Linkage Disequilibrium and Haplotype Studies of Chromosome 8p 11.1-21.1 Markers and Werner Syndrome

Werner syndrome (WS) is an autosomal recessive disorder, characterized as a progeroid syndrome, previously mapped to the 8p 11.1-21.1 region. Because WS is so rare, and because many patients are from consanguineous marriages, fine localization of the gene by traditional meiotic mapping methods is unlikely to succeed. Here we present the results of a search for a region that exhibits linkage disequilibrium with the disorder, under the assumption that identification of such a region may provide an alternative method of narrowing down the location of WRN, the gene responsible for WS. We present allele frequencies in Japanese and Caucasian cases and controls for D8S137, D8S131, D8S87, D8S278, D8S259, D8S283, fibroblast growth factor receptor 1, ankyrin 1, D8S339, and two polymorphisms in glutathione reductase (GSR), covering ~16.5 cM in total. We show that three of the markers examined—D8S339 and both polymorphisms in the GSR locus—show strong statistically significant evidence of disequilibrium with WRN in the Japanese population but not in the Caucasian population. In addition, we show that a limited number of haplotypes are associated with the disease in both populations and that these haplotypes define clusters of apparently related haplotypes that may identify as many as eight or nine independent WRN mutations in these two populations.     

Effects of ouabain on calcium paradox in rat hearts

The effects of ouabain (10(-7) to 10(-5) M) on the interrelationship between cell-cell contacts, resting tension, and creatine phosphokinase (CK) leakage owing to myocardial cell injury during Ca2+ paradox were studied in isolated perfused rat heart preparations. After perfusing for 15 min with Ca2+ -containing medium, hearts were perfused for 5 min with Ca2+ -free medium followed by a reperfusion with Ca2+ -containing medium for 5 min. This resulted in a transient increase in resting tension and a substantial release of CK into the perfusate during the calcium reperfusion period. These changes were accompanied by extensive structural damage in the myocardial cell, including formation of contraction bands, swelling of the mitochondria, and cell-cell separation. Inclusion of 10(-5) M ouabain for 5 min in the Ca2+ -containing perfusion medium prior to the start of Ca2+ -free perfusion resulted in a higher and sustained resting tension that was accompanied by a reduced loss of CK from the heart during Ca2+ reperfusion. In a histological examination of these ouabain exposed hearts, most of the structural changes owing to calcium paradox were apparent, but the cell-cell contacts were maintained. The results are consistent with the hypothesis that the loss of cell-cell contacts in the intercalated disc during the occurrence of Ca2+ paradox may be the cause of the delayed decline in the resting tension and is only partially responsible for the loss of CK. These differences in myocardial changes during Ca2+ paradox with or without ouabain may be due to the retention of calcium at certain crucial sites under the influence of ouabain.     

Histamine decreases left ventricular contractility in normal human subjects.

To determine whether histamine alters human left ventricular contractility we measured heart rate, calibrated carotid arterial pressure, and left ventricular dimensions (echocardiogram) in nine healthy volunteers. We assessed baseline contractility using the end-systolic pressure-dimension relationship and the end-systolic meridional wall stress-rate-corrected velocity of circumferential fiber shortening relationship determined over a wide range of afterloads using phenylephrine and nitroprusside infusions. We then infused histamine for 3-5 min at a dose predetermined to decrease mean arterial pressure by 20%, both before and after H1 receptor antagonist pretreatment (diphenhydramine 50 mg i.v.). Histamine decreased end-systolic pressure but, unlike an equally hypotensive infusion of nitroprusside, did not decrease end-systolic dimension or increase fractional shortening. Histamine also decreased velocity of circumferential fiber shortening at the same end-systolic meridional wall stress as controls (P < 0.05). These effects of histamine were inhibited by H1 antagonist pretreatment. We conclude that the dominant effect of histamine on the human heart is to decrease left ventricular contractility and that this decrease in contractility is dependent, at least partially, on H1-receptor activation.     

Have grass carp driven declines in macrophyte occurrence and diversity in the Vaal River,South Africa?

The Vaal River, South Africa, historically had a rich diversity of native submerged macrophytes with at least 13 species from 5 families recorded. Over the past 10 years there has been a noticeable reduction in the occurrence and diversity of submerged macrophytes in the river. It is possible that this is linked to the recent increase in the populations of invasive alien grass carp Ctenopharyngodon idella Cuvier & Valenciennes (Cyprinidae) in the river, where populations have been a concern since 2005. Grass carp invasions worldwide have been shown to have severe impacts on macrophyte biodiversity and ecosystem functioning. This fish is an aggressive feeder on submerged macrophytes, as well as being an ecosystem engineer that can change water and sediment chemistry.     

Soil Respiration in Semiarid Temperate Grasslands under Various Land Management

Soil respiration, a major component of the global carbon cycle, is significantly influenced by land management practices. Grasslands are potentially a major sink for carbon, but can also be a source. Here, we investigated the potential effect of land management (grazing, clipping, and ungrazed enclosures) on soil respiration in the semiarid grassland of northern China. Our results showed the mean soil respiration was significantly higher under enclosures (2.17μmol.m⁻².s⁻¹) and clipping (2.06μmol.m⁻².s⁻¹) than under grazing (1.65μmol.m⁻².s⁻¹) over the three growing seasons. The high rates of soil respiration under enclosure and clipping were associated with the higher belowground net primary productivity (BNPP). Our analyses indicated that soil respiration was primarily related to BNPP under grazing, to soil water content under clipping. Using structural equation models, we found that soil water content, aboveground net primary productivity (ANPP) and BNPP regulated soil respiration, with soil water content as the predominant factor. Our findings highlight that management-induced changes in abiotic (soil temperature and soil water content) and biotic (ANPP and BNPP) factors regulate soil respiration in the semiarid temperate grassland of northern China.     

A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types

The vaginal microbiota is important in women’s reproductive and overall health. However, the relationships between the structure, function and dynamics of this complex microbial community and health outcomes remain elusive. The objective of this study was to determine the phylogenetic range and abundance of prokaryotes in the vaginal microbiota of healthy, non-pregnant, ethnically diverse, reproductive-aged Canadian women. Socio-demographic, behavioural and clinical data were collected and vaginal swabs were analyzed from 310 women. Detailed profiles of their vaginal microbiomes were generated by pyrosequencing of the chaperonin-60 universal target. Six community state types (CST) were delineated by hierarchical clustering, including three Lactobacillus-dominated CST (L. crispatus, L. iners, L. jensenii), two Gardnerella-dominated (subgroups A and C) and an “intermediate” CST which included a small number of women with microbiomes dominated by seven other species or with no dominant species but minority populations of Streptococcus, Staphylococcus, Peptoniphilus, E. coli and various Proteobacteria in co-dominant communities. The striking correspondence between Nugent score and deep sequencing CST continues to reinforce the basic premise provided by the simpler Gram stain method, while additional analyses reveal detailed cpn60-based phylogeny and estimated abundance in microbial communities from vaginal samples. Ethnicity was the only demographic or clinical characteristic predicting CST, with differences in Asian and White women (p = 0.05). In conclusion, this study confirms previous work describing four cpn60-based subgroups of Gardnerella, revealing previously undescribed CST. The data describe the range of bacterial communities seen in Canadian women presenting with no specific vaginal health concerns, and provides an important baseline for future investigations of clinically important cohorts.     

Production of a presumptive chlorophyll catabolite in vitro: requirement for reduced ferredoxin

Senescent chloroplasts (gerontoplasts) isolated from primary leaves of barley (Hordeum vulgare L.) contained a group of fluorescent chlorophyll (Chl) compounds designated as FCC-2, FCC-3 and FCC-4. Compound FCC-2 represents an established catabolite of Chl-porphyrin and was the most abundant constituent of this group. One of the minor constituents, FCC-4, was produced in a reconstituted system composed of thylakoids and stroma. The generation of FCC-4 depended on oxygen and required reduced ferredoxin (Fd) which probably acts as a reductant of the putative oxygenating enzyme responsible for the cleavage of Chl-porphyrin. A typical assay mixture consisted of thylakoids and stroma (equalling 10⁸ gerontoplasts), Fd, NADPH and glucose-6-phosphate for NADPH-regeneration. The oxygenating enzyme appeared to be a stromal protein. However, enzyme activities associated with the thylakoids were also required for the production of FCC-4. The senescence-specific part of the reconstituted system resided in the thylakoids. Thus, FCC-4 was produced in assay mixtures of senescent thylakoids and stroma from presenescent chloroplasts, whereas combinations with presenescent thylakoids failed to yield appreciable amounts of this putative primary Chl-catabolite.     

Pyrosequencing of the Chaperonin-60 Universal Target as a Tool for Determining Microbial Community Composition

We compared dideoxy sequencing of cloned chaperonin-60 universal target (cpn60 UT) amplicons to pyrosequencing of amplicons derived from vaginal microbial communities. In samples pooled from a number of individuals, the pyrosequencing method produced a data set that included virtually all of the sequences that were found within the clone library and revealed an additional level of taxonomic richness. However, the relative abundances of the sequences were different in the two datasets. These observations were expanded and confirmed by the analysis of paired clone library and pyrosequencing datasets from vaginal swabs taken from four individuals. Both for individuals with a normal vaginal microbiota and for those with bacterial vaginosis, the pyrosequencing method revealed a large number of low-abundance taxa that were missed by the clone library approach. In addition, we showed that the pyrosequencing method generates a reproducible profile of microbial community structure in replicate amplifications from the same community. We also compared the taxonomic composition of a vaginal microbial community determined by pyrosequencing of 16S rRNA amplicons to that obtained using cpn60 universal primers. We found that the profiles generated by the two molecular targets were highly similar, with slight differences in the proportional representation of the taxa detected. However, the number of operational taxonomic units was significantly higher in the cpn60 data set, suggesting that the protein-encoding gene provides improved species resolution over the 16S rRNA target. These observations demonstrate that pyrosequencing of cpn60 UT amplicons provides a robust, reliable method for deep sequencing of microbial communities.Scientific interest in human microbial communities is growing, and basic concepts about the “human microbiome” are evolving rapidly (3, 34). Molecular phylogenetic analysis of 16S rRNA-encoding DNA sequences has revealed a vast diversity of uncultured microbial symbionts that influence animal physiology in ways only beginning to be understood. In particular, microbial species inhabiting the human vagina are thought to play an important role in host health (10). A shift in the composition of the vaginal microbiota from “normal” (Lactobacillus dominated) to a state defined as bacterial vaginosis (BV; increased abundance of gram-negative organisms) is associated with a range of negative outcomes, including pelvic inflammatory disease, preterm births, and the acquisition of sexually transmitted diseases (21, 22, 37). This observation has led to an increased interest in determining the composition of the vaginal microbiota by culture-independent methods (8, 11, 17, 25, 30, 35, 36). However, established cloning and sequencing techniques remain time- and labor-intensive, severely limiting the reach of phylogenetic or functional surveys of microbial communities across body sites, individuals, geographic areas, and scales of time.The advent of next-generation ultra-high-throughput sequencing technologies, in particular, the GS FLX (454 Life Sciences, Branford, CT), has removed an important quantitative barrier in molecular analysis by increasing the number of reads from a gene or genome by orders of magnitude in a single run (20). Unfortunately, the short average length of pyrosequencing reads (∼200 bp compared to ∼700 bp using dideoxy sequencing) presents a new set of problems. The results of recent application of this technology to analysis of 16S rRNA gene sequences from microbes in vaginal samples have demonstrated that short reads are more likely to generate matches to multiple sequences in the rRNA sequence database and that taxonomic and phylogenetic resolution was limited due to strong similarities between 16S rRNA sequences from closely related species (32).An alternative molecular target for microbial identification and phylogenetic analysis is cpn60, a gene that encodes the 60-kDa chaperonin or heat shock protein (HSP60/GroEL) (13). The cpn60 gene is universal in eubacteria and eukaryotes and an extensive, curated reference database is available (13) (http://cpndb.cbr.nrc.ca). The cpn60 universal target (UT) offers key advantages, including short target length (549 to 567 bp), sufficient resolving power to distinguish closely related species and subspecies, and a relatively uniform distribution of variability across the entire length of the target (9, 12). The use of the cpn60 UT has been well established for phylogenetic analysis of complex samples (4, 14) and has recently been applied to vaginal microbial communities (11). In the present study, we examined the feasibility of pyrosequencing for determining the composition of the vaginal microbiota using the cpn60 UT. We compared the microbial community structure generated by pyrosequencing of cpn60 amplicons using the GS FLX with dideoxy sequencing based on clone libraries generated from the same samples. In addition, we evaluated the microbial community profiles generated by pyrosequencing of cpn60 UT amplicons and 16S rRNA amplicons from the same vaginal samples.