Search is not available for this dataset
text
stringlengths 1
134k
| id
stringlengths 11
16
| article_id
stringlengths 8
10
| section_title
stringlengths 1
1.35k
| educational_score
float64 0.52
5.16
| domain
stringclasses 3
values | document_type
stringclasses 4
values | domain_scores
listlengths 3
3
| document_type_scores
listlengths 4
4
| language
stringclasses 38
values | language_score
float64 0
1
|
|---|---|---|---|---|---|---|---|---|---|---|
Universal occurrence of these sequences in all vertebrate classes was confirmed by their amplification using primers from human HoxD complex followed by Southern hybridization and sequencing (unpublished observation). Furthermore, using CR1, CR2 or CR3 as query we searched genomic sequences of variety of eukaryotes in available databases. This search indicated that these sequences are single copy and vertebrate specific. While these conserved regions appear to be a key component of the HoxD complex of all vertebrates looked at, we did not find such a degree of conservation in the flanking regions of other hox complexes ( HoxA , B and C ) of vertebrates. In order to trace back the evolutionary origin of such sequences, it will be of interest to investigate occurrence of these sequences at the corresponding region in the hox complexes of species of urochordata, cephalochordata or even agnatha. In the tunicate Oikopleura dioca , where hox genes are dispersed but the spatial pattern seen in other animals is still present , we did not find CR1, CR2 or CR3. Also, we did not find any significant conserved region corresponding to these CRs in the amphioxus genomic region that contains the cluster of hox genes. It appears, therefore, that these extremely conserved sequences have originated in the vertebrates where the hox complex has additional distinct features of tight clustering compared to the insect hox clusters and the temporal colinearity, not seen in invertebrates.
|
15462684_p2
|
15462684
|
Results and discussion
| 4.3018 |
biomedical
|
Study
|
[
0.9994463324546814,
0.00026647603954188526,
0.0002871897304430604
] |
[
0.9991872906684875,
0.00036425184225663543,
0.000367934990208596,
0.000080554535088595
] |
en
| 0.999996 |
Several recent reports using comparative genomics approach have identified conserved non-coding regions among different vertebrates but none to the degree that we report here. The mechanism that may require such a high degree of conservation is not known. It is not, therefore, immediately clear what precisely is the role of these sequences. EST database search revealed that part of CR1 and CR3 are transcribed without any significant ORF but no EST corresponding to CR2 or any other part of the 7 Kb region was found, Fig. 1 . A possible mechanism could involve RNA from this region that may function by base pairing to the genomic target sites. If that is the case, such high conservation could be expected. Role of transcription in the regulation of bithorax complex is emerging from recent studies .
|
15462684_p3
|
15462684
|
Results and discussion
| 4.125584 |
biomedical
|
Study
|
[
0.9995315074920654,
0.00015356161748059094,
0.00031491974368691444
] |
[
0.9991949200630188,
0.00045082339784130454,
0.00028742870199494064,
0.00006681180093437433
] |
en
| 0.999999 |
While such an extreme conservation of several hundred nucleotides over half a billion years in a region that does not code for any known proteins certainly implicates essential role for such sequences, probably in the regulation of HoxD complex, no known regulatory element requires such extreme conservation extending up to hundreds of base pairs. It is, therefore, likely that these elements could be components of a novel mechanism common to all vertebrates that regulates this gene complex. We are tempted to suggest that such a strongly conserved region from fish to human linked to a gene complex that is known to determine body axis formation may be the key determinant of molecular basis of early ontogeny. Early embryos of all vertebrates show striking similarity and we suggest that these elements may control the early expression pattern of HoxD which leads to similar pattern of the embryo shape. The gradient of conservation seen in this region from fish to human may further signify the evolutionary history of this locus and diversification of the morphological features along the anterior-posterior body axis of the vertebrate classes.
|
15462684_p4
|
15462684
|
Conclusions
| 4.481237 |
biomedical
|
Study
|
[
0.9994335770606995,
0.0002690117107704282,
0.00029743133927695453
] |
[
0.9971075654029846,
0.0008167882915586233,
0.0019335340475663543,
0.000142065022373572
] |
en
| 0.999997 |
The genomic sequences that contained Evx-2 and any of the Hoxd genes were downloaded and annotated using gene/ORF prediction tools. Similar approach was used for other hox complexes. Homology searches of the upstream sequences of HoxD region from human was carried out using the BLAST program of NCBI. The sequences that showed significant homology were further used to analyze the extent of homology by BLAST 2 program. The conserved regions from each sequence was obtained and subjected to multiple sequence analysis using Clustal X. In order to identify the expressed sequences corresponding to the conserved sequence, the conserved sequences along with the unique sequences were BLASTed against EST databases (human, mouse and dbEST).
|
15462684_p5
|
15462684
|
Sequence analysis
| 4.117322 |
biomedical
|
Study
|
[
0.9995854496955872,
0.00021351063332986087,
0.00020104942086618394
] |
[
0.9994028806686401,
0.0002306842798134312,
0.0003049249353352934,
0.00006151935667730868
] |
en
| 0.999997 |
The contigs that showed significant homology to the upstream sequences of human HoxD were annotated using the tBLASTx program and searching the translated amino acid sequence in the Swissprot database. Repeat masker program was used to look for repeat content. Genebank sequences used in this study are as follows: AC116665 Papio hamadryas , AF224263 Heterodontus francisci , AC015584 Mus musculus , AC009336 Homo sapiens , CAAB01000449 Fugu rubripes and NW_042732 Rattus norvegicus .
|
15462684_p6
|
15462684
|
Sequence analysis
| 4.094257 |
biomedical
|
Study
|
[
0.9996589422225952,
0.00014618401473853737,
0.0001947933778865263
] |
[
0.9977449178695679,
0.0018935450352728367,
0.00025585805997252464,
0.00010573791951173916
] |
en
| 0.999996 |
For the isolation of genomic DNA blood samples of human, chick and cobra ( Naja naja ) were used while liver tissue of mouse and muscle tissue of frog ( Bufo melanostictus ) and zebra fish were used. Standard protocol of DNA isolation was followed which included lysis, RNase A and proteinase K digestions followed by phenol/chloroform extraction and precipitation. Concentration and quality of the genomic DNA was checked on 0.7% agarose gel and UV absorption spectrophotometry. Based on the sequence of conserved regions primers were designed to amplify the three regions CR1, CR2 and CR3.
|
15462684_p7
|
15462684
|
DNA isolation, PCR amplification, sequencing and Southern hybridization
| 4.080852 |
biomedical
|
Study
|
[
0.9995976090431213,
0.00018221938807982951,
0.00022024694771971554
] |
[
0.9975252747535706,
0.0020376669708639383,
0.00033367835567332804,
0.00010342927271267399
] |
en
| 0.999998 |
Primers used in this study to amplify conserved regions from different vertebrate species were:CR1 forward- GAGGCTGTTCACACTGGTGG,CR1 reverse- ATCATGCTCTCTGATGGACC,CR2 forward- GCATCGTAATCAGTTCGGTC,CR2 reverse- TGATACAAGCTGATACCGTC,CR3 forward- GCTATTCAAAATGTTATTTGAG and CR3 reverse- CTGTAATGAAGAAAAGATTTATG.
|
15462684_p8
|
15462684
|
DNA isolation, PCR amplification, sequencing and Southern hybridization
| 3.719393 |
biomedical
|
Study
|
[
0.9989751577377319,
0.00017238137661479414,
0.0008524192380718887
] |
[
0.8997779488563538,
0.09902617335319519,
0.0008012156467884779,
0.0003946518700104207
] |
en
| 0.999998 |
The 25 μl reaction was performed using 100 ng template DNA and 5 pmol each of forward and reverse primers. PCR protocol was as follows: initial denaturation step of 94°C for 3 min was followed by 35 cycles of 94°C for 1 min, 57°C for 1 min and 72°C for 1.30 min and final extension step at 72°C for 7 min. Authenticity of the PCR products was confirmed by direct sequencing and Southern hybridization, using the corresponding human DNA as probe.
|
15462684_p9
|
15462684
|
DNA isolation, PCR amplification, sequencing and Southern hybridization
| 4.123801 |
biomedical
|
Study
|
[
0.999444305896759,
0.00035008572740480304,
0.0002055864460999146
] |
[
0.9923614263534546,
0.00703765731304884,
0.0003913983819074929,
0.00020948430756106973
] |
en
| 0.999995 |
An earlier version of this article was deposited in the 'Deposited Research' section of Genome Biology, , . While this manuscript was in reviewing process, a report comparing human genome to several other mammalian sequences identified many highly conserved noncoding sequences . Interestingly, this study also identified CR2 as uc.108 near HOXD and, in agreement to our observation, noted only a "core" conserved region in fish, suggesting that additional parts of the ultraconserved region were innovations after the common ancestor with fish.
|
15462684_p10
|
15462684
|
Note
| 3.43556 |
biomedical
|
Study
|
[
0.9985126852989197,
0.00016256871458608657,
0.0013246883172541857
] |
[
0.8693374395370483,
0.12231362611055374,
0.007305030710995197,
0.0010439965408295393
] |
en
| 0.999997 |
CS carried out the sequence analysis, PCR amplification and Southern analysis. SS participated in sequence analysis and DNA isolation from several organisms. AT carried out the sequencing of PCR products and participated in the sequence alignments. RKM conceived of the study, and participated in its design and coordination. All authors read and approved the final manuscript.
|
15462684_p11
|
15462684
|
Authors' contributions
| 0.89801 |
biomedical
|
Other
|
[
0.6469972133636475,
0.005728969816118479,
0.3472738265991211
] |
[
0.016952116042375565,
0.9780207276344299,
0.0035323549527674913,
0.0014947319868952036
] |
en
| 0.999996 |
Male factor infertility has been identified as the main or secondary cause in >40% of infertile couples. The number of office visits each year for infertility in the United States has risen from 600,000 in 1968 to 2 million by the 1990's. Semen analysis is a central component in male infertility evaluation . The present study was designed to evaluate the relationship of human semen parameters to season, age and smoking status.
|
15507127_p0
|
15507127
|
Background
| 3.290242 |
biomedical
|
Study
|
[
0.9986838698387146,
0.0005062224809080362,
0.0008099690894596279
] |
[
0.9986133575439453,
0.0009733947226777673,
0.00029332019039429724,
0.00011996485409326851
] |
en
| 0.999995 |
Seasonal variations in semen parameters have been reported in both fertile and infertile men . Saint Pol et al. found a significant seasonal variation in sperm count, with highest sperm counts in late winter and early spring and lowest concentration in late summer . There are several studies that suggest that an increase in age is associated with a decline in semen parameters . Paulson and coworkers identified an inverse association between age and total sperm count, but did not find an age related decrease in fertilization rate or a decrease in live birth rate in the oocyte donation model .
|
15507127_p1
|
15507127
|
Background
| 3.943504 |
biomedical
|
Study
|
[
0.9993834495544434,
0.00025281516718678176,
0.00036377584910951555
] |
[
0.8516040444374084,
0.0013140375958755612,
0.14678619801998138,
0.0002957279502879828
] |
en
| 0.999998 |
There is a consistent association between cigarette smoking and fertility in women . However, the data on cigarette smoking and measures of male fertility are less clear. Künzle et al. found an association between smoking and reduced semen quality while others found no strong relationship .
|
15507127_p2
|
15507127
|
Background
| 2.090302 |
biomedical
|
Study
|
[
0.9939423203468323,
0.0006626543472521007,
0.005394951440393925
] |
[
0.4702293872833252,
0.35863545536994934,
0.16893190145492554,
0.002203288022428751
] |
en
| 0.999998 |
The present study explores the relationship of human semen parameters with season, age and smoking status, while controlling for abstinence interval. In an earlier publication, we reported on the relationship between semen parameters, season, and age using data from a retrospective review of an existing laboratory database at the Massachusetts General Hospital Vincent Memorial Andrology Laboratory . The present study uses data from subjects recruited into an ongoing study exploring the relationship between environmental agents and semen parameters. There is no overlap with subjects from our earlier study.
|
15507127_p3
|
15507127
|
Background
| 3.872872 |
biomedical
|
Study
|
[
0.9993072748184204,
0.0003358369576744735,
0.00035695964470505714
] |
[
0.9993613362312317,
0.0002446011349093169,
0.0003230496949981898,
0.00007099770300555974
] |
en
| 0.999996 |
The Human Subject Internal Review Board committees of the Harvard School of Public Health and the Massachusetts General Hospital approved the study . Informed consent was obtained from each participant before entering the study.
|
15507127_p4
|
15507127
|
Study participants
| 1.23446 |
biomedical
|
Other
|
[
0.8764939308166504,
0.004401487298309803,
0.11910458654165268
] |
[
0.0471804253757,
0.950921356678009,
0.000982553930953145,
0.0009156182059086859
] |
en
| 0.999998 |
The study population consisted of patients (n = 306) presenting to the Vincent Memorial Andrology Laboratory of Massachusetts General Hospital (MGH) between January 2000 and January 2002 for semen analysis as a component of infertility evaluation. Of the 306 subjects, age was not available for five study subjects despite several attempts at follow up after the initial study visit. Sperm morphology was not performed on two subjects with azoospermia.
|
15507127_p5
|
15507127
|
Study participants
| 3.380291 |
biomedical
|
Study
|
[
0.9960254430770874,
0.003425591392442584,
0.0005488754832185805
] |
[
0.9981790781021118,
0.001359101152047515,
0.00020456041966099292,
0.0002573182573541999
] |
en
| 0.999996 |
Men were approached only if the referring physician had previously received a brief description of the study. The Andrologist approached patients and asked if they were willing to meet the research nurse to learn about the research study, noting that it was optional and not part of their clinic appointment. All patients approached had the opportunity to decide for themselves if they wanted to participate in the research study. Inclusion criteria for this study were: 1) scheduled for a routine semen analysis as a patient at the Vincent Memorial Andrology Laboratory, 2) either English or Spanish speaking, 3) age 18–54 years, 4) had not had a vasectomy, and 5) was not currently receiving hormone therapy.
|
15507127_p6
|
15507127
|
Study participants
| 2.766655 |
biomedical
|
Study
|
[
0.947422444820404,
0.04971034824848175,
0.0028672267217189074
] |
[
0.9821590781211853,
0.016197843477129936,
0.000361715181497857,
0.0012814173242077231
] |
en
| 0.999994 |
All subjects received an explanation of the study in a private setting prior to obtaining informed consent. Information on lifestyle, such as smoking history and medical history was obtained by nurse interview.
|
15507127_p7
|
15507127
|
Study participants
| 1.909386 |
biomedical
|
Study
|
[
0.9924180507659912,
0.0056051407009363174,
0.0019767668563872576
] |
[
0.9555040597915649,
0.04074579104781151,
0.0017544307047501206,
0.001995631493628025
] |
en
| 0.999994 |
From the date that semen specimen was produced, samples were classified by season as follows: winter = December, January, February; Spring = March, April, May; Summer = June, July, August; and Fall = September, October, November.
|
15507127_p8
|
15507127
|
Study participants
| 2.142228 |
biomedical
|
Study
|
[
0.9901378154754639,
0.001064940937794745,
0.008797255344688892
] |
[
0.7837429046630859,
0.21376913785934448,
0.0016064627561718225,
0.0008815110195428133
] |
en
| 0.999997 |
Semen was collected by masturbation in a private room in the hospital. The semen specimen was allowed to liquefy for at least 20 minutes in an incubator at 37°C and was analyzed within 60 minutes after collection. A routine semen analysis was performed which included the following parameters: semen volume, pH, sperm concentration, sperm motility, and sperm morphology.
|
15507127_p9
|
15507127
|
Collection of samples
| 3.836004 |
biomedical
|
Study
|
[
0.9963781237602234,
0.003378763794898987,
0.00024319582735188305
] |
[
0.896530032157898,
0.0993773341178894,
0.0016660242108628154,
0.002426557010039687
] |
en
| 0.999996 |
Volume was determined and sample color and viscosity were recorded. Semen pH was measured within one hour of ejaculation (Color pHast; EM Science, Gibbstown, NJ, USA).
|
15507127_p10
|
15507127
|
Semen volume and pH
| 3.308502 |
biomedical
|
Study
|
[
0.9988228678703308,
0.000629174814093858,
0.0005479818792082369
] |
[
0.9804776310920715,
0.01838424988090992,
0.0007271727081388235,
0.00041092681931331754
] |
en
| 0.999997 |
All fresh semen samples were analyzed for sperm concentration and motion parameters by the HTM-IVOS Semen analyzer (Hamilton-Thorn 10HTM-IVOS, Beverly, MA, USA). Setting parameters and the definition of measured sperm motion parameters for CASA were established by the manufacturer: (frames acquired: 30; frame rate: 60 Hz; straightness (STR) threshold: 80.0%; medium VAP cutoff: 25.0 um/s; and duration of tracking time: 0.38 sec). To measure both sperm concentration and motility, aliquots of semen samples (5 μl) were placed into a pre-warmed (37°C) Makler counting chamber (Sefi – Medical Instruments, Haifa, Israel). A minimum of 200 sperm from at least four different fields was analyzed from each specimen. Percent motile sperm was defined as World Health Organization (WHO) grade "a" sperm (rapidly progressive with velocity ≥ 25 μm/s at 37°C) plus "b" grade sperm (slow/sluggish progressive with velocity ≥ 5 μm/s but < 25 μm/s) .
|
15507127_p11
|
15507127
|
Concentration and motility
| 4.127629 |
biomedical
|
Study
|
[
0.999370276927948,
0.00047729737707413733,
0.00015252357115969062
] |
[
0.9986487030982971,
0.0006910891970619559,
0.0005463953129947186,
0.00011384787649149075
] |
en
| 0.999996 |
Using the "feathering" method at least two slides were derived from each fresh semen sample . The resulting thin-smear slide was allowed to air dry before staining which was carried out using a Diff-Quik staining kit, consisting of three solutions (Dade Behring AG, Düdingen, Switzerland). Slides were then mounted with a microscopy cover glass (Fisher Scientific, Pittsburgh, PA, USA).
|
15507127_p12
|
15507127
|
Morphology
| 3.835749 |
biomedical
|
Study
|
[
0.9985178112983704,
0.0009124601492658257,
0.0005696410080417991
] |
[
0.6908434629440308,
0.30619800090789795,
0.001629186561331153,
0.0013293838128447533
] |
en
| 0.999994 |
Morphological assessment was performed at a magnification of 100X with an oil immersion using a Nikon microscope (Nikon Company, Tokyo, Japan). As the slide was scored, the normal and abnormal spermatozoa (head defects, midpiece defects and tail defects) were noted. Sperm morphology was determined using the strict criteria by Kruger et al. . From each sample at least 200 spermatozoa was counted from two slides. Results were expressed as percentage of normal spermatozoa, head defects, midpiece defects and tail defects.
|
15507127_p13
|
15507127
|
Morphology
| 4.056767 |
biomedical
|
Study
|
[
0.9995948672294617,
0.00023963896092027426,
0.00016546390543226153
] |
[
0.9990298748016357,
0.0004953667521476746,
0.00040418782737106085,
0.00007055607420625165
] |
en
| 0.999998 |
Multiple regression analyses (SAS version 8.2, SAS Institute, Cary, NC, USA) was performed to investigate whether there were differences in semen parameters with respect to season, age, and smoking status. Winter was used as the reference season. We also investigated month-to-month variation in semen parameters. For each semen parameter, a separate multiple regression was performed. Semen analysis parameters were entered into the models both untransformed and after square root transformation because of their skewed distribution. Since the square root transformed results were similar to the untransformed results, and are simpler to interpret, only the untransformed results are presented. To explore whether the semen parameters and age relationships were linear, age was used as both a continuous and categorical variable (less than 30 years, 30 to 40 years, and greater than 40 years old). Abstinence time was modeled as an ordinal five-category variable (2 or fewer days, 3, 4, 5, and 6 or more days).
|
15507127_p14
|
15507127
|
Statistical analysis
| 4.026193 |
biomedical
|
Study
|
[
0.9995298385620117,
0.00027190044056624174,
0.00019829437951557338
] |
[
0.9993115663528442,
0.0002370169386267662,
0.0003896220587193966,
0.0000617785844951868
] |
en
| 0.999998 |
Subject's ages ranged from 18.2 to 54.3 years. The mean (± SD) age was 35.9 (± 5.6) years. The majority of the subjects (67%) were between 30 and 40 years old; only 11% were <30 years and 21% were >40 years old.
|
15507127_p15
|
15507127
|
Results
| 2.200905 |
biomedical
|
Study
|
[
0.9957559704780579,
0.0022501004859805107,
0.001993834041059017
] |
[
0.992424488067627,
0.00680565508082509,
0.00036938046105206013,
0.00040048902155831456
] |
en
| 0.999998 |
Mean sperm concentration was above the WHO reference values . Average (± SD) sperm concentration was 103 (± 95.5) M/ml with range = 0 – 655.4 M/ml. Mean (± SD) percent motility and percent normal morphology were 47.6% (± 25.5) and 6.9% (± 4.7), respectively. Mean (± SD) semen volume was 3.0 ml (± 1.6), with a range = 0.1 – 11.0. The mean (± SD) semen pH was 8.4 (± 0.3), with range = 6.8 – 9.0. Mean (± SD) abstinence interval was 1.7 (± 1.4) days. Distributions of semen parameters for the study population are presented in Table 1 .
|
15507127_p16
|
15507127
|
Results
| 4.069529 |
biomedical
|
Study
|
[
0.9987345337867737,
0.0011108326725661755,
0.00015470058133359998
] |
[
0.9987552165985107,
0.0006369423354044557,
0.0003909676452167332,
0.00021688362176064402
] |
en
| 0.999995 |
Seasonal variations in semen quality are shown in Table 2 . The number of semen samples obtained in the Spring, Summer, Fall, and Winter were 62, 81, 82, 81, respectively. Mean sperm concentration in the spring (137.2 million/ml) was significantly higher than in the winter (99.2 million/ml), summer (93.1 million /ml) and fall (90.6 million/ ml), (p-value < 0.05). These seasonal differences remained after adjusting for age and abstinence times. Figure 1 shows the month-to-month median sperm concentration across the study. Median sperm concentration by month was higher in March, April, May and June than all other months . Mean sperm motility also was higher in the spring (52.3%) than in the summer (47.7%), fall (47.1%) and winter (44.3%). This was higher when compared to winter ( p = 0.06).
|
15507127_p17
|
15507127
|
Results
| 4.08136 |
biomedical
|
Study
|
[
0.9992042183876038,
0.0005638747825287282,
0.00023194112873170525
] |
[
0.9993177652359009,
0.00020470513845793903,
0.00039481656858697534,
0.00008276863809442148
] |
en
| 0.999997 |
There were also seasonal variations in sperm morphology parameters. The mean percent normal morphology in Spring (7.5%) was greater than in Summer (6.7%), Fall (7.0%) or Winter (6.4%), though not statistically significant. These seasonal differences remained after adjusting for age and abstinence interval. Mean semen volume and pH were similar across season.
|
15507127_p18
|
15507127
|
Results
| 3.860734 |
biomedical
|
Study
|
[
0.9992144107818604,
0.0004419542383402586,
0.0003436241240706295
] |
[
0.9991282820701599,
0.0004626552981790155,
0.00033581428579054773,
0.00007326471677515656
] |
en
| 0.999996 |
There were no statistically significant relationships between age with semen volume, sperm concentration, percent motility, and percent normal morphology. However, there was little variability in age since the majority of men (> 65%) were between 30 and 40 years old.
|
15507127_p19
|
15507127
|
Results
| 2.444251 |
biomedical
|
Study
|
[
0.9975560903549194,
0.0012186039239168167,
0.0012253450695425272
] |
[
0.9904031753540039,
0.008746964856982231,
0.0005770775023847818,
0.00027277195476926863
] |
en
| 0.999998 |
In the present study, only 22 men were current smokers and 57 were ex-smokers. After controlling for age and abstinence time, there was no statistically significant relationship between semen quality and smoking status, though current smokers tended to have lower mean sperm concentration (83 million/ml) than never smokers (104 million/ml).
|
15507127_p20
|
15507127
|
Results
| 3.671373 |
biomedical
|
Study
|
[
0.9992098808288574,
0.00041852492722682655,
0.00037152558797970414
] |
[
0.9992952346801758,
0.00043421416194178164,
0.00020196502737235278,
0.00006862090958748013
] |
en
| 0.999997 |
Although there are numerous previously published studies investigating the relationship among semen parameters and season, age and smoking status, the data are not entirely consistent. To determine if these associations are robust, replication is required. It is the accumulation of consistent observations from epidemiological studies that provides confidence in the findings. Therefore, we believe the present study adds to the literature since it provides replication of seasonal trends in semen parameters. In addition, the present study was conducted in men residing in the Northeast region of the United States, an area with distinct seasons and one that has not been well represented in the literature on this topic. Our study has several strengths. The center selected as the site of this study (the Vincent Memorial Andrology Laboratory of Massachusetts General Hospital) has a large and readily accessible population of men seeking infertility evaluation. Based in a large tertiary care facility, the Andrology Laboratory draws patients from diverse backgrounds throughout the New England region of the United States, receiving referrals from physicians in the community and the medical center.
|
15507127_p21
|
15507127
|
Discussion
| 4.022864 |
biomedical
|
Study
|
[
0.999405026435852,
0.0003386703319847584,
0.00025630113668739796
] |
[
0.9993695616722107,
0.0002757655456662178,
0.00029141598497517407,
0.00006330890755634755
] |
en
| 0.999998 |
Our study also had potential limitations. Since it is known that there is within-person variability in semen parameters, using a single sample to characterize an individual may introduce measurement error, likely to be random. Another potential limitation is that it is possible that if some men recently moved to the New England area this may introduce bias. However, of the men in the study, 96% of them lived in New England area for at least 3 months prior to their semen analysis, the period of sperm development. Therefore, the concern with recent immigration to the New England area would be minimal.
|
15507127_p22
|
15507127
|
Discussion
| 3.394803 |
biomedical
|
Study
|
[
0.9989346861839294,
0.00040128998807631433,
0.0006639600032940507
] |
[
0.998977780342102,
0.000722701835911721,
0.0002174360997742042,
0.00008206441270885989
] |
en
| 0.999998 |
In the present study, we found higher sperm concentrations, motility and percent normal morphology in the spring than in other seasons. This may partially explain seasonal patterns of births in United States, where there is a deficit of spring births , conceived in the summer.
|
15507127_p23
|
15507127
|
Discussion
| 2.665853 |
biomedical
|
Study
|
[
0.9972183704376221,
0.00045945728197693825,
0.002322108019143343
] |
[
0.9966045618057251,
0.0029712789691984653,
0.00027636028244160116,
0.0001477952755521983
] |
en
| 0.999995 |
Our data are in agreement with previous reports of seasonal variation in sperm concentration with spring having the highest concentration. Gyllenborg et al. found high sperm counts in the spring as compared to the summer. Two other retrospective studies found peak sperm concentrations in the spring and winter . In our earlier publication, a retrospective review of semen analysis results from a different cohort of men, we found higher median sperm concentrations in the winter (111.6 million/mL) as compared to the fall (87.7 million/mL), with a median spring concentration of 90.0 million/mL . In our earlier study we were unable to control for abstinence interval, thus if winter abstinence times were longer than spring this may partially account for the differences between studies.
|
15507127_p24
|
15507127
|
Discussion
| 4.017674 |
biomedical
|
Study
|
[
0.999545156955719,
0.00024785639834590256,
0.00020699267042800784
] |
[
0.9947015643119812,
0.0003947292861994356,
0.004797674249857664,
0.00010601476242300123
] |
en
| 0.999997 |
Seasonal variations in sperm morphology were recently explored by Centola and Eberly in a large sample of California men . Although they did not find statistical significant seasonal variations in percent normal morphology, there were significant seasonal differences in percent tail defects, percent tapered forms, and percent immature sperm. In our earlier study we found higher median percentage of sperm with normal morphology in the winter (9.0%) as compared to spring (6.5%) . It is unclear why these results differed from the present study results. The literature on seasonal variations in sperm motility is largely inconsistent .
|
15507127_p25
|
15507127
|
Discussion
| 3.877254 |
biomedical
|
Study
|
[
0.9995772242546082,
0.00013789336662739515,
0.0002849445154424757
] |
[
0.9980448484420776,
0.0005563143640756607,
0.0013230654876679182,
0.00007577200449304655
] |
en
| 0.999997 |
Effects of temperature and hours of daylight may partially explain seasonal variations in semen quality. Sperm production in humans is known to decrease when testicular temperature is raised by experimental techniques . Normal spermatogenesis requires a temperature 2–3°C below rectal temperature . We think temperature and photoperiod may play a role in seasonal variations in semen quality. To explore this further, we are presently conducting a study collecting information on lifestyle factors, such as alcohol and drug use, environmental and occupational exposures, and personal factors such as stress. The information will allow us to further explore risk factors for altered semen quality.
|
15507127_p26
|
15507127
|
Discussion
| 3.581933 |
biomedical
|
Study
|
[
0.9993022680282593,
0.00017075684445444494,
0.0005270141991786659
] |
[
0.9881876111030579,
0.010656970553100109,
0.0009663973469287157,
0.00018895830726251006
] |
en
| 0.999998 |
Spermatogenesis occurs over approximately three months and does not seem to vary in duration among men . Chia et al. reported there were no significant month-to-month fluctuations in semen volume and sperm density among men who resided in the tropics , where there are minimal changes in temperature, unlike the seasonal variation of climate in the New England region. In our study, improved semen parameters in the spring may reflect spermatogenesis during the cold New England winter.
|
15507127_p27
|
15507127
|
Discussion
| 3.616782 |
biomedical
|
Study
|
[
0.9993876218795776,
0.00020197869162075222,
0.00041039648931473494
] |
[
0.9981138706207275,
0.0013847060035914183,
0.00041358472662977874,
0.00008784850069787353
] |
en
| 0.999995 |
While we did not find a relationship between age and semen parameters, there was little variability in age in our study population. In our earlier study we found inverse associations between age and sperm concentration, motility and morphology . However, the age range was larger in this earlier study. In another study, Schwartz and coworkers found an improvement in semen characteristics up to 25 years of age , followed by a leveling off and a subsequent decrease. However, the age relationships were not statistically significant for sperm count, semen volume, and the total number of spermatozoa. Statistically significant decreases in sperm concentration with advanced age were found among 29 'older' fathers (mean age 50.3 years) compared with those from 35 'younger' fathers (mean age 32.2 years) . A recent review of the literature by Kidd et al. suggested that increased age was associated with a decline in semen volume, sperm motility, and sperm morphology but not with sperm concentration .
|
15507127_p28
|
15507127
|
Discussion
| 3.942681 |
biomedical
|
Study
|
[
0.9993854761123657,
0.00034038405283354223,
0.000274092482868582
] |
[
0.9339202642440796,
0.0006922394968569279,
0.06512005627155304,
0.0002674513089004904
] |
en
| 0.999999 |
Studies have shown associations between cigarette smoking and infertility in women, time to conception, and risk of spontaneous abortion, as well as reduction in fecundity . Data on associations between cigarette smoking and male fertility are unclear . Hughes and Brennan reported that there were no consistent effects on semen quality among male smokers. Similarly, a survey of more than 4,000 European couples attempting to become pregnant failed to find an effect of male smoking on fecundity .
|
15507127_p29
|
15507127
|
Discussion
| 3.693343 |
biomedical
|
Study
|
[
0.9991230368614197,
0.0002140561700798571,
0.0006629861309193075
] |
[
0.8437069058418274,
0.0037261624820530415,
0.15221117436885834,
0.00035582444979809225
] |
en
| 0.999997 |
However, in contrast, in a cross-sectional study of men with proven fertility (n = 243), cigarette smoking was associated with significantly lower semen volume (but not other semen parameters) after adjusting for age and alcohol consumption . Results from a meta-analysis indicated that smokers' sperm density is on average 13–17% lower than that of nonsmokers . The available data suggest that cigarette smoking was associated with a significant decrease in sperm density, total sperm count, total motile sperm, and the percentage of normal forms .
|
15507127_p30
|
15507127
|
Discussion
| 4.011151 |
biomedical
|
Study
|
[
0.9996144771575928,
0.00018541677854955196,
0.00020005703845527023
] |
[
0.9857609868049622,
0.00040076705045066774,
0.013721260242164135,
0.00011701935000019148
] |
en
| 0.999996 |
In our study, only 22 men were current smokers and 57 were ex-smokers. After controlling for age and abstinence time, there was no significant relationship between semen quality and smoking status, though current smokers tended to have lower sperm concentration. The present study is ongoing and we will reexamine these relationships in a larger dataset. In addition, we are also collecting information on other lifestyle and personal factors, such as physical exercise, stress, and alcohol intake. Their relationship with semen parameters will be investigated in the future when we have a larger number of subjects.
|
15507127_p31
|
15507127
|
Discussion
| 3.058391 |
biomedical
|
Study
|
[
0.9988645315170288,
0.0004345618945080787,
0.0007008255342952907
] |
[
0.9984979629516602,
0.0011989742051810026,
0.00021656158787664026,
0.00008654136036057025
] |
en
| 0.999997 |
We found seasonal variations in sperm concentration and suggestive evidence of seasonal variation in sperm motility and percent sperm with normal morphology. Although smoking status was not a significant predictor of semen parameters, this may have been due to the small number of current smokers in the study.
|
15507127_p32
|
15507127
|
Conclusions
| 2.930642 |
biomedical
|
Study
|
[
0.9989122152328491,
0.0005417895154096186,
0.0005459484527818859
] |
[
0.9978436231613159,
0.0015733878826722503,
0.00043527211528271437,
0.00014767592074349523
] |
en
| 0.999998 |
The authors declare that they have no competing interests.
|
15507127_p33
|
15507127
|
Competeting interests
| 0.956449 |
other
|
Other
|
[
0.014629608951508999,
0.0016160424565896392,
0.9837543368339539
] |
[
0.004644680302590132,
0.9930703043937683,
0.0012706080451607704,
0.0010144523112103343
] |
en
| 0.999997 |
ZC, LG-B, IS, and RH all contributed equally to this work and reviewed the manuscript.
|
15507127_p34
|
15507127
|
Authors' contributions
| 0.829599 |
other
|
Other
|
[
0.016153287142515182,
0.0012326979776844382,
0.9826139807701111
] |
[
0.0019437490263953805,
0.9961600303649902,
0.0012520989403128624,
0.0006441068253479898
] |
en
| 0.999998 |
The ability to sharply curve membranes was a defining event in the evolution of early eukaryotes, allowing the formation of endomembrane systems . In modern eukaryotes, these systems have become elaborate internal membranes, such as the Golgi apparatus, the endoplasmic reticulum (ER), and the nuclear envelope (NE). To date three major kinds of transport vesicles, distinguished by the compositions of their protein coat complexes, have been shown to traffic between these internal membranes and the plasma membrane: First, the clathrin/adaptin complexes are responsible for endocytosis and vesicular trafficking between the Golgi, lysosomes, and endosomes; second, the COPI complex mediates intra-Golgi and Golgi-to-ER trafficking; and lastly, the COPII complex supports vesicle movement from the ER to the Golgi .
|
15523559_p0
|
15523559
|
Introduction
| 4.445391 |
biomedical
|
Study
|
[
0.9987975358963013,
0.0004040393396280706,
0.0007984890835359693
] |
[
0.8660776615142822,
0.008296815678477287,
0.12514038383960724,
0.00048520247219130397
] |
en
| 0.999999 |
The NE is contiguous with the ER and delineates the nucleus. It is made of an inner and outer membrane that together form a barrier between the nucleoplasm and the cytoplasm. This barrier is perforated by nuclear pore complexes (NPCs), which form pores between the inner and outer NE membranes by stabilizing a sharply curved section of connecting pore membrane. NPCs are approximately 50-MDa octagonally symmetric cylinders that function as the only known mediators of nucleocytoplasmic exchange; while permitting the free flow of small molecules, they restrict macromolecular trafficking to selected cargoes that are recognized by cognate transport factors. NPCs are found in all eukaryotic cells and are composed of a broadly conserved set of proteins, termed nups . Although the nups have been fully cataloged for both yeast (Saccharomyces) and vertebrates , there is currently little information concerning their origin and evolution. To this end, protein structures are helpful because it is easier to recognize similarities in structure than in sequence, especially for distantly related proteins. Thus, we have characterized the structures of seven proteins forming a core building block of the NPC, termed the yNup84 subcomplex in Saccharomyces and the vNup107–160 subcomplex in vertebrates. These structures reveal how the nuclear pore complex could have evolved from organisms with no analogous transport system.
|
15523559_p1
|
15523559
|
Introduction
| 4.565771 |
biomedical
|
Study
|
[
0.999229907989502,
0.0005055832443758845,
0.00026452282327227294
] |
[
0.9978538155555725,
0.0005917748785577714,
0.0013805885100737214,
0.00017379775817971677
] |
en
| 0.999996 |
The yNup84/vNup107–160 subcomplex has a molecular weight of approximately 600 kDa and has been shown in yeast to be flexible , presenting a considerable challenge to conventional experimental methods for structure determination; thus, we used a computational approach that relies on a database of experimentally determined structures . We first focused on the component nups of the yNup84 subcomplex: ySeh1, ySec13, yNup84, yNup85, yNup120, yNup133, and yNup145C, whose corresponding vertebrate homologs are, respectively, vSec13 l, vSec13R, vNup107, vNup75, vNup160, vNup133, and vNup96 . For putative domains in each of these nups, we first applied two threading programs to assign structure folds based on similarity to known protein structures (templates) (see Materials and Methods ). The corresponding sequence-structure alignments were refined and used to generate three-dimensional models of the nup domains, followed by evaluation of the models. Our analyses predicted that every nup in the yNup84/vNup107–160 subcomplex consists of a β-propeller domain, an α-solenoid domain, or both . β-propellers contain several blades arranged radially around a central axis, each blade consisting of a four-stranded antiparallel β-sheet; α-solenoid domains are composed of numerous pairs of antiparallel α-helices stacked to form a solenoid . While we have not defined the precise details of each domain, such as the exact shapes and numbers of propeller blades and solenoid repeats, the overall fold assignments for each nup are clear. These predictions indicate that yNup84, yNup85, and yNup145C all mainly consist of an α-solenoid domain, whereas yNup120 and yNup133 contain both an amino-terminal β-propeller and a large carboxyl-terminal α-solenoid region. Both ySec13 and ySeh1 are predicted to be almost entirely single-domain β-propellers of six and seven blades, respectively. These latter two proteins fall into the well-conserved class of tryptophan/aspartic acid (WD) repeat-containing β-propeller proteins. For both proteins, homology with the WD-repeat β-propellers has been reported previously and is confirmed here.
|
15523559_p2
|
15523559
|
Results
| 4.608211 |
biomedical
|
Study
|
[
0.9990214109420776,
0.0005923418211750686,
0.0003862062294501811
] |
[
0.9986341595649719,
0.0004102969542145729,
0.0007631391636095941,
0.00019245468138251454
] |
en
| 0.999998 |
We support our fold assignments using four considerations . First, both fold assignment programs returned their predictions with highly significant scores ( Tables S1–S7 ), and they predominantly assigned only the two predicted folds out of the approximately 1,000 different known fold types ( Tables S1–S7 ) . Moreover, while there are numerous variations corresponding to different proteins within each predicted fold type, the two different methods used for fold recognition often selected the same template proteins ( Tables S1–S7 ). Second, the evaluation of the atomic model for each nup was statistically significant when compared against the best models generated for random sequences of identical amino acid composition and length; all the nup models were at least six standard deviations away from the mean score of the random models . Third, secondary structure predictions from amino acid sequences alone indicate that all seven nups consist mainly of repetitive structures that largely match the secondary structures observed in their corresponding three-dimensional models . The agreement ranges from 58% to 87% of the residues for a three-state assignment (helix, strand, other). This agreement is the maximum possible level of consistency, given the approximately 75% accuracy of the secondary structure prediction methods .
|
15523559_p3
|
15523559
|
Results
| 4.237459 |
biomedical
|
Study
|
[
0.9994562268257141,
0.00030319407233037055,
0.00024056737311184406
] |
[
0.9991829991340637,
0.00017553156067151576,
0.0005593299865722656,
0.00008214211266022176
] |
en
| 0.999998 |
Finally, we provide direct biochemical evidence in support of our fold assignments, using proteolytic mapping of domain boundaries and loop locations in the seven nups . Tagged nups were purified from yeast extracts and incubated with the endoproteinases Asp-N (which hydrolyzes peptide bonds at the amino side of aspartic acid) or Lys-C (which hydrolyzes peptide bonds at the carboxylic side of lysines) while still attached to the magnetic beads via their proteolytically resistant tags. After digestion, proteolytic fragments that remained attached to the beads were separated by SDS-PAGE, and cleavage sites were determined either by molecular weight estimation of the fragments or by amino-terminal Edman sequencing ( Table 2 ). The regions predicted to form β-propellers were, as expected, extremely resistant to proteolysis . On the whole, the predicted α-solenoid regions were also resistant to proteolysis, although less so than the β-propellers. However, the major cleavages were found toward the end of the predicted α-solenoid domains, even in the most susceptible nup (yNup133). Strikingly, the strongest cleavages generally occurred in the border regions between the predicted domains, as is particularly evident for yNup133 and yNup120 . Hence, in every case, the regions that we predicted to form compact folded structures were proteolytically resistant, and the predicted linkers between these domains were proteolytically sensitive. This correlation provides support for all seven of our structural models. In addition, circular dichroism and Fourier transform infrared spectra reported for Nup85 are in agreement with our predictions, indicating a composition characteristic of α-solenoids (approximately 50% α-helical, 23% loops, 5% turns, and 10% β-sheet) . We expect our findings will spur efforts to determine the detailed atomic structures of nups; the rapid proteolytic domain mapping and molecular modeling techniques we have utilized here should aid these efforts.
|
15523559_p4
|
15523559
|
Results
| 4.442919 |
biomedical
|
Study
|
[
0.9992511868476868,
0.000497206172440201,
0.0002515979576855898
] |
[
0.9987325072288513,
0.00033881011768244207,
0.0007879363256506622,
0.00014075871149543673
] |
en
| 0.999997 |
Having established the domain folds for the yNup84 subcomplex, we also assigned domain folds in its vertebrate (i.e., human) and plant (i.e., Arabidopsis ) homologs. All seven nups from both human and Arabidopsis yielded identical domain fold assignments to their yeast counterparts ( Table S7 ), despite low primary sequence conservation among them . These findings indicate that the overall architecture of the yNup84/vNup107–160 subcomplex has been preserved throughout the eukaryotes. Hence, the yNup84/vNup107–160 subcomplex, which contributes nearly one-quarter of the mass of the NPC, is composed in the main of repetitive β-propellers and α-solenoids; taken together with other repetitive domain nups (such as the FG repeat nups), this suggests that a significant percentage of the NPC's bulk is composed of protein repeats .
|
15523559_p5
|
15523559
|
Results
| 4.269261 |
biomedical
|
Study
|
[
0.9994046688079834,
0.0002976205141749233,
0.00029769886168651283
] |
[
0.9993534684181213,
0.00021930165530648082,
0.0003576593881007284,
0.00006953973206691444
] |
en
| 0.999996 |
To gain insight into the function and origin of the yNup84/vNup107–160 subcomplex, we asked whether there are other known subcomplexes that share similar compositions and fold arrangements. A search of the entire SwissProt/TrEMBL database for entries that contain an amino-terminal β-propeller followed by an α-solenoid revealed that this specific architectural combination is absent from both bacteria and archaebacteria, and is found only in eukaryotic proteins, whose role (where known) is as components either of coated vesicles or of the yNup84/vNup107–160 subcomplex. Thus, the clathrin heavy chain, a major component of clathrin-coated vesicles, appears remarkably similar in domain architecture to both yNup120/vNup160 and yNup133/vNup133. All three proteins are composed of an amino-terminal β-propeller followed by an extended α-solenoid. Proteolysis of assembled clathrin cages leads to the release of an amino-terminal fragment of 52–59 kDa . This result is similar to our domain mapping results, where the proteolysis of yNup120 and yNup133 resulted in amino-terminal fragments of 45 kDa and 60 kDa, respectively. Strikingly, one component of the yNup84/vNup107–160 subcomplex, ySec13/vSec13R, is also a known vesicle-coating protein. Similarly, ySeh1/vSec13L, a close homolog of ySec13/vSec13R, is also associated with both the yNup84/vNup107–160 subcomplex and the vesicle-coating proteins . Together, these results point to an intimate connection between vesicle-coating complexes and the yNup84/vNup107–160 subcomplex.
|
15523559_p6
|
15523559
|
Results
| 4.603168 |
biomedical
|
Study
|
[
0.9990119934082031,
0.0006151867564767599,
0.00037271829205565155
] |
[
0.9984719157218933,
0.0004587135335896164,
0.0008718411554582417,
0.000197475659660995
] |
en
| 0.999997 |
In clathrin-coated vesicles, clathrin is attached via its amino-terminal domain to an adaptin complex. There are four types of adaptin complexes, all made of two large subunits that wrap around two small subunits. The bulk of each large subunit is made of an α-solenoid trunk . Similarly, the bulk of yNup84/vNup107, yNup85/vNup75, and yNup145C/vNup96 are also composed of α-solenoid trunks. Hence, the yNup84/vNup107–160 subcomplex resembles the clathrin/adaptin complex, in that the clathrin-like yNup120/vNup160 and yNup133/vNup133 are attached to the adaptin-like proteins yNup84/vNup107, yNup85/vNup75, and yNup145C/vNup96. This resemblance is further strengthened by our observation that the preferred templates for modeling the α-solenoid domains in the yNup84/vNup107–160 subcomplex were derived from proteins in vesicle coating complexes .
|
15523559_p7
|
15523559
|
Results
| 4.427029 |
biomedical
|
Study
|
[
0.9991989731788635,
0.0003191799914930016,
0.000481803115690127
] |
[
0.99852055311203,
0.0008624946349300444,
0.0005172951496206224,
0.0000996249946183525
] |
en
| 0.999996 |
Our analyses showed that the yNup84/vNup107–160 subcomplex and all three major classes of vesicle coating complexes can be linked together through their common architecture. As summarized in Figure 4 , these similarities include both previously reported relationships (e.g., between the clathrin/adaptin complexes and the COPI complexes) , and previously unsuspected relationships .
|
15523559_p8
|
15523559
|
Results
| 4.067476 |
biomedical
|
Study
|
[
0.9993263483047485,
0.0002298137842444703,
0.0004439260228537023
] |
[
0.9991140961647034,
0.0004236447566654533,
0.00040547692333348095,
0.000056821703765308484
] |
en
| 0.999997 |
The common architecture of the yNup84/vNup107–160 subcomplex and all three major classes of vesicle-coating complexes suggests that all of these complexes have common function in curving membranes. There is, in fact, circumstantial evidence for a role of the yNup84/vNup107–160 subcomplex in the establishment and maintenance of pore membrane curvature. Members of this complex, when disrupted in yeast, cause the uniformly distributed NPCs to cluster into patches in the plane of the NE , suggesting that impairment of yNup84 subcomplex function results in a suboptimal interaction of the NPC with its surrounding nuclear membranes.
|
15523559_p9
|
15523559
|
Results
| 4.356354 |
biomedical
|
Study
|
[
0.9994407296180725,
0.000242980953771621,
0.00031635674531571567
] |
[
0.9974431991577148,
0.0015222635120153427,
0.0009144776850007474,
0.00012007010809611529
] |
en
| 0.999996 |
As shown here, protein structure modeling is particularly useful in uncovering potential evolutionary and functional relationships that are refractory to classical approaches based on comparison of protein sequences alone. Our results show that clathrin/adaptin complexes, COPI complexes, COPII complexes, and the yNup84/vNup107–160 subcomplex all share a common molecular architecture. This commonality could have arisen by either convergent or divergent evolutionary pathways.
|
15523559_p10
|
15523559
|
Discussion
| 4.179555 |
biomedical
|
Study
|
[
0.9996086955070496,
0.00019721253192983568,
0.00019412230176385492
] |
[
0.99875807762146,
0.000438971008406952,
0.0007291389629244804,
0.0000738443632144481
] |
en
| 0.999995 |
In a convergent pathway, β-propeller and α-solenoid folds could have been independently utilized by both NPCs and vesicle-coating complexes at different stages of eukaryotic evolution. This possibility is supported by the high abundance of both fold types in eukaryotic genomes (which could potentially make their fusion in proteins or complexes relatively frequent) and the low sequence similarities between proteins of the NPC and vesicle coating complexes (which may suggest that they are not related).
|
15523559_p11
|
15523559
|
Discussion
| 4.2387 |
biomedical
|
Study
|
[
0.9994045495986938,
0.0001897200127132237,
0.0004057280602864921
] |
[
0.9945738911628723,
0.001960981171578169,
0.003346241544932127,
0.00011891813483089209
] |
en
| 0.999997 |
In a divergent pathway, NPCs and vesicle-coating complexes share these folds because both complex types could have originated from a common ancestor. In this scenario, a single “protocoatomer” would have been the progenitor for numerous vesicle coating complexes, as well as the yNup84/vNup107–160 subcomplex. Several lines of evidence support this latter hypothesis. First, the most confident models of the yNup84/vNup107–160 subcomplex proteins are based on structures of coated vesicle proteins . Second, the particular arrangement of an amino-terminal β-propeller followed by an α-solenoid appears to be unique to components of either vesicle coating complexes or of the yNup84/vNup107–160 subcomplex ( Protocol S1 ). Third, the overall composition of both complex types is similar, being mainly composed of proteins containing comparable distributions of β-propellers and α-solenoids . Fourth, both vesicle coating complexes and NPCs apparently share a common function: the bending and stabilizing of curved membranes. Fifth, the yNup84/vNup107–160 subcomplex actually contains bona fide vesicle coat components, Sec13 and Seh1. In light of these considerations, we favor the “protocoatomer” hypothesis, in which the NPCs and vesicle-coating complexes arose by a process of divergent evolution.
|
15523559_p12
|
15523559
|
Discussion
| 4.608692 |
biomedical
|
Study
|
[
0.9991508722305298,
0.0004479053313843906,
0.0004012699064332992
] |
[
0.9976091384887695,
0.000849113508593291,
0.0013583879917860031,
0.00018332798208575696
] |
en
| 0.999997 |
The lack of detectable sequence similarity between the proteins in the yNup84/vNup107–160 subcomplex and the coated vesicles is not surprising. Sequence comparisons of α-solenoid- and β-propeller-containing proteins suggest that these folds arose just before or around the time of the origin of eukaryotes, then rapidly duplicated and diversified . Both folds consist of repetitive structures, so the functional constraints on an individual repeat are weak, compared with the whole fold domain. It has been proposed that the robustness of these folds with respect to changes in their sequences permits their component repeats to individually lose their sequence similarity, eventually allowing the proteins they comprise to drift into new functions . Moreover, the lack of detectable sequence similarity for members of the same fold family is not necessarily an indicator of convergent evolution; obvious sequence similarities are often lost during long periods of evolution . The divergent pathway is also consistent with the conservation among members of the syntaxin family (key components of the vesicular transport machinery), which points to a similar early origin and rapid diversification of the eukaryotic endomembrane system . Based on these observations, we propose a single evolutionary origin for the structures maintaining both the endomembrane systems and the nucleus over models suggesting separate or even endosymbiotic origins for these structures.
|
15523559_p13
|
15523559
|
Discussion
| 4.750637 |
biomedical
|
Study
|
[
0.9989107847213745,
0.0005955824162811041,
0.0004935626056976616
] |
[
0.9955233335494995,
0.0008538764668628573,
0.0033499039709568024,
0.0002728916297201067
] |
en
| 0.999995 |
The current protocoatomer hypothesis posits that a simple coating module containing minimal copies of the two conserved folds evolved in protoeukaryotes as a mechanism to bend membranes into sharply curved sheets and invaginated tubules . The ability to so manipulate cell membranes represented a major evolutionary innovation that allowed, among other possibilities, the elaboration of internal membranes, phagotrophy, and endosymbiosis ; the importance of this ability is underscored by the presence of numerous types of membrane-curving devices in modern eukaryotes. As with clathrin, the flexibility of the α-solenoid in this simple module enabled the formation of curved membranes of various sizes. In addition, the α-solenoid repeat structure, together with the repeats in the β-propeller fold, provided the coating module with a large binding area. These features allowed the membrane-curving module to polymerize and form a coat, as well as to interact with other membrane-associated proteins. The endomembranes and their membrane-coating modules subsequently evolved to become more elaborate and specialized, with the partitioning of different functions into separate, interconnected compartments such as the ER, the Golgi, and the nucleus , each with their own specialized set of coating modules.
|
15523559_p14
|
15523559
|
Discussion
| 4.769326 |
biomedical
|
Study
|
[
0.9982315897941589,
0.0007662459393031895,
0.0010021876078099012
] |
[
0.8804125785827637,
0.005076338537037373,
0.1135825589299202,
0.0009285932756029069
] |
en
| 0.999997 |
In conclusion, we suggest that the progenitor of the NPC arose from a membrane-coating module that wrapped extensions of an early ER around the cell's chromatin. In this primitive NE, the coating modules would have originally formed the sharply curved membrane, creating large and freely permeable pores . These pores then closed to form the selectively permeable NPCs of modern eukaryotes . In doing so, they retained at their core a coating module as a relic of their evolutionary origins. This module, the yNup84/vNup107–160 subcomplex, may still serve to curve and stabilize the nuclear pore membrane in modern eukaryotes; as such, it would function as a key scaffold to form the NPCs, the portals of the nucleus. Our findings could thus provide an explanation for the origin of the nuclear pore complex (which until now has been a mystery) and may fill a significant gap in our understanding of the evolution of eukaryotes.
|
15523559_p15
|
15523559
|
Discussion
| 4.410246 |
biomedical
|
Study
|
[
0.9994093179702759,
0.0003348133177496493,
0.0002558992418926209
] |
[
0.9978882670402527,
0.0007313378155231476,
0.001234116731211543,
0.00014630271471105516
] |
en
| 0.999998 |
Only two domains in the seven nups have their folds assigned by sequence comparison to proteins of known structure . Therefore, to assign folds for as many target domains comprising the yNup84/vNup107–160 subcomplex as possible, we applied a structure-based approach consisting of iterative detection of potential template structures, their alignment to the target sequence, model building, and model assessment . Secondary structure was predicted from sequence by the PredictProtein and PSI-Pred servers.
|
15523559_p16
|
15523559
|
Untitled Section
| 4.161351 |
biomedical
|
Study
|
[
0.9995287656784058,
0.0002170172519981861,
0.00025431622634641826
] |
[
0.9991862177848816,
0.0005056793452240527,
0.00024201054475270212,
0.0000660713340039365
] |
en
| 0.999997 |
For each of the seven yeast nups and representative homologs, potentially related known structures were detected by the mGenThreader and FUGUE web servers ( Tables S1–S7 ). Several other servers gave similar results (unpublished data). To find out whether or not mGenThreader frequently identifies the β-propeller and α-solenoid folds as false positives, we randomly selected 20 sequences of known structure from each one of the structural classes and submitted them to mGenThreader. Using the same parameters as in our analysis of the nups, only two of these 140 sequences were incorrectly predicted to contain β-propeller or α-solenoid folds (unpublished data). Thus, we estimate the false positives rate for the nup fold assignments based on mGenThreader alone to be approximately 1%–2%.
|
15523559_p17
|
15523559
|
Detection of potential template structures
| 4.085015 |
biomedical
|
Study
|
[
0.9994558691978455,
0.000251442426815629,
0.0002927116001956165
] |
[
0.9994713664054871,
0.00020126951858401299,
0.0002751288120634854,
0.00005222762410994619
] |
en
| 0.999997 |
The matches obtained in the previous step provided an operational definition of a domain. They were either accepted or refined by manual and automated alignment. Manual realignment relied on sequence conservation and secondary structure predictions by PROF and PSI-PRED . The automatic realignments were obtained by SALIGN and T-Coffee . In the last iteration, the alignments and the models were refined by MOULDER, a genetic algorithm method for iterative alignment, model building, and model assessment .
|
15523559_p18
|
15523559
|
Alignment of the matched target-template pairs
| 4.113106 |
biomedical
|
Study
|
[
0.9991909861564636,
0.0003056503483094275,
0.0005033325869590044
] |
[
0.987330973148346,
0.01116913091391325,
0.0012955687707290053,
0.00020440944354049861
] |
en
| 0.999995 |
For each alignment, an all-atom model was built by comparative modeling based on satisfaction of spatial restraints as implemented in MODELLER .
|
15523559_p19
|
15523559
|
Model building
| 3.790486 |
biomedical
|
Study
|
[
0.9986973404884338,
0.0003850686189252883,
0.0009176481398753822
] |
[
0.9620018601417542,
0.036276090890169144,
0.0012811206979677081,
0.00044103062828071415
] |
en
| 0.999998 |
The fold assignment, alignment, and model building were repeated by varying the domain boundaries, target sequences for modeling, template structures, and their alignments. The aim was to improve model assessment by statistical potentials of ProsaII and DFIRE , and by a composite model evaluation criterion . The only importance of explicit model building in this analysis was to provide another semi-independent way to validate the fold assignments: If a model was assessed to have the correct fold, the initial fold assignment must have been correct. Beyond that, the models were not used.
|
15523559_p20
|
15523559
|
Model assessment.
| 4.08987 |
biomedical
|
Study
|
[
0.9991944432258606,
0.0003057662979699671,
0.0004998068325221539
] |
[
0.998988687992096,
0.000586412672419101,
0.00036185249336995184,
0.00006297616346273571
] |
en
| 0.999995 |
To search for proteins that resemble the domain architecture of clathrin, we queried MODBASE , our relational database of annotated comparative protein structure models, and Superfamily , a database of HMM-based structural assignments. Both databases assign folds to all available protein sequences that match at least one known protein structure. We first searched for any protein sequences that were matched to both β-propeller and α-solenoid structures. We used the broadest definitions of the β-propeller folds (b.66, b.67, b.68, b.69, b.70, for 4-, 5-, 6-, 7- and 8-bladed β-propellers, respectively) and α-solenoid folds (a.118) from the SCOP database (v1.65) . In MODBASE, we found 95 proteins predicted to contain both β-propeller and α-solenoid domains ( Protocol S1 ). Of these 95 proteins, 37 passed the following filters, ensuring clathrin-like characteristics: they had to be 800–2,000 residues long, the amino-terminal β-propeller domain had to be followed by a carboxyl-terminal α-solenoid domain, the β-propeller and α-solenoid domains each had to span at least 35% of the total length, and no other domain could be more than 25% of the total length. All of the 37 proteins were from eukaryotes. Their functions were assigned either as clathrin or unknown in the Swiss-Prot/TrEMBL database . Similar results were obtained by querying the Superfamily database .
|
15523559_p21
|
15523559
|
Domain combination search.
| 4.230372 |
biomedical
|
Study
|
[
0.9994651675224304,
0.00030887944740243256,
0.00022599502699449658
] |
[
0.9992517828941345,
0.0001985368289751932,
0.0004765251651406288,
0.00007319052383536473
] |
en
| 0.999997 |
Magnetic beads (2.8 μm Dynabeads M-270 Epoxy [#143.02; Dynal, Oslo, Norway]) were conjugated to rabbit IgG according to the manufacturer's instructions. Yeast cells carrying PrA-tagged versions of nups were grown and harvested as described previously . Cell pellets were frozen in liquid nitrogen and homogenized to a fine powder in a motorized grinder (#RM100; Retsch, Haan, Germany) continuously cooled with liquid nitrogen. The cell powder was thawed on ice and ten volumes of extraction buffer were added to cells and homogenized at 4 °C with a Polytron (Kinematica, Littau-Luzerne, Switzerland). The cell lysate was clarified by centrifugation (2,000 g for 5 min at 4 °C). The magnetic beads were added to the extract to a ratio of about 8 × 10 9 beads per g of cells. After incubation for 1 h at 4 °C, the beads were magnetically recovered. The beads were washed, resuspended in 50 μl of reaction buffer (according to the manufacturer's specifications), and Asp-N or Lys-C proteinase was added to give a weight ratio of 1:200 of proteinase to the tagged nup. After incubation at different time points at 37 °C, bead aliquots were removed and washed, and tagged fragments were eluted with 0.5 M NH 4 OH containing 0.5 mM EDTA. The eluant was vacuum-dried, resuspended in SDS-PAGE sample buffer, and separated on a 4%–12% bis-Tris gel (Invitrogen, Carlsbad, California, United States). Proteins were then either transferred electrophoretically to nitrocellulose or PVDF and probed with HRP-rabbit IgG , or analyzed by amino-terminal Edman sequencing .
|
15523559_p22
|
15523559
|
Proteolytic domain laddering.
| 4.244919 |
biomedical
|
Study
|
[
0.9994580149650574,
0.00033634566352702677,
0.00020567243336699903
] |
[
0.9977704286575317,
0.0015420762356370687,
0.0005544624873436987,
0.0001329705264652148
] |
en
| 0.999998 |
Uniprot accession numbers ( http://www.pir.uniprot.org ) for proteins discussed in this paper are as follows. Yeast: ySeh1 , ySec13 , yNup84 , yNup85 , yNup120 , yNup133 , and yNup145C . Human: vSec13 l (Q96EE3), vSec13R , vNup107 , vNup75 (Q9BW27), vNup160 , vNup133 (Q8WUM0), and vNup96 .
|
15523559_p23
|
15523559
|
Accession Numbers
| 2.105705 |
biomedical
|
Other
|
[
0.993287980556488,
0.0009113101405091584,
0.005800737999379635
] |
[
0.03848818317055702,
0.9594888687133789,
0.0009765640133991838,
0.0010463387006893754
] |
en
| 0.999996 |
Adult autoimmune thrombocytopenic purpura (ITP) is a chronic acquired organ-specific autoimmune thrombocytopenic syndrome . The low peripheral platelet concentration observed in ITP is the result of reduced platelet life span because of their early removal from the peripheral blood by the activated reticuloendothelial system of the spleen, liver or bone marrow, after their sensitization by autoantibodies that recognize their surface glycoprotein antigens . Apart from phagocytosis, destruction mechanisms include complement activation and direct cellular attack by T lymphocytes . Ineffective thrombocytopoiesis because of autoimmune attack of megakaryocytes in the bone marrow contributes to the thrombocytopenia with varying degrees among cases . The production of platelet autoantibodies by B-cells is driven by activated platelet-specific autoreactive T-cells . The phenotype of the disease-specific T helper cells has been shown to be skewed towards type 1 cytokine production .
|
15491502_p0
|
15491502
|
Background
| 4.583478 |
biomedical
|
Study
|
[
0.9991288781166077,
0.0006556281005032361,
0.00021546200150623918
] |
[
0.9089050889015198,
0.009087798185646534,
0.08070188760757446,
0.0013052496360614896
] |
en
| 0.999997 |
The spleen is considered to be the primary site of the autoimmune response where initiation, maintenance and regulation of the autoimmune attack take place. The spleen is the site of autoreactive T- and B-cell interaction and activation, and autoreactive anti-platelet antibody production . Platelet destruction is also sited mainly in the spleen in most patients .
|
15491502_p1
|
15491502
|
Background
| 3.882731 |
biomedical
|
Other
|
[
0.9992451667785645,
0.00037667909055016935,
0.0003782428102567792
] |
[
0.31239569187164307,
0.6575051546096802,
0.028629986569285393,
0.0014692022232338786
] |
en
| 0.999997 |
Splenectomy is followed by reduction of autoantibody peripheral blood titre . Spleen cells isolated from ITP patients produce antiplatelet immunoglobulin in in vitro cultures . The percentage of T- and B-cells with activated phenotype is far greater in the spleen than in the peripheral blood of ITP patients . The number of circulating autoreactive anti-platelet T- and B-cells declines after splenectomy that leads to clinical remission, whereas the peripheral blood concentration of CD3 + CD4 + , CD3 + CD8 + , CD3 + HLADR + , and CD3 + CD25 + cells increases significantly in ITP patients refractory to splenectomy . Changes in the histology of the spleen have been observed in ITP patients and include follicular hyperplasia, foam macrophages, and extramedullary hematopoiesis, among others .
|
15491502_p2
|
15491502
|
Background
| 4.325331 |
biomedical
|
Study
|
[
0.9995538592338562,
0.0003318172530271113,
0.00011429750156821683
] |
[
0.9963586926460266,
0.0006290667806752026,
0.0028259344398975372,
0.00018635991727933288
] |
en
| 0.999997 |
Splenectomy is the most clinically effective therapeutic intervention in ITP patients, resulting in complete remission in two thirds of the patients with more than 60% maintaining the therapeutic effect in the long term . Irrespective of clinical response, splenectomy seems to affect the natural history of the disease and to enhance the response of ITP patients to other treatments that follow .
|
15491502_p3
|
15491502
|
Background
| 3.767187 |
biomedical
|
Review
|
[
0.9968253374099731,
0.002610201947391033,
0.0005644432967528701
] |
[
0.02858647145330906,
0.057432714849710464,
0.9124414324760437,
0.0015394071815535426
] |
en
| 0.999997 |
Given the important immunoregulatory role of the spleen, we looked at the effects of splenectomy on immune activation and immune deviation indices in the peripheral blood of an ITP patient after splenectomy in association with peripheral platelet counts.
|
15491502_p4
|
15491502
|
Background
| 3.846972 |
biomedical
|
Study
|
[
0.9993364214897156,
0.0004691084031946957,
0.0001944571704370901
] |
[
0.9984153509140015,
0.0011014207266271114,
0.00025624767295084894,
0.0002269325777888298
] |
en
| 0.999995 |
A 42 year old woman presented in October 1999 in Patras University Hospital (PUH) with lower limb purpura and low platelet count (7 × 10 6 /L). Following clinical exclusion of causes of secondary thrombocytopenia the diagnosis of ITP was reached.
|
15491502_p5
|
15491502
|
Case presentation
| 2.454784 |
clinical
|
Clinical case
|
[
0.29659777879714966,
0.6941601634025574,
0.009242069907486439
] |
[
0.0027047726325690746,
0.011420253664255142,
0.0019342917948961258,
0.9839406609535217
] |
en
| 0.999999 |
The patient initially received glucocorticoid treatment to which she showed a temporary response until 6 months later when she relapsed. She was subsequently started on danazol without any clinical benefit. Intravenous immune globulin administration also proved ineffective after two 5-day cycles. As a result, the patient was subjected to splenectomy 9 months after the diagnosis with complete response, attaining platelet counts over 150 × 10 6 /L within 10 days after the operation. Five years later, she remains in clinical remission.
|
15491502_p6
|
15491502
|
Case presentation
| 3.318666 |
clinical
|
Clinical case
|
[
0.05506895110011101,
0.9408550262451172,
0.004075963515788317
] |
[
0.002730039181187749,
0.006075771991163492,
0.0024152740370482206,
0.988778829574585
] |
en
| 0.999997 |
Two consecutive blood samples were obtained from the patient, 3 and 7 months after splenectomy for the purposes of this study. A control group consisted of 11 adult healthy volunteers (6 women and 5 men, median age 40 years, range 18–65 years). Informed consent was obtained from the patient. PUH abides by the Helsinki declaration on ethical principles for medical research involving human subjects.
|
15491502_p7
|
15491502
|
Case presentation
| 2.721716 |
biomedical
|
Study
|
[
0.9966939687728882,
0.002699822187423706,
0.0006062122993171215
] |
[
0.9859585165977478,
0.011772490106523037,
0.000663897255435586,
0.001605152036063373
] |
en
| 0.999997 |
Peripheral blood mononuclear cells (PBMC) were prepared from each blood sample by centrifugation over a Ficoll-Paque gradient (Pharmacia, Sweden). The cells were cultured in vitro for 8 h with the addition of 20 ng/ml phorbol myristate acetate (PMA) and 1 μM ionomycin (Sigma, St-Louis, MI).
|
15491502_p8
|
15491502
|
Case presentation
| 4.046515 |
biomedical
|
Study
|
[
0.9995338916778564,
0.0003108335949946195,
0.00015528028598055243
] |
[
0.9967257976531982,
0.0025973350275307894,
0.0005516187520697713,
0.00012520054588094354
] |
en
| 0.999996 |
Total cellular RNA extracted from 10 6 cells was submitted to semiquantitative RT-PCR for the amplification of IL-2, IFN-γ, IL-4, IL-5, and IL-10 metagraphs . Primers and conditions for the RT-PCR are summarized in Table 1 . The PCR products were run on ethidium-stained agarose gels, photographed and quantified .
|
15491502_p9
|
15491502
|
Case presentation
| 4.078174 |
biomedical
|
Study
|
[
0.999617338180542,
0.0001780931488610804,
0.00020448978466447443
] |
[
0.9990308284759521,
0.0005805176915600896,
0.00032835116144269705,
0.000060360864154063165
] |
en
| 0.999997 |
A sharp decrease in the expression of the type-1 cytokines IL-2 and IFN-γ and their calculated sum expressing Th1 activity was observed at 7 months after splenectomy compared to 3 months after splenectomy ; this was accompanied by a parallel rise of platelet count from 190 × 10 6 /L to 265 × 10 6 /L. Regarding type-2 cytokine gene expression, IL-4 increased, IL-5 decreased, and IL-10 remained unchanged, whereas the change in Th2 activity (IL-4 units plus IL-5 units) was slight . The Th1/Th2 ratio {(IL-2+IFNγ)/(IL-4+IL-5)}, that reflects immune deviation, was accordingly greatly reduced 7 months post-splenectomy (Th1/Th2 = 1.3) compared to 3 months (Th1/Th2 = 3.5) . Mean Th1/Th2 ratio of the controls was 0.5 with 95% confidence intervals of the mean (0.15–0.85). The Th1/Th2 values at 3 months and at 7 months post-splenectomy lie at 6.25 and 1.6 standard deviations above the mean of the controls, respectively.
|
15491502_p10
|
15491502
|
Case presentation
| 4.232601 |
biomedical
|
Study
|
[
0.9994137287139893,
0.0003883897152263671,
0.00019791013619396836
] |
[
0.9992627501487732,
0.00022142226225696504,
0.0004223140131216496,
0.00009355191286886111
] |
en
| 0.999998 |
The above results show that in this patient type-1 polarization persists after removal of the spleen and attainment of clinical remission. This may mean that the spleen is not exclusively responsible for the coordination or the maintenance of the pathological immune response in this patient, provided that no accessory splenic tissue exists. Other disease centres may control the autoimmune reaction as well, such as the liver or the bone marrow. Alternatively, it is possible that ITP is the manifestation of a general immune system malfunction that pre-existed before the development of thrombocytopenia and persists after removal of what seems to be the effector of a manifestation of an autoimmune proclivity.
|
15491502_p11
|
15491502
|
Case presentation
| 4.15316 |
biomedical
|
Study
|
[
0.9982699155807495,
0.0016140863299369812,
0.00011606844782363623
] |
[
0.9811551570892334,
0.011867642402648926,
0.0024366441648453474,
0.004540429450571537
] |
en
| 0.999997 |
Unfortunately, a pre-splenectomy sample was not available for analysis. As a result, no conclusions can be drawn about the effect of splenectomy on the direction of change of Th1 activity. Based on phenotypic studies showing increased presence of T lymphocytes with activated phenotype after splenectomy in ITP patients , it is plausible that peripheral Th1 activity may have increased after splenectomy.
|
15491502_p12
|
15491502
|
Case presentation
| 3.350929 |
biomedical
|
Study
|
[
0.9993234872817993,
0.00021386361913755536,
0.00046266516437754035
] |
[
0.9876359105110168,
0.010917156003415585,
0.0011592913651838899,
0.00028764724265784025
] |
en
| 0.999998 |
The clinical remission may be due to the removal of a major platelet destruction site, although the underlying immune activity that drives the destruction may remain unaffected. Complete remission does not mean that increased platelet destruction has stopped after splenectomy. Platelet life span may still be shortened in this patient and/or her normal platelet count may be even higher than what was achieved after splenectomy.
|
15491502_p13
|
15491502
|
Case presentation
| 3.614579 |
biomedical
|
Other
|
[
0.9414550065994263,
0.05750676989555359,
0.0010382571490481496
] |
[
0.10120006650686264,
0.6496453881263733,
0.0053410218097269535,
0.24381348490715027
] |
en
| 0.999997 |
The pathological immune activity seems to decrease over time after splenectomy, as reflected by the lower Th1/Th2 ratio that is indicative of the degree of immune polarization. This may be explained by reduced stimulation of the immune system by activated spleen reticuloendothelial cells that present platelet antigens to T helper lymphocytes. In this way, it may be hypothesized that removal of one vital component of the self-attacking immune process can break the vicious circle that culminates in even greater immune activation, polarization, and platelet destruction. Removal of a major site of autoimmune activity may have abrogated recruitment of naïve T-cells. As a result, overall autoimmune activity wears off, as existing activated Th1 effector cells perish leaving behind a much smaller population of peripheral memory cells that retain the initial Th phenotype.
|
15491502_p14
|
15491502
|
Case presentation
| 4.347081 |
biomedical
|
Study
|
[
0.9994935989379883,
0.00036590854870155454,
0.00014043728879187256
] |
[
0.9972150325775146,
0.0010073252487927675,
0.0016101771034300327,
0.0001674115628702566
] |
en
| 0.999996 |
Another consideration that stems from the results of this case study is that immune polarization and immune deviation of the pathological response depend more on upregulation of type-1 mediators rather than on suppression of type-2 cytokines, or that type-2 response is inadequate to control excess type-1 response in active disease.
|
15491502_p15
|
15491502
|
Case presentation
| 3.886855 |
biomedical
|
Study
|
[
0.9976322650909424,
0.0021047128830105066,
0.0002628976944833994
] |
[
0.782875120639801,
0.19266892969608307,
0.007485297042876482,
0.016970612108707428
] |
en
| 0.999997 |
Clinical improvement after splenectomy is associated with reduced but not normalized immune activation and polarization in the patient studied. However, the spleen seems not to be absolutely necessary for the maintenance of the autoimmune reactivity.
|
15491502_p16
|
15491502
|
Conclusions
| 3.259851 |
biomedical
|
Study
|
[
0.9983764886856079,
0.0010966876288875937,
0.0005268110544420779
] |
[
0.8387442231178284,
0.1498844176530838,
0.008129616267979145,
0.0032418416813015938
] |
en
| 0.999996 |
The authors declare that they have no competing interests.
|
15491502_p17
|
15491502
|
Competing interests
| 0.956449 |
other
|
Other
|
[
0.014629608951508999,
0.0016160424565896392,
0.9837543368339539
] |
[
0.004644682165235281,
0.9930703043937683,
0.0012706087436527014,
0.0010144523112103343
] |
en
| 0.999997 |
FPP prepared the case report, performed the experiments and drafted the manuscript. AM conceived of the study, participated in its design and coordination and co-wrote the manuscript. Both authors read and approved the final manuscript.
|
15491502_p18
|
15491502
|
Authors' contributions
| 0.821541 |
other
|
Other
|
[
0.09306682646274567,
0.01020115241408348,
0.8967320322990417
] |
[
0.002868564100936055,
0.9938200116157532,
0.0012297243811190128,
0.0020816742908209562
] |
en
| 0.999995 |
The pre-publication history for this paper can be accessed here:
|
15491502_p19
|
15491502
|
Pre-publication history
| 1.031347 |
other
|
Other
|
[
0.013091341592371464,
0.0014214670518413186,
0.9854872226715088
] |
[
0.0015875872923061252,
0.997281551361084,
0.0006836647517047822,
0.0004471398133318871
] |
en
| 0.999997 |
Epithelial ovarian cancer is the fifth leading cause of death for women in the United States . Although early stage ovarian cancer can be effectively treated, symptoms of early disease are sufficiently vague that accurate diagnosis is often delayed until the cancer has progressed into more advanced stages . Treatment of early staged tumours (I through IIa) is associated with a 5-year survival rate of approximately 95% while survival rates drop to less than 30% when diagnosis is delayed until later stages (stage IIb through IV). To improve these statistics, effective early diagnosis and treatment strategies must be developed. Further knowledge of the genes and gene functional pathways involved in ovarian cancer are needed in order to develop these strategies.
|
15471544_p0
|
15471544
|
Background
| 3.968952 |
biomedical
|
Review
|
[
0.998245358467102,
0.0008490969194099307,
0.0009056442067958415
] |
[
0.08905192464590073,
0.014233946800231934,
0.8961560130119324,
0.0005581991281360388
] |
en
| 0.999994 |
Microarray technology has revolutionised the study of gene function by providing "snapshots" of global gene expression patterns from different normal and diseased tissues over multiple stages of development. Nowhere has the impact of this technology been more pronounced than in the field of cancer biology where gene expression profiling has been successfully used to objectively classify tumours and, in some instances, identify novel tumour sub-types . Microarray analyses have also been instrumental in the elucidation of new biological pathways that may be involved in tumour development, as well as, in the identification of new biomarkers of the disease and potential targets of therapeutic intervention.
|
15471544_p1
|
15471544
|
Background
| 4.230725 |
biomedical
|
Review
|
[
0.9923864603042603,
0.0035704246256500483,
0.004043050110340118
] |
[
0.010079050436615944,
0.009256472811102867,
0.9799341559410095,
0.0007303436868824065
] |
en
| 0.999996 |
Previous microarray studies of ovarian cancers have focused on the characterisation of differences between normal ovarian epithelial cells (and cell lines) and various types and stages of ovarian tumours . In this study, we focus on characterising differences between benign adenomas, borderline tumours of low malignant potential and malignant adenocarcinomas in order to identify changes associated with the acquisition of malignancy and to avoid the technical difficulties associated with obtaining sufficient amounts of normal ovarian surface epithelium. The ovarian tumour tissue samples used in these microarray studies were chosen to accurately represent the range of malignant potential observed clinically.
|
15471544_p2
|
15471544
|
Background
| 4.089621 |
biomedical
|
Study
|
[
0.9994959831237793,
0.00026884357794187963,
0.00023523181152995676
] |
[
0.9993675351142883,
0.00016712186334189028,
0.0004112691676709801,
0.00005416114436229691
] |
en
| 0.999996 |
We report here the results of applying clustering and statistical analyses to the microarray expression profiles of 18 ovarian tumours. Our findings indicate that gene expression profiling distinguished properly classify 92% of tumours in this study as benign or malignant. Samples taken from ovarian cancer patients who had been treated with chemotherapy prior to surgery were found not to cluster as a distinct group but rather with either the benign or malignant (not pre-treated) tumours. Chemotherapy patients whose tumours clustered with the benign group remained disease free for the duration of the study as evidenced by continued normal serum CA-125 levels. Profiling the functional categories of co-ordinately expressed genes revealed significant correlation between increased malignant potential and loss of IGF binding proteins, and cell adhesion molecules. In several instances co-ordinately expressed genes sharing functional categories also correlated with chromosomal location.
|
15471544_p3
|
15471544
|
Background
| 4.116992 |
biomedical
|
Study
|
[
0.9993100166320801,
0.0004790077218785882,
0.00021100020967423916
] |
[
0.9993552565574646,
0.00017193396342918277,
0.0003844158782158047,
0.00008833630272420123
] |
en
| 0.999998 |
To determine if gene expression profiling can distinguish between histologically determined tumour types, we analysed the profiles of 13 ovarian tumours (Table 1 ) by performing clustering using self-organising maps (SOM) and unsupervised hierarchical clustering (UHC). Self-organising maps are a type of mathematical cluster analysis used to recognise and classify features in complex multi-dimensional data . SOMs group samples into a user-defined number of clusters based on the similarity of the gene expression profiles. The set of thirteen samples was comprised of four benign adenomas (a_64, a_77, a_97, a_159), four borderline tumours of low malignant potential (b_15, b_65, b_72, b_120) and five malignant adenocarcinomas (c_2, c_4, c_23, c_66, c_79). Analysing all 12,590 probe set values from the 13 samples into four groups resulted in 92% of the samples being grouped into clusters consistent with their histopathological classification . One cluster (cluster 0) contained only adenocarcinomas, two clusters (clusters 1 and 2) contained only borderline tumours, and one cluster (cluster 3) contained all of the benign adenomas and one adenocarcinoma sample. In addition, the UHC of the entire data set produced essentially the same clusters as determined by SOM. The only difference between the SOM and UHC results was the stratification of borderline tumours, which are known to be a heterogeneous group of tumours. The SOM clustered the four borderline samples into one group of three borderlines (b_65, b_15, b_72) and one solitary sample (b_120) . However, the UHC clustered the four borderline samples into one group containing b_15 and b_120, and one group containing b_65, and b_72. Since c_79 was consistently misclassified, a second tissue sample of c_79 was analysed by microarray and clustered as above. This independently obtained expression profile for c_79 produced the same results.
|
15471544_p4
|
15471544
|
Unsupervised clustering of gene expression profiles can reliably identify ovarian tumour types
| 4.184562 |
biomedical
|
Study
|
[
0.9993815422058105,
0.0004010547127109021,
0.00021745845151599497
] |
[
0.9993357062339783,
0.0002076325035886839,
0.00036806706339120865,
0.0000885817498783581
] |
en
| 0.999997 |
Since many of the genes in our data set display no differential expression across the 13 tumours, their contribution to the SOM is negligible and can be considered noise. Removing genes whose expression pattern displayed insignificant variation (low standard deviation) across all samples, we reduced the data set to1000 probe sets. After removing probe sets representing the same gene, the reduced data set contained expression values representing 700 genes. The SOM and UHC of the reduced data set yielded identical clusters to those obtained using the entire data set .
|
15471544_p5
|
15471544
|
Unsupervised clustering of gene expression profiles can reliably identify ovarian tumour types
| 3.979186 |
biomedical
|
Study
|
[
0.9994292855262756,
0.00019686507584992796,
0.00037383942981250584
] |
[
0.999258816242218,
0.0004794022534042597,
0.00020000265794806182,
0.0000617572950432077
] |
en
| 0.999997 |
To determine the genes most highly correlated with each cluster identified by the SOM analysis, we performed a marker analysis on the reduced set of 700 genes. Marker analysis helps the user discover which genes are most closely correlated with a cluster and provides a measure of how significant that correlation is for each gene. Marker analysis measures the contribution of each gene to the SOM groupings based on a signal to noise ratio calculated from the difference in each gene's mean expression scaled by the sum of the standard deviations across all samples. To avoid having one cluster containing only one sample in the marker analysis, we grouped clusters cluster 1 and cluster 2 containing the borderline samples together, creating three clusters consisting of the benign adenomas and c79 (SOM_a), borderline adenocarcinomas (SOM_b), and the malignant adenocarcinomas (SOM_c). Genes highly correlated with each SOM group were expressed strongly in the tumour type associated with that SOM group and poorly expressed in the other SOM groups. It is interesting to note that the 10 genes highly correlated with SOM_a were expressed at intermediate levels in borderline tumours. Similarly, the 10 genes highly correlated with SOM_b were expressed at intermediate levels in the adenocarcinomas of SOM_c.
|
15471544_p6
|
15471544
|
Unsupervised clustering of gene expression profiles can reliably identify ovarian tumour types
| 4.107834 |
biomedical
|
Study
|
[
0.9995447993278503,
0.0002321456850040704,
0.00022309698397293687
] |
[
0.9994686245918274,
0.00020590992062352598,
0.00027506795595400035,
0.00005040840187575668
] |
en
| 0.999996 |
Five of the cancer patients in our study were treated with chemotherapy prior to surgery. We added the microarray profiles of these patient samples to our analysis in order to determine if they would cluster into a new distinct group or into one or more of the existing groups. The SOM and UHC clusters resulting from the analysis of all data (12,590 expression values) from all eighteen samples into four clusters differ only in the stratification of the borderline samples. The addition of the five samples from patients who received chemotherapy prior to surgery did not change the cluster assignments of the original thirteen samples. Clustering of the reduced set of 700 genes (see above), resulted in the same patterns of clustering as determined using the entire set of 12,590 expression values . Interestingly, the five samples from patients pre-treated with chemotherapy did not cluster together in a distinct group but rather were dispersed among the existing four clusters. Samples cc_29 and cc_76 clustered with the malignant adenocarcinomas, while samples cc_36 and cc_9 clustered with the benign adenomas. Sample cc_94 clustered with the borderline tumours.
|
15471544_p7
|
15471544
|
Gene expression profiles are correlated with recurrence
| 4.076863 |
biomedical
|
Study
|
[
0.9993459582328796,
0.000320234103128314,
0.00033384902053512633
] |
[
0.9995949864387512,
0.00016248997417278588,
0.00019034177239518613,
0.00005218951991992071
] |
en
| 0.999995 |
In an initial effort to test the possible clinical significance of the differential clustering of samples obtained from patients pre-treated with chemotherapy, we examined the post-operative history of these patients. One commonly used indicator of recurrence is the level of Cancer Antigen-125 (CA-125) in the blood . Although post-operative CA-125 levels were initially lowered to a significant extent in all of the patients pre-treated with chemotherapy, the levels remained consistently low in only those patients (cc_36, cc_9) whose microarray profiles clustered with the benign adenomas . The remaining patients displayed periodic recurrence requiring additional chemotherapy.
|
15471544_p8
|
15471544
|
Gene expression profiles are correlated with recurrence
| 4.052708 |
biomedical
|
Study
|
[
0.9991212487220764,
0.0006485882913693786,
0.00023006372794043273
] |
[
0.9993653893470764,
0.00027534502441994846,
0.0002560430148150772,
0.00010322062007617205
] |
en
| 0.999998 |
To identify genes whose differential expression correlate with malignant potential, we performed a statistical analysis comparing the expression profiles of the three tumour types examined in this study (benign adenoma, low malignant potential borderline adenocarcinoma, and malignant adenocarcinoma). Malignant adenocarcinoma sample c_79 was excluded from this analysis since both the SOM and UHC classification methods identified this sample as an outlier of the malignant adenocarcinoma group (see above). The F statistic was used to test equality of group means . Genes whose group means were identified as significantly different (p ≤ 0.001, 299 genes) in the ANOVA analysis were further analyzed using multiple comparison methods to determine which means differ from each other. The differences between group means for all pairwise combinations of groups were calculated and compared to the least significant difference. Genes were declared differentially expressed if the pairwise difference between group means was greater than the least significant difference. Probe sets duplicated between pairwise comparisons and probes sets with a fold change value below 2.0 were removed, leaving 163 unique genes differentially expressed between the tumour groups. The 15 differentially expressed genes with highest statistical significance are presented in Table 2 . The gene name, gene symbol, chromosomal location, functional classification, ANOVA rank and p-value of each of these 163 genes are attached as additional file 1 (complete list.txt).
|
15471544_p9
|
15471544
|
Significant differences in gene expression are associated with different ovarian tumour types
| 4.129075 |
biomedical
|
Study
|
[
0.9994320273399353,
0.00036050184280611575,
0.00020747595408465713
] |
[
0.9993888139724731,
0.0001649011974222958,
0.00036788554280065,
0.00007843289495212957
] |
en
| 0.999996 |
Hierarchical clustering was performed to visualise gene expression across tumour types for each of these 163 genes. All 12 tumours were correctly assigned as shown by the dendogram above the gene expression colour plot . Several features within the gene expression colour plot are worthy of note . Thirteen genes showed high expression in both adenoma and borderline. For forty genes expression levels in borderline tumours was intermediate between adenoma and cancer . Eight genes were highly expressed in either adenoma or borderline . And finally, thirteen genes showed high expression in both cancer and borderline .
|
15471544_p10
|
15471544
|
Significant differences in gene expression are associated with different ovarian tumour types
| 4.070776 |
biomedical
|
Study
|
[
0.9994055032730103,
0.0003034239634871483,
0.00029106123838573694
] |
[
0.9993383288383484,
0.0003291841421741992,
0.00026891243760474026,
0.00006361437408486381
] |
en
| 0.999997 |
Subsets and Splits
SQL Console for rntc/test-pp-aa
The query retrieves a sample of documents that are clinical cases with an educational score above 3, providing limited analytical value.
Clinical Cases Sample
Returns a sample of 100 clinical case documents, providing a basic overview of the document type's content.