title: Role of the amino acid mutations in the HA gene of H9N2 avian influenza virus under selective pressure in escape vaccine antibodies

abstract:
It has been well-documented that some amino acid mutations in hemagglutinin (HA) of H9N2 avian influenza virus (H9N2 virus) alter the viral antigenicity, but little is reported about the role of antibody escape mutations in escape vaccine antibodies. In this study, we found that the evolution of F/98 strain in chicken embryos or chickens resulted in significant differences in immune escape, and identify the contribution of HA mutations to the antigenic variation and immune escape of H9N2 virus. Among amino acid mutations in the HA of the antigen variant viruses occurring in embryonated chicken eggs and/or chickens with or without the selection pressure of vaccine antibodies, the mutations, S145N, Q164L, A168T, A198V, M224K and Q234L, affect the antigen drift of H9N2 virus. Specially, the A198V mutation, located at the receptor-binding site on the head domain of HA, significantly contributed the antigenic variation of H9N2 virus. The mutation A198V or Q234L significantly improved the receptor binding activity, while S145N mutation decreased the receptor binding activity. Single S145N mutation could promote viral escape from polyclonal antibodies (pAbs) by preventing Ab binding physically, and single A198V mutation could promote viral escape from pAbs by enhancing the receptor binding activity. Additionally, either the mutation S145N or A198V did interfere with the immunogenicity of the inactivated vaccine, resulting in reduction of the protective efficiency of H9N2 inactivated vaccine, which contributed escape from the antibody-based immunity. Our findings provided an important reference for the accurate evaluation of the role of the amino acids mutation in HA affecting the antigenicity of H9N2 virus on immune escape, and delivered a new perspective for monitoring the adaptive evolution of H9N2 virus.

ImportanceIn this study, the role of the HA mutations of H9N2 virus occurring with and without antibody selective pressure on escaping from the antibody-based immune response in host was analyzed. The results demonstrated that (i) the HA mutations S145N, Q164L, A168T, A198V, M224K, and Q234L occurring in the process of the adaptive evolution of H9N2 virus in embryonated chicken eggs and/or chickens could affect the antigenic variation of H9N2 virus. Among these mutations, the HA mutation A198V had the most significant effect on the antigenic variation; (ii) S145N mutation promoted viral escape from pAbs by preventing Abs binding physically; (iii) A198V mutation did promote viral escape from pAbs by enhancing the receptor binding activity; (iv) neither the HA mutation S145N or A198V interfered with the immunogenicity of the inactivated vaccine, resulting in reduction of the protective efficiency of H9N2 inactivated vaccine.


title: Decoding assembly of alpha-helical transmembrane pores through intermediate states

abstract: Membrane-active pore-forming alpha-helical peptides and proteins are well known for their dynamic assembly mechanism and it has been critical to delineate the pore-forming structures in the membrane. Previously, attempts have been made to elucidate their assembly mechanism and there is a large gap due to complex pathways by which these membrane-active pores impart their effect. Here we demonstrate the multi-step structural assembly pathway of alpha-helical peptide pores formed by a 37 amino-acid synthetic peptide, pPorU based on the natural porin from Corynebacterium urealyticum using single-channel electrical recordings. More specifically, we report detectable intermediates states during membrane insertion and pore formation of pPorU. The fully assembled pore is functional and exhibited unusually large stable conductance and voltage-dependent gating, generally applicable to a range of pore-forming proteins. Furthermore, we used rationally designed mutants to understand the role of specific amino acids in the assembly of these peptide pores. Mutant peptides that differ from wild-type peptides produced noisy, unstable intermediate states and low conductance pores, demonstrating sequence specificity in the pore-formation process supported by molecular dynamics simulations. We suggest that our study contributes to understanding the mechanism of action of alpha-helical pores and antimicrobial peptides and should be of broad interest to bioengineers to build peptide-based nanopore sensors.

category: biophysics


title: α-/γ-Taxilin are required for centriolar subdistal appendage assembly and microtubule organization

abstract: The centrosome, composed of a pair of centrioles (mother and daughter centrioles) and pericentriolar material, is mainly responsible for microtubule nucleation and anchorage in animal cells. The subdistal appendage (SDA) is a centriolar structure located at the subdistal region on the mother centriole, and it functions in microtubule anchorage. However, the molecular composition and detailed structure of SDA remain largely unknown. Here, we identified a-taxilin and r-taxilin as new SDA components, which form a complex via their coiled-coil domains and serve as a new subgroup during SDA hierarchical assembly. Their SDA localization is dependent on ODF2, and -taxilin recruits CEP170 to the SDA. Functional analyses suggest that -taxilin and {gamma}-taxilin are responsible for centrosomal microtubule anchorage during interphase, as well as for proper spindle orientation during metaphase. Altogether, our results shed light on the molecular components and functional understanding of the SDA hierarchical assembly and microtubule organization.

category: cell biology


title: Copper selects for siderophore-mediated virulence in Pseudomonas aeruginosa

abstract: Iron is essential for almost all bacterial pathogens and consequently it is actively withheld by their hosts. However, the production of extracellular siderophores enables iron sequestration by pathogens, increasing their virulence. Another function of siderophores is extracellular detoxification of non-ferrous metals. Here, we experimentally link the detoxification and virulence roles of siderophores by testing whether the opportunistic pathogen Pseudomonas aeruginosa displays greater virulence after exposure to copper. To do this, we incubated P. aeruginosa under different environmentally relevant copper regimes for either two or twelve days. Subsequent growth in a copper-free environment removed phenotypic effects, before we quantified pyoverdine production (the primary siderophore produced by P. aeruginosa), and virulence using the Galleria mellonella infection model. Copper selected for increased pyoverdine production, which was positively correlated with virulence. This effect increased with time, such that populations incubated with high copper for twelve days were the most virulent. Replication of the experiment with a non-pyoverdine producing strain of P. aeruginosa demonstrated that pyoverdine production was largely responsible for the change in virulence. Therefore we here show a direct link between metal stress and bacterial virulence, highlighting another dimension of the detrimental effects of metal pollution on human health.

category: ecology


title: A unique sulfotransferase-involving strigolactone biosynthetic route in Sorghum

abstract:
LOW GERMINATION STIMULANT 1 (LGS1) plays an important role in strigolactones (SLs) biosynthesis and Striga resistance in sorghum but the catalytic function remains unclear. Using the recently developed SL-producing microbial consortia, we examined the activities of sorghum MAX1 analogs and LGS1. Surprisingly, SbMAX1d (accession # XP_002458367) synthesized 18-hydroxy-carlactonoic acid (18-hydroxy-CLA) directly from carlactone (CL) through four-step oxidations, and addition of LGS1 led to the synthesis of both 5-deoxystrigol (5DS) and 4-deoxyorobanchol (4DO). Further biochemical characterization found that LGS1 functions after SbMAX1d by converting 18-hydroxy-CLA to 18-sulphate-CLA to provide an easier leaving group to afford a spontaneous formation of 5DS and 4DO. The unique functions of SbMAX1 and LGS1 imply a previously unknown synthetic route towards strigolactones.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/459372v1_ufig1.gif" ALT="Figure 1">
View larger version (12K):
org.highwire.dtl.DTLVardef@2252eeorg.highwire.dtl.DTLVardef@172a0f8org.highwire.dtl.DTLVardef@a630e4org.highwire.dtl.DTLVardef@d3e2b6_HPS_FORMAT_FIGEXP  M_FIG C_FIG

category: biochemistry


title: A high throughput bispecific antibody discovery pipeline

abstract: Bispecific antibodies (BsAbs) represent an emerging class of immunotherapy but inefficiency in the current BsAb discovery paradigm has limited their broad clinical availability. Here we report a high throughput, agnostic, single-cell-based BsAb functional screening pipeline, comprising molecular and cell engineering for efficient generation of BsAb library cells, followed by functional interrogation at the single-cell level to identify and sort positive clones and downstream sequence identification with single-cell PCR and sequencing and functionality characterization. Using a CD19xCD3 bispecific T cell engager (BiTE) as a model system, we demonstrate that our single cell platform possesses a high throughput screening efficiency of up to one and half million variant library cells per run and can isolate rare functional clones at low abundance of 0.008%. Using a complex CD19xCD3 BiTE-expressing cell library with approximately 22,300 unique variants comprising combinatorially varied scFvs, connecting linkers and VL/VH orientations, we have identified 98 unique clones including extremely rare ones ([~] 0.001% abundance). We also discovered BiTEs that exhibit novel properties contradictory to conventional wisdom, including harboring rigid scFv connecting peptide linkers yet with in vitro cytotoxicity comparable to that of clinically approved Blinatumomab. Through sequencing analyses on sorted BiTE clones, we discovered multiple design variable preferences for functionality including the CD19VL-VH- CD3VH-VL and CD19VH-VL-CD3VH-VL arrangements being the most favored orientation. Sequence analysis further interrogated the sequence composition of the CDRH3 domain in scFvs and identified amino acid residues conserved for function. We expect our single cell platform to not only significantly increase the development speed of high quality of new BsAb therapeutics for cancer and other disorders, but also enable identifying generalizable design principles for new BsAbs and other immunotherapeutics based on an in-depth understanding of the inter-relationships between sequence, structure, and function.

category: bioengineering


title: cDNA display coupled with next-generation sequencing for rapid activity-based screening: Comprehensive analysis of transglutaminase substrate preference

abstract: cDNA display is an in vitro display technology based on a covalent linkage between a protein and its corresponding mRNA/cDNA, where a stable complex is formed suitable for a wide range of selection conditions. A great advantage of cDNA display is the ability to handle enormous library size (1012) in a microtube scale, in a matter of days. To harness its benefits, we aimed at developing a platform which combines the advantages of cDNA display with high-throughput and accuracy of next-generation sequencing (NGS) for the selection of preferred substrate peptides of transglutaminase 2 (TG2), a protein cross-linking enzyme. After the optimization of the platform by the repeated screening of binary model libraries consisting of the substrate and non-substrate peptides at different ratios, screening and selection of combinatorial peptide library randomized at positions -1, +1, +2, and +3 from the glutamine residue was carried out. Enriched cDNA complexes were analyzed by NGS and bioinformatics, revealing the comprehensive amino acid preference of the TG2 at targeted positions of the peptide backbone. This is the first report on the cDNA display/NGS screening system to yield comprehensive data on TG substrate preference. Although some issues remain to be solved, this platform can be applied to the selection of other TGs and easily adjusted for the selection of other peptide substrates and even larger biomolecules.


title: Anterior Gradient-2 (AGR2) overexpression in colon cancer: a potential prognostic biomarker

abstract:
AimsColon cancer is one of the most common leading causes of death worldwide. Prognostic at an early stage is an efficient way to decrease mortality. The Endoplasmic Reticulum (ER)-resident protein anterior gradient-2 (AGR2), a Protein Disulfide Isomerase (PDI) is highly expressed in various solid tumours and is involved in tumour microenvironment-associated processes such as tumour growth, invasion and metastasis. This study aims at examining the expression of AGR2 protein in colon cancer as its prognostic value in such cancer remains inconclusive.

MethodsAGR2 protein expression was determined using immunohistochemistry on human tissue samples issued from a cohort of 82 colorectal carcinomas (Institut Bergonie, Bordeaux, France).

ResultsAGR2 protein expression was significantly higher in tumours than in adjacent non-tumour controls. AGR2 expression subgroup analyses indicated that AGR2 low expression in colon cancer patients was significantly associated with worse overall survival. Mucinous colon cancers exhibited higher AGR2 expression levels than non-mucinous cancers. Additionally, tumours with microsatellite instability (MSI) were characterised by a strong upregulation of AGR2 mRNA and protein expression despite an absence of MLH1/MSH2 mutations.

ConclusionOur findings indicate that high AGR2 protein expression is correlated with longer patient survival and that AGR2 overexpression is associated with MSI and mucinous-type colorectal cancers. Overall, AGR2 might serve as a biomarker to stratify colon tumours and to contribute to the prognosis of colon cancer patients.

category: cancer biology


title: Transcriptional regulation of HSCs in Aging and MDS reveals DDIT3 as a Potential Driver of Transformation

abstract:
Myelodysplastic syndromes (MDS) are hematopoietic stem cell (HSC) malignancies characterized by ineffective hematopoiesis, with increased incidence in elderly individuals. In this work, we analyzed the transcriptome of human HSCs purified from young and elderly healthy donors, as well as MDS patients, identifying transcriptional alterations following eight different patterns of expression. While aging-associated lesions seemed to predispose HSCs to myeloid transformation, disease-specific alterations may trigger MDS development. Among MDS-specific lesions, we detected the upregulation of the transcription factor DDIT3. Overexpression of DDIT3 in human healthy HSCs induced an MDS-like transcriptional state, and a delay in erythropoiesis. Such effect was associated with downregulation of transcription factors required for normal erythropoiesis, and with a failure in the activation of their transcriptional programs. Moreover, DDIT3 knockdown in CD34+ cells from MDS patients with anemia was able to restore erythropoiesis. These results identify DDIT3 as a driver of dyserythropoiesis, and a potential therapeutic target to restore the inefficient erythropoiesis characterizing MDS patients.

STATEMENT OF SIGNIFICANCEThis study defines how human aging and MDS development are characterized by transcriptional alterations in HSCs that follow different patterns, some of which may contribute to myeloid transformation. Among them, we demonstrate how MDS-specific upregulation of DDIT3 in HSCs induces dyserythropoiesis, while its knockdown in HSPCs from MDS patients restores proper erythroid differentiation.


title: Transcriptional regulation of HSCs in Aging and MDS reveals DDIT3 as a Potential Driver of Dyserythropoiesis


title: Magnetic fluctuations affect circadian patterns of locomotor activity in zebrafish

abstract: The locomotor activity of zebrafish (Danio rerio) has a pronounced, well-studied circadian rhythm. Under constant illumination, the period of free-running locomotor activity in this species usually becomes less than 24 hours. To evaluate the entraining capabilities of slow magnetic variations, zebrafish locomotor activity was evaluated at constant illumination and fluctuating magnetic field with a period of 26.8 hours. Lomb-Scargle periodogram revealed significant free-running rhythms of locomotor activity and related behavioral endpoints with a period close to 27 hours. Obtained results reveal the potential of slow magnetic fluctuations for entrainment of the circadian rhythms in zebrafish. The putative mechanisms responsible for the entrainment are discussed, including the possible role of cryptochromes.

category: physiology


title: Canopy health, but not Candidatus Liberibacter asiaticus Ct values, are correlated with fruit yield in Huanglongbing affected sweet orange trees.

abstract: In Florida, almost all citrus trees are infected with Huanglongbing (HLB), caused by the gram-negative, intracellular phloem limited bacteria Candidatus liberibacter asiaticus (CLas). Distinguishing between the severely and mildly sick trees is important for managing the groves and testing new HLB therapies. A mildly sick tree is one that produces higher fruit yield, compared to a severely sick tree, but measuring yields is laborious and time consuming. Here we characterized HLB affected sweet orange trees in the field in order to identify the specific traits that are correlated with the yields. We found that canopy volume, fruit detachment force (FDF) and the percentage of photosynthetically active radiation interception in the canopy (%INT) were positively correlated with fruit yields. Specifically, %INT measurements accurately distinguished between mild and severe trees in independent field trials. We could not find a difference in the Ct value between high and low producing HLB trees. Moreover, Ct values did not always agree with the number of CLas in the phloem that were visualized by transmission electron microscopy. Overall, our work identified an efficient way to distinguish between severe and mild HLB trees in Florida by measuring %INT and suggests that health of the canopy is more important for yields than the Ct value.

category: plant biology


title: Diet specialization in an insular population of coastal Peregrine Falcons

abstract: Individual diet specialization is known to occur in populations of generalist predators, where specific individuals develop specialist feeding strategies. Diet specialization has been reported in many raptor species, and it may be an important driver of intraspecific population structure. Here, we quantify the diet of five breeding pairs of Peregrine Falcons Falco peregrinus from an offshore island determined from prey remains collected over four breeding seasons. Three prey species accounted for 69.8 % of total prey frequency, with Manx Shearwater Puffinus puffinus the primary prey accounting for 47.3 % by frequency and 40.8 % by biomass. Herring Gull Larus argentatus was the second most important prey species by frequency (13.8 %) and biomass (29.8 %) followed by Domestic Pigeon Columba livia (frequency = 8.7 %, biomass = 7.0 %). Predation frequency on specific prey groups varied substantially between breeding pairs and months. Two pairs specialized on Manx Shearwater, one pair specialized on Herring Gull and Manx Shearwater, with the remaining two pairs having a relatively generalist diet of Manx Shearwaters, Domestic Pigeon and small passerines. Predation on Manx Shearwaters increased throughout the breeding season with a peak in total diet frequency of 63.8 % in July, with a concurrent decrease in Herring Gull predation frequency. Higher percentage of Manx Shearwater in the diet was able to explain 87 % of the variation in a narrower dietary breadth for the Peregrine pairs. Our results suggest individual diet specialization may be important for understanding population density in insular raptor populations.


title: Preventing co-infection: a viral strategy with short-term benefits and long-term drawbacks

abstract:
Viral superinfection occurs when multiple viral particles subsequently infect the same host. In nature, several viral species are found to have evolved diverse mechanisms to prevent superinfection (superinfection exclusion) but how this strategic choice impacts the fate of mutations in the viral population remains unclear. Using stochastic simulations, we find that genetic drift is suppressed when superinfection occurs, thus facilitating the fixation of beneficial mutations and the removal of deleterious ones. Interestingly, we also find that the competitive (dis)advantage associated with variations in life history parameters is not necessarily captured by the viral growth rate for either infection strategy. Putting these together, we then show that a mutant with superinfection exclusion will easily overtake a superinfecting population even if the latter has a much higher growth rate. Our findings suggest that while superinfection exclusion can negatively impact the long-term adaptation of a viral population, in the short-term it is ultimately a winning strategy.

Author summaryViral social behaviour has recently been receiving increasing attention in the context of ecological and evolutionary dynamics of viral populations. One fascinating and still relatively poorly understood example is superinfection or co-infection, which occur when multiple viruses infect the same host. Among bacteriophages, a wide range of mechanisms have been discovered that enable phage to prevent superinfection (superinfection exclusion) even at the cost of using precious resources for this purpose. What is the evolutionary impact of this strategic choice and why do so many phages exhibit this behaviour? Here, we conduct an extensive simulation study of a phage population to address this question. In particular, we investigate the fate of viral mutations arising in an environment with a constant supply of bacterial hosts designed to mimic a "turbidostat," as these are increasingly being used in laboratory evolution experiments. Our results show that allowing superinfection in the long-term yields a population which is more capable of adapting to changes in the environment. However, when in direct competition, mutants capable of preventing superinfection experience a very large advantage over their superinfecting counterparts, even if this ability comes at a significant cost to their growth rate. This indicates that while preventing superinfection can negatively impact the long-term prospects of a viral population, in the short-term it is ultimately a winning strategy.

category: evolutionary biology


title: Superinfection exclusion: a viral strategy with short-term benefits and long-term drawbacks


title: Immunity vs Sociality: Adaptive evolution tests suggest social lifestyle exerts greater selection pressures than host-pathogen coevolution in the bees

abstract:
Hosts and their parasites and pathogens are locked in antagonistic co-evolution. The genetic consequence of this can be seen in the rates of adaptive evolution in immunologically important loci in many taxa. As the risk of disease transmission increases we might also expect to see greater rates of adaptive evolution on genes of immune function. The evolution of sociality and its elaborations in insects represent enormous shift in disease transmission risk. Here, we examine whether sociality in the bees corresponds to changes in the rate of adaptive evolution in both classical canonical immune genes, and genes with putative immune functions identified from meta-analyses of honey-bee transcriptomic responses to infection. We find that measures of gene-wide adaptive evolution do not differ among canonical immune, non-canonical candidate immune, and background gene sets, but that branch-site adaptive evolution does increase with sociality regardless of gene category. Solitary species have greater rates of adaptive evolution in canonical immune genes than background genes, supporting the suggestion that social immune mechanisms may instead be the site of host-pathogen co-evolution in social species. We identify three genes with putative roles in immunity that warrant further attention (Vitel-logenin Vg, disks large 1 tumour suppressor, and the uncharacterised protein LOC100577972). There are more gene family changes after the origin of sociality across all gene classes, with contractions occur-ring after the elaboration of sociality to complex eusociality. There are few genes or functions under adaptive selection that appear to be shared outside of specific lineages, suggesting that evolution of the immune system may be specific to individual species and their pathogen interactions.

SignificanceInfectious disease drives rapid evolution of immune genes, but infection risk should be much higher in social species. To examine whether greater sociality drives faster immune system evolution we compared the rate of immune gene evolution in solitary, social, and highly eusocial bees. To account for possible novel immune genes in bees, we analysed classical immune genes alongside candidate immune genes inferred from other studies. Surprisingly, we find that solitary bees have the highest rate of immune gene evolution relative to background genes but that sociality is associated with rapid evolution across the whole genome. These findings suggest that 1) accelerated immune gene evolution is not universal, 2) immune gene evolution is moderated by sociality in that solitary species invest more into immune gene change, and 3) that social genomes are highly dynamic, which may obscure evolution at immunological loci. The types of immune genes and functions appear mostly lineage-specific, regardless of sociality, suggesting individual evolutionary his-tories exert more selection pressure than general patterns of greater pathogen exposure introduced by social living.


title: Clustering single cell CITE-seq data with a canonical correlation based deep learning method

abstract:
Single cell sequencing examines the sequence information from individual cells with optimized next generation sequencing (NGS) technologies. It provides researchers a higher resolution of cellular differences and a better understanding of the function of an individual cell in the context of its microenvironment. CITE-seq, or Cellular Indexing of Transcriptomes and Epitopes by sequencing, is one of the latest innovations in the domain of single cell sequencing. It enables researchers to simultaneously capture RNA and surface protein expression on the same cells so that we can correlate the two data types, identify biomarkers and better characterize cell phenotypes. Although multi-omics sequencing technologies developed rapidly, data analyzing methods tailored for multiomics sequencing data are lacking. Several serious problems have to be faced. An important one is how to integrate the information from different modalities, namely scRNA and protein data, efficiently.

In this paper, we introduce a canonical correlation based deep learning method called scCTClust for clustering analysis over CITE-seq data. We impute and extract the characteristics of the high dimensional RNA part of data with a ZINB model-based autoencoder. A t-kernel distance is introduced to measure the similarity between query cell and cluster centroids. And the protein data rectifies the feature extraction of scRNA data in a canonical correlation analysis(CCA) way. Extensive data experiments shows that scCTClust can precisely recover the dropout values for RNA sequencing data and extract authentic information from both modalities, getting a much better clustering result than state-of-the-art methods, no matter single-omic or multi-omics clustering algorithms.

category: bioinformatics


title: Methodological insights on proteogenomic approaches to enhance proteomics

abstract:
BackgroundProteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these large proteogenomic databases produce lower-sensitivity peptide identifications. Various strategies have been proposed to avoid this, including the generation of reduced transcriptome-informed protein databases (i.e., built from reference protein databases only retaining proteins whose transcripts are detected in the sample-matched transcriptome), which were found to increase peptide identification sensitivity. Here, we present a detailed evaluation of this approach.

ResultsFirst, we established that the increased sensitivity in peptide identification is in fact a statistical artifact, directly resulting from the limited capability of target-decoy competition to accurately model incorrect target matches when using excessively small databases. As anti-conservative FDRs are likely to hamper the robustness of the resulting biological conclusions, we advocate for alternative FDR control methods that are less sensitive to database size. Nevertheless, reduced transcriptome-informed databases are useful, as they reduce the ambiguity of protein identifications, yielding fewer shared peptides. Furthermore, searching the reference database and subsequently filtering proteins whose transcripts are not expressed reduces protein identification ambiguity to a similar extent, but is more transparent and reproducible.

ConclusionIn summary, using transcriptome information is an interesting strategy that has not been promoted for the right reasons. While the increase in peptide identifications from searching reduced transcriptome-informed databases is an artifact caused by the use of an FDR control method unsuitable to excessively small databases, transcriptome information can reduce ambiguity of protein identifications.


title: Proteogenomics: an analysis of how and when itenhances proteomics


title: Transcriptome-informed reduction of protein databases: an analysis of how and when proteogenomics enhances eukaryotic proteomics


title: Three-dimensional label-free histological imaging of whole organs by microtomy-assisted autofluorescence tomography

abstract:
Three-dimensional (3D) histology is vitally important to characterize disease-induced tissue heterogeneity at the individual cell level. However, it remains a scientific challenge for both high-quality 3D imaging and volumetric reconstruction. Here we propose a label-free, automated, and ready-to-use 3D histological imaging technique, termed microtomy-assisted autofluorescence tomography with ultraviolet excitation (MATE). With the combination of block-face imaging and serial microtome sectioning, MATE can achieve rapid and label-free imaging of paraffin-embedded whole organs at an acquisition speed of 1 cm3 per 4 hours with a voxel resolution of 1.2 x 1.2 x 10 m3. We demonstrate that MATE enables simultaneous visualization of cell nuclei, fiber tracts, and blood vessels in mouse/human brains without tissue staining or clearing. Moreover, diagnostic features, such as nuclear size and packing density, can be quantitatively extracted with high accuracy. MATE is augmented to the current slide-based 2D histology, holding great promise for facilitating histopathological interpretation at the cell level to analyze complex tissue heterogeneity in 3D.

Significance StatementConventional 3D histology based on spatial registration of serial histochemically-stained thin tissue slices is fundamentally labor-intensive and inaccurate. Here, we propose a rapid and label-free 3D histological imaging technique (i.e., MATE) that enables high-resolution imaging of complex whole organs without tissue staining or clearing. MATE is fully automated to provide a series of distortion- and registration-free images with intrinsic absorption-based contrast, demonstrating great potential as a routine tissue analysis tool that can seamlessly fit into the current clinical practice to facilitate the applications of histopathological interpretation at the subcellular level.

category: pathology


title: Lifespan analysis of dystrophic mdx fast-twitch muscle morphology and its impact on contractile function

abstract: Duchenne muscular dystrophy is caused by the absence of the protein dystrophin from skeletal muscle and is characterized by progressive cycles of necrosis/regeneration. Using the dystrophin deficient mdx mouse model we studied the morphological and contractile chronology of dystrophic skeletal muscle pathology in fast twitch EDL muscles from animals 4-22 months of age containing 100% regenerated muscle fibers. Catastrophically, the older age groups lost [~]80% of their maximum force after one eccentric contraction of 20% strain, with the greatest loss [~]93% recorded in senescent 22 month old mdx mice. In old age groups there was minimal force recovery [~]24% after 120 minutes, correlated with a dramatic increase in the number and complexity of branched fibers. This data supports our two-stage model where a "tipping point" is reached when branched fibers rupture irrevocably on eccentric contraction. These findings have important implications for pre-clinical drug studies and genetic rescue strategies.


title: Selective activation of BK channels in small-headed dendritic spines suppresses excitatory postsynaptic potentials

abstract:
Dendritic spines are the main receptacles of excitatory information in the brain. Their particular morphology, with a small head connected to the dendrite by a slender neck, has inspired theoretical and experimental work to understand how these structural features affect the processing, storage and integration of synaptic inputs in pyramidal neurons (PNs).

The activation of glutamate receptors in spines triggers a large voltage change as well as calcium signals at the spine head. Thus, voltage-gated and calcium-activated potassium channels located in the spine head likely play a key role in synaptic transmission. Here we study the presence and function of large conductance calcium-activated potassium (BK) channels in spines from layer 5 PNs. We find that BK channels are localized to dendrites and spines regardless of their size, but their activity can only be detected in spines with small head volumes ([≤] 0.09 {micro}m3), which reduces the amplitude of two-photon (2P) uncaging (u) excitatory postsynaptic potentials (EPSPs) recorded at the soma. In addition, we find that calcium signals in spines with small head volumes are significantly larger than those observed in spines with larger head volumes. In accordance with our experimental data, numerical simulations predict that synaptic inputs impinging onto spines with small head volumes generate voltage responses and calcium signals within the spine head itself that are significantly larger than those observed in spines with bigger head volumes, which are sufficient to activate spine BK channels. These results show that BK channels are selectively activated in small-headed spines, suggesting a new level of dendritic spine-mediated regulation of synaptic processing, integration, and plasticity in cortical PNs.

category: neuroscience


title: Mapping electromagnetic networks to haemodynamic networks in the human brain

abstract: Whole-brain neural communication is typically estimated from statistical associations among electromagnetic or haemodynamic time-series. The relationship between functional network architectures recovered from these two types of neural activity remains unknown. Here we map electromagnetic networks (measured using magnetoencephalography; MEG) to haemodynamic networks (measured using functional magnetic resonance imaging; fMRI). We find that the relationship between the two modalities is regionally heterogeneous and systematically follows the cortical hierarchy, with close correspondence in unimodal cortex and poor correspondence in transmodal cortex. Comparison with the BigBrain histological atlas reveals that electromagnetic-haemodynamic coupling is driven by laminar differentiation and neuron density, suggesting that the mapping between the two modalities can be explained by cytoarchitectural variation. Importantly, haemodynamic connectivity cannot be explained by electromagnetic activity in a single frequency band, but rather arises from the mixing of multiple neurophysiological rhythms. Correspondence between the two is largely driven by slower rhythms, particularly the beta (15-29 Hz) frequency band. Collectively, these findings demonstrate highly organized but only partly overlapping patterns of connectivity in MEG and fMRI functional networks, opening fundamentally new avenues for studying the relationship between cortical micro-architecture and multi-modal connectivity patterns.


title: Hierarchical decoupling of electromagnetic and haemodynamic cortical networks


title: Common and distinct neurofunctional representations of core and social disgust in the brain: An ALE meta-analysis and MACM characterization

abstract: Disgust represents a multifaceted defensive-avoidance response. On the behavioral level, the response includes withdrawal and a disgust-specific facial expression. While both serve the avoidance of pathogens, the latter additionally transmits social-communicative information. Given that common and distinct brain representation of the primary defensive-avoidance response (core disgust) and encoding of the social-communicative signal (social disgust) remain debated, we employed neuroimaging meta-analyses to (1) determine brain systems generally engaged in disgust processing, and (2) segregate common and distinct brain systems for core and social disgust. Disgust processing, in general, engaged a bilateral network encompassing the insula, amygdala, occipital and prefrontal regions. Core disgust evoked stronger reactivity in left-lateralized threat detection and defensive response network including amygdala, occipital and frontal regions while social disgust engaged a right-lateralized superior temporal-frontal network engaged in social cognition. Anterior insula, inferior frontal and fusiform regions were commonly engaged during core and social disgust, suggesting a common neural basis. We demonstrate a common and separable neural basis of primary disgust responses and encoding of associated social-communicative signals.


title: Common and distinct neurofunctional representations of core and social disgust in the brain: Coordinate-based and network meta-analyses


title: Characterization of Histone Lysine β-hydroxybutyrylation in bovine tissues, cells, and cumulus-oocyte complexes

abstract:
Besides their canonical roles as energy sources, short-chain fatty acids act as metabolic regulators of gene expression through the histone post-translational modifications. The ketone body {beta}-hydroxybutyrate (BHB) was shown to cause a novel type of epigenetic modification, Histone Lysine {beta}-hydroxybutyrylation (Kbhb), associated with genes upregulated in starvation-responsive metabolic pathways. Dairy cows increase BHB in early lactation and its effects on cellular epigenome are largely unknown. To unravel these effects, we sought and identified that Kbhb is present in bovine tissues in vivo and further confirmed that this epigenetic mark is responsive to BHB in bovine and human fibroblasts cultured in vitro in a dose-dependent manner. We also demonstrated that the maturation of cumulus-oocyte complexes with high concentrations of BHB did not affect the competence to complete meiotic maturation neither to develop until blastocyst stage. BHB treatment strongly induced H3K9bhb in cumulus cells, but this modification was only faintly detected in oocytes. Profiling the transcriptome in cumulus cells indicated that BHB treatment altered the expression of 345 genes. The down-regulated genes are mainly involved in glycolysis and ribosome assembly pathways, while the up-regulated genes are involved in mitochondrial metabolism and oocyte development. The specific genes and pathways altered by BHB treatment will provide entry points to carry out functional experiments aiming to mitigate problems and improve fertility in cattle suffering metabolic disorders. A key goal for future work will be to understand mechanistically how BHB transmits signals from the environment to affect cellular functions and the bovine epigenome.

Summary sentenceBeta-hydroxybutyrate induces Histone Lysine {beta}-hydroxybutyrylation in fibroblasts and cumulus-oocyte complexes, it alters the transcriptome in cumulus cells, but does not affect oocytes competence to resume meiosis and develop until blastocyst stage.

category: developmental biology


title: The temporal dynamics of the sea urchin regulome

abstract: In this work, we used Nanostring N-counter technology, to evaluate the mRNA expression level of more than 330 regulatory genes over 34-time points covering the first three days of development of the sea urchin larvae. The hierarchical clustering of the mRNAs expression levels has identified groups corresponding to the major developmental landmarks (e.g., maternal to zygotic transition and gastrulation). Furthermore, comparison with previous experiments indicates high reproducibility of mRNA level temporal dynamics across batches. Finally, we generated an online tool to visualize gene expression during sea urchin larval development. The site can be accessed at https://nanostring2021.herokuapp.com/.


title: How do I bite thee? Let me count the ways: Heterogeneity and temperature dependence in Ae. aegypti biting habits drive individual mosquito arbovirus transmission potential

abstract: In models of mosquito-borne transmission, biting rate is the most influential parameter, and understanding the role of temperature on this process is important for assessing the transmission potential of arboviruses like dengue (DENV). Further, the process of biting is assumed to be relatively homogeneous across individuals, with time-between-bites described by an exponentially distributed process. However, these assumptions have not been addressed through laboratory experimentation. We experimentally determined daily biting habits of Ae. aegypti at three temperatures (24{degrees}C, 28{degrees}C, and 32{degrees}C) and determined that there was a high degree of individual heterogeneity in biting habits (number of bites, timing of bites, etc.). There was a significantly higher proportion of females that bit at 28{degrees}C compared to both 24{degrees}C and 32{degrees}C. We further explored the consequences of biting heterogeneity using an individual-based model designed to examine whether a particular biting profile determines whether a mosquito is more or less likely to 1) become exposed given a single index case of DENV and 2) transmit to a susceptible individual. Our results indicate that biting is heterogeneous among individuals and this heterogeneity affects transmission potential of DENV. Understanding individual-level heterogeneity in biting is important and may suggest a role for high-frequency biters as significant contributors to the transmission of DENV.


title: Simultaneous expression of UV and violet SWS1 opsins expands the visual palette in a group of freshwater snakes.

abstract: Snakes are known to express a rod visual opsin and two cone opsins, only (SWS1, LWS), a reduced palette resulting from their supposedly fossorial origins. Dipsadid snakes in the genus Helicops are highly visual predators that successfully invaded freshwater habitats from ancestral terrestrial-only habitats. Here we report the first case of multiple SWS1 visual pigments in a vertebrate, simultaneously expressed in different photoreceptors and conferring both UV and violet sensitivity to Helicops snakes. Molecular analysis and in vitro expression confirmed the presence of two functional SWS1 opsins, likely the result of recent gene duplication. Evolutionary analyses indicate that each sws1 variant has undergone different evolutionary paths, with strong purifying selection acting on the UV-sensitive copy and dN/dS [~]1 on the violet-sensitive copy. Site-directed mutagenesis points to the functional role of a single amino acid substitution, Phe86Val, in the large spectral shift between UV and violet opsins. In addition, higher densities of photoreceptors and SWS1 cones in the ventral retina suggest improved acuity in the upper visual field possibly correlated with visually-guided behaviors. The expanded visual opsin repertoire and specialized retinal architecture are likely to improve photon uptake in underwater and terrestrial environments, and provide the neural substrate for a gain in chromatic discrimination, potentially conferring unique color vision in the UV-violet range. Our findings highlight the innovative solutions undertaken by a highly specialized lineage to tackle the challenges imposed by the invasion of novel photic environments and the extraordinary diversity of evolutionary trajectories taken by visual opsin-based perception in vertebrates.


title: STAAR Workflow: A cloud-based workflow for scalable and reproducible rare variant analysis

abstract:
SummaryWe developed the STAAR WDL workflow to facilitate the analysis of rare variants in whole genome sequencing association studies. The open-access STAAR workflow written in the workflow description language (WDL) allows a user to perform rare variant testing for both gene-centric and genetic region approaches, enabling genome-wide, candidate, and conditional analyses. It incorporates functional annotations into the workflow as introduced in the STAAR method in order to boost the rare variant analysis power. This tool was specifically developed and optimized to be implemented on cloud-based platforms such as BioData Catalyst Powered by Terra. It provides easy-to-use functionality for rare variant analysis that can be incorporated into an exhaustive whole genome sequencing analysis pipeline.

Availability and implementationThe workflow is freely available from https://dockstore.org/workflows/github.com/sheilagaynor/STAAR_workflow.

category: genetics


title: GABOLA: A Reliable Gap-Filling Strategy for de novo Chromosome-Level Assembly

abstract:
We propose a novel method, GABOLA, which utilizes long-range genomic information provided by accurate linked short reads jointly with long reads to improve the integrity and resolution of whole genome assemblies especially in complex genetic regions. We validated GABOLA on human and Japanese eel genomes. On the two human samples, we filled in more bases spanning 23.3Mbp and 46.2Mbp than Supernova assembler, covering over 3,200 functional genes which includes 8,500 exons and 15,000 transcripts. Among them, multiple genes related to various types of cancer were identified. Moreover, we discovered additional 11,031,487 base pairs of repeat sequences and 218 exclusive repeat patterns, some of which are known to be linked to several disorders such as neuron degenerative diseases. As for the eel genome, we successfully raised the genetic benchmarking score to 94.6% while adding 24.7 million base pairs. These results manifest the capability of GABOLA in the optimization of whole genome assembly and the potential in precise disease diagnosis and high-quality non-model organism breeding.

Availability: The docker image and source code of GABOLA assembler are available at https://hub.docker.com/r/lsbnb/gabola and https://github.com/lsbnb/gabola respectively.

category: genomics


title: Honest cues contribute to male choice for female guarding in a herbivorous spider mite.

abstract: Mate choice is a wide-spread phenomenon with important effects on ecological and evolutionary dynamics of successive generations. Increasing evidence shows that males can choose females if females vary in quality and these mating choices can strongly impact fitness. In the herbivorous spider mite Tetranychus urticae males engage in precopulatory mate guarding of quiescent females, and it is known that females vary in their time to sexual maturity and fecundity. However, our understanding of how males maximize their reproductive success and which female phenotypic traits are important cues for their mating decisions are still limited. In many arthropod species, female body size and pheromones are well known proxies for fecundity. These traits--and thus possibly male mating decisions--are however sensitive to environmental (dietary) stress. By allowing males to freely choose amongst many (synchronized) females in a controlled semi natural environment, we found that guarded females have a higher fecundity and are closer to sexual maturity than non-guarded females. Despite the fact that female body size was positively correlated with fecundity and significantly influenced by the environment, males did not discriminate on body size nor did we find evidence that they used other cues like cuticular pheromones or copying behavior (social cues). In conclusion we were able to show male mate preference for females that are closer to sexual maturity and have higher fecundity, but we were unable to identify the female traits that signal this information

category: animal behavior and cognition


title: ELeFHAnt: A supervised machine learning approach for label harmonization and annotation of single cell RNA-seq data

abstract: Annotation of single cells has become an important step in the single cell analysis framework. With advances in sequencing technology thousands to millions of cells can be processed to understand the intricacies of the biological system in question. Annotation through manual curation of markers based on a priori knowledge is cumbersome given this exponential growth. There are currently ~200 computational tools available to help researchers automatically annotate single cells using supervised/unsupervised machine learning, cell type markers, or tissue-based markers from bulk RNA-seq. But with the expansion of publicly available data there is also a need for a tool which can help integrate multiple references into a unified atlas and understand how annotations between datasets compare. Here we present ELeFHAnt: Ensemble learning for harmonization and annotation of single cells. ELeFHAnt is an easy-to-use R package that employs support vector machine and random forest algorithms together to perform three main functions: 1) CelltypeAnnotation 2) LabelHarmonization 3) DeduceRelationship. CelltypeAnnotation is a function to annotate cells in a query Seurat object using a reference Seurat object with annotated cell types. LabelHarmonization can be utilized to integrate multiple cell atlases (references) into a unified cellular atlas with harmonized cell types. Finally, DeduceRelationship is a function that compares cell types between two scRNA-seq datasets. ELeFHAnt can be accessed from GitHub at https://github.com/praneet1988/ELeFHAnt.


title: Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms

abstract: Studying isoform expression at the microscopic level has always been a challenging task. A classical example is kidney, where glomerular and tubulo-insterstitial compartments carry out drastically different physiological functions and thus presumably their isoform expression also differs. We aim at developing an experimental and computational pipeline for identifying isoforms at microscopic structure-level. We microdissed glomerular and tubulo-interstitial compartments from healthy human kidney tissues from two cohorts. The two compartments were separately sequenced with the PacBio RS II platform. These transcripts were then validated using transcripts of the same samples by the traditional Illumina RNA-Seq protocol, distinct Illumina RNA-Seq short reads from European Renal cDNA Bank (ERCB) samples, and annotated GENCODE transcript list, thus identifying novel transcripts. We identified 14,739 and 14,259 annotated transcripts, and 17,268 and 13,118 potentially novel transcripts in the glomerular and tubulo-interstitial compartments, respectively. Of note, relying solely on either short or long reads would have resulted in many erroneous identifications. We identified distinct pathways involved in glomerular and tubulointerstitial compartments at the isoform level.We demonstrated the possibility of micro-dissecting a tissue, incorporating both long- and short-read sequencing to identify isoforms for each compartment.


title: cILR: Competitive isometric log-ratio for taxonomicenrichment analysis

abstract:
Research in human associated microbiomes often involves the analysis of taxonomic count tables generated via high-throughput sequencing. It is difficult to apply statistical tools as the data is high-dimensional, sparse, and compositional. An approachable way to alleviate high-dimensionality and sparsity is to aggregate variables into pre-defined sets. Set-based analysis is ubiquitous in the genomics literature, and has demonstrable impact in improving interpretability and power of downstream analysis. Unfortunately, there is a lack of sophisticated set-based analysis methods specific to microbiome taxonomic data, where current practice often employs abundance summation as a technique for aggregation. This approach prevents comparison across sets of different sizes, does not preserve inter-sample distances, and amplifies protocol bias. Here, we attempt to fill this gap with a new single sample taxon enrichment method that uses a novel log-ratio formulation based on the competitive null hypothesis commonly used in the enrichment analysis literature. Our approach, titled competitive balances for taxonomic enrichment analysis (CBEA), generates sample-specific enrichment scores as the scaled log ratio of the subcomposition defined by taxa within a set and the subcomposition defined by its complement. We provide sample-level significance testing by estimating an empirical null distribution of our test statistic with valid p-values. Herein we demonstrate using both real data applications and simulations that CBEA controls for type I error even under high sparsity and high inter-taxa correlation scenarios. Additionally, it provides informative scores that can be inputs to downstream analyses such as prediction tasks.

Author summaryThe study of human associated microbiomes relies on genomic surveys via high-throughput sequencing. However, microbiome taxonomic data is sparse and high dimensional which prevents the application of standard statistical techniques. One approach to address this problem is to perform analyses at the level of taxon sets. Set-based analysis has a long history in the genomics literature, with demonstrable impact in improving both power and interpretability. Unfortunately, there is limited interest in developing new set-based tools tailored for microbiome taxonomic data given its unique features compared to other  omics data types. We developed a new tool to generate taxon set enrichment scores at the sample level through a novel log-ratio formulation based on the competitive null hypothesis. Our scores can be used for statistical inference at both the sample and population levels, as well as inputs to other downstream analyses such as prediction models. We demonstrate the performance of our method against competing approaches across both real data analyses and simulation studies.


title: CBEA: Competitive balances for taxonomic enrichmentanalysis


title: Gene Set Analysis for time-to-event outcome with the Generalized Berk-Jones statistic

abstract: Gene Set analysis allows to evaluate the impact of groups of genes on an outcome of interest, such as the occurrence of a disease. Through the definition of the gene sets, gene set analysis takes into account biological knowledge and makes it easier to interpret the results, while improving the statistical power compared to a gene-wise analysis. In the time-to-event context, few methods exist, but most of them do not take into account the correlation that occurs inside a gene set, which can be strong. As the Generalized Berk-Jones statistics showed great consistency and includes the correlation inside the test statistic, we adapted this method to the time-to-event context by using a Cox model. We compared our approach to other methods based on the Cox model, and showed that the Generalize Berk-Jones statistic offers great adaptability, meaning that it can be used in all kinds of data structures. We applied the different methods to two different contexts: Gliomas and Breast cancer. In terms of statistical power, we did offer similar results to the other Cox model methods, but with greater accuracy. In the breast cancer framework, we showed better statistical power than methods based on Kernel Machine score.


title: Real Age Prediction from the Transcriptome with RAPToR

abstract:
Transcriptomic data is often affected by uncontrolled variation among samples that can obscure and confound the effects of interest. This is frequently due to unintended differences in developmental stages between samples. The transcriptome itself can be used to estimate developmental progression, but existing methods require many samples and do not estimate a real developmental time.

Here we present RAPToR, a simple and precise computational method that estimates the real age of a sample from its transcriptome, exploiting existing time-series data as reference. RAPToR works with whole animal, dissected tissue and single-cell data, for the most common animal models, humans and even for nonmodel organisms lacking reference data. We show RAPToR estimated age improves differential expression analysis by recovering the signal of interest when confounded with age. RAPToR will be especially useful in large scale single organism profiling because it eliminates the need for accurate staging or synchronization before profiling.


title: Sex biases in cancer and autoimmune disease incidence are correlated across human tissues

abstract: Cancer occurs more frequently in men while autoimmune diseases (AIDs) occur more frequently in women. To explore whether these sex biases have a common basis, we collected 170 AID incidence studies from many countries for tissues that have both a cancer type and an AID that arise from that tissue. Analyzing a total of 182 country-specific, tissue-matched cancer-AID incidence rate sex bias data pairs, we find that, indeed, the sex biases observed in the incidence of AIDs and cancers that occur in the same tissue are positively correlated across human tissues. The common key factor whose levels across human tissues are most strongly associated with these incidence rate sex biases is the sex bias in the expression of the 37 genes encoded in the mitochondrial genome.


title: Sex biases in cancer and autoimmune disease incidence are strongly positively correlated with mitochondrial gene expression across human tissues


title: Liver-specific Deletion Of Small Heterodimer Partner Alters Enterohepatic Bile Acid Levels And Promotes Bile Acid-Mediated Proliferation In Male Mice.

abstract: Small heterodimer partner (Shp) regulates several metabolic processes, including bile acid levels, but lacks the conserved DNA binding domain. Phylogenetic analysis revealed conserved genetic evolution of Shp, Fxr, Cyp7a1 and Cyp27a1, underscoring the importance of these molecules in maintaining bile acid homeostasis. Shp, although primarily studied as a downstream target of Farnesoid X Receptor (Fxr), has a distinct hepatic role that is poorly understood. Here we report that liver-specific Shp knockout (LShpKO) mice have impaired negative feedback of Cyp7a1 and Cyp8b1 upon bile acid challenge and demonstrate that a single copy of the Shp gene is sufficient to maintain this response. LShpKO mice also exhibit elevated total bile acid pool with higher bile acid fraction in the intestine mimicking the 1% cholic acid (CA) fed control mice. Agonistic activation of Fxr (GW4064) in the LShpKO did not alter the elevated basal expression of Cyp8b1 but lowered Cyp7a1 expression. We found that deletion of Shp led to an enrichment of distinct motifs and pathways associated with circadian rhythm, amino and carboxylic acid metabolism, copper ion transport, and DNA synthesis. LShpKO livers displayed a higher basal proliferation that was exacerbated specifically with bile acid challenge but not with another liver mitogen, TCPOBOP (TC). Overall, our data indicate that hepatic SHP uniquely regulates certain proliferative and metabolic cues.


title: The effect of external lateral stabilization on energy cost of walking - A systematic review and meta-analysis

abstract: Previous studies have estimated the energy cost required for the control of medio-lateral stability in human walking by means of external lateral stabilization. Results were inconsistent, possibly due to differences in task constraints or stabilization devices. To better understand the effects of lateral stabilization on energy cost, we conducted a systematic review with meta-analysis of studies, which directly assessed effects of lateral stabilization on energy cost in healthy young adult participants (18-41 years old). We obtained individual participant data on net energy cost (J kg-1 m-1) from previously published studies. Across all studies reviewed, the net energy cost reduction during stabilized walking at preferred and zero step widths equaled to 0.05 {+/-} 0.35 (~2-3% reduction) and 0.25 {+/-} 0.29 J kg-1 m-1 (mean {+/-} s.d.) (~8-9% reduction), respectively. The effect of external lateral stabilization was significant only for walking at zero step width and without arm swing. Lateral stabilization devices with short rope length increased energy cost reduction. However, spring stiffness and habituation time did not influence energy cost reduction. We provide recommendations for improvement of lateral stabilization devices to avoid some of the confounding effects. External lateral stabilization reduces energy cost during walking by a small amount. It can be concluded that a small proportion of total energy cost is required to control medio-lateral stability; this proportion is larger when walking with narrow steps and without arm swing.


title: Unraveling the intracellular cross-talk governing the balance between TNFα mediated survival and apoptosis signaling

abstract: Tumor necrosis factor alpha (TNF), a pleiotropic cytokine, helps maintain a balance between proliferation and apoptosis in normal cells. This balance is often sacrificed in a diseased cell, such as that of a cancer, by preferring survival phenotype over apoptosis. Restoring this balance requires a detailed understanding of the causal intracellular mechanisms that govern TNF stimulated apoptotic response. In this study, we use a systems biology approach to unravel the interplay between the intracellular signaling markers that orchestrate apoptosis levels. Our approach deciphered the synergism between the early intracellular markers phosphorylated JNK (pJNK) and phosphorylated AKT (pAKT) that modulate the activation of Caspase3, an important apoptotic regulator. We demonstrate that this synergism depends critically on the survival pathway signaling mediated by NF{kappa}B which plays a dominant role in controlling the extent of the overall apoptotic response. By systematic inhibition of the signaling markers, we establish that the dynamic cross-talk between the pJNK and pAKT transients directs the apoptosis phenotype via accumulated Caspase3 response. Interestingly, superposition of the semi-quantitative correlation between apoptosis and Caspase3 transient levels on the proposed TNF network model permits quantification of the dynamic apoptotic response under different stimulation conditions. Thus, the predictive model can be leveraged towards arriving at useful insights that can identify potential targeted therapeutic strategies for altering apoptotic response.

category: systems biology


title: Dynamic analysis and control of a rice-pest system under transcritical bifurcations

abstract: Cultural methods were widely applied at an early stage of agricultural pest management but then replaced over time through pesticides with adverse effects on crop quality and the environment due to extensive and long-term use. In this study, we have reformulated a rice-pest-control model by first modelling a rice-pest system rigorously to then extend it to become an optimal control problem. We consider both, cultural methods and pesticides, and minimize thereby the density of agricultural pests, to increase the production of rice and to reduce gross annual losses. Pesticides have been applied only in an emergency scenario, which reduces environmental pollution and damage to nearby ecosystems. For the emergency case, we have developed a decision model to mitigate potential risks. The formulated models are verified by stability analysis at equilibrium points and investigated through transcritical bifurcations. Moreover, we have extensively confirmed our main results by numerical investigations and discussed the biological implications in more detail.


title: An individualized fMRI-based protocol to assess semantic memory in a heterogeneous multilingual population

abstract: The cognitive stimulation induced by multilingualism may slow down age-related memory impairment. However, a suitable neuroscientific framework to assess the influence of multilingualism on age-related memory processes is missing. We propose an experimental paradigm that assesses semantic memory processes using functional magnetic resonance imaging (fMRI). To this end, we modified the picture-word interference (PWI) task to be suitable for multilingual subjects undergoing functional magnetic resonance imaging (fMRI). In particular, stimulus material was prepared in multiple languages and closely matched in semantic properties, thus enabling participants to perform the experiment in a language of their choice. This paradigm was validated in a group (n = 62) of healthy elderly ([≥]64 years) multilingual subjects, all practicing three or more languages. Consistent with the engagement of semantic memory processes, we found that the encoding and recognition of semantically related vs. unrelated picture-word pairs evoked robust differences in behavior and the neural activity of parietal-temporal networks. These effects were not modulated by the language in which the task was performed. Based on this validation in a multilingual population, we conclude that the proposed paradigm will allow future studies to evaluate whether multilingualism aptitude engages neural systems in a manner that protects long-term memory from aging-related decline.


title: No substantial pre-existing B cell immunity against SARS-CoV-2 in healthy adults

abstract: Pre-existing immunity against SARS-CoV-2 may have critical implications for our understanding of COVID-19 susceptibility and severity. Various studies recently provided evidence of pre-existing T cell immunity against SARS-CoV-2 in unexposed individuals. In contrast, the presence and clinical relevance of a pre-existing B cell immunity remains to be fully elucidated. Here, we provide a detailed analysis of the B cell response to SARS-CoV-2 in unexposed individuals. To this end, we extensively investigated the memory B cell response to SARS-CoV-2 in 150 adults sampled pre-pandemically. Comprehensive screening of donor plasma and purified IgG samples for binding and neutralization in various functional assays revealed no substantial activity against SARS-CoV-2 but broad reactivity to endemic betacoronaviruses. Moreover, we analyzed antibody sequences of 8,174 putatively SARS-CoV-2-reactive B cells on a single cell level and generated and tested 158 monoclonal antibodies. None of the isolated antibodies displayed relevant binding or neutralizing activity against SARS-CoV-2. Taken together, our results show no evidence of relevant pre-existing antibody and B cell immunity against SARS-CoV-2 in unexposed adults.

category: immunology


title: TET1 controls Cxcl1 induction by DNA demethylation and promotes neutrophil recruitment during acute lung injury

abstract:
Neutrophils are rapidly recruited from the peripheral blood to the inflammatory site to initiate inflammatory response against pathogenic infections. The process to recruit neutrophils must be properly regulated since the abnormal accumulation of neutrophils can cause organ damage and dysfunction. The acute respiratory distress syndrome (ARDS)/acute lung injury (ALI) is a common cause of respiratory failure that is characterized by the infiltration of neutrophils and epithelial integrity disruption. Indeed, recent studies suggest a pathogenic role of neutrophils in the clinic severity of the coronavirus disease 2019 (COVID-19) ARDS. The chemokine CXCL1, which is rapidly induced by inflammatory stimuli, plays a key role in neutrophil influx during lung inflammation. The molecular basis of Cxcl1 induction is not fully understood. Here we report that TET1, a member of the ten eleven translocation (TET) methylcytosine dioxygenase protein family, displays a striking specificity in the regulation of gene expression in macrophages. RNA sequencing (RNA-seq) analysis showed that Tet1 disruption significantly altered the expression of only 48 genes that include Cxcl1 and several other genes known to be important for cell migration and trafficking in bone marrow derived macrophages (BMDMs) in response to LPS stimulation. TET1 regulates the induction of Cxcl1 by facilitating the DNA demethylation of the Cxcl1 promoter. In Tet1-/- mice, the induction of Cxcl1 was suppressed, resulting in defective neutrophil recruitment to the lung during LPS-induced acute lung injury. Our results identify a novel epigenetic mechanism that selectively controls Cxcl1 induction and neutrophil recruitment during acute lung injury.

Key PointsO_LITET1 has a striking specificity in macrophage gene regulation and controls Cxcl1 induction by inflammatory stimuli via DNA demethylation
C_LIO_LINeutrophil recruitment is defective in Tet1 deficient mice during acute lung injury
C_LI


title: Tafazzin deficiency in mouse mesenchymal stem cells potentiates their immunosuppression and impairs activated B lymphocyte immune function

abstract: Barth Syndrome (BTHS) is a rare X-linked genetic disorder caused by mutation in the TAFAZZIN gene which encodes the cardiolipin (CL) transacylase tafazzin (Taz). Taz deficiency in BTHS patients results in reduced CL in their tissues and a neutropenia which contributes to the risk of infections. However, the impact of Taz deficiency in other cells of the immune system is poorly understood. Mesenchymal stem cells (MSCs) are well known for their immune inhibitory function. We examined whether Taz-deficiency in murine MSCs impacted their ability to modulate lipopolysaccharide (LPS)-activated wild type (WT) murine B lymphocytes. MSCs from tafazzin knockdown (TazKD) mice exhibited a 50% reduction in CL compared to wild type (WT) MSCs. However, mitochondrial oxygen consumption rate and membrane potential were unaltered. In contrast, TazKD MSCs exhibited increased glycolysis compared to WT MSCs and this was associated with elevated proliferation, phosphatidylinositol-3-kinase expression and expression of the immunosuppressive markers indoleamine-2,3-dioxygenase, cytotoxic T-lymphocyte-associated protein 4, interleukin-10, and cluster of differentiation 59. When co-cultured with LPS-activated WT B cells, TazKD MSCs inhibited B cell proliferation and growth rate and reduced B cell secretion of IgM to a greater extent than B cells co-cultured with WT MSCs. In addition, co-culture of LPS-activated WT B cells with TazKD MSCs induced B cell differentiation toward potent immunosuppressive phenotypes including interleukin-10 secreting plasma cells and B regulatory cells compared to activated B cells co-cultured with WT MSCs. These results indicate that Taz deficiency in MSCs enhances MSCs-mediated immunosuppression of activated B lymphocytes.


title: An anti-SARS-CoV-2 non-neutralizing antibody with Fc-effector function defines a new NTD epitope and delays neuroinvasion and death in K18-hACE2 mice

abstract: Emerging evidence in animal models indicate that both neutralizing activity and Fc- mediated effector functions of neutralizing antibodies contribute to protection against SARS-CoV-2. It is unclear if antibody effector functions alone could protect against SARS-CoV-2. Here we isolated CV3-13, a non-neutralizing antibody from a convalescent individual with potent Fc-mediated effector functions that targeted the N- terminal domain (NTD) of SARS-CoV-2 Spike. The cryo-EM structure of CV3-13 in complex with SAR-CoV-2 spike revealed that the antibody bound from a distinct angle of approach to a novel NTD epitope that partially overlapped with a frequently mutated NTD supersite in SARS-CoV-2 variants. While CV3-13 did not alter the replication dynamics of SARS-CoV-2 in a K18-hACE2 transgenic mouse model, an Fc-enhanced CV3-13 significantly delayed neuroinvasion and death in prophylactic settings. Thus, we demonstrate that efficient Fc-mediated effector functions can contribute to the in vivo efficacy of anti-SARS-CoV-2 monoclonal antibodies in the absence of neutralization.

category: microbiology


title: RNA-Seq analysis and transcriptome assembly of Salicornia neei reveals powerful system for ammonium detoxification

abstract:
BackgroundSalicornia neei is a halophyte plant that has been proposed for use in the phytoremediation of the saline wastewater generated by land-based aquaculture, which usually contains elevated concentrations of ammonium resulting from protein metabolism. To identify the molecular mechanisms related to ammonium response, we analyzed the transcriptome of S. neei in response to growth in saline water containing 3 mM ammonium and the Michaelis-Menten ammonium removal biokinetics.

ResultsThe RNA sequencing generated a total of 14,680,108 paired-end reads from the control and stressed conditions. De novo assembly using the CLC Genomic Workbench produced 86,020 transcripts and a reference transcriptome with an N50 of 683 bp.

A total of 45,327 genes were annotated, representing 51.2% of the contig predicted from de novo assembly. As regards DEGs, a total of 9,140 genes were differentially expressed in response to ammonium in saline water; of these, 7,396 could be annotated against functional databases. The upregulated genes were mainly involved in cell wall biosynthesis, transmembrane transport and antiporter activities, including biological KEGG pathways linked to the biosynthesis of secondary metabolites, plant hormone signal transduction, autophagy, and nitrogen metabolism. In addiction, a set of 72 genes was directly involved in ammonium metabolism, including glutamine synthetase 1 (GLN1), glutamate synthase 1 (GLT1), and ferredoxin-dependent glutamate synthase chloroplastic (Fd-GOGAT). Finally, we observed that the ammonium uptake rate increased with increasing ammonium concentrations, and tended toward saturation in the range of 3 to 4 mM.

ConclusionOur results support the hypothesis that an ammonium detoxification system mediated by glutamine and glutamate synthase was activated in S. neei when exposed to ammonium and saline water. The present transcriptome profiling method could be useful when investigating the response of halophyte plants to saline wastewater from land-based aquaculture.


title: Depside and depsidone synthesis in lichenized fungi comes into focus through a genome-wide comparison of the olivetoric and physodic acid chemotype of Pseudevernia furfuracea

abstract: Primary biosynthetic enzymes involved in the synthesis of lichen polyphenolic compounds depsides and depsidones are Non-Reducing Polyketide Synthases (NR-PKSs), and cytochrome P450s (CytP450). However, for most depsides and depsidones the corresponding PKSs are unknown. Additionally, in non-lichenized fungi specific fatty acyl synthases (FASs) provide starters to the PKSs. Yet, the presence of such FASs in lichenized fungi remains to be investigated. Here we implement comparative genomics and metatranscriptomics to identify the most likely PKS and FASs for the synthesis of olivetoric and physodic acid, the primary depside and depsidone defining the two chemotypes of the lichen Pseudevernia furfuracea. We propose that the gene cluster PF33-1_006185, found in both chemotypes, is the most likely candidate for olivetoric and physodic acid biosynthesis. This is the first study to identify the gene cluster and the FAS likely responsible for physodic and olivetoric acid biosynthesis in a lichenized fungus. Our findings suggest that gene regulation and other epigenetic factors determine whether the mycobiont produces the depside or the depsidone, providing the first direct indication that chemotype diversity in lichens can arise through regulatory and not only through genetic diversity. Combining these results and existing literature, we propose a detailed scheme for depside/depsidone synthesis.


title: Evidence for a selective link between cooperation and individual recognition

abstract: The ability to recognize and discriminate among others is a frequent assumption of models of the evolution of cooperative behavior. At the same time, cooperative behavior has been proposed as a selective agent favoring the evolution of individual recognition abilities. While theory predicts that recognition and cooperation may co-evolve, data linking recognition abilities and cooperative behavior with fitness or evidence of selection are elusive. Here, we provide evidence of a fitness link between individual recognition and cooperation in the paper wasp Polistes fuscatus. Nest founding females in northern populations frequently form cooperative multiple foundress nests and possess highly variable facial patterns that mediate individual recognition. We describe a dearth of cooperative nesting, low phenotypic diversity, and a lack of individual recognition in southern populations. In a common garden experiment, northern co-foundress associations successfully reared offspring while all cooperative southern groups failed to rear any offspring, suggesting a fitness link between individual recognition and successful cooperation. Consistent with a selective link between individual recognition and cooperation, we find that rates of cooperative co-nesting correlate with identity-signaling color pattern diversity across the species range. Moreover, genomic evidence of recent positive selection on cognition loci likely to mediate individual recognition is substantially stronger in northern compared to southern P. fuscatus populations. Collectively, these data suggest that individual recognition and cooperative nesting behavior have co-evolved in P. fuscatus because recognition helps mediate conflict among co-nesting foundresses. This work provides evidence of a specific cognitive phenotype under selection because of social interactions, supporting the idea that social behavior can be a key driver of cognitive evolution.


title: Inhibitory Acetylation of Pyruvate Dehydrogenase Promotes Diastolic Dysfunction in Mice

abstract: Left ventricular diastolic dysfunction is a structural and functional condition that precedes the development of heart failure with preserved ejection fraction (HFpEF). The etiology of diastolic dysfunction includes alterations in fuel substrate metabolism that negatively impact cardiac bioenergetics, and may precipitate the eventual transition to heart failure. To date, the molecular mechanisms that regulate early changes in fuel metabolism leading to diastolic dysfunction remain unclear. In this report, we use a diet-induced obesity model and quantitative acetylproteomics in aged mice to show that inhibitory lysine acetylation of the pyruvate dehydrogenase (PDH) complex promotes energetic deficits and diastolic dysfunction in mouse hearts. Cardiomyocyte-specific deletion of the mitochondrial lysine acetylation regulatory protein GCN5L1 prevented hyperacetylation of the PDH complex subunit PDHA1, allowing aged obese mice to continue using pyruvate as a bioenergetic substrate in the heart. Our findings suggest that changes in mitochondrial protein lysine acetylation represent a key metabolic component of diastolic dysfunction that precedes the development of heart failure.


title: GCN5L1 promotes diastolic dysfunction by inhibiting cardiac pyruvate oxidation


title: Intersegmental coordination of the central pattern generator via interleaved electrical and chemical synapses in zebrafish spinal cord

abstract: A significant component of the repetitive dynamics during locomotion in vertebrates is generated within the spinal cord. The legged locomotion of mammals is most likely controled by a hierarchical, multi-layer spinal network structure, while the axial circuitry generating the undulatory swimming motion of animals like lamprey is thought to have only a single layer in each segment. Recent experiments have suggested a hybrid network structure in zebrafish larvae in which two types of excitatory interneurons (V2a-I and V2a-II) both make first-order connections to the brain and last-order connections to the motor pool. These neurons are connected by electrical and chemical synapses across segments. Through computational modeling and an asymptotic perturbation approach we show that this interleaved interaction between the two neuron populations allows the spinal network to quickly establish the correct activation sequence of the segments when starting from random initial conditions and to reduce the dependence of the intersegmental phase difference (ISPD) of the oscillations on the swimming frequency. The latter reduces the frequency dependence of the waveform of the swimming motion. In the model the reduced frequency dependence is largely due to the different impact of chemical and electrical synapses on the ISPD and to the significant spike-frequency adaptation that has been observed experimentally in V2a-II neurons, but not in V2a-I neurons. Our model makes experimentally testable predictions and points to a benefit of the hybrid structure for undulatory locomotion that may not be relevant for legged locomotion.


title: Conformational Change of Syntaxin-3b in Regulating SNARE Complex Assembly in the Ribbon Synapses

abstract: Neurotransmitter release of synaptic vesicles relies on the assembly of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex, consisting of syntaxin and SNAP-25 on the plasma membrane and synaptobrevin on the synaptic vesicle. The formation of the SNARE complex progressively zippers towards the membranes, which drives membrane fusion between the plasma membrane and the synaptic vesicle. However, the underlying molecular mechanism of SNARE complex regulation is unclear. In this study, we investigate the syntaxin-3b isoform found in the retinal ribbon synapses using single-molecule fluorescence resonance energy transfer (smFRET) to monitor the conformational changes of syntaxin-3b that modulate the SNARE complex formation. We found that syntaxin-3b is predominantly in a self-inhibiting closed conformation, inefficiently forming the ternary SNARE complex. Conversely, a phosphomimetic mutation (T14E) at the N-terminal region of syntaxin-3b promoted the open conformation, similar to the constitutively open form of syntaxin LE mutant. When syntaxin-3b is bound to Munc18-1, SNARE complex formation is almost completely blocked. Surprisingly, the T14E mutation of syntaxin-3b partially abolishes Munc18-1 regulation, acting as a conformational switch to trigger SNARE complex assembly. Thus, we suggest a model where the conformational change of syntaxin-3b induced by phosphorylation initiates the release of neurotransmitters in the ribbon synapses.


title: Age-related differences in immune dynamics during SARS-CoV-2 infection in rhesus macaques

abstract: Advanced age is a key predictor of severe COVID-19. To gain insight into this relationship, particularly with respect to immune responses, we utilized the rhesus macaque model of SARS-CoV-2 infection. Two cohorts of eight older (16-23 years) and eight younger (3-5 years) rhesus macaques were inoculated with SARS-CoV-2. Animals were evaluated using viral RNA quantification, clinical observations, thoracic radiographs, single-cell transcriptomics, multiparameter flow cytometry, multiplex immunohistochemistry, cytokine detection, and lipidomics analysis at pre-defined timepoints in various tissues. Differences in clinical signs, pulmonary infiltrates, and virus replication dynamics were limited between age cohorts. Transcriptional signatures of inflammation-associated genes in cells isolated from bronchoalveolar lavage fluid at 3 dpi revealed efficient mounting of innate immune defenses in both younger and older animals. These findings suggested that age did not substantially skew major facets of acute disease in this model. However, age-specific divergence of immune responses emerged during the post-acute phase of infection (7-21 dpi). Older animals exhibited sustained local inflammatory innate responses while local effector T-cell responses were induced earlier in the younger animals. Circulating lipid mediator and cytokine levels highlighted increased repair-associated signals in the younger animals, in contrast to persistent pro-inflammatory responses in the older animals. In summary, despite similar disease outcomes, multi-omics profiling in SARS-CoV-2-infected rhesus macaques suggests that age may delay or impair the induction of anti-viral cellular immune responses and delay efficient return to immune homeostasis following acute infection.


title: A unique form of collective epithelial migration is crucial for tissue fusion in the secondary palate and can overcome loss of epithelial apoptosis

abstract: Tissue fusion is an oft-employed process in morphogenesis which often requires the removal of the epithelia intervening multiple distinct primordia to form one continuous structure. In the mammalian secondary palate, a midline epithelial seam (MES) forms between two palatal shelves and must be removed to allow mesenchymal confluence. Abundant apoptosis and cell extrusion in this epithelial seam support their importance in its removal. However, by genetically disrupting the intrinsic apoptotic regulators BAX and BAK within the MES, we find a complete loss of cell death and cell extrusion, but successful removal of the MES, indicating that developmental compensation enables fusion. Novel static and live imaging approaches reveal that the MES is removed through a unique form of collective epithelial cell migration in which epithelial trails and islands stream through the mesenchyme to reach the oral and nasal epithelial surfaces. These epithelial trails and islands begin to express periderm markers while retaining expression of the basal epithelial marker {Delta}Np63, suggesting their migration to the oral and nasal surface is concomitant with their differentiation to an epithelial intermediate. Live imaging reveals anisotropic actomyosin contractility within epithelial trails that drives their peristaltic movement, and genetic loss of non-muscle myosin IIA-mediated actomyosin contractility results in dispersion of epithelial collectives and dramatic failure of normal MES migration. These findings demonstrate redundancy between cellular mechanisms of morphogenesis and reveal a crucial role for a unique form of collective epithelial migration during tissue fusion.


title: GPCR-G protein selectivity - a unified meta-analysis

abstract: Two-thirds of human hormones and one-third of clinical drugs act on membrane receptors that couple to G proteins to achieve appropriate functional responses. While G protein transducers from literature are annotated in the Guide to Pharmacology database, two recent large-scale datasets now expand the receptor-G protein  couplome. However, these three datasets differ in scope and reported G protein couplings giving different coverage and conclusions on GPCR-G protein signaling. Here, we report a common coupling map uncovering novel couplings supported by both large-scale studies, the selectivity/promiscuity of GPCRs and G proteins, and how the co-coupling and co-expression of G proteins compare to the families from phylogenetic relationships. The coupling map and insights on GPCR-G protein selectivity will catalyze advances in receptor research and cellular signaling towards the exploitation of G protein signaling bias in design of safer drugs.

category: pharmacology and toxicology


title: Common coupling map advances GPCR-G protein selectivity


title: In silico, In vitro Screening of Plant Extracts for Anti-SARS-CoV-2 Activity and Evaluation of Their Acute and Sub-Acute Toxicity

abstract:
BackgroundIn the absence of a specific drug for COVID 19, treatment with plant extracts could be an option worthy of further investigation.

PurposeTo screen the phytochemicals for Anti-SARS-CoV-2 in silico and evaluate their safety and efficacy in vitro and in vivo.

MethodThe phytochemicals for Anti-SARS-CoV-2 were screened in silico using molecular docking. The hits generated from in silico screening were subjected for extraction, isolation and purification. The anti-SARS-CoV-2 activity of plant extracts of Z. piperitum (ATRI-CoV-E1), W. somnifera (ATRI-CoV-E2), C. inophyllum (ATRI-CoV-E3), A. paniculata (ATRI-CoV-E4), and C. Asiatica (ATRI-CoV-E5). The in vitro safety and anti-SARS-CoV-2 activity of plant extracts were performed in VeroE6 cells using Remdesivir as positive control. The acute and sub-acute toxicity study was performed in Wistar male and female rats.

ResultsThe percentage of cell viability for ATRI-COV-E4, ATRI-COV-E5 and ATRI-COV-E2 treated VeroE6 cells were remarkably good on the 24th and 48th hour of treatment. The in vitro anti-SARS-CoV-2 activity of ATRI-COV-E4, ATRI-COV-E5 and ATRI-COV-E2 were significant for both E gene and N gene. The percentage of SARS-CoV-2 inhibition for ATRI-COV-E4 was better than Remdesivir. For E gene and N gene, Remdesivir showed IC50 of 0.15 {micro}M and 0.11 {micro}M respectively, For E gene and N gene, ATRI-CoV-E4 showed IC50 of 1.18 {micro}g and 1.16 {micro}g respectively. Taking the clue from in vitro findings, the plant extracts A. paniculata (ATRI-COV-E4), W. somnifera extract (ATRI-COV-E5) and C. asiatica extract (ATRI-COV-E2) were combined (ATRICOV 452) and evaluated for acute and sub-acute toxicity in Wistar male and female rats. No statistically significant difference in haematological, biochemical and histopathological parameters were noticed.

ConclusionThe study demonstrated the Anti-SARS-CoV-2 activity in vitro and safety of plant extracts in both in vitro and in vivo experimental conditions.


title: SARS-CoV-2 mRNA vaccination elicits robust and persistent T follicular helper cell response in humans

abstract: SARS-CoV-2 mRNA vaccines induce robust anti-spike (S) antibody and CD4+ T cell responses. It is not yet clear whether vaccine-induced follicular helper CD4+ T (TFH) cell responses contribute to this outstanding immunogenicity. Using fine needle aspiration of draining axillary lymph nodes from individuals who received the BNT162b2 mRNA vaccine, we show that frequency of TFH correlates with that of S-binding germinal center B cells. Mining of the responding TFH T cell receptor repertoire revealed a strikingly immunodominant HLADPB1* 04-restricted response to S167-180 in individuals with this allele, which is among the most common HLA alleles in humans. Paired blood and lymph node specimens show that while circulating S-specific TFH cells peak one week after the second immunization, S-specific TFH persist at nearly constant frequencies for at least six months. Collectively, our results underscore the key role that robust TFH cell responses play in establishing long-term immunity by this efficacious human vaccine.


title: Gut microbiota and age shape susceptibility to clostridial enteritis in lorikeets under human care

abstract:
BackgroundEnteritis is a common cause of morbidity and mortality in lorikeets that can be challenging to diagnose and treat. In this study, we examine gut microbiota in two lorikeet flocks with enteritis (Columbus Zoo and Aquarium - CZA; Denver Zoo - DZ). Since 2012, the CZA flock has experienced repeated outbreaks of enteritis despite extensive diet, husbandry, and clinical modifications. In 2018, both CZA and DZ observed a spike in enteritis. Recent research has revealed that the gut microbiota can influence susceptibility to enteropathogens. We hypothesized that a dysbiosis, or alteration in the gut microbial community, was making some lorikeets more susceptible to enteritis, and our goal was to characterize this dysbiosis and determine the features that predicted susceptibility.

ResultsWe employed 16S rRNA sequencing to characterize the cloacal microbiota in lorikeets (CZA n = 67, DZ n = 24) over time. We compared the microbiota of healthy lorikeets, to lorikeets with enteritis, and lorikeets susceptible to enteritis, with "susceptible" being defined as healthy birds that subsequently developed enteritis. Based on sequencing data, culture, and toxin gene detection in intestinal contents, we identified Clostridium perfringens type A (CZA and DZ) and C. colinum (CZA only) at increased relative abundances in birds with enteritis. Histopathology and immunohistochemistry further identified the presence of gram-positive bacilli and C. perfringens, respectively, in the necrotizing intestinal lesions. Finally, using Random Forests and LASSO models, we identified several features (young age and the presence of Rhodococcus fascians and Pseudomonas umsongensis) associated with susceptibility to clostridial enteritis.

ConclusionsWe identified C. perfringens type A and C. colinum associated with lorikeet necrohemorrhagic enteritis at CZA and DZ. Susceptibility testing of isolates lead to an updated clinical treatment plan which ultimately resolved the outbreaks at both institutions. This work provides a foundation for understanding gut microbiota features that are permissive to clostridial colonization and host factors (e.g. age, prior infection) that shape responses to infection.


title: Angicin, a novel bacteriocin of Streptococcus anginosus

abstract: As a conserved defense mechanism, many bacteria produce antimicrobial peptides, called bacteriocins, which give a colonization advantage in a multispecies environment. Here the first bacteriocin of Streptococcus anginosus, designated Angicin, is described. S. anginosus is commonly described as a commensal, however it also possesses a high pathogenic potential. Therefore, understanding factors contributing to its host colonization and persistence are important. A radial diffusion assay was used to identify S. anginosus BSU 1211 as a potent bacteriocin producer. By genetic mutagenesis the background of bacteriocin production and the bacteriocin gene itself were identified. Synthetic Angicin shows high activity against closely related streptococci, listeria and vancomycin resistant enterococci. It has a fast mechanism of action and causes a membrane disruption in target cells. Angicin, present in cell free supernatant, is insensitive to changes in temperature from -70 to 90 {degrees}C and pH values from 2-10, suggesting that it represents an interesting compound for potential applications in food preservation or clinical settings.


title: In vitro Functional Analysis of pgRNA Sites Regulating Assembly of Hepatitis B Virus.

abstract: The roles of RNA sequence/structure motifs, Packaging Signals (PSs), for regulating assembly of an HBV genome transcript have been investigated in an efficient in vitro assay containing only core protein (Cp) and RNA. Variants of three conserved PSs, within the genome of a strain not used previously, preventing correct presentation of a Cp-recognition loop motif are differentially deleterious for assembly of nucleocapsid-like particles (NCPs). Cryo-electron microscopy reconstruction of the T=4 NCPs formed with the wild-type gRNA transcript, reveal that the interior of the Cp shell is in contact with lower resolution density, potentially encompassing the arginine-rich protein domains and gRNA. Symmetry-relaxation of this reconstruction reveals that such contacts are made at every symmetry axis. We infer from their regulation of assembly that some of these contacts would involve gRNA PSs, and confirmed this by X-ray RNA footprinting. Mutation of the {varepsilon} stem-loop in the gRNA, where polymerase binds in vivo, produces a poor RNA assembly substrate with Cp alone, largely due to alterations in its conformation. The results show that RNA PSs regulate assembly of HBV genomic transcripts in vitro, and therefore may play similar roles in vivo, in concert with other molecular factors.


title: Foot-and-mouth disease virus localisation on follicular dendritic cells and sustained induction of neutralising antibodies is dependent on binding to complement receptors (CR2/CR1)

abstract:
Previous studies have shown after the resolution of acute infection and viraemia, foot- and-mouth disease virus (FMDV) capsid proteins and/or genome are localised in the light zone of germinal centres of lymphoid tissue in cattle and African buffalo. The pattern of staining for FMDV proteins was consistent with the virus binding to follicular dendritic cells (FDCs). We have now demonstrated a similar pattern of FMDV protein staining in mouse spleens after acute infection and showed FMDV proteins are colocalised with FDCs. Blocking antigen binding to complement receptor type 2 and 1 (CR2/CR1) prior to infection with FMDV significantly reduced the detection of viral proteins on FDCs and FMDV genomic RNA in spleen samples. Blocking the receptors prior to infection also significantly reduced neutralising antibody titres. Therefore, the binding of FMDV to FDCs and sustained induction of neutralising antibody responses are dependent on FMDV binding to CR2/CR1 in mice.

Author SummaryFoot and mouth disease virus causes a highly contagious acute vesicular disease, resulting in more than 50% of cattle, regardless of vaccination status, and almost 100% of African buffalo becoming persistently infected for long periods (months) of time. Yet, the mechanisms associated with establishment of persistent infections are still poorly understood. Infected animals are characterised by the presence of long-lived neutralising antibody titres, which contrast with the short-lived response induced by vaccination. We have used a mouse model to understand how foot and mouth disease virus is trapped and retained in the spleen for up to 28 days post infection and how the absence of antigen in the germinal centre prevents a sustainable neutralising antibody response, in the mouse. Our results highlight the importance of targeting antigen to FDCs to stimulate potent neutralising antibody responses after vaccination.