Statistical Mechanics Metrics in Pairing and Parsing In Silico and Phenotypic Data of a Novel Genetic NFκB1 (c.T638A) Variant

(1) Background: Mutations in NFκB1, a transcriptional regulator of immunomodulating proteins, are a known cause of inborn errors of immunity. Our proband is a 22-year-old male with a diagnosis of common variable immunodeficiency (CVID), cytopenias with massive splenomegaly, and nodular regenerative hyperplasia of the liver. Genetic studies identified a novel, single-point mutation variant in NFκB1, c. T638A p. V213E. (2) Methods: Next-generation panel sequencing of the patient uncovered a novel single-point mutation in the NFκB1 gene that was modeled using the I-TASSER homology-modeling software, and molecular dynamics were assessed using the YASARA2 software (version 20.14.24). (3) Results: This variant replaces valine with glutamic acid at position 213 in the NFκB1 sequence. Molecular modeling and molecular dynamic studies showed altered dynamics in and around the rel homology domain, ankyrin regions, and death domain of the protein. We postulate that these changes alter overall protein function. (4) Conclusions: This case suggests the pathogenicity of a novel variant using protein-modeling techniques and molecular dynamic simulations.

Genetic distance predicts trait differentiation at the subpopulation but not the individual level in eelgrass, Zostera marina

Ecological studies often assume that genetically similar individuals will be more similar in phenotypic traits, such that genetic diversity can serve as a proxy for trait diversity. Here, we explicitly test the relationship between genetic relatedness and trait distance using 40 eelgrass (Zostera marina) genotypes from five sites within Bodega Harbor, CA. We measured traits related to nutrient uptake, morphology, biomass and growth, photosynthesis, and chemical deterrents for all genotypes. We used these trait measurements to calculate a multivariate pairwise trait distance for all possible genotype combinations. We then estimated pairwise relatedness from 11 microsatellite markers. We found significant trait variation among genotypes for nearly every measured trait; however, there was no evidence of a significant correlation between pairwise genetic relatedness and multivariate trait distance among individuals. However, at the subpopulation level (sites within a harbor), genetic (FST) and trait differentiation were positively correlated. Our work suggests that pairwise relatedness estimated from neutral marker loci is a poor proxy for trait differentiation between individual genotypes. It remains to be seen whether genomewide measures of genetic differentiation or easily measured "master" traits (like body size) might provide good predictions of overall trait differentiation.

Multiple dimensions of intraspecific diversity affect biomass of eelgrass and its associated community

Genetic diversity within key species can play an important role in the functioning of entire communities. However, the extent to which different dimensions of diversity (e.g., the number of genotypes vs. the extent of genetic differentiation among those genotypes) best predicts functioning is unknown and may yield clues into the different mechanisms underlying diversity effects. We explicitly test the relative influence of genotypic richness and genetic relatedness on eelgrass productivity, biomass, and the diversity of associated invertebrate grazers in a factorial field experiment using the seagrass species, Zostera marina (eelgrass). Genotypic richness had the strongest effect on eelgrass biomass accumulation, such that plots with more genotypes at the end of the experiment attained a higher biomass. Genotypic diversity (richness + evenness) was a stronger predictor of biomass than richness alone, and both genotype richness and diversity were positively correlated with trait diversity. The relatedness of genotypes in a plot reduced eelgrass biomass independently of richness. Plots containing eelgrass with greater trait diversity also had a higher abundance of invertebrate grazers, while the diversity and relatedness of eelgrass genotypes had little effect on invertebrate abundance or richness. Our work extends previous findings by explicitly relating genotypic diversity to trait diversity, thus mechanistically connecting genotypic diversity to plot-level yields. We also show that other dimensions of diversity, namely relatedness, influence eelgrass performance independent of trait differentiation. Ultimately, richness and relatedness captured fundamentally different components of intraspecific variation and should be treated as complementary rather than competing dimensions of biodiversity affecting ecosystem functioning.

Microbiome succession during ammonification in eelgrass bed sediments

BACKGROUND

Eelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, also known as diagenesis, from plots at a field site in Bodega Bay, CA.

METHODS

Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n = 4 per plot) under a N₂ atmosphere, incubated them at in situ temperatures (15 °C) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at seven, 13 and 19 days to characterize changes in the relative abundances of microbial taxa throughout ammonification.

RESULTS

Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in predicted sulfur reducers (Desulfobacterales) and corresponding increases in predicted sulfide oxidizers (Thiotrichales). None of these changes in composition or richness were associated with variation in ammonification rates.

DISCUSSION

Our results showed that the microbiome of sediment from different plots followed similar successional patterns, which we infer to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g., elemental cycling and eelgrass-microbe interactions).

Response of a Habitat-Forming Marine Plant to a Simulated Warming Event Is Delayed, Genotype Specific, and Varies with Phenology

Growing evidence shows that increasing global temperature causes population declines and latitudinal shifts in geographical distribution for plants living near their thermal limits. Yet, even populations living well within established thermal limits of a species may suffer as the frequency and intensity of warming events increase with climate change. Adaptive response to this stress at the population level depends on the presence of genetic variation in thermal tolerance in the populations in question, yet few data exist to evaluate this. In this study, we examined the immediate effects of a moderate warming event of 4.5°C lasting 5 weeks and the legacy effects after a 5 week recovery on different genotypes of the marine plant Zostera marina (eelgrass). We conducted the experiment in Bodega Bay, CA USA, where average summer water temperatures are 14–15°C, but extended warming periods of 17–18°C occur episodically. Experimental warming increased shoot production by 14% compared to controls held at ambient temperature. However, after returning temperature to ambient levels, we found strongly negative, delayed effects of warming on production: shoot production declined by 27% and total biomass decreased by 50% relative to individuals that had not been warmed. While all genotypes’ production decreased in the recovery phase, genotypes that grew the most rapidly under benign thermal conditions (control) were the most susceptible to the detrimental effects of warming. This suggests a potential tradeoff in relative performance at normal vs. elevated temperatures. Modest short-term increases in water temperature have potentially prolonged negative effects within the species’ thermal envelope, but genetic variation within these populations may allow for population persistence and adaptation. Further, intraspecific variation in phenology can result in maintenance of population diversity and lead to enhanced production in diverse stands given sufficient frequency of warming or other stress events.

The relative importance of trait vs. genetic differentiation for the outcome of interactions among plant genotypes

Functional trait differences and genetic distance are increasingly used as metrics to predict the. outcome of species interactions and the maintenance of diversity. We apply these ideas to intraspecific diversity for the seagrass Zostera marina (eelgrass), by explicitly testing the influence of trait distance and genetic relatedness on the outcome of pairwise interactions among eelgrass genotypes. Increasing trait distance (but not relatedness) between eelgrass genotypes decreased the likelihood that both would persist over a year-long field experiment, contrary to our expectations based on niche partitioning. In plots in which one genotype excluded another, the biomass and growth of the remaining genotype increased with the trait distance and genetic relatedness of the initial pair, presumably due to a legacy of past interactions. Together these results suggest that sustained competition among functionally similar genotypes did not produce a clear winner, but rapid exclusion occurred among genotypes with distinct trait combinations. Borrowing from coexistence theory, we argue that fitness differences between genotypes with distinct traits overwhelmed any stabilizing effects of niche differentiation. Previously observed effects of eelgrass genetic diversity on performance may rely on nonadditive interactions among multiple genotypes or sufficient environmental heterogeneity to increase stabilizing forces and/or interactions.

The impact of prostate cancer on partners: a qualitative exploration

OBJECTIVE

Prostate cancer and its treatment can result in numerous physical and psychological morbidities for the patient as well as his partner. This qualitative study aimed to explore the experiences of intimate spouses or partners of men diagnosed and/or treated for prostate cancer to better understand the personal impact of prostate cancer on the partner.

METHODS

Twenty-seven partners participated in this study. Six focus groups were convened, and one in-depth interview was undertaken to explore the practical impact of prostate cancer on the intimate spouse/partner. All discussions were audio-recorded and transcribed and then coded using a thematic approach.

RESULTS

Six themes emerged: (a) The influence of the man's response to prostate cancer on the partner, (b) The need to be involved in treatment and medical decision making, (c) Supporting a man who is experiencing a loss of masculinity, (d) Degree of congruence between each partner's coping responses, (e) Constrained communication, and (f) Changed roles and increased practical management.

CONCLUSIONS

It is clear that prostate cancer impacts substantially on many areas of partner well-being. An effective intervention provided to this population seems warranted and may lead to improvements in partner well-being, assist the couple in lessening the impact of prostate cancer and its treatment on their relationship, and assist in the man's recovery.

Plant genotype and nitrogen loading influence seagrass productivity, biochemistry, and plant-herbivore interactions

Genetic variation within and among key species can have significant ecological consequences at the population, community, and ecosystem levels. In order to understand ecological properties of systems based on habitat-forming clonal plants, it is crucial to clarify which traits vary among plant genotypes and how they influence ecological processes, and to assess their relative contribution to ecosystem functioning in comparison to other factors. Here we used a mesocosm experiment to examine the relative influence of genotypic identity and extreme levels of nitrogen loading on traits that affect ecological processes (at the population, community, and ecosystem levels) for Zostera marina, a widespread marine angiosperm that forms monospecific meadows throughout coastal areas in the Northern Hemisphere. We found effects of both genotype and nitrogen addition on many plant characteristics (e.g., aboveground and belowground biomass), and these were generally strong and similar in magnitude, whereas interactive effects were rare. Genotypes also strongly differed in susceptibility to herbivorous isopods, with isopod preference among genotypes generally matching their performance in terms of growth and survival. Chemical rather than structural differences among genotypes drove these differences in seagrass palatability. Nitrogen addition uniformly decreased plant palatability but did not greatly alter the relative preferences of herbivores among genotypes, indicating that genotype effects are strong. Our results highlight that differences in key traits among genotypes of habitat-forming species can have important consequences for the communities and ecosystems that depend on them and that such effects are not overwhelmed by known environmental stressors.

Prophylactic ergometrine-oxytocin versus oxytocin for the third stage of labour

BACKGROUND

The routine prophylactic administration of an uterotonic agent is an integral part of active management of the third stage of labour, helping to prevent postpartum haemorrhage (PPH). The two most widely used uterotonic agents are: ergometrine-oxytocin (Syntometrine) (a combination of oxytocin 5 international units (iu) and ergometrine 0.5 mg) and oxytocin (Syntocinon).

OBJECTIVES

To compare the effects of ergometrine-oxytocin with oxytocin in reducing the risk of PPH (blood loss of at least 500 ml) and other maternal and neonatal outcomes.

SEARCH STRATEGY

We searched the Cochrane Pregnancy and Childbirth Group trials register (May 2003).

SELECTION CRITERIA

Randomised trials comparing ergometrine-oxytocin use with oxytocin use in women having the third stage of labour managed actively.

DATA COLLECTION AND ANALYSIS

We independently assessed trial eligibility and quality and extracted data. We contacted study authors for additional information.

MAIN RESULTS

Six trials were included (9332 women). Compared with oxytocin, ergometrine-oxytocin was associated with a small reduction in the risk of PPH using the definition of PPH of blood loss of at least 500 ml (odds ratio 0.82, 95% confidence interval 0.71 to 0.95). This advantage was found for both a dose of 5 iu oxytocin and a dose of 10 iu oxytocin, but was greater for the lower dose. There was no difference detected between the groups using either 5 or 10 iu for the stricter definition of PPH of blood loss at least 1000 ml. Adverse effects of vomiting, nausea and hypertension were more likely to be associated with the use of ergometrine-oxytocin. When heterogeneity between trials was taken into account there were no statistically significant differences found for the other maternal or neonatal outcomes.

REVIEWER'S CONCLUSIONS

The use of ergometrine-oxytocin as part of the routine active management of the third stage of labour appears to be associated with a small but statistically significant reduction in the risk of PPH when compared to oxytocin for blood loss of 500 ml or more. No statistically significant difference was observed between the groups for blood loss of 1000 ml or more. A statistically significant difference was observed in the presence of maternal side-effects, including elevation of diastolic blood pressure, vomiting and nausea, associated with ergometrine-oxytocin use compared to oxytocin use. Thus, the advantage of a reduction in the risk of PPH, between 500 and 1000 ml blood loss, needs to be weighed against the adverse side-effects associated with the use of ergometrine-oxytocin.

Genetic interactions of conserved regions in the DEAD-box protein Prp28p

The yeast PRP28 g ene has been implicated in nuclear precursor messenger RNA (pre-mRNA) splicing, a two-step reaction involved in a multitude of RNA structural alterations. Prp28p, the gene product of PRP28 , is a member of the evolutionarily conserved DEAD-box proteins (DBPs). Members of DBPs are involved in a variety of RNA-related biochemical processes, presumably by their putative RNA helicase activities. Prp28p has been speculated to play a role in melting the duplex between U4 and U6 small nuclear RNAs (snRNAs), leading to the formation of an active spliceosome. To study the function of Prp28p and its interactions with other components of the splicing machinery, we have isolated and characterized a large number of prp28 conditional mutants. Strikingly, many of these prp28 mutations are localized in the highly conserved motifs found in all the DBPs. Intragenic reversion analysis suggests that regions of motifs II, III and V, as well as of motifs I and IV, in Prp28p are likely to be in close proximity to each other. Our results thus provide the first hint of the local structural arrangement for Prp28p, and perhaps for other DBPs as well.

Use of nutrition support in patients with AIDS: a four-year retrospective review

A series of 55 patients with AIDS and opportunistic infections were admitted a total of 75 times to Robert Wood Johnson University Hospital over a 4-year period, and supplemental nutrition support--intravenous (IV), enteral, or both--was given during 32 of these admissions. Use of nutrition support was correlated retrospectively with pretreatment nutritional status, length of hospital stay (LOS), and survival and was found to be positively correlated with weight loss greater than or equal to 10% or weight less than or equal to 90% of ideal body weight (p less than 0.001), admission hemoglobin less than or equal to 10g (p less than 0.001), and LOS less than or equal to 21 days (p less than or equal to 0.003). Nutrition support intervention did not correlate with survival, admission total lymphocyte count (TLC), or serum albumin level. Survival was negatively correlated with LOS (p less than or equal to 0.04) and continuous daily fever for greater than or equal to 6 days (p less than 0.001). Survival was also significantly lower in patients who received IV rather than enteral nutrition support (p less than or equal to 0.03). Weight loss, admission TLC, albumin, and hemoglobin levels did not correlate with survival. These results suggest that nutrition support generally was given to the sickest patients with AIDS. There was no measurable benefit associated with use of supplemental nutritional support in this series. Properly designed trials will be necessary to define the optimum route, timing, and type of nutritional support for patients with AIDS.