title: An amphipathic and cationic antimicrobial peptide kills colistin resistant Gram-negative pathogens in vivo

abstract:
New antibiotics are needed against multidrug resistant Gram-negative pathogens that have compromised global health systems. Antimicrobial peptides are generally considered promising lead candidates for the next generation of antibiotics but have not fulfilled this expectation. Here we demonstrate activity of a cationic amphipathic undecapeptide (ChIP; Charge change Independent Peptide) against a wide panel of multidrug resistant Gram-negative pathogens. Importantly, the antimicrobial activity of ChIP is independent of the surface charge changes that confer colistin resistance through modification of Lipid A, while decreased activity of ChIP correlates with GlcN1 tri-acylation of Lipid A. In an in vivo peritonitis mouse model ChIP displays excellent activity against both colistin sensitive and resistant Escherichia coli and Acinetobacter baumannii strains.

Author SummaryAntimicrobial peptides hold promise as novel treatment options for diseases caused by multidrug resistant bacteria. Here we present evidence that the ChIP peptide, comprised of 11 D-amino acids, is active against a variety of Gram-negative bacteria that ranks high on the WHO list of critically important pathogens. ChIP initially interacts with the Gram-negative outer membrane, independent of its surface charge, followed by entry into the periplasm and permeabilization of the inner membrane, leading to bacterial cell death. Detailed analyses of the outer membrane indicate that the acylation pattern of lipopolysaccharides plays an important role for ChIP activity. In a mouse infection model, ChIP display excellent activity in reducing bacterial numbers for both Escherichia coli and Acinetobacter baumannii. Importantly, ChIP is highly efficient against bacteria resistant to colistin, an antibiotic normally considered as a last resort treatment of infections caused by multidrug resistant Gram-negative bacteria.


title: The mating type transcription factor MAT1-1-1 from the fungal human pathogen Aspergillus fumigatus: synthesis, purification, and crystallization of the DNA binding domain.

abstract:
Mating type (MAT) loci are the most important and significant regulators of sexual reproduction and development in ascomycetous fungi. Usually, they encode two transcription factors (TFs), named MAT1-1-1 or MAT1-2-1. Mating-type strains carry only one of the two TF genes, which control expression of pheromone and pheromone receptor genes, involved in the cell-cell recognition process. The present work presents the crystallization for the alpha1 (1) domain of MAT1-1-1 from the human pathogenic fungus Aspergillus fumigatus (AfMAT1-1-1). Crystals were obtained for the complex between a polypeptide containing the 1 domain and DNA carrying the AfMAT1-1-1 recognition sequence. A streak seeding technique was applied to improve native crystal quality, resulting in diffraction data to 3.2 [A] resolution. Further, highly redundant data sets were collected from the crystals of selenomethionine-substituted AfMAT1-1-1 with a maximum resolution of 3.2 [A]. This is the first report of structural studies on the 1 domain MAT regulator involved in the mating of ascomycetes.

SynopsisAn optimized purification and crystallization protocol together with initial X-ray datasets are described for this mating type transcription factor from human pathogenic fungus Aspergillus fumigatus.

category: microbiology


title: Seasonal resistome diversity and dissemination of WHO priority antibiotic-resistant pathogens in Lebanese estuaries

abstract: Anthropogenic activities are demonstrated to be the key drivers of antimicrobial resistance (AMR) dissemination in the environment. Lebanese rivers that lead to the Mediterranean Sea were sampled at estuaries sites, under high anthropogenic pressure, in spring 2017 and winter 2018 to study seasonal variation of antimicrobial-resistant bacteria (ARBs) and antimicrobial resistance genes (ARGs). Methods: A combined approach using culture techniques and high throughput qPCR identified hotspots for antimicrobial resistance and anthropogenic pressure in particular locations along the Lebanese coast. Results: Multi-resistant Gram-negative (Enterobacterales and Pseudomonas spp) and Gram-positive bacterial pathogens were isolated. A high abundance of certain ARGs (vanB, blaBIC-1, blaGES, tetM, and mcr-1) was detected in 5 Lebanese estuaries. The relative abundance of ARGs was highest in winter and areas with high anthropogenic activities and population growth with an influx of refugees. Conclusion: Qualitative analysis of ARB and the analysis of the Lebanese estuaries resistome revealed critical levels of contamination with pathogenic bacteria and provided significant information about the spread of ARGs in anthropogenically impacted estuaries.


title: Broad antiviral effects of Echinacea purpurea against SARS-CoV-2 variants of concern and potential mechanism of action

abstract:
BackgroundSARS-CoV-2 variants of concern (VOC) represent an alarming threat as they show altered biological behavior and may escape vaccination effectiveness. Some exhibit increased pathogenicity and transmissibility compared to the original wild type WUHAN (Hu-1). Broad-spectrum antivirals could complement and further enhance preventive benefits achieved through SARS-CoV-2 vaccination campaigns

MethodsThe anti-coronavirus activity of Echinacea purpurea (Echinaforce(R) extract, EF) against (i) VOCs B1.1.7 (alpha), B.1.351.1 (beta), P.1 (gamma), B1.617.2 (delta), AV.1 (Scottish) and B1.525 (eta), (ii) SARS-CoV-2 spike (S) protein-pseudotyped viral particles and reference strain OC43 as well as (iii) wild-type SARS-CoV-2 (Hu-1) were analyzed. Molecular dynamics (MD) were applied to study interaction of Echinaceas phytochemical markers with known pharmacological viral and host cell targets.

ResultsEF extract broadly inhibited propagation of all investigated SARS-CoV-2 VOCs as well as entry of SARS-CoV-2 pseudoparticles at EC50s ranging from 3.62 to 12.03 {micro}g/ml. Preventive addition of 20 {micro}g/ml EF to epithelial cells significantly reduced sequential infection with SARS-CoV-2 (Hu-1) as well as with the common human strain OC43. MD analyses showed constant binding affinities to Hu-1, B1.1.7, B.1.351, P.1 and B1.617.2-typic S protein variants for alkylamides, caftaric acidand feruoyl-tartaric acid in EF extract. They further indicated that the EF extract could possibly interact with TMPRSS-2, a serine protease required for virus endocytosis.

ConclusionsEF extract demonstrated stable antiviral activity across 6 tested VOCs, which is likely due to the constant affinity of the contained phytochemical marker substances to all spike variants. A possible interaction of EF with TMPRSS-2 partially would explain cell protective benefits of the extract by inhibition of endocytosis. EF may therefore offer a supportive addition to vaccination endeavors in the control of existing and future SARS-CoV-2 virus mutations.


title: An mRNA silencing mechanism reliant on the cooperation between REGE-1/Regnase-1 and RLE-1/Roquin-1

abstract: Regnase-1 is an evolutionarily conserved endoribonuclease, degrading diverse mRNAs important, among others, for immune homeostasis, development, and cancer. There are two competing models of Regnase-1 mediated mRNA silencing. One model postulates that Regnase-1 works together with another RNA-binding protein, Roquin-1. The other model proposes that the two proteins function separately. Studying the C. elegans Regnase-1 ortholog, REGE-1, we have uncovered a functional relationship between REGE-1 and the nematode counterpart of Roquin-1, RLE-1. While REGE-1 and RLE-1 associate with mRNA independently of each other, both proteins are essential for mRNA silencing. Intriguingly, the functional interdependence between REGE-1 and RLE-1 is reminiscent of the proposed cooperation between mammalian Regnase-1 and Roquin-1, which may underlie a prototypic silencing mechanism involving both proteins.

category: molecular biology


title: Adeno-associated virus type 2 (AAV2) uncoating is a stepwise process and is linked to structural reorganization of the nucleolus

abstract:
Nucleoli are membrane-less structures located within the nucleus and are known to be involved in many cellular functions, including stress response and cell cycle regulation. Besides, many viruses can employ the nucleolus or nucleolar proteins to promote different steps of their life cycle such as replication, transcription and assembly. While adeno-associated virus type 2 (AAV2) capsids have previously been reported to enter the host cell nucleus and accumulate in the nucleolus, both the role of the nucleolus in AAV2 infection, and the viral uncoating mechanism remain elusive. In all prior studies on AAV uncoating, viral capsids and viral genomes were not directly correlated on the single cell level, at least not in absence of a helper virus. To elucidate the properties of the nucleolus during AAV2 infection and to assess viral uncoating on a single cell level, we combined immunofluorescence analysis for detection of intact AAV2 capsids and capsid proteins with fluorescence in situ hybridization for detection of AAV2 genomes. The results of our experiments provide evidence that uncoating of AAV2 particles occurs in a stepwise process that is completed in the nucleolus and supported by alteration of the nucleolar structure.

Author SummaryAdeno-associated virus (AAV) capsids have been reported to enter the host cell nucleus and accumulate in the nucleolus. However, both the role of the nucleolus in AAV2 infection as well as the viral uncoating mechanism remain unknown. Here, we provide evidence that uncoating of the AAV2 particle is a stepwise process that is completed in the nucleolus and supported by alteration of the nucleolar morphology.


title: Adenine Base Editing in vivo with a Single Adeno-Associated Virus Vector

abstract: Base editors (BEs) have opened new avenues for the treatment of genetic diseases. However, advances in delivery approaches are needed to enable disease targeting of a broad range of tissues and cell types. Adeno-associated virus (AAV) vectors remain one of the most promising delivery vehicles for gene therapies. Currently, most BE/guide combinations and their promoters exceed the packaging limit (~5 kb) of AAVs. Dual-AAV delivery strategies often require high viral doses that impose safety concerns. In this study, we engineered an adenine base editor using a compact Cas9 from Neisseria meningitidis (Nme2Cas9). Compared to the well-characterized Streptococcus pyogenes Cas9-containing ABEs, Nme2-ABE possesses a distinct PAM (N4CC) and editing window, exhibits fewer off-target effects, and can efficiently install therapeutically relevant mutations in both human and mouse genomes. Importantly, we show that in vivo delivery of Nme2-ABE and its guide RNA by a single-AAV vector can efficiently edit mouse genomic loci and revert the disease mutation and phenotype in an adult mouse model of tyrosinemia. We anticipate that Nme2-ABE, by virtue of its compact size and broad targeting range, will enable a range of therapeutic applications with improved safety and efficacy due in part to packaging in a single-vector system.


title: Pre-treatment of Nile tilapia (Oreochromis niloticus) with ozone nanobubbles improve efficacy of heat-killed Streptococcus agalactiae immersion vaccine

abstract:
Nanobubble technology has shown appealing technical benefits and potential applications in aquaculture. We recently found that treatment with ozone nanobubbles (NB-O3) activated expression of several immune-related genes leading to effective response to subsequent exposure to fish pathogens. In this study, we investigated whether pre-treatment of Nile tilapia (Oreochromis niloticus) with NB-O3 can enhance specific immune responses and improve efficacy of immersion vaccination against Streptococcus agalactiae. Spleen and head kidney of fish in the vaccinated groups showed a substantial upregulation in expression levels of three immunoglobulin classes(IgM, IgD, and IgT) compared with the unvaccinated control groups. At day 21 post-immunization, the relative expression was greatest (approx. 3.2 to 4.1 folds). Both systemic and mucosal IgM antibodies were elicited in vaccinated groups. As the result, the cumulative survival rate of the vaccinated groups was found to be higher than that of the unvaccinated groups, with a relative percent survival (RPS) ranging from 52.9-70.5%. However, fish in the vaccinated groups that received pre-treatment with NB-O3, bacterial antigen uptakes, expression levels of IgM, IgD, and IgT, as well as the specific-IgM antibody levels and percent survival, were all slightly or significantly higher than that of the vaccinated group without pre-treatment with NB-O3. Taken together, our findings suggest that utilizing pre-treatment with NB-O3 may improve the immune response and efficacy of immersion vaccination in Nile tilapia.

HighlightsO_LIImmune response and efficacy of a heat-killed Streptococcus agalactiae immersion vaccine for Nile tilapia with and without pre-treatment with NB-O3 were accessed.
C_LIO_LIBacterial antigen uptake in the NB-O3-VAC compared to the AT-VAC groups was increased 1.32 and 1.80-fold at 3 and 6 h post-vaccination, respectively.
C_LIO_LIVaccinated group that received pre-treatment with NB-O3 had slightly to significantly higher levels of IgM, IgD, and IgT mRNA expression; IgM levels; and survival rate.
C_LIO_LIPre-treatment with NB-O3 may be a novel strategy for improving efficacy of immersion vaccine in aquaculture
C_LI


title: A rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A

abstract: Sirtuin 6 (SIRT6) is a deacylase and mono-ADP ribosyl transferase (mADPr) enzyme involved in multiple cellular pathways implicated in the regulation of aging and metabolism. Targeted sequencing identified a SIRT6 allele containing two linked substitutions (N308K/A313S) as enriched in Ashkenazi Jewish (AJ) centenarians as compared to AJ control individuals. Characterization of this SIRT6 (centSIRT6) allele demonstrated it to be a stronger suppressor of LINE1 retrotransposons, confer enhanced stimulation of DNA double strand break repair, and more robust cancer cell killing compared to the wild type. Surprisingly, centSIRT6 displayed weaker deacetylase activity, but stronger mADPr activity, over a range of NAD+ concentrations and substrates. Additionally, centSIRT6 displayed a stronger interaction with Lamin A/C (LMNA), which correlated with enhanced ribosylation of LMNA. Our results suggest that enhanced SIRT6 function contributes to human longevity by improving genome maintenance via increased mADPr activity and enhanced interaction with LMNA.


title: Oxoglutarate dehydrogenase coordinates myofibril growth by maintaining amino acid homeostasis

abstract: Myofibrils are long intracellular cables specific to muscles, composed mainly of actin and myosin filaments. The actin and myosin filaments are organized into repeated units called sarcomeres, which form the myofibril cables. Muscle contraction is achieved by the simultaneous shortening of sarcomeres and for a highly coordinated contraction to occur all sarcomeres should have the same size. Muscles have evolved a variety of ways to ensure sarcomere homogeneity, one example being the controlled oligomerization of Zasp proteins that sets the diameter of the myofibril. To understand how Zasp proteins effect myofibril growth, we looked for Zasp-binding proteins at the Z-disc. We found that the E1 subunit of the oxoglutarate dehydrogenase complex is recruited to the Z-disc by Zasp52 and is required to sustain myofibril growth. By making specific mutants, we show that its enzymatic activity is important for myofibril growth, and that the other two subunits of the complex are also required for myofibril formation. Using super resolution microscopy, we revealed the overall organization of the complex at the Z-disc. Then, using metabolomic analysis, we uncovered an amino acid balance defect affecting protein synthesis, that we also confirmed by genetic tools. In summary, we show that Zasp controls the local amino acid pool responsible for myofibril growth by recruiting the OGDH complex to the Z-disc.

category: cell biology


title: Transcription Factor RFX3 Stabilizes Mammary Basal Cell Identity

abstract: The myoepithelial cell compartment of the murine postnatal mammary gland is generated from basal cap cells in the terminal end bud and maintained by self-renewal. Transdifferentiation to the luminal lineage does not normally occur but can be induced by DNA damage, luminal cell death or transplantation into a recipient mammary fat pad. Myoepithelial cells cultivated in vitro can also transdifferentiate towards the luminal lineage. Little is known about the molecular mechanisms and gene regulatory networks underlying this plasticity. Using a transgenic mouse (Tg11.5kb-GFP) that marks cap cells with GFP, we discovered that mature myoepithelial cells placed in culture begin to express GFP within [~]24 hrs and later express the Keratin 8 (K8) luminal marker. Cell tracking showed that most K8+ cells arose from GFP+ cells, suggesting that myoepithelial cells de-differentiate towards a progenitor state before changing lineage. Differential gene expression analysis, comparing pure GFP+ cap cells with mature myoepithelial cells, identified multiple transcription factors that iRegulon predicted might regulate the myoepithelial to cap cell transition. Knockout of one of these genes, Regulatory Factor 3 (Rfx3), significantly reduced the population of GFP+ cells and increased differentiation to the K8+ luminal lineage. Rfx3 knockout also reduced mammosphere growth and mammary gland regeneration efficiency in a transplantation assay, but had no effect on proliferation in vitro. Together, these data support a key role for Rfx3 in the stabilization of the mammary basal cell lineages.


title: A mutation associated with Charcot-Marie-Tooth disease enhances the formation of stable dynamin 2 complexes in cells

abstract: Mutations in dynamin 2 (DNM2) have been associated with two distinct motor disorders, Charcot-Marie-Tooth neuropathies (CMT) and centronuclear myopathy (CNM). The majority of these mutations are clustered in the pleckstrin homology domain (PHD) which engage in intramolecular interactions that suppress dynamin self-assembly and GTPase activation. CNM mutations in the PHD interferes with these intramolecular interactions, thereby blocking the formation of the auto-inhibited state. CMT mutations are located primarily on the opposite surface of the PHD, which is specialized for lipid PIP2 binding. It has been speculated that the distinct locations and interactions of residues mutated in CMT and CNM explain why each set of mutations cause either one disease or the other, despite their close proximity within the PHD sequence. We show that at least one CMT-causing mutant, lacking residues 555DEE557 ({Delta}DEE), displays this inability to undergo auto-inhibition as observed in CNM-linked mutants. This {Delta}DEE deletion mutant induces the formation of abnormally large cytoplasmic inclusions similar to those observed for CNM-linked mutant R369W. We also found substantially reduced migration from the membrane of the {Delta}DEE deletion mutant. These findings call into question the molecular mechanism currently believed to underlie the absence of pathogenic overlap between DNM2-dependent CMT and CNM.


title: Entangled architecture of rough endoplasmic reticulum (RER) and vacuoles enables topological damping in cytoplasm of an ultra-fast giant cell

abstract: Cellular systems are known to exhibit some of the fastest movements in the biological world 1-3 - but little is known as to how single cells can dissipate this energy rapidly and adapt to such large accelerations without sub-cellular damage. To study intracellular adaptations under extreme forces - we investigate Spirostomum ambiguum - a giant cell (1-4mm in length) well known to exhibit ultrafast contractions (50% of body length) within 5 msec with a peak acceleration of 15g. 2,4 Utilizing transmitted electron microscopy (TEM) and confocal imaging, we discover a novel association of rough endoplasmic reticulum (RER) and vacuoles throughout the cell - forming a contiguous fenestrated cubic membrane architecture that topologically entangles these two organelles. A nearly uniform inter-organelle spacing of 60nm is observed between RER and vacuoles, closely packing the entire cell. Using an overdamped molecular dynamics simulation, 5 we demonstrate how this unique entangled metamaterial responds to external loads by rapidly dissipating energy and helps preserve spatial relationships between organelles. Because this dynamics arises primarily from entanglement of two networks incurring jamming transition at a subcritical volume fraction 6 - we term this phenomena "topological damping". Our findings suggest a new mechanical role of RER-vacuolar meshwork as a metamaterial capable of dissipating energy in an ultra-fast contraction event.


title: Lessons from the meiotic recombination landscape of the ZMM deficient budding yeast Lachancea waltii

abstract:
Meiotic recombination has been deeply characterized in a few model species only, notably in the budding yeast Saccharomyces cerevisiae. Interestingly, most members of the ZMM pathway that implements meiotic crossover interference in S. cerevisiae have been lost in Lachancea yeast species after the divergence of Lachancea kluyveri from the rest of the clade. This suggests major differences in the control of crossover distribution. After investigating meiosis in L. kluyveri, we determined the meiotic recombination landscape of Lachancea waltii and identified several characteristics that should help understand better the underlying mechanisms. Such characteristics include systematic regions of loss of heterozygosity (LOH) in L. waltii hybrids, compatible with dysregulated Spo11-mediated DNA double strand breaks (DSB) independently of meiosis. They include a higher recombination rate in L. waltii than in L. kluyveri despite the lack of multiple ZMM pro-crossover factors. L. waltii exhibits an elevated frequency of zero-crossover bivalents as L. kluyveri but opposite to S. cerevisiae. L. waltii gene conversion tracts lengths are comparable to those observed in S. cerevisiae and shorter than in L. kluyveri despite the lack of Mlh2, a factor limiting conversion tracts size in S. cerevisiae. L. waltii recombination hotspots are not shared with either S. cerevisiae or L. kluyveri, showing that meiotic recombination hotspots can evolve at a rather limited evolutionary scale within budding yeasts. Finally, in line with the loss of several ZMM genes, we found only residual crossover interference in L. waltii likely coming from the modest interference existing between recombination precursors.

Significance statementStudying non-model species is relevant to understand better biological processes by shedding light on their evolutionary variations. Here we chose the non-model budding yeast Lachancea waltii to study meiotic recombination. In sexually reproducing organisms, meiotic recombination shuffles parental genetic combinations notably by crossovers that cluster in hotspots at the population level. We found remarkable variations compared to both the canonical Saccharomyces cerevisiae model and another close relative Lachancea kluyveri. Such variations notably include the loss in L. waltii of a layer of regulation of crossover distribution that is otherwise conserved in budding yeasts and mammals. They also include the lack of conservation of crossover hotspots across the Lachancea species while crossover hotspots are remarkably stable across the Saccharomyces species.

Highlights- Extensive LOH events in L. waltii intraspecific hybrids
- No conservation of the recombination hotspots across the Lachancea genus
- Reduced but not suppressed crossover interference in the absence of the ZMM pathway
- Similar gene conversion tract lengths in L. waltii, S. cerevisiae, and L. kluyveri despite the lack of MLH2 in L. waltii

category: genetics


title: Absolute Scaling of Single-Cell Transcriptomes Reveals Pervasive Hypertranscription in Adult Stem and Progenitor Cells

abstract:
Hypertranscription facilitates biosynthetically demanding cellular state transitions through global upregulation of the nascent transcriptome. Despite its potential widespread relevance, documented examples of hypertranscription remain few and limited predominantly to early development. This limitation is in large part due to the fact that modern sequencing approaches, including single-cell RNA sequencing (scRNA-seq), generally assume similar levels of transcriptional output per cell. Here, we use molecule counting and spike-in normalization to develop absolute scaling of single-cell RNA sequencing data. Absolute scaling enables an estimation of total transcript abundances per cell, which we validate in embryonic stem cell (ESC) and germline data and apply to adult mouse organs at steady-state or during regeneration. The results reveal a remarkable dynamic range in transcriptional output among adult cell types. We find that many different multipotent stem and progenitor cell populations are in a state of hypertranscription, including in the hematopoietic system, intestine and skin. Hypertranscription marks cells with multilineage potential in adult organs, is redeployed in conditions of tissue injury, and can precede by 1-2 days bursts of proliferation during regeneration. In addition to the association between hypertranscription and the stem/progenitor cell state, we dissect the relationship between transcriptional output and cell cycle, ploidy and secretory behavior. Our analyses reveal a common set of molecular pathways associated with hypertranscription across adult organs, including chromatin remodeling, DNA repair, ribosome biogenesis and translation. Our findings introduce an approach towards maximizing single-cell RNA-seq profiling. By applying this methodology across a diverse collection of cell states and contexts, we put forth hypertranscription as a general and dynamic cellular program that is pervasively employed during development, organ maintenance and regeneration.

SUMMARY STATEMENTAbsolute scaling of single-cell transcriptomic data reveals highly dynamic global levels of transcription across adult cell lineages

category: genomics


title: The anti-angiogenic compound dimethyl fumarate inhibits the serine synthesis pathway and increases glycolysis in endothelial cells

abstract: A pathological and persistent angiogenesis is observed in several diseases like retinopathies, diabetes, psoriasis and cancer. Dimethyl fumarate, an ester from the Krebs cycle intermediate fumarate, is approved as a drug for the treatment of psoriasis and multiple sclerosis, and its anti-angiogenic activity has been reported in vitro and in vivo. However, it is not known whether dimethyl fumarate is able to modulate endothelial cell metabolism, considered an essential feature for the angiogenic switch. By means of different experimental approximations, including proteomics, isotope tracing and metabolomics experimental approaches, in this work we studied the possible role of dimethyl fumarate in endothelial cell energetic metabolism. We demonstrate for the first time that dimethyl fumarate promotes glycolysis and diminishes cell respiration, which could be a consequence of a down-regulation of serine and glycine synthesis through inhibition of PHGDH activity in endothelial cells. This new target can open a new field of study regarding the mechanism of action of dimethyl fumarate.

category: biochemistry


title: Modelling biochemical gradients in vitro to control cell compartmentalization in a microengineered 3D model of the intestinal epithelium

abstract: Gradients of signaling pathways within the intestinal stem cell (ISC) niche are instrumental for cellular compartmentalization and tissue function, yet how are they formed and sensed by the epithelium is still not fully understood. Here we present a new in vitro model of the small intestine based on primary epithelial cells (i), apically accessible (ii), with native tissue mechanical properties and controlled mesh size (iii), 3D villus-like architecture (iv), and precisely controlled biomolecular gradients of the ISC niche (v). Biochemical gradients are formed through the hydrogel-based scaffolds by free diffusion from a source to a sink chamber. To confirm the establishment of spatiotemporally controlled gradients, we employ light-sheet fluorescence microscopy and in-silico modelling. The ISC niche biochemical gradients coming from the stroma and applied along the villus axis lead to the in vivo-like compartmentalization of the proliferative and differentiated cells, while changing the composition and concentration of the biochemical factors affects the cellular organization along the villus axis. This novel 3D in vitro intestinal model derived from organoids recapitulates both the villus-like architecture and the gradients of ISC biochemical factors, thus opening the possibility to study in vitro the nature of such gradients and the resulting cellular response.

category: bioengineering


title: Modeling of microRNA-derived disease network repurposes methotrexate for the prevention and therapy of abdominal aortic aneurysm in mice

abstract: Abdominal aortic aneurysm (AAA) is a highly lethal vascular disease characterized by permanent dilatation of the abdominal aorta. The main purpose of the current study is to search for noninvasive medical therapies for abdominal aortic aneurysm (AAA), for which there is currently no effective drug therapy. Network medicine represents a cutting-edge technology, as analysis and modeling of disease networks can provide critical clues regarding the etiology of specific diseases and which therapeutics may be effective. Here, we proposed a novel algorithm to quantify disease relations based on a large accumulated microRNA-disease association dataset and then built a disease network that covered 15 disease classes and included 304 diseases. Analysis revealed a number of patterns for these diseases; for example, diseases tended to be clustered and coherent in the network. Surprisingly, we found that AAA showed the strongest similarity with rheumatoid arthritis and systemic lupus erythematosus, both of which are autoimmune diseases, suggesting that AAA could be one type of autoimmune disease in etiology. Based on this observation, we further hypothesized that drugs for autoimmune disease could be repurposed for the prevention and therapy of AAA. Finally, animal experiments confirmed that methotrexate, a drug for autoimmune disease, was able to prevent the formation and inhibit the development of AAA.

category: bioinformatics


title: A convergent malignant phenotype in B-cell acute lymphoblastic leukemia involving the splicing factor SRRM1

abstract: A significant proportion of B-cell acute lymphoblastic leukemia (B-ALL) patients remains with a dismal prognosis due to yet undetermined mechanisms. We performed a comprehensive multicohort analysis of gene fusions, gene expression, and RNA splicing alterations to uncover molecular signatures potentially linked to the observed poor outcome. We identified 84 fusions with significant allele frequency across patients. We identified an expression signature that predicts high risk independently of the gene fusion background. This signature includes the upregulation of the splicing factor SRRM1, which potentially impacts splicing events associated with poor outcomes through protein-protein interactions with other splicing factors. Experiments in B-ALL cell lines provided further evidence for the role of SRRM1 on cell survival, proliferation, and invasion. Our findings reveal a convergent mechanism of aberrant RNA processing that sustains a malignant phenotype independently of gene fusions and could complement current clinical strategies in B-ALL.

category: cancer biology


title: Metabolitin-based molecular drug delivery by targeting GPR158 in glioblastoma

abstract: Glioblastoma multiforme (GBM) is a lethal form of intracranial tumor. One of the obstacles to treat GBM is the blood-brain barrier which limit the transportation of drugs into the tumor site. Here, based on our previous study on metabolitin (MTL) and osteocalcin, we generated a molecular drug delivery system that consisted of metabolitin and small molecules such as fluorescent dye or peptide drugs for diagnosis and treatment. And we designed a GBM diagnostic probe (MTL-ICG) and therapeutic peptide drug (MTL-NBD) that can cross the blood-brain barrier (BBB). In a NIR animal live imaging system, we found MTL-ICG can penetrate cross BBB and label the GBM site. The in vitro experiment showed that MTL-NBD had inhibitory effect on GBM cell line (U87-MG). Besides, after orthotopic transplantation of GBM into mouse cortex, treatment of MTL-NBD intravenously showed inhibition trend, which were similar with the effect of NBD, a known anti-tumor polypeptide drug. In addition, we found the GPR158, the receptor of osteocalcin, was also high expressed in grafting site. Taken together, these findings suggest that MTL is a promising cell penetrating peptide targeting GPR158 in GBM, which provide a novel delivery tool for GBM.


title: Mitochondrial Dysfunction is a Driver for SP-2509 Drug Resistance in Ewing Sarcoma

abstract: Expression of the fusion oncoprotein EWS/FLI causes Ewing sarcoma, an aggressive pediatric tumor characterized by widespread epigenetic deregulation. These epigenetic changes are targeted by novel lysine specific demethylase-1 (LSD1) inhibitors, which are currently in early phase clinical trials. Single agent targeted therapy often induces resistance, and successful clinical development requires knowledge of resistance mechanisms, enabling the design of effective combination strategies. Here, we used a genome-scale CRISPR-Cas9 loss-of-function screen to identify genes whose knockout (KO) conferred resistance to the LSD1 inhibitor SP- 2509 in Ewing sarcoma cell lines. Multiple genes required for mitochondrial electron transport chain (ETC) complexes III and IV function were hits in our screen. We validated this finding using genetic and chemical approaches including CRISPR KO, ETC inhibitors, and mitochondrial depletion. Further global transcriptional profiling revealed that altered complex III/IV function disrupted the oncogenic program mediated by EWS/FLI and LSD1 and blunted the transcriptomic response to SP-2509. These findings demonstrate that mitochondrial dysfunction modulates SP-2509 efficacy and suggest that new therapeutic strategies combining LSD1 with agents which prevent mitochondrial dysfunction may benefit patients with this aggressive malignancy.


title: Endoplasmic reticulum oxidoreductin (ERO) provides resilience against reductive stress and hypoxic conditions by mediating luminal redox dynamics

abstract:
Oxidative protein folding in the endoplasmic reticulum (ER) depends on the coordinated action of protein disulfide isomerases and ER oxidoreductins (EROs). Strict dependence of ERO activity on molecular oxygen as the final electron acceptor implies that oxidative protein folding and other ER processes are severely compromised under hypoxia. While many key players involved in oxidative protein folding are known, our understanding of how redox homeostasis in the ER is maintained and how EROs, the Cys residues of nascent proteins, and the luminal glutathione redox buffer interact is limited. Here, we isolated viable ero1 ero2 double mutants largely deficient in ERO activity, which rendered the mutants highly sensitive to reductive stress and hypoxia. To elucidate the specific redox dynamics in the ER lumen in vivo, we expressed the glutathione redox potential (EGSH) sensor Grx1-roGFP2iL-HDEL with a midpoint potential of -240 mV in the ER of Arabidopsis plants. We found EGSH values of -241 mV in wild-type plants, which is less oxidizing than previously estimated. In the ero1 ero2 mutants, luminal EGSH was reduced further to -253 mV. Recovery to reductive ER stress, as induced by acute exposure to dithiothreitol, was delayed in ero1 ero2 mutants. The characteristic signature of EGSH dynamics in the ER lumen triggered by hypoxia was affected in the ero1 ero2 mutant reflecting a disrupted balance of reductive and oxidizing inputs, including nascent polypeptides and glutathione entry. The ER redox dynamics can now be dissected in vivo, revealing a central role of EROs as major redox integrators to promote luminal redox homeostasis.

One sentence summaryDynamic monitoring the ER luminal glutathione redox potential highlights the role of EROs in defining redox conditions and the interplay between different redox inputs during hypoxia and reductive stress.

category: plant biology


title: Spatial Meta-transcriptomes of human and murine intestines

abstract: We developed an analysis pipeline that can extract microbial sequences from Spatial Transcriptomic data and assign taxonomic labels to them, generating a spatial microbial abundance matrix in addition to the default host expression one, enabling simultaneous analysis of host expression and microbial distribution. We applied it on both human and murine intestinal datasets and validated the spatial microbial abundance information with alternative assays. Finally, we present a few biological insights that can be gained from this novel data. In summary, this proof of concept work demonstrated the feasibility of Spatial Meta-transcriptomic analysis, and pave the way for future experimental optimization.

category: systems biology


title: Progressive alterations of striatal polysomal architecture in a mouse model of Huntington's disease

abstract: Given their highly polarized morphology and functional singularity, neurons require precise spatial and temporal control of protein synthesis. Alterations in protein translation have been implicated in the development and progression of a wide range of neurological and neurodegenerative disorders, including Huntingtons disease (HD). We examined the architecture of polysomes in their native brain context by performing 3D electron tomography of striatal tissue from the zQ175 knock-in mouse model of HD. Results revealed progressive remodelling towards a more compacted polysomal architecture, an effect that coincided with the emergence and progression of HD related symptoms. This aberrant architecture is compatible with ribosome stalling phenomena. In fact, we also detected an increase in the striatal expression of the stalling relief factor EIF5A2. Polysomal sedimentation gradients showed a significant increase in the accumulation of free 40S ribosomal subunits in zQ175 striatal samples. Together, these findings indicate that changes in the architecture of the protein synthesis machinery may underlie translational alterations associated with HD, thus opening new avenues for understanding the progression of this disease.

category: neuroscience


title: Progressive alterations in polysomal architecture in a mouse model of Huntington's disease


title: Effects of active and passive enrichment regimes on fecal glucocorticoid metabolite levels in captive Indian leopards (Panthera pardus fusca)

abstract: Environmental enrichment improves health and wellbeing of zoo animals. To test this hypothesis, we used Indian leopards, one of the popular zoo animals, as a model system to understand effects of active (interacting) and passive (noninteracting) enrichment elements on stress hormone levels of captive individuals. We included three enrichment categories, category  A (having both active: large size cage, and passive: controlled temperature, playback of forest sounds and sound proof glasses to filter visitors noise, enrichment elements), category  B (active enrichment type I, small size cage with air coolers), and category C (active enrichment type II, medium size cage without air coolers) for the leopards (n=14) housed in two Indian zoos. We standardized a non-invasive method to measure fecal glucocorticoid metabolite (fGCM) levels in captive leopards. The standardized fGCM assay was further validated by analysing samples from free-ranging leopards, as well. The fGCM levels (Mean{+/-}SE) were 10.45{+/-}2.01 and 0.95{+/-}0.003g/g dry wt of feces in captive and free-ranging leopards, respectively. Our results demonstrated that fGCM levels of leopards in categories B and C were significantly (P<0.05) different from each other, thus, indicating cage size (an active enrichment element) as an important factor in influencing the physiology of the sampled animals. Overall, the findings of the study will contribute towards informing policies for management of the Indian leopards.

category: ecology


title: Pose-gait analysis for cetaceans with biologging tags

abstract: Biologging tags are a key enabling tool for investigating cetacean behavior and locomotion in their natural habitat. Identifying and then parameterizing gait from movement sensor data is critical for these investigations. But how best to characterize gait from tag data remains an open question. Further, the location and orientation of the tag on an animal in the field are variable and can change multiple times during deployment. As a result, the relative orientation of the tag with respect to (wrt) the animal must be determined before a wide variety of further analyses. Currently, custom scripts that involve specific manual heuristics methods tend to be used in the literature. These methods require a level of knowledge and experience that can affect the reliability and repeatability of the analysis. The authors of this work argue that an animals gait is composed of a sequence of body poses observed by the tag, demonstrating a specific spatial pattern in the data that can be utilized for different purposes. This work presents an automated data processing pipeline (and software) that takes advantage of the common characteristics of pose and gait of the animal to 1) Identify time instances associated with occurrences of relative motion between the tag and animal; 2) Identify the relative orientation of tag wrt the animals body for a given data segment; and 3) Extract gait parameters that are invariant to pose and tag orientation. The authors included biologging tag data from bottlenose dolphins, humpback whales, and beluga whales in this work to validate and demonstrate the approach. Results show that the average relative orientation error of the tag wrt the dolphins body after processing was within 11 degrees in roll, pitch, and yaw directions. The average precision and recall for identifying relative tag motion were 0.87 and 0.89, respectively. Examples of the resulting pose and gait analysis demonstrate the potential of this approach to enhance studies that use tag data to investigate movement and behavior. MATLAB source code and data presented in the paper were made available to the public (https://github.com/ding-z/cetacean-pose-gait-analysis.git), with suggestions related to tag data processing practices provided in this paper. The proposed analysis approach will facilitate the use of biologging tags to study cetacean locomotion and behavior.

category: animal behavior and cognition


title: Pentoxifylline-induced Protein Expression Change in RAW 264.7 Cells as Determined by Immunoprecipitation-based High Performance Liquid Chromatography

abstract: Although pentoxifylline (PTX) was identified as a competitive non-selective phosphodiesterase inhibitor, its pharmacological effect has not been clearly elucidated. The present study explored the effect of low dose 10 g/mL PTX (therapeutic dose) compared to high dose 300 g/mL PTX (experimental dose) in RAW 264.7 cells through immunoprecipitation-based high performance liquid chromatography (IP-HPLC), immunohistochemistry, and western blot. 10 g/mL PTX increased the expression of proliferation (Ki-67, PCNA, cyclin D2, cdc25A), epigenetic modification (KDM4D, PCAF), protein translation (DOHH, DHPS, eIF5A1), RAS signaling (KRAS, pAKT1/2/3, PI3K), NFkB signaling (NFkB, GADD45, p38), protection (HSP70, SOD1, GSTO1/2), neuromuscular differentiation (NSE{gamma}, myosin-1a, desmin), osteoblastic differentiation (BMP2, RUNX2, osterix), acute inflammation (TNF, IL-1, CXCR4), innate immunity ({beta}-defensin 1, lactoferrin, TLR-3, -4), cell-mediated immunity (CD4, CD8, CD80), while decreased the expression of ER stress (eIF2, eIF2AK3, ATF6), fibrosis (FGF2, CTGF, collagen 3A1), and chronic inflammation (CD68, MMP-2, -3, COX2) versus the untreated controls. The activation of proliferation by 10 g/mL PTX was also supported by the increase of cMyc-MAX heterodimer and {beta}-catenin-TCF1 complex in double IP-HPLC. 10 g/mL PTX enhanced FAS-mediated apoptosis but diminished p53-mediated apoptosis, and downregulated many angiogenesis proteins (angiogenin, VEGF-A, and FLT4), but upregulated HIF1, VEGFR2, and CMG2 reactively. Whereas, 300 g/mL PTX consistently decreased proliferation, epigenetic modification, RAS and NFkB signaling, neuromuscular and osteoblastic differentiation, but increased apoptosis, ER stress, and fibrosis compared to 10 g/mL PTX. These data suggest PTX has different biological effect on RWA 264.7 cells depending on the concentration of 10 g/mL and 300 g/mL PTX. The low dose 10 g/mL PTX enhanced RAS/NFkB signaling, proliferation, differentiation, and inflammation, particularly, it stimulated neuromuscular and osteoblastic differentiation, innate immunity, and cell-mediated immunity, but attenuated ER stress, fibrosis, angiogenesis, and chronic inflammation, while the high dose 300 g/mL PTX was found to alleviate the 10 g/mL PTX-induced biological effects, resulted in the suppression of RAS/NFkB signaling, proliferation, neuromuscular and osteoblastic differentiation, and inflammation.

category: pharmacology and toxicology


title: Genetic evidence that uptake of the fluorescent analog 2NBDG occurs independently of known glucose transporters

abstract: The fluorescent derivative of glucose, 2-Deoxy-2-[(7-nitro-2,1,3-benzoxadiazol-4-yl)-amino]-D-glucose (2NBDG), is a widely used surrogate reagent to visualize glucose uptake in live cells at single cell resolution. Using a model of CRISPR-Cas9 gene editing in 5TGM1 myeloma cells, we demonstrate that ablation of the glucose transporter gene Slc2a1 abrogates radioactive glucose uptake but has no effect on the magnitude or kinetics of 2NBDG import. Extracellular 2NBDG, but not NBD-fructose was transported by plasma cells into the cytoplasm suggesting specific activity that is unlinked to glucose import and that of chemically similar compounds. RNA-Seq analysis of primary plasma cells and the 5TGM1 myeloma cell line revealed expression of other candidate glucose transporters. Yet, deletion of these transporters individually or in combination with one another also had no impact on 2NBDG uptake. Ablation of the genes in the Slc29 and Slc35 families of nucleoside and nucleoside sugar transporters as well as the ATP-binding cassette (ABC) transporter family also failed to impact 2NBDG import. Thus, cellular uptake of 2NBDG is promoted by an unknown mechanism and is not a faithful indicator of glucose transport.

category: immunology


title: Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

abstract: Laboratory mice are widely studied as models of mammalian biology, including the microbiota. However, much of the taxonomic and functional diversity of the mouse gut microbiome is missed in current metagenomic studies, because genome databases have not achieved a balanced representation of the diverse members of this ecosystem. Towards solving this problem, we used flow cytometry and low-coverage sequencing to capture the genomes of 764 single cells from the stool of three laboratory mice. From these, we generated 298 high-coverage microbial genome assemblies, which we annotated for open reading frames and phylogenetic placement. These genomes increase the gene catalog and phylogenetic breadth of the mouse microbiota, adding 135 novel species with the greatest increase in diversity to the Muribaculaceae and Bacteroidaceae families. This new diversity also improves the read mapping rate, taxonomic classifier performance, and gene detection rate of mouse stool metagenomes. The novel microbial functions revealed through our single-cell genomes highlight previously invisible pathways that may be important for life in the murine gastrointestinal tract.


title: Salubrinal induces fetal hemoglobin expression via the stress-signaling pathway in human sickle erythroid progenitors and sickle cell disease mice

abstract: Sickle cell disease (SCD) is an inherited blood disorder caused by a mutation in the HBB gene leading to hemoglobin S production and polymerization under hypoxia conditions leading to vaso-occlusion, chronic hemolysis, and progressive organ damage. This disease affects [~]100,000 people in the United States and millions worldwide. An effective therapy for SCD is fetal hemoglobin (HbF) induction by pharmacologic agents such as hydroxyurea, the only Food and Drug Administration-approved drug for this purpose. Therefore, the goal of our study was to determine whether salubrinal (SAL), a selective protein phosphatase 1 inhibitor, induces HbF expression through the stress-signaling pathway by activation of p-eIF2 and ATF4 trans-activation in the {gamma}-globin gene promoter. Sickle erythroid progenitors treated with 24{micro}M SAL increased F-cells levels 1.4-fold (p=0.021) and produced an 80% decrease in reactive oxygen species. Western blot analysis showed SAL enhanced HbF protein by 1.6-fold (p=0.0441), along with dose-dependent increases of p-eIF2 and ATF4 levels. Subsequent treatment of SCD mice by a single intraperitoneal injection of SAL (5mg/kg) produced peak plasma concentrations at 6 hours. Chronic treatments of SCD mice with SAL mediated a 2.3-fold increase in F-cells (p=0.0013) and decreased sickle erythrocytes supporting in vivo HbF induction.


title: Comparison of biological features of wild European rabbit mesenchymal stem cells derived from different tissues.

abstract: Although the European rabbit is an "endangered" species and a notorious biological model, the analysis and comparative characterization of new tissue sources of rabbit mesenchymal stem cells (rMSCs) has not been well studied. Here we report for the first time the isolation and characterization of rMSCs derived from an animal belonging to a natural rabbit population within the species native region. New rMSC lines were isolated from different tissues: oral mucosa (rOM-MSC), dermal skin (rDS-MSC), subcutaneous adipose tissue (rSCA-MSC), ovarian adipose tissue (rOA-MSC), oviduct (rO-MSC), and mammary gland (rMG-MSC). The six rMSC lines showed plastic adhesion with fibroblast-like morphology and were all shown to be positive for CD44 and CD29 expression (characteristic markers of MSCs), and negative for CD34 or CD45 expression. In terms of pluripotency features, all rMSC lines expressed NANOG, OCT4, and SOX2. Furthermore, all rMSC lines cultured under osteogenic, chondrogenic, and adipogenic conditions showed differentiation capacity. In conclusion, this study describes the isolation and characterization of new rabbit cell lines from different tissue origins, with a clear mesenchymal pattern. We show that rMSC do not exhibit differences in terms of morphological features, expression of the cell surface, and intracellular markers of pluripotency and in vitro differentiation capacities, attributable to their tissue of origin.


title: Characterization of metabolic compartmentalization in the liver using spatially resolved metabolomics

abstract: Cells adapt their metabolism to physiological stimuli, and metabolic heterogeneity exists between cell types, within tissues, and subcellular compartments. The liver plays an essential role in maintaining whole-body metabolic homeostasis and is structurally defined by metabolic zones. These zones are well-understood on the transcriptomic level, but have not been comprehensively characterized on the metabolomic level. Mass spectrometry imaging (MSI) can be used to map hundreds of metabolites directly from a tissue section, offering an important advance to investigate metabolic heterogeneity in tissues compared to extraction-based metabolomics methods that analyze tissue metabolite profiles in bulk. We established a workflow for the preparation of tissue specimens for matrix-assisted laser desorption/ionization (MALDI) MSI and achieved broad coverage of central carbon, nucleotide, and lipid metabolism pathways. We used this approach to visualize the effect of nutrient stress and excess on liver metabolism. Our data revealed a highly organized metabolic compartmentalization in livers, which becomes disrupted under nutrient stress conditions. Fasting caused changes in glucose metabolism and increased the levels of fatty acids in the circulation. In contrast, a prolonged high-fat diet (HFD) caused lipid accumulation within liver tissues with clear zonal patterns. Fatty livers had higher levels of purine and pentose phosphate related metabolites, which generates reducing equivalents to counteract oxidative stress. This MALDI MSI approach allowed the visualization of liver metabolic compartmentalization at high resolution and can be applied more broadly to yield new insights into metabolic heterogeneity in vivo.


title: Metabolic properties of murine kidney mitochondria

abstract: We show that mitochondria from the kidney of mice (MKM), rat brain (RBM), and heart (RHM) oxidize long-chain fatty acids at high rates in all metabolic states only in the presence of any other mitochondrial metabolites: succinate, glutamate, or pyruvate. All supporting substrates increased several folds the respiration rates in State 4 and State 3. The stimulations of the State 3 respiration with palmitoyl-carnitine + malate oxidation (100%) were: with succinate in MKM 340%, RBM 370%, and RHM 340%; with glutamate - MKM 200%, RBM 270%, and RHM 270%; and with pyruvate - MKM 150%, RBM 260%, and RHM 280%. The increases in O2 consumption in State 4 were due to increased leakage of electrons to produce superoxide radicals (O2*). Earlier, we have shown that the brain and heart mitochondria possess a strong intrinsic inhibition of succinate oxidation to prevent the excessive O2* production at diminished functional loads. We show that kidney mitochondria lack the intrinsic inhibition of SDH. The new methodology to study {beta}-oxidation of LCFAs opens the opportunity to study energy metabolism under normal and pathological conditions, particularly in the organs that utilize LCFAs as the main energy source.


title: Gross anatomy of the gluteal and posterior thigh muscles in koalas based on their innervations

abstract: There are not many descriptions of the muscle morphology of marsupials, despite the fact that they should show diversity according to the adaptation and dispersal to a variety of environments. Most of the previous studies regarding the gross anatomy of marsupials were conducted in the 1800 - 1900s, and many issues still remain that need to be reexamined. For instance, the muscle identification had been performed based only on their attachments and thus, muscle descriptions are often inconsistent among the studies. These classic studies often do not include figures or photographs, so the discrepancies in the descriptions of the muscles could only be verified by performing the muscle identification again with a more reliable method. This problem can be solved by performing muscle identification by innervation. This method, which focuses on the ontogenic origin of the muscle as opposed to the attachment site, is prone to individual and interspecies variation and is a common technique in recent anatomical research. This technique is more reliable than previous methods and is suitable for comparison with other taxa (i.e., eutherians). In this study, we first conducted muscle identification based on innervation in the gluteal and posterior thighs of koalas in order to reorganize the anatomical knowledge of marsupials. This is because the gluteus and posterior thighs of koalas are the areas where previous studies have been particularly inconsistent. We dissected five individual koalas and clarified discrepancies in previous studies, as well as investigated the unique muscle morphology and their function in koalas. Specifically, the koalas gluteal muscle group is suitable for abduction, while the posterior thigh muscles are particularly suitable for flexion. In the future, we will update the anatomical findings of marsupials in the same way to clarify the adaptive dissipation process of marsupials, as well as to contribute to the understanding of the evolutionary morphology of mammals.

category: zoology


title: Inactivation of SARS-CoV-2 and influenza A virus by spraying hypochlorous acid solution and hydrogen peroxide solution in the form of Dry Fog

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is transmitted by droplet and contact infection. SARS-CoV-2 that adheres to environmental surfaces remains infectious for several days. We herein attempted to inactivate SARS-CoV-2 and influenza A virus adhering to an environmental surface by spraying aerosolized hypochlorous acid solution and hydrogen peroxide solution in the form of Dry Fog (fog that does not wet objects even if touched). SARS-CoV-2 and influenza virus were dried on plastic plates and placed into a test chamber for inactivation by the Dry Fog spraying of disinfectants. The results obtained showed that Dry Fog spraying inactivated SARS-CoV-2 and influenza A virus in time- and exposed disinfectant amount-dependent manners. SARS-CoV-2 was more resistant to the virucidal effects of aerosolized hypochlorous acid solution and hydrogen peroxide solution than influenza A virus; therefore, higher concentrations of spray solutions were required to inactivate SARS-CoV-2 than influenza A virus. The present results provide important information for the development of a strategy that inactivates SARS-CoV-2 and influenza A virus on environmental surfaces by spatial spraying.

category: microbiology


title: Temporally precise movement-based predictions in the mouse auditory cortex

abstract: Many of the sensations experienced by an organism are caused by their own actions, and accurately anticipating both the sensory features and timing of self-generated stimuli is crucial to a variety of behaviors. In the auditory cortex, neural responses to self-generated sounds exhibit frequency-specific suppression, suggesting that movement-based predictions may be implemented early in sensory processing. Yet it remains unknown whether this modulation results from a behaviorally specific and temporally precise prediction, nor is it known whether corresponding expectation signals are present locally in the auditory cortex. To address these questions, we trained mice to expect the precisely timed acoustic outcome of a forelimb movement using a closed-loop sound-generating lever. Dense neuronal recordings in the auditory cortex revealed suppression of responses to self-generated sounds that was specific to the expected acoustic features, specific to a precise time within the movement, and specific to the movement that was coupled to sound during training. Predictive suppression was concentrated in L2/3 and L5, where deviations from expectation also recruited a population of prediction-error neurons that was otherwise unresponsive. Recording in the absence of sound revealed abundant movement signals in deep layers that were biased toward neurons tuned to the expected sound, as well as temporal expectation signals that were present throughout the cortex and peaked at the time of expected auditory feedback. Together, these findings reveal that predictive processing in the mouse auditory cortex is consistent with a learned internal model linking a specific action to its temporally precise acoustic outcome, while identifying distinct populations of neurons that anticipate expected stimuli and differentially process expected versus unexpected outcomes.


title: Characterizing the Behavioral and Neuroendocrine Features of Susceptibility and Resilience to Social Stress

abstract: Evaluating and coping with stressful social events as they unfold is a critical strategy in overcoming them without long-lasting detrimental effects. Individuals display a wide range of responses to stress, which can manifest in a variety of outcomes for the brain as well as subsequent behavior. Chronic Social Defeat Stress (CSDS) in mice has been widely used to model individual variation following a social stressor. Following a course of repeated intermittent psychological and physical stress, mice diverge into separate populations of social reactivity: resilient (socially interactive) and susceptible (socially avoidant) animals. A rich body of work reveals distinct neurobiological and behavioral consequences of this experience that map onto the resilient and susceptible groups. However, the range of factors that emerge over the course of defeat have not been fully described. Therefore, in the current study, we focused on characterizing behavioral, physiological, and neuroendocrine profiles of mice in three separate phases: before, during, and following CSDS. We found that following CSDS, traditional read-outs of anxiety-like and depression-like behaviors do not map on to the resilient and susceptible groups. By contrast, behavioral coping strategies used during the initial social stress encounter better predict which mice will eventually become resilient or susceptible. In particular, mice that will emerge as susceptible display greater escape behavior on Day 1 of social defeat than those that will emerge as resilient, indicating early differences in coping mechanisms used between the two groups. We further show that the social avoidance phenotype in susceptible mice is specific to the aggressor strain and does not generalize to conspecifics or other strains, indicating that there may be features of threat discrimination that are specific to the susceptible mice. Our findings suggest that there are costs and benefits to both the resilient and susceptible outcomes, reflected in their ability to cope and adapt to the social stressor.


title: Arousal elevation drives the development of oscillatory vocal output

abstract: Adult behaviors, such as vocal production, often exhibit temporal regularity. In contrast, their immature forms are more irregular. We ask whether the coupling of motor behaviors with arousal changes give rise to temporal regularity. Do they drive the transition from variable to regular motor output over the course of development? We used marmoset monkey vocal production to explore this putative influence of arousal on the nonlinear changes in their developing vocal output patterns. Based on a detailed analysis of vocal and arousal dynamics in marmosets, we put forth a general model incorporating arousal and auditory-feedback loops for spontaneous vocal production. Using this model, we show that a stable oscillation can emerge as the baseline arousal increases, predicting the transition from stochastic to periodic oscillations observed during marmoset vocal development. We further provide a solution for how this model can explain vocal development as the joint consequence of energetic growth and social feedback. Together, we put forth a plausible mechanism for the development of arousal-mediated adaptive behavior.


title: Models for Evaluation of Biological Age Based on Multi-omics

abstract: Aging is a complex process of systemic degeneration at multiple cellular and tissue levels that has a complex mechanism. Individuals age at different rates, and there is a high degree of aging heterogeneity. Therefore, it is inaccurate to judge an individuals degree of aging by their chronological age. We performed transcriptome-focused multi-omics analyses (including transcriptomics, DNA methylation, proteomics, cytokine and telomere analysis, and single-cell transcriptome sequencing) on 139 healthy individuals aged 23 to 88 years. We systematically analyzed linear and non-linear changes in gene expression throughout aging. Genes with similar expression trajectories were enriched in similar biological pathways, including the PI3K-AKT signaling pathway and the inflammatory response. Through DNA methylation detection, we found that the expression of the top genes correlated with age was affected by methylation in the gene promoter region. These genes had no significant correlation with the expression of downstream proteins, but they were enriched in PI3K-AKT-associated proteins. Single-cell transcriptome sequencing showed that the expression of these genes did not significantly change in different cell subtypes, which proves that the gene expression changes were caused by internal age-related cellular changes rather than cell composition changes. We designed a transcriptome age clock and a methylation age clock using a set of 787 genes. Our models can accurately predict age with a mean absolute error (MAE) of 5.203 and 3.28, respectively, which is better than previously established aging models. The accuracy of our model was further verified by the detection of telomeres, which can identify accelerated aging of individuals.


title: KRAS G12D can be targeted by potent salt-bridge forming inhibitors

abstract: KRAS mutation occurs in nearly 30% of human cancers, yet the most prevalent and oncogenic KRAS mutation (G12D) still lacks inhibitors. Herein, we explored the formation of a salt-bridge between KRASs Asp12 residue and a series of potent inhibitors. Our ITC results show that these inhibitors bind to and inhibit both GDP-bound and GTP-bound KRAS G12D, and our crystallographic studies revealed the structural basis of inhibitor binding in the switch-II pocket, experimentally confirming the formation of a salt-bridge between the piperazine moiety of the inhibitors and the 12D residue of the mutant protein. Among KRAS family proteins and mutants, both ITC and enzymatic assays support the selectivity of the inhibitors for KRAS G12D, and the inhibitors disrupt the KRAS-CRAF interaction. We also observed inhibition of cancer cell proliferation and inhibition of MAPK signaling by a representative inhibitor (TH-Z835); however, since this was not fully dependent on KRAS mutation status, it is possible that our inhibitors may have off-target effects via non-KRAS small GTPases. Experiments with a mouse model of pancreatic cancer showed that TH-Z835 significantly reduced tumor volume and synergized with an anti-PD-1 antibody. Collectively, our study demonstrates proof-of-concept for a salt-bridge, induced-fit pocket strategy for KRAS G12D, which warrants future medicinal chemistry efforts for optimal efficacy and minimized off-target effects.


title: Combined Pan-, Population-, and Phylo-Genomic Analysis of Aspergillus fumigatus Reveals Population Structure and Lineage-Specific Diversity

abstract: Aspergillus fumigatus is a deadly agent of human fungal disease, where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on de novo assemblies offer a promising alternative to reference-based genomics, with the potential to address the full genetic repertoire of a species. Here, we use a combination of population genomics, phylogenomics, and pan-genomics to assess population structure and recombination frequency, phylogenetically structured gene presence-absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes in A. fumigatus. We provide evidence for three primary populations of A. fumigatus, structured by both gene variation (SNPs and indels) and distinct gene presence-absence variation with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism, suggesting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. A. fumigatus demonstrated exceptionally high levels of recombination and one of the largest fungal pan-genomes reported to date including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference genome-based approach for evaluating intraspecific variation, and the power of combined genomic approaches to elucidate population structure, genetic diversity, and putative ecological drivers of clinically relevant fungi.


title: Fatquant: An automated image analysis tool for identification of fat cells in heterogeneous hematoxylin and eosin tissue sections.

abstract:
Hematoxylin and eosin (H and E) is one of the common histological staining techniques that provides information on the tissue cytoarchitecture. Adipose (fat) cells accumulation in pancreas has been shown to impact beta cell survival and its endocrine function. The current automated tools available for fat analysis are suited for white adipose tissue which is homogeneous and easier to segment unlike heterogeneous tissues such as pancreas where fat cells continue to play critical physiopathological functions. In the current study, we present an automated fat analysis tool, Fatquant, where mathematical formula to calculate diagonal of a square drawn inside circle is utilized for identification and analysis of fat cells in heterogeneous H and E tissue sections. Using histological images of pancreas from a publicly available database, we show an area accuracy overlap of 89-93% between manual versus automated algorithm based fat cell detection.

Author SummaryWe have developed an automated tool, Fatquant, for identification of fat cells in complex hematoxylin and eosin tissue sections such as pancreas which can aid the pathologist for detection and analysis. Fatquant is unique as current fat automated tools work well for homogeneous white adipose tissue but not for other tissue samples.


title: Unexpected short- and long-term effects of chronic adolescent HU-210 exposure on emotional behavior

abstract:
Chronic adolescent cannabinoid receptor agonist exposure has been shown to lead to persistent increases in depressive-like behaviors. This has been a key obstacle to the development of cannabinoid-based therapeutics. However, most of the published work has been performed with only three compounds, namely {Delta}9-tetrahydrocannabinol, CP55,940 and WIN55,212-2. Hypothesizing that different compounds may lead to distinct outcomes, we herein used the highly potent CB1R/CB2R full agonist HU-210, and first aimed at replicating cannabinoid-induced long-lasting effects, by exposing adolescent female Sprague-Dawley rats to increasing doses of HU-210, for 11 days and testing them at adulthood, after a 30-day drug washout. Surprisingly, HU-210 did not significantly impact adult anxious- or depressive-like behaviors. We then tested whether chronic adolescent HU-210 treatment resulted in short-term (24h) alterations in depressive-like behavior. Remarkably, HU-210 treatment simultaneously induced marked antidepressant- and prodepressant-like responses, in the modified forced swim (mFST) and sucrose preference tests (SPT), respectively. Hypothesizing that mFST results were a misleading artifact of HU-210-induced behavioral hyperreactivity to stress, we assessed plasmatic noradrenaline and corticosterone levels, under basal conditions and following an acute swim-stress episode. Notably, we found that while HU-210 did not alter basal noradrenaline or corticosterone levels, it greatly augmented the stress-induced increase in both.

Our results show that, contrary to previously studied cannabinoid receptor agonists, HU-210 does not induce persisting depressive-like alterations, despite inducing marked short-term increases in stress-induced reactivity. By showing that not all cannabinoid receptor agonists may induce long-term negative effects, these results hold significant relevance for the development of cannabinoid-based therapeutics.


title: Brassica napus genes Rlm4 and Rlm7, conferring resistance to Leptosphaeria maculans, are alleles of the Rlm9 wall-associated kinase-like resistance locus

abstract: Brassica napus (canola/rapeseed) race specific resistance genes against blackleg disease, caused by the ascomycete fungus Leptosphaeria maculans, have been commonly used in canola breeding. To date; LepR3, Rlm2 and Rlm9 R genes against L. maculans have been cloned from B. napus. LepR3 and Rlm2 are Receptor Like Proteins (RLP) and the recently reported Rlm9 is a Wall Associated Kinase-Like (WAKL) protein. Rlm9 located on chromosome A07 is closely linked with Rlm3, Rlm4, RLm7 genes. Recognition of AvrLm5-9 and AvrLm3 by their corresponding Rlm9 and Rlm3 proteins is masked in the presence of AvrLm4-7. Here we report cloning of Rlm4 and Rlm7 by generating genome sequence of the doubled haploid (DH) B. napus cv Topas DH16516 introgression lines Topas-Rlm4 and Topas-Rlm7. Candidate Rlm4 and Rlm7 genes were identified form the genome sequence and gene structures were determined by mapping RNA-sequence reads, generated from infected cotyledon tissues, to the genome of Topas-Rlm4 and Topas-Rlm7. Rlm4 and Rlm7 genomic constructs with their native promoters were transferred into the blackleg susceptible B. napus cv Westar N-o-1. Complementation of resistance response in the transgenic Westar:Rlm4 and Westar:Rlm7 that were inoculated with L. maculans transgenic isolates 2367:AvrRlm4-7 or 2367:AvrLm7 confirmed the function of Rlm4 and Rlm7 genes. Wild type L. maculans isolate 2367 that does not contain AvrLm4-7 or AvrLm7, and transgenic 2367:AvrLm3 and 2367:AvrLm5-9 did not induce resistance proving the specificity of Rlm4 and Rlm7 response. Rlm4 and Rlm7 alleles are also allelic to Rlm9. Rlm4 and Rlm7 genes encode WAKL proteins. Comparison of highly homologous sequences of Rlm4 and Rlm7 with each other and with the sequence of additional alleles, using whole genome sequencing of additional 128 lines, identified a limited number of point mutation located within the predicted extracellular receptor domains.


title: Brain injury environment critically influences the connectivity of transplanted neurons

abstract:
Cell transplantation is a promising approach for the reconstruction of neuronal circuits after brain damage. Transplanted neurons integrate with remarkable specificity into circuitries of the mouse cerebral cortex affected by neuronal ablation. However, it remains unclear how neurons perform in a local environment undergoing reactive gliosis, inflammation, macrophage infiltration and scar formation, as in traumatic brain injury (TBI). To elucidate this, we transplanted cells from the embryonic mouse cerebral cortex into TBI-injured, inflamed-only, or intact cortex of adult mice. Brain-wide quantitative connectomics unraveled graft inputs from correct regions across the brain in all conditions, with pronounced quantitative differences: scarce in intact and inflamed brain, versus exuberant after trauma. In the latter, excessive synapse pruning follows the initial overshoot of connectivity resulting in only a few connections left. Proteomic profiling identifies candidate molecules involved in the synaptic yield, a pivotal parameter to tailor for functional restoration of neuronal circuits.

TeaserNeuronal grafts in a brain area affected by trauma receive excessive yet mostly vulnerable inputs from host circuits.


title: Modeling Synaptic Effects of Anesthesia and its Cortical Cholinergic Reversal

abstract:
General anesthetics work through a variety of molecular mechanisms while resulting in the common end point of sedation and loss of consciousness. Generally, the administration of common inhalation anesthetics induces decreases in synaptic excitation while promoting synaptic inhibition. Animal studies have shown that, during anesthesia, exogenously induced increases in acetylcholine-mediated effects in the brain can elicit wakeful-like behavior despite the continued presence of the anesthetic. Less investigated, however, is the question of whether the brains electrophysiological activity is also restored to pre-anesthetic levels and quality by such interventions. Here we apply a computational model of a network composed of excitatory and inhibitory neurons to simulate the network effects of changes in synaptic inhibition and excitation due to anesthesia and its reversal by muscarinic receptor-mediated cholinergic effects. We use a differential evolution algorithm to fit model parameters to match measures of spiking activity, neuronal connectivity, and network dynamics recorded in the visual cortex of rodents during anesthesia with desflurane in vivo. We find that facilitating muscarinic receptor effects of acetylcholine on top of anesthetic-induced synaptic changes predicts reversal of the neurons spiking activity, functional connectivity, as well as pairwise and population interactions. Thus, our model results predict a possible neuronal mechanism for the induced reversal of the effects of anesthesia on post synaptic potentials, consistent with experimental behavioral observations.

Author SummaryHere, we apply a computational model of a network composed of excitatory and inhibitory neurons to simulate the network effects of changes in synaptic inhibition and excitation due to anesthesia and we investigate the possibility of its reversal by muscarinic receptor-mediated cholinergic effects. Specifically, we use a differential evolution algorithm to fit model parameters to match dynamics recorded in the visual cortex of rodents during anesthesia with desflurane in vivo. We find that changes of the fitted synaptic parameters in response to the increasing desflurane concentration matched those established by neurophysiology. Further, our results demonstrate that the cellular effects induced by anesthesia can be mitigated by the changes in cellular excitability due to acetylcholine.


title: Virtual reality-based sensorimotor adaptation shapes subsequent spontaneous and naturalistic stimulus-driven brain activity

abstract:
Our everyday life summons numerous novel sensorimotor experiences, to which our brain needs to adapt in order to function properly. However, tracking plasticity of naturalistic behaviour and associated brain modulations is challenging. Here we tackled this question implementing a prism adaptation training in virtual reality (VRPA) in combination with functional neuroimaging. Three groups of healthy participants (N=45) underwent VRPA (with a spatial shift either to the left/right side, or with no shift), and performed fMRI sessions before and after training. To capture modulations in free-flowing, task-free brain activity, the fMRI sessions included resting state and free viewing of naturalistic videos. We found significant decreases in spontaneous functional connectivity between large-scale cortical networks - namely attentional and default mode/fronto-parietal networks - only for adaptation groups. Additionally, VRPA was found to bias visual representations of naturalistic videos, as following rightward adaptation, we found upregulation of visual response in an area in the parieto-occipital sulcus (POS) in the right hemisphere. Notably, the extent of POS upregulation correlated with the size of the VRPA induced after-effect measured in behavioural tests. This study demonstrates that a brief VRPA exposure is able to change large-scale cortical connectivity and correspondingly bias the representation of naturalistic sensory inputs.

Significance statementIn the current work, we tested how a brief sensorimotor experience changes subsequent brain activity and connectivity. Using virtual reality (VR) as a tool for sensorimotor training opens a window for creating otherwise impossible sensory experiences and sensorimotor interactions. Specifically, we studied how VR adaptation training in ecological conditions modulates spontaneous functional connectivity and brain representation of naturalistic real-life-like stimuli. Previous adaptation studies used artificial, lab-designed setups both during adaptation and while measuring subsequent aftereffects. Testing brain response while observing naturalistic stimuli and in resting state allowed us to stay as close as possible to naturalistic real-life-like conditions, not confounded by performance during a task. The current work demonstrates how rapid changes in free-flowing brain activity and connectivity occur following short-term VR visuomotor adaptation training in healthy individuals. Moreover, we found a link between sensory responses to naturalistic stimuli and adaptation-induced behavioural aftereffect, thus demonstrating a common source of training-induced spatial recalibration, which affects both behaviour and brain representations of naturalistic stimuli. These findings might have meaningful implications both for understanding the mechanisms underlying visuomotor plasticity in healthy individuals and for using VR adaptation training as a tool for rehabilitating brain-damaged patients suffering from deficits in spatial representation.


title: biPACT: a method for three-dimensional visualization of mouse spinal cord circuits of long segments with high resolution

abstract:
BackgroundThe spatial complexity of neuronal circuits in the central nervous system is a hurdle in understanding and treating brain and spinal cord injuries. Although several methods have recently been developed to render the spinal cord transparent and label specific neural circuits, three-dimensional visualization of long segments of spinal cord with high resolution remains challenging.

New MethodWe present a method that combines tissue staining of neuronal tracts traced with biotinylated dextran amine (BDA) and a modified passive clarity clearing protocol to describe individual fibers in long segments of mouse spinal cord.

ResultsCorticospinal tract was traced with BDA with a mouse model of thoracic spinal cord injury. The spinal cord was stained and cleared in two weeks with four solutions: staining solution, hydrogel solution, clearing solution, and observation solution. The samples were observed with a light-sheet microscope, and three-dimensional reconstruction was performed with ImageJ software. High resolution-images comparable with tissue sections were obtained continuously and circumferentially. By tiling, it was possible to obtain high-resolution images of long segments of the spinal cord. The tissue could be easily re-stained in case of fading,

Comparison with Existing MethodsThe present method does not require special equipment, can label specific circuits without genetic technology, and re-staining rounds can be easily implemented. It enables to visualize individual neural fiber of specific neural circuit in long spinal cord segments.

ConclusionsBy using simple neural staining, and clearing methods, it was possible to acquire a wide range of high-resolution three-dimensional images of the spinal cord.

HighlightsO_LINo special devices or genetic tracers are required for a new clearing method
C_LIO_LINeuronal fibers are individually depicted in long segments of mouse spinal cord.
C_LIO_LIRe-staining of neuronal fiber is possible.
C_LIO_LIStereotaxic observation is achieved by 3-D reconstruction with open-source software.
C_LI


title: Impaired dynamics of prefrontal beta-band networks during cognitive action control in Parkinson's disease

abstract:
Among the cognitive symptoms that are associated with Parkinsons disease (PD), alterations in cognitive action control (CAC) are commonly reported in patients. CAC enables the suppression of an automatic action, in favor of a goal-directed one. The implementation of CAC is time-resolved and arguably associated with dynamic changes in functional brain networks. However, the electrophysiological functional networks involved, their dynamic changes, and how these changes are affected by PD, still remain unknown. In this study, to address this gap of knowledge, 21 PD patients and 10 healthy controls (HC) underwent a Simon task while high-density electroencephalography (HD-EEG) was recorded. Source-level dynamic connectivity matrices were estimated using the phase-locking value in the beta (12-25 Hz) and gamma (30-45 Hz) frequency bands. Temporal independent component analyses were used as a dimension reduction tool to isolate the group-specific brain network states that were dominant during the task. Typical microstate metrics were quantified to investigate the presence of these states at the subject-level. Our results first confirmed that PD patients experienced difficulties in inhibiting automatic responses during the task. At the group-level, HC displayed a significant functional network state that involved typical CAC-related prefrontal and cingulate nodes (e.g., inferior frontal cortex). Both group- and subject-level analyses showed that this network was less present in PD to the benefit of other networks involving lateralized temporal and insular components. The presence of this prefrontal network was associated with decreased reaction time. In the gamma band, two networks (fronto-cingulate and fronto-temporal) followed one another in HC, while 3 partially overlapping networks that included fronto-temporal, fronto-occipital and cross-hemispheric temporal connections were found in PD. At the subject-level, differences between PD and HC were less marked. Altogether, this study showed that the functional brain networks observed during CAC and their temporal changes were different in PD patients as compared to HC, and that these differences partially relate to behavioral changes. This study also highlights that task-based dynamic functional connectivity is a promising approach in understanding the cognitive dysfunctions observed in PD and beyond.

HighlightsO_LICognitive action control is associated with dynamic functional networks
C_LIO_LIPrefrontal and cingulate beta connectivity are prominent in healthy controls
C_LIO_LIPD patients have different dynamic networks in which prefrontal nodes are absent
C_LIO_LIThe occurrence of prefrontal beta networks was associated with a decreased reaction time
C_LIO_LIFunctional networks in the gamma band were temporally organized in HC, but overlapping in PD patients
C_LI


title: Neuroimaging signature associated with symptom exacerbation in early-stage psychosis

abstract: Recent reports have indicated that the occurrence of symptom exacerbation in early-stage psychosis could result in brain changes, which are likely to underlie the poorer disease outcome. Thus, it is important to identify neuroimaging signature associated with symptom exacerbation in early-stage psychosis. We studied 85 patients with psychosis within two years after onset and 94 healthy controls (HC). The patient group was subdivided into two groups: 54 patients who did not experience major symptom exacerbation between the onset and study enrollment (P1), and 31 patients who experienced major symptom exacerbation (P2). We analyzed three brain imaging measures derived from resting-state functional MRI, such as global efficiency, nodal efficiency, and resting-state functional connectivity (rs-FC). After excluding some brain imaging measures that were potentially affected by clinical variables, we conducted a comparison between overall patient group and HC group as well as comparsions between HC, P1, and P2 groups for these three types of brain imaging measures, respectively. By integrating the information, we pinned down the dorsal anterior cingulate cortex and thalamus as key hubs in the context of several large-scale brain networks associated with symptom exacerbations in early-stage psychosis. Our study implies the importance of considering neural mechanism associated with symptom exacerbations in early stages of psychotic disorders.


title: Synthesis and Evaluation of Acridone and Xanthone Epoxides with Anti-MRSA and Anti-MSSA Activity

abstract: A series of acridone and xanthone-based compounds bearing 1,2-epoxypropyl or 1,2-propanediol substituents were synthesized and evaluated for activity against MRSA and MSSA bacterial strains. The results indicate a correlation exists between the number of epoxide groups and activity, with peak MIC values observed for bis-epoxy derivatives. Both activity and heathy cell toxicity was shown to decrease with the addition of a third epoxy group. The corresponding ring-opened diol analogs were devoid of activity, demonstrating the critical function of the epoxide in mediating antimicrobial activity. The most active compounds were also screened using a regulated antisense RNA expression library. The results show no increase in activity against cells sensitized by down-regulation of the most common drug targets, including DNA gyrase, DNA topoisomerase, tRNA synthetase, and the fatty acid biosynthesis pathway. The compounds are postulated to function as membrane disrupting agents, similar to the xanthone natural product -mangostin.


title: Regenerated crustacean limbs are precise replicas

abstract: Animals can regenerate complex organs, yet this frequently results in imprecise replicas of the original structure. In the crustacean Parhyale, embryonic and regenerating legs differ in gene expression dynamics but produce apparently similar mature structures. We examine the fidelity of Parhyale leg regeneration using complementary approaches to investigate microanatomy, sensory function, cellular composition and cell molecular profiles. We find that regeneration precisely replicates the complex microanatomy and spatial distribution of external sensory organs, and restores their sensory function. Single-nuclei sequencing shows that regenerated and uninjured legs are indistinguishable in terms of cell type composition and transcriptional profiles. This remarkable fidelity highlights the ability of organisms to achieve identical outcomes via distinct processes.

category: developmental biology


title: There and Back to the Present: An Evolutionary Tale on Biological Diversity

abstract: Ecologists often agree on the importance of macroevolution for niche-mediated distribution of biological diversity along environmental gradients. Yet, macroevolutionary diversification and dispersal in time and space generate uneven geographic distribution of phylogenetic pools, which affects the imprint let by macroevolution on local species pools. In this article we introduce an individual-based simulation approach coupled to Approximate Bayesian Computation (ABC) that allows to parameterize the adaptation rate of species niche positions along the evolution of a monophyletic lineage, and the intensity of dispersal limitation, associated with the distribution of biological diversity between assemblages potentially connected by dispersal (metacommunity). The analytical tool was implemented in an R package called mcfly. We evaluated the statistical performance of the analytical framework using simulated datasets, which confirmed the suitability of the analysis to estimate adaptation rate and dispersal limitation parameters. Further, we evaluated the role played by niche evolution and dispersal limitation on species diversity distribution of Phyllostomidae bats across the Neotropics. The framework proposed here shed light on the links between niche evolution, dispersal limitation and the distribution of biological diversity, and thereby improved our understanding of evolutionary imprints on ecological patterns. Perhaps more importantly, it offers new possibilities for solving the eco-evolutionary puzzle.


title: Coevolution of the olfactory organ and its receptor repertoire in ray-finned fishes

abstract: Ray-finned fishes (Actinopterygii) perceive their environment through a range of sensory modalities, including olfaction 1,2. Anatomical diversity of the olfactory organ suggests that olfaction is differentially important among species 1,3,4. To explore this topic, we studied the evolutionary dynamics of the four main gene families (OR, TAAR, ORA/VR1 and OlfC/VR2) 5 coding for olfactory receptors in 185 species of ray-finned fishes. The large variation in the number of functional genes, between 28 in the Ocean Sunfish Mola mola and 1317 in the Reedfish Erpetoichthys calabaricus, is the result of parallel expansions and contractions of the four main gene families. Several ancient and independent simplifications of the olfactory organ are associated with massive gene losses. In contrast, polypteriforms, which have a unique and complex olfactory organ, have almost twice as many olfactory receptor genes as any other ray-finned fish. These observations suggest a functional link between morphology of the olfactory organ and richness of the olfactory receptor repertoire. Further, our results demonstrate that the genomic underpinning of olfaction in ray-finned fishes is heterogeneous and presents a dynamic pattern of evolutionary expansions, simplifications and reacquisitions.

category: evolutionary biology


title: Combining biomarker and virus phylogenetic models improves epidemiological source identification

abstract:
To identify and stop active HIV transmission chains new epidemiological techniques are needed. Here, we describe the development of a multi-biomarker augmentation to phylogenetic inference of the underlying transmission history in a local population. HIV biomarkers are measurable biological quantities that have some relationship to the amount of time someone has been infected with HIV. To train our model, we used five biomarkers based on real data from serological assays, HIV sequence data, and target cell counts in longitudinally followed, untreated patients with known infection times. The biomarkers were modeled with a mixed effects framework to allow for patient specific variation and general trends, and fit to patient data using Markov Chain Monte Carlo (MCMC) methods. Subsequently, the density of the unobserved infection time conditional on observed biomarkers were obtained by integrating out the random effects from the model fit. This probabilistic information about infection times was incorporated into the likelihood function for the transmission history and phylogenetic tree reconstruction, informed by the HIV sequence data. To critically test our methodology, we developed a coalescent-based simulation framework that generates phylogenies and biomarkers given a specific or general transmission history. Testing on many epidemiological scenarios showed that biomarker augmented phylogenetics can reach 90% accuracy under idealized situations. Under realistic within-host HIV evolution, involving substantial within-host diversification and frequent transmission of multiple lineages, the average accuracy was at about 50% in transmission clusters involving 5-50 hosts. Realistic biomarker data added on average 16 percentage points over using the phylogeny alone. Using more biomarkers improved the performance. Shorter temporal spacing between transmission events and increased transmission heterogeneity reduced reconstruction accuracy, but larger clusters were not harder to get right. More sequence data per infected host also improved accuracy. We show that the method is robust to incomplete sampling, and we evaluate real HIV-1 transmission clusters. The technology presented here could allow for better prevention programs by providing data for locally informed and tailored strategies.

AUTHOR SUMMARYWhile phylogenetic methods have been successfully used to infer transmission patterns on many scales, substantial uncertainty about the corresponding transmission history has remained. Here, we introduce a formal inference framework for the simultaneous use of HIV biomarkers and HIV sequences derived from persons who may have infected each other. We created a flexible system that can use up to five biomarkers to estimate the time of infection of each person, with the appropriate uncertainty given by an empirical probability distribution. These time-of-infection distributions were jointly modelled with the HIV phylogenetic tree estimation to produce possible transmission histories. We show that adding biomarkers substantially limits the possible transmission histories. This makes it possible to identify transmission risks, to assess confidence in source attributions, and to make efficient resource allocations to prevent further transmissions in local epidemics.


title: Spontaneous parthenogenesis in the parasitoid wasp Cotesia typhae: low frequency anomaly or evolving process?

abstract: Hymenopterans are haplodiploids and unlike most other Arthropods they do not possess sexual chromosomes. Sex determination typically happens via the ploidy of individuals: haploids become males and diploids become females. Arrhenotoky is believed to be the ancestral reproduction mode in Hymenopterans, with haploid males produced parthenogenetically, and diploid females produced sexually. However, a number of transitions towards thelytoky (diploid females produced parthenogenetically) have appeared in Hymenopterans, and in most cases populations or species are either totally arrhenotokous or totally thelytokous. Here we present the case of Cotesia typhae (Fernandez-Triana), a Braconidae that produces parthenogenetic females at a low frequency. The phenotyping of two laboratory strains and one natural population showed that this frequency is variable, and that this rare thelytokous phenomenon also happens in the wild. Moreover, mated females from one of the laboratory strains produce a few parthenogenetic daughters among a majority of sexual daughters. The analysis of daughters of heterozygous virgin females allowed us to show that a mechanism similar to automixis with central fusion is very likely at play in C. typhae. This mechanism allows some parts of the genome to remain heterozygous, especially at the chromosomes centromeres, which can be advantageous depending on the sex determination system involved. Lastly, in most species, the origin of thelytoky is either bacterial or genetic, and an antibiotic treatment as well as PCR experiments did not demonstrate a bacterial cause in C. typhae. The unusual case of low parthenogenetic frequency described in this species constitutes another example of the fascinating diversity of sex determination systems in Arthropods.