title: Structure of mycobacterial CIII2CIV2 respiratory supercomplex bound to the tuberculosis drug candidate telacebec (Q203)

abstract: The imidazopyridine telacebec, also known as Q203, is one of only a few new classes of compounds in more than fifty years with demonstrated antituberculosis activity in humans. Telacebec inhibits the mycobacterial respiratory supercomplex composed of complexes III and IV (CIII2CIV2). In mycobacterial electron transport chains, CIII2CIV2 replaces canonical CIII and CIV, transferring electrons from the intermediate carrier menaquinol to the final acceptor, molecular oxygen, while simultaneously transferring protons across the inner membrane to power ATP synthesis. We show that telacebec inhibits the menaquinol:oxygen oxidoreductase activity of purified Mycobacterium smegmatis CIII2CIV2 at concentrations similar to those needed to inhibit electron transfer in mycobacterial membranes and Mycobacterium tuberculosis growth in culture. We then used electron cryomicroscopy (cryoEM) to determine structures of CIII2CIV2 both in the presence and absence of telacebec. The structures suggest that telacebec prevents menaquinol oxidation by blocking two different menaquinol binding modes to prevent CIII2CIV2 activity.


title: Ca2+-dependent liquid-liquid phase separation underlies intracellular Ca2+ stores.

abstract: Endoplasmic/sarcoplasmic reticulum Ca2+ stores are essential to myriad cellular processes, however, the structure of these stores is largely unknown and existing models neither explain observations made in vivo nor sufficiently account for physiological data. We investigate CASQ1 - the major Ca2+ binding protein of skeletal muscle - and discover Ca2+-dependent liquid-liquid phase separation activity. The intrinsic disorder of CASQ1 underlies this activity and is regulated via phosphorylation by the secretory pathway kinase FAM20C. This novel divalent cation driven condensation demonstrates liquid-liquid phase separation occurs within the endoplasmic/sarcoplasmic reticulum, mechanistically explains efficient Ca2+ buffering and storage, and represents a largely unexplored mechanism of divalent-cation driven protein association.

category: biochemistry


title: The fruit fly Anastrepha obliqua harbors three kingdoms of life in its intestinal tract.

abstract: The fruit fly Anastrepha obliqua is an economically important pest for mango fruits in Mexico. The sterile insect technique is used to control this pest; it involves mass production and release of sterile flies to reduce reproduction of the wild population. As noted in different tephritidae, the performance of sterile males may be affected by the assimilation of nutrients under mass-rearing conditions. In the wild, the flys life cycle suggests the acquisition of different organisms that could modulate fitness and physiology of the fly. Therefore, the microorganisms lodged in the gut may be determinative. For A. obliqua, there is no information regarding microorganisms other than bacteria. This study analyzed bacteria, fungi, and archaea communities in the A. obliqua gut through denaturing gradient gel electrophoresis (DGGE) profile of 16S and 18S ribosomal DNA markers. Besides, 16S sequencing and phylogenetic analysis provided a better description of bacteria, and archaea communities. We found that wild flies presented higher microbial diversity than laboratory samples. Phylogeny analyses of wild samples suggest the presence of microbial species related to fructose assimilation while laboratory microbial species suggest the presence of microorganisms leading to a specialized metabolism to process yeast as result of the consumption of an artificial diet. Here, the archaea kingdom is suggested as an important player in fly metabolism. This is the first report of the intestinal microbial (bacteria, archaea and fungi) composition of A. obliqua, which will aid in our understanding of the role of microorganisms in the development and physiology of the flies.

category: microbiology


title: Dietary Exposure to Antibiotic Residues Facilitates Metabolic Disorder by Altering the Gut Microbiota and Bile Acid Composition

abstract:
Antibiotics used as growth promoters in livestock and animal husbandry can be detected in animal-derived food. Epidemiological studies have implicated that exposure to these antibiotic residues in food may be associated to childhood obesity. Herein, the effect of exposure to residual dose of tylosin--an antibiotic growth promoter--on host metabolism and gut microbiota was explored in vivo. Theoretical maximal daily intake (TMDI) doses of tylosin were found to facilitate high-fat diet-induced obesity, induce insulin resistance, and perturb the composition of gut microbiota in mice. The obesity-related phenotypes were transferrable to germ-free recipient mice, indicating that the effects of TMDI dose of tylosin on obesity and insulin resistance occurred mainly via alteration of the gut microbiota. Tylosin TMDI exposure restricted to early life, which is the critical period of gut microbiota development, altered the abundance of specific bacteria related to host metabolic homeostasis later in life. Moreover, early-life exposure to tylosin TMDI was sufficient to modify the ratio of primary to secondary bile acids, thereby inducing lasting metabolic consequences via the downstream FGF15 signaling pathway. Altogether, these findings demonstrate that exposure to very low dose of antibiotic residues, whether continuously or in early life, can exert long-lasting effects on host metabolism by altering gut microbiota and its metabolites.

ImportanceEvidence has indicated that chronic exposure to antibiotic residues in food could contribute to obesity. However, few studies have investigated the effect of chronic exposure to very low-dose antibiotic residue in food (~1000-fold lower than the therapeutic dose) on gut microbiota and host metabolism. Our study demonstrates that even with limited exposure in early life, a residual dose of tylosin causes lasting metabolic disturbances through altering gut microbiota and its metabolites. Our findings reveal that the gut microbiota is susceptible to previously ignored environmental factors.


title: Light-dependent synthesis of a nucleotide second messenger controls bacterial motility

abstract: Nucleotide second messengers are universally crucial factors for the signal transduction of various organisms. In prokaryotes, cyclic nucleotide messengers are involved in the bacterial life cycle and function, such as virulence, biofilm formation, and others mainly via gene regulation. Here we show that the swimming motility of a soil bacterium is rapidly modulated by cyclic adenosine monophosphate (cAMP) synthesized upon light exposure. Analysis of a loss-of-photoresponsivity mutant obtained by transposon random mutagenesis determined the novel sensory gene, and its expression in Escherichia coli through codon optimization revealed the light-dependent synthesis of cAMP. GFP labeling showed the localization of the photoresponsive enzyme at the cell poles where flagellar motors reside. The present findings highlight the new role of cAMP that rapidly controls the flagella-dependent bacterial motility and the global distribution of the discovered photoactivated cyclase among diverse microbial species.


title: Life on leaves : uncovering temporal dynamics in Arabidopsis' leaf microbiota

abstract: Leaves are primarily responsible for the plants photosynthetic activity. Thus, changes in the phyllosphere microbiota, which includes deleterious and beneficial microbes, can have far reaching effects on plant fitness and productivity. In this context, identifying the processes and microorganisms that drive the changes in the leaf microbiota over a plants lifetime is crucial. In this study we analyzed the temporal dynamics in the leaf microbiota of Arabidopsis thaliana, integrating both compositional changes and changes in microbe-microbe interactions via the study of microbial networks. Field-grown Arabidopsis were used to follow leaf bacterial, fungal and oomycete communities, throughout the plants growing season (extending from November to March), over three consecutive years. Our results revealed the existence of conserved time patterns, with microbial communities and networks going through a stabilization phase (decreasing diversity and variability) at the beginning of the plants growing season. Despite a high turnover in these communities, we identified 19  core taxa persisting in Arabidopsis leaves across time and plant generations. With the hypothesis these microbes could be playing key roles in the structuring of leaf microbial communities, we conducted a time-informed microbial network analysis which showed core taxa are not necessarily highly connected network  hubs and  hubs alternate with time. Our study shows that leaf microbial communities exhibit reproducible dynamics and patterns, suggesting it could be possible to predict and drive these microbial communities to desired states.


title: Development of Kaptive databases for Vibrio parahaemolyticus O- and K-antigen serotyping

abstract: Vibrio parahaemolyticus is an important food-borne human pathogen and is divided in 16 O-serotypes and 71 K-serotypes. Agglutination tests are still the gold standard for serotyping, but many V. parahaemolyticus isolates are not typable by agglutination. An alternative for agglutination tests is serotyping using genome sequence data. In this study, we manually identified all known O- and K-loci from V. parahaemolyticus isolates which we serotyped and sequenced, and extracted additional O- and K-loci from publicly available genomes. We developed Kaptive databases for all O- and K-loci after manual curation of the loci. These Kaptive databases with the identified V. parahaemolyticus O- and K -loci can be used to identify the O- and K-serotypes of V. parahaemolyticus isolates from genome sequences.


title: Gut-derived metabolites influence neurodevelopmental gene expression and Wnt signalling events in a germ-free zebrafish model

abstract: Small molecule metabolites produced by the microbiome are known to be neuroactive and are capable of directly impacting the brain and central nervous system, yet there is little data on the contribution of these metabolites to the earliest stages of neural development and neural gene expression. Here, we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. Overall, we did not observe any gross morphological changes between treatments but did observe a significant decrease in neural gene expression in embryos raised germ-free, which was rescued with the addition of zebrafish metabolites. Specifically, we identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA-Seq analysis. Of these, 42 were rescued with the treatment of zebrafish gut-derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Consistent with the ontology analysis, we found alterations in the development of Wnt dependent events which is rescued in the GF embryos treated with metabolites.

category: molecular biology


title: Cdt1 inhibits CMG helicase in early S phase to separate origin licensing from DNA synthesis

abstract:
A fundamental concept in eukaryotic DNA replication is the temporal separation of G1 origin licensing from S phase origin firing. Re-replication and genome instability ensue if licensing occurs after DNA synthesis has started. In humans and other vertebrates, the E3 ubiquitin ligase CRL4Cdt2 starts to degrade the licensing factor Cdt1 after origins fire, raising the question of how cells prevent re-replication in early S phase. Here, using quantitative microscopy, we show that Cdt1 inhibits DNA synthesis during an overlap period when cells fire origins while Cdt1 is still present. Cdt1 inhibits DNA synthesis by suppressing CMG helicase progression at replication forks through the MCM-binding domain of Cdt1, and DNA synthesis commences once Cdt1 is degraded. Thus, instead of separating licensing from firing to prevent re-replication in early S phase, cells separate licensing from DNA synthesis through Cdt1-mediated inhibition of CMG helicase after firing.

Highlights- Cdt1 is present together with fired origins of replication at the start of S phase
- Cdt1 delays DNA synthesis by inhibiting CMG helicase progression after origins fire
- Cdt1 inhibits CMG helicase progression through the MCM-binding domain of Cdt1

category: cell biology


title: CatSper mediates the chemotactic behavior and motility of the ascidian sperm

abstract: Sperm motility, including chemotactic behavior, is regulated by changes in the intracellular Ca2+ concentration. The cation channel of sperm (CatSper), plays an important role in the regulation of intracellular Ca2+ concentration. In mammals, CatSper is the only Ca2+ channel that functions in the sperm, and the mice that lack the genes for the subunits of CatSper, which make up the pore region of the Ca2+ channel, are infertile due to the inhibition of hyperactivation of the sperm. CatSper is also thought to be involved in chemotaxis in sea urchins. In contrast, in the ascidian, Ciona intestinalis, the sperm-activating and -attracting factor (SAAF) interacts with Ca2+/ATPase, which is a Ca2+-pump. Although the existence of CatSper genes has been reported, it is not clear whether CatSper is the specific Ca2+ channel that functions in the ascidian sperm. Therefore, in this study, we generated Catsper3 knockout (KO) animals that found that they were significantly less motile, with few motile sperms not exhibiting any chemotactic behavior. These results suggest that CatSper plays important roles in the spermatogenesis and basic motility mechanisms of sperms in both ascidians and mammals.

category: developmental biology


title: Constitutive gene expression differs in three brain regions important for cognition in neophobic and non-neophobic house sparrows (Passer domesticus)

abstract: Neophobia (aversion to new objects, food, and environments) is a personality trait that affects the ability of wildlife to adapt to new challenges and opportunities. Despite the ubiquity and importance of this trait, the molecular mechanisms underlying repeatable individual differences in neophobia in wild animals are poorly understood. We evaluated wild-caught house sparrows (Passer domesticus) for neophobia in the lab using novel object tests. We then selected the most and least neophobic individuals (n=3 of each) and extracted RNA from four brain regions involved in learning, memory, threat perception, and executive function: striatum, dorsomedial hippocampus, medial ventral arcopallium, and caudolateral nidopallium (NCL). Our analysis of differentially expressed genes (DEGs) used 11,889 gene regions annotated in the house sparrow reference genome for which we had an average of 25.7 million mapped reads/sample. PERMANOVA identified significant effects of brain region, phenotype (neophobic vs. non-neophobic), and a brain region by phenotype interaction. Comparing neophobic and non-neophobic birds revealed constitutive differences in DEGs in three of the four brain regions examined: hippocampus (12% of the transcriptome significantly differentially expressed), striatum (4%) and NCL (3%). DEGs included important known neuroendocrine mediators of learning, memory, executive function, and anxiety behavior, including serotonin receptor 5A, dopamine receptors 1, 2 and 5 (downregulated in neophobic birds), and estrogen receptor beta (upregulated in neophobic birds). These results suggest that some of the behavioral differences between phenotypes may be due to underlying gene expression differences in the brain. The large number of DEGs in neophobic and non-neophobic birds also implies that there are major differences in neural function between the two phenotypes that could affect a wide variety of behavioral traits beyond neophobia.

category: animal behavior and cognition


title: Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immuno-staining

abstract: Detection of nucleic acids within sub-cellular compartments is key to understanding their function. Determining the intracellular distribution of nucleic acids requires quantitative retention and estimation of their association with different organelles by immunofluorescence microscopy. This is important also for the delivery of nucleic acid therapeutics which depends on endocytic uptake and endosomal escape. However, the current methods fail to preserve the majority of exogenously delivered nucleic acids in the cytoplasm. To solve this problem, by monitoring Cy5-labeled mRNA delivered to primary human adipocytes via lipid nanoparticles (LNP), we optimized cell fixation, permeabilization and immuno-staining of a number of organelle markers, achieving quantitative retention of mRNA and allowing visualization of levels which escape detection using conventional procedures. Additionally, we demonstrated the protocol to be effective on exogenously delivered siRNA, miRNA, as well as endogenous miRNA. Our protocol is compatible with RNA probes of single molecule fluorescence in-situ hybridization (smFISH) and molecular beacon, thus demonstrating that it is broadly applicable to study a variety of nucleic acids.


title: A native mass spectrometry-based assay for rapid assessment of the empty/full capsid ratio in AAV gene therapy products

abstract: Adeno-associated virus (AAV)-based cell and gene therapy is a rapidly developing field, requiring analytical methods for detailed product characterization. One important quality attribute of AAV products that requires monitoring is the amounts of residual empty capsids following downstream processing. Traditionally, empty and full particles are quantified via analytical ultracentrifugation as well as anion exchange chromatography using ultraviolet or fluorescence detection. Here, we present a native mass spectrometry-based approach to assess the ratio of empty to full AAV-capsids without the need for excessive sample preparation. We report rapid determination of the amount of empty particles in AAV5 and AAV8 samples, with results correlating well with more conventional analysis strategies, demonstrating the potential of state-of-the-art mass spectrometry for the characterization of viral particles.


title: Identification of genetic markers and wood properties that predict wood biorefinery potential in aspen bioenergy feedstock (Populus tremula).

abstract: Wood represents the majority of the biomass on lands, and it constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, meaning that feedstocks must be improved. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior biorefinery tree feedstocks. We recorded as many as 65 wood-related and growth traits in a population of European aspen natural genotypes. These traits included three growth and field performance traits, 20 traits for wood chemical composition, 17 traits for wood anatomy and structure, and 25 wood saccharification traits as indicators of bioconversion potential. We used statistical modelling to determine which wood traits best predict bioconversion yield traits. This way, we identified a core set of wood properties that predict bioprocessing traits. Several of these predictor traits showed high broad-sense heritability, suggesting potential for genetic improvement of feedstocks. Finally, we performed genome-wide association study (GWAS) to identify genetic markers for yield traits or for wood traits that predict yield. GWAS revealed only a few genetic markers for saccharification yield traits, but many more SNPs were associated with wood chemical composition traits, including predictors traits for saccharification. Among them, 16 genetic markers associated specifically with lignin chemical composition were situated in and around two genes which had not previously been associated with lignin. Our approach allowed linking aspen wood bioprocessing yield to wood properties and the underlying genetics, including the discovery of two new potential regulator genes for wood chemical composition.

category: plant biology


title: PECAn, a pipeline for image processing and statistical analysis of complex mosaic 3D tissues

abstract: Investigating organ biology requires sophisticated methodologies to induce genetically distinct clones within a tissue. Microscopic analysis of such samples produces information-rich 3D images. However, the 3D nature and spatial anisotropy of clones makes sample analysis challenging and slow and limits the amount of information that can be extracted manually. Here we have developed a pipeline for image processing and statistical data analysis which automatically extracts sophisticated parameters from complex multi-genotype 3D images. The pipeline includes data handling, machine-learning-enabled segmentation, multivariant statistical analysis, and graph generation. This enables researchers to run rigorous analyses on images and videos at scale and in a fraction of the time, without requiring programming skills. We demonstrate the power of this pipeline by applying it to the study of Minute cell competition. We find an unappreciated sexual dimorphism in Minute competition and identify, by statistical regression analysis, tissue parameters that model and predict competitive death.


title: Do pesticide residues have enduring negative effect on macroinvertebrates and vertebrates in fallow rice paddies?

abstract: Rice is one of the most important staple food in the world, with irrigated rice paddies largely converted from natural wetlands. The effectiveness of rice fields in help preserve species depends partially on management practices, including the usage of pesticides. However, related studies have focused predominately on the cultivation period, leaving the effects of soil pesticide residues on aquatic invertebrates during the fallow periods little explored; other animals, such as waterbirds, also rely on aquatic invertebrates in flooded fallow fields for their survival. We therefore investigated vertebrates and macroinvertebrates (terrestrial and aquatic) on rice stands and in flooded water during cultivation and fallow periods in organic and conventional rice fields in Taiwan. Association of environmental factors with terrestrial and aquatic organisms was also analyzed. In total, 32,880 individuals of 144 invertebrate families and 381 individuals of 15 vertebrate families were recorded after nine samplings each for six organic and six conventional rice fields. Family richness and abundance of all invertebrates (terrestrial and aquatic) were higher in organic than in conventional fields during the cultivation period, but were similar between the two agricultural practices during the fallow period. Richness and abundance of terrestrial invertebrates in both organic and conventional fields increased with the progression of rice cultivation, so did the differences between the two practices. Richness of aquatic invertebrates was mostly constant across the sampling period, while abundance increased but differences decreased during the fallow period. Richness and abundance of terrestrial invertebrates were positively associated with ambient temperature and height of rice stand. Abundance of aquatic invertebrates were positively associated with pH value and amount of dissolved oxygen but negatively associated with water temperature. Richness and abundance of all vertebrates and each of the constituting groups (fish, amphibian, reptile, bird, and migratory waterbird) were statistically similar between the two practices although abundance of migratory waterbirds in organic fields were two times those in conventional fields during the fallow period. Our study suggested accumulated effects of pesticides on suppressing terrestrial invertebrates during the cultivation period, but diminishing effects of pesticide residues on repressing aquatic invertebrates during the fallow period. This comprehensive study provided a holistic picture on macroinvertebrate and vertebrate fauna, as well as ramifications of pesticide usage, in a representative Southeast Asia rice paddy ecosystem. Further study should compare rice fields with natural wetlands to better assess how to capitalize on agroecosystems for biodiversity conservation.

category: ecology


title: Selection-Enriched Genomic Loci (SEGL) Reveals Genetic Loci for Environmental Adaptation and Photosynthetic Productivity in Chlamydomonas reinhardtii.

abstract:
This work demonstrates an approach to produce and select hybrid algal strains exhibiting increased photosynthetic productivity under multiple environmental conditions. This simultaneously addresses two major impediments to improving algal bioenergy production: 1) generating new genetic variants with improved performance; and 2) disentangling complex interactions between genetic and physiological factors contributing to these improvements. We pooled progeny generated from mating two environmental isolates of the green alga Chlamydomonas reinhardtii and cultured the pools under multiple environmental conditions. Strains from the outcompeting populations showed substantial (in some cases over 3 fold) increases in productivity over the parental lines under certain environments related to biomass production, including laboratory conditions as well as hyperoxia, fluctuating light, high salinity and high temperature. The results indicate that C. reinhardtii has remarkable, untapped, directed evolution capacity that may be harnessed using breeding and competition approaches. The populations were deep sequenced at multiple time points to identify "Selection-Enriched Genomic Loci" (SEGL) that accumulated in the populations, and thus likely confer increased fitness under the respective environmental conditions. With improved resolution, SEGL mapping can identify allelic combinations used for targeted breeding approaches, generating elite algal lines with multiple desirable traits, as well as to further understand the genetic and mechanistic bases of photosynthetic productivity.

Significance StatementIncreasing the photosynthetic efficiency of algae during biomass production is perhaps the most critical hurdle for economically sustainable algal based biofuels. This presents unique challenges because modifications designed to increase photosynthesis often result in decreased fitness, due to production of toxic reactive oxygen species when photosynthesis is not adequately regulated. These problems are exacerbated under natural and outdoor production environments because of the complex nature of photosynthesis and the multifaceted interactions between genetic, environmental and physiological factors. Here, we demonstrate a high throughput biotechnological screening approach that simultaneously produces algal strains with highly increased autotrophic productivity and identifies genomic loci contributing to these improvements. Our results demonstrate that Chlamydomonas reinhardtii exhibits high directed evolutionary capacity readily accessed through breeding and selection.

category: evolutionary biology


title: Fast and flexible processing of large FRET image stacks using the FRET-IBRA toolkit

abstract:
Ratiometric time-lapse FRET analysis requires a robust and accurate processing pipeline to eliminate bias in intensity measurements on fluorescent images before further quantitative analysis can be conducted. This level of robustness can only be achieved by supplementing automated tools with built-in flexibility for manual ad-hoc adjustments. FRET-IBRA is a modular and fully parallelized configuration file-based tool written in Python. It simplifies the FRET processing pipeline to achieve accurate, registered, and unified ratio image stacks. The flexibility of this tool to handle discontinuous image frame sequences with tailored configuration parameters further streamlines the processing of outliers and time-varying effects in the original microscopy images. FRET-IBRA offers cluster-based channel background subtraction, photobleaching correction, and ratio image construction in an all-in-one solution without the need for multiple applications, image format conversions, and/or plug-ins. The package accepts a variety of input formats and outputs TIFF image stacks along with performance measures to detect both the quality and failure of the background subtraction algorithm on a per frame basis. Furthermore, FRET-IBRA outputs images with superior signal-to-noise ratio and accuracy in comparison to existing background subtraction solutions, whilst maintaining a fast runtime. The FRET-IBRA package has been extensively used in quantifying the spatial distribution of calcium ions during pollen tube growth under mechanical constraints. Benchmarks against existing tools clearly demonstrate the need for FRET-IBRA in extracting reliable insights from FRET microscopy images of dynamic physiological processes at high spatial and temporal resolution. The source code for Linux and Mac operating systems is released under the BSD license and, along with installation instructions, test images, example configuration files, and a step-by-step tutorial, is freely available at github.com/gmunglani/fret-ibra.

Author SummaryFRET is a fundamental imaging technique used to generate fluorescence signals sensitive to molecular conformations and interactions. Despite its wide use and the large body of literature on the theoretical steps required to process images generated from this procedure, we were unable to locate a tool that contained the entire processing workflow, whilst allowing the user the flexibility to adjust parameters for maximum accuracy and runtime efficiency. FRET-IBRA was thus created to be an all-in-one, open-source, parallel solution to process FRET images, while eliminating complications arising from repeated image format conversions. Besides enhancing the background subtraction algorithm for FRET images, several additional options were implemented for the user to extract the cleanest signal possible for their specific use case. FRET-IBRA is primarily built for flexibility when handling large image stacks by supporting sequences of image frames to be treated independently, greatly reducing time spent on splitting and concatenating image stacks. In accuracy and speed benchmarks against more general background subtraction packages, FRET-IBRA was able to provide the cleanest results with a fast runtime, leading to reliable analysis without additional tuning.

category: bioinformatics


title: EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on Ensemble Learning

abstract:
Classification of proteins into their respective functional categories remains a long-standing key challenge in computational biology. Machine Learning (ML) based discriminative algorithms have been used extensively to address this challenge; however, the presence of small-sized, noisy, unbalanced protein classification datasets where high sequence similarity does not always imply identical functional properties have prevented robust prediction performance. Herein we present a ML method, Ensemble method for enZyme Classification (EnZymClass), that is specifically designed to address these issues. EnZymClass makes use of 47 alignment-free feature extraction techniques as numerically encoded descriptors of protein sequences to construct a stacked ensemble classification scheme capable of categorizing proteins based on their functional attributes. We used EnZymClass to classify plant acyl-ACP thioesterases (TEs) into short, long and mixed free fatty acid substrate specificity categories. While general guidelines for inferring substrate specificity have been proposed before, prediction of chain-length preference from primary sequence has remained elusive. EnZymClass achieved high classification metric scores on the TE substrate specificity prediction task (average accuracy score of 0.8, average precision and recall scores of 0.87 and 0.89 respectively on medium-chain TE prediction) producing accuracy scores that are about twice as effective at avoiding misclassifications than existing similarity-based methods of substrate specificity prediction. By applying EnZymClass to a subset of TEs in the ThYme database, we identified two acyl-ACP TE, ClFatB3 and CwFatB2, with previously uncharacterized activity in E. coli fatty acid production hosts. We incorporated modifications into ClFatB3 established in prior TE engineering studies, resulting in a 4.2-fold overall improvement in observed C10 titers over the wildtype enzyme.

EnZymClass can be readily applied to other protein classification challenges and is available at: https://github.com/deeprob/ThioesteraseEnzymeSpecificity

Author SummaryThe natural diversity of proteins has been harnessed to serve specialized applications in various fields, including medicine, renewable chemical production, and food and agriculture. Acquiring and characterizing new proteins to meet a given application, however, can be an expensive process, requiring selection from thousands to hundreds of thousands of candidates in a database and subsequent experimental screening. Using amino acid sequence to predict a proteins function has been demonstrated to accelerate this process, however standard approaches require information on previously characterized proteins and their respective sequences. Obtaining the necessary amount of data to accurately infer sequence-function relationships can be prohibitive, especially with a low-throughput testing cycle. Here, we present EnZymClass, a model that is specifically designed to work with small to medium-sized protein sequence datasets and retain high prediction performance of function. We applied EnZymClass to predict the presence or absence of a desired function among acyl-ACP thioesterases, a key enzyme class used in the production of renewable oleochemicals in microbial hosts. By training EnZymClass on only 115 functionally characterized enzyme sequences, we were able to successfully detect two plant acyl-ACP thioesterases with the desired specialized function among 617 sequences in the ThYme database.


title: Ring-shaped multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by the ADP/ATP exchange inhibition

abstract:
Circadian clocks tick a rhythm with a nearly 24-hour period in various organisms. The clock proteins of cyanobacteria, KaiA, KaiB, and KaiC, compose a minimum circadian clock. The slow KaiB-KaiC complex formation, which is essential in determining the clock period, occurs when the C1 domain of KaiC binds ADP produced by ATP hydrolysis. KaiC is considered to promote this complex formation by inhibiting the backward process, ADP/ATP exchange, rather than activating the forward process, ATP hydrolysis. Remarkably, although inhibition of backward process, in general, decelerates the whole process, KaiC oppositely accelerates the complex formation. In this article, by building a novel reaction model, we investigate the molecular mechanism of the simultaneous promotion and acceleration of the complex formation, which may play a significant role in keeping the period invariant under environmental perturbations. Based on several experimental results, we assume in this model that six KaiB monomers cooperatively and rapidly binds to C1 with the stabilization of the binding-competent conformation of C1 only when C1 binds six ADP. We find the cooperative KaiB binding effectively separates the pre-binding process of C1 into a fast transformation to binding-competent C1 requiring multiple ATP hydrolyses and its slow backward transformation. Since the ADP/ATP exchange retards the forward process, its inhibition results in the acceleration of the complex formation. We also find that, in a simplified monomeric model where KaiB binds to a KaiC monomer independently of the other monomers, the ADP/ATP exchange inhibition cannot accelerate the complex formation. In summary, we conclude that the ring-shaped hexameric form of KaiC enables the acceleration of the complex formation induced by the backward process inhibition because the cooperative KaiB binding arises from the structure of KaiC.

Author summaryCircadian clocks tick a rhythm with a nearly 24-hour period in various organisms. The cyanobacterial circadian clock has attracted much attention because of its simplicity, composed of only three proteins, KaiA, KaiB, and KaiC. The rate of the slow KaiB-KaiC complex formation, which plays an essential role in the period determination, is mainly regulated by the ATP hydrolysis (forward process) and the ADP/ATP exchange (backward process) of KaiC. KaiC promotes the complex formation by inhibiting the backward process rather than activating the forward process. Remarkably, although inhibition of backward process, in general, slows down the whole process, KaiC oppositely accelerates the complex formation. In this article, we investigate the molecular mechanism of this acceleration by building a novel mathematical model based on several significant experimental results. We find the cooperative binding of six KaiB to a KaiC hexamer, which arises from the ring-shaped hexameric structure of KaiC, effectively separates the pre-binding process into a fast transformation to the binding-competent KaiC requiring multiple ATP hydrolyses and its slow backward transformation. Since the ADP/ATP exchange retards the forward process, its inhibition results in the acceleration of the complex formation.

category: biophysics


title: Social experience alters oxytocinergic modulation in the nucleus accumbens of female prairie voles

abstract: Social relationships are dynamic and evolve with shared and personal experiences. Whether the functional role of social neuromodulators also evolves with experience to shape the trajectory of relationships is unknown. We utilized pair bonding in the socially monogamous prairie voles as an example of socio-sexual experience that dramatically alters behaviors displayed toward other individuals. We investigated oxytocin-dependent modulation of excitatory synaptic transmission in the nucleus accumbens as a function of pair bonding status. We found that an oxytocin receptor agonist decreases the amplitude of spontaneous Excitatory Postsynaptic Currents (EPSCs) in sexually naive virgin, but not pair-bonded, female voles, while it increases the amplitude of electrically evoked EPSCs in paired voles, but not in virgins. This oxytocin-dependent potentiation of synaptic transmission relies on the de novo coupling between oxytocin receptor signaling and endocannabinoid CB1 receptor signaling in pair bonded voles. Blocking CB1 receptors after pair bond formation increases the occurrence of a specific form of social rejection - defensive upright response - that is displayed towards the partner but not towards a novel individual. Altogether, our results demonstrate that oxytocins action in the nucleus accumbens is changed through social experience in a way that regulates the trajectory of social interactions as the relationship with the partner unfolds, potentially promoting the maintenance of a pair bond by inhibiting aggressive responses. These results provide a mechanism by which social experience and context shift oxytocinergic signaling to impact neural and behavioral responses to social cues.

category: neuroscience


title: Outer membrane vesicles derived from Klebsiella pneumoniae are a driving force for horizontal gene transfer

abstract:
Gram-negative bacteria release outer membrane vesicles (OMVs) into the extracellular environment. Recent studies recognized these vesicles as vectors to horizontal gene transfer, however the parameters that mediate OMVs transfer within bacterial communities remain unclear. The present study highlights for the first time the transfer of plasmids containing resistance genes via OMVs derived from Klebsiella pneumoniae (K. pneumoniae). This mechanism confers DNA protection and it is plasmid copy number dependent with a ratio of 3.6 time among high copy-number plasmid (pGR) versus low copy number plasmid (PRM) and the transformation efficiency was 3.6 times greater. Therefore, the DNA amount in the vesicular lumen and the efficacy of horizontal gene transfer was strictly dependent on the identity of the plasmid. Moreover, the role of K. pneumoniae-OMVs in interspecies transfer was described. The transfer ability was not related to the phylogenetic characteristics between the donor and the recipient species. K. pneumoniae-OMVs transferred plasmid to Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa and Burkholderia cepacia. These findings address the pivotal role of K. pneumoniae-OMVs as vectors for antimicrobial resistance genes spread, contributing to the development of antibiotic resistance in the microbial communities.

Author summaryK. pneumoniae is an important opportunistic pathogen that affects several host districts, in particular respiratory and urinary tracts. Hospital-acquired K. pneumoniae infections lead to a 50% mortality rate correlated with rapid acquisition of antibiotic resistance. Currently, the increasing rate of antibiotic resistance among K. pneumoniae isolates is a major concern worldwide. The spread of multidrug-resistant K. pneumoniae strains renders current therapeutic options ineffective. Like all Gram-negative bacteria, K. pneumoniae secretes OMVs. OMVs are spherical structures, with a diameter between 50-250 nm, originating from the outer membrane. OMVs biogenesis allows bacteria to interact with the external environment, increasing bacterial survival under stressful conditions and regulating microbial interactions within bacterial communities. Few evidence recognized OMVs as vectors for horizontal gene transfer, contributing to the spread of resistance. In this scenario, the present study examines the potential role of K. pneumoniae-OMVs in inter- and intra-species diffusion of {beta}-lactam resistance.


title: Inhibition of Ras1-MAPK pathways for hypha formation by novel drug candidates in Candida albicans

abstract:
The opportunistic human fungal pathogen Candida albicans has morphogenesis as a virulence factor. The morphogenesis of C. albicans is closely related to pathogenicity (1). Ras1 in C. albicans is an important switch in the MAPK pathway for morphogenesis (2, 3). The MAPK pathway is important for the virulence, such as cell growth, morphogenesis, and biofilm formation (4, 5). Ume6 is a well-known transcriptional factor for hyphal-specific genes (6). Despite numerous studies, as a recent issue, it is necessary to develop a new drug that uses a different pathway mechanism to inhibit resistant C. albicans strains caused by chronic prescription of azole or echinocandin drugs, which are mainly used. Here, we show that the small carbazole derivatives attenuated the pathogenicity of C. albicans through inhibition of the Ras1/MAPK pathway. We found that the small molecules inhibit morphogenesis through repressing protein and RNA levels in Ras/MAPK related genes including UME6 and NRG1. Furthermore, we found the antifungal effect of the small molecules in vivo using a candidiasis murine model. We anticipate our findings are that the small molecules are the promising compounds for the development of new antifungal agents for the treatment of systemic candidiasis and possibly for other fungal diseases.

Author summaryThe infection by the opportunistic human fungal pathogen Candida albicans occurs mainly in immunocompetent and immunocompromised humans, such as AIDS patients, immunosuppressant-treated organ transplant patients, and recent COVID-19 patients. Morphogenesis which the ability to switch between yeast and hyphal growth forms is one of the representative virulence factors of C. albicans. Here, we describe novel small molecules that show antifungal effects such as the inhibition of the morphogenesis and the biofilm formation, and maintenance of biofilm. Moreover, we found that these small molecules had antifungal activity in mouse experiments, and confirmed that they were also effective in drug-resistant C. albicans strains. Studies of some small molecules with structures similar to ours have already been reported to exhibit growth inhibitory activity against bacteria and Candida species. However, the mechanism of action of these molecules has not been elucidated. In this study, we demonstrated, for the first time, the mechanism by which these two small molecules inhibit C. albicans pathogenicity through inhibition of specific pathways. Our study, through the research of the mechanism of action of novel small molecules, provides new insights into the development of drug candidates not only for wild-type C. albicans, but also for strains resistant to existing drugs.


title: Human Papillomavirus Type 16 E6 induces cell competition

abstract:
High risk human papillomavirus (HPV) infections induce squamous epithelial tumors in which the virus replicates. Initially, the virus-infected epithelial cells are untransformed, but expand in both number and area at the expense of normal squamous epithelial cells. How this occurs is unknown, but is presumed to be due to viral oncogene expression. We have developed an in vitro assay in which colonies of post-confluent HPV16 expressing cells outcompete confluent surrounding normal keratinocytes for surface area. The enhanced cell competition induced by the complete HPV16 genome is conferred by E6 expression alone, and not by individual expression of E5 or E7. In traditional oncogene assays, E7 is a more potent oncogene than E6, but such assays do not include interaction with normal surrounding cells. These new results separate classic oncogenicity that is primarily conferred by E7, from cell competition that we show is primarily conferred by E6, and provides a new biological role for E6 oncoproteins from high risk human papillomaviruses.

ImportanceHigh risk papillomavirus infections induce epithelial tumors, some of which evolve into malignancies. The development and maintenance of cancer is due to the virally encoded E6 and E7 oncoproteins. How a virally infected keratinocyte out-competes normal uninfected keratinocytes has been unknown. The present work shows that the enhanced competition of HPV16-infected cells is primarily due to the expression of the E6 oncoprotein and not the E7 or E5 oncoproteins. This work shows the importance of measuring oncoprotein traits in the context of cell competition with uninfected cells, and shows the potential of papillomavirus oncoproteins to be novel genetic probes for the analysis of cell competition.


title: Zeb2 DNA-binding sites in ES cell derived neuroprogenitor cells reveal autoregulation and align with neurodevelopmental knockout mouse and disease phenotypes.

abstract:
Perturbation and mechanistic studies have shown that the DNA-binding transcription factor Zeb2 controls cell fate decision, differentiation and/or maturation in multiple cell lineages in embryos and after birth. In cultured embryonic stem cells (ESCs) Zeb2s strong upregulation is necessary for their exit from primed pluripotency and entering neural and general differentiation. We engineered mouse ESCs to produce epitope-tagged Zeb2 from one of its two endogenous alleles. Using crosslinking ChIP-sequencing, we mapped for the first time 2,432 DNA-binding sites of Zeb2 in ESC-derived neuroprogenitor cells (NPCs). A new, major site maps promoter-proximal to Zeb2 itself, and its homozygous removal demonstrates that Zeb2 autoregulation is necessary to elicit proper Zeb2 effects in ESC[->]NPC differentiation. We then cross-referenced all Zeb2 DNA-binding sites with transcriptome data from Zeb2 perturbations in ESCs, ventral forebrain in mouse embryos, and adult neurogenesis. While the characteristics of these neurodevelopmental systems differ, we find interesting overlaps. Collectively, these new results obtained in ESC-derived NPCs significantly add to Zeb2s role as neurodevelopmental regulator as well as the causal gene in Mowat-Wilson Syndrome. Also, Zeb2 was found to map to loci mutated in other human congenital syndromes, making variant or disturbed levels of ZEB2 a candidate modifier principle in these.

Significance statementZeb2 is needed for exit from primed pluripotency and differentiation of ESCs and being studied in various cell lineages and tissues/organs in knockouts and adult mice. Phenotyping has mainly documented transcriptomes of Zeb2-mutant affected cell types, but ChIP-seq data are still not available to document Zeb2s direct target loci as repressor or activator of transcription. This study maps for the first time the Zeb2 genome-wide binding sites in ESC-derived neuroprogenitors, and discovered Zeb2 autoregulation. Cross-referencing these ChIP-seq data with transcriptome profiles of Zeb2 perturbation further explains Mowat-Wilson Syndrome defects and proposes ZEB2 as candidate modifier gene in other syndromes.


title: Micronutrient supplements with iron promote disruptive protozoan and fungal communities in the developing infant gut

abstract: Supplementation with micronutrients, including vitamins, iron and zinc, is a key strategy to alleviate child malnutrition. However, adverse events resulting in gastrointestinal disorders, largely associated with iron, has resulted in ongoing debate over their administration. To better understand their impact on gut microbiota, we analysed the bacterial, protozoal, fungal and helminth communities of stool samples collected from children that had previously been recruited to a cluster randomized controlled trial of micronutrient supplementation in Pakistan. We show that while bacterial diversity was reduced in supplemented children, vitamins and iron may promote colonization with distinct protozoa and mucormycetes, whereas the addition of zinc ameliorates this effect. In addition to supplements, residence in a rural versus urban setting is an important determinant of eukaryotic composition. We suggest that the risks and benefits of such interventions may be mediated in part through eukaryotic communities, in a manner dependent on setting.


title: mDrop-seq: Massively parallel single-cell RNA-seq of Saccharomyces cerevisiae and Candida albicans

abstract: Advances in high-throughput single-cell mRNA sequencing (scRNA-seq) have been limited till date by technical challenges like tough cell walls and low RNA quantity that prevented transcriptomic profiling of microbial species at throughput. We present microbial Drop-seq or mDrop-seq, a high-throughput scRNA-seq technique that is used on two yeast species, Saccharomyces cerevisiae, a popular model organism and Candida albicans, a common opportunistic pathogen. We benchmarked mDrop-seq for sensitivity and specificity and used it to profile 35,109 S. cerevisiae cells to detect variation in mRNA levels between them. As a proof of concept, we quantified expression differences in heat-shocked S. cerevisiae using mDrop-seq. We detected differential activation of stress response genes within a seemingly homogenous population of S. cerevisiae under heat-shock. We also applied mDrop-seq to C. albicans cells, a polymorphic and clinically relevant yeast species with thicker cell wall compared to S. cerevisiae. Single cell transcriptomes in 39,705 C. albicans cells was characterized using mDrop-seq under different conditions, including exposure to fluconazole, a common anti-fungal drug. We noted differential regulation in stress response and drug target pathways between C. albicans cells, changes in cell cycle patterns and marked increases in histone activity. These experiments are among the first high throughput single cell RNA-seq on different yeast species and demonstrate mDrop-seq as an affordable, easily implementable, and scalable technique that can quantify the variability in gene expression in different yeast species. We hope that mDrop-seq will lead to better understanding of genetic variation in yeasts in response to stimuli and find immediate applications in investigating drug resistance and infection outcome.

category: genomics


title: Mouse Antibodies with Activity Against the SARS-CoV-2 D614G and B.1.351 Variants

abstract: With the rapid spread of SARS-CoV-2 variants, including those that are resistant to antibodies authorized for emergency use, it is apparent that new antibodies may be needed to effectively protect patients against more severe disease. Differences between the murine and human antibody repertoires may allow for the isolation of murine monoclonal antibodies that recognize a different or broader range of SARS-CoV-2 variants than the human antibodies that have been characterized so far. We describe mouse antibodies B13 and O24 that demonstrate neutralizing potency against SARS-CoV-2 Wuhan (D614G) and B.1.351 variants. Such murine antibodies may have advantages in protecting against severe symptoms when individuals are exposed to new SARS-CoV-2 variants.


title: SARS-CoV-2 genome sequencing with Oxford Nanopore Technology and Rapid PCR Barcoding in Bolivia

abstract: SARS-CoV-2 genomic surveillance has Illumina technology as the golden standard. However, Oxford Nanopore Technology (ONT) provides significant improvements in accessibility, turnaround time and portability. Characteristics that gives developing countries the opportunity to perform genome surveillance. The most used protocol to sequence SARS-CoV-2 with ONT is an amplicon-sequencing protocol provided by the ARTIC Network which requires DNA ligation. Ligation reagents can be difficult to obtain in countries like Bolivia. Thus, here we provide an alternative for library preparation using the rapid PCR barcoding kit (ONT). We mapped more than 3.9 million sequence reads that allowed us to sequence twelve SARS-CoV-2 genomes from three different Bolivian cities. The average sequencing depth was 324X and the average genome length was 29527 bp. Thus, we could cover in average a 98,7% of the reference genome. The twelve genomes were successfully assigned to four different nextstrain clades (20A, 20B, 20E and 20G) and we could observe two main lineages of SARS-CoV-2 circulating in Bolivia. Therefore, this alternative library preparation for SARS-CoV-2 genome sequencing is effective to identify SARS-CoV-2 variants with high accuracy and without the need of DNA ligation. Hence, providing another tool to perform SARS-CoV-2 genome surveillance in developing countries.


title: T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations

abstract: Rapidly appearing SARS-CoV-2 mutations can affect T cell epitopes, which can help the virus to evade either CD8 or CD4 T-cell responses. We developed T-cell COVID-19 Atlas (T-CoV, https://t-cov.hse.ru) - the comprehensive web portal, which allows one to analyze how SARS-CoV-2 mutations alter the presentation of viral peptides by HLA molecules. The data are presented for common virus variants and the most frequent HLA class I and class II alleles. Binding affinities of HLA molecules and viral peptides were assessed with accurate in silico methods. The obtained results highlight the importance of taking HLA alleles diversity into account: mutation-mediated alterations in HLA-peptide interactions were highly dependent on HLA alleles. For example, we found that the essential number of peptides tightly bound to HLA-B*07:02 in the reference Wuhan variant ceased to be tight binders for the Indian (Delta) and the UK (Alpha) variants. In summary, we believe that T-CoV will help researchers and clinicians to predict the susceptibility of individuals with different HLA genotypes to infection with variants of SARS-CoV-2 and/or forecast its severity.


title: Nonclinical Safety and Immunogenicity of an rVSV-ΔG-SARS-CoV-2-S vaccine in mice, hamsters, rabbits and pigs

abstract: rVSV-{Delta}G-SARS-CoV-2-S is a clinical stage (Phase 2) replication competent recombinant vaccine against SARS-CoV-2. Nonclinical safety, immunogenicity and efficacy studies were conducted in 4 animal species, using multiple dose levels (up to 108 PFU/animal) and various dosing regimens. There were no treatment related mortalities in any study, or any noticeable clinical signs. Compared to unvaccinated controls, hematology and biochemistry parameters were unremarkable and no adverse histopathological findings gave cause for safety concern in any of the studies. There was no viral shedding in urine, nor viral RNA detected in whole blood or serum samples 7 days post vaccination. The rVSV-{Delta}G-SARS-CoV-2-S vaccine immune response gave rise to neutralizing antibodies, cellular immune response, and increased lymphocytic cellularity in the spleen germinal centers and regional lymph node. No evidence for neurovirulence was found in C57BL/6 immune competent mice or in highly sensitive IFNAR KO mice. Vaccine virus replication and distribution in K18 hACE2 transgenic mice showed a gradual clearance from the vaccination site with no vaccine virus recovered from the lungs. The rVSV-{Delta}G-SARS-CoV-2-S vaccine was well tolerated locally and systemically and elicited an effective immunogenic response up to the highest dose tested, supporting further clinical development.

category: pharmacology and toxicology


title: A Newcastle disease virus-vector expressing a prefusion-stabilized spike protein of SARS-CoV-2 induces protective immune responses against prototype virus and variants of concern in mice and hamsters

abstract: Rapid development of coronavirus disease 2019 (COVID-19) vaccines and expedited authorization for use and approval has been proven beneficial to mitigate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread and given hope in this desperate situation. It is believed that sufficient supplies and equitable allocations of vaccines are necessary to limit the global impact of the COVID-19 pandemic and the emergence of additional variants of concern. We have developed a COVID-19 vaccine based on Newcastle disease virus (NDV) that can be manufactured at high yields in embryonated eggs. Here we provide evidence that the NDV vector expressing an optimized spike antigen (NDV-HXP-S), upgraded from our previous construct, is a versatile vaccine that can be used live or inactivated to induce strong antibody responses and to also cross-neutralize variants of concern. The immunity conferred by NDV-HXP-S effectively counteracts SARS-CoV-2 infection in mice and hamsters. It is noteworthy that vaccine lots produced by existing egg-based influenza virus vaccine manufacturers in Vietnam, Thailand and Brazil exhibited excellent immunogenicity and efficacy in hamsters, demonstrating that NDV-HXP-S vaccines can be quickly produced at large-scale to meet global demands.

category: immunology


title: Sex-dependent Lupus Ruminococcus blautia gnavus strain induction of zonulin-mediated intestinal permeability and autoimmunity

abstract: Imbalances in the gut microbiome are suspected as contributors to the pathogenesis of Systemic Lupus Erythematosus, and our studies and others have documented that patients with active Lupus nephritis have expansions of the obligate anaerobe, Ruminococcus blautia gnavus (RG). To investigate whether the RG strains in Lupus patients have in vivo pathogenic properties, we colonized C57BL/6 mice with individual RG strains from healthy adults or those from Lupus patients. These strains had a similar capacity for murine intestinal colonization, in antibiotic-preconditioned specific-pathogen-free, as well as germ-free adults, and their neonatally colonized litters. Lupus-derived RG strains induced high levels of intestinal permeability that was significantly greater in female than male mice, whereas the RG species-type strain (ATCC29149/VPI C7-1) from a healthy donor had little or no effects. Lupus RG strain-induced functional alterations were associated dysregulated occluden transcript production in the ileal wall as well as raised serum levels of zonulin, a regulator of tight junction formation between cells that form the gut barrier. Notably, the level of Lupus RG-induced intestinal permeability was significantly correlated with serum IgG anti RG cell-wall lipoglycan antibodies, and to anti-native DNA autoantibodies that are a biomarker for SLE. Strikingly, gut permeability was completely reversed by oral treatment with larazotide acetate, an octapeptide that is a specific molecular antagonist of zonulin. Taken together, these studies document a molecular pathway by which RG strains from Lupus patients induce a leaky gut and autoimmunity that have been implicated in the pathogenesis of flares of clinical Lupus disease.


title: Vibrio cholerae motility in aquatic and mucus-mimicking environments

abstract:
Cholera disease is caused by Vibrio cholerae infecting the lining of the small intestine and results in severe diarrhea. V. choleraes swimming motility is known to play a crucial role in pathogenicity and may aid the bacteria in crossing the intestinal mucus barrier to reach sites of infection, but the exact mechanisms are unknown. The cell can be either pushed or pulled by its single polar flagellum, but there is no consensus on the resulting repertoire of motility behaviors.

We use high-throughput 3D bacterial tracking to observe V. cholerae swimming in buffer, in viscous solutions of the synthetic polymer PVP, and in mucin solutions that may mimic the host environment. We perform a statistical characterization of its motility behavior on the basis of large 3D trajectory datasets. We find that V. cholerae performs asymmetric run-reverse-flick motility, consisting of a sequence of a forward run, reversal, and a shorter backward run, followed by a turn by approximately 90{degrees}, called a flick, preceding the next forward run. Unlike many run-reverse-flick swimmers, V. choleraes backward runs are much shorter than its forward runs, resulting in an increased effective diffusivity. We also find that the swimming speed is not constant, but subject to frequent decreases. The turning frequency in mucin matches that observed in buffer. Run-reverse-flick motility and speed fluctuations are present in all environments studied, suggesting that these behaviors may also occur in natural aquatic habitats as well as the host environment.

ImportanceCholera disease produces vomiting and severe diarrhea and causes approximately 100,000 deaths per year worldwide. The disease is caused by the bacterium Vibrio cholerae colonizing the lining of the small intestine. V. choleraes ability to swim is known to increase its infectivity, but the underlying mechanisms are not known. One possibility is that swimming may aid in crossing the protective mucus barrier that covers the lining of the small intestine. Our work characterizing how V. cholerae swims in environments that mimic properties of the host environment may advance the understanding of how motility contributes to infection.


title: Direct Observation of Electrically Conductive Pili Emanating from Geobacter sulfurreducens

abstract:
Geobacter sulfurreducens is a model microbe for elucidating the mechanisms for extracellular electron transfer in several biogeochemical cycles, bioelectrochemical applications, and microbial metal corrosion. Multiple lines of evidence previously suggested that electrically conductive pili (e-pili) are an essential conduit for long-range extracellular electron transport in G. sulfurreducens. However, it has recently been reported that G. sulfurreducens does not express e-pili and that filaments comprised of multi-heme c-type cytochromes are responsible for long-range electron transport. This possibility was directly investigated by examining cells, rather than filament preparations, with atomic force microscopy. Approximately 90 % of the filaments emanating from wild-type cells had a diameter (3 nm) and conductance consistent with previous reports of e-pili harvested from G. sulfurreducens or heterologously expressed in E. coli from the G. sulfurreducens pilin gene. The remaining 10% of filaments had a morphology consistent with filaments comprised of the c-type cytochrome OmcS. A strain expressing a modified pilin gene designed to yield poorly conductive pili expressed 90 % filaments with a 3 nm diameter, but greatly reduced conductance, further indicating that the 3 nm diameter conductive filaments in the wild-type strain were e-pili. A strain in which genes for five of the most abundant outer-surface c-type cytochromes, including OmcS, was deleted yielded only 3 nm diameter filaments with the same conductance as in the wild-type. These results demonstrate that e-pili are the most abundant conductive filaments expressed by G. sulfurreducens, consistent with previous functional studies demonstrating the need for e-pili for long-range extracellular electron transfer.

ImportanceElectroactive microbes have significant environmental impacts as well as applications in bioenergy and bioremediation. The composition, function, and even existence of electrically conductive pili (e-pili) has been one of the most contentious areas of investigation in electromicrobiology, in part because e-pili offer a mechanism for long-range electron transport that does not involve the metal co-factors common in much of biological electron transport. This study demonstrates that e-pili are abundant filaments emanating from Geobacter sulfurreducens, which serves as a model for long-range extracellular electron transfer in direct interspecies electron transfer, dissimilatory metal reduction, microbe-electrode exchange, and corrosion caused by direct electron uptake from Fe(0). The methods described in this study provide a simple strategy for evaluating the distribution of conductive filaments throughout the microbial world with an approach that avoids artifactual production and/or enrichment of filaments that may not be physiologically relevant.


title: ZomB is essential for chemotaxis of Vibrio alginolyticus by the rotational direction control of the polar flagellar motor

abstract:
Bacteria exhibit chemotaxis by controlling flagellar rotation to move toward preferred places or away from non-preferred places. The change in rotation is triggered by the binding of the chemotaxis signaling protein CheY to the C-ring in the flagellar motor. Some specific bacteria, including Vibrio spp. and Shewanella spp. have a single transmembrane protein called ZomB. ZomB is essential for controlling the flagellar rotational direction in Shewanella putrefaciens and Vibrio parahaemolyticus. In this study, we confirmed that the zomB deletion results only in the counterclockwise (CCW) rotation of the motor in Vibrio alginolyticus as previously reported in other bacteria. We found that ZomB is not required for the clockwise (CW) rotation-fixing phenotype caused by mutations in fliG and fliM, and that ZomB is essential for CW rotation induced by overproduction of CheY. Purified ZomB proteins form multimers, indicating that ZomB functions as a complex. ZomB may interact with a protein involved in the flagellar rotation, stator proteins or rotor proteins. We found that ZomB is a new player in chemotaxis and is required for the rotational control in addition to CheY in Vibrio alginolyticus.

ImportanceBacterial chemotaxis is performed by the control of the flagellar rotation. CheY and ZomB control the rotational direction of the flagellar motor in Vibrio spp. and Shewanella spp. In this study, we characterized ZomB in Vibrio alginolyticus, which is essential for the clockwise rotation of the motor.


title: The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA

abstract:
BackgroundSalt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons.

ResultsA marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora.

ConclusionsThe S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially-mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i.) Enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii.) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root and rhizosphere associated prokaryotes detoxify sulfide in the root zone while potentially transferring fixed C and N to the host plant.


title: Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: Application to direct RNA sequencing on nanopores.

abstract: Understanding transcriptomes requires documenting the structures, modifications, and abundances of RNAs as well as their proximity to other molecules. The methods that make this possible depend critically on enzymes (including mutant derivatives) that act on nucleic acids for capturing and sequencing RNA. We tested two 3 nucleotidyl transferases, Saccharomyces cerevisiae poly(A) polymerase and Schizosaccharomyces pombe Cid1, for the ability to add base and sugar modified rNTPs to free RNA 3 ends, eventually focusing on Cid1. Although unable to polymerize {Psi}TP or 1me{Psi}TP, Cid1 can use 5meUTP and 4thioUTP. Surprisingly, Cid1 can use inosine triphosphate to add poly(I) to the 3 ends of a wide variety of RNA molecules. Most poly(A) mRNAs efficiently acquire a uniform tract of about 50 inosine residues from Cid1, whereas non-poly(A) RNAs acquire longer, more heterogeneous tails. Here we test these activities for use in direct RNA sequencing on nanopores, and find that Cid1-mediated poly(I)-tailing permits detection and quantification of both mRNAs and non-poly(A) RNAs simultaneously, as well as enabling the analysis of nascent RNAs associated with RNA polymerase II. Poly(I) produces a different current trace than poly(A), enabling recognition of native RNA 3 end sequence lost by in vitro poly(A) addition. Addition of poly(I) by Cid1 offers a broadly useful alternative to poly(A) capture for direct RNA sequencing on nanopores.


title: Human airway lineages derived from pluripotent stem cells reveal the epithelial responses to SARS-CoV-2 infection

abstract:
There is an urgent need to understand how SARS-CoV-2 infects the airway epithelium and in a subset of individuals leads to severe illness or death. Induced pluripotent stem cells (iPSCs) provide a near limitless supply of human cells that can be differentiated into cell types of interest, including airway epithelium, for disease modeling. We present a human iPSC-derived airway epithelial platform, composed of the major airway epithelial cell types, that is permissive to SARS-CoV-2 infection. Subsets of iPSC-airway cells express the SARS-CoV-2 entry factors ACE2 and TMPRSS2. Multiciliated cells are the primary initial target of SARS-CoV-2 infection. Upon infection with SARS-CoV-2, iPSC-airway cells generate robust interferon and inflammatory responses and treatment with remdesivir or camostat methylate causes a decrease in viral propagation and entry, respectively. In conclusion, iPSC-derived airway cells provide a physiologically relevant in vitro model system to interrogate the pathogenesis of, and develop treatment strategies for, COVID-19 pneumonia.

Highlights and eTOC blurbO_LISubsets of human iPSC-airway epithelial cells express SARS-Co-V entry factors ACE2 and TMPRSS2.
C_LIO_LIiPSC-airway cells are permissive to SARS-CoV-2 infection via multiciliated cells.
C_LIO_LISARS-CoV-2 infection of iPSC-airway leads to a robust interferon and inflammatory response.
C_LIO_LIiPSC-airway is a physiologically relevant model to study SARS-CoV-2 infection.
C_LI


title: Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements

abstract: A year after the World Health Organisation (WHO) declared COVID-19 as a pandemic, much has been learned regarding SARS-CoV-2 epidemiology, vaccine production, and disease treatment. Whole-genome sequencing (WGS) has played a significant role in contributing to our understanding of the epidemiology and biology of this virus. In this paper, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asia and the impact of technological development, access to resources, and demography of individual countries on its uptake. Using Oxford Nanopore Technology (ONT), Nottingham-Indonesia Collaboration for Clinical Research and Training (NICCRAT) initiative has facilitated collaboration between the University of Nottingham and a team in Research Centre for Biotechnology, Indonesian Institute of Sciences (Lembaga Ilmu Pengetahuan Indonesia/LIPI) to carry out a small number of SARS-CoV-2 WGS in Indonesia. The ONT offers sequencing advantages that fit within the Indonesian context. Analyses of SARS-CoV-2 genomes deposited on GISAID from Southeast and East Asian countries reveal the importance of collecting clinical and demographic metadata and the importance of open access and data sharing. Lineage and phylogenetic analyses per 1 June 2021 found that: 1) B.1.466.2 variants were the most predominant in Indonesia, with mutations in the spike protein including D614G at 100%, N439K at 99.1%, and P681R at 69.7% frequency, 2) The variants of concern (VoCs) B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta) were first detected in Indonesia in January 2021, 3) B.1.470 was first detected in Indonesia and spread to the neighbouring regions, and 4) The highest rate of virus transmissions between Indonesia and the rest of the world appears to be through interactions with Singapore and Japan, two neighbouring countries with a high degree of access and travels to and from Indonesia.


title: Investigating the conformational dynamics of SARS-CoV-2 NSP6 protein with emphasis on non-transmembrane 91-112 & 231-290 regions

abstract:
The NSP6 protein of SARS-CoV-2 is a transmembrane protein, with some regions lying outside the membrane. Besides, a brief role of NSP6 in autophagosome formation, this is not studied significantly. Also, there is no structural information available till date. Based on the prediction by TMHMM server for transmembrane prediction, it is found that the N-terminal residues (1-11), middle region residues (91-112) and C-terminal residues (231-290) lies outside the membrane. Molecular Dynamics (MD) simulations showed that NSP6 consisting of helical structures, whereas membrane outside lying region (91-112) showed partial helicity, which further used as model and obtain disordered type conformation after 1.5 microsecond. Whereas, the residues 231-290 has both helical and beta sheet conformations in its structure model. A 200ns simulations resulted in the loss of beta sheet structures, while helical regions remained intact. Further, we have characterized the residue 91-112 by using reductionist approaches. The NSP6 (91-112) was found disordered like in isolation, which gain helical conformation in different biological mimic environmental conditions. These studies can be helpful to study NSP6 (91-112) interactions with host proteins, where different protein conformation might play significant role. The present study adds up more information about NSP6 protein aspect, which could be exploited for its host protein interaction and pathogenesis.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/451329v1_ufig1.gif" ALT="Figure 1">
View larger version (29K):
org.highwire.dtl.DTLVardef@1b6e8aborg.highwire.dtl.DTLVardef@165564eorg.highwire.dtl.DTLVardef@551f7org.highwire.dtl.DTLVardef@1485518_HPS_FORMAT_FIGEXP  M_FIG C_FIG The schematic representation of NSP6 membrane topology and conformational dynamics of residue 91-112. The N-terminal and C-terminal are shown in cytoplasmic side based on the experimental evidence on coronaviruses reported by Oostra et al., 2008. The membrane anchoring domain are shown based on the TMHMM server prediction.


title: An Autoantigen Profile from Jurkat T-Lymphoblasts Provides a Molecular Guide for Investigating Autoimmune Sequelae of COVID-19

abstract: In order to understand autoimmune phenomena contributing to the pathophysiology of COVID-19 and post-COVID syndrome, we have been profiling autoantigens (autoAgs) from various cell types. Although cells share numerous autoAgs, each cell type gives rise to unique COVID-altered autoAg candidates, which may explain the wide range of symptoms experienced by patients with autoimmune sequelae of SARS-CoV-2 infection. Based on the unifying property of affinity between autoantigens (autoAgs) and the glycosaminoglycan dermatan sulfate (DS), this paper reports 140 candidate autoAgs identified from proteome extracts of human Jurkat T-cells, of which at least 105 (75%) are known targets of autoantibodies. Comparison with currently available multi-omic COVID-19 data shows that 125 (89%) of DS-affinity proteins are altered at protein and/or RNA levels in SARS-CoV-2-infected cells or patients, with at least 94 being known autoAgs in a wide spectrum of autoimmune diseases and cancer. Protein alterations by ubiquitination and phosphorylation in the viral infection are major contributors of autoAgs. The autoAg protein network is significantly associated with cellular response to stress, apoptosis, RNA metabolism, mRNA processing and translation, protein folding and processing, chromosome organization, cell cycle, and muscle contraction. The autoAgs include clusters of histones, CCT/TriC chaperonin, DNA replication licensing factors, proteasome and ribosome proteins, heat shock proteins, serine/arginine-rich splicing factors, 14-3-3 proteins, and cytoskeletal proteins. AutoAgs such as LCP1 and NACA that are altered in the T cells of COVID patients may provide insight into T-cell responses in the viral infection and merit further study. The autoantigen-ome from this study contributes to a comprehensive molecular map for investigating acute, subacute, and chronic autoimmune disorders caused by SARS-CoV-2.


title: Genomes of novel Myxococcota reveal severely curtailed machineries for predation and cellular differentiation

abstract:
Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, non-soil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes, and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of thirteen distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g. FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine-learning approaches based on a set of 634 genes informative of social lifestyle predicted a non-social behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities, but encoded genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 Mya in response to the rise of soil as a distinct habitat on earth.

ImportanceThe Myxococcota is a phylogenetically coherent bacterial lineage that exhibits unique social traits. Cultured Myxococcoat are predominantly aerobic soil-dwelling microorganisms that are capable of predation and fruiting body formation. However, multiple yet-uncultured lineages within the Myxococcota has been encountered in a wide range of non-soil, predominantly anaerobic habitats; and the metabolic capabilities, physiological preferences, and capacity of social behavior of such lineages remains unclear. Here, we analyzed genomes recovered from a metagenomic analysis of an anoxic freshwater spring in Oklahoma, USA that represent novel, yet-uncultured, orders and families in the Myxococcota. The genomes appear to lack the characteristic hallmarks for social behavior encountered in Myxococcota genomes, and displayed a significantly smaller genome size and a smaller number of genes encoding biosynthetic gene clusters, peptidases, signal transduction systems, and transcriptional regulators. Such perceived lack of social capacity we confirmed through detailed comparative genomic analysis of thirteen pathways associated with Myxococcota social behavior, as well as the implementation of machine learning approaches to predict social behavior based on genome composition. Metabolically, these novel Myxococcota are predicted to be strict anaerobes, utilizing fermentation, nitrate rductio, and dissimilarity sulfate reduction for energy acquisition. Our result highlight the broad patterns of metabolic diversity within the yet-uncultured Myxococcota and suggest that the evolution of predation and fruiting body formation in the Myxococcoat has occurred in response to soil formation as a distinct habitat on earth.


title: Alkane-priming of Beauveria bassiana strains to improve biocontrol of the redbanded stink bug Piezodorus guildinii and the bronze bug Thaumastocoris peregrinus

abstract: Insect Epicuticle hydrocarbons (CHC) are known to be important determinants in the susceptibility degree of insects to fungal entomopathogens. Five Beauveria bassiana isolates were phenotypically analyzed regarding their response to CHC nutrition and their pathogenicity and virulence towards high fungal-susceptible Thaumastocoris peregrinus and low fungal-susceptible Piezodorus guildinii, which are important hemipteran pests in eucalyptus and soybean plantations, respectively. Two of these isolates, resulting the most (ILBB308) and the least (ILBB299) virulent to P. guildinii, were also evaluated at gene expression level after growth on n-pentadecane. B. bassiana most virulent isolate ILBB308 showed the lowest growth on most evaluated CHC media. However, this isolate distinctively induced most of the analyzed genes involved in CHC assimilation, cuticle degradation and stress tolerance. Virulence towards low susceptibility P. guildinii was enhanced in both hypervirulent ILB308 and hypovirulent ILBB299 isolates after growth on n-pentadecane as the sole carbon source, whereas virulence enhancement towards high susceptibility T. peregrinus was not observed in alkane-grown fungi. Virulence enhancement towards P. guildinii could be mostly explained by a priming effect produced by CHC on the induction of some genes related to hydrocarbon assimilation in ILB 205 and ILB 308, such as hydrophobin (Bbhyd2) and cytochrome P450 genes (BbCyp52g11 and BbCyp52x1), and partially by the induction of genes related to cuticle degradation (Bbchit and Bbcdep1) and stress tolerance (Bbsod1) observed only in ILB308.


title: Entering into a self-regulated learning mode prevents detrimental effect of feedback removal on memory

abstract: Recently, we provided causal evidence that self-regulated dopamine signaling enhanced long-term memory formation in the absence of any external feedback or reward (Ripolles et al., 2016, 2018) if a congruent meaning inferred from semantic context (DA-dependent learning), while DA-signals were absent if no congruent meaning could be inferred (DA-independent learning). Here, we investigated the interaction of self-regulated learning with externally-regulated DA-signalling by providing external performance feedback in the first or second half of trials. We found that removing feedback during DA-dependent learning lowered subsequent recognition rates a day later, whereas recognition remained high in the group which received feedback only in the second half. In contrast, feedback modestly enhanced recognition rates for both groups for DA-independent learning. Our findings suggest that external reinforcers can selectively impair DA-dependent memories if internal DA-dependent processes are not already established and highlights the relevance of self-regulated learning in education to support stable memory formation.


title: Visual perturbation of balance suggests impaired neuromuscular stability but intact visuo-motor control in Parkinson's disease

abstract:
Postural instability marks one of the most disabling features of Parkinsons disease (PD), but only reveals itself after affected brain areas have already been significantly damaged. Thus, there is a need to detect deviations in balance and postural control before visible symptoms occur. In this study, we visually perturbed balance in the anterior-posterior direction using sinusoidal oscillations of a moving room in virtual reality at different frequencies. We tested three groups: individuals with PD under dopaminergic medication, an age-matched control group, and a group of young healthy adults. We tracked their centre of pressure and their full-body motion. We investigated sway amplitudes and applied newly introduced phase-locking analyses to investigate responses across participants bodies. Patients exhibited significantly higher sway amplitudes as compared to the control subjects. However, their sway was phase-locked to the visual motion like that of age-matched and young healthy adults. Furthermore, all groups successfully compensated for the visual perturbation by - most likely reflexively - phase-locking their sway to the stimulus. As frequency of the perturbation increased, distribution of phase-locking (PL) across the body revealed a shift of the highest PL-values from the upper body towards the hip-region for young healthy adults, which could not be observed in patients and elderly healthy adults. Our findings suggest an impaired neuromuscular stability, but intact visuomotor processing in early stages of PD, while less flexibility to adapt postural strategy to different perturbations revealed to be an effect of age rather than disease.

New & NoteworthyA better understanding of visuomotor control in Parkinsons disease (PD) potentially serves as a tool for earlier diagnosis, which is crucial for improving patients quality of life. In our study, we assess body sway responses to visual perturbations of the balance control system in patients with early-to-mid stage PD, using motion tracking along with recently established phase-locking techniques. Our findings suggest patients at this stage to have an impaired muscular stability but intact visuomotor control.


title: Dual-lipid metabolomics revealed the communication of MTB or MB with Bovine alveolar macrophages in lipid metabolisms

abstract:
M. tuberculosis(MTB) and M. bovis(MB) of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of the notorious infectious disease tuberculosis(TB) in a range of mammals, including cattle and human. The lipid composition of MTB/MB performed imperative function as invading host macrophage. In the present study, a dual-lipid metabolomics were used to elucidate the differences in lipid composition of MTB and MB and the different responses in lipid metabolisms of bovine alveolar macrophage challenged by MTB/MB. The lipid metabolomics of MTB and MB indicated that there were significant differences in lipid composition of both bacteria that the level of various lipids belonged to Glycerophospholipids, Sterol Lipids, Fatty Acyls and Polyketides exhibited differences between MTB and MB. Meanwhile, both MTB and MB with different lipid composition could invoked different responses in lipid metabolisms of the host macrophage. MTB infection mainly induced the increase in content of Polyketides and Glycerophospholipids in macrophages, whereas MB infection induced the level of Glycerophospholipids and Sterol Lipids of macrophages. Furthermore, we identified TAG 13:0-18:5-18:5 of MTB and PC(16:1(9E)/0:0), PI(20:2(11Z,14Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)), 4,6-Decadiyn-1-ol isovalerate and LacCer(d18:1/24:1(15Z)) of MB caused the different variations in lipid metabolisms of macrophage following MTB/MB attacks, respectively. Finally, we proposed MTB and MB with different lipid compositions could successfully colonize in macrophage by different mechanisms that MTB could promote the formation of foam cells of macrophage for its colonization and development, while MB mainly through suppressing the macrophage autophagy to escape the immune responses of host.

ImportanceThe differences in lipid composition of MTB and MB and the different responses in lipid metabolisms of bovine alveolar macrophage challenged by MTB/MB were elucidated in this study. The lipid composition of MTB and MB exhibited significantly different patterns, which could induced different responses of the host macrophage during the infection process of MTB or MB, respectively. MTB infection mainly induced the increase in content of Polyketides and Glycerophospholipids in macrophages, whereas MB infection induced the level of Glycerophospholipids and Sterol Lipids of macrophages.The results presented here thus provides a comprehensively dual-lipid metabolomics profile in MTB/MB and MTB/MB-attacked macrophages, which deepened our understanding of the interaction between host and pathogens in lipid metabolisms.


title: LI-Seq: A Cost-Effective, Low Input DNA method for Whole Genome Library Preparation

abstract:
O_LISamples from species of high conservation concern are often low in total genomic DNA. Whole Genome Sequencing (WGS) can provide many insights that can be used to aid in species conservation, but current methods for working with low quality and low input samples can be cost prohibitive for population level genomic analyses. Thus, there is an urgent need for a cost-effective method of preparing WGS libraries from low input DNA samples.
C_LIO_LITo bridge the gap between sampling techniques commonly used in conservation genetics that yield low quality and low input DNA and the powerful tool of WGS, we developed LI-Seq, a more efficient method that successfully produces libraries from low quality DNA with as low input as 0.48 ng of DNA, with an average final library size of 300-500 base pairs.
C_LIO_LISequencing results suggest no difference in sequencing quality or coverage between low quality, low input and high quality, high input starting material using our protocol. We conclude that our new method will facilitate high-throughput WGS on low quality, low input samples, thus expanding the power of genomic tools beyond traditional high quality samples.
C_LI

category: genetics


title: DiMeLo-seq: a long-read, single-molecule method for mappingprotein-DNA interactions genome-wide

abstract: Molecular studies of genome regulation often rely on the ability to map where specific proteins interact with genomic DNA. Existing techniques for mapping protein-DNA interactions genome-wide rely on DNA amplification methods followed by sequencing with short reads, which dissociates joint binding information at neighboring sites, removes endogenous DNA methylation information, and precludes the ability to reliably map interactions in repetitive regions of the genome. To address these limitations, we created a new protein-DNA mapping method, called Directed Methylation with Long-read sequencing (DiMeLo-seq), which methylates DNA near each target proteins DNA binding site in situ, then leverages the ability to distinguish methylated and unmethylated bases on long, native DNA molecules using long-read, single-molecule sequencing technologies. We demonstrate the optimization and utility of this method by mapping the interaction sites of a variety of different proteins and histone modifications across the human genome, achieving a single-molecule binding site resolution of less than 200 bp. Furthermore, we mapped the positions of the centromeric histone H3 variant CENP-A in repetitive regions that are unmappable with short reads, while simultaneously analyzing endogenous CpG methylation and joint binding events on single molecules. DiMeLo-seq is a versatile method that can provide multimodal and truly genome-wide information for investigating protein-DNA interactions.


title: The orexigenic force of olfactory palatable food cues in sated rats

abstract:
BackgroundEnvironmental cues recalling palatable foods are ubiquitous and motivate eating beyond metabolic need, yet the timing of this response and whether it can develop towards a non-palatable readily available food remain elusive. Although there is increasing evidence indicating that external stimuli in the olfactory modality can communicate with the major hub in the feeding neurocircuitry, the hypothalamic arcuate nucleus (Arc), the identity of hypothalamic substrates has been only partially uncovered.

MethodsUsing a palatable home-cage hidden-food paradigm, we investigate the ability of olfactory food cues to promote chow overconsumption in sated male rats, together with their impact on meal pattern. We likewise explore, by means of an immediate early gene marker, the neural mechanisms involved, including the possible engagement of the orexigenic ghrelin system.

ResultsOlfactory detection of a familiar palatable food shifts diurnal patterns towards an increase in meal frequency to cause persistent overconsumption of chow in sated conditions. In line with the orexigenic response observed, sensing the palatable food in the environment stimulates food-seeking and risk-taking behavior, and also triggers release of active ghrelin. Olfactory food cues recruit intermingled populations of cells embedded within the feeding circuitry within the Arc, including, notably, those containing the ghrelin receptor, even when food is not available for consumption.

ConclusionsThese data demonstrate leverage of ubiquitous food cues, not only for palatable food-searching, but also to powerfully drive food consumption in ways that resonate with heightened hunger, for which the orexigenic ghrelin system is implicated.


title: Traip Mitotic Function Controls Brain Size

abstract: Microcephaly is a developmental failure to achieve proper brain size and neuron number. Mutations in diverse genes are linked to microcephaly, including several with DNA damage repair (DDR) functions; however, it is not well understood how these DDR gene mutations limit brain size. One such gene is TRAIP, which has multiple known functions in DDR. We characterized the Drosophila ortholog Traip, finding that loss of Traip causes a brain-specific defect in the Mushroom Body (MB). Traip mutant (traip-) MBs had reduced size and fewer neurons, but no neurodegeneration, consistent with human primary microcephaly disorders. Reduced neuron numbers in traip- were explained by premature caspase-dependent cell death of MB neuroblasts (MB-NBs). Many traip- MB-NBs had prominent chromosome bridges in anaphase, along with polyploidy, aneuploidy, or micronuclei. We found no evidence for an interphase DNA repair role for Traip in MB-NBs; instead, proper MB development requires Traip function during mitosis, where Traip localizes to centrosomes and mitotic spindles. Our results suggest that proper brain size is ensured by the recently described role for TRAIP in unloading stalled replication forks in mitosis, which suppresses DNA bridges and neural stem cell death to promote proper neuron number. Further, the mitotic nature of traip- MB-NB defects and Traip localization suggest a closer etiological link between DDR microcephaly genes like Traip and the centrosome/spindle-related genes more commonly associated with microcephaly.


title: What is behavior? No seriously, what is it?

abstract: Studying  behavior lies at the heart of many disciplines. Nevertheless, academics rarely provide an explicit definition of what  behavior actually is. What range of definitions do people use, and how does that vary across disciplines? To answer these questions we have developed a survey to probe what constitutes  behavior. We find that academics adopt different definitions of behavior according to their academic discipline, animal model that they work with, and level of academic seniority. Using hierarchical clustering, we identify at least six distinct types of  behavior which are used in seven distinct operational archetypes of  behavior. Individual respondents have clear consistent definitions of behavior, but these definitions are not consistent across the population. Our study is a call for academics to clarify what they mean by  behavior wherever they study it, with the hope that this will foster interdisciplinary studies that will improve our understanding of behavioral phenomena.