Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions

Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization of interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early mutations improve cooperativity by manifesting in synergistic epistasis between genomes of the mutually interacting species. Specifically, we have characterized evolutionary trajectories of syntrophic interactions of Desulfovibrio vulgaris (Dv) with Methanococcus maripaludis (Mm) by longitudinally monitoring mutations accumulated over 1000 generations of nine independently evolved communities with analysis of the genotypic structure of one community down to the single-cell level. We discovered extensive parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance within many evolution lines of a rare lineage of Dv that retained sulfate-respiration (SR+) capability, which is not required for metabolic cross-feeding. An in-depth investigation revealed that synergistic epistasis across pairings of Dv and Mm genotypes had enhanced cooperativity within SR− and SR+ assemblages, enabling their coexistence within the same community. Thus, our findings demonstrate that cooperativity of a mutualism can improve through synergistic epistasis between genomes of the interacting species, enabling the coexistence of mutualistic assemblages of generalists and their specialized variants.Subject terms: Microbial ecology, Population genetics, Symbiosis, Population dynamics, Molecular evolution     

Functional characterization of prostaglandin E2 inducible osteogenic colony forming units in cultures of cells isolated from the neonatal rat calvarium

Prostaglandin E₂ (PGE₂) increases the number of mineralized nodules that form in cultures of rat calvarial (RC) cells. The purpose of our study was to characterize PGE₂-inducible osteogenic colony forming units (CFU-Os) by determining their number, the cell populations from which they were released, their specific responsive period to PGE₂, and their proliferating and differentiating characteristics under the stimulation of PGE₂. Limiting dilution analysis was used to determine the number of PGE₂-inducible CFU-Os. Sequential digestion of intact rat parietal bones with collagenase isolated 5 subpopulations of RC cells that were used to estimate the cell populations where PGE₂-inducible CFU-Os resided. The responsive period of PGE₂-inducible CFU-Os to PGE₂ was evaluated by treating cultures of mixed RC cells for all possible combinations of days 1–10, 11–20, and 21–30. PGE₂ effects on proliferation and differentiation of CFU-Os were evaluated by comparing the DNA synthesis and AP activity in subpopulations I and IV on days 3, 6, and 9. Results showed: (1) PGE₂-inducible CFU-Os represent 0.27% of cells in the mixed RC population, (2) the majority of determined and PGE₂-inducible CFU-Os were found in the subpopulations released during the 60–100 min digestion periods, (3) the response of PGE₂-inducible CFU-Os is limited to the first 10 days of culture, and (4) PGE₂-stimulated nodule formation is associated with an early increase in DNA synthesis and a sustained increase in alkaline phosphatase activity. We conclude that, functionally, PGE₂-inducible CFU-Os are slowly proliferating AP negative cells primarily found in the subpopulations III-V. PGE₂ stimulates them to proliferate and become AP+, and function as determined CFU-Os to form mineralized nodules in vitro. © 1996 Wiley-Liss, Inc.     

Challenges in the clinical utility of the serum test for HER2 ECD

Approximately 15-30% of breast cancers over-express the HER2/neu receptor. Historically, over-expression of HER2/neu has been identified using IHC or FISH, both of which are invasive approaches requiring tissue samples. Recent evidence has shown that some tumors identified as "negative" using these methods can respond to HER2/neu targeted therapy. Shedding of the extracellular domain (ECD) of the receptor into the circulation has led to the development of a serum test of HER2 ECD as an additional approach to probe HER2/neu overexpression. The serum test will be able to monitor the dynamic changes of HER2 status over the course of disease progression. Some studies further suggest that the serum HER2 ECD level and its change may serve as a biomarker to reflect patients' response to therapy. Yet more than 10years after the first serum HER2 ECD test was approved by the FDA, serum HER2 testing has yet to be widely used in clinical practice. In this article we will review the progress of the serum HER2 ECD test and discuss some obstacles impeding its incorporation into broad clinical practice. We will also discuss recent improvements in the sensitivity and specificity of the assay that offer some hope for the future of serum HER2 test.     

Habitat Features Predict Carrying Capacity of a Recovering Marine Carnivore

The recovery of large carnivore species from over-exploitation can have socioecological effects; thus, reliable estimates of potential abundance and distribution represent a valuable tool for developing management objectives and recovery criteria. For sea otters (Enhydra lutris), as with many apex predators, equilibrium abundance is not constant across space but rather varies as a function of local habitat quality and resource dynamics, thereby complicating the extrapolation of carrying capacity (K) from one location to another. To overcome this challenge, we developed a state-space model of density-dependent population dynamics in southern sea otters (E. l. nereis), in which K is estimated as a continuously varying function of a suite of physical, biotic, and oceanographic variables, all described at fine spatial scales. We used a theta-logistic process model that included environmental stochasticity and allowed for density-independent mortality associated with shark bites. We used Bayesian methods to fit the model to time series of survey data, augmented by auxiliary data on cause of death in stranded otters. Our model results showed that the expected density at K for a given area can be predicted based on local bathymetry (depth and distance from shore), benthic substrate composition (rocky vs. soft sediments), presence of kelp canopy, net primary productivity, and whether or not the area is inside an estuary. In addition to density-dependent reductions in growth, increased levels of shark-bite mortality over the last decade have also acted to limit population expansion. We used the functional relationships between habitat variables and equilibrium density to project estimated values of K for the entire historical range of southern sea otters in California, USA, accounting for spatial variation in habitat quality. Our results suggest that California could eventually support 17,226 otters (95% CrI = 9,739–30,087). We also used the fitted model to compute candidate values of optimal sustainable population abundance (OSP) for all of California and for regions within California. We employed a simulation-based approach to determine the abundance associated with the maximum net productivity level (MNPL) and propose that the upper quartile of the distribution of MNPL estimates (accounting for parameter uncertainty) represents an appropriate threshold value for OSP. Based on this analysis, we suggest a candidate value for OSP (for all of California) of 10,236, which represents 59.4% of projected K. © 2021 The Authors. The Journal of Wildlife Management published by Wiley Periodicals LLC on behalf of The Wildlife Society.     

A complex plasma plant sterol locus on mouse chromosome 14 has at least two genes regulating intestinal sterol absorption

We previously identified two inbred mouse strains, C57BL/6J and CASA/Rk, with different plasma plant sterol levels. An intercross between these strains revealed a broad plasma plant sterol locus on chromosome 14, which peaked at 17 centimorgan (cM) with a maximum logarithm of the odds score of 9.9. Studies in a chromosome 14 congenic strain, 14KK, with a 4-60 cM CASA/Rk interval on the C57BL/6J background revealed that males, but not females, had decreased plasma plant sterol levels and intestinal cholesterol absorption. In two subcongenic strains, 14PKK and 14DKK, with 4-19.5 and 19.5-60 cM CASA/Rk intervals, respectively, both males and females had decreased plasma plant sterol levels and decreased intestinal cholesterol absorption. Compatible with the decreased plasma plant sterol phenotype, 14PKK mice had increased biliary plant sterol excretion, whereas 14DKK mice did not. Therefore, gender-dependent interactions of genes at the 14PKK and 14DKK intervals are likely to underlie the 14KK interval effect on plasma plant sterol levels and sterol absorption from the intestine. These studies confirm the plasma plant sterol locus on mouse chromosome 14 and provide evidence that there are at least two sets of genes operating: one set affecting intestinal sterol absorption and biliary excretion, and the other set mainly affecting intestinal sterol absorption.     

Overexpression of a bacterial indole-3-acetyl-l-aspartic acid hydrolase in Arabidopsis thaliana

Transgenic Arabidopsis lines (ecotype Col-0) carrying the Enterobacter agglomerans IaaspH gene under CaMV 35S promoter control were more sensitive to exogenous indole-3-acetyl aspartic acid (IAA-Asp) and metabolized [2'-¹⁴C]IAA-Asp more rapidly than control lines. Free IAA, total IAA and IAN levels in independent transgenic lines that accumulated IaaspH mRNA varied insignificantly from control levels, yet IAA-Asp levels were significantly reduced. The transgenic lines were grown in a variety of conditions and subjected to morphometric analysis. All three lines showed statistically significant differences in rosette diameter (in soil), root and hypocotyl length (on agar). These effects were transient in some cases and did not manifest themselves under all growth conditions tried. The two independent lines with single T-DNA insertions had lower seed set compared to control lines.     

KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis

Mass spectrometry (MS)‐based quantitative phosphoproteomics has become a key approach for proteome‐wide profiling of phosphorylation in tissues and cells. Traditional experimental design often compares a single treatment with a control, whereas increasingly more experiments are designed to compare multiple treatments with respect to a control. To this end, the development of bioinformatic tools that can integrate multiple treatments and visualise kinases and substrates under combinatorial perturbations is vital for dissecting concordant and/or independent effects of each treatment. Here, we propose a hypothesis driven kinase perturbation analysis (KinasePA) to annotate and visualise kinases and their substrates that are perturbed by various combinatorial effects of treatments in phosphoproteomics experiments. We demonstrate the utility of KinasePA through its application to two large‐scale phosphoproteomics datasets and show its effectiveness in dissecting kinases and substrates within signalling pathways driven by unique combinations of cellular stimuli and inhibitors. We implemented and incorporated KinasePA as part of the “directPA” R package available from the comprehensive R archive network (CRAN). Furthermore, KinasePA also has an interactive web interface that can be readily applied to annotate user provided phosphoproteomics data ( http://kinasepa.pengyiyang.org ).     

Mapping quantitative trait loci (QTL) in sheep. IV. Analysis of lactation persistency and extended lactation traits in sheep

Background

In sheep dairy production, total lactation performance, and length of lactation of lactation are of economic significance. A more persistent lactation has been associated with improved udder health. An extended lactation is defined by a longer period of milkability. This study is the first investigation to examine the presence of quantitative trait loci (QTL) for extended lactation and lactation persistency in sheep.

Methods

An (Awassi × Merino) × Merino single-sire backcross family with 172 ewes was used to map QTL for lactation persistency and extended lactation traits on a framework map of 189 loci across all autosomes. The Wood model was fitted to data from multiple lactations to estimate parameters of ovine lactation curves, and these estimates were used to derive measures of lactation persistency and extended lactation traits of milk, protein, fat, lactose, useful yield, and somatic cell score. These derived traits were subjected to QTL analyses using maximum likelihood estimation and regression analysis.

Results

Overall, one highly significant (LOD > 3.0), four significant (2.0 < LOD < 3.0) and five suggestive (1.7 < LOD < 2.0) QTL were detected across all traits in common by both mapping methods. One additional suggestive QTL was identified using maximum likelihood estimation, and four suggestive (0.01 < P < 0.05) and two significant (P < 0.01) QTL using the regression approach only. All detected QTL had effect sizes in the range of 0.48 to 0.64 SD, corresponding to QTL heritabilities of 3.1 to 8.9%. The comparison of the detected QTL with results in cattle showed conserved linkage regions. Most of the QTL identified for lactation persistency and extended lactation did not coincide. This suggests that persistency and extended lactation for the same as well as different milk yield and component traits are not controlled by the same genes.

Conclusion

This study identified ten novel QTL for lactation persistency and extended lactation in sheep, but results suggest that lactation persistency and extended lactation do not have a major gene in common. These results provide a basis for further validation in extended families and other breeds as well as targeting regions for genome-wide association mapping using high-density SNP arrays.     

Characterization of secreted recombinant <Emphasis Type="Italic">Toxoplasma gondii</Emphasis> surface antigen 2 (SAG2) heterologously expressed by the yeast <Emphasis Type="Italic">Pichia pastoris</Emphasis>

The surface antigen 2 (SAG2) gene of the protozoan parasite, Toxoplasma gondii, was cloned and extracellularly expressed in the yeast Pichia pastoris. The effectiveness of the secreted recombinant SAG2 (rSAG2-S) as a serodiagnosis reagent was assessed by western blots and ELISA. In the western blot assay, rSAG2-S reacted with all Toxoplasma-antibody positive human serum samples but not with Toxoplasma-negative samples. In the ELISA, rSAG2-S yielded sensitivity rates ranging from 80% (IgG negative, IgM positive) to 100% (IgG positive, IgM negative). In vivo experiments showed that serum from mice immunized with rSAG2-S reacted specifically with the native SAG2 of T. gondii. These mice were protected when challenged with live cells of T. gondii.