title: A cationic lipid site at the outward transmembrane face of a pentameric ligand-gated ion channel

abstract: Pentameric ligand-gated ion channels (pLGICs) are crucial mediators of electrochemical signal transduction from bacteria to humans. Lipids play an important role in regulating pLGIC function, yet the structural basis for specific pLGIC-lipid interactions remains poorly understood. The bacterial channel ELIC recapitulates several properties of eukaryotic pLGICs, including activation by the neurotransmitter GABA and sensitivity to lipids, offering a simplified model system for structure-function studies. In this study, functional effects of non-canonical amino acid substitution of W206 at the top of the M1-helix, combined with detergent interactions observed in recent X-ray structures, are consistent with this region being the location of a lipid binding site on the outward face of the ELIC transmembrane domain. Coarse-grained and atomistic molecular dynamics simulations revealed preferential binding of lipids containing a positive charge, particularly involving interactions with residue W206 consistent with cation-{pi} binding. Polar contacts from the principal subunit, particularly M3 residue Q264, further supported lipid binding via headgroup ester linkages. Aromatic residues were identified at analogous sites in a handful of eukaryotic family members, including the human GABAA receptor subunit {varepsilon}, suggesting conservation of relevant interactions in other evolutionary branches. Further mutagenesis experiments indicated that mutations at this site in {varepsilon}-containing GABAA receptors can change the apparent affinity of the agonist response to GABA, consistent with a potential role of this site in channel gating. In conclusion, this work is a detailed case study in type-specific lipid interactions at an evolutionarily distinctive pLGIC site, with implications for lipid modulation and lipophilic drug design.


title: 2,3,7,8-Tetrachlorodibenzo-p-dioxin elicited decreases in cobalamin inhibits methylmalonyl-CoA mutase activity redirecting propionyl-CoA metabolism to the β-oxidation-like pathway resulting in hepatic accumulation of the toxic intermediate acrylyl-CoA

abstract: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a persistent environmental contaminant and the prototypical ligand for the aryl hydrocarbon receptor (AhR). AhR mediates the effects of TCDD and related compounds, including the reprograming of intermediate metabolism. Untargeted metabolomics analysis of hepatic extracts prepared from mice orally gavaged with TCDD every 4 days for 28 days identified the dose-dependent induction of acrylyl-CoA, a highly reactive toxic intermediate produced during the metabolism of propionyl-CoA in the cobalamin (Cbl)-independent {beta}-oxidation-like pathway. Acrylyl-CoA is a biomarker of inborn errors of metabolism associated with propionic and methylmalonic acidemia associated with Cbl deficiency, transport and/or defects in Cbl-dependent methylmalonyl-CoA mutase (MUT). Although TCDD repressed gene expression for both the canonical Cbl-dependent carboxylase and the alternate Cbl-independent {beta}-oxidation-like pathways, inhibition occurred only at 30 g/kg TCDD while acrylyl-CoA levels increased at ~3 g/kg. In contrast, TCDD decreased serum Cbl and hepatic cobalt levels at ~3 g/kg TCDD consistent with the dosedependent increase in acrylyl-CoA levels. TCDD elicited negligible effects on the expression of genes associated with Cbl absorption, transport, trafficking and derivatization to 5-deoxy-adenosylcobalamin (AdoCbl), the required MUT cofactor. In addition, TCDD induced the decarboxylation of cis-aconitate to itaconate by Acod1. Itaconate can then be activated to itaconyl-CoA, a MUT suicide inactivator that forms an adduct with AdoCbl, blocking MUT activity and reducing Cbl levels. Collectively, these results suggest MUT activity was impaired due to Cbl depletion by TCDD causing propionyl-CoA metabolism to be redirected to the alternate Cbl-independent {beta}-oxidation-like pathway resulting in hepatic acrylyl-CoA accumulation.

category: pharmacology and toxicology


title: Analysing and simulating energy-based models in biology using BondGraphTools

abstract: Like all physical systems, biological systems are constrained by the laws of physics. However, mathematical models of biochemistry frequently neglect the conservation of energy, leading to unrealistic behaviour. Energy-based models that are consistent with conservation of mass, charge and energy have the potential to aid the understanding of complex interactions between biological components, and are becoming easier to develop with recent advances in experimental measurements and databases. In this paper, we motivate the use of bond graphs (a modelling tool from engineering) for energy-based modelling and introduce, BondGraphTools, a Python library for constructing and analysing bond graph models. We use examples from biochemistry to illustrate how BondGraphTools can be used to automate model construction in systems biology while maintaining consistency with the laws of physics.

category: systems biology


title: Loss of STAT5 in adipocytes increases subcutaneous fat mass via sex-dependent and depot-specific pathways

abstract: The STAT (Signal Transducers and Activators of Transcription) family of transcription factors contributes to adipocyte development and function. STAT5A and STAT5B are induced during adipocyte differentiation and are primarily activated by growth hormone (GH). Studies in mice lacking adipocyte GH receptor or STAT5 support their roles in lipolysis-mediated reduction of adipose tissue mass. We have generated a mouse model lacking both STAT5 genes specifically in adipocytes (STAT5AKO). Notably, both sexes of STAT5AKO mice have increased inguinal adipose tissue without any changes in gonadal fat mass. However, both depots exhibit substantial differences in fat cell size. Study of STAT5AKO mice also have revealed that GHs ability to induce insulin resistance is dependent upon STAT5 in adipocytes, but its ability to reduce adipose tissue mass is STAT5 independent. Additional observations, which were not predicted, indicate that the causes and regulation of increased fat mass in STAT5AKO mice are sex- and depot-dependent.

category: cell biology


title: Weak effect of Gypsy retrotransposon bursts on Sonneratia alba salt stress gene expression

abstract:
Background and AimsTransposable elements (TEs) are an important source of genetic diversity and can be co-opted for the regulation of host genes. However, to what extent the pervasive TE colonization of plant genomes has contributed to stress adaptation remains controversial. Plants inhabiting harsh environments in nature provide a unique opportunity to answer this question.

MethodsWe compared TE compositions and their evolutionary dynamics in the genomes of two mangrove species: the pioneer Sonneratia alba and its less salt-tolerant relative S. caseolaris. Age distribution, strength of purifying selection and the removal rate of LTR (long terminal repeat) retrotransposons were estimated. Phylogenetic analysis of LTR retrotransposons and their distribution in the genome of S. alba were surveyed. Small RNA sequencing and whole-genome bisulfite sequencing was conducted using leaves of S. alba. Expression pattern of LTR retrotransposons and their nearby genes were examined using RNA-seq data of S. alba under different salt treatments.

Key ResultsS. alba possesses more TEs than S. caseolaris. Particularly, many more young Gypsy LTR retrotransposons have accumulated in S. alba than in S. caseolaris despite an increase in purifying selection against TE insertions. The top two most abundant Gypsy families in S. alba preferentially insert in gene-poor regions. They are under relaxed epigenetic repression, probably due to the presence of CHROMO domains in their 3-ends. Although a considerable number of TEs in S. alba showed differential expression under salt stress, only four copies were significantly correlated with their nearby genes in expression levels. One such TE-gene pair involves Abscisic acid 8-hydroxylase 3 functioning in abscisic acid catabolism.

ConclusionsThis study sheds light on the evolutionary dynamics and potential function of TEs in an extremophile. Our results suggest that the conclusion on co-option of TEs should be cautious even though activation of TEs by stress might be prevalent.

category: evolutionary biology


title: Bile salt hydrolases deplete conjugated bile acids and erode gut barrier integrity in non-alcoholic steatohepatitis

abstract: Altered host-microbe interactions and increased intestinal permeability have been implicated in the pathogenesis of a range of diseases. However, the mechanisms by which gut microbes affect epithelial barrier integrity remain unclear. Few host-produced metabolites that protect against epithelial damage have been identified, and whether microbial metabolism of host factors alters intestinal barrier function is unknown. Here, we investigate the effects of bacterial metabolism of host-produced bile acid (BA) metabolites on epithelial barrier integrity. We observe that rats fed a choline-deficient, high-fat diet (CDAHFD) exhibit reduced abundance of host-produced conjugated BAs in the intestine at early timepoints coinciding with increased permeability. We show that in vitro, conjugated BAs protect gut epithelial monolayers from damage caused by bacterially produced unconjugated BAs through micelle formation. We then demonstrate that inhibition of BA deconjugation using a small molecule inhibitor of gut bacterial bile salt hydrolase (BSH) enzymes prevents development of pathologic intestinal permeability and hepatic inflammation in CDAHFD-fed rats. Finally, we show that the predominant conjugated BAs in humans protect against epithelial barrier disruption in vitro. Our study identifies a protective role for conjugated BAs in intestinal epithelial barrier function and suggests that rational manipulation of microbial BA metabolism could be leveraged to regulate gut barrier integrity.

category: physiology


title: Inhibition of microbial deconjugation of micellar bile acids protects against intestinal permeability and liver injury


title: C9ORF72 dipeptide repeat proteins disrupt formation of GEM bodies and induce aberrant accumulation of survival of motor neuron protein

abstract: A GGGGCC repeat expansion in the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS), a devastating motor neuron disease. In the neurons of ALS patients, dipeptide repeat proteins (DPRs) are produced from repeat-containing RNAs by an unconventional form of translation, and some of these proteins, especially those containing poly(glycine-arginine) and poly(proline-arginine), are toxic to neurons. Gemini of coiled bodies (GEMs) are nuclear structures that harbor survival of motor neuron (SMN) protein, and SMN is essential for the assembly of U-rich small nuclear ribonucleoproteins (snRNPs) that are central for splicing. We previously reported that GEMs are lost and that snRNP biogenesis is misregulated in the motor neurons of ALS patients. Here we show that DPRs interfere with GEM formation and proper SMN localization in HeLa cells and iPSC-derived motor neurons from an ALS patient with the C9ORF72 mutation. The accumulation of poly(glycine-arginine) markedly reduced the number of GEMs and caused the formation of aberrant cytoplasmic RNA granules that sequestered SMN. These findings indicate the functional impairment of SMN in motor neurons expressing DPRs and may provide a mechanism to explain the vulnerability of motor neurons of C9ORF72-ALS patients.

category: neuroscience


title: Lateralized deficits in arousal processing after insula lesions: behavioral and autonomic evidence

abstract: A large body of evidence ascribes a pivotal role in emotion processing to the insular cortex. However, the complex structure and lateralization of emotional deficits following insular damage are not understood. Here, we investigated emotional ratings of valence and arousal and skin conductance responses (SCR) to a graded series of emotionally arousing scenes in patients with left (n = 10) or right (n = 9) insular damage and in healthy controls (n = 18). We found a significant reduction in overall SCRs, arousal ratings and valence extremity scores in right-lesioned patients, as compared to left-lesioned patients and healthy controls. Additional analyses of correlations between subjective arousal ratings resp. SCR and normative arousal ratings revealed that both lesion groups had evaluative and physiological difficulties to discover changes in stimulus arousal. Although no group differences emerged on overall ratings of valence, analysis of correlations between subjective and normative valence ratings displayed markedly reduced accuracy in right-lesioned patients, as compared to left-lesioned patients and healthy controls. Our findings support the hypothesis that the left and right insulae subserve different functions in emotion processing, potentially due to asymmetrical representations of autonomic information in the left and right human forebrain. The right insula may serve as integral node for sympathetic arousal and cognitive affective processing.


title: Integrated multi-omics investigations reveal the key role of synergistic microbial networks in removing plasticizer di-(2-ethylhexyl) phthalate from estuarine sediments

abstract:
Di-(2-ethylhexyl) phthalate (DEHP) is the most widely used plasticizer worldwide with an annual global production of over eight million tons. Because of its improper disposal, endocrine-disrupting DEHP often accumulates in estuarine sediments in industrialized countries at sub-millimolar levels, resulting in adverse effects on both ecosystems and human beings. The microbial degraders and biodegradation pathways of DEHP in O2-limited estuarine sediments remain elusive. Here, we employed an integrated meta-omics approach to identify the DEHP degradation pathway and major degraders in this ecosystem. Estuarine sediments were treated with DEHP or its derived metabolites, o-phthalic acid and benzoic acid. The rate of DEHP degradation in denitrifying mesocosms was two times slower than that of o-phthalic acid, suggesting that side-chain hydrolysis of DEHP is the rate-limiting step of anaerobic DEHP degradation. On the basis of microbial community structures, functional gene expression, and metabolite profile analysis, we proposed that DEHP biodegradation in estuarine sediments is mainly achieved through synergistic networks between denitrifying proteobacteria. Acidovorax and Sedimenticola are the major degraders of DEHP side-chains; the resulting o-phthalic acid is mainly degraded by Aestuariibacter through the UbiD-dependent benzoyl-CoA pathway. We isolated and characterized Acidovorax sp. strain 210-6 and its extracellular hydrolase, which hydrolyzes both alkyl side-chains of DEHP. Interestingly, genes encoding DEHP/MEHP hydrolase and phthaloyl-CoA decarboxylase--key enzymes for side-chain hydrolysis and o-phthalic acid degradation, respectively--are flanked by transposases in these proteobacterial genomes, indicating that DEHP degradation capacity is likely transferred horizontally in microbial communities.

ImportanceXenobiotic phthalate esters (PAE) have been produced on a considerably large scale for only 70 years. The occurrence of endocrine-disrupting di-(2-ethylhexyl) phthalate (DEHP) in environments has raised public concern, and estuarine sediments are major DEHP reservoirs. Our multi-omics analyses indicated that complete DEHP degradation in O2-limited estuarine sediments depends on synergistic microbial networks between diverse denitrifying proteobacteria and uncultured candidates. Our data also suggest that the side-chain hydrolysis of DEHP, rather than o-phthalic acid activation, is the rate-limiting step in DEHP biodegradation within O2-limited estuarine sediments. Therefore, deciphering the bacterial ecophysiology and related biochemical mechanisms can help facilitate the practice of bioremediation in O2-limited environments. Furthermore, the DEHP hydrolase genes of active DEHP degraders can be used as molecular markers to monitor environmental DEHP degradation. Finally, future studies on the directed evolution of identified DEHP/MEHP hydrolase would bring a more catalytically efficient DEHP/MEHP hydrolase into practice.

category: microbiology


title: A species-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for preimplantation development

abstract:
Retrotransposons mediate gene regulation in multiple developmental and pathological processes. Here, we characterized the transient retrotransposon induction in preimplantation development of eight mammalian species. While species-specific in sequences, induced retrotransposons exhibit a similar preimplantation profile, conferring gene regulatory activities particularly through LTR retrotransposon promoters. We investigated a mouse-specific MT2B2 retrotransposon promoter, which generates an N-terminally truncated, preimplantation-specific Cdk2ap1{Delta}N isoform to promote cell proliferation. Cdk2ap1{Delta}N functionally contrasts to the canonical Cdk2ap1, which represses cell proliferation and peaks in mid-gestation stage. The mouse-specific MT2B2 element is developmentally essential, as its deletion abolishes Cdk2ap1{Delta}N, reduces cell proliferation and impairs embryo implantation. Intriguingly, Cdk2ap1{Delta}N is evolutionarily conserved across mammals, driven by species-specific promoters. The distinct preimplantation Cdk2ap1{Delta}N expression across different mammalian species correlates with their different duration in preimplantation development. Hence, species-specific transposon promoters can yield evolutionarily conserved, alternative protein isoforms, bestowing them with new functions and species-specific expression to govern essential biological divergence.

One Sentence SummaryIn mammalian preimplantation embryos, retrotransposon promoters generate conserved gene isoforms, confer species-specific expression, and perform essential developmental functions.

category: developmental biology


title: Convergent evolution of a novel blood-red nectar pigment in vertebrate-pollinated flowers

abstract:
Nesocodon mauritianus (Campanulaceae) produces a blood-red nectar that has been proposed to serve as a visual attractant for pollinator visitation. Here we show that the nectars red color is derived from a novel alkaloid termed nesocodin. The first nectar produced is acidic and pale yellow in color, but slowly becomes alkaline before taking on its characteristic red color. Three enzymes secreted into the nectar are either necessary or sufficient for pigment production, including (1) a carbonic anhydrase that creates an alkaline environment, (2) an aryl alcohol oxidase that generates sinapaldehyde, a pigment precursor, and (3) a ferritin-like catalase that protects nesocodin from degradation by hydrogen peroxide. Our findings demonstrate how these three enzymatic activities allow for the condensation of sinapaldehyde and proline to form a novel pigment with a stable imine bond, which in turn is attractive to Phelsuma geckos, the presumed pollinators of Nesocodon. We also identify nesocodin in the red nectar of the distantly related Jaltomata herrerae and provide evidence for convergent evolution of this trait. While the overall enzymatic activities required for red pigment formation in both Nesocodon and J. herrerae nectars are identical, the associated genes encoding the enzymes are not orthologous and, in the case of the aryl alcohol oxidase, even belong to different protein families. This work cumulatively identifies a novel, convergently evolved trait in two vertebrate-pollinated species, suggesting the red pigment is selectively favored and that only a limited number of compounds are likely to underlie this adaptation.

SignificanceNearly 90% of flowering plants produce nectar to attract pollinators. Beyond sugars, many types of nectar solutes play important ecological roles; however, the molecular basis for the diversity of nectar composition across species is less explored. One rare trait among flowering plants is the production of colored nectar, which may function to attract and guide prospective pollinators. Our findings indicate convergent evolution of a red-colored nectar across two distantly related plant species. Behavioral data show that the red pigment attracts diurnal geckos, a presumed pollinator of one of these plants. These findings join a growing list of examples of distinct biochemical and molecular mechanisms underlying evolutionary convergence, and provide a fascinating system for testing how interactions across species drive the evolution of novel pigments in an understudied context.


title: Biofilm-forming capacity of Escherichia coli isolated from cattle and beef packing plants: relation to virulence attributes, stage of processing, antimicrobial interventions, and heat tolerance

abstract:
Despite the importance of biofilm formation in contamination of meat by pathogenic Escherichia coli at slaughter plants, drivers for biofilm have been unclear. To identify selection pressures for biofilm, we evaluated 745  Top 7 from cattle and 700 generic E. coli from two beef slaughter plants for motility, expression of curli and cellulose, and biofilm-forming potential. Top 7 were also screened for serogroup, stx1, stx2, eae and rpoS. Generic E. coli were compared by source (hide of carcass, hide-off carcass, processing equipment) before and after implementation of antimicrobial hurdles. The proportion of E. coli capable of forming biofilms was lowest (7.1%; P < 0.05) for cattle isolates and highest (87.3%; P < 0.05) from equipment. Only one enterohemorrhagic E. coli (EHEC) was an extremely-strong biofilm-former, in contrast to 73.4% of E. coli from equipment. Isolates from equipment after sanitation had a greater biofilm-forming capacity (P < 0.001) than those before sanitation. Most Top 7 were motile and expressed curli, although these traits along with expression of cellulose and presence of rpoS were not necessary for biofilm formation. In contrast, isolates capable of forming biofilms on equipment were almost exclusively motile and able to express curli. Results of the present study indicate that cattle would rarely carry EHEC capable of making strong biofilms to slaughter plants. However, if biofilm-forming EHEC contaminated equipment, current antimicrobial hurdles would inadvertently perpetuate the most robust biofilm-forming strains. Accordingly, new and effective anti-biofilm hurdles are required for meat-processing equipment, to reduce future instances of food-borne disease.

ImportanceAs the majority of enterohemorrhagic E. coli (EHEC) are not capable of forming biofilms, sources were undetermined of the biofilm-forming EHEC isolated from  high-event periods in beef slaughter plants. This study demonstrated that sanitation procedures used on beef-processing equipment inadvertently select for survival of the most robust biofilm-forming strains of E. coli. Cattle only rarely carry EHEC capable of forming strong biofilms (1/745 isolates evaluated), but sanitation of equipment markedly increased (P < 0.001) biofilm-forming capacity of E. coli. In contrast, chilling carcasses for 3 days at 0{degrees}C reduced (P < 0.05) biofilm-forming capacity of E. coli. Consequently, an additional anti-biofilm hurdle for meat-processing equipment, perhaps involving cold exposure, is necessary to further reduce the risk of food-borne disease.


title: The influence of sex, hormone status, and growth rate on dietary isotope fractionation: a case study with laboratory rats

abstract:
Stable isotope analysis is increasingly used to discern ecological differences within and among species, especially those difficult to observe. In applied ecological studies, variations in stable isotope composition are often attributed to foraging behavior or trophic ecology rather than fractionation during metabolic processes. One physiological difference among individuals is gonadal hormone levels, which affects food intake, metabolism, and locomotor activity. However, it is unclear how these effects- isolated from ecology- affect metabolic dynamics and expression in stable isotope analysis. Here, we test the linkage between gonadal hormones and isotopic heterogeneity among individuals with captive rats. We found that sex and removal of gonadal hormones are factors either individually or interactive for {delta}15N and {delta}13C values in serum and blood as well as {delta}15N values of muscle and liver. Furthermore, the degree of fractionation in these tissues is related to growth rate. Gonadectomization also affected isotopic composition for liver {delta}13C values and kidney {delta}15N values, but fat {delta}13C values were affected only by sex. The pattern of differentiation between groups was most different for kidney {delta}15N and {delta}13C values, which also had the largest isotopic variability among groups. Overall, isotopic variation within one tissue for the four groups demonstrated up to 1{per thousand} difference in {delta}13C and {delta}15N values suggesting that sex based within population variations should into consideration these potential physiological effects.

What is already knownThere are isotopic differences between diet and various consumer tissues with variability among individuals, which is often characterized based on captive feeding studies. Effects of protein quality and quantity, variable growth rate based on ontogeny, and differences between sexes have been tested thus far in experiments. Furthermore, it is known that gonadal hormones affect energy regulation with difference in weight gain, which suggest differences in extent and rate of biochemical processes.

What this study addsThis study demonstrates effects of gonadal hormone status with metabolic biochemistry by using stable isotopes of carbon and nitrogen as dietary tracers. We find that gonadal hormone status accounts for some isotopic heterogeneity among individuals, which should be considered when interpreting stable isotope data from wild specimens. Rather than attributing isotopic differences to ecological factors, such as foraging preference, there may be underlying physiological processes that differentiate groups based on ontogeny and sex.

category: ecology


title: A numerical framework for genetic hitchhiking in populations of variable size

abstract:
Natural selection on beneficial or deleterious alleles results in an increase or decrease, respectively, of their frequency within the population. Due to chromosomal linkage, the dynamics of the selected site affect the genetic variation at nearby neutral loci in a process commonly referred to as genetic hitchhiking. Changes in population size, however, can yield patterns in genomic data that mimic the effects of selection. Accurately modeling these dynamics is thus crucial to understanding how selection and past population size changes impact observed patterns of genetic variation.

Here, we model the evolution of haplotype frequencies with the Wright-Fisher diffusion to study the impact of selection on linked neutral variation. Explicit solutions are not known for the dynamics of this diffusion when selection and recombination act simultaneously. Thus, we present a method for numerically evaluating the Wright-Fisher diffusion dynamics of two linked loci separated by a certain recombination distance when selection is acting. We can account for arbitrary population size histories explicitly using this approach. A key step in the method is to express the moments of the associated transition density, or sampling probabilities, as solutions to ordinary differential equations. Numerically solving these differential equations relies on a novel accurate and numerically efficient technique to estimate higher order moments from lower order moments.

We demonstrate how this numerical framework can be used to quantify the reduction and recovery of genetic diversity around a selected locus over time and elucidate distortions in the site-frequency-spectra of neutral variation linked to loci under selection in various demographic settings. The method can be readily extended to more general modes of selection and applied in likelihood frameworks to detect loci under selection and infer the strength of the selective pressure.

category: genetics


title: Healthier decisions in the cued-attribute food choice paradigm have high test-retest reliability across five task repetitions over 14 days

abstract: Food choice paradigms are commonly used to study decision mechanisms, individual differences, and intervention efficacy. Here, we measured behavior from twenty-three healthy young adults who completed five repetitions of a cued-attribute food choice paradigm over two weeks. This task includes cues prompting participants to explicitly consider the healthiness of the food items before making a selection, or to choose naturally based on whatever freely comes to mind. We found that the average patterns of food choices following both cue types and ratings about the palatability (i.e. taste) and healthiness of the food items were similar across all five repetitions. At the individual level, the test-retest reliability for choices in both conditions and healthiness ratings was excellent. However, test-retest reliability for taste ratings was only fair, suggesting that estimates about palatability may vary more from day to day for the same individual.

category: animal behavior and cognition


title: Methodological considerations when assessing mitochondrial respiration and biomarkers for mitochondrial content in human skeletal muscle

abstract:
BackgroundThe assessment of mitochondrial respiration and mitochondrial content are two common measurements in the fields of skeletal muscle research and exercise science. However, to verify the validity of the observed changes in both mitochondrial respiration and mitochondrial content following an intervention such as exercise training, it is important to determine the reliability and reproducibility of the experimental design and/or techniques employed. We examined the repeatability of widely used methodologies for assessing mitochondrial respiration and mitochondrial content, respectively; the measurement of maximal mitochondrial oxidative phosphorylation in permeabilized muscle fibres using high-resolution respirometry, and the measurement of citrate synthase activity as a biomarker for mitochondrial content in a microplate with spectrophotometer.

ResultFor mitochondrial respiration, the coefficient of variation for repeated measurements using muscle sampled from same biopsy decreased from 12.7% to 11% when measured in triplicate with outliers excluded, rather than in duplicate. The coefficient of variation was 9.7% for repeated muscle biopsies sampled across two separated days. For measurements of citrate synthase activity, the coefficient of variation was 3.5% of three technical repeats on the same plate, 10.2% for duplicate analyses using the same muscle lysate when conducted in the same day, and 30.5% when conducted four weeks apart.

ConclusionWe have provided evidence for important technical considerations when measuring mitochondrial respiration with human skeletal muscle: 1) the relatively large technical variability can be reduced by increasing technical repeats and excluding outliers; 2) the biological variability and absolute mitochondrial respiration value of the participants should be considered when estimating the required sample size; 3) a new threshold of 15% for the increase in respiration rate after the addition of cytochrome c test for testing mitochondrial outer membrane integrity. When analysing citrate synthase activity, our evidence suggests it is important to consider the following: 1) all samples from the same study should be homogenized and measured at the same time using the same batch of freshly made chemical reagents; 2) biological variability should be considered when detecting small change in mitochondrial content; 3) the relative change should be used to compare the outcomes from different studies.


title: Rice MEL2 regulates the timing of meiotic transition as a component of cytoplasmic RNA granules

abstract: Cytoplasmic RNA granules play important roles in gene expression at the post-transcriptional level. In this study, we found that the rice RNA-binding protein MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2), which contributes to the control of meiotic entry timing, was a constituent of RNA granules, frequently associating with processing bodies and stress granules in the cytoplasm of premeiotic spore mother cells. MEL2 has four conserved domains and a large intrinsically disordered region, which is often responsible for formation and maintenance of granular structures. MEL2-like proteins with diverse domain structures are widely conserved in land plants and charophyte algae. In basal land plants, MEL2-like proteins are exclusively expressed in the sporophyte, which expresses meiotic genes, suggesting the functional conservation of MEL2 among land plant species. We propose here that MEL2 participates in post-transcriptional regulation of meiotic genes as a component of RNA granules to ensure proper timing of the meiotic transition.

category: plant biology


title: Astrocytes render memory flexible

abstract:
Cognitive flexibility is an essential ability to adapt to changing environment and circumstances. NMDAR has long been implicated in cognitive flexibility, but the precise molecular and cellular mechanism is not well understood. Here, we report that astrocytes regulate NMDAR tone through Best1-mediated glutamate and D-serine release, which is critical for cognitive flexibility. Co-release of D-serine and glutamate is required for not only homosynaptic LTD but also heterosynaptic LTD, which is induced at unstimulated synapses upon release of norepinephrine and activation of astrocytic 1-AR during homosynaptic LTP. Remarkably, heterosynaptic LTD at unstimulated synapses during memory acquisition is required for later repotentiation LTP during reversal learning, laying a foundation for flexible memory and cognitive flexibility. Our study sheds light on the pivotal role of astrocytes in orchestrating multiple synapses during memory formation and determining the fate of consolidated memory to be retained as a flexible memory.

HighlightsO_LIAstrocytes regulate NMDAR tone via Best1-mediated glutamate and D-serine release
C_LIO_LIActivation of astrocytic 1-AR induces heterosynaptic LTD via NMDAR tone
C_LIO_LIHeterosynaptic LTD is required for repotentiation LTP and spatial reversal learning
C_LIO_LIAstrocytic regulation of NMDAR tone is critical for metaplasticity and flexible memory
C_LI


title: Identifying Brain Regions Related to Word Prediction During Listening to Japanese Speech by Combining a LSTM Language Model and MEG

abstract: Recently, a neuroscientific approach has revealed that humans understand language while subconsciously predicting the next word from the preceding context. Most studies on human word prediction have investigated the correlations between brain activity while reading or listening to sentences on functional magnetic resonance imaging (fMRI) and the predictive difficulty of each word in a sentence calculated by the N-gram language model. However, because of its low temporal resolution, fMRI is not optimal for identifying the changes in brain activity that accompany language comprehension. In addition, the N-gram language model is a simple computational structure that does not account for the structure of the human brain. Furthermore, it is necessary for humans to retain information prior to the N-1 word in order to form a contextual understanding of a presented story. Therefore, in the present study, we measured brain activity using magnetoencephalography (MEG), which has a higher temporal resolution than fMRI, and calculated the prediction difficulty of words using a long short-term memory language model (LSTMLM), which is based on a neural network inspired by the structure of the human brain and has longer information retention than the N-gram language model. We then identified the brain regions involved in language prediction during Japanese-language speech listening using encoding and decoding analyses. In addition to surprisal-related regions revealed in previous studies, such as the superior temporal gyrus, fusiform gyrus, and temporal pole, we also found relationships between surprisal and brain activity in other regions, including the insula, superior temporal sulcus, and middle temporal gyrus, which are believed to be involved in longer-term, sentence-level cognitive processing.


title: Multiple forms of working memory emerge from synapse-astrocyte interactions

abstract: Competing accounts propose that working memory (WM) is subserved either by persistent activity in single neurons, or by time-varying activity across a neural population, or by activity-silent mechanisms carried out by hidden internal states of the neural population. While WM is traditionally regarded to originate exclusively from neuronal interactions, cortical networks also include astrocytes that can modulate neural activity. We propose that different mechanisms of WM can be brought forth by astrocyte-mediated modulations of synaptic transmitter release. In this account, the emergence of different mechanisms depends on the networks spontaneous activity and the geometry of the connections between synapses and astrocytes.


title: Efficacy of a Broadly Neutralizing SARS-CoV-2 Ferritin Nanoparticle Vaccine in Nonhuman Primates

abstract:
The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants stresses the continued need for next-generation vaccines that confer broad protection against coronavirus disease 2019 (COVID-19). We developed and evaluated an adjuvanted SARS-CoV-2 Spike Ferritin Nanoparticle (SpFN) vaccine in nonhuman primates (NHPs). High-dose (50 {micro}g) SpFN vaccine, given twice within a 28 day interval, induced a Th1-biased CD4 T cell helper response and a peak neutralizing antibody geometric mean titer of 52,773 against wild-type virus, with activity against SARS-CoV-1 and minimal decrement against variants of concern. Vaccinated animals mounted an anamnestic response upon high-dose SARS-CoV-2 respiratory challenge that translated into rapid elimination of replicating virus in their upper and lower airways and lung parenchyma. SpFNs potent and broad immunogenicity profile and resulting efficacy in NHPs supports its utility as a candidate platform for SARS-like betacoronaviruses.

One-Sentence SummaryA SARS-CoV-2 Spike protein ferritin nanoparticle vaccine, co-formulated with a liposomal adjuvant, elicits broad neutralizing antibody responses that exceed those observed for other major vaccines and rapidly protects against respiratory infection and disease in the upper and lower airways and lung tissue of nonhuman primates.

category: immunology


title: CCR2 Regulates Vaccine-Induced Mucosal T cell Memory to Influenza A Virus

abstract:
Elicitation of lung tissue-resident memory CD8 T cells (TRMs) is a goal of T-cell based vaccines against respiratory viral pathogens such as influenza A virus (IAV). Chemokine receptor 2 (CCR2)-dependent monocyte trafficking plays an essential role in the establishment of CD8 TRMs in lungs of IAV-infected mice. Here, we used a combination adjuvant-based subunit vaccine strategy that evokes multifaceted (TC1/TC17/TH1/TH17) IAV nucleoprotein-specific lung TRMs, to determine whether CCR2 and monocyte infiltration are essential for vaccine-induced TRM development and protective immunity to IAV in lungs. Following intranasal vaccination, neutrophils, monocytes, conventional dendrtitic cells (DCs) and monocyte-derived DCs internalized and processed vaccine antigen in lungs. We also found that Basic Leucine Zipper ATF-Like Transcription Factor 3 (BATF-3)-dependent DCs were essential for eliciting T cell responses, but CCR2 deficiency enhanced the differentiation of CD127HI/KLRG-1LO, OX40+veCD62L+ve and mucosally imprinted CD69+veCD103+ve effector and memory CD8 T cells in lungs and airways of vaccinated mice. Mechanistically, increased development of lung TRMs, induced by CCR2 deficiency was linked to dampened expression of T-bet, but not altered TCF-1 levels or T cell receptor signaling in CD8 T cells. T1/T17 functional programming, parenchymal localization of CD8/CD4 effector and memory T cells, recall T cell responses and protective immunity to a lethal IAV infection were unaffected in CCR2-deficient mice. Taken together, we identified a negative regulatory role for CCR2 and monocyte trafficking in mucosal imprinting and differentiation of vaccine-induced TRMs. Mechanistic insights from this study may aid the development of T-cell-based vaccines against respiratory viral pathogens including IAV and SARS-CoV-2.

ImportanceWhile antibody-based immunity to influenza A virus (IAV) is type and sub-type specific, lung and airway-resident memory T cells that recognize conserved epitopes in the internal viral proteins are known to provide heterosubtypic immunity. Hence, broadly protective IAV vaccines need to elicit robust T-cell memory in the respiratory tract. We have developed a combination adjuvant-based IAV nucleoprotein vaccine that elicits strong CD4 and CD8 T cell memory in lungs and protects against H1N1 and H5N1 strains of IAV. In this study, we examined the mechanisms that control vaccine-induced protective memory T cells in the respiratory tract. We found that trafficking of monocytes into lungs might limit the development of anti-viral lung-resident memory T cells, following intranasal vaccination. These findings suggested that strategies that limit monocyte infiltration can potentiate vaccine-induced frontline T-cell immunity to respiratory viruses such as IAV and SARS-CoV-2.


title: COVID-19: A need for new rather than repurposed antiviral drugs.

abstract:
BackgroundSARS-CoV-2 infection, the causative agent of COVID-19, has resulted in over 2,500,000 deaths to date1. Although vaccines are becoming available, treatment options remain limited. Repurposing of compounds could reduce the time, cost, and risks associated with the development of new drugs and has been the focus of many clinical studies.

Here, we summarise available evidence on 29 FDA-approved compounds, from in vitro results to clinical trials, focussing on remdesivir, galidesivir and favipiravir, and test 29 antiviral compounds activity in vitro.

MethodsA comprehensive search strategy was used to retrieve trials and publications related to antiviral compounds with potential efficacy to treat coronaviruses. These data were used to prioritise testing of a panel of antiviral drugs in vitro against patient isolates of SARS-CoV-2. An in vitro screen was carried out to determine the activity of 29 FDA-approved compounds.

Results625 clinical trials investigated 16 repurposed antiviral candidate compounds for the treatment of COVID-19. In vitro studies identified ten drug candidates with demonstrable anti-SARS-CoV-2 activity, including favipiravir, remdesivir, and galidesivir. To validate these findings, a drug screen was conducted using two cell lines and wildtype isolates of SARS-CoV-2 isolated from patients in the UK. While eight drugs with anti-SARS-CoV-2 activity were identified in vitro, activity in clinical trials has, as yet failed to demonstrate a strong effect on mortality.

ConclusionsSo far, no repurposed antiviral has shown a strong effect on mortality in clinical studies. The urgent need for novel antivirals in this pandemic is clear, despite the costs and time associated with their development.

Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSRepurposing of existing compounds for the treatment of COVID-19 has been the focus of many in vitro studies and clinical trials, saving time, costs and risks associated with the research and development of new compounds.

Added value of this studyWe reviewed the literature for 29 FDA-approved compounds with previously reported (or suspected) anti-SARS-CoV-2 activity and found 625 clinical trials that have been undertaken on 16 different drugs. We determined if repurposed antivirals are suitable for clinical trials based on previously published data, and conducted an additional in vitro screen using locally circulating strains in the UK (PHE2 and GLA1). We report the difference in IC50 from published data using Wuhan1/Wash1 strains with PHE2 and GLA1, including IC50 values below 100M for galidesivir in wild-type virus. Given the limited success of repurposed compounds in the treatment of COVID-19, we comment on the urgent need for new antivirals specifically targeting SARS-CoV-2.

Implications of all the available evidenceOur data show that most prospective compounds for repurposing show no anti-SARS-CoV-2 activity, and antiviral activity in vitro does not always translate to clinical benefit. So far, no repurposed compound has shown a strong effect on mortality in clinical studies. Drugs, including monoclonal antibody therapies, that have been developed to target SARS-CoV-2 virus itself have shown most promise.


title: The Nestin neural enhancer is essential for normal levels of endogenous Nestin in neuroprogenitors but is not required for embryo development

abstract: Enhancers are vitally important during embryonic development to control the spatial and temporal expression of genes. Recently, large scale genome projects have identified a vast number of putative developmental regulatory elements. However, the proportion of these that have been functionally assessed is relatively low. While enhancers have traditionally been studied using reporter assays, this approach does not characterise their contribution to endogenous gene expression. We have studied the murine Nestin (Nes) intron 2 enhancer, which is widely used to direct exogenous gene expression within neural progenitor cells in cultured cells and in vivo. We generated CRISPR deletions of the enhancer region in mice and assessed their impact on Nes expression during embryonic development. Loss of the Nes neural enhancer significantly reduced Nes expression in the developing CNS by as much as 82%. By assessing NES protein localization, we also show that this enhancer region contains repressor element(s) that inhibit Nes expression within the vasculature. Previous reports have stated that Nes is an essential gene, and its loss causes embryonic lethality. We also generated 2 independent Nes null lines and show that both develop without any obvious phenotypic effects. Finally, through crossing of null and enhancer deletion mice we provide evidence of trans-chromosomal interaction of the Nes enhancer and promoter.


title: Unsupervised temporal consistency improvement for microscopy video segmentation with Siamese networks

abstract: We introduce a simple mechanism by which a CNN trained to perform semantic segmentation of individual images can be re-trained - with no additional annotations - to improve its performance for segmentation of videos. We put the segmentation CNN in a Siamese setup with shared weights and train both for segmentation accuracy on annotated images and for segmentation similarity on unlabelled consecutive video frames. Our main application is live microscopy imaging of membrane-less organelles where the fluorescent groundtruth for virtual staining can only be acquired for individual frames. The method is directly applicable to other microscopy modalities, as we demonstrate by experiments on the Cell Segmentation Benchmark. Our code is available at https://github.com/kreshuklab/learning-temporal-consistency.

category: bioinformatics


title: Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike protein and the human ACE2 receptor

abstract: The association of the receptor binding domain (RBD) of SARS-CoV-2 viral spike with human angiotensin converting enzyme (hACE2) represents the first required step for viral entry. Amino acid changes in the RBD have been implicated with increased infectivity and potential for immune evasion. Reliably predicting the effect of amino acid changes in the ability of the RBD to interact more strongly with the hACE2 receptor can help assess the public health implications and the potential for spillover and adaptation into other animals. Here, we introduce a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born electrostatic solvation, hydrogen-bonding, {pi}-{pi} packing and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity using the decomposed energy terms as descriptors. The computational base achieves an accuracy of 82.2% in terms of correctly classifying single amino-acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient r of 0.69 between predicted and experimentally calculated binding affinities. Both metrics are calculated using a 5-fold cross validation test. Our method thus sets up a framework for effectively screening binding affinity change with unknown single and multiple amino-acid changes. This can be a very valuable tool to predict host adaptation and zoonotic spillover of current and future SARS-CoV-2 variants.

category: biophysics


title: Neurogenesis-mediated forgetting of complex paired-associates memories

abstract: The hippocampus is a critical structure involved in many forms of learning and memory. It is also one of the only regions in the adult mammalian brain that continues to generate new neurons throughout adulthood. This process of adult neurogenesis may increase the plasticity of the hippocampus which could be beneficial for learning but has also been demonstrated to decrease the stability of previously acquired memories. Here we test whether increased production of new neurons following the formation of a gradually acquired paired-associates task will result in forgetting of this type of memory. We trained mice in a touchscreen-based object/location task and then increased neurogenesis using voluntary exercise. Our results indicate that mice with increased neurogenesis show poor recall of the previously established memory. When subsequently exposed to a reversal task we also show that mice with increased neurogenesis require fewer correction trials to acquire the new task contingencies. This suggests that prior forgetting reduces perseveration on the now outdated memory. Together our results add to a growing body of literature which indicates the important role of adult neurogenesis in destabilizing previously acquired memories to allow for flexible encoding of new memories.


title: Modelling the efficacy of Neprilysin from various species in degrading different Amyloid-beta peptides: Potential application in therapeutics of Alzheimers disease

abstract: Recombinant neprilysin due to its degradation potential against Amyloid-{beta} (A{beta}) peptides has been looked at as a potential therapeutic candidate for treating Alzheimers disease (AD). However the enzymatic activity of neprilysin against different A{beta} peptides can variable which significantly limits the therapeutic optimization. Using the molecular interaction analysis and modelling it against the known enzyme-substrate kinetics, this study developed a novel approach to predicting biosimilar enzyme-substrate kinetics. The known enzyme-substrate kinetics of human recombinant neprilysin with A{beta}1-40 peptide was used as the prototype to assess the affinity and efficacy of various inter and intra-species neprilysin- A{beta} peptide enzyme kinetics based on the relative molecular interaction analysis. Significant inter and intra-species variations in neprilysin- A{beta} peptide enzyme kinetics was observed which further validated the need for optimizing enzyme kinetics tailored to specific substrate degradation. The novel enzyme kinetics modelling approach described in this study can be helpful in the developing of recombinant enzymes/peptides for personalised therapeutic applications.

category: biochemistry


title: Effect of temperature and loading frequency on the performance of vertical subsurface flow constructed wetlands: Modelling study using HYDRUS

abstract: Constructed wetlands are used in wastewater treatment for the removal of organic matter, nutrients, pathogens and other pollutants from water. The diversity of chemical, physical and biological processes taking place inside constructed wetlands (CWs) make them difficult systems for accurate quantitative description through conventional modelling approaches. However, existing modelling tools can bring valuable insight into important phenomena and interactions that might remain otherwise neglected. In this study the CW2D module under HYDRUS - 2D is used to identify the possible mechanisms by which temperature and loading frequency impacts the performance of the vertical subsurface flow constructed wetlands (VSSFCWs). An improvement on CWs design and operation guidelines in warm regions is intended. Case studies of a VSSFCW at 10{degrees}C, 20{degrees}C and 30{degrees}C treating septic tank effluent are simulated with parameters adjusted for high temperature conditions. The simulation results suggest oxygen limitation as possibly constraining nitrification capacity at high temperatures. Simulations also suggest that higher loading frequencies enhance performance and capacity. This detailed mechanistic modelling study aims at bringing insight into possible non trivial interactions and mechanisms in CWs such that in conjunction with a necessary experimental validation, should lead to enhanced operation and design in warm regions.

category: bioengineering


title: FPM app: an open-source application for simple and intuitive Fourier ptychographic reconstruction

abstract:
SummaryFourier ptychographic microscopy (FPM) is a computational microscopy technique that enables large field of view and high-resolution microscopic imaging of biological samples. However, the FPM does not yet have an adequately capable open-source software. In order to fill this gap we are presenting novel, simple, universal, semi-automatic and highly intuitive graphical user interface (GUI) open-source application called the FPM app enabling wide-scale robust FPM reconstruction. Apart from implementing the FPM in accessible GUI app, we also made several improvements in the FPM image reconstruction process itself, making the FPM more automatic, noise-robust and faster.

Availability and ImplementationFPM app was implemented in MATLAB and all MATLAB codes along with standalone executable version of the FPM app and the online documentation are freely accessible at https://github.com/MRogalski96/FPM-app. Our exemplary FPM datasets may be downloaded at https://bit.ly/2MxNpGb.


title: LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data

abstract: Linked-Reads technologies, popularized by 10x Genomics, combine the high-quality and low cost of short-reads sequencing with a long-range information by adding barcodes that tag reads originating from the same long DNA fragment. Thanks to their high-quality and long-range information, such reads are thus particularly useful for various applications such as genome scaffolding and structural variant calling. As a result, multiple structural variant calling methods were developed within the last few years. However, these methods were mainly tested on human data, and do not run well on non-human organisms, for which reference genomes are highly fragmented, or sequencing data display high levels of heterozygosity. Moreover, even on human data, most tools still require large amounts of computing resources. We present LEVIATHAN, a new structural variant calling tool that aims to address these issues, and especially better scale and apply to a wide variety of organisms. Our method relies on a barcode index, that allows to quickly compare the similarity of all possible pairs of regions in terms of amount of common barcodes. Region pairs sharing a sufficient number of barcodes are then considered as potential structural variants, and complementary, classical short reads methods are applied to further refine the breakpoint coordinates. Our experiments on simulated data underline that our method compares well to the state-of-the-art, both in terms of recall and precision, and also in terms of resource consumption. Moreover, LEVIATHAN was successfully applied to a real dataset from a non-model organism, while all other tools either failed to run or required unreasonable amounts of resources. LEVIATHAN is implemented in C++, supported on Linux platforms, and available under AGPL-3.0 License at https://github.com/morispi/LEVIATHAN.


title: ENNAVIA is an innovative new method which employs neural networks for antiviral and anti-coronavirus activity prediction for therapeutic peptides

abstract: Viruses represent one of the greatest threats to human health, necessitating the development of new antiviral drug candidates. Antiviral peptides often possess excellent biological activity and a favourable toxicity profile, and therefore represent a promising field of novel antiviral drugs. As the quantity of sequencing data grows annually, the development of an accurate in silico method for the prediction of peptide antiviral activities is important. This study leverages advances in deep learning and cheminformatics to produce a novel sequence-based deep neural network classifier for the prediction of antiviral peptide activity. The method out-performs the existent best-in-class, with an external test accuracy of 93.9%, Matthews correlation coefficient of 0.87 and an Area Under the Curve of 0.93 on the dataset of experimentally validated peptide activities. This cutting-edge classifier is available as an online web server at https://research.timmons.eu/ennavia, facilitating in silico screening and design of peptide antiviral drugs by the wider research community.


title: Bacterial cell shape control by nutrient-dependent synthesis of cell division inhibitors

abstract:
By analysing cell shape and size of the bacterium Bacillus subtilis under nutrient perturbations, protein depletion, and antibiotic treatments we find that cell geometry is extremely robust, reflected in a well-conserved scaling relation between surface area (S) and volume (V), S ~ V{gamma}, with{gamma} = 0.85. We develop a molecular model supported by single-cell simulations to predict that the surface-to-volume scaling exponent{gamma} is regulated by nutrient-dependent production of metabolic enzymes that act as cell division inhibitors in bacteria. Using theory that is supported by experimental data, we predict the modes of cell shape transformations in different bacterial species and propose a mechanism of cell shape adaptation to different nutrient perturbations. For organisms with high surface-to-volume scaling exponent{gamma} , such as B. subtilis, cell width is not sensitive to growth rate changes, whereas organisms with low{gamma} , such as A. baumannii, cell shape adapts readily to growth rate changes.

SIGNIFICANCEHow bacteria regulate their size and shapes to optimise their growth fitness in different nutrient environments remains largely unknown. By analysing the surface area and volume of rod-shaped B. subtilis exposed to different nutrient conditions and antibiotics we find that cells preserve a power law scaling between surface area and volume. We show that the surface-to-volume scaling is extremely robust and is regulated by nutrient-dependent synthesis of cell division inhibitors. By analysing different bacterial types, we find that cells conserve the surface-to-volume scaling exponent that is typical for each species, implying distinct mechanisms for morphological adaptation in each organism.


title: Fluid Menisci and In Vitro Particle Dosimetry of Submerged Cells

abstract: Understanding the mechanisms of interaction between cells and particulate nanomaterials lies in the heart of assessing the hazard associated with nanoparticles. The paradigm of toxicology requires quantifying and interpreting dose-response relationships, and cells cultured in vitro and exposed to particle dispersions rely on mathematical models that estimate the received nanoparticle dose. Yet, none of these models acknowledges the fact that aqueous cell-culture media wet the inner surface of hydrophilic open wells, which results in curved fluid-air interface called meniscus. We show that omitting this phenomenon leads to a nontrivial but systematic error and twists the fundamental concept of nanotoxicology. Given that reproducibility and harmonization between meta analyses, in vitro, in silico, and in vivo studies must be improved, we present an adequate mathematical model that greatly advances such efforts.

category: pharmacology and toxicology


title: A tau class Glutathione-S-Transferase (OsGSTU5) acts as a negative regulator of VirE2 interaction with T-DNA during Agrobacterium infection in rice

abstract: During Agrobacterium-mediated transformation (AMT), T-DNA along with several virulence proteins like VirD2, VirE2, VirE3, VirD5, and VirF enter into the plant cytoplasm. VirE2 is supposed to serve as single-stranded DNA binding (SSB) protein and assist the cytoplasmic trafficking of T-DNA inside the host cell. In the present study, a rice glutathione-S-transferase (OsGSTU5) that interacts with VirE2 protein in plant cytoplasm has been identified. OsGSTU5 is observed to be involved in post-translational glutathionylation of VirE2 protein (gVirE2). In silico analysis revealed that  gVirE2+ssDNA complex is structurally less stable than  VirE2+ ssDNA complex. The gel shift activity confirms the attenuated SSB property of gVirE2 over VirE2 protein under in vitro condition. Moreover, knock-down and overexpression OsGSTU5 phenotypes of rice showed increased and decreased T-DNA expression, respectively after Agrobacterium infection. The present finding convincingly establishes the role of OsGSTU5 as defense protein in rice that can further serve as an important target for modulation of AMT efficiency in rice.


title: Respiration aligns perception with neural excitability

abstract: Recent studies from the field of interoception have highlighted the link between bodily and neural rhythms during action, perception, and cognition. The mechanisms underlying functional body-brain coupling, however, are poorly understood, as are the ways in which they modulate behaviour. We acquired respiration and human magnetoencephalography (MEG) data from a near-threshold spatial detection task to investigate the trivariate relationship between respiration, neural excitability, and performance. Respiration was found to significantly modulate perceptual sensitivity as well as posterior alpha power (8 - 13 Hz), a well-established proxy of cortical excitability. In turn, alpha suppression prior to detected vs undetected targets underscored the behavioural benefits of heightened excitability. Notably, respiration-locked excitability changes were maximised at a respiration phase lag of around - 30{degrees} and thus temporally preceded performance changes. In line with interoceptive inference accounts, these results suggest that respiration actively aligns sampling of sensory information with transient cycles of heightened excitability to facilitate performance.


title: Brain image-derived phenotypes yield insights into causal risk of psychiatric disorders using a Mendelian randomization study

abstract: Brain imaging-derived phenotypes (IDPs) serve as underlying functional intermediates in psychiatric disorders, both of which are highly polygenic and heritable. Observational studies have elucidated the correlation between IDPs and psychiatric disorders, yet no systematic screening of IDPs to confer the causal liability in such disorders. We conducted a bidirectional two-sample Mendelian randomization framework to explore the causality of 1,901 IDPs on 10 psychiatric disorders and established the BrainMR database (http://brainmr.online/idp2psy/Index.php). We identified 17 causalities in forward MR analyses and 14 causalities in reverse MR analyses, which all rigorously examined them through various sensitivity analyses. The top significant relationship in forward was a unit lower volume of right central lateral of the thalamic nuclei, which was causally associated with an increased anorexia nervosa risk with an estimated OR of 0.52 (95% CI 0.41-0.64, P = 3.32 x 10-9). In reverse, the top significant IDP to be affected was the area of superior segment of the circular sulcus of the insula in the right hemisphere, which was increased by the reason of SCZ risk with an estimated association effect size of 0.068 (95% CI 0.046-0.090, P = 1.12 x 10-6). Overall, our study provides unique insights into causal pathways of psychiatric disorders at the imaging levels.


title: Synchronized Neural Activity Indexes Engagement with Spoken Stories under Acoustic Masking

abstract: Older people with hearing problems often experience difficulties understanding speech in the presence of background sound. As a result, they may disengage in social situations, which has been associated with negative psychosocial health outcomes. Measuring listening (dis-)engagement during challenging listening situations has received little attention thus far. We recruit young, normal-hearing human adults (both sexes) and investigate how speech intelligibility and engagement during naturalistic story listening is affected by the level of acoustic masking (12-talker babble) at different signal-to-noise ratios (SNRs). In Experiment 1, we observed that word-report scores were above 80% for all but the lowest SNR (-3 dB SNR) we tested, at which performance dropped to 54%. In Experiment 2, we calculated inter-subject correlation (ISC) using electroencephalography (EEG) data to identify dynamic spatial patterns of shared neural activity evoked by the stories. ISC has previously been used as a neural measure of participants engagement with naturalistic materials. Our results show that ISC was stable across all but the lowest SNRs, despite reduced speech intelligibility. Comparing ISC and intelligibility demonstrated that word-report performance declined more strongly with decreasing SNR compared to ISC. Our measure of neural engagement suggests that individuals remain engaged in story listening despite missing words due to background noise. Our work provides a potentially fruitful approach to investigate listener engagement with naturalistic, spoken stories that may be used to investigate (dis)engagement in older adults with hearing impairment.


title: Synchronized Neural Activity Indexes Engagement with Spoken Stories Despite Acoustic Masking


title: Neural activity during story listening is synchronized across individuals despite acoustic masking


title: Brain virtual histology with X-ray phase-contrast tomography Part II: 3D morphologies of amyloid-β plaques in Alzheimer's disease models

abstract:
While numerous transgenic mouse strains have been produced to model the formation of amyloid-{beta} (A{beta}) plaques in the brain, efficient methods for whole-brain 3D analysis of A{beta} deposits are lacking. Moreover, standard immunohistochemistry performed on brain slices precludes any shape analysis of A{beta} plaques. The present study shows how in-line (propagation-based) X-ray phase-contrast tomography (XPCT) combined with ethanol-induced brain sample dehydration enables hippocampus-wide detection and morphometric analysis of A{beta} plaques. Performed in three distinct Alzheimer mouse strains, the proposed workflow identified differences in signal intensity and 3D shape parameters: 3xTg displayed a different type of A{beta} plaques, with a larger volume and area, greater elongation, flatness and mean breadth, and more intense average signal than J20 and APP/PS1. As a label-free non-destructive technique, XPCT can be combined with standard immunohistochemistry. XPCT virtual histology could thus become instrumental in quantifying the 3D spreading and the morphological impact of seeding when studying prion-like properties of A{beta} aggregates in animal models of Alzheimers disease. This is Part II of a series of two articles reporting the value of in-line XPCT for virtual histology of the brain; Part I shows how in-line XPCT enables 3D myelin mapping in the whole rodent brain and in human autopsy brain tissue.

HighlightsO_LIX-ray phase-contrast tomography (XPCT) enables whole brain detection of A{beta} plaques
C_LIO_LIMorphometric parameters of A{beta} plaques may be readily retrieved from XPCT data
C_LIO_LINew shape parameters were successfully extracted from three Alzheimers disease models
C_LIO_LIA Fiji-based "biologist-friendly" analysis workflow is proposed and shared
C_LIO_LIXPCT is a powerful virtual histology tool that requires minimal sample preparation
C_LI

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/436908v2_ufig1.gif" ALT="Figure 1">
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title: MEG cortical microstates: spatiotemporal characteristics, dynamic functional connectivity and stimulus-evoked responses

abstract: EEG microstate analysis is a useful approach for studying brain states - nicknamed  atoms of thought - and their fast transitions in healthy cognition and disease. A key limitation of conventional microstate analysis is that it must be performed at the sensor level, and therefore gives limited anatomical insight into the cortical mechanisms underpinning these states. In this study, we generalise the microstate methodology to be applicable to source-reconstructed electrophysiological data. Using simulations of a neural-mass network model, we first established the validity and robustness of the proposed method. Using MEG resting-state data, we uncovered ten microstates with distinct spatial distributions of cortical activation. Multivariate pattern analysis demonstrated that source-level MEG microstates were associated with distinct functional connectivity patterns. Using a passive auditory paradigm, we further demonstrated that the occurrence probability of MEG microstates were altered by evoked auditory responses, exhibiting a hyperactivity of the microstate including the auditory cortex. Our results support the use of MEG source-level microstates as a data-driven method for investigating brain dynamic activity and connectivity at the millisecond scale.


title: Calcium-Permeable AMPA Receptor Activity and GluA1 Trafficking in the Basolateral Amygdala Regulate the Positive Reinforcing Effects of Alcohol

abstract: Addiction is viewed as maladaptive glutamate-mediated neuroplasticity that is regulated, in part, by calcium-permeable AMPA receptor (CP-AMPAR) activity. However, the contribution of CP-AMPARs to alcohol-seeking behavior remains to be elucidated. We evaluated CP-AMPAR activity in the basolateral amygdala (BLA) as a potential target of alcohol that also regulates alcohol self-administration in C57BL/6J mice. Operant self-administration of sweetened alcohol increased spontaneous EPSC frequency in BLA neurons that project to the nucleus accumbens as compared to behavior-matched sucrose controls indicating an alcohol-specific upregulation of synaptic activity. Bath application of the CP-AMPAR antagonist NASPM decreased evoked EPSC amplitude only in alcohol self-administering mice indicating alcohol-induced synaptic insertion of CP-AMPARs in BLA projection neurons. Moreover, NASPM infusion in the BLA dose-dependently decreased the rate of operant alcohol self-administration providing direct evidence for CP-AMPAR regulation of alcohol reinforcement. Since most CP-AMPARs are GluA1-containing, we asked if alcohol alters the activation state of GluA1-containing AMPARs. Immunocytochemistry results showed elevated GluA1-S831 phosphorylation in the BLA of alcohol as compared to sucrose mice. To investigate mechanistic regulation of alcohol self-administration by GluA1-containing AMPARs, we evaluated the necessity of GluA1 trafficking using a TET-ON AAV encoding a dominant-negative GluA1 c-terminus (GluA1ct) that blocks activity-dependent synaptic delivery of native GluA1-containing AMPARs. GluA1ct expression in the BLA reduced alcohol self-administration with no effect on sucrose controls. These results show that CP-AMPAR activity and GluA1 trafficking in the BLA mechanistically regulate the reinforcing effects of sweetened alcohol. Pharmacotherapeutic targeting these mechanisms of maladaptive neuroplasticity may aid medical management of alcohol use disorder.


title: A State Space Modeling Approach to Real-Time Phase Estimation

abstract: Brain rhythms have been proposed to facilitate brain function, with an especially important role attributed to the phase of low frequency rhythms. Understanding the role of phase in neural function requires interventions that perturb neural activity at a target phase, necessitating estimation of phase in real-time. Current methods for real-time phase estimation rely on bandpass filtering, which assumes narrowband signals and couples the signal and noise in the phase estimate, adding noise to the phase and impairing detections of relationships between phase and behavior. To address this, we propose a state space phase estimator for real-time tracking of phase. By tracking the analytic signal as a latent state, this framework avoids the requirement of bandpass filtering, separately models the signal and the noise, accounts for rhythmic confounds, and provides credible intervals for the phase estimate. We demonstrate in simulations that the state space phase estimator outperforms current state-of-the-art real-time methods in the contexts of common confounds such as broadband rhythms, phase resets and co-occurring rhythms. Finally, we show applications of this approach to in vivo data. The method is available as a ready-to-use plug-in for the OpenEphys acquisition system, making it widely available for use in experiments.


title: Cannabinoid signaling promotes the reprogramming of Muller glia into proliferating progenitor cells.

abstract:
Endocannabinoids (eCB) are lipid-based neurotransmitters that are known to influence synaptic function in the visual system. eCBs are also known to suppress neuroinflammation in different pathological states. However, nothing is known about the roles of the eCB system during reprogramming of Muller glia (MG) into proliferating progenitor-like cells in the retina. Accordingly, we used the chick and mouse model to characterize expression patterns of eCB-related genes and applied pharmacological agents to examine how the eCB system impacts glial reactivity and the capacity of MG to become Muller glia-derived progenitor cells (MGPCs). We probed single cell RNA-seq libraries to identify eCB-related genes and identify cells with dynamic patterns of expression in damaged retinas. MG and inner retinal neurons expressed the eCB receptor CNR1, as well as enzymes involved in eCB metabolism. In the chick, intraocular injections of 2-Arachidonoylglycerol (2-AG) and Anandamide (AEA) potentiated the formation of MGPCs. Consistent with these findings, CNR1-agonists and MGLL-inhibitor promoted reprogramming, whereas CNR1-antagonist and inhibitors of eCB synthesis suppressed reprogramming. Surprisingly, retinal microglia were largely unaffected by increases or decreases in eCB signaling in both chick and mouse models. However, eCB-signaling suppressed the activation of NFkB-reporter in MG in damaged mouse retinas. We conclude that the eCB system in the retina influences the reactivity of MG and is important for regulating glial reactivity and the reprogramming of MG into proliferating MGPCs, but not for regulating the reactivity of immune cells in the retina.

Main PointsMuller glia express CNR1 receptor and endocannabinoid synthesis genes.

Endocannabinoids after retinal damage promote the formation of Muller glia derived progenitor cells in chick.

Endocannabinoids reduce NFkB activity in mouse Muller glia.

category: molecular biology


title: Identification of a new, Rab14-dependent, endo-lysosomal pathway

abstract: Cells can endocytose material from the surrounding environment. Endocytosis and endosome dynamics are controlled by proteins of the small GTPase Rab family. Several endocytosis pathways have been described (e.g. clathrin-mediated endocytosis, macropinocytosis, CLIC/GEEC pathway). Besides possible recycling routes to the plasma membrane and various organelles, these pathways all appear to funnel the endocytosed material to Rab5-positive early endosomes that then mature into Rab7-positive late endosomes/lysosomes. By studying the uptake of a series of cell-penetrating peptides (CPPs) used in research and clinic, we have discovered a second endocytic pathway that moves material to late endosomes/lysosomes and that is fully independent of Rab5 and Rab7 but requires the Rab14 protein. This newly identified pathway differs from the conventional Rab5-dependent endocytosis at the stage of vesicle formation already and is not affected by a series of compounds that inhibit the Rab5-dependent pathway. The Rab14-dependent pathway is also used by physiological cationic molecules such as polyamines and homeodomains found in homeoproteins. Rab14 is expressed by the last eukaryotic common ancestor. The Rab14-dependent pathway may therefore correspond to a primordial endosomal pathway taken by cationic cargos.

category: cell biology


title: Patterns and mechanisms underlying ecoregion delineation in North American freshwater plants

abstract:
AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSAimC_ST_ABSBiogeographical regionalisations are actively studied in different ecosystems, because they increase our understanding on fundamental broad{square}scale patterns and can help us in the establishment of conservation areas. Thus, we studied how well existing freshwater ecoregions describe geographical delineation for inland water plants and which ecogeographical gradients explain them.

LocationNorth America, excluding Mexico and remote islands.

TaxonFreshwater vascular plants of all taxa and different functional groups.

MethodsUsing newly available fine-grained data on freshwater plant distributions, we calculated internal homogeneity and cross-boundary heterogeneity among neighbouring ecoregions. We further integrated measures of community dissimilarity to assess whether the degree of within-ecoregion homogeneity and distinctness are driven by their relationships to species replacements and richness differences, and explored how a complex suite of ecogeographical mechanisms and plant life forms affect ecoregion delineation using spatially explicit regression routines.

ResultsWe found a clear geographical patterning of ecoregion robustness for North American freshwater plants, with their communities being more internally homogeneous and more similar to one another in polar and subtropical inland waters. Surprisingly, the degree of internal homogeneity and ecoregion distinctness were almost equally driven by species replacements and richness differences. Considering different life forms, ecoregion delineation performed best for emergent and floating-leaved plants. Finally, within-ecoregion homogeneity and distinctness were best explained by annual mean temperature and terrain ruggedness, respectively, with mean water alkalinity, ecoregion area and Late Quaternary Ice Age legacies having supplementary effects.

Main conclusionsOur findings emphasise that geographical regionalisations founded on a particular organismal group are not applicable for all taxa. Our study is a promising starting point for further investigations of geographical delineations for different freshwater taxa. These updated regionalisations can then be used for conserving different biotas in freshwaters, which are currently among the most threatened ecosystems in the world.

SO_SCPLOWTATEMENTC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWOFC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSIGNIFICANCEC_SCPLOWIn biogeographical regionalisation biota is categorized to meaningful geographical units, such as ecoregions. However, ecoregions delineated for a particular group of organisms may not be applicable to another assemblages. We studied how ecoregions founded on fish are suitable for freshwater plants across North America. Our findings suggest that these ecoregions did not show consistent robustness for freshwater plants in North America. This study is a promising starting point for further investigations of geographical delineations for different freshwater taxa, having also value in conservation planning and management.


title: Spatiotemporal patterns in Golden-cheeked Warbler breeding habitat quality and quantity

abstract: The Golden-cheeked Warbler, Setophaga chrysoparia, is a migratory songbird listed as endangered under the federal Endangered Species Act that breeds exclusively in central Texas and is heavily impacted by habitat conversion. The species relies on mixed Ashe-juniper and oak woodlands for nest-building and shelter during spring and early summer months. Using land cover data spanning the last 25 years, we conduct a geospatial analysis to quantify changes and\ identify shifts in breeding habitat quantity and quality. Since 1985, 13% of all forests within the warblers breeding range were disturbed, with greater incidences near San Antonio (32%) and Austin (24%) metropolitan areas. Additionally, data show a 45% decrease in high-quality habitat (i.e., intact mixed or evergreen core forests) and a decrease in patch size. Habitats within protected areas see a less sharp decline in habitat quality and large increases in warbler sightings, but these only represent 10% of all highest-quality habitat in the breeding range. Drastic declines in habitat quality suggest that generalized metrics of conversion may underestimate true habitat loss as degradation may impact the ecological viability of remaining forests for warbler nesting. Further evidence suggests that the few protected areas within the Texas range continue to play a significant role in warbler breeding. This information will assist researchers and managers prioritizing conservation action and will inform upcoming species status determinations.


title: Comparing two circular distributions: advice for effective implementation of statistical procedures in biology

abstract: Many biological variables, often involving timings of events or directions, are recorded on a circular rather than linear scale, and need different statistical treatment for that reason. A common question that is asked of such circular data involves comparison between two groups or treatments: Are the populations from which the two samples drawn differently distributed around the circle? For example, we might ask whether the distribution of directions from which a stalking predator approaches its prey differs between sunny and cloudy conditions; or whether the time of day of mating attempts differs between lab mice subject to one of two hormone treatments. An array of statistical approaches to these questions have been developed. We compared 18 of these (by simulation) in terms of both abilities to control type I error rate near the nominal value, and statistical power. We found that only eight tests offered good control of type I error in all our test situations. Of these eight, we are able to identify Watsons U2 test and MANOVA based on trigonometric functions of the data as offering the best power in the overwhelming majority of our test circumstances. There was often little to choose between these tests in terms of power, and no situation where either of the remaining six tests offered substantially better power than either of these. Hence, we recommend the routine use of either Watsons U2 test or MANOVA when comparing two samples of circular data.


title: Cooperation among c-subunits of FoF1-ATP synthase in rotation-coupled proton translocation

abstract: In FoF1-ATP synthase, proton translocation through Fo drives rotation of the c-subunit oligomeric ring relative to the a-subunit. Recent studies suggest that in each step of the rotation, key glutamic acid residues in different c-subunits contribute to proton release to and proton uptake from the a-subunit. However, no studies have demonstrated cooperativity among c-subunits toward FoF1-ATP synthase activity. Here, we addressed this using Bacillus PS3 ATP synthase harboring c-ring with various combinations of wild-type and cE56D, enabled by genetically fused single-chain c-ring. ATP synthesis and proton pump activities were decreased by a single cE56D mutation and further decreased by double cE56D mutations. Moreover, activity further decreased as the two mutation sites were separated, indicating cooperation among c-subunits. Similar results were obtained for proton transfer-coupled molecular simulations. Simulations revealed that prolonged proton uptake in mutated c-subunits is shared between two c-subunits, explaining the cooperation observed in biochemical assays.


title: Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data

abstract: 1Gene co-expression measurements are widely used in computational biology to identify coordinated expression patterns across a group of samples, which may indicate that these genes are controlled by the same transcriptional regulatory program, or involved in common biological processes. Gene co-expression is generally estimated from RNA-Seq data, which are generally normalized to remove technical variability. Here, we find and demonstrate that certain normalization methods, in particular quantile-based methods, can introduce false-positive associations between genes, and that this can consequently hamper downstream co-expression network analysis. Quantile-based normalization can, however, be extremely powerful. In particular when preprocessing large-scale heterogeneous data, quantile-based normalization can be applied to remove technical variability while maintaining global differences in expression for samples with different biological attributes. We therefore developed CAIMAN, a method to correct for false-positive associations that may arise from normalization of RNA-Seq data. CAIMAN utilizes a Gaussian mixture model to fit the distribution of gene expression and to adaptively select the threshold to define lowly expressed genes, which are prone to form false-positive associations. Thereafter, CAIMAN corrects the normalized expression for these genes by removing the variability across samples that might lead to false-positive associations. Moreover, CAIMAN avoids arbitrary gene filtering and retains associations to genes that only express in small subgroups of samples, highlighting its potential future impact on network modeling and other association-based approaches in large-scale heterogeneous data.


title: Tissue flow through pores: a computational study

abstract: AO_SCPLOWBSTRACTC_SCPLOWCell migration is of major importance for the understanding of phenomena such as morphogenesis, cancer metastasis, or wound healing. In many of these situations cells are under external confinement. In this work we show by means of computer simulations with a Cellular Potts Model (CPM) that the presence of a bottleneck in an otherwise straight channel has a major influence on the internal organisation of an invading cellular monolayer and the motion of individual cells therein. Comparable to a glass or viscoelastic material, the cell sheet is found to exhibit features of both classical solids and classical fluids. The local ordering on average corresponds to a regular hexagonal lattice, while the relative motion of cells is unbounded. Compared to an unconstricted channel, we observe that a bottleneck perturbs the formation of regular hexagonal arrangements in the epithelial sheet and leads to pile-ups and backflow of cells near the entrance to the constriction, which also affects the overall invasion speed. The scale of these various phenomena depends on the dimensions of the different channel parts, as well as the shape of the funnel domain that connects wider to narrower regions.


title: Too little, too late: transcription during imbibition of lethally aged soybean seeds is weak and delayed, but not aberrant

abstract:
O_TBL View this table:
org.highwire.dtl.DTLVardef@116f1e7org.highwire.dtl.DTLVardef@163aa97org.highwire.dtl.DTLVardef@54d174org.highwire.dtl.DTLVardef@8342f3org.highwire.dtl.DTLVardef@1a08df1_HPS_FORMAT_FIGEXP  M_TBL C_TBL O_LIThis study investigates alive to dead signals in seeds that aged during cool, dry storage. Signals may invoke abrupt, lethal metabolic pathways or reflect effects of accumulated small injuries which impair recovery from life in the dry state.
C_LIO_LICohorts of soybean (Glycine max cv.  Williams 82) seeds were stored for 3, 19 and 22 years. Transcriptomes of dry embryonic axes and axes 24 hours after imbibition (HAI) were sequenced to determine gene expression patterns. These cohorts showed about <2, 40, and ~99% mortality, respectively, in response to storage and aging.
C_LIO_LIA total of 19,340 genes were significantly differentially expressed (SDE) in imbibed axes compared to dry axes. Gene expression patterns of imbibed axes clustered into three groups that represented high, low, and no germination potential (GP). There were 17,360 SDE genes in high-GP axes and 4,892 SDE genes, mostly upregulated, in no-GP axes. Transcriptomes of no-GP axes were similar to healthy axes at 3 HAI.
C_LIO_LISlow transcription, not transcription errors or novel expression pathways, portends failure to transition from seed to seedling. We conclude that the signature of death in dry aged seeds arises from metabolism that is "too little and too late."
C_LI


title: Mathematical Models of Retinitis Pigmentosa: The Trophic Factor Hypothesis

abstract: Retinitis pigmentosa (RP) is the term used to denote a group of inherited retinal-degenerative conditions that cause progressive sight loss. Individuals with this condition lose their light-sensitive photoreceptor cells, known as rods and cones, over a period of years to decades; degeneration starting in the retinal periphery, and spreading peripherally and centrally over time. RP is a rod-cone dystrophy, meaning that rod health and function are affected earlier and more severely than that of cones. Rods degenerate due to an underlying mutation, whereas the reasons for cone degeneration are unknown. A number of mechanisms have been proposed to explain secondary cone loss and the spatio-temporal patterns of retinal degeneration in RP. One of the most promising is the trophic factor hypothesis, which suggests that rods produce a factor necessary for cone survival, such that, when rods degenerate, cone degeneration follows. In this paper we formulate and analyse mathematical models of RP under the trophic factor hypothesis. These models are constructed as systems of reaction-diffusion partial differential equations in one spatial dimension, and are solved and analysed using a combination of numerical and analytical methods. We predict the conditions under which cones will degenerate following the loss of a patch of rods from the retina, the critical trophic factor treatment rate required to prevent cone degeneration following rod loss and the spatio-temporal patterns of cone loss that would result if the trophic factor mechanism alone were responsible for retinal degeneration.

category: systems biology


title: Extrasynaptic GABA waves underlie epileptiform rhythms in the hippocampal network

abstract: Synchronised rhythmic activity of the brain is thought to arise from neuronal network behaviours that rely on synaptic signalling between individual cells. This notion has been a basis to explain periodic epileptiform discharges that are driven by interneuronal networks. However, interneuronal discharges not only engage cell-cell GABAergic transmission but also control the extracellular GABA concentration ([GABA]e) and thus tonic GABAA receptor conductance (Gtonic) across the cell population. At the same time, the firing activity of interneurons shows a bell-shaped dependence on Gtonic, suggesting an innate susceptibility to self-sustained oscillations. Here, we employ patch-clamp GABA  sniffer and fast two-photon excitation imaging of GABA sensor to show that periodic epileptiform discharges are preceded by a region-wide, rising wave of extracellular GABA. Neural network simulations based on such observations reveal that it is the volume-transmitted, extrasynaptic actions of GABA targeting multiple off-target cells that drives synchronised interneuronal spiking prompting periodic epileptiform bursts. We validate this hypothesis using simultaneous patch-clamp recordings from multiple nerve cells, selective optogenetic stimulation of fast-spiking interneurons, and by revealing the role of GABA uptake. Our findings thus unveil a key role of extrasynaptic, volume-transmitted GABA actions in enabling and pacing regenerative rhythmic activity in brain networks.


title: Volume-transmitted GABA waves drive epileptiform rhythms in the hippocampal network


title: Pseudomonas aeruginosa isolates defective in function of the LasR quorum sensing regulator are frequent in diverse environmental niches

abstract: The saprophyte Pseudomonas aeruginosa is a versatile opportunistic pathogen causing infections in immunocompromised individuals. To facilitate its adaptation to a large variety of niches, this bacterium exploits population density-dependant gene regulation systems called quorum sensing. In P. aeruginosa, three distinct but interrelated quorum sensing systems (las, rhl and pqs) regulate the production of many survival and virulence functions. In prototypical strains, the las system, through its transcriptional regulator LasR, is important for the full activation of the rhl and pqs systems. Still, LasR-deficient isolates have been reported, mostly sampled from the lungs of people with cystic fibrosis, where they are considered selected by the chronic infection environment. In this study, we show that a defect in LasR activity appears to be an actually widespread mechanism of adaptation in this bacterium. Indeed, we found abundant LasR-defective isolates sampled from hydrocarbon-contaminated soils, hospital sink drains, and meat/fish market environments, using an approach based on phenotypic profiling, supported by gene sequencing. Interestingly, several LasR-defective isolates maintain an active rhl system or are deficient in pqs system signaling. The high prevalence of a LasR-defective phenotype among environmental P. aeruginosa isolates questions the role of quorum sensing in niche adaptation.


title: Isolation and Purification of Lipoarabinomannan from Urine of Adults with Active Tuberculosis

abstract: Lipoarabinomannan (LAM) is a cell wall component of Mycobacterium tuberculosis that is excreted in the urine of persons with active tuberculosis (TB). Limited diagnostic sensitivity of LAM immunoassays has been due to selecting antibodies against LAM derived from in vitro cultured M. tuberculosis, rather than LAM purified from in vivo clinical urine specimens. Urinary LAM (uLAM) is critical to enable the development of and/or screening of novel uLAM-specific antibodies but is typically dilute and in heterogeneous mixtures with other urine components. We used physical, enzymatic, and chemical processes for the scaled isolation and purification of uLAM. The purified material may then be used to develop more sensitive uLAM diagnostic tests for active TB disease.


title: Neuronal ribosomes dynamically exchange ribosomal proteins in a context-dependent manner.

abstract: Owing to their morphological complexity and dense network connections, neurons modify their proteomes locally, using mRNAs and ribosomes present in the neuropil (tissue enriched for dendrites and axons). Although ribosome biogenesis largely takes place in the nucleus and perinuclear region, neuronal ribosomal protein (RP) mRNAs have been frequently detected remotely, in dendrites and axons. Here, using imaging and ribosome profiling, we directly detected the RP mRNAs and their translation in the neuropil. Combining brief metabolic labeling with mass spectrometry, we found that a group of RPs quickly associated with translating ribosomes in the cytoplasm and that this incorporation is independent of canonical ribosome biogenesis. Moreover, the incorporation probability of some RPs was regulated by location (neurites vs. cell bodies) and changes in the cellular environment (in response to oxidative stress). Our results suggest new mechanisms for the local activation, repair and/or specialization of the translational machinery within neuronal processes, potentially allowing remote neuronal synapses a rapid solution to the relatively slow and energy-demanding requirement of nuclear ribosome biogenesis.