title: Autoregulation dependent and independent mechanisms are responsible for the systemic control of nodule formation by the plant N demand

abstract: In legumes interacting with rhizobia the formation of symbiotic organs responsible for the acquisition of atmospheric nitrogen is depending of the plant nitrogen (N) demand. We discriminated between local and systemic impact of nitrogen on nodule formation using Medicago truncatula plants cultivated in split-root systems. We obtained evidence of the control of nodule formation by whole plant systemic N-satisfaction signaling but obtained little evidence of a local control by mineral nitrogen. We characterized the impact of systemic N signaling on the root transcriptome reprogramming associated to nodule formation. We identified, large genes clusters displaying common expression profiles in response to systemic N signaling enriched in particular fonctions required during these biological processes. We found evidence of a strong effect of SUNN in the control by systemic N signaling of many genes involved in the early interaction with rhizobium as well as organogenesis supporting a role of autoregulation pathway in systemic N signaling. However, we also found evidence that major SUNN independent systemic N signaling controls were maintained in the mutant. This study shed light on the unexpected high complexity of the control of nodule formation by systemic N signaling, that probably involves multiple pathways.


title: Systematic monitoring of photosynthetically-derived oxidative signals using a 2-Cys peroxiredoxin-based redox probe

abstract:
Transmission of reductive cues from the photosynthetic electron transport chain to redox-regulated proteins plays a crucial role in activating chloroplast metabolism. However, deciphering the role of their counterbalanced oxidative signals is challenging due to monitoring difficulties. Here, we demonstrate the light-depended redox modification of chloroplast-targeted 2-Cys peroxiredoxins and introduce peroxiredoxin-based biosensors to monitor photosynthetically-derived oxidative signals. By employing a set of genetically encoded biosensors, we show the induction of oxidative signals under habitual light intensities and their inverse relationship with NADPH levels, unraveling the combined activity of reducing and oxidizing signals in fine-tuning chloroplast metabolism. A faster increase in carbon assimilation rates during photosynthesis induction phase was measured in plants deficient in 2-Cys peroxiredoxins compared to wild-type, suggesting the involvement of oxidative signals in attenuating photosynthesis under variable light environments. We suggest that oxidative signals measured by peroxiredoxin-based biosensors reflect the limitation to photosynthesis imposed by the redox regulatory system.

One-Sentence SummaryA genetically encoded biosensor unmasked the dominant role of photosynthetically-derived oxidative signals under habitual conditions.

category: plant biology


title: Systematic monitoring of photosynthetically-derived oxidative signals by a peroxiredoxin-based biosensor


title: Systematic monitoring of 2-Cys peroxiredoxin-derived redox signals unveiled its role in attenuating carbon assimilation rate


title: 'Phytopathological strolls' in the dual context of COVID-19 lockdown and IYPH2020: transforming constraints into an opportunity for public education about plant pathogens

abstract: The experience presented here relates to 2020, a particularly timely year for plant disease-related communication ( International Year of Plant Health IYPH2020), but also a unique year because of the COVID-19 pandemic. Our goal was to illustrate the diversity and beauty of fungal plant pathogens through a naturalist approach that could be followed by any amateur. We achieved this end through  phytopathological strolls, in which we observed and determined the origin of symptoms on diseased plants found in our garden, in the local streets, in nearby open spaces, and sharing this matter with a broad public. The lockdown imposed in France created an additional motivation to take up the challenge, and to involve our children, even under strong constraints, such as movement restrictions. We observed and described fungal pathogens through hundreds of photographs, shared our findings with a large audience on Twitter, and received feedback. The material used was deliberately simple and transportable: a digital reflex camera, an old microscope, a mobile phone, some books and an Internet connexion. Between March 17, 2020 and June 20, 2021 we found 196 plant pathogens, including 97 rusts, 27 powdery mildews and 28 septoria-like diseases. We discuss here the importance of promoting searches for plant pathogens, their description and conservation, through a combination of classical approaches and digital tools in tune with the times, such as Twitter, by treating pathogen identification like a detective game and, more surprisingly, by making use of the addictive nature of collection approaches, drawing a parallel with Pokemon Go.

category: microbiology


title: Light spectra trigger divergent gene expression in barley cultivars

abstract:
Light spectra influence barley development, causing a diverse range of responses among cultivars that are poorly understood. Here, we exposed three barley genotypes with different light sensitivities to two light sources: fluorescent bulbs, over-representing green and red wavebands, and metal halide lamps, with a more balanced spectrum. We used RNA sequencing to identify the main genes and pathways involved in the different responses, and RT-qPCR to validate the expression values. Different grades of sensitivity to light spectra were associated with transcriptional reprogramming, plastid signals, and photosynthesis. The genotypes were especially divergent in the expression of genes regulated by transcription factors from MADS-box, WRKY, and NAC families, and in specific photoreceptors such as phytochromes and cryptochromes. Variations in light spectra also affected the expression of circadian clock, flowering time, and frost tolerance genes, among others, resembling plant responses to temperature. The relation between PPD-H1, HvVRN1, and HvFT1 expression might explain genotypic differences. Light-sensitive genotypes experienced a partial reversion of the vernalization process and senescence-related stress under the less favorable light quality conditions. The observed light-quality sensitivities reveal a complex mechanism of adaptation to regions with specific light quality features and/or possible regulation of light spectra in plant development during early spring.

HighlightDevelopment genes were affected by light quality in the barley varieties tested. Different grades of sensitivity were related to the expression of transcription factors, senescence, light signaling and cold-regulated genes.


title: Pelagic larval polyclads that practice macrophagous carnivory

abstract: We report evidence that hatchling polyclads of several genera feed in the plankton on large prey. These ciliated swimmers, despite apparently lacking means to concentrate food or even detect it at a distance, subdue and consume fast-moving active-swimming plankters such as crustacean larvae and copepods, or molluskan veligers. We describe feeding events in captivity using videomicroscopy, and identify several wild-caught predatory pelagic polyclad larvae to genus or species level by DNA barcoding. Remarkably, one of these types is identified unambiguously with a species previously observed as Mullers larvae, which live as conventional planktotrophs on an inferred diet of small phytoflagellates. Therefore we conclude first that while so-called "direct-developing" polyclad flatworms may hatch with juvenile-like morphology, at least some of these are functionally larvae. Second, that some species of polyclad have at least a triphasic life cycle, with a first larval stage living in the plankton on primary producers followed by a second larval stage living in the plankton by macrophagous carnivory, before presumably settling to the benthos for adult life.

category: zoology


title: Impact of the B.1.1.7 variant on neutralizing monoclonal antibodies recognizing diverse epitopes on SARS-CoV-2 Spike

abstract: The interaction of the SARS-CoV-2 Spike receptor binding domain (RBD) with the ACE2 receptor on host cells is essential for viral entry. RBD is the dominant target for neutralizing antibodies and several neutralizing epitopes on RBD have been molecularly characterized. Analysis of circulating SARS-CoV-2 variants has revealed mutations arising in the RBD, the N-terminal domain (NTD) and S2 subunits of Spike. To fully understand how these mutations affect the antigenicity of Spike, we have isolated and characterized neutralizing antibodies targeting epitopes beyond the already identified RBD epitopes. Using recombinant Spike as a sorting bait, we isolated >100 Spike-reactive monoclonal antibodies from SARS-CoV-2 infected individuals. ~45% showed neutralizing activity of which ~20% were NTD-specific. None of the S2-specific antibodies showed neutralizing activity. Competition ELISA revealed that NTD-specific mAbs formed two distinct groups: the first group was highly potent against infectious virus, whereas the second was less potent and displayed glycan-dependant neutralization activity. Importantly, mutations present in B.1.1.7 Spike frequently conferred resistance to neutralization by the NTD-specific neutralizing antibodies. This work demonstrates that neutralizing antibodies targeting subdominant epitopes need to be considered when investigating antigenic drift in emerging variants.

category: immunology


title: Multi-specific DARPin(R) therapeutics demonstrate very high potency against mutated SARS-CoV-2 variants in vitro

abstract: SARS-CoV-2 has infected millions of people globally and continues to undergo evolution. Emerging variants can be partially resistant to vaccine induced immunity and therapeutic antibodies, emphasizing the urgent need for accessible, broad-spectrum therapeutics. Here, we report a comprehensive study of ensovibep, the first trispecific clinical DARPin candidate, that can simultaneously engage all three units of the spike protein trimer to potently inhibit ACE2 interaction, as revealed by structural analyses. The cooperative binding of the individual modules enables ensovibep to retain inhibitory potency against all frequent SARS-CoV-2 variants, including Omicron BA.1 and BA.2, as of February 2022. Moreover, viral passaging experiments show that ensovibep, when used as a single agent, can prevent development of escape mutations comparably to a cocktail of monoclonal antibodies (mAb). Finally, we demonstrate that the very high in vitro antiviral potency also translates into significant therapeutic protection and reduction of pathogenesis in Roborovski dwarf hamsters infected with either the SARS-CoV-2 wild-type or the Alpha variant. In this model, ensovibep prevents fatality and provides substantial protection equivalent to the standard of care mAb cocktail. These results support further clinical evaluation and indicate that ensovibep could be a valuable alternative to mAb cocktails and other treatments for COVID-19.


title: Multispecific DARPin(R) therapeutics demonstrate very high potency against SARS-CoV-2 variants in vitro


title: Ensovibep, a novel trispecific DARPin candidate that protects against SARS-CoV-2 variants


title: Why do species get a thin slice of π? Revisiting Lewontin's Paradox of Variation

abstract: Neutral theory predicts that genetic diversity increases with population size, yet observed levels of diversity across metazoans vary only two orders of magnitude while population sizes vary over several. This unexpectedly narrow range of diversity is known as Lewontins Paradox of Variation (1974). While some have suggested selection constrains diversity, tests of this hypothesis seem to fall short. Here, I revisit Lewontins Paradox to assess whether current models of linked selection are capable of reducing diversity to this extent. To quantify the discrepancy between pairwise diversity and census population sizes across species, I combine previously-published estimates of pairwise diversity from 172 metazoan taxa with estimates of census sizes. Using phylogenetic comparative methods, I show this relationship is significant accounting for phylogeny, but with high phylogenetic signal and evidence that some lineages experience shifts in the evolutionary rate of diversity deep in the past. Additionally, I find a negative relationship between recombination map length and census size, suggesting abundant species have less recombination and experience greater reductions in diversity due to linked selection. However, I show that even using strong selection parameter estimates, models of linked selection are unlikely to explain the observed relationship between diversity and census sizes across species.

category: evolutionary biology


title: Summix: A method for detecting and adjusting for population structure in genetic summary data

abstract: Publicly available genetic summary data have high utility in research and the clinic including prioritizing putative causal variants, polygenic scoring, and leveraging common controls. However, summarizing individual-level data can mask population structure resulting in confounding, reduced power, and incorrect prioritization of putative causal variants. This limits the utility of publicly available data, especially for understudied or admixed populations where additional research and resources are most needed. While several methods exist to estimate ancestry in individual-level data, methods to estimate ancestry proportions in summary data are lacking. Here, we present Summix, a method to efficiently deconvolute ancestry and provide ancestry-adjusted allele frequencies from summary data. Using continental reference ancestry, African (AFR), Non-Finnish European (EUR), East Asian (EAS), Indigenous American (IAM), South Asian (SAS), we obtain accurate and precise estimates (within 0.1%) for all simulation scenarios. We apply Summix to gnomAD v2.1 exome and genome groups and subgroups finding heterogeneous continental ancestry for several groups including African/African American ([~]84% AFR, [~]14% EUR) and American/Latinx ([~]4% AFR, [~]5% EAS, [~]43% EUR, [~]46% IAM). Compared to the unadjusted gnomAD AFs, Summixs ancestry-adjusted AFs more closely match respective African and Latinx reference samples. Even on modern, dense panels of summary statistics, Summix yields results in seconds allowing for estimation of confidence intervals via block bootstrap. Given an accompanying R package, Summix increases the utility and equity of public genetic resources, empowering novel research opportunities.

category: genetics


title: Unfazed: parent-of-origin detection for large and small de novo variants

abstract:
SummaryUnfazed is a command-line tool to determine the parental gamete of origin for de novo mutations from paired-end Illumina DNA sequencing reads. Unfazed uses variant information for a sequenced trio to identify the parental gamete of origin by linking phase-informative inherited variants to de novo mutations using read-based phasing. It achieves a high success rate by chaining reads into haplotype groups, thus increasing the search space for informative sites. Unfazed provides a simple command-line interface and scales well to large inputs, determining parent-of-origin for nearly 30,000 de novo variants in under 60 hours.

AvailabilityUnfazed is available at https://github.com/ibelyeu/unfazed.

category: genomics


title: Who infects Whom? - Reconstructing infection chains of Mycobacterium avium ssp. paratuberculosis in an endemically infected dairy herd by use of genomic data

abstract: Recent evidence of circulation of multiple strains within herds and mixed infections of cows marks the beginning of a rethink of our knowledge on Mycobacterium avium ssp. paratuberculosis (MAP) epidemiology. Strain typing opens new ways to investigate MAP transmission. This work presents a method for reconstructing infection chains in a setting of endemic Johnes disease on a well-managed dairy farm. By linking genomic data with demographic field data, strain-specific differences in spreading patterns could be quantified for a densely sampled dairy herd. Mixed infections of dairy cows with MAP are common, and some strains spread more successfully. Infected cows remain susceptible for co-infections with other MAP genotypes. The model suggested that cows acquired infection from 1-4 other cows and spread infection to 0-17 individuals. Reconstructed infection chains supported the hypothesis that high shedding animals that started to shed at an early age and showed a progressive infection pattern represented a greater risk for spreading MAP. Transmission of more than one genotype between animals was recorded. In this farm with a good MAP control management program, adult-to-adult contact was proposed as the most important transmission route to explain the reconstructed networks. For each isolate, at least one more likely ancestor could be inferred. Our study results help to capture underlying transmission processes and to understand the challenges of tracing MAP spread within a herd. Only the combination of precise longitudinal field data and bacterial strain type information made it possible to trace infection in such detail.


title: A high-throughput radioactivity-based assay for screening SARS-CoV-2 nsp10-nsp16 complex

abstract: Frequent outbreaks of novel coronaviruses (CoVs), highlighted by the current SARS-CoV-2 pandemic, necessitate the development of therapeutics that could be easily and effectively administered world-wide. The conserved mRNA-capping process enables CoVs to evade their host immune system and is a target for antiviral development. Nonstructural protein (nsp) 16 in complex with nsp10 catalyzes the final step of coronaviral mRNA-capping through its 2-O-methylation activity. Like other methyltransferases, SARS-CoV-2 nsp10-nsp16 complex is druggable. However, the availability of an optimized assay for high-throughput screening (HTS) is an unmet need. Here, we report the development of a radioactivity-based assay for methyltransferase activity of nsp10-nsp16 complex in a 384-well format, and kinetic characterization, and optimization of the assay for HTS (Z'-factor: 0.83). Considering the high conservation of nsp16 across known CoV species, the potential inhibitors targeting SARS-CoV-2 nsp10-nsp16 complex may also be effective against other emerging pathogenic CoVs.

category: biochemistry


title: Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

abstract: Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness as well as DFT properties. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, the proposed kinase inhibitors and a few of the predicted nucleotidyl transferase inhibitors significantly inhibited the aforementioned enzymatic activity. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.

category: bioinformatics


title: Molecular dynamics simulation study of effects of key mutations in SARS-CoV-2 on protein structures

abstract: SARS-CoV-2 has been spreading rapidly since 2019 and has produced large-scale mutations in the genomes. The mutation in genes may lead to changes in protein structure, which would have a great impact on the epidemiological characteristics. In this study, we selected the key mutations of SARS-CoV-2 from a real-time monitoring tool, including D614G, A222V, N501Y, T716I, S982A, D1118H of spike (S) protein, and performed molecular dynamics (MD) simulations on single-site mutant D614G, double-site mutant D614G&A222V and penta-site mutant N501Y&D614G&T716I&S982A&D1118H to investigate their effects on protein structure and stability using molecular dynamics (MD) simulations. The results suggested that D614G improved the stability of S protein, while D614G&A222V and N501Y&D614G&T716I&S982A&D1118H showed an increased solvent accessible surface area and they might enhance the ability of protein to react with the outside environment. Our findings could complement the mechanistic link between genotype--phenotype--epidemiological characteristics in the study of SARS-CoV-2. We also found no significant difference between the antigenicity of S protein and the mutants through Ellipro, which may reference for vaccine development and application.


title: Molecular dynamics simulation study reveals effects of key mutations on spike protein structure in SARS-CoV-2


title: Enabling multiscale variation analysis with genome graphs

abstract:
BackgroundStandard approaches to characterising genetic variation revolve around mapping reads to a reference genome and describing variants in terms of differences from the reference; this is based on the assumption that these differences will be small and provides a simple coordinate system. However this fails, and the coordinates break down, when there are diverged haplotypes at a locus (e.g. one haplotype contains a multi-kilobase deletion, a second contains a few SNPs, and a third is highly diverged with hundreds of SNPs). To handle these, we need to model genetic variation that occurs at different length-scales (SNPs to large structural variants) and that occurs on alternate backgrounds. We refer to these together as multiscale variation.

ResultsWe model the genome as a directed acyclic graph consisting of successive hierarchical subgraphs ("sites") that naturally incorporate multiscale variation, and introduce an algorithm for genotyping, implemented in the software gramtools. This enables variant calling on different sequence backgrounds. In addition to producing regular VCF files, we introduce a JSON file format based on VCF, which records variant site relationships and alternate sequence backgrounds.

We show two applications. First, we benchmark gramtools against existing state-of-the-art methods in joint-genotyping 17 M. tuberculosis samples at long deletions and the overlapping small variants that segregate in a cohort of 1,017 genomes. Second, in 706 African and SE Asian P. falciparum genomes, we analyse a dimorphic surface antigen gene which possesses variation on two diverged backgrounds which appeared to not recombine. This generates the first map of variation on both backgrounds, revealing patterns of recombination that were previously unknown.

ConclusionsWe need new approaches to be able to jointly analyse SNP and structural variation in cohorts, and even more to handle variants on different genetic backgrounds. We have demonstrated that by modelling with a directed, acyclic and locally hierarchical genome graph, we can apply new algorithms to accurately genotype dense variation at multiple scales. We also propose a generalisation of VCF for accessing multiscale variation in genome graphs, which we hope will be of wide utility.


title: Fibroblast activation protein regulates natural killer cell migration, extravasation and tumor infiltration

abstract:
Natural killer (NK) cells play critical roles in physiologic and pathologic conditions such as pregnancy, infection, autoimmune disease and cancer. In cancer, numerous strategies have been designed to exploit the cytolytic properties of NK cells, with variable success. A major hurdle to NK-cell focused therapies is NK cell recruitment to and infiltration into tumors. While the chemotaxis pathways regulating NK recruitment to different tissues are well delineated, the mechanisms human NK cells employ to physically migrate are ill-defined. We show for the first time that human NK cells express fibroblast activation protein (FAP), a cell surface protease previously thought to be primarily expressed by activated fibroblasts. FAP degrades the extracellular matrix to facilitate cell migration and tissue remodeling. We used novel in vivo zebrafish and in vitro 3D culture models to demonstrate that FAP regulates NK cell migration, extravasation, and infiltration into tumors, ultimately affecting tumor cell lysis. These findings demonstrate the necessity of proteolytic migration in NK cell function, suggest novel mechanisms of action of FAP targeting drugs, and provide an entirely new way to regulate NK cell activity.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/429622v2_ufig1.gif" ALT="Figure 1">
View larger version (47K):
org.highwire.dtl.DTLVardef@9b2025org.highwire.dtl.DTLVardef@5b5e79org.highwire.dtl.DTLVardef@976566org.highwire.dtl.DTLVardef@18230c5_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Individuals at risk for developing rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential

abstract: Rheumatoid arthritis (RA) is an autoimmune disease characterized in seropositive individuals by the presence of anti-cyclic citrullinated protein (CCP) antibodies. RA is linked to the intestinal microbiota, yet the association of microbes with CCP serology and their contribution to RA is unclear. We describe intestinal phage communities of individuals at risk for developing RA, with or without anti-CCP antibodies, whose first degree relatives have been diagnosed with RA. We show that at-risk individuals harbor intestinal phage compositions that diverge based on CCP serology, are dominated by Lachnospiraceae phages, and originate from disparate ecosystems. These phages encode unique repertoires of auxiliary metabolic genes (AMGs) which associate with anti-CCP status, suggesting that these phages directly influence the metabolic and immunomodulatory capability of the microbiota. This work sets the stage for the use of phages as preclinical biomarkers and provides insight into a possible microbial-based causation of RA disease development.


title: The promiscuous and highly mobile resistome of a superbug.

abstract: Antimicrobial resistance (AR) is a major global threat to public health. Understanding the population dynamics of AR is critical to restrain and control this issue. However, no study has provided a global picture of the resistome of Acinetobacter baumannii, a very important nosocomial pathogen. Here we analyze 1450+ genomes (covering > 40 countries and > 4 decades) to infer the global population dynamics of the resistome of this species. We show that gene flow and horizontal transfer have driven the dissemination of AR genes in A. baumannii. We found considerable variation in AR gene content across lineages. Although the individual AR gene histories have been affected by recombination, the AR gene content has been shaped by the phylogeny. Furthermore, many AR genes have been transferred to other well-known pathogens, such as Pseudomonas aeruginosa or Klebsiella pneumoniae. Finally, despite using this massive data set, we were not able to sample the whole diversity of AR genes, which suggests that this species has an open resistome. Ours results highlight the high mobilization risk of AR genes between important pathogens. On a broader perspective, this study gives a framework for an emerging perspective (resistome-centric) on the genome epidemiology (and surveillance) of bacterial pathogens.


title: MSX2 safeguards syncytiotrophoblast fate of human trophoblast stem cells

abstract: The majority of placental pathologies are associated with failures in trophoblast differentiation, yet the underlying transcriptional regulation is poorly understood. Here, we use human trophoblast stem cells to elucidate the function of the transcription factor MSX2 in trophoblast specification. We show that depletion of MSX2 de-represses the syncytiotrophoblast program, while forced expression of MSX2 blocks it. We demonstrate that a large proportion of the affected genes are directly bound and regulated by MSX2 and identify components of the SWI/SNF complex as its strong interactors. Our findings uncover the pivotal role of MSX2 in cell fate decisions that govern human placental development and function.

category: molecular biology


title: Oxidant-Resistant LRRC8A/C Anion Channels Support Superoxide Production by Nox1

abstract:
Tumor necrosis factor- (TNF) activates NADPH Oxidase 1 (Nox1) in vascular smooth muscle cells (VSMCs), producing superoxide (O2*-) required for subsequent signaling. LRRC8 family proteins A-E comprise volume-regulated anion channels (VRACs). The required subunit LRRC8A physically associates with Nox1, and VRAC activity is required for Nox activity and the inflammatory response to TNF. LRRC8 channel currents are modulated by oxidants, suggesting that oxidant sensitivity and proximity to Nox1 may play a physiologically relevant role. In VSMCs, LRRC8C knockdown (siRNA) recapitulated the effects of siLRRC8A, inhibiting TNF-induced extracellular and endosomal O2*- production, receptor endocytosis, NF-{kappa}B activation, and proliferation. In contrast, siLRRC8D potentiated NF-{kappa}B activation. Nox1 co-immunoprecipitated with 8C and 8D, and co-localized with 8D at the plasma membrane and in vesicles. We compared VRAC currents mediated by homomeric and heteromeric 8C and 8D channels expressed in HEK293 cells. The oxidant chloramine T (ChlorT, 1 mM) weakly inhibited LRRC8C, but potently inhibited 8D currents. ChlorT exposure also greatly reduced subsequent current block by DCPIB, implicating external sites of oxidation. Substitution of the extracellular loop domains (EL1, EL2) of 8D onto 8C conferred significantly stronger ChlorT-dependent inhibition. 8A/C channel activity is thus more effectively maintained in the oxidized microenvironment expected to result from Nox1 activation at the plasma membrane. Increased ratios of 8D:8C expression may potentially depress inflammatory responses to TNF. LRRC8A/C channel downregulation represents a novel strategy to reduce TNF-induced inflammation.

Key PointsO_LILRRC8A-containing anion channels associate with Nox1 and regulate superoxide production and TNF signaling. Here we show that .LRRC8C and 8D also co-immunoprecipitate with Nox1 in vascular smooth muscle cells.
C_LIO_LILRRC8C knockdown inhibited TNF-induced O2*- production, receptor endocytosis, NF-{kappa}B activation, and proliferation while LRRC8D knockdown enhanced NF-{kappa}B activation. Significant changes in LRRC8 isoform expression in human atherosclerosis and psoriasis suggest compensation for increased inflammation.
C_LIO_LIThe oxidant chloramine-T (ChlorT, 1 mM) weakly ([~]25%) inhibited 8C currents but potently ([~]80%) inhibited 8D currents. Substitution of the two extracellular loop (EL) domains of 8D onto 8C conferred significantly stronger ChlorT-dependent inhibition.
C_LIO_LIChlorT also impaired current block by DCPIB, which occurs through interaction with EL1, further implicating external sites of oxidation.
C_LIO_LI8A/C channels most effectively maintain activity in an oxidized microenvironment, as is expected to result from Nox1 activity at the plasma membrane.
C_LI

category: cell biology


title: hC9ORF78 localizes to kinetochores and is required for proper chromosome segregation.

abstract:
C9ORF78 is a poorly characterized protein found in diverse eukaryotes. Previous work indicated overexpression of hC9ORF78 (aka HCA59) in malignant tissues indicating a possible involvement in growth regulatory pathways. Additional studies in fission yeast and humans uncover a potential function in regulating the spliceosome. In studies of GFP-tagged hC9ORF78 we observed a dramatic reduction in protein abundance in cells grown to confluence and/or deprived of serum growth factors. Serum stimulation induced synchronous re-expression of the protein in HeLa cells. This effect was also observed with the endogenous protein. Overexpressing either E2F1 or N-Myc resulted in elevated hC9ORF78 expression potentially explaining the serum-dependent upregulation of the protein. Immunofluorescence analysis indicates that hC9ORF78 localizes to nuclei in interphase but does not appear to concentrate in speckles as would be expected for a splicing protein. Surprisingly, a subpopulation of hC9ORF78 co-localizes with ACA, Mad1 and Hec1 in mitotic cells suggesting that this protein may associate with kinetochores or centromeres. Furthermore, knocking-down hC9ORF78 caused mis-alignment of chromosomes in mitosis. These studies uncover novel mitotic function and subcellular localization of cancer antigen hC9ORF78.

SUMMARY STATEMENThC9ORF78 regulates chromosome segregation.


title: Proteolysis of fibrillin-2 microfibrils is essential for normal skeletal development

abstract: The embryonic extracellular matrix (ECM) undergoes transition to mature ECM as development progresses, yet specific transition mechanisms ensuring ECM proteostasis and their regulatory impact are poorly defined. Fibrillin microfibrils are macromolecular ECM complexes serving structural and regulatory roles. In mice, Fbn1 and Fbn2, encoding major microfibrillar components, are strongly expressed during embryogenesis, but fibrillin-1 is the major component observed in adult tissue microfibrils. Here, analysis of mouse Adamts6 and Adamts10 mutant embryos, lacking these homologous secreted metalloproteases individually and in combination, along with in vitro analysis of microfibrils, measurement of ADAMTS6-fibrillin affinities and N-terminomics identification of ADAMTS6-cleaved sites, demonstrates a transcriptionally adapted system for fibrillin-2 proteolysis that contributes to postnatal fibrillin-1 dominance. The lack of ADAMTS6, alone and in combination with ADAMTS10 led to excess fibrillin-2 in perichondrium, with impaired skeletal development resulting from a drastic reduction of aggrecan, cartilage link protein and impaired BMP, but not TGF{beta} signaling in cartilage. Although ADAMTS6 cleaves fibrillin-1 and fibrillin-2 as well as fibronectin, which provides the initial scaffold for microfibril assembly, primacy of the protease-substrate relationship between ADAMTS6 and fibrillin-2 was unequivocally established by reversal of these defects in Adamts6-/- embryos by genetic reduction of Fbn2, but not Fbn1.

category: developmental biology


title: Global spread and evolutionary history of HCV subtype 3a

abstract: Studies have shown that HCV subtype 3a had likely been circulating in South Asia before its global spread. However, the time and route of this dissemination remain unclear. For the first time, we generated host and virus genome-wide data for more than 500 patients infected with HCV subtype 3a from the UK, North America, Australia and New Zealand. We used the host genomic data to infer the ancestry of the patients and used this information to investigate the epidemic history of HCV subtype 3a. We observed that viruses from hosts of South Asian ancestry clustered together near the root of the tree, irrespective of the sampling country and that they were more diverse than viruses from other host ancestries. We also inferred that three independent transmission events resulted in the spread of the virus from South Asia to the UK, North America and the Australian continent. This initial spread happened during or soon after the end of the second world war. This was followed by an exponential growth in the effective population size of HCV subtype 3a worldwide and many independent transmissions between the UK, North America and Australian continent. Using both host and virus genomic information can be highly informative in studying the virus epidemic history especially in the context of chronic infections.


title: Variation in predicted COVID-19 risk among lemurs and lorises

abstract: The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.


title: Understanding of the 2-oxoglutarate dehydrogenase and 2-oxoadipate dehydrogenase assembly with the E2o core relevant to a hybrid complex formation

abstract: The 2-oxoglutarate (OG) dehydrogenase complex (OGDHc) is a key enzyme in the tricarboxylic acid cycle (TCA) and comprises multiple copies of three components: 2-oxoglutarate dehydrogenase (hE1o), dihydrolipoamide succinyltransferase (hE2o), and dihydrolipoamide dehydrogenase (hE3). The OGDHc is one of the major regulators of mitochondrial metabolism through NADH and reactive oxygen species levels and impacts cell metabolic and cell signaling pathways through the coupling of OG metabolism to gene transcription, related to tumor cell proliferation and aging. The reduced OGDHc activity is linked to a number of neurodegenerative diseases. Evidence was obtained for the formation of a hybrid 2-oxo acid dehydrogenase complex between the OGDHc and its homologue 2-oxoadipate (OA) dehydrogenase (hE1a) in the L-lysine metabolic pathway, suggesting a potential cross-talk between the two distinct metabolic pathways. These findings raised fundamental questions about assembly of hE1a and hE1o to the hE2o core. Due to the lack of an atomic structure of the OGDHc from any sources, and of knowledge about exact distribution of components around the E2 core, hydrogen/deuterium exchange (HDX-MS) and chemical cross-linking mass spectrometry (CL-MS) have been carried out in binary hE1o-hE2o, hE1a-hE2o, hE1o-hE3 and hE2o-hE3 sub-complexes followed by structural modeling. Here we report findings that revealed some similarities in the assembly of hE1o and hE1a to the hE2o core. At the same time, three regions of the hE2o core comprising residues 191-208, 273-288, and 370-386 revealed a different binding mode to hE1o and hE1a, suggesting that hE2o can differentiate between these two proteins that may have physiological consequences.


title: RNA polymerase II clusters form in line with liquid phase wetting of chromatin

abstract: It is essential for cells to control which genes are transcribed into RNA. In eukaryotes, two major control points are recruitment of RNA polymerase II (Pol II) into a paused state and subsequent pause release to begin transcript elongation. Pol II associates with macromolecular clusters during recruitment, but it remains unclear how Pol II recruitment and pause release might affect these clusters. Here, we show that clusters exhibit morphologies that are in line with wetting of chromatin by a liquid phase enriched in recruited Pol II. Applying instantaneous structured illumination microscopy and stimulated emission double depletion microscopy to pluripotent zebrafish embryos, we find recruited Pol II associated with large clusters, and elongating Pol II with dispersed clusters. A lattice kinetic Monte Carlo model representing recruited Pol II as a liquid phase reproduced the observed cluster morphologies. In this model, chromatin is a copolymer chain containing regions that attract or repel recruited Pol II, supporting droplet formation by wetting or droplet dispersal, respectively.

category: biophysics


title: Discovery of a first-in-class inhibitor of the PRMT5-substrate adaptor interaction

abstract: PRMT5 and its substrate adaptor proteins (SAPs), pICln and Riok1, are synthetic lethal dependencies in MTAP-deleted cancer cells. SAPs share a conserved PRMT5 binding motif (PBM) which mediates binding to a surface of PRMT5 distal to the catalytic site. This interaction is required for methylation of several PRMT5 substrates, including histone and spliceosome complexes. We screened for small molecule inhibitors of the PRMT5-PBM interaction and validated a compound series which binds to the PRMT5-PBM interface and directly inhibits binding of SAPs. Mode of action and structure determination studies revealed that these compounds form a covalent bond between a halogenated pyridazinone group and cysteine 278 of PRMT5. Optimization of the starting hit produced a lead compound, BRD0639, which engages the target in cells, disrupts the PRMT5-RIOK1 complex, and reduces substrate methylation. BRD0639 is a first-in-class PBM-competitive small molecule that can support studies of PBM-dependent PRMT5 activities and the development of novel PRMT5 inhibitors that selectively target these functions.

category: cancer biology


title: Exaggerated cytokine production in human peripheral blood mononuclear cells by recombinant SARS-CoV-2 spike glycoprotein S1 and its inhibition by dexamethasone

abstract: An understanding of the pathological inflammatory mechanisms involved in SARS-CoV-2 virus infection is necessary in order to discover new molecular pharmacological targets for SARS-CoV-2 cytokine storm. In this study, the effects of a recombinant SARS-CoV-2 spike glycoprotein S1 was investigated in human peripheral blood mononuclear cells (PBMCs). Stimulation of PBMCs with spike glycoprotein S1 (100 ng/mL) resulted in significant elevation in the production of TNF, IL-6, IL-1{beta} and IL-8. However, pre-treatment with dexamethasone (100 nM) caused significant reduction in the release of these cytokines. Further experiments revealed that S1 stimulation of PBMCs increased phosphorylation of NF-{kappa}B p65 and I{kappa}B, and I{kappa}B degradation. DNA binding of NF-{kappa}B p65 was also significantly increased following stimulation with spike glycoprotein S1. Treatment of PBMCs with dexamethasone (100 nM) or BAY11-7082 (1 {micro}M) resulted in inhibition of spike glycoprotein S1-induced NF-{kappa}B activation. Activation of p38 MAPK by S1 was blocked in the presence of dexamethasone and SKF 86002. CRID3, but not dexamethasone pre-treatment produced significant inhibition of S1-induced activation of NLRP3/caspase-1. Further experiments revealed that S1-induced increase in the production of TNF, IL-6, IL-1{beta} and IL-8 was reduced in the presence of BAY11-7082 and SKF 86002, while CRID3 pre-treatment resulted in the reduction of IL-1{beta} production. These results suggest that SARS-CoV-2 spike glycoprotein S1 stimulated PBMCs to release pro-inflammatory cytokines through mechanisms involving activation of NF-{kappa}B, p38 MAPK and NLRP3 inflammasome. It is proposed that the clinical benefits of dexamethasone in COVID-19 is possibly due to its anti-inflammatory activity in reducing SARS-CoV-2 cytokine storm.

category: pharmacology and toxicology


title: Induction of exaggerated cytokine production in human peripheral blood mononuclear cells by a recombinant SARS-CoV-2 spike glycoprotein S1 and its inhibition by dexamethasone


title: Glutamatergic dysfunction precedes neuron loss in cerebral organoids with MAPT mutation.

abstract: Frontotemporal dementia (FTD) due to MAPT mutation causes pathological accumulation of tau and glutamatergic cortical neuronal death by unknown mechanisms. We used human induced pluripotent stem cell (iPSC)-derived cerebral organoids expressing tau-V337M and isogenic corrected controls to discover early alterations due to the mutation that precede neurodegeneration. At 2 months, mutant organoids show upregulated expression of MAPT, and glutamatergic signaling pathways and regulators including the RNA-binding protein ELAVL4. Over the following 4 months, mutant organoids accumulate splicing changes, disruption of autophagy function and build-up of tau and P-tau S396. By 6 months, tau-V337M organoids show specific loss of glutamatergic neurons of layers affected in patients. Mutant neurons are susceptible to glutamate toxicity which was rescued pharmacologically by treatment with the PIKFYVE kinase inhibitor apilimod. Our results demonstrate a sequence of events that precede cell death, revealing molecular pathways associated with glutamate signaling as potential targets for therapeutic intervention in FTD.

category: neuroscience


title: Revisiting a GWAS peak in Arabidopsis thaliana reveals possible confounding by genetic heterogeneity

abstract: Genome-wide association studies (GWAS) have become a standard approach for exploring the genetic basis of phenotypic variation. However, correlation is not causation, and only a tiny fraction of all associations have been experimentally confirmed. One practical problem is that a peak of association does not always pinpoint a causal gene, but may instead be tagging multiple causal variants. In this study, we reanalyze a previously reported peak associated with flowering time traits in Swedish in Arabidopsis thaliana. The peak appeared to pinpoint the AOP2/AOP3 cluster of glucosinolate biosynthesis genes, which is known to be responsible for natural variation in herbivore resistance. Here we propose an alternative hypothesis, by demonstrating that the AOP2/AOP3 flowering association can be wholly accounted for by allelic variation in two flanking genes with clear roles in regulating flowering: NDX1, a regulator of the main flowering time controller FLC, and GA1, which plays a central role in gibberellin synthesis and is required for flowering under some conditions. In other words, we propose that the AOP2/AOP3 flowering-time association is yet another example of a spurious, "synthetic" association, arising from trying to fit a single-locus model in the presence of two statistically associated causative loci.


title: Cell type classification and discovery across diseases, technologies and tissues reveals conserved gene signatures and enables standardized single-cell readouts

abstract: Autoimmune diseases are a major cause of mortality1,2. Current treatments often yield severe insult to host tissue. It is hypothesized that improved "precision medicine" therapies will target pathogenic cells selectively and thus reduce or eliminate severe side effects, and potentially induce robust immune tolerance3. However, it remains challenging to systematically identify which cellular phenotypes are present in cellular ensembles. Here, we present a novel machine learning approach, Signac, which uses neural networks trained with flow-sorted gene expression data to classify cellular phenotypes in single cell RNA-sequencing data. We demonstrate that Signac accurately classified single cell RNA-sequencing data across diseases, technologies, species and tissues. Then we applied Signac to identify known and novel immune-relevant precision medicine candidate drug targets (n = 12) in rheumatoid arthritis. A full release of this workflow can be found at our GitHub repository (https://github.com/mathewchamberlain/Signac).


title: How public reaction to disease information across scales and the impacts of vector control methods influence disease prevalence and control efficacy

abstract: With the development of social media, the information about vector-borne disease incidence over broad spatial scales can cause demand for local vector control before local risk exists. Anticipatory intervention may still benefit local disease control efforts; however, infection risks are not the only focal concerns governing public demand for vector control. Concern for environmental contamination from pesticides and economic limitations on the frequency and magnitude of control measures also play key roles. Further, public concern may be focused more on ecological factors (i.e., controlling mosquito populations) or on epidemiological factors (i.e., controlling infection-carrying mosquitoes), which may lead to very different control outcomes. Here we introduced a generic Ross-MacDonald model, incorporating these factors under three spatial scales of disease information: local, regional, and global. We tailored and parameterized the model for Zika virus transmitted by Aedes aegypti mosquito. We found that overreaction caused by larger-scale incidence information could decrease average human infections per patch breeding capacity, however, the associated increase in total control effort plays a larger role, which leads to an overall decrease in control efficacy. The shift of focal concerns from epidemiological to ecological risk could relax the negative effect of overreaction on control efficacy when mosquito breeding capacity populations are expected to be large. This work demonstrates that, depending on expected total mosquito breeding capacity population size, and weights of different focal concerns, large-scale disease information can reduce disease infections without lowering control efficacy. Our findings provide guidance for vector-control strategies by considering public reaction through social media.

category: ecology


title: Inferring time-lagged causality using the derivative of single-cell expression

abstract:
Many computational methods have been developed for inferring causality among genes using cross-sectional gene expression data, such as single-cell RNA sequencing (scRNA-seq) data. However, due to the limitations of scRNA-seq technologies, time-lagged causal relationships may be missed by existing methods. In this work, we propose a method, called causal inference with time-lagged information (CITL), to infer time-lagged causal relationships from scRNA-seq data by assessing conditional independence between the changing and current expression levels of genes. CITL estimates the changing expression levels of genes by "RNA velocity". We demonstrate the accuracy and stability of CITL for inferring time-lagged causality on simulation data against other leading approaches. We have applied CITL to real scRNA data and inferred 878 pairs of time-lagged causal relationships, with many of these inferred results supported by the literature.

Author summaryComputational causal inference is a promising way to survey causal relationships between genes efficiently. Though many causal inference methods have been applied to gene expression data, none considers the time-lagged causal relationship, which means that some genes may take some time to affect their target genes with several reactions. If relationships between genes are time-lagged, the existing methods assumptions will be violated. The relationships will be challenging to recognize. We demonstrate that this is indeed the case through simulation. Therefore, we develop a method for inferring time-lagged causal relationships of single-cell gene expression data. We assume that a time-lagged causal relationship should present a strong association between the cause and the effects changing. To calculate such correlation, we first estimate the derivative of gene expression using the information from unspliced transcripts. Then, we use conditional independent tests to search gene pairs satisfying our assumption. Our results suggest that we could accurately infer time-lagged causal gene pairs validated by published literature. This method may complement gene regulatory analysis and provide candidate gene pairs for further controlled experiments.


title: SamQL: A Structured Query Language and filtering tool for the SAM/BAM file format

abstract: The Sequence Alignment/Map Format Specification (SAM) is one of the most widely used file formats in computational biology today and several tools have been developed to process it and use it. It is a flexible file format, used by many bioinformaticians on a daily basis. Despite its flexibility, SAM encoded files can often be difficult to query and understand. As genomic data are rapidly growing, structured and efficient queries on data encoded in SAM/BAM files is becoming critical. Importantly, any new tools should be able to support existing large datasets without requiring any data transformations. Here we introduce SamQL, an SQL-like query language for the SAM format with intuitive syntax that supports complex and efficient queries on top of SAM/BAM files and that can replace commonly used Bash one-liners employed by many bioinformaticians. SamQL is a complete query language that we envision as a step to a structured database engine for genomics. SamQL is written in Go, taking advantage of modern multicore compute systems and is freely available as standalone program and as an open-source library released under an MIT license, https://github.com/maragkakislab/samql/.


title: Sex Differences in Solute and Water Handling in the Human Kidney: Modeling and Functional Implications

abstract:
Besides the excretion of metabolic wastes, the kidneys regulate homeostasis of electrolytes, pH, metabolites, volume and blood pressure. Sex differences in kidney function and blood pressure have been widely described across many species. Immunoblot analysis has revealed that the kidney of a female rat is not simply a smaller version of a male kidney. Rather, male and female rat kidneys exhibit dimorphic patterns of transporter expression and salt handling, the functional implications of which have been analyzed in a series of previously published modeling studies of rat kidney function. In the present study, we extend the analysis to the human kidney: we developed sex-specific models of solute and water transport in the human kidney, and identified epithelial transport parameters, consistent with patterns found in male and female rats, that yield urine output and excretion rates consistent with known human values. The model predicts that the lower sodium hydrogen exchanger 3 (NHE3) activity in women reduces the fractional reabsorption of Na+, K+, Cl-, and water along the proximal tubule, compared to men, and that the larger load on the distal nephron can be handled by enhanced activities in key Na+ transporter such as epithelial sodium channel (ENaC) and sodium chloride cotransporter (NCC) in women. Model simulations further indicate that the larger distal transport capacity and proximal transport reserve may better prepare women for elevated demands of pregnancy and lactation. The larger distal transport capacity may also contribute to reduced efficacy of angiotensin converting enzyme inhibitors to lower blood pressure in women.

Author summaryThe kidneys maintain homeostasis by controlling the amount of water, ions, and other substances in the blood. That function is accomplished by the nephrons, which transform glomerular filtrate into urine by an exquisite transport process mediated by a number of membrane transporters. Recently, the distribution of renal transporters along the nephron has been shown to be markedly different between male and female rodents. We postulate that similar sexual dimorphism exists between men and women, and we seek to reveal its physiological implications. We hypothesize that the larger abundance of a renal Na+ transport in the proximal tubules in females may also better prepare them for the fluid retention adaptations required during pregnancy and lactation, durint which renal and systemic hemodynamics are both drastically altered by the marked volume expansion and vasodilation. Also, kidneys play a key role in blood pressure regulation, and a popular class of anti-hypertensive medications, angiotensin converting enzymes (ACE) inhibitors, have been reported to be less effective in women. Model simulations suggest that the blunted natriuretic and diuretic effects of ACE inhibition in women can be attributed, in part, to their higher distal baseline transport capacity.

category: physiology


title: 'Nepotistic journals: a survey of biomedical journals.

abstract:
ContextConvergent analyses in different disciplines support the use of the Percentage of Papers by the Most Prolific author (PPMP) as a red flag to identify journals that can be suspected of questionable editorial practices. We examined whether this index, complemented by the Gini index, could be useful for identifying cases of potential editorial bias, using a large sample of biomedical journals.

MethodsWe extracted metadata for all biomedical journals referenced in the National Library of Medicine, with any attributed Broad Subject Terms, and at least 50 authored (i.e. by at least one author) articles between 2015 and 2019, identifying the most prolific author (i.e. the person who signed the most papers in each particular journal). We calculated the PPMP and the 2015-2019 Gini index for the distribution of articles across authors. When the relevant information was reported, we also computed the median publication lag (time between submission and acceptance) for articles authored by any of the most prolific authors and that for articles not authored by prolific authors. For outlier journals, defined as a PPMP or Gini index above the 95th percentile of their respective distributions, a random sample of 100 journals was selected and described in relation to status on the editorial board for the most prolific author.

Results5 468 journals that published 4 986 335 papers between 2015 and 2019 were analysed. The PPMP 95th percentile was 10.6% (median 2.9%). The Gini index 95th percentile was 0.355 (median 0.183). Correlation between the two indices was 0.35 (95CI 0.33 to 0.37). Information on publication lag was available for 2 743 journals. We found that 277 journals (10.2%) had a median time lag to publication for articles by the most prolific author(s) that was shorter than 3 weeks, versus 51 (1.9%) journals with articles not authored by prolific author(s). Among the random sample of outlier journals, 98 provided information about their editorial board. Among these 98, the most prolific author was part of the editorial board in 60 cases (61%), among whom 25 (26% of the 98) were editors-in-chief.

DiscussionIn most journals publications are distributed across a large number of authors. Our results reveal a subset of journals where a few authors, often members of the editorial board, were responsible for a disproportionate number of publications. The papers by these authors were more likely to be accepted for publication within 3 weeks of their submission. To enhance trust in their practices, journals need to be transparent about their editorial and peer review practices.

category: scientific communication and education


title: Selection of stimulus parameters for enhancing slow wave sleep events with a Neural-field theory thalamocortical computational model

abstract:
Slow-wave sleep cortical brain activity, conformed by slow-oscillations and sleep spindles, plays a key role in memory consolidation. The increase of the power of the slow-wave events, obtained by auditory sensory stimulation, positively correlates to memory consolidation performance. However, little is known about the experimental protocol maximizing this effect, which could be induced by the power of slow-oscillation, the number of sleep spindles, or the timing of both events co-occurrence. Using a mean-field model of thalamocortical activity, we studied the effect of several stimulation protocols, varying the pulse shape, duration, amplitude, and frequency, as well as a target-phase using a closed-loop approach. We evaluated the effect of these parameters on slow-oscillations (SO) and sleep-spindles (SP), considering: (i) the power at the frequency bands of interest, (ii) the number of SO and SP, (iii) co-occurrences between SO and SP, and (iv) synchronization of SP with the up-peak of the SO. The first three targets are maximized using a decreasing ramp pulse with a pulse duration of 50 ms. Also, we observed a reduction in the number of SO when increasing the stimulus energy by rising its amplitude. To assess the target-phase parameter, we applied closed-loop stimulation at 0{o}, 45{o}, and 90{o} of the phase of the narrow-band filtered ongoing activity, at 0.85 Hz as central frequency. The 0{o} stimulation produces better results in the power and number of SO and SP than the rhythmic or aleatory stimulation. On the other hand, stimulating at 45{o} or 90{o} change the timing distribution of spindles centers but with fewer co-occurrences than rhythmic and 0{o} phase. Finally, we propose the application of closed-loop stimulation at the rising zero-cross point using pulses with a decreasing ramp shape and 50 ms of duration for future experimental work.

Author summaryDuring the non-REM (NREM) phase of sleep, events that are known as slow oscillations (SO) and spindles (SP) can be detected by EEG. These events have been associated with the consolidation of declarative memories and learning. Thus, there is an ongoing interest in promoting them during sleep by non-invasive manipulations such as sensory stimulation. In this paper, we used a computational model of brain activity that generates SO and SP, to investigate which type of sensory stimulus -shape, amplitude, duration, periodicity- would be optimal for increasing the events frequency and their co-occurrence. We found that a decreasing ramp of 50 ms duration is the most effective. The effectiveness increases when the stimulus pulse is delivered in a closed-loop configuration triggering the pulse at a target phase of the ongoing SO activity. A desirable secondary effect is to promote SPs at the rising phase of the SO oscillation.


title: The purine nucleoside phosphorylase pnp-1 regulates epithelial cell resistance to infection  in C. elegans

abstract:
Intestinal epithelial cells are subject to attack by a diverse array of microbes, including intracellular as well as extracellular pathogens. While defense in epithelial cells can be triggered by pattern recognition receptor-mediated detection of microbe-associated molecular patterns, there is much to be learned about how they sense infection via perturbations of host physiology, which often occur during infection. A recently described host defense response in the nematode C. elegans called the Intracellular Pathogen Response (IPR) can be triggered by infection with diverse natural intracellular pathogens, as well as by perturbations to protein homeostasis. From a forward genetic screen, we identified the C. elegans ortholog of purine nucleoside phosphorylase pnp-1 as a negative regulator of IPR gene expression, as well as a negative regulator of genes induced by extracellular pathogens. Accordingly, pnp-1 mutants have resistance to both intracellular and extracellular pathogens. Metabolomics analysis indicates that C. elegans pnp-1 likely has enzymatic activity similar to its human ortholog, serving to convert purine nucleosides into free bases. Classic genetic studies have shown how mutations in human purine nucleoside phosphorylase cause immunodeficiency due to T-cell dysfunction. Here we show that C. elegans pnp-1 acts in intestinal epithelial cells to regulate defense. Altogether, these results indicate that perturbations in purine metabolism are likely monitored as a cue to promote defense against epithelial infection in the nematode C. elegans.

Author summaryAll life requires purine nucleotides. However, obligate intracellular pathogens are incapable of generating their own purine nucleotides and thus have evolved strategies to steal these nucleotides from host cells in order to support their growth and replication. Using the small roundworm C. elegans, we show that infection with natural obligate intracellular pathogens is impaired by loss of pnp-1, the C. elegans ortholog of the vertebrate purine nucleoside phosphorylase (PNP), which is an enzyme involved in salvaging purines. Loss of pnp-1 leads to altered levels of purine nucleotide precursors and increased expression of Intracellular Pathogen Response genes, which are induced by viral and fungal intracellular pathogens of C. elegans. In addition, we find that loss of pnp-1 increases resistance to extracellular pathogen infection and increases expression of genes involved in extracellular pathogen defense. Interestingly, studies from 1975 found that mutations in human PNP impair T-cell immunity, whereas our findings here indicate C. elegans pnp-1 regulates intestinal epithelial immunity. Overall, our work indicates that host purine homeostasis regulates resistance to both intracellular and extracellular pathogen infection.


title: The impact of genetic background and sex on the phenotype of IL-23 induced murine arthritis

abstract:
BackgroundOverexpression of IL-23 in adult mice by means of hydrodynamic tail vein injection of IL-23 minicircles has been reported to result in spondyloarthritis-like disease. The impact of genetic background and sex on the disease phenotype in this model has not been investigated.

MethodsWe compared male B10.RIII mice with male C57BL/6 mice, and male with female B10.RIII mice after hydrodynamic injection of IL-23 enhanced episomal vector (EEV) at 8-12 weeks of age. We monitored clinical arthritis scores, paw swelling, and body weight. Animals were euthanized after two weeks and tissues were harvested for histology, flow cytometry and gene expression analysis. Serum cytokine levels were determined by ELISA.

FindingsMale B10.RIII mice developed arthritis in the forepaws and feet within 6 days after IL-23 EEV injection; they also exhibited psoriasis-like skin disease, colitis, weight loss, and osteopenia. In contrast to previous reports, we did not observe spondylitis or uveitis. Male C57BL/6 mice injected with IL-23 EEV had serum IL-23 levels comparable with B10.RIII mice and developed skin inflammation, colitis, weight loss, and osteopenia but failed to develop arthritis. Female B10.RIII mice had more severe arthritis than male B10.RIII mice but did not lose weight.

ConclusionsSystemic IL-23 overexpression results in spondyloarthritis-like disease in B10.RIII mice. The development of extra-articular manifestations but absence of arthritis in C57BL/6 mice suggests organ-specific genetic control mechanisms of IL-23 driven inflammation. Discrepancies regarding the phenotype of IL-23 induced disease in different labs and the sexual dimorphism observed in this study warrant further exploration.


title: A unique GCN5 histone acetyltransferase complex controls erythrocyte invasion and virulence in the malaria parasite Plasmodium falciparum

abstract:
The histone acetyltransferase GCN5-associated SAGA complex is evolutionarily conserved from yeast to human and functions as a general transcription co-activator in global gene regulation. In this study, we identified a divergent GCN5 complex in Plasmodium falciparum, which contains two plant homeodomain (PHD) proteins (PfPHD1 and PfPHD2) and a plant apetela2 (AP2)-domain transcription factor (PfAP2-LT). To dissect the functions of the PfGCN5 complex, we generated parasites with the bromodomain deletion in PfGCN5 and the PHD domain deletion in PfPHD1. The two deletion mutants closely phenocopied each other, exhibiting significantly reduced merozoite invasion of erythrocytes and elevated sexual conversion. These domain deletions caused dramatic decreases not only in histone H3K9 acetylation but also in H3K4 trimethylation, indicating synergistic crosstalk between the two euchromatin marks. Domain deletion in either PfGCN5 or PfPHD1 profoundly disturbed the global transcription pattern, causing altered expression of more than 60% of the genes. At the schizont stage, these domain deletions were linked to specific downregulation of merozoite genes involved in erythrocyte invasion, many of which harbor the DNA-binding motifs for AP2-LT and/or AP2-I, suggesting targeted recruitment of the PfGCN5 complex to the invasion genes by these specific transcription factors. Conversely, at the ring stage, PfGCN5 or PfPHD1 domain deletions disrupted the mutually exclusive expression pattern of the entire var gene family, which encodes the virulent factor PfEMP1. Correlation analysis between the chromatin state and alteration of gene expression demonstrated that up- and down-regulated genes in these mutants are highly correlated with the silenct and active chromatin states in the wild-type parasite, respectively. Collectively, the PfGCN5 complex represents a novel HAT complex with a unique subunit composition including the AP2 transcription factor, which signifies a new paradigm for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist.

Author SummaryEpigenetic regulation of gene expression plays essential roles in orchestrating the general and parasite-specific cellular pathways in the malaria parasite Plasmodium falciparum. Using tandem affinity purification and proteomic characterization, we identified a divergent transcription co-activator - the histone acetyltransferase GCN5-associated complex in P. falciparum, which contains nine core components, including two PHD domain proteins (PfPHD1 and PfPHD2) and a plant apetela2-domain transcription factor. To understand the functions of the PfGCN5 complex, we performed gene disruption in two subunits of this complex, PfGCN5 and PfPHD1. We found that the two deletion mutants displayed very similar growth phenotypes, including significantly reduced merozoite invasion rates and elevated sexual conversion. These two mutants were associated with dramatic decreases in histone H3K9 acetylation and H3K4 trimethylation, which led to global changes in chromatin states and gene expression. Genes significantly affected by the PfGCN5 and PfPHD1 gene disruption include those participating in parasite-specific pathways such as invasion, virulence, and sexual development. In conclusion, this study presents a new model of the PfGCN5 complex for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist.

category: microbiology


title: Bridging Between Material Properties Of Proteins And The Underlying Molecular Interactions

abstract: In this work, we develop a novel method that bridges between material properties of proteins, particularly the modulus of elasticity, and the underlying molecular interactions. To this end, we employ both an all-atom normal mode analysis (NMA) model with the CHARMM force field and an elastic solid model for proteins and protein interfaces. And the "bridge" between the two models is a common physical property that they both can predict: the magnitude of thermal vibrations. This connection allows one to calibrate the Youngs moduli of proteins and protein interface regions. We find that the elastic moduli of proteins are mostly in the range of a few Gpa to 10 Gpa, while the elastic moduli of the interface regions are about an order smaller. The work is significant as it represents the first attempt to systematically compute the moduli of elasticity of proteins from molecular interactions.


title: Rapid divergence in independent aspects of the compatibility phenotype in the Spiroplasma/Drosophila interaction.

abstract: Heritable symbionts represent important components of host biology, both as antagonistic reproductive parasites and as beneficial protective partners. An important component of heritable microbes biology is their ability to establish in new host species, a process equivalent to a host shift for an infectiously transmitted parasite or pathogen. For a host shift to occur, the symbiont must be compatible with the host: it must not cause excess pathology, must have good vertical transmission, and possess a drive phenotype that enables spread. Classically, compatibility has been considered a declining function of genetic distance between novel and ancestral host species. Here we investigate the evolutionary lability of compatibility to heritable microbes by comparing the capacity for a symbiont to establish in two novel host species equally related to the ancestral host. Compatibility of the protective Spiroplasma from D. hydei with D. simulans and D. melanogaster was tested. The Spiroplasma had contrasting compatibility in these two host species. The transinfection showed pathology and low vertical transmission in D. melanogaster but was asymptomatic and transmitted with high efficiency in D. simulans. These results were not affected by the presence/absence of Wolbachia in either of the two species. The pattern of protection was not congruent with that for pathology/transmission, with protection being weaker in the D. simulans, the host in which Spiroplasma was asymptomatic and transmitted well. Further work indicated pathological interactions occurred in D. sechellia and D. yakuba, indicating that D. simulans was unusual in being able to carry the symbiont without damage. The differing compatibility of the symbiont with these closely related host species emphasises first the rapidity with which host-symbiont compatibility evolves despite compatibility itself not being subject to direct selection, and second the independence of the different components of compatibility (pathology, transmission, protection). This requirement to fit three different independently evolving aspects of compatibility, if commonly observed, is likely to be a major feature limiting the rate of host shifts. Moving forward, the variation between sibling species pairs observed above provides an opportunity to identify the mechanisms behind variable compatibility between closely related host species, which will drive hypotheses as to the evolutionary drivers of compatibility variation.


title: Alien chromatin but not Fhb7 confers Fusarium head blight resistance in wheat breeding

abstract:
The lack of resistance resources is a major bottleneck for wheat Fusarium head blight (FHB) resistance breeding. Three wheat-Th. elongatum FHB resistant translocation lines have been developed and used for wheat breeding without yield penalty. Transcriptomic analysis identified a derivative glutathione S-transferase transcript T26102, which was homologous to Fhb7 and induced dramatically by Fusarium graminearum. Unlike other studies, Fhb7 homologs were detected not only in Thinopyrum but also in Elymus, Leymus, Pseudoroegeria and Roegeria. We also found that several wheat-Th. ponticum derivatives carrying Fhb7 and its homologs were highly susceptible to FHB. Moreover, the transgenic plants expressing Fhb7 and its homolog on different backgrounds did not improve the FHB resistance.

One Sentence SummaryThe GST-encoding Fhb7 candidate cannot improve Fusarium head blight resistance in wheat breeding.


title: Alien chromatin other than the GST-encoding Fhb7 candidate confers Fusarium head blight resistance in wheat breeding


title: Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations

abstract: Genome-wide association studies rely on the statistical inference of untyped variants, called imputation, to increase the coverage of genotyping arrays. However, the results are often suboptimal in populations underrepresented in existing reference panels and array designs, since the selected single nucleotide polymorphisms (SNPs) may fail to capture population-specific haplotype structures, hence the full extent of common genetic variation. Here, we propose to sequence the full genome of a small subset of an underrepresented study cohort to inform the selection of population-specific add-on SNPs, such that the remaining array-genotyped cohort could be more accurately imputed. Using a Tanzania-based cohort as a proof-of-concept, we demonstrate the validity of our approach by showing improvements in imputation accuracy after the addition of our designed addon SNPs to the base H3Africa array.


title: Does colour impact attention towards 2D images in geckos?

abstract: Animals are exposed to different visual stimuli that influence how they perceive and interact with their environment. Visual information such as shape and colour can help the animal detect, discriminate and make appropriate behavioural decisions for mate selection, communication, camouflage, and foraging. In all major vertebrate groups, it has been shown that certain species can discriminate and prefer certain colours and that colours may increase the response to a stimulus. However, because colour is often studied together with other potentially confounding factors, it is still unclear to what extent colour discrimination plays a crucial role in the perception of and attention towards biologically relevant and irrelevant stimuli. To address these questions in reptiles, we assessed the response of three gecko species Correlophus ciliatus, Eublepharis macularius, and Phelsuma laticauda to familiar and novel 2D images in colour or grayscale. We found that while all species responded more often to the novel than to the familiar images, colour information did not influence object discrimination. We also found that the duration of interaction with images was significantly longer for the diurnal species, P. laticauda, than for the two nocturnal species, but this was independent from colouration. Finally, no differences among sexes were observed within or across species. Our results indicate that geckos discriminate between 2D images of different content independent of colouration, suggesting that colouration does not increase detectability or intensity of the response. These results are essential for uncovering which visual stimuli produce a response in animals and furthering our understanding of how animals use colouration and colour vision.

category: animal behavior and cognition


title: Polar and non-polar fractions of deep fried edible oils induce differential cytotoxicity and hemolysis

abstract: Edible oils are the essential part of diet, however, deep frying process induce oxidative changes in these oils, making them unsuitable for consumption. Deep frying generates various noxious polar and non-polar aldehydes and carbonyls, which may be polar or non-polar in nature. The present study thus evaluated the cytotoxic and hemolytic effects of polar and non-polar fractions of different deep fried edible oils. There observed a significantly elevated level of lipid peroxidation products in the polar fraction of deep fried sunflower (FSO-P) and rice bran oils (FRO-P). The treatment with these fractions induced cytotoxicity in cultured colon epithelial cells, with a higher intensity in FSO-P and FRO-P. Further, an increased TBARS level and catalase activity in RBCs treated with FSO-P and FRO-P led to hemolysis. In comparison, the fried coconut oil (FCO) fractions were less toxic and hemolytic; in addition, the non-polar fraction was more toxic, compared to FCO-P fraction.


title: Extending the Near Infrared Emission Range of Indium Phosphide Quantum Dots for Multiplexed In Vivo Imaging

abstract: This report of the reddest emitting indium phosphide quantum dots (InP QDs) to date demonstrates tunable, near infrared (NIR) photoluminescence and fluorescence multiplexing in the first optical tissue window with a material that avoids toxic constituents. This synthesis overcomes the InP synthesis "growth bottleneck" and extends the emission peak of InP QDs deeper into the first optical tissue window using an inverted QD heterostructure. The ZnSe/InP/ZnS core/shell/shell structure is designed to produce emission from excitons with heavy holes confined in InP shells wrapped around larger-bandgap ZnSe cores and protected by a second shell of ZnS. The InP QDs exhibit InP shell thickness-dependent tunable emission with peaks ranging from 515 - 845 nm. The high absorptivity of InP leads to effective absorbance and photoexcitation of the QDs with UV, visible, and NIR wavelengths in particles with diameters of eight nanometers or less. These nanoparticles extend the range of tunable direct-bandgap emission from InP-based nanostructures, effectively overcoming a synthetic barrier that has prevented InP-based QDs from reaching their full potential as NIR imaging agents. Multiplexed lymph node imaging in a mouse model shows the potential of the NIR-emitting InP particles for in vivo imaging.

category: bioengineering


title: The biochemical resolving power of fluorescence lifetime imaging

abstract: A deeper understanding of spatial resolution has led to innovations in microscopy and the disruption of biomedical research, as with super-resolution microscopy. To foster similar advances in time-resolved and spectral imaging, we have previously introduced the concept of  biochemical resolving power in fluorescence microscopy. Here, we apply those concepts to investigate how the instrument response function (IRF), sampling conditions, and photon-statistics limit the biochemical resolution of fluorescence lifetime microscopy. Using Fisher information analysis and Monte Carlo simulations, we reveal the complex dependencies between photon-statistics and the IRF, permitting us to quantify resolution limits that have been poorly understood (e.g., the minimum resolvable decay time for a given width of the IRF and photon-statistics) or previously underappreciated (e.g., optimization of the IRF for biochemical detection). With this work, we unravel common misunderstandings on the role of the IRF and provide theoretical insights with significant practical implications on the design and use of time-resolved instrumentation.


title: The biochemical resolving power of fluorescence lifetime imaging: untangling the roles of the instrument response function and photon-statistics


title: Molecular diagnosis and prognosis of cancers of unknown-primary (CUPs): progress from a microRNA-based droplet digital PCR assay

abstract: Metastasis is responsible for the majority of cancer-related deaths. Particularly challenging is the management of metastatic cancer of unknown primary site (CUP), whose tissue-of-origin (TOO) remains undetermined even after expensive investigations. CUP therapy is rather unspecific and poorly effective. Molecular approaches developed to identify CUPs potential tissue-of-origin, can overcome some of these issues. In this study, we applied a pre-determined set of microRNAs (miRNAs) to infer the TOO of 53 metastatic cancers of unknown or uncertain origin. We designed a molecular assay to quantify 89 miRNAs at the copy number level, using EvaGreen-based Droplet Digital PCR. We assessed miRNA expression in 159 samples including primary tumors from 17 tumor classes (reference set), metastases of known and unknown origin. We applied two different statistical models for class prediction to obtain CUPs most probable TOOs. Specifically, we used the shrunken centroids using PAMR (Prediction Analysis of Microarrays for R) and the least absolute shrinkage and selection operator (LASSO) models. The molecular test was successfully applied to FFPE samples and provided a site-of-origin identification within one-week from the biopsy procedure. The most frequently predicted origins were gastrointestinal, pancreas, breast and lung. The assay was applied to multiple metastases from the same CUP, collected from different metastatic sites: the molecular prediction revealed an impressive agreement in site-of-origin prediction, intrinsically validating our assay. The final prediction was compared with the clinico-pathological hypothesis of primary site. Moreover, a panel of 14 miRNAs proved to have prognostic value and being associated with overall survival. Our study demonstrated that miRNA expression profiling in CUP samples could be employed as diagnostic and prognostic test. Our molecular analysis can be performed on-request, concomitantly with standard diagnostic workup and in association with genetic profiling, to offer valuable indication about the possible primary site, thereby supporting treatment decisions.

category: pathology


title: Plant pathogens convergently evolved to counteract redundant nodes of an NLR immune receptor network

abstract: In plants, NLR (nucleotide-binding domain and leucine-rich repeat-containing) proteins can form receptor networks to confer hypersensitive cell death and innate immunity. One class of NLRs, known as NRCs (NLR required for cell death), are central nodes in a complex network that protects against multiple pathogens and comprises up to half of the NLRome of solanaceous plants. Given the prevalence of this NLR network, we hypothesized that pathogens convergently evolved to secrete effectors that target NRC activities. To test this, we screened a library of 167 bacterial, oomycete, nematode and aphid effectors for their capacity to suppress the cell death response triggered by the NRC-dependent disease resistance proteins Prf and Rpi-blb2. Among five of the identified suppressors, one cyst nematode protein and one oomycete protein suppress the activity of autoimmune mutants of NRC2 and NRC3, but not NRC4, indicating that they specifically counteract a subset of NRC proteins independently of their sensor NLR partners. Whereas the cyst nematode effector SPRYSEC15 binds the nucleotide-binding domain of NRC2 and NRC3, the oomycete effector AVRcap1b suppresses the response of these NRCs via the membrane trafficking-associated protein NbTOL9a (Target of Myb 1-like protein 9a). We conclude that plant pathogens have evolved to counteract central nodes of the NRC immune receptor network through different mechanisms. Coevolution with pathogen effectors may have driven NRC diversification into functionally redundant nodes in a massively expanded NLR network.

category: plant biology


title: How much does habitat isolation drive forest bird morphology?

abstract: Rapid environmental change caused by humans has become a major concern for wildlife conservationists. But phenotypic and evolutionary responses of species to such change may often be swift enough to prevent their collapse. Several North American bird species living in boreal forests now have more pointed wings (a proxy for sustained ight efficiency), than they had a century ago. This remarkable pattern has been hypothesized as resulting from selective pressures favoring colonization of isolated habitat. Additionally, aerodynamics predict that heavier birds can achieve faster ight, a further advantage for exploring isolated habitats. We tested whether birds establishing territories in isolated areas have more pointed wings and are heavier than con-specifics found in more densely populated areas. Wing shapes of wild-caught adults from 21 passerine bird species did not generally support this prediction. However individuals with large body mass relative to their species were found more frequently in isolated habitats. Our results offer partial support for the isolation hypothesis at the landscape scale. We encourage further work at coarser, regional, scales to further examine whether wing shape and body mass evolutionarily respond to habitat isolation.

category: zoology


title: Examination of digital images from Macaulay Library to determine avian molt strategies: A case study on molts and plumages in eight species of North American hummingbirds

abstract: I examined a total of 27,581 images of 6.345 individuals from the Cornell Lab of Ornithologys Macaulay Library to clarify conflicting reports on molt and plumage strategies in eight species of hummingbirds that breed or have bred primarily in the southwestern United States. Fixed replacement sequences from two nodes among primaries and two nodes among secondaries were found without exception, conforming to the findings of previous studies. I concluded that the preformative molt is limited to partial in three species, partial to incomplete in three species, partial to complete in one species, and complete in one species. These molt strategies could be interpreted as having differentiated through synapomorphy, with species between currently recognized clades varying in the extent of their preformative molts; however, given the plastic nature of molt strategies, I predict that this variation will be shaped more by environmental factors than by synapomorphy. Results of this study additionally clarify molt terminology in Trochilidae as based on homologies and establish new criteria for age determinations. The Macaulay Library clearly provides an important resource for the investigation of avian molts and plumages. The results of a validation exercise that I conducted indicate that banders and field ornithologists with a wide range of previous experience can collect accurate data in this manner. I present a road map for such studies and suggest many other questions on avian molt that can also be investigated, including how timing of molts vary geographically and by habitat and how remigial replacement sequences proceed in little-known bird families. I encourage contributors to the Macaulay Library to take and upload images of birds in molt or in worn plumages.


title: Inhibiting glycogen synthase kinase 3 suppresses TDP-43-mediated neurotoxicity in a caspase-dependant manner

abstract: Amyotrophic lateral sclerosis-frontotemporal dementia (ALS-FTD) is a progressive and ultimately fatal disease spectrum characterised by 43-kDa TAR DNA-binding protein (TDP-43) pathology. Current disease modifying drugs have modest effects and novel therapies are sorely needed. We previously showed that deletion of glycogen synthase kinase-3 (GSK3) suppresses TDP-43-mediated motor neuron degeneration in Drosophila. Here, we investigated the potential of GSK3 inhibition to ameliorate TDP43-mediated toxicity in mammalian neurons. Expression of TDP-43 was found to both activate GSK3 and promote caspase mediated cleavage of TDP-43. Inhibition of GSK3 reduced the abundance of full-length and cleaved TDP-43 in rodent neurons expressing wild-type or disease-associated mutant TDP-43 and also ameliorated neurotoxicity. Our results suggest that TDP-43 turnover is promoted by GSK3 inhibition in a caspase-dependent manner, and that targeting GSK3 activity could have therapeutic value.


title: A modular platform for engineering function ofnatural and synthetic biomolecular condensates

abstract: Phase separation is emerging as a universal principle for how cells use dynamic subcompartmentalization to organize biochemical reactions in time and space1,2. Yet, whether the emergent physical properties of these biomolecular condensates are important for their biological function remains unclear. The intrinsically disordered protein PopZ forms membraneless condensates at the poles of the bacterium Caulobacter crescentus and selectively sequesters kinase-signaling cascades to regulate asymmetric cell division3-5. By dissecting the molecular grammar underlying PopZ phase separation, we find that unlike many eukaryotic examples, where unstructured regions drive condensation6,7, a structured domain of PopZ drives condensation, while conserved repulsive features of the disordered region modulate material properties. By generating rationally designed PopZ mutants, we find that the exact material properties of PopZ condensates directly determine cellular fitness, providing direct evidence for the physiological importance of the emergent properties of biomolecular condensates. Our work codifies a clear set of design principles illuminating how sequence variation in a disordered domain alters the function of a widely conserved bacterial condensate. We used these insights to repurpose PopZ as a modular platform for generating synthetic condensates of tunable function in human cells.


title: 14-3-3ζ-depletion impairs mammary gland development in the mouse

abstract: The 14-3-3 family of proteins have roles in regulating several key cellular processes. While their significant structural and functional homology had informed the idea that these proteins acted redundantly, it is now becoming clear that individual family members may have tissue and context specific functions, highlighting the need for a more nuanced understanding of these important proteins. Here, we demonstrate that mice deficient in 14-3-3{zeta} exhibit developmental defects of the mammary epithelium, associated with dysregulation of key transcription factors involved in the maintenance of mammary stem cell populations. We believe that this model will be prove useful for investigating the role of 14-3-3{zeta} in the maintenance of mammary stem cell populations and elucidating the transcriptional networks driving specification of the mammary epithelium.


title: Exotic bifurcations in three connected populations with Allee effect

abstract: We consider three connected populations with strong Allee effect, and give a complete classification of the steady state structure of the system with respect to the Allee threshold and the dispersal rate, describing the bifurcations at each critical point where the number of steady states change. One may expect that by increasing the dispersal rate between the patches, the system would become more well-mixed hence simpler. However, we show that it is not always the case, and the number of steady states may (temporarily) increase by increasing the dispersal rate. Besides sequences of pitchfork and saddle-node bifurcations, we find triple-transcritical bifurcations and also a sun-ray shaped bifurcation where twelve steady states meet at a single point then disappear. The major tool of our investigations is a novel algorithm that decomposes the parameter space with respect to the number of steady states and find the bifurcation values using cylindrical algebraic decomposition with respect to the discriminant variety of the polynomial system.


title: Ground cover presence in organic olive orchards affects the interaction of natural enemies against Prays oleae, promoting an effective egg predation

abstract: The olive moth, Prays oleae, is one of the most common insects that damages olives in the Mediterranean region. The establishment of ground cover within olive orchards has been promoted in this region in recent years to avoid erosion and soil degradation. Nevertheless, its role as a shelter for natural enemies of pests has been controversial. In this study, we have investigated the effectiveness of the biological control of P. oleae in organic olive orchards with ground cover (mowed) and without ground cover (tilled). For this, (1) we assessed the relationship between predated eggs and the abundance of natural enemies in both types of orchards; (2) we compared both the potential damage of the pest and the egg hatching in the two types of orchards; and (3) we examined the interaction amongst families of natural enemies and P. oleae (as adults and as predated eggs). The results showed that there is a high rate of predation in the studied olive orchards, 81% of the eggs were predated, 12.2% hatched, and 6.9% were live eggs. However, mowed orchards were more effective for controlling P. oleae by means of egg predation rather than tilled orchards, i.e., in mowed orchards, whilst the potential damage of the pest was higher, egg hatching was rather low. The structure of the adult arthropod community, i.e., the composition and abundance of families of natural enemies did not differ between the orchards, but the abundance of the families Anthocoridae, Miridae and Scelionidae was significantly higher in the mowed orchards. Finally, the interaction amongst natural enemies and P. oleae showed that the families that better explained the effects on egg predation were Aeolothripidae, Anthocoridae, Miridae, Chrysopidae (predators), and Formicidae (omnivore). We discuss the results in terms of ecological interactions of trophic guilds and we conclude that the establishment and maintenance of ground cover in organic olive orchards, at least in June and July, is of great significance because it positively affects the egg predation of P. oleae. This effect is especially significant when there is a low abundance of natural enemies in the olive orchards.