abstract: Bacterial microcompartments are organelle-like structures composed entirely of proteins. They have evolved to carry out several distinct and specialized metabolic functions in a wide variety of bacteria. Their outer shell is constructed from thousands of tessellating protein subunits, encapsulating enzymes that carry out the internal metabolic reactions. The shell proteins are varied, with single, tandem and permuted versions of the PF00936 protein family domain comprising the primary structural component of their polyhedral architecture, which is reminiscent of a viral capsid. While considerable amounts of structural and biophysical data have been generated in the last 15 years, current resources present challenges for understanding the functional and structural properties of microcompartments (MCPs) and their diversity. In order to make the remarkable structural features of bacterial microcompartments accessible to a broad community of scientists and non-specialists, we developed MCPdb: The Bacterial Microcompartment Database (https://mcpdb.mbi.ucla.edu/). MCPdb is a comprehensive resource that categorizes and organizes known microcompartment protein structures and their larger assemblies. To emphazise the critical roles symmetric assembly and architecture play in microcompartment function, each structure in the MCPdb is validated and annotated with respect to: (1) its predicted natural assembly state (2) tertiary structure and topology and (3) the metabolic compartment type from which it derives. The current database includes 134 structures and is available to the public with the anticipation that it will serve as a growing resource for scientists interested in understanding protein-based metabolic organelles in bacteria.


title: Working memory relates to individual differences in speech category learning: Insights from computational modeling and pupillometry

abstract: Across two experiments, we examine the relationship between individual differences in working memory (WM) and the acquisition of non-native speech categories in adulthood. While WM is associated with individual differences in a variety of learning tasks, successful acquisition of speech categories is argued to be contingent on WM-independent procedural-learning mechanisms. Thus, the role of WM in speech category learning is unclear. In Experiment 1, we show that individuals with higher WM acquire non-native speech categories faster and to a greater extent than those with lower WM. In Experiment 2, we replicate these results and show that individuals with higher WM use more optimal, procedural-based learning strategies and demonstrate more distinct speech-evoked pupillary responses for correct relative to incorrect trials. We propose that higher WM may allow for greater stimulus-related attention, resulting in more robust representations and optimal learning strategies. We discuss implications for neurobiological models of speech category learning.

category: neuroscience


title: Resolving the graft ischemia-reperfusion injury during liver transplantation at the single cell resolution

abstract: Ischemia-reperfusion injury (IRI) remains the major reason for impaired donor graft function and increased mortality post-liver transplantation. The mechanism of IRI involves multiple pathophysiological processes and numerous types of cells. However, a systematic and comprehensive single-cell transcriptional profile of intrahepatic cells during liver transplantation is still unclear. We performed a single-cell transcriptome analysis of 14,313 cells from liver tissues collected from pre-procurement, at the end of preservation and 2 h post-reperfusion. We made detailed annotations of mononuclear phagocyte, endothelial cell, NK/T, B and plasma cell clusters, and we described the dynamic changes of the transcriptome of these clusters during IRI and the interaction between mononuclear phagocyte clusters and other cell clusters. In addition, we found that TNFAIP3 interacting protein 3 (TNIP3), specifically and highly expressed in Kupffer cell clusters post-reperfusion, may have a protective effect on IRI. In summary, our study provides the first dynamic transcriptome map of intrahepatic cell clusters during liver transplantation at single-cell resolution.

category: cell biology


title: Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process

abstract: Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, maturation, and differentiation are still under debate. To date, only discrete and inconsistent information on the classification of shrimp hemocytes has been reported, showing that the morphological characteristics are not sufficient to resolve their actual roles. Our present study using single-cell RNA sequencing, revealed nine types of hemocytes of Marsupenaeus japonicus based on their transcriptional profiles. We identified markers of each subpopulation and the differentiation pathways involved in their maturation. We also discovered cell growth factors that might play crucial roles in hemocyte differentiation. Different immune roles among these subpopulations were suggested from the analysis of differentially expressed immune-related genes. These results provide a unified classification of shrimp hemocytes, which improves the understanding of its immune system.


title: Bioengineered embryoids mimic post-implantation development in vitro

abstract: The difficulty of studying post-implantation development in mammals has sparked a flurry of activity to develop in vitro models, termed embryoids, based on self-organizing pluripotent stem cells. Previous approaches to derive embryoids either lack the physiological morphology and signaling interactions, or are not yet optimal for modeling post-gastrulation development. Here, we report a bioengineering-inspired approach aimed at addressing this gap. A high-throughput cell aggregation approach was employed to simultaneously coax mouse embryonic stem cells (ESCs) into hundreds of uniform epiblast-like (EPI) aggregates in a solid matrix-free manner. When co-cultured with mouse trophoblast stem cell (TSC) aggregates, the resulting hybrid structures initiate gastrulation-like events and undergo axial morphogenesis to yield structures, termed EpiTS embryoids, with a pronounced anterior development, including brain-like regions. We identify the presence of an epithelium in EPI aggregates as the major determinant for the axial morphogenesis and anterior development seen in EpiTS embryoids. Our results demonstrate the potential of EpiTS embryoids to study peri-gastrulation development in vitro.

category: developmental biology


title: Dynamic adult tracheal plasticity drives stem cell adaptation to changes in intestinal homeostasis.

abstract: Coordination of stem cell function by local and niche-derived signals is essential to preserve adult tissue homeostasis and organismal health. The vasculature is a prominent component of multiple stem cell niches. However, its role in adult intestinal homeostasis remains largely understudied. Here, we uncover a previously unrecognised crosstalk between adult intestinal stem cells (ISCs) in Drosophila and the vasculature-like tracheal system, which is essential for intestinal regeneration. Following damage to the intestinal epithelium, gut-derived reactive oxygen species (ROS) activate tracheal HIF-1 and bidirectional FGF/FGFR signaling, leading to reversible remodelling of gut-associated terminal tracheal cells and ISC proliferation following damage. Unexpectedly, ROS-induced adult tracheal plasticity involves downregulation of the tracheal specification factor trachealess (trh) and upregulation of IGF2 mRNA-binding protein (IGF2BP2/Imp). Our results reveal a novel intestine/vasculature interorgan communication program, which is essential to adapt stem cells response to the proliferative demands of the intestinal epithelium.


title: Occurrences of protonated base triples in RNA are determined by their cooperative binding energies and specific functional requirements

abstract: With wide ranging diversity in their geometries, binding strengths and chemical properties, noncanonical base pairs are equipped to intricately regulate and control the structural dynamics of RNA molecules. Protonation of nucleobases adds to the diversity. Compared to the unprotonated scenario, on one hand they open up new alternatives for base pairing interactions (Class I) while on the other, they modulate the geometry and stability of existing base pairing interactions (Class II). In both cases, compensation of the energetic cost associated with nucleobase protonation at physiological pH, can be understood in terms of protonation induced restructuring of charge distribution. This not only leads to modifications in existing base-base interactions but often also leads to additional stabilizing interactions, resulting in the formation of protonated base triples. Here we report our detailed quantum chemical studies, in conjunction with structural bioinformatics based analysis of RNA crystal and NMR structure datasets, probing into the contribution of such protonated triples in the structural dynamics of RNA. Our studies revealed more than 55 varieties of protonated triples in RNA, some of which occur recurrently within conserved structural motifs present in rRNAs, tRNAs and in other synthetic RNAs. Our studies suggest that high occurrence frequencies are associated with protonated triples which satisfy the specific structural requirements of conserved motifs where they occur. For example, protonated triples with flexible geometries are involved in the formation of tertiary contacts between different distant motifs. Stabilization of protonated base pairs, through the induction of additional energetically cooperative interactions, appears to be another factor. These results provide significant insights into the sequence-structure-function relationships in RNA.

category: biophysics


title: Simultaneous association of grip effort with snack food items does not change preferences

abstract: Effort is typically considered aversive such that rewards requiring less effort are preferred over identical value rewards that require greater effort, commonly referred to as "effort discounting". Although effort has been repeatedly shown to be weighed as a cost, there are indications to suggest that under some conditions it may increase preferences. An example for how effort affects preferences is the  contrast effect were items that follow effort production gain value. In the current study we examined whether the association of grip effort with snack food items would change preferences. In four experiments, we first identified each participants individual preferences of snack food items and subjective maximal grip force. We then associated different effort levels with items of similar preference. Finally, we tested for changes in preferences following the effort association. Across the four studies, effort association had no effect on preferences. Using Bayesian analyses, we conclude that simultaneous association of effort does not change preferences in our studies and call for a replication effort of previous findings.


title: Natural protection from type 1 diabetes in Non Obese Diabetic (NOD) mice is characterised by a unique pancreatic islet phenotype

abstract: The non-obese diabetic (NOD) mouse develops spontaneous type 1 diabetes, with some features of disease that are very similar to the human disease. However, a proportion of NOD mice are naturally-protected from developing diabetes, and currently studies characterising this cohort are very limited. Here, using both immunofluorescence and multi-parameter flow cytometry we focus on the pancreatic islet morphology and immune infiltrate observed in naturally-protected NOD mice. We show that naturally-protected NOD mice are characterised by an increased frequency of insulin-containing, smaller sized, pancreatic islets. Although mice remain diabetes free, florid immune infiltrate remains. However, this immune infiltrate is skewed towards a regulatory phenotype in both T and B-cell compartments. Pancreatic islets have an increased frequency of IL-10 producing B cells and associated cell surface markers. Resident memory CD69+CD8+ T cells show a significant shift towards reduced CD103 expression, while CD4+ T cells have increased FoxP3+CTLA4+ expression. These data indicate that naturally-protected NOD mice have a unique islet signature and provide new insight into regulatory mechanisms within pancreatic islets.

category: immunology


title: Computational identification and characterization of antigenic properties of Rv3899c of Mycobacterium tuberculosis and its interaction with Human leukocyte antigen (HLA)

abstract: Tuberculosis (TB) is the second largest infectious disease that kills 1.2 million people annually worldwide. A rise in drug-resistant TB cases demands continued efforts towards the discovery & development of drugs and vaccines. In the recent past, though novel drugs have been added to the current TB regimen [1], research on new vaccine candidates needs a greater thrust. Secretory proteins of H37Rv are frequently studied for their antigenicity and their scope as protein subunit vaccines decrees further analysis. In this study, Rv3899c of H37Rv emerges as a potential vaccine candidate on its evaluation by several bioinformatics tools. It is a non-toxin, secretory protein with an  immunoglobulin-like fold which does not show similarity with a human protein. We found Rv3899c homologs in several mycobacterial species and its antigenic score (0.54) to compare well with the known immunogens such as ESAT-6 (0.56) and Rv1860 (0.52). Structural examination of Rv3899c predicted ten antigenic peptides, an accessibility profile of the antigenic determinants constituting B-cell epitope rich regions and a low Abundance of Antigenic Regions (AAR) value. Significantly, our study shows ESX-2 secretion system proteins and antigenic PE/PPE proteins of H37Rv as the interacting partners of Rv3899c. Further, molecular docking predicted Rv3899c to interact with human leukocyte antigen HLA-DRB1*04:01 through its antigenically conserved motif (RAAEQQRLQRIVDAVARQEPRISWAAGLRDDGTT). Interestingly, the binding affinity was observed to increase on citrullation of its Arg1 residue. Taken together, the computational characterization and predictive information suggest Rv3899c to be a promising TB vaccine candidate, which should be examined and validated experimentally.


title: Global transcriptome analysis of Stenotrophomonas maltophilia in response to growth at human body temperature

abstract:
Stenotrophomonas maltophilia (Smal) is a typical example of an environmental originated opportunistic human pathogen, which can thrive at different habitats including the human body and can cause a wide range of infections. It must cope with heat stress during transition from the environment to the human body as the physiological temperature of the human body (37 {square}) is higher than environmental niches (22-30 {square}). Interestingly, S. rhizophila a phylogenetic neighbour of Smal within genus Stenotrophomonas is unable to grow at 37 {square}. Thus, it is crucial to understand how Smal is adapted to human body temperature, which could suggest its evolution as an opportunistic human pathogen. In this study, we have performed comparative transcriptome analysis of S. maltophilia grown at 28 {square} and 37 {square} as temperature representative for environmental niches and human body respectively. RNA-Seq analysis revealed several interesting findings showing alterations in gene expression levels at 28 {square} and 37 {square}, which can play an important role during infection. We have observed downregulation of genes involved in cellular motility, energy production and metabolism, replication and repair whereas upregulation of VirB/D4 Type IV secretion system, aerotaxis, cation diffusion facilitator family transporter and LacI family transcriptional regulators at 37 {square}. Microscopy and plate assays corroborated altered expression of genes involved in motility. The results obtained enhance our understanding of the strategies employed by S. maltophilia during adaptation towards the human body.

Impact statementStenotrophomonas maltophilia (Smal) is a WHO listed multidrug resistant nosocomial pathogen. Interestingly, S. maltophilia species can grow both at 28 {square} and 37 {square} unlike its closest taxonomic relative, i.e., S. rhizophila and also majority species belonging this genus. Hence this ability to grow at 37 {square}, i.e., human body temperature might have played key role in the unique success and emergence of this species as opportunistic human pathogen. Using transcriptome sequencing, we have identified set of genes which are differentially regulated at 37 {square} and investigated their evolutionary history. This study has revealed regulation of genes involved in motility, metabolism, energy, replication, transcription, aerotaxis and a type IV secretion system might have a role in successful adaption to a distinct lifestyle. The findings will be helpful in further systematic studies on understanding and management of an emerging human pathogen such as Smal.

category: microbiology


title: Imaging cytoplasmic lipid droplets in vivo with fluorescent perilipin 2 and perilipin 3 knockin zebrafish

abstract: Cytoplasmic lipid droplets are highly dynamic storage organelles; their rapid synthesis, expansion, and degradation, as well as their varied interactions with other organelles allow cells to maintain lipid homeostasis. While the molecular details of lipid droplet dynamics are currently a very active area of investigation, this work has been primarily performed in cultured cells and in vitro systems. By taking advantage of the powerful transgenic and in vivo imaging opportunities afforded by the zebrafish model system, we have built a suite of tools to allow lipid droplets to be studied in real-time from the subcellular to the whole organism level. Fluorescently-tagging the lipid droplet associated proteins, perilipin 2 and perilipin 3, in the endogenous loci, permits visualization of lipid droplets in the intestine, liver, lateral line and adipose tissue. Using these transgenic lines we have found that perilipin 3 is rapidly loaded on intestinal lipid droplets following a high fat meal and then largely replaced by perilipin 2 a few hours later. These powerful new tools will facilitate studies on the role of lipid droplets in different tissues and under different genetic and physiological manipulations.


title: Estuarine molecular bycatch as a landscape-wide biomonitoring tool

abstract: Environmental DNA analysis is rapidly transforming biodiversity monitoring and bolstering conservation applications worldwide. This approach has been assisted by the development of metabarcoding PCR primers that are suited for detection of a wide range of taxa. However, little effort has gone into exploring the value of the non-target DNA sequences that are generated in every survey, but subsequently discarded. Here we demonstrate that fish-targeted markers widely employed in aquatic biomonitoring can also detect birds and mammals present in the surrounding habitats. We showcase this feature in three temperate estuaries over multiple seasons, where dozens of bird and mammal species offer valuable insights into spatial and temporal faunal variation. Our results indicate that existing metabarcode sequence data sets are suitable for mining and exploration of this  molecular by-catch, and that any future eDNA-based surveys can be designed to accommodate this enhanced property of this widely applicable tool.

category: ecology


title: Molecular population genetics of Sex-lethal (Sxl) in the D. melanogaster species group - a locus that genetically interacts with Wolbachia pipientis in Drosophila melanogaster

abstract: Sex-lethal (Sxl) is the sex determination switch in Drosophila, and also plays a critical role in germ-line stem cell (GSC) daughter differentiation in Drosophila melanogaster. Three female-sterile alleles at Sxl in Drosophila melanogaster were previously shown to genetically interact to varying degrees with the maternally inherited endosymbiont Wolbachia pipientis. Given this genetic interaction and W. pipientis ability to manipulate reproduction in Drosophila, we carried out a careful study of both the population genetics (within four Drosophila species) and molecular evolutionary analysis (across 20 Drosophila species) of Sxl. Consistent with earlier studies, we find that selective constraint has played a prominent role in Sxls molecular evolution within Drosophila, but we also observe patterns that suggest both episodic bursts of protein evolution and recent positive selection at Sxl. The episodic nature of Sxls protein evolution is discussed in light of its genetic interaction with W. pipientis.

category: evolutionary biology


title: Competition and environmental gradients structure Canidae assemblages across the planet

abstract: The phylogenetic information of assemblages carries the signature of ecological and evolutionary processes that assembled these communities. Identifying the mechanisms that shape communities is not simple, as they can vary spatially. Here, we investigated how the phylogenetic structure of Canidae across the globe is affected by the environment and competition. We first identified phylogenetically clustered and overdispersed assemblages of canids over the planet taking into account regional pools of species in South and North America, Eurasia, and Africa. Then, we applied Structural Equation Models in these communities in order to identify the effect of temperature, vegetation cover, human impact, and body size dissimilarity on the spatial distribution of the phylogenetic information of canids. Only southern South America and the Middle East had strong phylogenetic clustered patterns, while the rest of the planet predominantly showed overdispersed assemblages. Body size dissimilarity and vegetation cover were the most important variables to explain the spatial patterns of phylogenetic structure in clustered and overdispersed communities, respectively. Canidae community composition across the world presents significant patterns of clustering and overdispersion, which vary following mainly the environmental gradient, suggesting habitat filtering as the main force acting on Canidae assemblages.


title: Competition and environmental gradients structure assemblages of Canidae across the planet


title: Determinants of the rate of molecular evolution in fission yeast

abstract: Which variables determine the rate of gene and protein sequence evolution is a central question in evolutionary genomics. In the model organism fission yeast (Schizosaccharomyces pombe), the determinants of the rate of sequence evolution have yet to be determined. Previous studies in other organisms have typically found gene expression levels to be most significant, with numerous other variables identified as having a smaller impact. Here, partial least squares regression (PLS) and partial correlation analysis are used to model sequence evolution rates in the fission yeast genome by a range of variables. Variable importance in projection (VIP) scores as well as partial correlation coefficients are calculated for each variable, and used as estimates of the influence of each independent variable on sequence evolution rate. Unlike many previous studies in other organisms, centrality in the PPI network is shown to be the most important variable, and gene expression found to be less influential. Considerable heterogeneity is found in the influence of different gene ontology terms as well as amino acid composition. However, the majority of variance in constraint in fission yeast remains unexplained by this study, indicating that variables not yet considered and stochastics probably have considerable impact on the rate of molecular evolution.

category: genomics


title: Network centrality is the most important variable determining gene sequence evolution rates in Schizosaccharomyces pombe


title: Poor adult nutrition impairs learning and memory in a parasitoid wasp

abstract: Animals have evolved cognitive abilities whose impairment can incur dramatic fitness costs. While malnutrition is known to impact brain development and cognitive functions in vertebrates, little is known in insects, whose small brain appears particularly vulnerable to environmental stressors. Here, we investigated the influence of diet quality on learning and memory in the parasitoid wasp Venturia canescens. Newly emerged adults were exposed for 24h to either honey, sucrose solution 20%, sucrose solution 10%, or no food, before being conditioned in an olfactory associative learning task in which an odor (orange) was associated to a reward (host larvae). Wasps fed honey showed 3.5 times higher learning performances and 1.5 times longer memory retention times than wasps fed sucrose solutions and starved wasps. Poor diets also reduced longevity and fecundity. Our results demonstrate the importance of early adult nutrition for optimal cognitive function in these parasitoid wasps that must quickly develop olfactory memories for choosing high quality hosts for their progeny.

category: animal behavior and cognition


title: MBASR: Workflow-simplified ancestral state reconstruction of discrete traits with MrBayes in the R environment

abstract: Ancestral state reconstruction (ASR) is a critical tool in comparative biology. Given a phylogenetic tree and observed trait states for taxa at the trees tips, ASR aims to model ancestral trait states at the trees internal nodes. Thus, the pattern, tempo, and frequency of a characters evolution can be considered in a phylogenetic framework. Software programs that perform discrete trait ASR analyses are variably complex in terms of workflow steps, input formats, user interfaces, settings and execution commands, and the organization of output. MBASR (acronym for MrBayes Ancestral States with R) is an R language toolkit that highly automates the ASR workflow and uses the machinery of the popular phylogenetics software MrBayes. Input data files are simple, analysis can be setup and run with a single R function, and statistical output is concisely organized and immediately interpretable. Use requires minimal knowledge of the most basic R commands and no experience with the MrBayes program. The MBASR toolkit can be freely downloaded from GitHub.

category: bioinformatics


title: Structural basis for Potassium transport by KdpFABC

abstract: KdpFABC is an oligomeric K+ transport complex in prokaryotes that maintains ionic homeostasis under stress conditions. The complex comprises a channel-like subunit (KdpA) from the Superfamily of K+ Transporters and a pump-like subunit (KdpB) from the superfamily of P-type ATPases. Recent structural work has defined the architecture and generated contradictory hypotheses for the transport mechanism. Here, we use substrate analogs to stabilize four key intermediates in the reaction cycle and determine the corresponding structures by cryo-EM. We find that KdpB undergoes conformational changes consistent with other representatives from the P-type superfamily, whereas KdpA, KdpC and KdpF remain static. We observe a series of spherical densities that we assign as K+ or water and which define a pathway for K+ transport. This pathway runs through an intramembrane tunnel in KdpA and delivers ions to sites in the membrane domain of KdpB. Our structures suggest a mechanism where ATP hydrolysis is coupled to K+ transfer between alternative sites in the membrane domain of KdpB, ultimately reaching a low-affinity site where a water-filled pathway allows release of K+ to the cytoplasm.


title: Weakly-Coupled Oscillators with Long-Distance Correlation as a Model of Human Atrial Fibrillation

abstract: I.Atrial Fibrillation (AF) is a chronic, progressive, and heterogeneous disease, which exhibits irregular and chaotic atrial electrical activity. The exact mechanisms of AF have remained elusive. The complexity of the atrial signals, irregular period, and the non-local nature of AF make it very difficult to characterize its spatiotemporal organization. This paper presents a set of data-processing tools to find and evaluate the intracardiac signals in AF based on synchronization theory. Specifically, a graph-theoretical algorithm is developed to prune spurious detections of atrial complexes (spikes). The processing pipeline was applied to 10 intracardiac recordings obtained during ablation procedures in patients with paroxysmal or persistent AF. The AF cases were classified into three main types. Type I (n=3) is defined as the presence of a single driver that dominates both atria and is consistent with the mother rotor hypothesis. The majority of the cases had more than one driver and were classified as types II (n=4) and III (n=3). The drivers, i.e., the interacting organized areas, in type II have significantly different peak frequencies and are only weakly coupled. The drivers in type III have close frequencies, are moderately interacting, and show evidence of transient intermittent phase-locking (intermittency). In addition, a long-distance correlation between channels from the left and right atria was observed. The theory of synchronization is a useful conceptual framework to process and analyze AF and can provide mechanistic insight into AF and the effect of various interventions.


title: GENPPI: standalone software for creating protein interaction networks from genomes

abstract:
MotivationBacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationships that are capable of being annotated only from genomes are conserved gene neighbourhoods (CNs), phylogenetic profiles (PPs), and gene fusions. At present, there is no standalone software that enables networks of interactions among proteins to be created using these three evolutionary characteristics with efficient and effective results.

ResultsWe developed GENPPI software for the ab initio prediction of interaction networks using predicted proteins from a genome. In our case study, we employed 50 genomes of the genus Corynebacterium. Based on the PP relationship, GENPPI differentiated genomes between the ovis and equi biovars of the species Corynebacterium pseudotuberculosis and created groups among the other species analysed. If we inspected only the CN relationship, we could not entirely separate biovars, only species. Our software GENPPI was determined to be efficient because, for example, it creates interaction networks from the central genomes of 50 species/lineages with an average size of 2200 genes in less than 40 minutes on a conventional computer. Our software is compelling because the interaction networks that it creates reflect evolutionary relationships among species and were obtained in average nucleotide identity (ANI) analyses. Additionally, this software enables the user to define how he or she intends to explore the PP and CN characteristics through various parameters, enabling the creation of customized interaction networks. For instance, users can set parameters regarding the genus, metagenome, or pangenome. In addition to the parameterization of GENPPI, it is also the users choice regarding which set of genomes he or she is going to study.

AvailabilityThe source code in the Common Lisp language, binary files for different operating systems, and GENPPI software tutorials are available at {{github.com/santosardr/genppi}}.

Contactsantosardr@ufu.br

Supplementary informationSupplementary data are available at Bioinformatics online.

category: systems biology


title: Subclinical Mastitis in Dairy Cows is Associated with Changes in Salivary Serum Amylase-A, Social Behavior and Activity Profiles

abstract: The aim of this study was to identify detailed changes in behavior, and in salivary serum amyloid A (SAA), associated with subclinical mastitis. This included standard sickness behaviors (which form part of an adaptive response to conserve energy, minimize heat loss and facilitate recovery following infection and inflammation) and lesser-studied behaviors, that are biologically predicted to change at low-level infection, and therefore particularly relevant for detecting subclinical mastitis (here labelled  luxury behaviors). SAA is a physiological marker of systemic inflammation, with levels in milk and serum already known to increase during subclinical mastitis. We investigated whether the same was true for SAA in cow saliva. Data were collected for n = 34 commercial barn-housed dairy cows, tested in 17 matched-pairs. Each pair comprised a cow with subclinical mastitis (SCM) and a healthy control (CTRL), identified using somatic cell count (SCC) (SCM: SCC >200 x1000 cells/ml; CTRL: SCC <100 x1000 cells/ml). SCM cows were selected for study ad-hoc, at which point they were paired with a CTRL cow, based upon parity and calving date; consequently, the full data set was accrued over several months. Data were collected for each pair over 3 days: SCC (l4:00-l5:00h) Day 1; behavior (24h from 00:00h) Day 2; salivary serum amyloid-A (SAA) Day 3. We report, for the first time, that an increase in salivary SAA occurs during subclinical mastitis; SAA was higher in SCM cows and demonstrated a positive (weak) correlation with SCC. The behavioral comparisons revealed that SCM cows had reductions in activity (behavioral transitions and distance moved), social exploration, social reactivity (here: likelihood to move away/be displaced following receipt of agonism), performance of social grooming and head butts, and the receipt of agonistic non-contact challenges. In addition, SCM cows received more head swipes, and spent a greater proportion of time lying with their head on their flank than CTRL cows. SCM cows also displayed an altered feeding pattern; they spent a greater proportion of feeding time in direct contact with two conspecifics, and a lower proportion of feeding time at self-locking feed barriers, than CTRL cows. Behavioral measures were found to correlate, albeit loosely, with serum SAA in a direction consistent with predictions for sickness behavior. These included positive correlations with both lying duration and the receipt of all agonistic behavior, and negative correlations with feeding, drinking, the performance of all social and all agonistic behavior, and social reactivity. We conclude that changes in salivary SAA, social behavior, and activity offer potential in the detection of subclinical mastitis and recommend further investigation to substantiate and refine our findings.

category: zoology


title: Changes in Behavior and Salivary Serum Amyloid A in cows with Subclinical Mastitis


title: Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains

abstract: Recent advances in neuroscience make the extraction of full neuronal morphology at whole brain dataset available. To produce quality morphometry at large scale, it is highly desirable but extremely challenging to efficiently handle petabyte-scale high-resolution whole brain imaging database. Here, we developed a multi-level method to produce high quality somatic, dendritic, axonal, and potential synaptic morphometry, which was made possible by utilizing necessary petabyte hardware and software platform to optimize both the data and workflow management. Our method also boosts data sharing and remote collaborative validation. We highlight a petabyte application dataset involving 62 whole mouse brains, from which we identified 50,233 somata of individual neurons, profiled the dendrites of 11,322 neurons, reconstructed the full 3-D morphology of more than one thousand neurons including their dendrites and full axons, and detected million scale putative synaptic sites derived from axonal boutons. Analysis and simulation of these data indicate the promise of this approach for modern large-scale morphology applications.


title: MorphoHub: A Platform for Petabyte-Scale Multi-Morphometry Generation


title: A novel approach to the empirical characterization of learning in biological systems

abstract:
Learning to execute precise, yet complex, motor actions through practice is a trait shared by most organisms. Here we develop a novel experimental approach for the comprehensive investigation and characterization of the learning dynamics of practiced motion. Following the dynamical systems framework, we consider a high-dimensional behavioral space in which a trial-by-trial sequence of motor outputs defines a trajectory that converges to a fixed point - the desired motor output. In this scenario, details of the internal dynamics and the trial-by-trial learning mechanism cannot be disentangled from behavioral noise for nonlinear systems or even well estimated for linear systems with many parameters. To overcome this problem, we introduce a novel approach: the sporadic application of systematic target perturbations that span the behavioral space and allow us to estimate the linearized dynamics in the vicinity of the fixed point. The steady-state Lyapunov equation then allows us to identify the noise covariance. We illustrate the method by analyzing sequence-generating neural networks with either intrinsic or extrinsic noise, at time resolutions that span from spike timing to spiking rates. We demonstrate the utility of our approach in experimentally plausible and realizable settings and show that this method can fully characterize the linearized between-trials learning dynamics as well as extract meaningful internal properties of the unknown mechanism that drives the motor output within each trial. We then illustrate how the approach can be extended to nonlinear learning dynamics through a flexible choice of the basis and magnitude of perturbations.

Significance statementMovement control ties brain activity to measurable external actions in real time, providing a useful tool for both neuroscientists interested in the emergence of stable behavior and biomedical engineers interested in the design of neural prosthesis and brain-machine interfaces. We approach the question of motor skill learning by introducing artificial errors through a novel perturbative scheme amenable to analytic examination in the linearized regime close to the desired behavior. Numerical simulations then demonstrate how to probe the learning dynamics in both linear and nonlinear systems. These findings stress the usefulness of analyzing responses to deliberately induced errors and the importance of properly designing such perturbation experiments. Our approach provides a novel generic tool for monitoring the acquisition of motor skills.


title: A multimodal metabolomics approach to elucidate the trigger components of rumen fluid for larval exsheathment in a model gastrointestinal parasitic nematode, Haemonchus contortus.

abstract:
BackgroundMetabolomics is a powerful and sensitive approach for investigating low molecular weight metabolite profiles present in rumen biofluids to identify potential roles of metabolites in rumen microbiome and understanding host-level regulatory mechanisms associated with animal production.

FindingsRumen samples from sheep grazed on a mixed ryegrass and clover pasture diet, were fractionated based on molecular weight and analysed using metabolomics and lipidomics to detect the small molecules present in ovine rumen fluid fractions.

ConclusionsUntargeted metabolomics provides a detailed snapshot of the ovine ruminal fluid metabolome that can be used as reference for future studies on ovine rumen fluid or as a comparator for other ruminant species. All data and metadata are available for download in the MetaboLights database.

category: molecular biology


title: Non-targeted multimodal metabolomics and lipidomics data from ovine rumen fluid fractions


title: Evolutionary processes driving the rise and fall of Staphylococcus aureus ST239, a dominant hybrid pathogen

abstract: Staphylococcus aureus ST239 has been one of the most successful epidemic MRSA strains, and one of the leading causes of healthcare-associated MRSA infections. Here we investigate the evolution of ST239 using a combination of computational and experimental approaches. ST239 is thought to have emerged by a large scale chromosomal replacement event in which an ST8 clone acquired approximately 600 kb of DNA from an ST30 clone. Analysis of large-scale genomic data sets allowed us to confirm and refine the model of the origin of ST239. Importantly, we found that ST239 originated between the 1920s and 1945, implying that this MRSA lineage evolved at least 14 years before the clinical introduction of methicillin. Molecular evolution within ST239 has been dominated by purifying selection, although we found some evidence that the acquired region of the genome has evolved rapidly as a result of relaxed selective constraints. Crucially, we found that ST239 isolates have low competitive ability relative to both ST30 and ST8, demonstrating that this hybrid lineage is characterized by low fitness. We also found evidence of positive selection in a small number of genes involved in antibiotic resistance and virulence, suggesting that ST239 has evolved towards an increasingly pathogenic lifestyle. Collectively, these results support the view that low fitness has driven the recent decline of ST239, and highlight the challenge of using evolutionary approaches to understand the dynamics of pathogenic bacteria.


title: GeneFriends 2021: Updated co-expression databases and tools for human and mouse genes and transcripts

abstract: Gene co-expression analysis has emerged as a powerful method to provide insights into gene function and regulation. The rapid growth of publicly available RNA-sequencing (RNA-seq) data has created opportunities for researchers to employ this abundant data to help decipher the complexity and biology of genomes. Co-expression networks have proven effective for inferring relationship between the genes, for gene prioritization and for assigning function to poorly annotated genes based on their co-expressed partners. To facilitate such analyses we created previously an online co-expression tool for humans and mice entitled GeneFriends. To continue providing a valuable tool to the scientific community, we have updated the GeneFriends database. Here, we present the latest version of GeneFriends, which includes updated gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples. GeneFriends is freely available at http://www.genefriends.org/


title: Selective enhancement of neural coding in V1 underlies fine discrimination learning in tree shrew.

abstract: Visual discrimination improves with training, a phenomenon that is thought to reflect plastic changes in the responses of neurons in primary visual cortex (V1). However, the identity of the neurons that undergo change, the nature of the changes, and the consequences of these changes for other visual behaviors remain unclear. Using chronic in vivo 2-photon calcium imaging to monitor the responses of neurons in V1 of tree shrews learning a Go/No-Go fine orientation discrimination task, we find increases in neural population measures of discriminability for task-relevant stimuli that correlate with performance and depend on a select subset of neurons with preferred orientations that include the rewarded stimulus and nearby orientations biased away from the non-rewarded stimulus. Learning is accompanied by selective enhancement in the response of these neurons to the rewarded stimulus that further increases their ability to discriminate the task stimuli. These changes persist outside of the trained task and predict observed enhancement and impairment in performance of other discriminations, providing evidence for selective persistent learning-induced plasticity in V1 with significant consequences for perception.


title: Targeting glucose metabolism sensitizes pancreatic cancer to MEK inhibition

abstract: Pancreatic ductal adenocarcinoma (PDAC) is almost universally lethal. A critical unmet need exists to explore essential susceptibilities in PDAC and identify druggable targets for tumor maintenance. This is especially challenging in the context of PDAC, in which activating mutations of KRAS oncogene (KRAS*) dominate the genetic landscape. By using an inducible KrasG12D-driven p53 deficient PDAC mouse model (iKras model), we demonstrate that RAF-MEK-MAPK signaling is the major effector for oncogenic Kras-mediated tumor maintenance. However, MEK inhibition has minimal therapeutic effect as single agent for PDAC both in vitro and in vivo. Although MEK inhibition partially downregulates the transcription of glycolysis genes, it surprisingly fails to suppress the glycolysis flux in PDAC cell, which is a major metabolism effector of oncogenic KRAS. Accordingly, In vivo genetic screen identified multiple glycolysis genes as potential targets that may sensitize tumor cells to MAPK inhibition. Furthermore, inhibition of glucose metabolism with low dose 2-deoxyglucose (2DG) in combination with MEK inhibitor dramatically induces apoptosis in KrasG12D-driven PDAC cell in vitro, inhibits xenograft tumor growth and prolongs the overall survival of genetically engineered mouse PDAC model. Molecular and metabolism analyses indicate that co-targeting glycolysis and MAPK signaling results in apoptosis via induction of lethal ER stress. Together, our work suggests that combinatory inhibition of glycolysis and MAPK pathway may serve as an alternative approach to target KRAS-driven PDAC.

category: cancer biology


title: A non-adaptive demographic mechanism for genome expansion in Streptomyces

abstract: The evolution of microbial genome size is driven by gene acquisition and loss events that occur at scales from individual genomes to entire pangenomes. The equilibrium between gene gain and loss is shaped by evolutionary forces, including selection and drift, which are in turn influenced by population demographics. There is a well-known bias towards deletion in microbial genomes, which promotes genome streamlining. Less well described are mechanisms that promote genome expansion, giving rise to the many microbes, such as Streptomyces, that have unusually large genomes. We find evidence of genome expansion in Streptomyces sister-taxa, and we hypothesize that a recent demographic range expansion drove increases in genome size through a non-adaptive mechanism. These Streptomyces sister-taxa, NDR (northern-derived) and SDR (southern-derived), represent recently diverged lineages that occupy distinct geographic ranges. Relative to SDR genomes, NDR genomes are larger, have more genes, and their genomes are enriched in intermediate frequency genes. We also find evidence of relaxed selection in NDR genomes relative to SDR genomes. We hypothesize that geographic range expansion, coupled with relaxed selection, facilitated the introgression of non-adaptive horizontally acquired genes, which accumulated at intermediate frequencies through a mechanism known as genome surfing. We show that similar patterns of pangenome structure and genome expansion occur in a simulation that models the effects of population expansion on genome dynamics. We show that non-adaptive evolutionary phenomena can explain expansion of microbial genome size, and suggest that this mechanism might explain why some bacteria with large genomes can be found in soil.


title: Local genetic context shapes the function of a gene regulatory network

abstract: Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks.


title: Inter- and intra-specific variation in hair cortisol concentrations of Neotropical bats

abstract: Quantifying hair cortisol has become popular in wildlife ecology for its practical advantages for evaluating health. Before hair cortisol levels can be reliably interpreted however, it is key to first understand the intrinsic factors explaining intra- and interspecific variation. Bats are an ecologically diverse group of mammals that allow studying such variation. Given that many bat species are threatened or have declining populations in parts of their range, non-invasive tools for monitoring colony health and identifying cryptic stressors are needed to efficiently direct conservation efforts. Here we describe intra- and interspecific sources of variation in hair cortisol levels in 18 Neotropical bat species from Mexico and Belize. We found that fecundity is an important ecological trait explaining interspecific variation in bat hair cortisol. Other ecological variables such as colony size, roost durability, and basal metabolic rate did not explain hair cortisol variation among species. At the individual level, females exhibited higher hair cortisol levels than males, and the effect of body mass varied among species. Overall, our findings help validate and accurately apply hair cortisol as a monitoring tool in free-ranging bats.


title: Dynamics on the web: spiders use physical rules to solve complex tasks in mate search and competition

abstract: A long-standing question in animal behaviour is how organisms solve complex tasks. Here we explore how the dynamics of animal behaviour in the ubiquitous tasks of mate-search and competition can arise from a physics-based model of effective interactions. Male orb-weaving spiders of the genus Trichonephila are faced with the daunting challenge of entering the web of a much larger and potentially cannibalistic female, approaching her, and fending off rival males. The interactions that govern the dynamics of males within the confined two-dimensional arena of the females web are dominated by seismic vibrations. This unifying modality allows us to describe the spiders as interacting active particles, responding only to effective forces of attraction and repulsion due to the female and rival males. Our model is based on a detailed analysis of experimental spider trajectories, obtained during the approach of males towards females, and amidst their interactions with rival males of different sizes. The dynamics of spider particles that emerges from our theory allows us to explain a puzzling relationship between the density of males on the web and the reproductive advantages of large males. Our results provide strong evidence that the simple physical rules at the basis of our model can give rise to complex fitness related behaviours in this system.


title: Computationally scalable regression modeling for large-scale clinical omics data with ParProx

abstract: Statistical analysis of ultrahigh-dimensional omics scale data has long depended on univariate hypothesis testing. With growing data features and samples, the obvious next step is to establish multivariable association analysis as a routine method for understanding genotype-phenotype associations. Here we present ParProx, a state-of-the-art implementation to optimize overlapping group lasso regression models for time-to-event and classification analysis, guided by biological priors through coordinated variable selection. ParProx not only enables model fitting for ultrahigh-dimensional data within the architecture for parallel or distributed computing, but also allows users to obtain interpretable regression models consistent with known biological relationships among the independent variables, a feature long neglected in statistical modeling of omics data. We demonstrate ParProx using three different omics data sets of moderate to large numbers of variables, where we use genomic regions and pathways to arrive at sparse regression models comprised of biologically related independent variables. ParProx is naturally applicable to a wide range of studies using ultrahigh-dimensional omics data, ranging from genome-wide association analysis to single cell sequencing studies where multivariable modeling is computationally intractable.


title: Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx


title: Temporal order of mutations influences cancer initiation dynamics

abstract: Cancer is a set of genetic diseases that are driven by mutations. It was recently discovered that the temporal order of genetic mutations affects the cancer evolution and even the nature of the decease itself. The mechanistic origin of these observations, however, remain not well understood. Here we present a theoretical model for cancer initiation dynamics that allows us to quantify the impact of the temporal order of mutations. In our approach, the cancer initiation process is viewed as a set of stochastic transitions between discrete states defined by the different numbers of mutated cells. Using a first-passage analysis, probabilities and times before the cancer initiation are explicitly evaluated for two alternative sequences of two mutations. It is found that the probability of cancer initiation is determined only by the first mutation, while the dynamics is specified by both mutations. In addition, it is shown that the acquisition of a mutation with higher fitness before mutation with lower fitness increases the probability of the tumor formation but delays the cancer initiation. Theoretical results are explained using effective free-energy landscapes.


title: The Arabidopsis Calcium Sensor Calmodulin-like 38 Regulates Stress Granule Autophagy and Dynamics during Low Oxygen Stress and Re-aeration Recovery

abstract: In response to the energy crisis resulting from submergence stress and hypoxia, Arabidopsis limits non-essential mRNAs translation, and accumulate cytosolic stress granules (SG). SGs are phase-separated mRNA-protein particles that partition transcripts for various fates: storage, degradation, or return to translation after stress alleviation. Here, it is shown that RNA stress granules are dynamically regulated during hypoxia stress and aerobic recovery via two phases of autophagy that require the AAA+ ATPase CDC48 and the calcium sensor Calmodulin-like 38 (CML38). CML38 is a core hypoxia response-protein that associates with hypoxia-induced SGs. We show that CML38 is essential for SG autophagy during extended hypoxia. Further, cml38 mutants show disorganized SG morphology during extended hypoxia, suggesting a role in SG formation and maintenance. We also show that upon the return of aerobic conditions, intracellular calcium and CML38 are necessary for SG breakdown and turnover, and for upregulating autophagy. cml38 mutants not only lose these responses, but also have aberrant, sustained autophagosome accumulation during the reoxygenation recovery phase. The findings suggest that CDC48 RNA granule autophagy ("granulophagy") is conserved in plants, and that the hypoxia-induced calcium sensor CML38 regulates SG autophagy during anaerobic stress as well as during the reprogramming phase associated with reoxygenation.

category: plant biology


title: Cepo uncovers cell identity through differential stability

abstract: We present Cepo, a method to generate cell-type-specific gene statistics of differentially stable genes from single-cell RNA-sequencing (scRNA-seq) data to define cell identity. Cepo outperforms current methods in assigning cell identity and enhances several cell identification applications such as cell-type characterisation, spatial mapping of single cells, and lineage inference of single cells.


title: The sensitivity of third party punishment to the framing effect and its brain mechanism

abstract:
People as third-party observers, without direct self-interest, may punish norm violators to maintain social norms. However, third-party judgment and the follow-up punishment might be susceptible to the way we frame (i.e., verbally describe) a norm violation. We conducted a behavioral and a neuroimaging experiment to investigate the above phenomenon, which we call "third-party framing effect." In these experiments, participants observed an anonymous player A decided whether to retain her/his economic benefit while exposing player B to a risk of physical pain (described as "harming others" in one condition and "not helping others" in the other condition), then they had a chance to punish player A at their own cost. Participants were more willing to execute third-party punishment under the harm frame compared to the help frame, manifesting as a framing effect. Self-reported moral outrage toward player A mediated the relationship between empathy toward player B and the framing effect size. Correspondingly, the insula (possibly related to empathy) and cerebellum (possibly related to anger) were activated more strongly under the harm frame than the help frame. Functional connectivity between these regions showed strongest weight when predicting the framing effect size. These findings shed light on the psychological and neural mechanisms of the third-party framing effect.

Graphic abstract

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title: Rapid mechanical stimulation of inner-ear hair cells by photonic pressure

abstract: Hair cells, the receptors of the inner ear, detect sounds by transducing mechanical vibrations into electrical signals. From the top surface of each hair cell protrudes a mechanical antenna, the hair bundle, which the cell uses to detect and amplify auditory stimuli, thus sharpening frequency selectivity and providing a broad dynamic range. Current methods for mechanically stimulating hair bundles are too slow to encompass the frequency range of mammalian hearing and are plagued by inconsistencies. To overcome these challenges, we have developed a method to move individual hair bundles with photonic force. This technique uses an optical fiber whose tip is tapered to a diameter of a few micrometers and endowed with a ball lens to minimize divergence of the light beam. Here we describe the fabrication, characterization, and application of this optical system and demonstrate the rapid application of photonic force to vestibular and cochlear hair cells.


title: Distinct T cell chromatin landscapes in scleroderma subtypes

abstract: Systemic sclerosis (SSc; scleroderma) is a poorly understood autoimmune rheumatic disease that primarily affects women. The clinical hallmark is hardening of the skin, but internal organ dysfunction is the leading cause of death. Diagnosis and treatment are complicated by heterogeneity within the disease including variable lethality, fibrosis severity, serum autoantibody production, and internal organ involvement. Important gaps remain in our knowledge of the exact molecular and cellular pathways underlying distinct SSc subtypes. Herein, we identify genome-wide chromatin accessibility profiles of peripheral CD4+ T cells to distinguish and better understand the observed heterogeneity in SSc patients. We identify a link between serum anticentromere autoantibody (ACA) subtype and elevated levels of T helper 2 (Th2) cells and increased chromatin access at gene loci encoding fibrosis-driving Th2 cytokines IL4, IL13, and IL4 receptor. Biological sex followed by autoantibody subtype are the predominant variables associated with differences in CD4+ T cell epigenomic profiles, while mycophenolate mofetil treatment appeared to have no effect. These results suggest new mechanistic basis and therapeutic strategies to address SSc, especially the ACA+ subtype that is associated with pulmonary arterial hypertension.


title: Recovery of high-quality assembled genomes via single-cell genome-guided binning of metagenome assembly

abstract:
BackgroundObtaining high-quality (HQ) reference genomes from microbial communities is crucial for understanding the phylogeny and function of uncultured microbes in complex microbial ecosystems. Despite the improved bioinformatic approaches to generate curated metagenome-assembled genomes (MAGs), existing metagenomic binners often fail to obtain reliable MAGs, and thus, they are nowhere comparable to genomes sequenced from isolates in terms of strain level resolution. Here, we present a single-cell genome-guided metagenome binning (MetaSAG) to reconstruct the strain-resolved genomes from microbial communities at once.

ResultsMetaSAG employs single-cell amplified genomes (SAGs) generated with microfluidic technology as binning guides to recover improved draft genomes with the metagenomic data. To assess the performance of reconstructing genomes from various microbial communities, we compared MetaSAG with four conventional metagenomic binners using a cell mock community, human gut microbiota, and skin microbiota samples. MetaSAG showed precise contig binning and higher recovery rates (>97%) of rRNA and plasmids compared to conventional binners in genome reconstruction from the cell mock community. In human microbiota samples, MetaSAG recovered the largest number of genomes with a total of 103 gut microbial genomes (21 HQ and 65 showed >90% completeness) and 45 skin microbial genomes (10 HQ and 40 showed >90% completeness), respectively. Conventional binners recovered one Staphylococcus hominis genome, whereas MetaSAG recovered two S. hominis genomes from the identical skin microbiota sample. Single-cell sequencing indicated that these S. hominis genomes clearly derived from two distinct strains harboring specifically different plasmids. We found that all conventional S. hominis MAGs had substantial lack or excess of the genome sequences and contamination of other Staphylococcus bacteria (S. epidermidis).

ConclusionsMetaSAG enabled us to obtain the strain-resolved genomes in the mock community and human microbiota samples by assigning metagenomic sequences correctly and covering both highly conserved genes such as rRNA genes and unique extrachromosomal elements, including plasmids. MetaSAG will provide HQ genomes that are difficult to obtain with metagenomic analyses alone and will facilitate the understanding of microbial ecosystems by elucidating detailed metabolic pathways and horizontal gene transfer networks through microbial genomes. MetaSAG is available at https://github.com/kojiari/metasag.


title: Recovery of high-quality assembled genomes via metagenome binning guided with single-cell amplified genomes


title: Mobilization of antibiotic resistance genes differ by resistance mechanism

abstract: The degree to which antibiotic resistance genes (ARGs) are mobilized by insertion sequence (IS) elements, plasmids, and integrons has a strong association with their likelihood to function as resistance determinants. This stems from genetic decontextualization where strong promoters often present in IS elements and integrons and the copy number effect of plasmids contribute to high expression of accessory genes. Here, we screen all complete bacterial RefSeq genomes for ARGs. The genetic contexts of detected ARGs are investigated for IS elements, integrons, plasmids, and phylogenetic dispersion. The ARG-MOB scale is proposed which indicates how mobilized detected ARGs are in bacterial genomes. Antibiotic efflux genes are rarely mobilized and it is concluded that these are often housekeeping genes that are not decontextualized to confer resistance through overexpression. Even 80% of {beta}-lactamases have never, or very rarely, been mobilized in the 15,790 studied genomes. However, some ARGs are indeed mobilized and co-occur with IS elements, plasmids, and integrons. These results have consequences for the design and interpretation of studies screening for resistance determinants, as mobilized ARGs pose a more concrete risk to human health, especially under heterologous expression, than groups of ARGs that have only been shown to confer resistance in cloning experiments.


title: Nuclear m6A reader Ythdc1 regulates the scaffold function of LINE1 in mouse ESCs

abstract: N6-methyladenosine (m6A) on chromosome-associated regulatory RNAs (carRNAs), including repeat RNAs, play important roles in tuning the chromatin state and transcription1. Among diverse RNA-chromatin interacting modes, the nuclear RNA scaffold is considered important for trans-interactions2,3 but has not yet been connected with m6A yet. Here, we found that Ythdc1 played indispensable roles in the embryonic stem cell (ESC) self-renewal and differentiation potency, and these roles highly depended on its m6A-binding ability. Ythdc1 deficiency in ESCs resulted in decreased rRNA synthesis and the activation of 2-cell (2C) embryo-specific transcriptional program, and these observations recapitulated the transcriptome defects induced by dysfunction of the long interspersed nuclear element-1 (LINE1)-scaffold, which were unrelated to the direct targeting of Ythdc1. A detailed analysis revealed that Ythdc1 recognized m6A on LINE1 and was physically involved in the formation of the LINE1-Nucleolin partnership and the chromatin recruitment of Kap1. In summary, our study reveals a new link between m6A and the RNA scaffold and thus provides a new regulatory model for the crosstalk between RNA and the chromatin epigenome.


title: Mitofusins 1 and 2 collaborate to fuel pancreatic beta cell insulin release via regulation of both mitochondrial structure and DNA content

abstract: The dynamin-like GTPases Mitofusin 1 and 2 (Mfn1 and Mfn2) are essential for mitochondrial function, which has been principally attributed to their regulation of fission/fusion dynamics. Here, we report that Mfn1 and 2 are critical for glucose-stimulated insulin secretion (GSIS) primarily through control of mitochondrial DNA (mtDNA) content. Whereas Mfn1 and Mfn2 individually were dispensable for glucose homeostasis, combined Mfn1/2 deletion in {beta}-cells reduced mtDNA content, impaired mitochondrial morphology and networking, and decreased respiratory function, ultimately resulting in severe glucose intolerance. Importantly, gene dosage studies unexpectedly revealed that Mfn1/2 control of glucose homeostasis was dependent on maintenance of mtDNA content, rather than mitochondrial structure. Mfn1/2 maintain mtDNA content by regulating the expression of the crucial mitochondrial transcription factor Tfam, as Tfam overexpression ameliorated the reduction in mtDNA content and GSIS in Mfn1/2-deficient {beta}-cells. Thus, the primary physiologic role of Mfn1 and 2 in {beta}-cells is coupled to the preservation of mtDNA content rather than mitochondrial architecture, and Mfn1 and 2 may be promising targets to overcome mitochondrial dysfunction and restore glucose control in diabetes.


title: Mitofusin 1 and 2 regulation of mitochondrial DNA content is a critical determinant of glucose homeostasis


title: Is earlier reproduction associated with higher or lower survival? Antagonistic results between individual and population scales in the blue tit

abstract: Although it has been shown that phenology can respond to temporal environmental variation in free ranging populations of several species, little is known about the mechanisms of these responses and their effects on demography, and in particular on survival. Exploring phenological responses and their associated consequences on survival can be achieved at two distinct scales: the population scale, which focusses on a set of common responses to environmental conditions, and the individual scale, focusing on the relative position of each individual in the distribution of survival and phenology under particular conditions. In this study, we apply capture-mark-recapture multistate modelling on a 38-year monitoring dataset of blue tits (Cyanistes caeruleus) to investigate the effects of breeding phenology and some demographic covariates (breeding density, average and individual breeding success) on adult survival, at both population and individual scales. Our analysis revealed that (i) at the population scale, early breeding years are followed by lower average adult survival. (ii) At the individual level, earlier breeders within the population have higher subsequent survival than later breeders, although this relationship is reversed in years with very harsh conditions, e.g. warm spring and high breeding density. (iii) High individual relative breeding success is also associated with higher subsequent survival and explains more survival variation than relative phenology. Overall, our study indicates that, although earlier breeding is associated with a survival cost at the population level, substantial intrapopulation hererogeneity shapes a positive association between earlier breeding, breeding success and survival at the individual level.


title: High regional and intra-generic variation in susceptibility to mass bleaching in Indo-Pacific coral species

abstract:
AimMass bleaching is a major threat to reef-building corals and the ecosystems they underpin. Here, we identified regional variation in the nature of this threat in terms of the bleaching-susceptibility of individual coral species on some Indian Ocean and Pacific Ocean reefs.

Location22 sites in the central Great Barrier Reef, Australia (GBR) and 30 sites in the central Maldives Archipelago (MA).

Time period2002 for the GBR and 2016 for the MA.

Major taxa studiedCorals (Order Scleractinia).

MethodsFollowing marine heat-wave conditions, timed in-situ surveys were used to record bleaching responses (tissue colour) of large samples of individual coral colonies. Responses of 106 shared species were analysed for sites with similar levels of temperature stress, depth of occurrence and mortality. In each region, phylogenetic mixed models were used to partition the effects on responses of species of deep-time phylogeny, contemporary history and local-scale, among-site variability.

ResultsRelative susceptibility to bleaching varied widely between regions: only 27 of the 106 shared species were in the same quartile for relative susceptibility in both regions. Few species were highly susceptible in both regions. Closely related species varied widely in their individual susceptibilities. Phylogenetic effects were moderate in both regions, but contemporary phenotypic effects indicative of recent evolution and acclimatization were greater in the MA, consistent with a stronger history of recent bleaching.

Main conclusionsThe high regional and intra-generic variation in coral bleaching-susceptibility described here suggests there may be important differences in the extent to which these Indian and Pacific Ocean coral populations are exhibiting responses to deep-time evolutionary changes on the one hand, versus recent adaptation, on the other. There is a concerning scarcity of this type of data, by which coral species most at risk from bleaching in particular regions may be more accurately identified.


title: Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat

abstract: Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite of its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGAtAt genepool and its domestication history would further its use for wheat improvement. We report the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGAtAt genepool. We show that the extant GGAtAt genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGAtAt wheats, revealed group-, and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. We discuss the origin and domestication history of the GGAtAt lineages in the context of state-of-the-art archaeobotanical finds. We shed new light on the complex evolutionary history of the GGAtAt wheat genepool. We provide the basis for an increased use of the GGAtAt wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.


title: anonymizeBAM: Versatile anonymization of human sequence data for open data sharing

abstract: The risks associated with re-identification of human genetic data are severely limiting open data sharing in life sciences. Here, we developed anonymizeBAM, a versatile tool for the anonymization of genetic variant information present in sequence data. Applying anonymizeBAM to single-cell RNA-seq and ATAC-seq datasets confirmed the complete removal of donor-related genetic information. Therefore, the accurate generation of de-identified sequence data will re-enable open sharing in sequencing-based studies for improved transparency, reproducibility, and innovation.


title: Biop-C: A Method for Chromatin Interactome Analysis of Solid Cancer Needle Biopsy Samples

abstract: A major challenge in understanding the 3D genome organization of cancer samples is the lack of a method adapted to solid cancer needle biopsy samples. Here we developed Biop-C, a modified in situ Hi-C method, and applied it to characterize three nasopharyngeal cancer patient samples. We identified Topologically-Associated Domains (TADs), chromatin interaction loops, and Frequently Interacting regions (FIREs) at key oncogenes in nasopharyngeal cancer from Biop-C heat maps. Our results demonstrate the utility of our Biop-C method in investigating the 3D genome organization in solid cancers, and the importance of 3D genome organization in regulating oncogenes in nasopharyngeal cancer.


title: Deciphering 3D Human Sphygmopalpation Pulse Patterns using "X-ray" Images Acquired from Tactile Robotic Fingers

abstract: Sphygmopalpation at specific locations of human wrists has been used as a medical measurement technique in China since the Han Dynasty (202 BC - 220 AD); it is now generally accepted that traditional Chinese medicine (TCM) doctors are able to decipher 28 types of basic pulse patterns using their fingertips. This TCM technique of examining individual arterial pulses by palpation has undergone an upsurge recently in popularity as a low-cost and non-invasive diagnostic technique for monitoring patient health status. We have developed a pulse sensing platform for studying and digitalizing arterial pulse patterns via a TCM approach. This platform consists of a robotic hand with three fingers for pulse measurement and an artificial neural network (ANN) together with pulse signal preprocessing for pulse pattern recognition. The platforms previously reported by other research groups or marketed commercially exhibit one or more of the following imperfections: a single channel for data acquisition, low sensitivity and rigid sensors, lack of control of the applied pressure, and in many reported works, lack of an intelligent data analysis system. The platform presented here features up to three-dimensional (3D) tactile sensing channels for recording data and uses highly sensitive capacitive MEMS (microelectromechanical systems) flexible sensing arrays, pressure-feedback-controlled robotic fingers, and machine learning algorithms. We also proposed a methodology of obtaining "X-ray" image of pulse information constructed based on the sensing data from 3 locations and 3 applied pressures (i.e., mimicking TCM doctors), which contains all arterial pulse information in both spatial and temporal spans, and which could be used as an input to a deep learning algorithm. By applying our developed platform and algorithms, 3 types of consistent pulse patterns, i.e., "Hua" [Formula], "Xi" [Formula], and "Chen" [Formula], as described by TCM doctors", could be identified in a selected group of 3 subjects who were diagnosed by TCM practitioners. We have shown the classification rates is 98.7% in training process and 84.2% in testing result for these 3 basic pulse patterns. The high classification rate of the developed platform could lead to further development of a high-level artificial intelligence system incorporating knowledge from TCM - the robotics finger system could become a standard clinical equipment for digitalizing and visualizing human arterial pulses

category: bioengineering


title: A bioreactor for controlled electromechanical stimulation of developing scaffold-free constructs

abstract:
Bioreactors are commonly used to apply biophysically-relevant stimulations to tissue-engineered constructs in order to explore how these stimuli influence tissue development, healing, and homeostasis. These bioreactors offer great flexibility as key features of the stimuli (e.g., duty cycle, frequency, amplitude, duration) can be controlled to elicit a desired cellular response. Controlled delivery of mechanical and/or electrical stimulation has been shown to improve the structure and function of engineered tissue constructs, compared to unstimulated controls, for applications in various musculoskeletal soft tissues. However, most bioreactors that apply mechanical and electrical stimulations, do so to a scaffold after the construct has developed, preventing study of the influence these stimuli have on early construct development. Thus, there is a need for a bioreactor that allows the direct application of mechanical and electrical stimulation to constructs as they develop, to enable such exploration and to better mimic key aspects of tissue development. Hence, the objective of this study was to develop and calibrate a bioreactor to deliver precise mechanical and electrical stimulation, either independently or in combination, to developing scaffold-free tissue constructs. Standard Flexcell Tissue Train plates were modified with stainless steel loading pins and stimulating electrodes to integrate direct mechanical and electrical stimulation, respectively, into our established scaffold-free, single-fiber engineering platform. Linear calibration curves were established, then used to apply precise dynamic mechanical and electrical stimulations, over a range of physiologically relevant strains (0.50, 0.70, 0.75, 1.0, 1.5%) and voltages (1.5, 3.5 V), respectively. Once calibrated, applied mechanical and electrical stimulations were not statistically different from their desired target values, and were consistent whether delivered independently or in combination. Indeed, concurrent delivery of mechanical and electrical stimulation resulted in a negligible change in mechanical (< 2%) and electrical (<1%) values, from their independently-delivered values. With this calibrated bioreactor, we can apply precise, controlled, reproducible mechanical and electrical stimulations, alone or in combination, to scaffold-free, tissue engineered constructs as they develop, to explore how these stimuli can be leveraged to advance and accelerate functional tissue engineering in a variety of musculoskeletal soft tissues.

IMPACT STATEMENTAs the importance of biophysical stimulation in tissue engineering continues to be recognized and incorporated, this bioreactor provides a platform to further our understanding of the roles independent or combined mechanical and electrical stimulation have in tissue development and functional maturation, and may inform future tissue engineering approaches for clinical applications.


title: PepNN: a deep attention model for the identification of peptide binding sites

abstract: Protein-peptide interactions play a fundamental role in facilitating many cellular processes, but remain underexplored experimentally and difficult to model computationally. Here, we present PepNN-Struct and PepNN-Seq, structure and sequence-based approaches for the prediction of peptide binding sites on a protein given the sequence of a peptide ligand. A main difficulty for the prediction of peptide-protein interactions is the flexibility of peptides and their tendency to undergo conformational changes upon binding. To account for this behaviour, we developed a novel reciprocal attention module that simultaneously updates the encodings of peptide and protein residues and explicitly enforces the symmetry in the updates, allowing for information flow and reflecting the biochemical reality of conformational changes in the peptide. PepNN additionally makes use of modern graph neural network layers that are effective at learning representations of molecular structure. Finally, to compensate for the scarcity of peptide-protein complex structural information, we make use of available protein-protein complex and protein sequence information through a series of transfer learning steps. PepNN-Struct achieves state-of-the-art performance on the task of identifying peptide binding sites, with a ROC AUC of 0.893 and an MCC of 0.483 on an independent test set. Beyond prediction of binding sites on proteins with a known peptide ligand, we also show that the developed models make reasonable peptide-agnostic predictions, allowing for the identification of novel peptide binding proteins.


title: COT: an efficient Python tool for detecting marker genes among many subtypes

abstract: We develop an accurate and efficient method to detect marker genes among many subtypes using subtype-enriched expression profiles. We implement a Cosine based One-sample Test (COT) Python software that is easy to use and applicable to multi-omics data. We demonstrate the performance and utility of COT on gene expression and proteomics data acquired from tissue or cell subtypes. Formulated as a one-sample test with Cosine similarity test statistic in scatter space, the detected de novo marker genes will allow biologists to perform a more comprehensive and unbiased molecular characterization, deconvolution and classification of complex tissue or cell subtypes.


title: Native structure of the RhopH complex, a key determinant of malaria parasite nutrient acquisition

abstract: The RhopH complex is implicated in malaria parasites ability to invade and create new permeability pathways in host erythrocytes, but its mechanisms remain poorly understood. Here we enrich the endogenous RhopH complex in a native soluble form, comprising RhopH2, CLAG3.1 and RhopH3, directly from parasite cell lysates and determine its atomic structure using cryo electron microscopy, mass spectrometry, and the cryoID program. This first direct observation of an exported P. falciparum transmembrane protein--in a soluble, trafficking state and with atomic details of buried putative membrane-insertion helices--offers insights into assembly and trafficking of RhopH and other parasite-derived complexes to the erythrocyte membrane. Our study demonstrates the potential endogenous structural proteomics approach holds for elucidating the molecular mechanisms of hard-to-isolate complexes in their native, functional forms.


title: Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region

abstract:
The T cell antigen receptor (TCR-CD3) complex initiates T cell activation following recognition of peptides presented by Major Histocompatibility Complex (pMHC)-encoded proteins. The ligation of pMHC to TCR{beta} induces Src family kinases activity via the cytoplasmic tails of the CD3{delta}{varepsilon}, CD3{gamma}{varepsilon} and {zeta}{zeta} dimers. The TCR-CD3 topology is well understood, but little is known about its conformational dynamics and arrangement of its cytoplasmic tails, limiting our grasp of the signalling mechanism. Here, we investigated the entire TCR-CD3 embedded in an asymmetric lipid bilayer using molecular modelling and multi-scale molecular dynamics simulations. Our study demonstrates conformational changes in the extracellular and transmembrane domains, and the arrangement of the TCR-CD3 cytoplasmic tails. The TCR{beta} variable regions were the most flexible in the extracellular domain. The cytoplasmic tails formed highly interlaced structures while some tyrosine sidechains within the immunoreceptor tyrosine-based activation motifs (ITAMs) of the CD3{varepsilon} and {zeta} subunits dynamically penetrated the hydrophobic core of the bilayer. Ionic interactions between the cytoplasmic tails and phosphatidylinositol phosphates (PIP2 and PIP3) in the inner leaflet of the lipid bilayer led to the formation of a distinct annular lipid fingerprint around the TCR-CD3 complex. These results combined with available experiential data increase our understanding of the TCR-CD3 activation mechanism and highlight the importance of membrane lipids in regulating T cell activation.

Significance statementThe T cell receptor (TCR-CD3) detects antigenic peptides displayed by major histocompatibility complexes (pMHC) to instigate activation of T cell adaptive immunity. Despite significant structural and functional knowledge of TCR-CD3 topology, the membrane interactions and dynamics of its cytoplasmic moieties remain elusive. Interactions of TCR-CD3 cytoplasmic tails with membrane lipids may regulate their phosphorylation by Src-family kinases, the first intracellular event required for T cell activation. Using the static 3D structure of TCR-CD3 resolved by cryo-electron microscopy, we provide novel insights into the protein-lipid interactions of the complete TCR-CD3 embedded in a bilayer closely mimicking its native membrane environment. Our study sheds light on the dynamics of the TCR-CD3 at near-atomic resolution and further aids in deciphering its activation mechanism.


title: Hydroxyapatite pellets as versatile model surfaces for systematic studies on enamel

abstract: Research into materials for medical application draws inspiration from naturally occurring or synthesized surfaces, just like many other research directions. For medical application of materials, particular attention has to be paid to biocompatibility, osseointegration and bacterial adhesion behavior. To understand their properties and behavior, experimental studies with natural materials such as teeth are strongly required. The results, however, may be highly case-dependent because natural surfaces have the disadvantage of being subject to wide variations, for instance in their chemical composition, structure, morphology, roughness, and porosity. A synthetic surface which mimics enamel in its performance with respect to bacterial adhesion and biocompatibility would, therefore, facilitate systematic studies much better. In this study, we discuss the possibility of using hydroxyapatite (HAp) pellets to simulate the surfaces of teeth and show the possibility and limitations of using a model surface. We performed single-cell force spectroscopy with single Staphylococcus aureus cells to measure adhesion-related parameters such as adhesion force and rupture length of adhesins binding to HAp and enamel. We also examine the influence of blood plasma and saliva on the adhesion properties of S. aureus. The results of these measurements are matched to water wettability, elemental composition of the samples and the change in the macromolecules adsorbed over time. We found that the adhesion properties of S. aureus were similar on both samples under all conditions: Significant decreases in adhesion strength were found equally in the presence of saliva or blood plasma on both surfaces. We therefore conclude that HAp pellets are a good alternative for natural dental material. This is especially true when slight variations in the physicochemical properties of the natural materials may affect the experimental series.


title: Transcriptomic analyses of MYCN-regulated genes in anaplastic Wilms' tumour cell lines reveals oncogenic pathways and potential therapeutic vulnerabilities

abstract:
The MYCN proto-oncogene is deregulated in many cancers, most notably in neuroblastoma where MYCN gene amplification identifies a clinical subset with very poor prognosis. Gene expression and DNA analyses have also demonstrated over-expression of MYCN mRNA, as well as focal amplifications, copy number gains and presumptive change of function mutations of MYCN in Wilms tumours with poorer outcome, including tumours with diffuse anaplasia. Surpisingly, however, the expression and functions of the MYCN protein in Wilms tumours still remain obscure.

In this study, we assessed MYCN protein expression in primary Wilms tumours using immunohistochemistry of tissue microarrays. We found MYCN protein to be expressed in tumour blastemal cells, and absent in stromal and epithelial components. For functional studies, we used two anaplastic Wilms tumour cell-lines, WiT49 and 17.94, to study the biological and transcriptomic effects of MYCN depletion. We found that MYCN knockdown consistently led to growth suppression but not cell death. RNA sequencing identified 561 MYCN-regulated genes shared by WiT49 and 17.94 cell-lines. As expected, numerous cellular processes were downstream of MYCN. MYCN positively regulated the miRNA regulator and known Wilms tumour oncogene LIN28B, the genes encoding methylosome proteins PRMT1, PRMT5 and WDR77, and the mitochondrial translocase genes TOMM20 and TIMM50. MYCN repressed genes included the developmental signalling receptor ROBO1 and the stromal marker COL1A1.

Importantly, we found that MYCN also repressed the presumptive Wilms tumour suppressor gene REST, with MYCN knockdown resulting in increased REST protein and concomitant repression of REST target genes. Together, our study identifies regulatory axes that interact with MYCN, providing novel pathways for potential targeted therapeutics for poor prognosis Wilms tumour.


title: The PELOTA-HBS1 Complex Orchestrates mRNA Translation Surveillance and PDK1-mediated Plant Growth and Development

abstract: The quality control system for messenger RNA is fundamental for cellular activities in eukaryotes. To elucidate the molecular mechanism of 3-Phosphoinositide-Dependent Protein Kinase1 (PDK1), an essential regulator throughout growth and development of eukaryotes, a forward genetic approach was employed to screen for suppressors of the loss-of-function T-DNA insertional pdk1.1 pdk1.2 double mutant in Arabidopsis. Notably, the severe growth attenuation of pdk1.1 pdk1.2 is rescued by sop21 (suppressor of pdk1.1 pdk1.2) that harbours a loss-of-function mutation in PELOTA1 (PEL1). PEL1 is a homologue of mammalian PELOTA and yeast DOM34, which form a heterodimeric complex with the GTPase HBS1, responsible for ribosome rescue to assure the quality and fidelity of mRNA molecules. Genetic analysis further reveals that the dysfunction of PEL1-HBS complex fails to degrade the T-DNA-disrupted, truncated but functional PDK1 transcripts, thus rescuing pdk1.1 pdk1.2. Our studies demonstrate the functionality and identify the essential functions of a homologous PELOTA-HBS1 complex in higher plant, and provide novel insights into the mRNA quality control mechanism.


title: The pathway of starch synthesis in Arabidopsis thaliana leaves

abstract:
Many plants accumulate transitory starch reserves in their leaves during the day to buffer their carbohydrate supply against fluctuating light conditions, and to provide carbon and energy for survival at night. It is universally accepted that transitory starch is synthesized from ADP-glucose (ADPG) in the chloroplasts. However, the consensus that ADPG is made in the chloroplasts by ADPG pyrophosphorylase has been challenged by a controversial proposal that ADPG is made primarily in the cytosol, probably by sucrose synthase (SUS), and then imported into the chloroplasts. To resolve this long-standing controversy, we critically re-examined the experimental evidence that appears to conflict with the consensus pathway. We show that when precautions are taken to avoid artefactual changes during leaf sampling, Arabidopsis thaliana mutants that lack SUS activity in mesophyll cells (quadruple sus1234) or have no SUS activity (sextuple sus123456) have wild-type levels of ADPG and starch, while ADPG is 20 times lower in the pgm and adg1 mutants that are blocked in the classical pathway of starch synthesis. We conclude that the ADPG needed for starch synthesis in leaves is synthesized primarily by ADPG pyrophosphorylase in the chloroplasts.

Significance statementMutant analysis shows that sucrose synthase makes no significant contribution to transitory starch synthesis in Arabidopsis leaves, resolving a 20-year old controversy about one of the most important pathways of photosynthetic metabolism.


title: The Flowering Time Regulator FLK Controls Pathogen Defense in Arabidopsis thaliana

abstract: Plant disease resistance is a complex process that is maintained in an intricate balance with development. Increasing evidence indicates the importance of post-transcriptional regulation of plant defense by RNA binding proteins. The K homology (KH) repeat is an ancient RNA binding motif found in proteins from diverse organisms. The role of KH domain proteins in pathogen resistance is not well known. From a genetic screen aimed to uncover novel defense genes in Arabidopsis, we identified a new allele of the canonical flowering regulatory gene, FLOWERING LOCUS KH Domain (FLK), encoding a putative triple KH-repeat protein. In addition to late flowering, the flk mutants exhibited decreased resistance to the bacterial pathogen Pseudomonas syringae and increased resistance to the necrotrophic fungal pathogen Botrytis cinerea. We found that the flk mutations compromised basal defense and defense signaling mediated by salicylic acid and led to increased reactive oxygen species (ROS) scavenging, likely through FLKs regulation of the ROS scavenging enzyme catalases. RNA-seq data revealed that major defense signaling genes are regulated by FLK, providing a molecular basis for FLKs contribution to pathogen defense. Together our data support that FLK is a multifunctional protein regulating pathogen defense and development of plants.


title: Cell-Free Characterization of Coherent Feed-Forward Loop-Based Synthetic Genetic Circuit

abstract: Regulatory pathways inside living cells employ feed-forward architectures to fulfill essential signal processing functions that aide in the interpretation of various types of inputs through noise-filtering, fold-change detection and adaptation. Although it has been demonstrated computationally that a coherent feed-forward loop (CFFL) can function as noise filter, a property essential to decoding complex temporal signals, this motif has not been extensively characterized experimentally or integrated into larger networks. Here we use post-transcriptional regulation to implement and characterize a synthetic CFFL in an Escherichia coli cell-free transcription-translation system and build larger composite feed-forward architectures. We employ microfluidic flow reactors to probe the response of the CFFL circuit using both persistent and short, noise-like inputs and analyze the influence of different circuit components on the steady-state and dynamics of the output. We demonstrate that our synthetic CFFL implementation can reliably repress background activity compared to a reference circuit, but displays low potential as a temporal filter, and validate these findings using a computational model. Our results offer practical insight into the putative noise-filtering behavior of CFFLs and show that this motif can be used to mitigate leakage and increase the fold-change of the output of synthetic genetic circuits.

category: synthetic biology


title: Real-Time Three-Dimensional Tracking of Single Vesicles Reveals the Abnormal Motion and Vesicle Pools of Synaptic Vesicles in Neurons of Huntington's Disease Mice

abstract: Although defective synaptic transmission was suggested to play a role in neurodegenerative diseases, the dynamics and vesicle pools of synaptic vesicles during neurodegeneration remain elusive. Here, we performed real-time three-dimensional tracking of single synaptic vesicles in cortical neurons from a mouse model of Huntingtons disease (HD). Vesicles in HD neurons had a larger net displacement and radius of gyration compared with wild-type neurons. Vesicles with a high release probability (Pr) were interspersed with low-Pr vesicles in HD neurons, whereas high-Pr and low-Pr vesicle pools were spatially separated in wild-type neurons. Non-releasing vesicles in HD neurons had an abnormally high prevalence of irregular oscillatory motion. These abnormal dynamics and vesicle pools were rescued by overexpressing Rab11, and the abnormal irregular motion was rescued by jasplakinolide. These results suggest the abnormal dynamics and vesicle pools of synaptic vesicles in the early stages of HD, suggesting a possible pathogenic mechanism of neurodegenerative diseases.

category: neuroscience