title: Effects of BCG vaccination on donor unrestricted T cells in humans

abstract: Antigen classes other than proteins can be presented to T cells by near-monomorphic antigen-presenting molecules such as CD1, MR1, and butyrophilin 3A1. We sought to define the roles of donor unrestricted T (DURT) cells, including MR1-reactive MAIT cells, CD1b-reactive glucose monomycolate (GMM)-specific T cells, CD1d-reactive NKT cells, and {gamma}{delta} T cells, in vaccination against Mycobacterium tuberculosis. We characterized DURT cells following primary bacille Calmette-Guerin (BCG) vaccination in infants or BCG-revaccination in adults. BCG (re)vaccination did not modulate peripheral blood frequencies, T cell activation or memory profiles of MAIT cells, CD1b-restricted GMM-specific and germline-encoded mycolyl-reactive (GEM) cells or CD1d- restricted NKT cells. By contrast, BCG vaccination was associated with increased frequencies of {gamma}{delta} T cells as well as a novel subset of IFN-{gamma}-expressing CD4+ T cells with a CD26+CD161+TRAV1-2- phenotype in infants. More studies are required to understand the full potential of DURT cells in new TB vaccine strategies.


title: The in vivo RNA structurome of the malaria parasite Plasmodium falciparum, a protozoan with an A/T-rich transcriptome

abstract: Plasmodium falciparum, a protozoan parasite and causative agent of human malaria, has one of the most A/T-biased genomes sequenced to date. This may give the genome and the transcriptome unusual structural features. Recent progress in sequencing techniques has made it possible to study the secondary structures of RNA molecules at the transcriptomic level. Thus, in this study we produced the in vivo RNA structurome of a protozoan parasite with a highly A/U-biased transcriptome. We showed that it is possible to probe the secondary structures of P. falciparum RNA molecules in vivo using two different chemical probes, and obtained structures for more than half of all transcripts in the transcriptome. These showed greater stability (lower free energy) than the same structures modelled in silico, and structural features appeared to influence translation efficiency and RNA decay. Finally, we compared the P. falciparum RNA structurome with the predicted RNA structurome of an A/T-balanced species, P. knowlesi, finding a bias towards lower overall transcript stability and more hairpins and multi-stem loops in P. falciparum. This unusual protozoan RNA structurome will provide a basis for similar studies in other protozoans and also in other unusual genomes.

category: microbiology


title: Understanding Lactobacillus paracasei and Streptococcus oralis biofilm interactions through agent-based modeling

abstract:
As common commensals residing on mucosal tissues, Lactobacillus species are known to encourage health, while recent findings highlight the pathogenic roles of Streptococcus species in these environments. In this study we used a combination of in vivo imaging experiments and computational modeling to explore biofilm interactions between Streptococcus oralis, an accessory pathogen in oral Candidiasis, and Lactobacillus paracasei, an organism with known probiotic properties. A computational agent-based model was created where the two species only interact by competing for space and nutrients. Quantification of bacterial growth in live biofilms indicated that S. oralis biomass and cell numbers were much lower than predicted by the model. Two subsequent models were then created to examine more complex interactions between these species, one where L. paracasei secretes a surfactant, and another where L. paracasei secretes an inhibitor of S. oralis growth. Further biofilm experiments support the hypothesis that L. paracasei may secrete an inhibitor of S. oralis growth, although they do not exclude that a surfactant could also be involved. This contribution shows how agent-based modeling and experiments can be used in synergy to address multiple species biofilm interactions, with important roles in mucosal health and disease.

IMPORTANCEWe previously discovered a role of the oral commensal Streptococcus oralis as an accessory pathogen. S. oralis increases the virulence of Candida albicans infections in murine oral candidiasis and epithelial cell models through mechanisms which promote the formation of tissue-damaging biofilms. Lactobacillus species have known inhibitory effects on biofilm formation of many microbes, including Streptococcus species. Agent-based modeling has great advantages as a means of exploring multifaceted relationships between organisms in complex environments such as biofilms. Here we used an iterative collaborative process between experimentation and modeling to reveal aspects of the mostly unexplored relationship between S. oralis and L. paracasei in biofilm growth. The inhibitory nature of L. paracasei on S. oralis in biofilms may be exploited as a means of preventing or alleviating mucosal fungal infections.


title: Antimicrobial activity and degradation of superhydrophobic magnesium substrates in bacterial media

abstract: The interest in magnesium-based materials is promoted by their biocompatibility, bioresorbability, and by their recently found antibacterial potential. Until now the widespread use of magnesium alloys in different corrosive environments was inhibited by their weakly controllable degradation rate and poorly understood microbiologically induced corrosion behavior. To better understand the degradation and usability of magnesium-based alloys, in this study we have fabricated the superhydrophobic coatings on top of magnesium-based alloy and analyzed the behavior of this alloy in bacterial dispersions of Pseudomonas aeruginosa and Klebsiella pneumoniae cells in phosphate buffered saline. It was shown that immersion of such coatings into bacterial dispersions causes notable changes in the morphology of the samples, dependent on the bacterial dispersion composition and the type of bacterial strain. The interaction of superhydrophobic coatings with the bacterial dispersion caused the formation of biofilms and sodium polyphosphate films, which provided enhanced barrier properties for magnesium dissolution and hence for dispersion medium alkalization, eventually leading to inhibition of magnesium substrate degradation. Electrochemical data obtained for superhydrophobic samples continuously contacted with the corrosive bacterial dispersions during 48 h indicated a high level of anti-corrosion protection.


title: Large-scale CRISPRi and transcriptomics of Staphylococcus epidermidis identify genetic factors implicated in commensal-pathogen lifestyle versatility

abstract:
Staphylococcus (S.) epidermidis is a ubiquitous human commensal skin bacterium that is also one of the most prevalent nosocomial pathogens. The genetic factors underlying this remarkable lifestyle plasticity are incompletely understood, much due to the difficulties of genetic manipulation, precluding high-throughput functional profiling of this species. To probe S. epidermdis versatility to survive across a diversity of skin sites and infection niches, we developed a large-scale CRISPR interference (CRISPRi) screen complemented by transcriptional profiling (RNA-seq) across 24 diverse environmental conditions and piloted a droplet-based CRISPRi approach to enhance throughput and sensitivity. We identified putative essential genes, importantly, revealing amino acid metabolism as crucial to survival across diverse environments and demonstrated the importance of trace metal uptake for survival under multiple stress conditions. We identified pathways significantly enriched and repressed across our range of stress and nutrient limited conditions, demonstrating the considerable plasticity of S. epidermidis in responding to environmental stressors. We postulate a mechanism by which nitrogen metabolism is linked to lifestyle versatility in response to hyperosmotic challenges, such as those encountered on human skin. Finally, we examined S. epidermidis survival under acid stress and hypothesize a role for cell wall modification as a vital component of the survival response in acidic conditions. Taken together, this study integrates large scale CRISPRi and transcriptomics data across multiple environments to provide insights into a keystone member of the human skin microbiome. Our results additionally provide a valuable benchmarking analysis for CRISPRi screens and are rich resource for other staphylococcal researchers.

Author summaryStaphylococcus epidermidis is an important bacteria of the skin microbiome. While it has an important role in skin health, it can also be a major infectious agent, especially in bloodstream and catheter infections. Understanding the underlying genes and pathways that contribute to S. epidermidis ability to have both health and disease-associated abilities will be important to promoting the former and targeting the latter. Yet the function of many S. epidermidis genes, particularly in skin and infection environments, remains unknown. We developed a CRISPRi platform to knock down the function of S. epidermidis genes to better understand to what degree they are essential for growth in these environments. We complemented this gene essentiality data with gene expression data in the same environments to understand how regulation of these genes contribute to S. epidermidis survival. These large-scale data generated numerous hypotheses for new genetic links to S. epidermidis growth versatility.


title: Librator, a platform for optimized sequence editing, design, and expression of influenza virus proteins

abstract: Artificial mutagenesis and chimeric/mosaic protein engineering have laid the foundation for antigenic characterization1 and universal vaccine design2-4 for influenza viruses. However, many methods used for influenza research and vaccine development require sequence editing and protein expression, limiting their applicability and the progress of related research to specialists. Rapid tools allowing even novice influenza researchers to properly analyze and visualize influenza protein sequences with accurate nomenclature are needed to expand the research field. To address this need, we developed Librator, a system for analyzing and designing protein sequences of influenza virus Hemagglutinin (HA) and Neuraminidase (NA). With Librators graphical user interface (GUI) and built-in sequence editing functions, biologists can easily analyze influenza sequences and phylogenies, automatically port sequences to visualize structures, then readily mutate target residues and design sequences for antigen probes and chimeric/mosaic proteins efficiently and accurately. This system provides optimized fragment design for Gibson Assembly5 of HA and NA expression constructs based on peptide conservation of all historical HA and NA sequences, ensuring fragments are reusable and compatible, allowing for significant reagent savings. Use of Librator will significantly facilitate influenza research and vaccine antigen design.


title: Early life stress affects the miRNA cargo in epididymal extracellular vesicles in mouse

abstract:
Sperm RNA can be modified by environmental factors and has been implicated in communicating signals about changes in a fathers environment to the offspring. The RNA composition of sperm is influenced during its final stage of maturation in the epididymis by extracellular vesicles released by epididymal cells. We studied the effect of exposure to stress in postnatal life on the transcriptome of epididymal extracellular vesicles using a mouse model of transgenerational transmission. We found that the small RNA signature of epididymal extracellular vesicles, particularly miRNAs, is altered in adult males exposed to postnatal stress. miRNAs changes correlate with differences in the expression of their target genes in sperm and zygotes generated from that sperm. These results suggest that stressful experiences in early life can have persistent biological effects on the male reproductive tract that may in part be responsible for the transmission of the effects of exposure to the offspring.

Summary SentencemiRNA cargo of extracellular vesicles in cauda epididymis is changed by paternal exposure to early life stress, which correlates with differences in the expression of their target genes in sperm and zygotes generated from that sperm

category: molecular biology


title: Melbournevirus-encoded histone doublets are recruited to virus particles and form destabilized nucleosome-like structures

abstract:
The organization of genomic DNA into defined nucleosomes has long been viewed as a hallmark of eukaryotes. This paradigm has been challenged by the identification of  minimalist histones in archaea, and more recently by the discovery of genes that encode fused remote homologs of the four eukaryotic histones in Marseilleviridae, a subfamily of giant viruses that infect amoebae. We demonstrate that viral doublet histones localize to the cytoplasmic viral factories after virus infection, and ultimately to mature virions. CryoEM structures of viral nucleosome-like particles show strong similarities to eukaryotic nucleosomes, despite the limited sequence identify. The unique connectors that link the histone chains contribute to the observed instability of viral nucleosomes, and some histone tails assume structural roles. Our results further expand the range of  organisms that have nucleosomes and suggest a specialized function of histones in the biology of these unusual viruses.

One Sentence SummarySome large DNA viruses encode fused histone doublets that are targeted to viral factories and assemble into open nucleosome-like structures.


title: TNF drives AKI-to-CKD transition downstream of proximal tubule EGFR

abstract:
Proximal-tubule-cell EGFR activation mediates tubule cell proliferation and repair early after kidney injury, while sustained EGFR activation causes kidney fibrosis. Inflammation is a key driver of AKI-to-CKD transition and fibrosis, but mechanisms of EGFR-driven profibrotic responses are not well understood. In a mouse model of AKI-to-CKD transition and CKD progression, we show that EGFR-inhibition significantly reduced kidney expression of many immunoregulatory molecules already by day two after injury, including the potent inflammatory cytokine tumor-necrosis-factor (TNF). Single nuclei RNA-sequencing analysis showed that macrophages were among the main early cellular sources of TNF in the injured kidney. In vitro, EGFR activation in macrophages increased macrophage TNF expression, while EGFR inhibition in vivo reduced kidney macrophage accumulation, as early as two days after injury. Thus, profibrotic EGFR signaling increases kidney TNF levels both directly and indirectly. TNF inhibition did not alter tubule EGFR activation and in contrast to EGFR inhibition did not reduce early macrophage accumulation in the kidney, suggesting that TNF does not promote early infiltration of immune cells in the kidney, but rather regulates profibrotic functions of kidney and/or immune cells. TNF inhibition with etanercept in vivo in AKI-injured mice downregulated a number of cytokines, including TNF itself. This cytokine downregulation overlapped with EGFR inhibition, and additional non-overlapping downregulated cytokines shared the same functions, predicting that TNF inhibition would prevent AKI-to-CKD transition like EGFR inhibition. Indeed, TNF-inhibition with etanercept reduced AKI-induced fibrosis to the same degree as the EGFR-inhibition, while the combination of both treatments showed no additive effect. In conclusion, our results identify TNF as a downstream effector of profibrotic EGFR activation and motivate the examination of TNF pathway inhibition in human AKI or CKD.

Translational statementProximal tubule epidermal-growth-factor (EGFR) activation in mice and likely also in humans drives inflammation in the kidney after acute-kidney-injury (AKI) and causes chronic-kidney-disease (CKD) with fibrosis in a process termed AKI-to-CKD transition. Recent retrospective data shows that patients treated with TNF inhibitors show decreased incidence and progression of CKD. Our current work shows that TNF inhibition in mice is equally as effective as EGFR inhibition in preventing AKI-to-CKD transition and fibrosis. Thus, our results have translational potential and may stimulate examination of short-term TNF inhibition in AKI to prevent AKI-to-CKD transition or possibly of longer-term TNF inhibition in CKD to prevent CKD progression.

category: cell biology


title: EGFR-driven profibrotic signals in AKI-to-CKD transition are blocked by TNF inhibition: Opportunities for etanercept treatment


title: Nopp140-chaperoned 2'-O-methylation of small nuclear RNAs in Cajal bodies ensures splicing fidelity

abstract: Spliceosomal small nuclear RNAs (snRNAs) are modified by small Cajal body (CB) specific ribonucleoproteins (scaRNPs) to ensure snRNP biogenesis and pre-mRNA splicing. However, the function and subcellular site of snRNA modification are largely unknown. We show that CB localization of the protein Nopp140 is essential for concentration of scaRNPs in that nuclear condensate; and that phosphorylation by casein kinase 2 (CK2) at some 80 serines targets Nopp140 to CBs. Transiting through CBs, snRNAs are apparently modified by scaRNPs. Indeed, Nopp140 knockdown-mediated release of scaRNPs from CBs severely compromises 2-O-methylation of spliceosomal snRNAs, identifying CBs as the site of scaRNP catalysis. Additionally, alternative splicing patterns change indicating that these modifications in U1, U2, U5, and U12 snRNAs safeguard splicing fidelity. Given the importance of CK2 in this pathway, compromised splicing could underlie the mode of action of small molecule CK2 inhibitors currently considered for therapy in cholangiocarcinoma, hematological malignancies, and COVID-19.


title: ERK3-MK5 signaling regulates myogenic differentiation and muscle regeneration by promoting FoxO3 degradation

abstract: The physiological functions and downstream effectors of the atypical mitogen-activated protein kinase ERK3 remain to be characterized. We recently reported that mice expressing catalytically-inactive ERK3 (Mapk6KD/KD) exhibit a reduced post-natal growth rate as compared to control mice. Here, we show that genetic inactivation of ERK3 impairs post-natal skeletal muscle growth and adult muscle regeneration after injury. Loss of MK5 phenocopies the muscle phenotypes of Mapk6KD/KD mice. At the cellular level, genetic or pharmacological inactivation of ERK3 or MK5 induces precocious differentiation of C2C12 or primary myoblasts, concomitant with MyoD activation. Reciprocally, ectopic expression of activated MK5 inhibits myogenic differentiation. Mechanistically, we show that MK5 directly phosphorylates FoxO3, promoting its degradation and reducing its association with MyoD. Depletion of FoxO3 rescues in part the premature differentiation of C2C12 myoblasts observed upon inactivation of ERK3 or MK5. Our findings reveal that ERK3 and its substrate MK5 act in a linear signaling pathway to control post-natal myogenic differentiation.


title: Proton pump inhibitors inhibit PHOSPHO1 activity and matrix mineralisation in vitro

abstract: Proton pump inhibitors (PPIs) have been associated with an increased risk of fragility fractures in pharmaco-epidemiological studies. The mechanism is unclear but it has been speculated that by neutralising gastric acid, they may reduce intestinal calcium absorption, causing secondary hyperparathyroidism and bone loss. Here we investigated that hypothesis that the skeletal effects of PPI might be mediated by inhibitory effects on the bone-specific phosphatase PHOSPHO1. We found that the all PPI tested potential inhibited the activity of PHOSPHO1 with IC50 ranging between 0.73M for esomeprazole to 19.27M for pantoprazole. In contrast, these PPIs did not inhibit TNAP activity. We also found that mineralisation of bone matrix in primary osteoblast cultures inhibited by several PPI in a concentration dependent manner. In contrast, the histamine-2 receptor antagonists (H2RA) nizatidine, famotidine, cimetidine and ranitidine had no inhibitory effects on PHOSPHO1 activity. Our experiments shown for the first time that PPI inhibit PHOSPHO1 activity and matrix mineralisation in vitro revealing a potential mechanism by which these widely used drugs are associated with the risk of fractures.


title: ATXN10 is required for embryonic heart development and maintenance of epithelial cell phenotypes in the adult kidney and pancreas

abstract: Atxn10 is a gene known for its role in cytokinesis during the cell cycle and is associated with Spinocerebellar Ataxia (SCA10), a slowly progressing cerebellar syndrome caused by an intragenic pentanucleotide repeat expansion. Atxn10 is also implicated in the ciliopathy syndromes Nephronophthisis (NPHP) and Joubert Syndrome (JBTS), which are caused by disruption of cilia function leading to nephron loss, impaired renal function, and cerebellar hypoplasia. How Atxn10 disruption contributes to these disorders remains unknown. Here we generated Atxn10 congenital and conditional mutant mouse models. Our data indicate that while ATXN10 protein can be detected around the base of the cilium as well as in the cytosol, its loss does not cause overt changes in cilia formation or morphology. Congenital loss of Atxn10 results in embryonic lethality around E10.5 associated with pericardial effusion and loss of trabeculation. Similarly, tissue specific loss of ATXN10 in the developing endothelium (Tie2-Cre) and myocardium (cTnT-Cre) also results in embryonic lethality with severe cardiac malformations occurring in the latter. Using an inducible Cagg-CreER to disrupt Atxn10 systemically, we show that ATXN10 is also required for survival in adult mice. Loss of ATXN10 results in severe pancreatic and renal abnormalities leading to lethality within a few weeks post ATXN10 deletion in adult mice. Evaluation of these phenotypes further identified rapid epithelial to mesenchymal transition (EMT) in these tissues. In the pancreas, the phenotype includes signs of both acinar to ductal metaplasia and EMT with aberrant cilia formation and severe defects in glucose homeostasis related to pancreatic insufficiency or defects in feeding or nutrient intake. Collectively this study identifies ATXN10 as an essential protein for survival.

category: developmental biology


title: Embryo-to-embryo variability in RNAi knockdown efficiency of dKDM5/lid in Drosophila melanogaster

abstract: We used the maternal-Gal4 shRNA system to knock down expression of dKDM5/lid in Drosophila melanogaster embryos, and analyzed the efficacy of the knockdown by qRT-PCR. Although average relative expression of lid was significantly lower in knockdown conditions compared to the driver-only control, we observed a wide and overlapping range of relative gene expression between individual control and knockdown embryos.

category: genetics


title: Metabolic adaptation to progressive mitochondrial dysfunction in aging POLGD257A mice

abstract: A decline in mitochondrial function is associated with neurodegeneration and aging. Progressive mitochondrial defects have diverse metabolic consequences that could drive some of the pathophysiological changes that occur with aging. Here, we comprehensively characterized metabolic alterations in PolgD257A mitochondrial DNA mutator mice. Plasma alanine increased dramatically with time, with lactate and other organic acids accumulating to a lesser extent. These changes were reflective of increased glycolysis, rapid gluconeogenesis, and hypoglycemia. Tracing with [15N]ammonium revealed impairment of the urea cycle and diversion to purine catabolism. We also measured alterations in the lipidome, observing a general reduction in canonical lipids and the accumulation of 1-deoxysphingolipids, which are synthesized from alanine via promiscuous serine palmitoyltransferase activity. Consistent with 1-deoxysphingolipids association with peripheral neuropathy, PolgD257A mice exhibited thermal hypoalgesia. These results highlight the distinct changes that occur in carbon and nitrogen metabolism upon mitochondrial impairment and key metabolic mechanisms which can drive aging-associated neuropathy.

category: biochemistry


title: Widespread reorganisation of the regulatory chromatin landscape facilitates resistance to inhibition of oncogenic ERBB2 signalling.

abstract: Oesophageal adenocarcinoma (OAC) patients show poor survival rates and there are few targeted molecular therapies available. However, components of the receptor tyrosine kinase (RTK) driven pathways are commonly mutated in OAC, typified by high frequency amplifications of the RTK ERRB2. ERBB2 can be therapeutically targeted, but this has limited clinical benefit due to the acquisition of drug resistance. Here we examined how OAC cells respond to ERBB2 inhibition through altering their regulatory chromatin landscapes and rewiring their gene regulatory networks to acquire a reversible resistant state. ERBB2 inhibition triggers widespread remodelling of the accessible chromatin landscape. This remodelling is accompanied by the activation of the transcriptional regulators HNF4A and PPARGC1A. Initially, inhibition of cell cycle associated gene expression programmes is observed, with compensatory increases in the programmes driving changes in metabolic activity. PPARGC1A is instrumental in promoting a switch to dependency on oxidative phosphorylation and both PPARGC1A and HNF4A are required for the acquisition of resistance to ERBB2 inhibition. Our work therefore reveals the molecular pathways that support the acquisition of a resistant state and points to potential new therapeutic strategies to combat drug resistance.

category: cancer biology


title: Caveolae Impacts Cellular RNA Levels through Transcription and Translational Processes

abstract: Caveolae are membrane domains that provide mechanical strength to cells and localize signaling molecules. Caveolae are composed of caveolin-1 or -3 (Cav1/3) molecules that assemble into domains with the help of cavin-1. Besides organizing caveolae, cavin-1, also known as Polymerase I and Transcript Release Factor (PTRF), promotes ribosomal RNA transcription in the nucleus. Cell expression of Cav1 and cavin-1 are linked. Here, we find that deforming caveolae by subjecting cells to mild osmotic stress (300 to 150 mOsm), changes the levels of cellular proteins (GAPDH, Hsp90 and Ras) change only when Cav1/cavin-1 levels are reduced suggesting link between caveolae deformation and protein expression. We find that this link may be due to relocalization of cavin-1 from the plasma membrane to the nucleus upon caveolae deformation caused by osmotic stress. Cavin-1 relocalization is also seen when Cav1-Gq contacts change upon stimulation with carbachol. Cav1 and cavin-1 levels have profound effects on the amount of cytosolic RNA and the size distribution of these RNAs that in turn impact the ability of cells to form stress granules and RNA-processing bodies (p-bodies) that protect mRNA when cells are subjected to environmental stress. Studies using a cavin-1 knock-out cell line show adaptive changes in cytosolic RNA levels but a reduced ability to form stress granules. Our studies show that caveolae, through release of cavin-1, communicates mechanical and chemical cues to the cell interior to impact transcriptional and translational processes.

category: physiology


title: Biomolecular mechanisms for signal differentiation

abstract: Cells can sense temporal changes of molecular signals, allowing them to predict environmental vari-ations and modulate their behaviour. This paper elucidates the underlying biomolecular mechanisms of time derivative computation, facilitating the design of reliable synthetic differentiator devices for a variety of applications, ultimately expanding our understanding of cell behaviour. In particular, we describe and analyse three alternative biomolecular topologies that work as signal differentiators of high accuracy to arbitrary input signals around their nominal operation. We propose strategies to preserve their performance even in the presence of high-frequency input signal components, which are detrimental to the performance of most differentiators. We found that the core of the proposed topologies appears in natural regulatory networks and we further discuss their biological relevance. The simple structure of our designs makes them promising tools for realizing derivative control action in synthetic biology.

category: synthetic biology


title: Actin-based myosin XXI (13) molecular motor is involved in early phase of Leishmania cytokinesis

abstract: Leishmania genome encodes for two isoforms of myosin, but only Myosin XXI (Myo21), which is a novel form of myosin in that it contains two ubiquitin associated-like (UBA) domains towards the end of its tail structure, is expressed in both the promastigote and amastigote forms of this protozoan. Earlier studies have shown that in Leishmania promastigotes Myo21 besides localizing throughout the cell body and flagellum, it is prominently localized to the base of the flagellum. It has further been shown that this protein in the promastigotes plays an important role in regulating the cell morphology, motility, flagellum dynamics, growth and intracellular trafficking, As Myo21 depletion has been shown to result in reduced cell growth in culture, we considered it of interest to investigate whether the observed effect of Myo21 on the cell growth is mediated through its possible role in Leishmania cell division cycle. For this, we prepared heterozygous Myo21 mutants of Leishmania promastigotes (Myo21+/-cells) and then analyzed their morphology, growth and cell division cycle, using wild type Leishmania promastigotes (Myo21+/+ cells) as control. The cell division cycle was analyzed by employing flow cytometry and immunofluorescence microscopy. Flow cytometric analysis revealed that the G2/M to G1 phase transition in Myo21+/- cell is significantly delayed, as compared to Myo21+/+ cells. Immunofluorescence confocal microscopic analysis indicated that Myo21+/- cells encountered a significant delay in initiation of cytokinesis, which was mainly due to delay in the flagellar pocket division. Further analysis revealed that actin-based Myo21 motor is essentially required in the initiation phase of Leishmania cytokinesis.


title: Hybridization and cryptic speciation in the Tropical Eastern Pacific octocoral genus Pacifigorgia

abstract: The shallow waters of the Tropical Eastern Pacific (TEP) harbor a species-rich octocoral fauna, with seven genera and 124 octocoral species described to date for the region. Of these lineages, Pacifigorgia, with 35 species, is by far the most speciose and abundant shallow-water octocoral occurring in the region. The speciation mechanisms resulting in this remarkable diversity remain speculative, despite the extensive taxonomic and molecular systematic research conducted so far in the TEP. Using genome-wide SNP markers, we provide evidence for hybridization and extensive cryptic speciation in Pacifigorgia, suggesting that the genus diversity has been underestimated by traditional and molecular systematic research. Our study highlights the difficulties faced by both traditional taxonomy and single-marker based molecular approaches to characterize octocoral diversity and evolution, and the role genome-wide molecular studies coupled to morphological research play to advance our understanding of this group.

category: evolutionary biology


title: Generating realistic cell samples for gene selection in scRNA-seq data: A novel generative framework

abstract:
High dimensional, small sample size (HDSS) scRNA-seq data presents a challenge to the gene selection task in single cell. Conventional gene selection techniques are unstable and less reliable due to the fewer number of available samples which affects cell clustering and annotation. Here, we present an improved version of generative adversarial network (GAN) called LSH-GAN to address this issue by producing new realistic samples and combining this with the original scRNA-seq data. We update the training procedure of the generator of GAN using locality sensitive hashing which speeds up the sample generation, thus maintains the feasibility of applying gene selection procedures in high dimension scRNA-seq data. Experimental results show a significant improvement in the performance of benchmark feature (gene) selection techniques on generated samples of one synthetic and four HDSS scRNA-seq data. Comprehensive simulation study ensures the applicability of the model in the feature (gene) selection domain of HDSS scRNA-seq data.

AvailabilityThe corresponding software is available at https://github.com/Snehalikalall/LSH-GAN

category: bioinformatics


title: Cluster Size Distribution of Cells Disseminating from a Primary Tumor

abstract:
The first stage of the metastatic cascade often involves motile cells emerging from a primary tumor either as single cells or as clusters. These cells enter the circulation, transit to other parts of the body and finally are responsible for growth of secondary tumors in distant organs. The mode of dissemination is believed to depend on the EMT nature (epithelial, hybrid or mesenchymal) of the cells. Here, we calculate the cluster size distribution of these migrating cells, using a mechanistic computational model, in presence of different degree of EMT-ness of the cells; EMT is treated as given rise to changes in their active motile forces () and cell-medium surface tension ({Gamma}). We find that, for ( > min, {Gamma} > 1), when the cells are hybrid in nature, the mean cluster size, [Formula], where min increases with increase in {Gamma}. For {Gamma} [≤] 0, [Formula], the cells behave as completely mesenchymal. In presence of spectrum of hybrid states with different degree of EMT-ness (motility) in primary tumor, the cells which are relatively more mesenchymal (higher ) in nature, form larger clusters, whereas the smaller clusters are relatively more epithelial (lower ). Moreover, the heterogeneity in  is comparatively higher for smaller clusters with respect to that for larger clusters. We also observe that more extended cell shapes promote the formation of smaller clusters. Overall, this study establishes a framework which connects the nature and size of migrating clusters disseminating from a primary tumor with the phenotypic composition of the tumor, and can lead to the better understanding of metastasis.

Author summaryIn the process of metastasis, tumor cells disseminate from the primary tumor either as single cells or multicellular clusters. These clusters are potential contributor to the initiation of secondary tumor in distant organs. Our computational model captures the size distribution of migrating clusters depending on the adhesion and motility of the cells (which determine the degree of their EMT nature). Furthermore, we investigate the effect of heterogeneity of cell types in the primary tumor on the resultant heterogeneity of cell types in clusters of different sizes. We believe that the understanding the formation and nature of these clusters, dangerous actors in the deadly aspect of cancer progression, will be useful for improving prognostic methods and eventually better treatments.


title: A model of naturalistic decision making in preference tests

abstract:
Decisions as to whether to continue with an ongoing activity or to switch to an alternative are a constant in an animals natural world, and in particular underlie foraging behavior and performance in food preference tests. Stimuli experienced by the animal both impact the choice and are themselves impacted by the choice, in a dynamic back and forth. Here, we present model neural circuits, based on spiking neurons, in which the choice to switch away from ongoing behavior instantiates this back and forth, arising as a state transition in neural activity. We analyze two classes of circuit, which differ in whether state transitions result from a loss of hedonic input from the stimulus (an "entice to stay" model) or from aversive stimulus input (a "repel to leave" model). In both classes of model, we find that the mean time spent sampling a stimulus decreases with increasing value of the alternative stimulus, a fact that we linked to the inclusion of depressing synapses in our model. The competitive interaction is much greater in "entice to stay" model networks, which has qualitative features of the marginal value theorem, and thereby provides a framework for optimal foraging behavior. We offer suggestions as to how our models could be discriminatively tested through the analysis of electrophysiological and behavioral data.

Author summaryMany decisions are of the ilk of whether to continue sampling a stimulus or to switch to an alternative, a key feature of foraging behavior. We produce two classes of model for such stay-switch decisions, which differ in how decisions to switch stimuli can arise. In an "entice-to-stay" model, a reduction in the necessary positive stimulus input causes switching decisions. In a "repel-to-leave" model, a rise in aversive stimulus input produces a switch decision. We find that in tasks where the sampling of one stimulus follows another, adaptive biological processes arising from a highly hedonic stimulus can reduce the time spent at the following stimulus, by up to ten-fold in the "entice-to-stay" models. Along with potentially observable behavioral differences that could distinguish the classes of networks, we also found signatures in neural activity, such as oscillation of neural firing rates and a rapid change in rates preceding the time of choice to leave a stimulus. In summary, our model findings lead to testable predictions and suggest a neural circuit-based framework for explaining foraging choices.

category: neuroscience


title: Tubulin Acetylation Promotes Penetrative Capacity of Cells Undergoing Radial Intercalation

abstract: The post-translational modification of tubulin provides a wide diversity of differential functions to microtubule networks. Here we address the role of tubulin acetylation on the penetrative capacity of cells undergoing radial intercalation in the skin of Xenopus embryos. Radial intercalation is the process by which cells move apically and penetrate the epithelial barrier via inserting into the outer epithelium. As such there are two opposing forces that regulate the ability of cells to intercalate: the restrictive forces of the epithelial barrier versus the penetrative forces of the intercalating cell. By positively and negatively modulating tubulin acetylation specifically in the intercalating cells, the timing of intercalation can be altered such that cells with more acetylated microtubules penetrate the epithelium faster. Moreover, the Xenopus epithelium is a complex array of variable types of vertices and we find that intercalating cells preferentially penetrate at higher order "rosette" vertices as opposed to the more prevalent tricellular vertices. We observed differential timing in the ability of cells to penetrate different types of vertices, indicating lower order vertices represent more restrictive sites of insertion. Interestingly, we are able to shift the accessibility of early intercalating cells towards the more restrictive tricellular junctions by modulating the level of tubulin acetylation and the subsequent penetrative capacity of intercalating cells. Overall our data implicate tubulin acetylation in driving tissue penetration of intercalating cells.


title: Gonococcal invasion into epithelial cells depends on both cell polarity and ezrin

abstract: Neisseria gonorrhoeae (GC) establishes symptomatic infection in women from the cervix, lined with heterogeneous epithelial cells from non-polarized stratified at the ectocervix to polarized columnar at the endocervix. We have previously shown that GC differentially colonize and transmigrate across the ecto and endocervical epithelia. However, whether and how GC invade into heterogeneous cervical epithelial cells is unknown. This study examined GC entry of epithelial cells with various properties, using human cervical tissue explant and non-polarized/polarized epithelial cell line models. While adhering to non-polarized and polarized epithelial cells at similar levels, GC invaded into non-polarized more efficiently than polarized epithelial cells. The enhanced GC invasion in non-polarized epithelial cells was associated with increased ezrin phosphorylation, F-actin and ezrin recruitment to GC adherent sites, and the elongation of GC-associated microvilli. Inhibition of ezrin phosphorylation inhibited F-actin and ezrin recruitment and microvilli elongation, leading to a reduction in GC invasion. The reduced GC invasion in polarized epithelial cells was associated with non-muscle myosin II-mediated F-actin disassembly and microvilli ablation at GC adherence sites. Surprisingly, intraepithelial GC were only detected inside epithelial cells shed from the cervix, but neither in the ectocervix nor the endocervix, by immunofluorescence microscopy. We observed similar ezrin and F-actin recruitment in exfoliated cervical epithelial cells but not in those that remained in the ectocervical epithelium, as the luminal layer of ectocervical epithelial cells expressed ten-fold lower levels of ezrin than those beneath. However, GC inoculation induced F-actin reduction and myosin recruitment in the endocervix, similar to what was seen in polarized epithelial cells. Thus, polarized expression of ezrin at the apical surface of epithelial cells inhibits GC invasion, while non-polarized expression of ezrin promotes GC invasion by driving actin accumulation and microvilli elongation.


title: Blood vessels regulate primary motor neuronal pathfinding in zebrafish via exosome contained microRNA-22

abstract: A precise neuro-vascular communication is crucial to orchestrate directional migration and patterning of the complex vascular network and neural system. However, how blood vessels are involved in shaping the proper neuronal formation has not been fully understood. So far, limited studies have reported the discovery and functions of microRNAs (miRNAs) in guiding vascular and neural pathfinding. Currently, we showed that the deficiency of miRNA-22a, an endothelial-enriched miRNA, caused dramatic pathfinding defects both in intersegmental vessels (ISVs) and primary motor neurons (PMNs) in zebrafish embryos. Furthermore, we found the specific inhibition of miR-22a in ECs resulted in the patterning defects of both ISVs and PMNs. However, neuronal block of miR-22a mainly led to the axonal defects of PMN. Then we demonstrated that endothelial miR-22a regulates PMNs axonal navigation via exosome pathway. Sema4c was identified as a potential target of miR-22a through transcriptomic analysis and in silico analysis. Furthermore, luciferase assay and EGFP sensor assay in vivo confirmed the binding of miR-22a with 3-UTR of sema4c. In addition, Down-regulation of sema4c in the miR-22a morphants significantly neutralized the aberrant patterning of vascular and neural networks. Our study revealed that miR-22a acted as a dual guidance cue coordinating vascular and neuronal patterning and expanded the repertoire of guidance molecules, which might be of use therapeutically to guide vessels and nerves in the relevant diseases that affect both systems.


title: Water Stress and Disruption of Mycorrhizae Induce Parallel Shifts in Phyllosphere Microbiome Composition

abstract: Water and nutrient limitation are key stressors that affect plant health and ecosystem function. These environmental factors impact both soil- and root-associated microbial communities, and systemically alter plant physiology, but it is less clear how they affect aboveground plant-microbe interactions. Through experimental manipulations in the field and growth chamber, we examined the interacting effects of irrigation, soil fertility, and root mycorrhizal associations on bacterial and fungal communities of the tomato phyllosphere (Solanum lycopersicum). Both water stress and mycorrhizal disruption reduced bacterial richness within plants, homogenized bacterial community diversity among plants, and reduced the relative abundance of dominant fungal taxa. We observed striking parallelism in the individual microbial taxa affected by irrigation and mycorrhizal associations. Given the increasingly understood role of the phyllosphere in shaping plant health and pathogen susceptibility, these results offer an additional mechanism by which belowground conditions shape plant fitness.

category: ecology


title: Hunter-gatherer foraging networks promote information transmission

abstract: Central-place foraging, where foragers return to a central location (or home), is a key feature of hunter-gatherer social organization. Central-place foraging could have significantly changed hunter-gatherers use of space and mobility, and altered social networks and increased opportunities for information exchange. We evaluated whether central-place foraging patterns facilitate information transmission and considered the potential roles of environmental conditions and mobility strategies. We built an agent-based central-place foraging model where agents move according to a simple optimal foraging rule, and can encounter other agents as they move across the environment. They either forage close to their home within a given radius or move the location of their home to new areas. We analyzed the interaction networks arising across different environments and mobility strategies. We found that, at intermediate levels of environmental heterogeneity and mobility, central-place foraging increased global and local network efficiencies as well as the rate of contagion-based information transmission (simple and complex). We also assessed the effect of population density on the resultant networks and found that central-place mobility strategies can further improve information transmission in larger populations. Our findings suggest that the combination of foraging and movement strategies, as well as the underlying environmental conditions that characterized early human societies, may have been a crucial precursor in our species unique capacity to innovate, accumulate and rely on complex culture.


title: How the footprint of history shapes the evolution of digital organisms

abstract: Goulds thought experiment of "replaying lifes tape" provides a conceptual framework for experiments that quantify the contributions of adaptation, chance, and history to evolutionary outcomes. For example, we can empirically measure how varying the depth of history in one environment influences subsequent evolution in a new environment. Can this "footprint of history"--the genomic legacy of prior adaptation--grow too deep to overcome? Can it constrain adaptation, even with intense selection in the new environment? We investigated these questions using digital organisms. Specifically, we evolved ten populations from one ancestor under identical conditions. We then replayed evolution from three time points in each populations history (corresponding to shallow, intermediate, and deep history) in two new environments (one similar and one dissimilar to the prior environment). We measured the contributions of adaptation, chance, and history to the among-lineage variation in fitness and genome length in both new environments. In both environments, variation in genome length depended largely on history and chance, not adaptation, indicating weak selection. By contrast, adaptation, chance, and history all contributed to variation in fitness. Crucially, whether the depth of history affected adaptation depended on the environment. When the ancestral and new environments overlapped, history was as important as adaptation to the fitness achieved in the new environment for the populations with the deepest history. However, when the ancestral and novel environments favored different traits, adaptation overwhelmed even deep history. This experimental design for assessing the influence of the depth of history is promising for both biological and digital systems.


title: Genetic variants associated mRNA stability in lung

abstract:
Expression quantitative trait loci (eQTLs) analyses have been widely used to identify genetic variants associated with gene expression levels to understand what molecular mechanisms underlie genetic traits. The resultant eQTLs might affect the expression of associated genes through transcriptional or post-transcriptional regulation. In this study, we attempt to distinguish these two types of regulation by identifying genetic variants associated with mRNA stability of genes (stQTLs). Specifically, we computationally inferred mRNA stability of genes based on RNA-seq data and performed association analysis to identify stQTLs. Using the Genotype-Tissue Expression (GTEx) lung RNA-Seq data, we identified a total of 142,801 stQTLs for 3,942 genes and 186,132 eQTLs for 4,751 genes from 15,122,700 genetic variants for 13,476 genes, respectively. Interesting, our results indicated that stQTLs were enriched in the CDS and 3UTR regions, while eQTLs are enriched in the CDS, 3UTR, 5UTR, and upstream regions. We also found that stQTLs are more likely than eQTLs to overlap with RNA binding protein (RBP) and microRNA (miRNA) binding sites. Our analyses demonstrate that simultaneous identification of stQTLs and eQTLs can provide more mechanistic insight on the association between genetic variants and gene expression levels.

Author SummaryIn the past decade, many studies have identified genetic variants associated with gene expression level (eQTLs) in different phenotypes, including tissues and diseases. Gene expression is the result of cooperation between transcriptional regulation, such as transcriptional activity, and post-transcriptional regulation, such as mRNA stability. Here, we present a computational framework that take advantage of recently developed methods to estimate mRNA stability from RNA-Seq, which is widely used to estimate gene expression, and then to identify genetic variants associated with mRNA stability (stQTLs) in lung tissue. Compared to eQTLs, we found that genetic variants that affects mRNA stability are more significantly located in the CDS and 3UTR regions, which are known to interact with RNA-binding proteins (RBPs) or microRNAs to regulate stability. In addition, stQTLs are significantly more likely to overlap the binding sites of RBPs. We show that the six RBPs that most significantly bind to stQTLs are all known to regulate mRNA stability. This pipeline of simultaneously identifying eQTLs and stQTLs using only RNA-Seq data can provide higher resolution than traditional eQTLs study to better understand the molecular mechanisms of genetic variants on the regulation of gene expression.


title: Defects in autophagy lead to selective in vivo changes in turnover of cytosolic and organelle proteins in Arabidopsis

abstract:
Identification of autophagic protein cargo in plants by their abundance in autophagy related genes (ATG) mutants is complicated by changes in both protein synthesis and protein degradation. To detect autophagic cargo, we measured protein degradation rate in shoots and roots of Arabidopsis atg5 and atg11 mutant plants. These data show that less than a quarter of proteins changing in abundance are probable cargo and revealed roles of ATG11 and ATG5 in degradation of specific cytosol, chloroplast and ER-resident proteins, and a specialized role for ATG11 in degradation of proteins from mitochondria and chloroplasts. Our data support a role for autophagy in degrading glycolytic enzymes and the chaperonin containing T-complex polypeptide-1 complex. Autophagy induction by Pi limitation changed metabolic profiles and the protein synthesis and degradation rates of atg5 and atg11 plants. A general decrease in the abundance of amino acids and increase in several secondary metabolites in autophagy mutants was consistent with altered catabolism and changes in energy conversion caused by reduced degradation rate of specific proteins. Combining measures of changes in protein abundance and degradation rates, we also identify ATG11 and ATG5 associated protein cargo of low Pi induced autophagy in chloroplasts and ER-resident proteins involved in secondary metabolism.

Single Sentence SummaryProtein cargo of autophagy in plants can be discovered by identifying proteins that increase in abundance and decrease in degradation rate in mutants deficient in autophagy machinery

category: plant biology


title: Cerebellar neuronal dysfunction accompanies early motor symptoms in Spinocerebellar Ataxia Type 3 and is partially alleviated upon chronic citalopram treatment

abstract:
Spinocerebellar Ataxia Type 3 (SCA3) is an adult-onset, progressive ataxia. SCA3 presents with ataxia before any gross neuropathology. A feature of many cerebellar ataxias is aberrant cerebellar output that contributes to motor dysfunction. We examined whether abnormal cerebellar output was present in the CMVMJD135 SCA3 mouse model and, if so, whether it correlated with the disease onset and progression. In vivo recordings showed that the activity of deep cerebellar nuclei neurons, the main output of the cerebellum, was altered. The aberrant activity correlated with the onset of ataxia. However, although the severity of ataxia increased with age, the severity of the aberrant cerebellar output was not progressive. The abnormal cerebellar output, however, was accompanied with non-progressive abnormal activity of their upstream synaptic inputs, the Purkinje cells. In vitro recordings indicated that alterations in both intrinsic Purkinje cell pacemaking and in their synaptic inputs contributed to abnormal Purkinje cell activity. These findings implicate abnormal cerebellar physiology as an early, consistent contributor to pathophysiology in SCA3, and suggest that the aberrant cerebellar output could be an appropriate therapeutic target in SCA3.

Summary StatementIn a mouse model of Spinocerebellar ataxia type 3 aberrant cerebellar physiology is apparent early in disease, before overt neuronal pathology or neuronal death.


title: Cerebellar Neuronal Dysfunction Accompanies Early Motor Symptoms in Spinocerebellar Ataxia Type 3


title: Inferred Clades of Transposable Elements in Drosophila Suggest Co-evolution with piRNAs

abstract: Transposable elements (TEs) are self-replicating "genetic parasites" ubiquitous to eukaryotic genomes. In addition to conflict between TEs and their host genomes, TEs of the same family are in competition with each other. They compete for the same genomic niches while experiencing the same regime of copy-number selection. This suggests that competition among TEs may favor the emergence of new variants that can outcompete their ancestral forms. To investigate the sequence evolution of TEs, we developed a method to infer clades: collections of TEs that share SNP variants and represent distinct TE family lineages. We applied this method to a panel of 85 Drosophila melanogaster genomes and found that the genetic variation of several TE families shows significant population structure that arises from the population- specific expansions of single clades. We used population genetic theory to classify these clades into younger versus older clades and found that younger clades are associated with a greater abundance of sense and antisense piRNAs per copy than older ones. Further, we find that the abundance of younger, but not older clades, is positively correlated with antisense piRNA production, suggesting a general pattern where hosts preferentially produce antisense piRNAs from recently active TE variants. Together these findings suggest a pattern whereby new TE variants arise by mutation and then increase in copy number, followed by the host producing antisense piRNAs that may be used to silence these emerging variants.


title: Patterns of piRNA regulation in Drosophila revealed through transposable element clade inference


title: Ornament, armament, or toolkit? Modelling how population size drives the evolution of birdsong, a functional cultural trait

abstract: Oscine songbirds have been an important study system for social learning, particularly because their learned songs provide an analog for human languages and music. Here we propose a different analogy; from an evolutionary perspective, could a birds song be more like an arrowhead than an aria? We modify a model of human tool evolution to accommodate cultural evolution of birdsong: each song learner chooses the most skilled available tutor to emulate, and each is more likely to produce an inferior copy than a superior one. Similarly to human tool evolution, we show that larger populations foster improvements in song over time, even when learners restrict their pool of tutors to a subset of individuals. We also demonstrate that songs could be simplified instead of lost after population bottlenecks if lower-quality traits are easier to imitate than higher-quality ones. We show that these processes could plausibly generate empirically observed patterns of song evolution, and we make predictions about the types of song elements most likely to be lost when populations shrink. More broadly, we aim to connect the modeling approaches used in human and non-human systems, moving toward a cohesive theoretical framework that accounts for both cognitive and demographic processes.

category: animal behavior and cognition


title: Metaphloem development in the Arabidopsis root tip

abstract:
The phloem transport network is a major evolutionary innovation that enabled plants to dominate terrestrial ecosystems. In the growth apices, the meristems, apical stem cells continuously produce early, so-called protophloem. This is easily observed in Arabidopsis root meristems, where the differentiation of individual protophloem sieve element precursors into interconnected, conducting sieve tubes is laid out in a spatio-temporal gradient. The mature protophloem eventually collapses as the neighboring metaphloem takes over its function further distal from the stem cell niche. Compared to protophloem, metaphloem ontogenesis is poorly characterized, primarily because its visualization is challenging. Here we describe an improved protocol to investigate metaphloem development in Arabidopsis root tips in combination with a set of new molecular markers. We found that mature metaphloem sieve elements are only observed in the late post-meristematic root although their specification is initiated as soon as protophloem sieve elements enucleate. Moreover, unlike protophloem sieve elements, metaphloem sieve elements only differentiate once they have fully elongated. Finally, our results suggest that metaphloem differentiation is not directly controlled by protophloem-derived cues but rather follows a distinct, robust developmental trajectory.

Summary statementMetaphloem sieve element differentiation in Arabidopsis roots follows a robust developmental trajectory.


title: Diversity in somatic DNA repair efficiencies between commercial inbred maize lines and native Central American purple landraces

abstract: Maize is a staple food all over the world. Models for climate change suggest that, in the future, cloud formation might be reduced in the tropics increasing the exposure to Ultraviolet-B (UV-B) radiation, a DNA-damaging agent. UV-B (290 to 320 nm) has been shown to affect yield in maize. In this project we have determined the differences in DNA repair efficiencies between U.S. inbred lines B73 and Mo17, and Central American purple landraces from Guatemala and Costa Rica. Our results from single cell electrophoresis experiments (Comet Assay) suggest that the landrace Pujagua Santa Cruz (P1, Costa Rican) was resistant to damage caused by the radiomimetic agent zeocin (24h/100 micrograms per mL), while landrace Pujagua La Cruz (P2, Costa Rican) was able to repair DNA damage after one hour. On the other hand, line Mo17 (Missouri, USA) was unable to repair the damage, while B73 (Iowa, USA) and the landraces Jocopilas (Guatemalan), Orotina Congo (Costa Rican) and Talamanca (Costa Rican) were partially able to repair DNA damage. High Resolution Melting (HRM) curve analysis of putative homologous DNA repair gene ZeaATM1 showed that both P1 and P2 had differences in the melting temperatures for this gene compared to B73 and Mo17, while P1 showed additional differences in ZeaSOG1, ZeaRAD51 and ZeaBRCA1, suggesting that in this landrace the presence of polymorphisms may be common among key genes for this pathway. Taken together our results suggest that key adaptive differences in DNA repair efficiencies exist between inbred lines and landraces of maize and that some Central America landraces could be used as a valuable pool of alleles for plant breeding aiming to increase tolerance to radiation.


title: Text has been revised, image definition has been revised.


title: Stability of microbiota in vineyard soils across consecutive years.

abstract:
Agricultural soils harbor rich and diverse microbial communities that have a deep influence on soil properties and productivity. Large scale studies have shown the impact of environmental parameters like climate or chemical composition on the distribution of bacterial and fungal species. Comparatively, little data exists documenting how soil microbial communities change between different years. Quantifying the temporal stability of soil microbial communities will allow us to better understand the relevance of the differences between environments and their impact on ecological processes on the global and local scale.

We characterized the bacterial and fungal components of the soil microbiota in ten vineyards in two consecutive years. Despite differences of species richness and diversity between the two years, we found a general stability of the taxonomic structure of the soil microbiota. Temporal differences were smaller than differences due to geographical location, vineyard land management or differences between sampling sites within the same vineyard. Using machine learning, we demonstrated that each site was characterized by a distinctive microbiota, and we identified a reduced set of indicator species that could classify samples according to their geographic origin across different years with high accuracy.

ImportanceThe temporal stability of the soil microbiota is important to understand the relevance of the differences that are found in response to a variety of environmental factors. By comparing fungal and bacterial microbiota from samples collected in the same sites in two consecutive years, we found a remarkable stability of both components, with characteristic differences between bacteria and fungi. Our work fills an important gap toward the definition of a microbial cartography of agricultural soils.


title: Design of the recombinant influenza neuraminidase antigen is crucial for protective efficacy

abstract:
Supplementing influenza vaccines with recombinant neuraminidase (rNA) remains a promising approach for improving the suboptimal efficacy. However, correlations among rNA designs, properties, and protection have not been systematically investigated. Here, we performed a comparative analysis of several rNAs produced from different construct designs using the baculovirus/insect cell system. The rNAs were designed with different tetramerization motifs and NA domains from a recent H1N1 vaccine strain (A/Brisbane/02/2018) and were analyzed for enzymatic properties, antigenicity, thermal and size stability, and protection in mice. We found that rNAs containing the NA head-domain versus the full-ectodomain possess distinct enzymatic properties and that the molecular size stability is tetramerization domain-dependent, whereas protection is more contingent on the combination of the tetramerization and NA domains. Following single-dose immunizations, a rNA possessing the full-ectodomain, non-native enzymatic activity, and the tetramerization motif from the human vasodilator-stimulated phosphoprotein provided substantially higher protection than a rNA possessing the head-domain, native activity and the same tetramerization motif. In contrast, these two rNAs provided comparable protection when the tetramerization motif was exchanged with the one from the tetrabrachion protein. These findings demonstrate that the rNA design is crucial for the protective efficacy and should be thoroughly evaluated for vaccine development, as the unpredictable nature of the heterologous domain combination can result in rNAs with similar key attributes but vastly differ in protection.

IMPORTANCEFor several decades it has been proposed that influenza vaccines could be supplemented with recombinant neuraminidase (rNA) to improve the efficacy. However, some key questions for manufacturing stable and immunogenic rNA remain to be answered. We show here that the tetramerization motifs and NA domains included in the rNA construct design can have a profound impact on the biochemical, immunological and protective properties. We also show that the single-dose immunization regimen is more informative for assessing the rNA immune response and protective efficacy, which is surprisingly more dependent on the specific combination of NA and tetramerization domains than common attributes for evaluating NA. Our findings may help to optimize the design of rNAs that can be used to improve or develop influenza vaccines.


title: Animal lifestyle changes acceptable mass limits for attached tags

abstract:
O_LIAnimal-attached devices have transformed our understanding of vertebrate ecology. To minimize tag-related harm for these studies, researchers have long advocated that tag masses should not exceed 3% of the animals body mass. However, this proposition ignores tag forces generated as a result of animal movement.
C_LIO_LIUsing data from collar-attached accelerometers on diverse free-ranging terrestrial animals, we detail a tag-based acceleration method (TbAM) in which we quantify animal athleticism in terms of fractions of animal movement time devoted to different collar-recorded accelerations. The varying accelerations are converted to forces imposed on the animals based on the acceleration and tag mass and allow derivation of defined force limits, including those amounting to 3% of the animals mass, for specified fractions of any animals active time.
C_LIO_LIWe demonstrate how species athleticism is the principal determinant of tag forces, whereas body mass is of little importance. Forces exerted by  3% tags were mostly equivalent to 4-19% of the animals masses during moving, with a maximum of 54% in a hunting cheetah. Cumulative frequency curves of tag acceleration for periods when animals were active, all showed a characteristic sigmoid pattern, which was displaced further to the right as higher acceleration activities accounted for an increasing proportion of any animals time. Specifying that tags should exert forces that are less than 3% of the animals body mass for 95% of the time led to corrected tag masses constituting between 1.6% and 2.98% of our study animals masses, with values depending on animal athleticism.
C_LIO_LIRecognition that animal athleticism affects tag forces of their carriers fundamentally changes how acceptable tag mass limits should be determined by ethics bodies. In order to have a scientifically robust acceptable threshold to limit the forces experienced by an animal carrier, we suggest practitioners derive a similar cumulative acceleration profile for their study species and use a minimum of the 95% limits on the plot (although higher limits may be more appropriate).
C_LI

category: zoology


title: Sleep-dependent upscaled excitability and saturated neuroplasticity in the human brain: From brain physiology to cognition

abstract: Sleep strongly affects synaptic strength, making it critical for cognition, especially learning, and memory formation. Whether and how sleep deprivation modulates human brain physiology and cognition is not well understood. Here we examined how overnight sleep deprivation vs sufficient sleep affects (a) cortical excitability, as measured by transcranial magnetic stimulation (TMS), (b) inducibility of LTP-and-LTD-like plasticity via transcranial direct current stimulation (tDCS), and (c) learning, memory and attention. The results suggest that sleep deprivation upscales cortical excitability due to enhanced glutamate-related cortical facilitation and decreased and/or reversed GABAergic cortical inhibition. Furthermore, tDCS-induced LTP-like plasticity abolishes while LTD-like plasticity converts to excitatory LTP-like plasticity under sleep deprivation. This is associated with increased EEG theta activity, which is related to sleep pressure. Finally, we show that learning and memory formation, behavioral counterparts of plasticity, and working memory and attention, which rely on cortical excitability, are impaired during sleep deprivation. Our data suggest that upscaled brain excitability, and altered plasticity, due to sleep deprivation, are associated with impaired cognitive performance.


title: Sleep-dependent upscaled excitability, saturated neuroplasticity, and modulated cognition in the human brain


title: Heterotypic Aβ interactions facilitate amyloid assembly and modify amyloid structure

abstract: It is still unclear why pathological amyloid deposition initiates in specific brain regions, nor why specific cells or tissues are more susceptible than others. Amyloid deposition is determined by the self-assembly of short protein segments called aggregation-prone regions (APRs) that favour cross-{beta} structure. Here we investigated whether A{beta} amyloid assembly can be modified by heterotypic interactions between A{beta} APRs and short homologous segments in otherwise unrelated human proteins. We identified heterotypic interactions that accelerate A{beta} assembly, modify fibril morphology and affect its pattern of deposition in vitro. Moreover, we found that co-expression of these proteins in an A{beta} reporter cell line promotes A{beta} amyloid aggregation. Importantly, reanalysis of proteomics data of A{beta} plaques from AD patients revealed an enrichment in proteins that share homologous sequences to the A{beta} APRs, suggesting heterotypic amyloid interactions may occur in patients. Strikingly, we did not find such a bias in plaques from overexpression models in mouse. Based on these data, we propose that heterotypic APR interactions may play a hitherto unrealised role in amyloid-deposition diseases.


title: Coherent activity at three major lateral hypothalamic neural outputs controls the onset of motivated behavior responses

abstract: The lateral hypothalamus (LH) plays an important role in motivated behavior. However, it is not known how LH neural outputs dynamically signal to major downstream targets to organize behavior. We used multi-fiber photometry to show that three major LH neural outputs projecting to the dorsal raphe nucleus (DRN), ventral tegmental area (VTA), and lateral habenula (LHb) exhibit significant coherent activity in mice engaging motivated responses, which decrease during immobility. Mice engaging active coping responses exhibit increased activity at LH axon terminals that precedes an increase in the activity of serotonin neurons and dopamine neurons, indicating that they may play a role in initiating active responses stemming from LH signal transmissions. The optogenetic activation of LH axon terminals in either the DRN, VTA, or LHb was sufficient to increase mobility but had different effects on passive avoidance and sucrose consumption, suggesting that LH outputs use complementary mechanisms to control behavioral responses. Our results support the notion that the three LH neural outputs play complementary roles in initiating motivated behaviors.


title: Virus-Targeted Transcriptomic Analyses Implicate Ranaviral Interaction with Host Interferon Response in Frog Virus 3-infected Frog Tissues

abstract:
Frog Virus 3 (FV3) is a large dsDNA virus that cause global infections in amphibians, fish and reptiles, and contribute to amphibian declines. FV3s genome contains near 100 putative open reading frames (ORFs). Previous studies have classified these coding genes into temporal classes as immediate early, delayed early and late viral transcripts based on their sequential expression during FV3 infection. To genome-wide characterize ranaviral gene expression, we performed a whole transcriptomic analysis (RNA-Seq) using total RNA samples containing both viral and cellular transcripts from FV3-infected Xenopus laevis adult tissues using two FV3 strains, a wild type (FV3-WT) and an ORF64R-deleted recombinant (FV3-{Delta}64R). In samples from the infected intestine, liver, spleen, lung and especially kidney, a FV3-targeted transcriptomic analysis mapped reads spanning the full-genome coverage at [~]10x depth on both positive and negative strands. By contrast, reads were only mapped to partial genomic regions in samples from the infected thymus, skin and muscle. Extensive analyses validated the expression of almost all annotated 98 ORFs and profiled their differential expression in a tissue-, virus-, and temporal class-dependent manners. Further studies identified several putative ORFs that encode hypothetical proteins containing viral mimicking conserved domains found in host interferon (IFN) regulatory factors (IRFs) and IFN receptors. This study provides the first comprehensive genome-wide viral transcriptome profiling during infection and across multiple amphibian host tissues that will serve as instrumental reference. It also presents evidence implying that ranaviruses like FV3 have acquired previously unknown molecular mimics interfering with host IFN signaling during evolution.

ImportanceFrog Virus 3 (FV3), are large dsDNA viruses that cause devastating infections globally in amphibians, fish and reptiles, and contribute to catastrophic amphibian declines. FV3s large genome encodes near 100 coding genes, of which most have been functionally uncharacterized in the viral pathogenesis. Using a whole transcriptomic analysis (RNA-Seq) in FV3-infected amphibian samples, we determined a genome-wide virus transcriptome and profiled their differential expression in a tissue-, virus-, and temporal class-dependent manners. Further studies identified several putative ORFs that encode hypothetical proteins containing viral mimicking conserved domains found in host interferon (IFN) regulatory factors (IRFs) and IFN receptors. This study provides the first comprehensive genome-wide viral transcriptome profiling during infection and across multiple amphibian host tissues that will serve as instrumental reference. It also presents evidence implying that ranaviruses like FV3 have acquired previously unknown molecular mimics interfering with host IFN signaling during evolution.


title: A qnr-plasmid allows aminoglycosides to induce SOS in Escherichia coli

abstract:
The plasmid-mediated quinolone resistance (PMQR) genes have been shown to promote high-level bacterial resistance to fluoroquinolone antibiotics, potentially leading to clinical treatment failures.

In Escherichia coli, sub-inhibitory concentrations (sub-MIC) of the widely used fluoroquinolones are known to induce the SOS response. Interestingly, the expression of several PMQR qnr genes is controlled by the SOS master regulator.

During the characterization of a small qnrD-plasmid carried in E. coli, we observed that the aminoglycosides become able to induce the SOS response in this species, thus leading to the transcription of qnrD.

We found that induction of the SOS response is due to nitric oxide (NO) accumulation in presence of sub-MIC of aminoglycosides. We demonstrated that the NO accumulation is driven by two plasmid genes, ORF3 and ORF4, whose products act at two levels. ORF3 encode a FAD-binding oxidoreductase which helps NO synthesis, while ORF4 code for an FNR-type transcription factor, related to an O2-responsive regulator of hmp expression, able to repress the Hmp-mediated NO detoxification pathway of E. coli.

Thus, this discovery, that other major classes of antibiotics may induce the SOS response could have worthwhile implications for antibiotic stewardship efforts in preventing the emergence of resistance.


title: Genome assemblies of three closely related leaf beetle species (Galerucella spp).

abstract: Galerucella (Coleoptera: Chrysomelidae) is a leaf beetle genus that has been extensively used for ecological and evolutionary studies. It has also been used as biological control agent against invading purple loosestrife in North America, with large effects on biodiversity. Here we report genome assembly and annotation of three closely related Galerucella species: G. calmariensis, G. pusilla and G. tenella. The three assemblies have a genome size ranging from 460Mb to 588Mb, with N50 from 31,588kb to 79.674kb, containing 29,202 to 40,929 scaffolds. Using an ab initio evidence-driven approach, 30,302 to 33,794 protein-coding genes were identified and functionally annotated. These draft genomes will contribute to the understanding of host-parasitoid interactions, evolutionary comparisons of leaf beetle species and future population genomics studies.

category: genomics


title: Chromatin-interacting transposon RNAs linking to the core trans-inhibition circuitry for embryonic stem cell identity

abstract: Transposable DNA sequences constitute more than half of the human and mouse genomes. A large number of non-coding RNAs, named as transposon RNAs, are derived from these transposable elements. The cis-regulatory function of transposable DNA elements, such as LINE-1 and Alu has been largely explored. But the biological roles of transposon RNAs arent well understood. Here, investigations of RNA-chromatin interactions provide us with comprehensive evidence that specific families of transposon RNAs play roles in trans-regulation linking to the core inhibition circuitry for embryonic stem cell identity. Alternative modes of the RNA-DNA hybrid duplex and protein-recruited RNA scaffold are required for the regulatory activities of transposon RNAs. LINE-1 RNAs co-locating with KAP1 form a negative feedback loop stabilizing the transcription of LINE-1 DNA elements via RNA-DNA hybrids. In another way LINE-1 RNAs, together with the reprogramming three factors and Polycomb repressive complexes, participate in the inhibition on dozens of differentiation-relative genes.


title: Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace

abstract: mTORC1 is a kinase complex regulating cell growth, proliferation and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted mTORC1 with DEPTOR to understand its function. We find that DEPTOR is a unique partial mTORC1 inhibitor that may have evolved to preserve feedback inhibition of PI3K. Counterintuitively, mTORC1 activated by RHEB or oncogenic mutation is much more potently inhibited by DEPTOR. Although DEPTOR partially inhibits mTORC1, mTORC1 prevents this inhibition by phosphorylating DEPTOR, a mutual antagonism that requires no exogenous factors. Structural analyses of the mTORC1/DEPTOR complex showed DEPTORs PDZ domain interacting with the mTOR FAT region, and the unstructured linker preceding the PDZ binding to the mTOR FRB domain. Here we show, in contrast to previous cellular studies, that both the PDZ and linker regions are essential for inhibition, and it is likely that interaction with the FRB is crucial to the unique partial inhibition.


title: Defining the KRAS-regulated kinome in KRAS-mutant pancreatic cancer

abstract: Oncogenic KRAS drives cancer growth by activating diverse signaling networks, not all of which have been fully delineated. We set out to establish a system-wide profile of the KRAS-regulated kinase signaling network (kinome) in KRAS-mutant pancreatic ductal adenocarcinoma (PDAC). We knocked down KRAS expression in a panel of six cell lines, and then applied Multiplexed Inhibitor Bead/Mass Spectrometry (MIB/MS) chemical proteomics to monitor changes in kinase activity and/or expression. We hypothesized that depletion of KRAS would result in downregulation of kinases required for KRAS-mediated transforming activities, and in upregulation of other kinases that could potentially compensate for the deleterious consequences of the loss of KRAS. We identified 15 upregulated and 13 downregulated kinases in common across the panel. In agreement with our hypothesis, all 15 of the upregulated kinases have established roles as cancer drivers (e.g., SRC, TGFBR1, ILK), and pharmacologic inhibition of the upregulated kinase, DDR1, suppressed PDAC growth. Interestingly, 11 of the 13 downregulated kinases have established driver roles in cell cycle progression, particularly in mitosis (e.g., WEE1, Aurora A, PLK1). Consistent with a crucial role for the downregulated kinases in promoting KRAS-driven proliferation, we found that pharmacologic inhibition of WEE1 also suppressed PDAC growth. The unexpected paradoxical activation of ERK upon WEE1 inhibition led us to inhibit both WEE1 and ERK concurrently, which caused further potent growth suppression and enhanced apoptotic death than WEE1 inhibition alone. We conclude that system-wide delineation of the KRAS-regulated kinome can identify potential therapeutic targets for KRAS-mutant pancreatic cancer.


title: DNA methylation affects pre-mRNA transcriptional initiation and processing in Arabidopsis

abstract:
BackgroundDNA methylation may regulate pre-mRNA transcriptional initiation and processing, thus affecting gene expression. Unlike animal cells, plants, especially Arabidopsis thaliana, have relatively low DNA methylation levels, limiting our ability to observe any correlation between DNA methylation and pre-mRNA processing using typical short-read sequencing. However, with newly developed long-read sequencing technologies, such as Oxford Nanopore Technology Direct RNA sequencing (ONT DRS), combined with whole-genome bisulfite sequencing, we were able to precisely analyze the relationship between DNA methylation and pre-mRNA transcriptional initiation and processing using DNA methylation-related mutants.

ResultsUsing ONT DRS, we generated more than 2 million high-quality full-length long reads of native mRNA for each of the wild type Col-0 and mutants defective in DNA methylation, identifying a total of 117,474 isoforms. We found that low DNA methylation levels around splicing sites tended to prevent splicing events from occurring. The lengths of the poly(A) tail of mRNAs were positively correlated with DNA methylation. DNA methylation before transcription start sites or around transcription termination sites tended to result in gene-silencing or read-through events.

Furthermore, using ONT DRS, we identified novel transcripts that we could not have otherwise, since transcripts with intron retention and fusion transcripts containing the uncut intergenic sequence tend not to be exported to the cytoplasm. Using the met1-3 mutant with activated constitutive heterochromatin regions, we confirmed the effects of DNA methylation on pre-mRNA processing.

ConclusionThe combination of ONT DRS with whole-genome bisulfite sequencing was a powerful tool for studying the effects of DNA methylation on splicing site selection and pre-mRNA processing, and therefore regulation of gene expression.


title: Mechanisms Underlying the Complex Dynamics of Temperature Entrainment by a Circadian Clock

abstract:
Autonomously oscillating circadian clocks resonate with daily environmental (zeitgeber) rhythms to organize physiology around the solar day. While entrainment properties and mechanisms have been studied widely and in great detail for light-dark cycles, entrainment to daily temperature rhythms remains poorly understood despite that they are potent zeitgebers.

Here we investigate the entrainment of the chronobiological model organism Neurospora crassa, subject to thermocycles of different periods and fractions of warm versus cold phases, mimicking seasonal variations. Depending on the properties of these thermocycles, regularly entrained rhythms, period-doubling (frequency demultiplication) but also irregular aperiodic behavior occurs. We demonstrate that the complex nonlinear phenomena of experimentally observed entrainment dynamics can be understood by molecular mathematical modeling.

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category: systems biology


title: Genome sequence of Pseudopithomyces chartarum, causal agent of facial eczema (pithomycotoxicosis) in ruminants, and identification of the putative sporidesmin toxin gene cluster

abstract:
Facial eczema (FE) in grazing ruminants is a debilitating liver syndrome induced by ingestion of sporidesmin, a toxin belonging to the epipolythiodioxopiperazine class of compounds. Sporidesmin is produced in spores of the fungus Pseudopithomyces chartarum, a microbe which colonises leaf litter in pastures. New Zealand has a high occurrence of FE in comparison to other countries as animals are fed predominantly on ryegrass, a species that supports high levels of Pse. chartarum spores. The climate is also particularly conducive for Pse. chartarum growth. Here, we present the genome of Pse. chartarum and identify the putative sporidesmin gene cluster. The Pse. chartarum genome was sequenced using single molecule real-time sequencing (PacBio) and gene models identified. Loci containing genes with homology to the aspirochlorine, sirodesmin PL and gliotoxin cluster genes of Aspergillus oryzae, Leptosphaeria maculans and Aspergillus fumigatus, respectively, were identified by tBLASTn. We identified and annotated an epipolythiodioxopiperazine cluster at a single locus with all the functionality required to synthesise sporidesmin.

HighlightsO_LIThe whole genome of Pseudopithomyces chartarum has been sequenced and assembled.
C_LIO_LIThe genome is 39.13 Mb, 99% complete, and contains 11,711 protein coding genes.
C_LIO_LIA putative sporidesmin A toxin (cause of facial eczema) gene cluster is described.
C_LIO_LIThe genomes of Pse. chartarum and the Leptosphaerulina chartarum teleomorph differ.
C_LIO_LIComparative genomics is required to further resolve the Pseudopithomyces clade.
C_LI


title: TranSyT, the Transport Systems Tracker

abstract: The importance and rate of development of genome-scale metabolic models have been growing for the last years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGEs release, software development for automatic integration of transport reactions into models has stalled. Here we present the Transport Systems Tracker (TranSyT), the next iteration of TRIAGE. Unlike its predecessor, TranSyT does not rely on manual curation to expand its internal database, derived from highly-curated records retrieved from the Transporters Classification Database and complemented with information from other data sources. TranSyT compiles information regarding transporters families, transport proteins, and derives reactions into its internal database, making it available for rapid annotation of complete genomes. All transport reactions have GPR associations and can be exported with identifiers from four different metabolite databases. TranSyT is currently available as a plugin for merlin v4.0 and an app for KBase.


title: TranSyT, an innovative framework for identifying transport systems


title: SmProt: a reliable repository with comprehensive annotation of small proteins identified from ribosome profiling

abstract: Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance of small proteins has been revealed in current years, along with the discovery of their diverse functions. However, systematic annotation of small proteins is still insufficient. SmProt was specially developed to provide valuable information on small proteins for scientific community. Here we present the update of SmProt, which emphasizes reliability of translated sORFs, genetic variants in translated sORFs, disease-specific sORFs translation events or sequences, and significantly increased data volume. More components such as non-AUG translation initiation, function, and new sources are also included. SmProt incorporated 638,958 unique small proteins curated from 3,165,229 primary records, which were computationally predicted from 419 ribosome profiling (Ribo-seq) datasets and collected from the literature and other sources originating from 370 cell lines or tissues in 8 species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Saccharomyces cerevisiae, Caenorhabditis elegans, and Escherichia coli). In addition, small protein families identified from human microbiomes were collected. All datasets in SmProt are free to access, and available for browse, search, and bulk downloads at http://bigdata.ibp.ac.cn/SmProt/.


title: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

abstract:
MotivationSpatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissuespecific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary.

ResultsWe describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the users computer or through a web application.

AvailabilityspatialLIBD is available at bioconductor.org/packages/spatialLIBD.

Supplementary informationSupplementary data are available at Bioinformatics online.


title: Factorization-based Imputation of Expression in Single-cell Transcriptomic Analysis (FIESTA) recovers Gene-Cell-State Relationships

abstract:
MotivationSingle cell RNA sequencing (scRNA-seq) is a powerful gene expression profiling technique that is presently revolutionizing the study of complex cellular systems in the biological sciences. Existing single-cell RNA-sequencing methods suffer from sub-optimal target recovery leading to inaccurate measurements including many false negatives. The resulting  zero-inflated data may confound data interpretation and visualization.

ResultsSince cells have coherent phenotypes defined by conserved molecular circuitries (i.e. multiple gene products working together) and since similar cells utilize similar circuits, information about each each expression value or  node in a multi-cell, multi-gene scRNA-Seq data set is expected to also be predictable from other nodes in the data set. Based on this logic, several approaches have been proposed to impute missing values by extracting information from non-zero measurements in a data set. In this study, we applied non-negative matrix factorization approaches to a selection of published scRNASeq data sets to recommend new values where original measurements are likely to be inaccurate and where  zero measurements are predicted to be false negatives. The resulting imputed data model predicts novel cell type markers and expression patterns more closely matching gene expression values from orthogonal measurements and/or predicted literature than the values obtained from other previously published imputation approaches.

Contactbenjamin.spike@hci.utah.edu

Availability and implementationFIESTA is written in R and is available at https://github.com/elnazmirzaei/FIESTA and https://github.com/TheSpikeLab/FIESTA.


title: Effect of the shrimp farming wastes as co-feed on growth performance and digestibility of juvenile grey mullet, Mugil cephalus

abstract: A feeding trial was carried out to evaluate the utilization of residual nutrients from a shrimp farming wastes as co-feed in different proportions in juvenile grey mullets. Four treatments were designed offering shrimp farming wastes at 0, 33, 66, and 100%. The 4 % of feed respecting the total biomass of each experimental tank was offered daily. The total feed ratio was completed with commercial feed for marine fish in the treatments where it was needed. At the end of the feeding trial, final weight, weight gain, relative weight gain, and thermal growth coefficient were reduced in the fish when increasing the amount of SFW as feed. However, the fish showed a digestive capacity to use residual nutrients up to 66 %, increasing their initial weight by up to 25 %. The increase of shrimp farming waste as feed negatively affected the whole-body proximal composition. The digestibility results showed that the fish could digest up to 41 % of the shrimp farming waste protein. Results suggest that juvenile grey mullets are capable of utilizing residual nutrients from shrimp farming waste. However, it is necessary to use an alternative feed source to induce an optimal growth performance for the juvenile grey mullets. It is also recommended that mullets be fed with formulated feed to meet their nutritional requirements to maintain the protein and lipid content of the whole-body under culture conditions.


title: Tractography-based targeting of ventral intermediate nucleus: A comparison between conventional stereotactic targeting and diffusion tensor imaging-based targeting

abstract:
BackgroundThe ventral intermediate (VIM) nucleus of the thalamus is the main target for lesioning using magnetic resonance imaging (MRI) guided focused ultrasound (MRgFUS) or deep brain stimulation (DBS). Targeting of VIM still depends on standard stereotactic coordinates, which do not account for inter-individual variability. Several approaches have been proposed including visualization of dentato-rubro-thalamic tract (DRTT) using diffusion tensor imaging tractography.

ObjectiveTo compare probabilistic tracking of DRTT with deterministic tracking of DRTT and stereotactic coordinates to identify the most appropriate approach to target VIM.

MethodsIn this retrospective study, we assessed the VIM targeted using stereotactic coordinates, deterministic and probabilistic tracking of DRTT in 19 patients with essential tremor who underwent DBS with VIM targeted using microelectrode recordings. We subsequently determined the positions of VIM derived from these three approaches and compared with that of DBS lead position using paired sample t-tests.

ResultsThe probabilistic tracking of DRTT was significantly anterior to the lead (1.45 {+/-} 1.61 mm (P< 0.0001)), but not in the medial/lateral position (-0.29{+/-}2.42 mm (P=0.50)). Deterministic tracking of DRTT was significantly lateral (2.16 {+/-} 1.94 mm (P< 0.0001)) and anterior to the lead (1.66 {+/-} 2.1 mm (P< 0.0001)). The stereotactic coordinates were significantly lateral (2.41 {+/-} 1.41 mm (P< 0.0001)) and anterior (1.23 {+/-} 0.89 mm (P< 0.0001)) to the lead.

ConclusionProbabilistic tracking of DRTT was found to be superior in targeting VIM compared to deterministic tracking and stereotactic coordinates.


title: Mapping vestibular and visual contributions to angular head velocity tuning in the cortex

abstract: Neurons that signal the direction and angular velocity of head movements (AHV cells) are critically important to process visual and spatial information. However, it has been challenging to isolate the sensory modality that drives them and to comprehensively map their cortical distribution. To address this, we developed a method that enables rotating awake, head-fixed mice under a two-photon microscope in a visual environment. Starting in layer 2/3 of the retrosplenial cortex, a key area for vision and navigation, we found that a significant fraction of rotation-sensitive neurons report AHV. These tuning properties depend on vestibular input because they persist in darkness and are reduced when replaying visual flow to stationary animals. When mapping the spatial extent, we found AHV cells in all cortical areas that we explored, including motor, somatosensory, visual- and posterior parietal cortex. Notably, the vestibular and visual contributions to AHV are area dependent. Thus, many cortical circuits have access to AHV, enabling a diverse integration with sensorimotor and cognitive information.


title: Extracellular adenosine induces hypersecretion of IL-17A by T-helper 17 cells through the adenosine A2a receptor to promote neutrophilic inflammation

abstract: Extracellular adenosine, produced from ATP secreted by neuronal or immune cells, may play a role in endogenous regulation of inflammatory responses. However, the underlying molecular mechanisms are largely unknown. Here, we show that adenosine primes hypersecretion of interleukin (IL)-17A by CD4+ T cells via T cell receptor activation. This hypersecretion was also induced by an adenosine A2a receptor (A2aR) agonist, PSB0777. In addition, an A2aR antagonist (Istradefylline), and inhibitors of adenyl cyclase, protein kinase A, and cAMP response element binding protein (which are signaling molecules downstream of the Gs protein coupled with the A2aR), suppressed IL-17A production, suggesting that activation of A2aR induces IL-17A production by CD4+ T cells. Furthermore, immune subset studies revealed that adenosine induced hypersecretion of IL-17A by T-helper (Th)17 cells. These results indicate that adenosine is an endogenous modulator of neutrophilic inflammation. Administration of an A2aR antagonist to mice with experimental autoimmune encephalomyelitis led to marked amelioration of symptoms, suggesting that suppression of adenosine-mediated IL-17A production is an effective treatment for Th17-related autoimmune diseases.

category: immunology