title: Slc7a8 deletion is protective against diet-induced obesity and attenuates lipid accumulation in multiple organs

abstract:
Adipogenesis, through adipocyte hyperplasia and/or hypertrophy, leads to increased adiposity, giving rise to obesity. A genome-wide transcriptome analysis of adipogenesis in human adipose derived stromal/stem cells identified SLC7A8 (Solute Carrier Family 7 Member 8) as a potential novel mediator. This study has investigated the role of SLC7A8 in adipose tissue biology using a mouse model of diet-induced obesity. slc7a8 knockout (KO) and wildtype (WT) C57BL/6J mice were fed either a control diet (CD) or a high-fat diet (HFD) for 14 weeks. On HFD, both WT and KO (WTHFD and KOHFD) gained significantly more weight than their CD counterparts. However, KOHFD gained significantly less weight than WT HFD. KOHFD significantly reduced the level of glucose intolerance observed in WTHFD. KOHFD significantly reduced both adipocyte mass and hypertrophy in inguinal, mesenteric, perigonadal and brown adipose depots, with a corresponding decrease in macrophage infiltration. Additionally, KOHFD decreased lipid accumulation in the liver, heart, gastrocnemius muscle, lung, and kidney. This study demonstrates that targeting SLC7A8 protects against diet-induced obesity by reducing lipid accumulation in multiple organs, and thereby has the potential to mitigate the development of obesity-associated comorbidities.

Author summaryThe development of obesity can be attributed to adipocyte hypertrophy or hyperplasia leading to increased adiposity. The C57BL/6 mouse is an excellent model used to study metabolic syndromes often associated with obesity development. Mice fed on a high-fat diet are susceptible to weight gain leading to the development of obesity and its associated metabolic syndrome. Here, we report findings from targeting a novel human adipogenic gene (SLC7A8) in condition of obesity development using a mouse model of diet-induced obesity (DIO). The results indicate that deleting slc7a8 in mice significantly protects against DIO and improves glucose metabolism. Also, deficiency in slc7a8 was observed to significantly attenuates adipocyte hypertrophy in white and brown adipose tissues, and reduced lipid accumulation in many organs. Furthermore, inflammation was significantly reduced in adipose tissues and liver of slc7a8 deficient mice in condition of DIO. Overall, results from this study shows that slc7a8 is an important molecular regulator of obesity development and mediates its function by reducing lipid accumulation in multiple organs. Hence, SLC7A8 could serve as a potential therapeutic target to combat the development of obesity and other pathophysiological conditions associated with excess lipid accumulation in organs.


title: KTD1 is a yeast defense factor against K28 killer toxin

abstract: Secreted protein toxins are widely used weapons in conflicts between organisms. Killer yeast produce killer toxins that inhibit the growth of nearby sensitive yeast. We investigated variation in resistance to the killer toxin K28 across diverse natural isolates of the Saccharomyces cerevisiae population and discovered a novel defense factor, which we named KTD1, that is an important determinant of K28 toxin resistance. KTD1 is a member of the DUP240 gene family of unknown function. We uncovered a putative role of DUP240 proteins in killer toxin defense and identified a region that is undergoing rapid evolution and is critical to KTD1s protective ability. Our findings implicate KTD1 as a key factor in the defense against killer toxin K28.

category: genetics


title: Evolution of diapause in the African turquoise killifish by remodeling ancient gene regulatory landscape

abstract: Suspended animation states such as hibernation or diapause allow organisms to survive extreme environments. But the mechanisms underlying the evolution of these extreme survival states are unknown. The African turquoise killifish has evolved diapause as a form of suspended development to survive the complete drought that occurs every year in its habitat. Here we show that many gene duplicates - paralogs - exhibit specialized expression in diapause versus normal development in the African turquoise killifish. Surprisingly, paralogs with specialized expression in diapause are evolutionarily very ancient, and they are also present even in vertebrates that do not exhibit diapause. Profiling the chromatin accessibility landscape among different fish species reveals an evolutionarily recent increase in chromatin accessibility at these very ancient paralogs, suggesting rewiring of their regulatory landscape. The increase in chromatin accessibility in the African turquoise killifish is linked to the presence of new binding sites for transcription factors (e.g., FOXO, REST, and PPAR), due to both de novo mutations and transposable element insertion. Interestingly, accessible chromatin regions in diapause are enriched for lipid metabolism genes. By performing lipidomics in different fish species, we uncover a specific lipid profile in African turquoise killifish embryos in diapause. Notably, select very long-chain fatty acids are high in diapause, suggesting they may be used for long-term survival in this state. Together, our multi-omic analysis indicates that diapause is driven by regulatory innovation of very ancient gene programs that are critical for survival. Our work also suggests a mechanism for how complex adaptations evolve in nature and offers strategies by which a suspended animation program could be reactivated in other species for long-term preservation.

category: genomics


title: Genomic adaptation in the CAZyome and specialised metabolism of the plant-associated Streptomyces violaceusniger clade

abstract: Streptomycetes are Gram-positive actinobacteria largely represented in the plant root microbiota. The genetic determinants involved in the presence of Streptomyces in the rhizosphere are largely unknown and can rely on the ability to degrade plant-derived compounds such as cell-wall polysaccharides and on the production of specialised metabolites. To address whether Streptomyces strains recruited into root microbiota share genomic specificities related to these two functions, we engaged a comparative genomic analysis using a newly sequenced rhizospheric strain, Streptomyces sp. AgN23 and strains from the phylogenetically related S. violaceusniger clade. This analysis enlightens a shared prominent CAZyome potentially involved in plant polysaccharides degradation and a strong conservation of antimicrobials biosynthetic clusters (rustmicin, mediomycin, niphimycin, nigericin) as well as plant bioactive compounds (nigericin, echosides, elaiophylin). Taken together, our work supports the hypothesis that specific hydrolytic enzymes and specialised metabolites repertoires may play important roles in the development of Streptomyces strains in the rhizosphere.


title: Development of amyloid beta gold nanorod aggregates as optoacoustic probes

abstract: Propagation of small amyloid beta (A{beta}) aggregates (or seeds) has been suggested as a potential mechanism of Alzheimers disease progression. Monitoring the propagation of A{beta} seeds in an organism would enable testing of this hypothesis and, if confirmed, provide mechanistic insights. This requires a contrast agent for long-term tracking of the seeds. Gold nanorods combine several attractive features for this challenging task, in particular, their strong absorbance in the infrared (enabling optoacoustic imaging) and the availability of several established protocols for surface functionalization. In this work, polymer-coated gold nanorods were conjugated with anti-A{beta} antibodies and specifically attached to pre-formed A{beta} seeds. The resulting complexes were characterized for their optical properties by UV/Vis spectroscopy and multispectral optoacoustic tomography. The complexes retained their biophysical properties, i.e. their ability to seed A{beta} fibril formation. They remained stable in biological media for at least 2 days and showed no toxicity to SH-SY5Y neuroblastoma cells up to 1.5 nM and 6 M of gold nanorods and A{beta} seeds, respectively. Taken together, this study describes the first steps in the development of probes for monitoring the spread of A{beta} seeds in animal models.

category: biochemistry


title: In silico modeling and interactive profiling of BPH resistant R genes with elicitor molecules of rice planthoppers

abstract: Brown planthopper resistant NBS-LRR specific R genes (Bph9, Bph14, Bph18, Bph26) have been reported in rice. BPH specific R genes were clustered with other R genes of rice on chromosome 12 (Bph9, Bph18, Bph26) and 3 (Bph14). Motif analysis of BPH specific R genes showed the predominant motifs as CC, NBS and LRR regions. Bph9, Bph18 and Bph26 R genes exhibited high degree of sequence similarity in their CC and NBS region and are considered as functional alleles of BPH resistance at chromosome 12. LRR region of BPH genes were interacting with the elicitor molecules of planthoppers and are the potential lignad binding site. Bph14 exhibited more number of LRR repeats and were interacting efficiently with all the tested salivary elictor molecules of planthoppers. Bph18 with no LRR region exhibited reduced interaction efficiency with the tested elicitor molecules of planthoppers. Our in silico studies confirms that Bph14 R gene resistance protein to be a promising candidate for providing broad spectrum resistance against planthoppers of rice. The study further provides new avenues to investigate the mechanism of receptor-ligand recognition and signaling mechanism against rice planthoppers.

category: plant biology


title: Multi-trait and multi-environment Bayesian analysis to predict the G x E interaction in flood-irrigated rice

abstract: The biggest challenge for the reproduction of flood-irrigated rice is to identify superior genotypes that present development of high-yielding varieties with specific grain qualities, resistance to abiotic and biotic stresses in addition to superior adaptation to the target environment.Thus, the objectives of this study were to propose a multi-trait and multi-environment Bayesian model to estimate genetic parameters for the flood-irrigated rice crop. To this end, twenty-five rice genotypes belonging to the flood-irrigated rice breeding program were evaluated. Grain yield and flowering were evaluated in the agricultural year 2017/2018. The experimental design used in all experiments was a randomized block design with three replications. The Markov Chain Monte Carlo algorithm was used to estimate genetic parameters and genetic values. The flowering is highly heritable by the Bayesian credibility interval: h2 = 0.039-0.80, and 0.02-0.91, environment 1 and 2, respectively. The genetic correlation between traits was significantly different from zero in the two environments (environment 1: -0.80 to 0.74; environment 2: -0.82 to 0.86. The relationship of CVe and CVg higher for flowering in the reduced model (CVg/CVe= 5.83 and 13.98, environments 1 and 2, respectively). For the complete model, this trait presented an estimate of the relative variation index of: CVe= 4.28 and 4.21, environments 1 and 2, respectively. In summary, the multi-trait and multi-environment Bayesian model allowed a reliable estimate of the genetic parameter of flood-irrigated rice. Bayesian analyzes provide robust inference of genetic parameters. Therefore, we recommend this model for genetic evaluation of flood-irrigated rice genotypes, and their generalization, in other crops. Precise estimates of genetic parameters bring new perspectives on the application of Bayesian methods to solve modeling problems in the genetic improvement of flood-irrigated rice.


title: Effects of electroacupuncture on the expression of hypothalamic neuropeptide Y and ghrelin in pubertal rats with polycystic ovary syndrome

abstract:
BackgroundPolycystic ovary syndrome often starts in puberty, and its pathogenesis is not clear. This study aimed to explore the pathogenesis of pubertal polycystic ovary syndrome (PCOS) and assess the therapeutic effect of electroacupuncture on pubertal PCOS.

MethodsDihydrotestosterone (DHT) was used to induce rat models of pubertal PCOS. pubertal rats with PCOS were randomly divided into a model group (M), an electroacupuncture group (EA), and a sham acupuncture group (SA). Age-matched normal rats were regarded as normal controls (N). Rats were treated with EA or SA five times a week for 25 minutes during their 6th-7th week. At the end of the experiment, we observed any changes in ovarian morphology; detected levels of metabolic indices in serum, the hypothalamus and pancreas.

ResultsEA significantly improved estrous cycle disorders and the ovarian polycystic morphology in pubertal rats with PCOS, but SA only improved disorders of the estrous cycle. The serum levels of insulin, neuropeptide Y(NPY) and fasting blood glucose(FBG) increased significantly, while the serum levels of ghrelin(GHRL) decreased in the model group. After treatment with EA, the levels of NPY and FBG went into decrease, whereas the levels of GHRL and insulin increased. There was few differences in the hypothalamic expression of galanin (GAL), galanin-like peptide (GALP) and ghrelin receptor(GHSR) between the four groups. The upregulation of NPY mRNA and neuropeptide Y2 receptor(NPY2R) mRNA and the downregulation of GHRL protein and mRNA in the hypothalamus, and the increased expression of NPY and NPY2R as well as the decreased expression of GHRL in the arcuate nucleus (ARC) can be rescued by EA. But, surprisingly, SA seem to make no difference to the levels of FBG and insulin, and the protein expression of ghrelin in the hypothalamus and ARC. Co-expression of kisspeptin and GHSR, and co-expression of gonadotrophin releasing hormone(GnRH) and NPY2R were observed in ARC. No differences were found between groups in protein of GAL, GALP and GHRL expression in the pancreas. Neither EA nor SA can attenuate the upregulated kisspeptin protein expression in the pancreas of PCOS model rats.

ConclusionsEA and SA improved the symptoms of pubertal PCOS rats, and the mechanism might be associated with regulating hypothalamic NPY and ghrelin levels.

category: neuroscience


title: Estimated quantity of swine virus genomes based on quantitative PCR analysis in spray-dried porcine plasma samples collected from multiple manufacturing plants.

abstract: This survey was conducted to estimate the incidence and level of potential viral contamination in commercially collected porcine plasma. Samples of spray dried porcine plasma (SDPP) were collected over a 12-month period from eight spray drying facilities in Spain, England, Northern Ireland, Brazil, Canada, and the United States. In this survey, viral load for several porcine pathogens including SVA, TGEV, PRRSV (EU and US strains), PEDV, PCV2, SIV, SDCoV and PPV were determined by qPCR. Regression of Ct on TCID50 of serial diluted stock solution of each virus allowed the estimate of potential viral level in SDPP and unprocessed liquid plasma (using typical solids content of commercially collected porcine plasma). In this survey SVA, TGEV or SDCoV were not detected in any of the SDPP samples. Brazil SDPP samples were free of PRRSV and PEDV. Samples of SDPP from North America primarily contained the PRRSV-US strain while the European samples contained the PRRSV-EU strain (except for one sample from each region containing a low estimated level of the alternative PRRSV strain). Estimated viral level tended to be low ranging from <1.0 log10 TCID50 to <2.5 log10 TCID50. Estimated level of SIV was the exception with a very low incidence rate but higher estimated viral load <3.9 log10 TCID50. In summary, the incidence of potential viral contamination in commercially collected porcine plasma was variable and estimated virus level in samples containing viral DNA/RNA was low.

category: microbiology


title: Profiling RT-LAMP tolerance of sequence variation for SARS-CoV-2 RNA detection

abstract: The ongoing SARS-CoV-2 pandemic has necessitated a dramatic increase in our ability to conduct molecular diagnostic tests, as accurate detection of the virus is critical in preventing its spread. However, SARS-CoV-2 variants continue to emerge, with each new variant potentially affecting widely-used nucleic acid amplification diagnostic tests. RT-LAMP has emerged as a quick, inexpensive diagnostic alternative to RT-qPCR, but has not been studied as thoroughly. Here we interrogate the effect of SARS-CoV-2 sequence mutations on RT-LAMP amplification, creating 572 single point mutation "variants" covering every position of the LAMP primers in 3 SARS-CoV-2 assays and analyzing their effects with over 4,500 RT-LAMP reactions. Remarkably, we observed only minimal effects on amplification speed and no effect on detection sensitivity, highlighting RT-LAMP as an extremely robust technique for viral RNA detection. Additionally, we describe the use of molecular beacons to sensitively identify variant RNA sequences. Together these data add to the growing body of knowledge on the utility of RT-LAMP and increase its potential to further our ability to conduct molecular diagnostic tests outside of the traditional clinical laboratory environment.

category: molecular biology


title: Alternative strategy to induce CRISPR-mediated genetic changes in hematopoietic cells

abstract: Acute Myeloid Leukaemia is a complex heterogenous disease caused by clonal expansion of undifferentiated myeloid precursors. Recently, several haematological models have been developed with CRISPR/Cas9, using viral vectors, because blood cells are hard to transfect. To avoid virus disadvantages, we have developed a strategy to generate CRISPR constructs, by means of PCR, which any lab equipped with basic technology can implement. These PCR-generated constructs enter easily into hard-to-transfect cells. After testing its functionality by editing MYBL2 gene in HEK293 cells, we successfully introduced the R172 mutation in IDH2 gene in NB4 cells that expresses constitutively the Cas9 nuclease. Comparing our methodology with ribonucleoprotein strategies, we found that mutation introduction efficiency was similar between both methodologies, and no off-target events were detected. Our strategy represents a valid alternative to introduce desired mutations in hard to transfect leukemic cells, avoiding using huge vectors or viral transduction.


title: Impact of Grain for Green Project on Water Resources and Ecological Water Stress in Yanhe River Basin

abstract: Grain for Green project (GGP) initialed by China government since 1999 has achieved substantial achievements accompanied with surface runoff decrease in the Loess Plateau but impacts of large-scale afforestation on regional water resources are uncertain. Hence, the objective of this study is to explore the impact of land use change on generalized water resources and ecological water stress using blue and green water concept taking Yanhe River Basin as a case study. Soil and Water Assessment Tool (SWAT) is applied to quantify summary of green and blue water which is defined as generalized water resources, ecological water requirement of vegetation (forest and grass), agricultural water footprint and virtual water flow are considered as regional water requirements. Land use types of 1980 (scenario I), 2017 (scenario II) are input in SWAT model while keeps other parameters constant in order to isolate the influence of land use changes. Results show that average annual difference of blue, green and generalized water resources is -72.08 million m3, 24.34 million m3, -47.74 million m3 respectively when simulation results of scenario II subtracts scenario I and it presents that land use change caused by GGP leads to decrease in blue and generalized water resources whereas increase in green water resources. SURQ in scenario I is more than that in scenario IIin all the study period from 1980-2017, green water storage in scenario I is more than that in scenario II in all the study period except in 1998; whereas LATQ in scenario I is less than that in scenario II except in 2000 and 2015, GWQ in 1992, 2000 and 2015, green water flow in 1998. Blue water, green water storage and green water flow in scenario II is less than that in scenario I in the whole basin, 12.89 percent of the basin and 99.21 percent of the basin respectively. Total WF increases from 1995 to 2010 because forest WF increases significantly in this period though agricultural WF and grass WF decreases. Ecological water stress index has no obvious temporal change trend in both land use scenarios but ecological water stress index in scenario II is more than that in scenario I which illustrates that GGP leads to increase of ecological water stress from perspective of generalized water resources

category: ecology


title: Female choice can explain the fertilization pattern in oaks

abstract: We extend a two-step lottery model of Craft et al. to test the hypothesis that oak trees pursue a form of within-flower female choice to increase the diversity of fathers. Oak trees produce six ovules per flower while maturing just one acorn. When assuming a random ovule selection - which is a natural assumption in the absence of other hypotheses - observed fertilization patterns in oaks cannot be explained: long-distance fertilization is unusually common, even as nearby oak trees may be absent as pollen donors. Our model demonstrates how producing multiple ovules per flower permits selection for rare, distant fathers. The number of ovules per flower that maximizes paternal diversity increases with the number of trees. We introduce a cost function for ovule production for which six ovules per flower balance these costs with the benefits of diversifying fathers. Using data from two published field studies, 7 of 8 investigated maternal oaks had actual paternal diversity indices (average diversity index of 15.42) that fit the female choice hypothesis (estimated diversity of 14.66) significantly better than assuming a random selection from the six available ovules (estimated diversity of 7.649). A third field study permitted us to compare paternity by distance classes for two maternal trees. Both fit the female choice model better than random ovule selection.


title: Regulation of skeletal muscle metabolism and contraction performance via teneurin-latrophilin action.

abstract: Skeletal muscle regulation is responsible for voluntary muscular movement in vertebrates. The genes of two essential proteins, teneurins and latrophilins (LPHN), evolving in ancestors of multicellular animals, form a ligand-receptor pair, and are now shown to be required for skeletal muscle function. Teneurins possess a bioactive peptide, termed the teneurin C-terminal associated peptide (TCAP) that interacts with the LPHNs to regulate skeletal muscle contractility strength and fatigue by an insulin-independent glucose importation mechanism. CRISPR-based knockouts and siRNA-associated knockdowns of LPHN-1 and-3 shows that TCAP stimulates an LPHN-mediated cytosolic Ca2+ signal transduction cascade to increase energy metabolism and enhance skeletal muscle function via increases in type-1 oxidative fiber formation and reduce the fatigue response. Thus, the teneurin/TCAP-LPHN system is presented as a novel mechanism likely to regulate the energy requirements and performance of skeletal muscle.

category: physiology


title: Treatment of waste stabilization pond effluent using natural zeolite for irrigation potential

abstract: Direct utilization of treated effluent from natural treatment systems for irrigation can be challenging on sensitive plants due to high levels of salinity. Post-treatment of such an effluent prior to its applicability in irrigation can be of significant importance. In this study, the wastewater from a natural treatment plant was treated using a lab-scale filtration system with zeolite as a filter material. Three different column depths (0.5 m, 0.75 m, and 1 m) were used to investigate the effect of column depth on the treatment efficiency of the media. The suitability of the raw wastewater and the treated effluent from each column for irrigation purposes was investigated. The water quality parameters investigated were; electrical conductivity (EC), total dissolved solids (TDS), sodium (Na+), calcium (Ca2+), and magnesium (Mg2+). From the analysis results, it was observed that the column depth had a significant influence on the removal efficiency of the pollutants. Where the removal efficiency was observed to be increasing with the increase in the column depth. The highest removal efficiency (94.58%) was achieved from the combination of electrical conductivity and 1 m column depth, while the lowest removal efficiency (10.05%) was observed from the combination of calcium and 0.5 m column depth. The raw wastewater fell mostly into a "very high" hazard, which is class four (C4) based on electrical conductivity and class four (S4) based sodium adsorption ratio; making it unsuitable for irrigation purposes. However, the status improved after the treatment using different column depths.

category: scientific communication and education


title: PU.1 expression defines distinct functional activities in the phenotypic HSC compartment in a mouse model of inflammatory stress

abstract: The transcription factor PU.1 is a critical regulator of lineage fate in blood-forming hematopoietic stem cells (HSC). In response to inflammatory signals, PU.1 expression is increased in HSC, activating myeloid differentiation genes while repressing cell cycle and protein synthesis genes. To address potential functional heterogeneity arising in the phenotypic HSC compartment due to changes in PU.1 expression, here we fractionated phenotypic HSC using the SLAM code in conjunction with PU.1 expression levels using the PU.1-EYFP reporter mouse strain. While PU.1lo SLAM cells contain extensive long-term repopulating activity and a molecular signature corresponding to HSC activity at steady state, under inflammatory conditions the PU.1lo SLAM fraction is comprised almost entirely of HSC-like cells containing extensive short-term megakaryocytic potential. Our data demonstrate that the phenotypic HSC gate is heterogenous, and that similar PU.1 transcription factor levels can be tied to distinct functional activities under steady-state and inflammatory conditions.

category: cell biology


title: Trisomy 21 increases microtubules and disrupts centriolar satellite localization

abstract:
Trisomy 21, the cause of Down syndrome, causes a 0.5-fold protein increase of the chromosome 21-resident gene Pericentrin (PCNT) and reduces primary cilia formation and signaling. Here we investigate the mechanisms by which PCNT imbalances disrupt cilia. Using isogenic RPE-1 cells with increased chromosome 21 dosage, we find PCNT protein accumulates around the centrosome as a pericentrosomal cluster of enlarged cytoplasmic puncta that localize along and at MT ends. Cytoplasmic PCNT puncta impact the intracellular MT trafficking network required for primary cilia, as the PCNT puncta sequester cargo peripheral to centrosomes in what we call pericentrosomal crowding. The centriolar satellite proteins, PCM1, CEP131 and CEP290, important for ciliogenesis, accumulate at sites of enlarged PCNT puncta in trisomy 21 cells. Reducing PCNT when chromosome 21 ploidy is elevated is sufficient to decrease PCNT puncta, reestablish a normal density of MTs around the centrosome, restore ciliogenesis to wild type levels and decrease pericentrosomal crowding. A transient reduction in MTs also decreases pericentrosomal crowding and partially rescues ciliogenesis in trisomy 21 cells, indicating that increased PCNT leads to defects in the microtubule network deleterious to normal centriolar satellite distribution. We propose that chromosome 21 aneuploidy disrupts MT-dependent intracellular trafficking required for primary cilia.

TOCMcCurdy et al explore why elevated Pericentrin in trisomy 21 negatively impacts primary cilia formation and signaling. They find that elevated Pericentrin produces more pericentrosomal puncta that associates with and increases microtubules. Changes to Pericentrin and microtubules mislocalizes centriolar satellites in a pericentrosomal crowd.


title: The regenerative response of cardiac interstitial cells

abstract: Understanding how certain animals are capable of regenerating their hearts will provide much needed insights into how this process can be induced in humans in order to reverse the damage caused by myocardial infarction. Currently, it is becoming increasingly evident that cardiac interstitial cells play crucial roles during cardiac regeneration. To understand how interstitial cells behave during cardiac regeneration, we performed single-cell RNA sequencing (scRNA-seq) of regenerating zebrafish hearts. Using a combination of immunohistochemistry, chemical inhibition and novel transgenic animals, we were able to investigate the role of cell type specific responses during cardiac regeneration. This approach allowed us to identify a number of important regenerative mechanisms within the interstitial cell populations. Here, we provide here a detailed insight into how interstitial cells behave during cardiac regeneration and identify a number of novel features of these cells which will serve to increase our understanding of how this process could eventually be induced in humans.


title: Epidermal Stratification Requires Retromer-Mediated Desmoglein-1 Recycling

abstract: Sorting and trafficking transmembrane cargo is essential for tissue development and homeostasis. However, the importance of intracellular trafficking in the development and regeneration of stratified epidermis has not been investigated. Here we identify the interaction between VPS35, an essential component of the retromer endosomal trafficking complex, and the desmosomal cadherin, Desmoglein 1 (Dsg1). Dsg1 is specifically expressed in stratified tissues and when properly localized on the plasma membrane, promotes epidermal stratification. We show that the retromer drives Dsg1 recycling from the endo-lysosomal system to the plasma membrane to support keratinocyte stratification and differentiation. The retromer enhancing chaperone, R55 promotes the plasma membrane localization of Dsg1 and a Dsg1 mutant associated with Severe dermatitis, multiple Allergies, and Metabolic wasting (SAM) syndrome, enhancing the ability of SAM-Dsg1 to promote stratification. Our work provides the first evidence for retromer function in epidermal regeneration and identifies it as a potential therapeutic skin disease target.


title: Activation of transient receptor potential vanilloid 4 is involved in pressure overload-induced cardiac hypertrophy

abstract: Previous studies, including our own, have demonstrated that transient receptor potential vanilloid 4 (TRPV4) is expressed in hearts and implicated in cardiac remodeling and cardiac dysfunction. However, the effects of TRPV4 on pressure overload-induced cardiac hypertrophy remain unclear. In this study, we found that TRPV4 expression was significantly increased in mouse hypertrophic hearts, human failing hearts, and neurohormone-induced hypertrophic cardiomyocytes. Deletion of TRPV4 attenuated transverse aortic constriction (TAC)-induced cardiac hypertrophy, cardiac dysfunction, fibrosis, inflammation, and the activation of NF{kappa}B - NOD-like receptor pyrin domain-containing protein 3 (NLRP3) in mice. In vitro, TRPV4 inhibition decreased the neurohormone-induced cardiomyocyte hypertrophy and the increase of intracellular Ca2+ concentration. TRPV4 agonist triggered Ca2+ influx and evoked the phosphorylation of Ca2+/calmodulin-dependent protein kinase II (CaMKII) but these effects were abolished by removing extracellular Ca2+ or TRPV4 inhibition. More importantly, TAC or neurohormone stimulation-induced CaMKII phosphorylation was significantly blocked by TRPV4 inhibition. Finally, we showed that CaMKII inhibition significantly inhibited the phosphorylation of NF{kappa}B induced by TRPV4 activation. Our results suggest that TRPV4 activation contributed to pressure overload-induced cardiac hypertrophy. This effect was associated with upregulated Ca2+/ CaMKII mediated the activation of NF{kappa}B-NLRP3. Thus, TRPV4 may represent a potential therapeutic drug target for cardiac hypertrophy.


title: A basement membrane discovery pipeline uncovers network complexity, new regulators, and human disease associations

abstract: Basement membranes (BMs) are ubiquitous extracellular matrices whose composition remains elusive, limiting our understanding of BM regulation and function. By developing a bioinformatic and in vivo discovery pipeline, we define a network of 222 human proteins localized to BMs. Network analysis and screening in C. elegans and zebrafish identified new BM regulators, including ADAMTS, ROBO, and TGF{beta}. More than 100 BM-network genes associate with human phenotypes and by screening 63,039 genomes from families with rare disorders, we discovered loss-of-function variants in LAMA5, MPZL2, and MATN2, and show they regulate BM composition and function. This cross-disciplinary study establishes the immense complexity and role of BMs in human health.


title: The novel conserved NAD+ binding micropeptide SGHRT regulates mitochondrial function and metabolism in human cardiomyocytes

abstract: AbstractsNicotinamide adenine dinucleotide (NAD) is a critical metabolite and coenzyme for multiple metabolic pathways and cellular processes (1-4). In this study, we identified Singheart, SGHRT as a nuclear genome-encoded NAD+-binding mitochondrial micropeptide. SGHRT, present in both monomeric and dimeric forms, binds directly to NAD, but not NADH or flavin adenine dinucleotide (FAD). Localized to the inner mitochondrial membrane and mitochondrial matrix, SGHRT interacts with the mitochondrial enzymes Succinate-CoA Ligase and Succinate Dehydrogenase. SGHRT deletion in human embryonic stem cell derived cardiomyocytes disrupted mitochondria morphology, decreased total NAD and ATP abundance, and resulted in defective TCA cycle metabolism, the electron transport chain and in Ox-Phos processes. These results comprise the first report of an NAD+-binding micropeptide, SGHRT, required for mitochondrial function and metabolism.


title: Aldehyde dehydrogenase 3A1 deficiency leads to mitochondrial dysfunction and impacts salivary gland stem cell self-renewal, differentiation and survival

abstract: Adult salivary stem/progenitor cells (SSPC) have an intrinsic property to self-renew in order to maintain tissue architecture and homeostasis. Adult salivary glands have been documented to harbor SSPC, which have been shown to play a vital role in the regeneration of the glandular structures post radiation damage. We have previously demonstrated that activation of aldehyde dehydrogenase 3A1 (ALDH3A1) after radiation reduced aldehyde accumulation in SSPC, leading to less apoptosis and improved salivary function. We subsequently found that sustained pharmacological ALDH3A1 activation is critical to enhance regeneration of murine submandibular gland after radiation damage. Further investigation shows that ALDH3A1 function is crucial for SSPC self-renewal and differentiation even in the absence of radiation stress. Salivary glands from Aldh3a1-null mice have fewer acinar structures than wildtype mice. ALDH3A1 deletion or pharmacological inhibition in SSPC leads to a decrease in mitochondrial DNA copy number, lower expression of mitochondrial specific genes and proteins, structural abnormalities, lower membrane potential, and reduced cellular respiration. Loss or inhibition of ALDH3A1 also elevates ROS levels and accumulation of ALDH3A1 substrate 4-hydroxynonenal (4-HNE, a lipid peroxidation product), leading to decreased survival of murine SSPC that can be rescued by treatment with 4-HNE specific carbonyl scavengers. Our data indicate that ALDH3A1 activity protects mitochondrial function and is important for the development and regeneration activity of SSPC. This knowledge will help to guide our translational strategy of applying ALDH3A1 activators in the clinic to prevent radiation-related hyposalivation in head and neck cancer patients.


title: Bcl-xL restricts transcriptional, morphological and functional decompensation of β-cell mitochondria under chronic glucose excess

abstract: In the progression of diabetes, pancreatic islet {beta}-cells respond to increased metabolic demand with functional compensation, followed by pathogenic decompensation of mitochondria-dependent insulin secretion. It is not clear what mechanisms drive, or control, mitochondrial decompensation. Here, we report that anti-apoptotic Bcl-xL maintains mitochondrial integrity in {beta}-cells under non-apoptotic levels of glucose stress. Prolonged glucose excess causes transcriptional reprogramming of glycolysis and {beta}-cell identity genes, while sensitizing glucose-stimulated Ca2+ signaling and insulin secretion. Deletion of Bcl-xL amplifies this insulin hypersecretion and increases mitochondrial fusion, mitochondrial volume, and oxygen consumption, whereas ATP-coupled respiration and mitochondrial hyperpolarization become impaired. Of note, Bcl-xL-deficient {beta}-cells have impaired Pgc-1 expression, and develop specific defects in the expression of Tfam, mitochondrial ribosomal genes, and OXPHOS components under glucose stress. Bcl-xL limits high glucose-induced mitochondrial ROS (mitoROS) levels and pharmacological normalization of mitoROS in Bcl-xL KO cells rescues glucose-induced defects in mitochondrial gene expression and changes to {beta}-cell identity. Our data identify mitoROS as a primary retrograde driver of transcriptional re-wiring in {beta}-cells exposed to excess glucose, and reveal Bcl-xL as an important safeguard against transcriptional and functional decompensation of {beta}-cell mitochondria. Bcl-xL and mitoROS may thus be viable targets to prevent early {beta}-cell dysfunction and the progression of diabetes.


title: Disentangling single-cell omics representation with a power spectral density-based feature extraction

abstract: Emerging single-cell technologies provide high-resolution measurements of distinct cellular modalities opening new avenues for generating detailed cellular atlases of many and diverse tissues. The high dimensionality, sparsity, and inaccuracy of single cell sequencing measurements, however, can obscure discriminatory information, mask cellular subtype variations and complicate downstream analyses which can limit our understanding of cell function and tissue heterogeneity. Here, we present a novel pre-processing method (scPSD) inspired by power spectral density analysis that enhances the accuracy for cell subtype separation from large-scale single-cell omics data. We comprehensively benchmarked our method on a wide range of single-cell RNA-sequencing datasets and showed that scPSD pre-processing, while being fast and scalable, significantly reduces data complexity, enhances cell-type separation, and enables rare cell identification. Additionally, we applied scPSD to transcriptomics and chromatin accessibility cell atlases and demonstrated its capacity to discriminate over 100 cell types across the whole organism and across different modalities of single-cell omics data.

category: bioinformatics


title: ProS-GNN: Predicting effects of mutations on protein stability using graph neural networks

abstract:
MotivationPredicting protein stability change upon variation through computational approach is a valuable tool to unveil the mechanisms of mutation-induced drug failure and help to develop immunotherapy strategies. However, some machine learning based methods tend to be overfitting on the training data or show anti-symmetric biases between direct and reverse mutations. Moreover, this field requires the methods to fully exploit the limited experimental data.

ResultsHere we pioneered a deep graph neural network based method for predicting protein stability change upon mutation. After mutant part data extraction, the model encoded the molecular structure-property relationships using message passing and incorporated raw atom coordinates to enable spatial insights into the molecular systems. We trained the model using the S2648 and S3412 datasets, and tested on the Ssym and Myoglobin datasets. Compared to existing methods, our proposed method showed competitive high performance in data generalization and bias suppression with ultra-low time consumption. Furthermore, method was applied to predict the Pyrazinamides Gibbs free energy change for a real case study.

Availabilityhttps://github.com/shuyu-wang/ProS-GNN.

Contactvincentwang622@126.com


title: Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver

abstract: In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily fluctuations of RNA accumulation and affecting the distribution of transcripts in different subcellular compartments. Our study analysed the nuclear and cytoplasmic, poly(A) and total transcriptomes of mouse livers collected over the course of a day. These data provide a genome-wide temporal inventory of enrichment in subcellular RNA, and revealed specific signatures of splicing, nuclear export and cytoplasmic mRNA stability related to transcript and gene lengths. Combined with a mathematical model describing rhythmic RNA profiles, we could test the rhythmicity of export rates and cytoplasmic degradation rates of approximately 1400 genes. With nuclear export times usually much shorter than cytoplasmic half-lives, we found that nuclear export contributes to the modulation and generation of rhythmic profiles of 10% of the cycling nuclear mRNAs. This study contributes to a better understanding of the dynamic regulation of the transcriptome during the day-night cycle.

category: systems biology


title: Multi-omics analysis reveals cross-organism interactions in coral holobiont

abstract: Corals create an ecosystem, called a holobiont, with intracellular algae (zooxanthellae) and resident bacteria. Zooxanthellae and some bacteria play major roles in the physiological properties of the coral host. However, because of the difficulties in experimental verification of cross-organism interactions, the mechanisms underpinning these interactions are largely unknown. To address this, we here generated and then analyzed multi-omics datasets for corals, zooxanthellae, and bacteria collected at Okinawa, Japan, from November 2014 to September 2016. Using cross-organism co-expression analysis, we successfully characterized the host-alga relationship in the coral holobiont. Specifically, we observed that the coral host dominates the zooxanthellae. The multi-omics analysis also suggested that infection with coral-associated bacteria Endozoicomonas likely involves coral-like ephrin ligands, triggering an immune response of the coral host. This study highlights the potential of the multi-omics approach to elucidate coral-microbe interactions.


title: MeDUsA: A novel system for automated axon quantification to evaluate neuroaxonal degeneration

abstract:
BackgroundDrosophila is an excellent model organism for studying human neurodegenerative diseases (NDs), and the rough eye phenotype (REP) assay is a convenient experimental system for analysing the toxicity of ectopically expressed human disease genes. However, the association between REP and axonal degeneration, an early sign of ND, remains unclear. To address this question, we developed a method to evaluate axonal degeneration by quantifying the number of retinal R7 axons in Drosophila; however, it requires expertise and is time-consuming. Therefore, there is a need for an easy-to-use software that can automatically quantify the axonal degeneration.

ResultWe created MeDUsA (a  method for the quantification of degeneration using fly axons), which is a standalone executable computer program based on Python that combines a pre-trained deep-learning masking tool with an axon terminal counting tool. This software automatically quantifies the number of axons from a confocal z-stack image series. Using this software, we have demonstrated for the first time directly that axons degenerate when the causative factors of NDs (Syn, Tau, TDP-43, HTT) were expressed in the Drosophila eye. Furthermore, we compared axonal toxicity of the representative causative genes of NDs and their pathological alleles with REP and found no significant correlation between them.

ConclusionsMeDUsA rapidly and accurately quantifies axons in Drosophila eye. By simplifying and automating time-consuming manual efforts requiring significant expertise, it enables large-scale, complex research efforts on axonal degeneration, such as screening to identify genes or drugs that mediate axonal toxicity caused by ND disease proteins.

category: pathology


title: Urinary bladder enlargement across nine rodent models of diabetes: correlations with glucose and insulin levels

abstract: The urinary bladder is markedly enlarged in the type 1 diabetes mellitus model of streptozotocin (STZ)-injected rats, but much less data exist for models of type 2 diabetes (T2DM). Diabetic polyuria has been proposed to explain bladder enlargement. We have collected data on bladder weight and blood glucose from 16 studies representing 9 distinct rodent diabetes (7 T2DM) and obesity models; some included arms with diets and/or pharmacological treatments. Data were analyzed for bladder enlargement and for correlations between bladder weight on the one and glucose levels on the other hand. Our data confirm major bladder enlargements in STZ rats, minor if any enlargement in fructose-fed rats, db/db mice and mice on a high-fat diet. For the first time we report bladder weight data on 5 other models with presence and degree of bladder enlargement being heterogeneous across models. Bladder weight was correlated with plasma glucose in some but not other models, but correlations were moderate to weak except for RIP-LMCV mice. We conclude that the presence and extent of bladder enlargement varies markedly across diabetes models, particularly TD2M models; our data do not support the idea that bladder enlargement is primarily driven by glucose levels/glucosuria.

category: pharmacology and toxicology


title: Intestinal Gluconeogenesis Regulates Brown and White Adipose Tissues Functions in mice

abstract:
ObjectiveIntestinal gluconeogenesis, via the initiation of a gut-brain nervous circuit, accounts for the metabolic benefits linked to dietary proteins or fermentable fibre in rodents and has been positively correlated with the rapid amelioration of body weight after gastric bypass surgery in obese humans. In particular, the activation of intestinal gluconeogenesis moderates the development of hepatic steatosis accompanying obesity. In this study, we investigated the specific effects of intestinal gluconeogenesis on adipose tissue metabolism, independently of its induction by nutritional manipulation.

MethodsWe used two transgenic mouse models of suppression or overexpression of G6PC, the catalytic subunit of glucose-6 phosphatase, the key enzyme of endogenous glucose production, specifically in the intestine.

ResultsUnder a hypercaloric diet, mice with a genetic overexpression of intestinal gluconeogenesis showed a lower adiposity and higher thermogenic capacities than wild-type mice, featuring marked browning of white adipose tissue and prevention of the whitening of brown adipose tissue. Suppression of sympathetic nervous signalling in brown adipose tissue impairs the activation of thermogenesis. Conversely, mice with genetic suppression of intestinal gluconeogenesis exhibit an increase in adiposity under standard diet, associated with a decreased expression of markers of thermogenesis in both the brown and white adipose tissues.

ConclusionIntestinal gluconeogenesis is sufficient in itself to activate the sympathetic nervous system and prevent the expansion and the metabolic alterations of brown and white adipose tissues metabolism under high calorie diet, thus preventing the development of obesity. These data increase knowledge of the mechanisms of weight reduction in gastric bypass surgery and pave the way of new approaches to prevent or cure obesity.


title: Perception of a conserved family of plant signalling peptides by the receptor kinase HSL3

abstract: Plant genomes encode hundreds of secreted peptides; however, relatively few have been characterised. We report here an uncharacterised, stress-induced family of plant signalling peptides, which we call CTNIPs. Based on the role of the common co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) in CTNIP-induced responses, we identified the orphan receptor kinase HAESA-LIKE 3 (HSL3) as the CTNIP receptor via a proteomics approach. CTNIP binding, ligand-triggered complex formation with BAK1, and induced downstream responses all involve HSL3. Notably, the HSL3-CTNIP signalling module is evolutionarily ancient, predating the divergence of extant angiosperms. The identification of this signalling module will help establish its physiological role and provides a resource to understand further receptor-ligand co-evolution.


title: Nuclear Export of Drosophila PERIOD contributes to temperature compensation of the circadian clock

abstract: Circadian clocks are self-sustained molecular oscillators controlling daily changes of behavioral activity and physiology. For functional reliability and precision the frequency of these molecular oscillations must be stable at different environmental temperatures, known as  temperature compensation. Despite being an intrinsic property of all circadian clocks, this phenomenon is not well understood at the molecular level. Here we use behavioral and molecular approaches to characterize a novel mutation in the period (per) clock gene of Drosophila melanogaster, which alters a predicted nuclear export sequence (NES) of the PER protein. We show that this new perI530A allele leads to progressively longer behavioral periods and clock oscillations with increasing temperature in both clock neurons and peripheral clock cells. While the mutant PERI530A protein shows normal circadian fluctuations and post-translational modifications at cool temperatures, increasing temperatures lead to both, severe amplitude dampening and hypophosphorylation of PERI530A. We further show that PERI530A displays reduced repressor activity at warmer temperatures, presumably because it cannot inactivate the transcription factor CLOCK (CLK). With increasing temperatures nuclear accumulation of PERI530A within clock neurons is increased, suggesting that PER is normally exported out of the nucleus at warm temperatures. Consequently, downregulating the nuclear export factor CRM1 also leads to temperature-dependent changes of behavioral rhythms. In summary, our results suggest that the PER NES and the nuclear export of clock proteins play an important role in temperature compensation of the Drosophila circadian clock.


title: Psychological stress disrupts intestinal epithelial cell function and mucosal integrity through microbe and host-directed processes

abstract: Psychological stress alters the gut microbiota and predisposes individuals to increased risk for enteric infections and chronic bowel conditions. Intestinal epithelial cells (IECs) are responsible for maintaining homeostatic interactions between the gut microbiota and its host. In this study, we hypothesized that disruption to colonic IECs is a key factor underlying stress-induced disturbances to intestinal homeostasis. Conventionally raised (CONV-R) and germ-free (GF) mice were exposed to a social disruption stressor (Str) to ascertain how stress modifies colonic IECs, the mucosal layer, and the gut microbiota. RNA sequencing of IECs isolated from CONV-R mice revealed a robust pro-inflammatory (Saa1, Il18), pro-oxidative (Duox2, Nos2), and antimicrobial (Reg3b/g) transcriptional profile as a result of Str. This response occurred concomitant to mucus layer thinning and signs of microbial translocation. In contrast to their CONV-R counterparts, IECs from GF mice or mice treated with broad spectrum antibiotics exhibited no detectable transcriptional changes in response to Str. Nevertheless, IECs from Str-exposed GF mice exhibited an altered response to ex vivo bacterial challenge (increased dual Oxidase-2 [Duox2] and nitric oxide synthase-2 (Nos2)), indicating that STR primes host IEC pro-oxidative responses. In CONV-R mice stress-induced increases in colonic Duox2 and Nos2 (ROS generating enzymes) strongly paralleled changes to microbiome composition and function, evidencing Str-mediated ROS production as a primary factor mediating gut-microbiota dysbiosis. In conclusion, a mouse model of social stress disrupts colonic epithelial and mucosal integrity, a response dependent on an intact microbiota and host stress signals. Together these preclinical findings may provide new insight into mechanisms of stress-associated bowel pathologies in humans.

category: immunology


title: The Atomic-Level Physiochemical Determinants of T Cell Receptor Dissociation Kinetics

abstract: The rational design of T Cell Receptors (TCRs) for immunotherapy has stagnated due to a limited understanding of the dynamic physiochemical features of the TCR that elicit an immunogenic response. The physiochemical features of the TCR-peptide major histocompatibility complex (pMHC) bond dictate bond lifetime which, in turn, correlates with immunogenicity. Here, we: i) characterize the force-dependent dissociation kinetics of the bond between a TCR and a set of pMHC ligands using Steered Molecular Dynamics (SMD); and ii) implement a machine learning algorithm to identify which physiochemical features of the TCR govern dissociation kinetics. Our results demonstrate that the total number of hydrogen bonds between the CDR2{beta}-MHC({beta}), CDR1-Peptide, and CDR3{beta}-Peptide are critical features that determine bond lifetime. We propose that amino acid substitutions to these hypervariable regions of the TCR can efficiently manipulate immunogenicity and thus be used in the rational design of TCRs for immunotherapy.


title: Optimized Multicolour Immunofluorescence Panel for Cattle B Cell Phenotyping by an 8-Colour, 10-Parameter Panel

abstract: This 8-colour, 10-parameter panel has been optimised to distinguish between functionally distinct subsets of cattle B cells in both fresh and cryopreserved peripheral blood mononuclear cells (PBMCs). Existing characterised antibodies against cell surface molecules (immunoglobulin light chain (S-Ig(L)), CD20, CD21, CD40, CD71 and CD138) enabled the discrimination of 24 unique populations within the B cell population. This allows the identification of five putative functionally distinct B cell subsets critical to infection and vaccination responses; 1) naive B cells (BNaive), 2) regulatory B cells (BReg), 3) memory B cells (BMem), 4) plasmablasts (PB) and 5) plasma cells (PC). Although CD3 and CD8 can be included as an additional dump channel, it does not significantly improve the panels ability to separate "Classical" B cells. This panel will promote better characterisation and tracking of B cell responses in cattle as well as other bovid species as the reagents are likely to cross react.


title: The route of vaccine administration determines whether blood neutrophils undergo long-term phenotypic modifications

abstract:
Innate immunity modulates adaptive immunity and defines the magnitude, quality, and longevity of antigen-specific T- and B- cell immune memory. Various vaccine and administration factors influence the immune response to vaccination, including the route of vaccine delivery.

We studied the dynamics of innate cell responses in blood using a preclinical model of non-human primates immunized with a live attenuated vaccinia virus, Modified vaccinia virus Ankara (MVA), and mass cytometry. We previously showed that MVA induces a strong, early, and transient innate response, but also late phenotypic modifications of blood myeloid cells after two months when injected subcutaneously. Here, we show that the early innate effector cell responses and plasma inflammatory cytokine profiles differ between subcutaneous and intradermal vaccine injection. Additionally, we show that the intradermal administration fails to induce more highly activated/mature neutrophils long after immunization, in contrast to subcutaneous administration.

Different batches of antibodies, staining protocols and generations of mass cytometers were used to generate the two datasets that were compared. Mass cytometry data were analyzed in parallel using the same analytical pipeline based on three successive clustering steps, including SPADE, and categorical heatmaps were compared using the Manhattan distance to measure the similarity between cell cluster phenotypes.

Overall, we show that the vaccine per se is not sufficient for the late phenotypic modifications of innate myeloid cells, which are evocative of innate immune training. Its route of administration is also crucial, likely by influencing the early innate response, and systemic inflammation, and the vaccine biodistribution.


title: Hoxb5 reprograms murine multipotent blood progenitors into hematopoietic stem cell-like cells

abstract: The expression of transcription factor Hoxb5 specifically marks the functional hematopoietic stem cells (HSC) in mice. However, our recent work demonstrated that ectopic expression of Hoxb5 exerted little effect on HSC but could convert B cell progenitors into functional T cells in vivo. Thus, cell type- and development stage-specific roles of Hoxb5 in hematopoietic hierarchy await more extensive exploration. Here, with a mouse strain engineered with conditional expression of Hoxb5, we unveiled that induced expression of Hoxb5 in mouse multipotent progenitor cells (MPP) led to the generation of a de novo Sca1+cKit+Mac1+CD48+ (Mac1+CD48+SK) cell type, which has the ability to repopulate long-term multi-lineage hematopoiesis in serial transplant recipients. RNA-seq analyses showed that Mac1+CD48+SK cells exhibited an acquired machinery of DNA replication and cell division, which resembled nature fetal liver HSC cells (FL HSC). In short, our current study uncovers that Hoxb5 is able to empower MPP with self-renewal potential, thereby providing new strategies to reprogram blood progenitor cells into HSC-like cells.


title: The Isl1/Shh/Wnt5a cascade controls the invasion of myoblasts by tuning the CXCL12/CXCR4 axis during tongue morphogenesis

abstract: The migration and invasion of myoblast cells derive from the occipital somites is critical for tongue morphogenesis. However, the molecular mechanisms underlying myoblast migration and invasion remain elusive. In this study, we report that transcription factor Isl1 is required for tongue development. Loss of Isl1 in the distal mandibular epithelium results in aglossia due to the defect of myoblast cells invasion. In the absence of Isl1 expression, myoblast cells in the first branchial arch fail to migrate into the presumptive tongue primordium. Down-regulation of Shh was detected in the distal mandibular epithelium after Isl1 deletion. As a downstream target gene of Shh, Wnt5a attracts the migration of mesenchymal cells expressing chemokine ligand 12 (CXCL12). CXCL12+ mesenchymal cells in the Isl1 mutant embryo fail to migrate to the distal region but accumulate in a relatively small proximal domain of the first branchial arch. CXCL12 serves as a bidirectional cue for myoblasts that express its receptor CXCR4, attracting CXCR4+ myoblasts invasion at low concentration but repelling at high concentration. The defect in the distal migration of CXCL12+ mesenchymal cells leads to a high local concentration of CXCL12, thereby preventing the invasion of CXCR4+ myoblasts. In addition, transgenic activation of Ihh alleviates the defect in tongue development and rescues the invasion of myoblasts, corroborating the functional involvement of Hedgehog signaling in tongue development. In summary, this study provides the first line of genetic evidence for the Isl1/Shh/Wnt5a cascade to regulate myoblasts invasion by tuning the CXCL12/CXCR4 axis.

category: developmental biology


title: Aggregation pheromone 4-vinylanisole promotes the synchrony of sexual maturation in female locusts

abstract: Reproductive synchrony generally occurs in various group-living animals; however, the underlying mechanisms remain largely unexplored. Here, we report that aggregation pheromone, 4-vinylanisole, plays a key role in promoting sexual maturation synchrony of female adults in the migratory locust, Locusta migratoria, a worldwide agricultural pest species that can form huge swarms with millions of individuals. Gregarious female locusts display significant synchrony of sexual maturation and oviposition whereas solitarious females and olfactory deficiency mutants do not. Only the presence of gregarious male adults can stimulate sexual maturation synchrony of female adults. Of the volatiles emitted abundantly by gregarious male adults, only 4-vinylanisole induces female sexual maturation synchrony, whereas this effect is abolished in mutants of 4- vinylanisole receptor. Interestingly, 4-vinylanisole mainly accelerates oocyte maturation of young females aged at middle developmental stages (3-4 days post adult eclosion). Juvenile hormone/vitellogenin pathway mediates female sexual maturation triggered by 4-vinylanisole. Our results highlight a "catch-up" strategy by which gregarious females synchronize their oocyte maturation and oviposition by time-dependent endocrinal response to 4-vinylanisole.


title: Identifying barriers to gene flow and hierarchical conservation units from seascape genomics: a modelling framework applied to a marine predator

abstract: The ongoing decline of large marine vertebrates must be urgently mitigated, particularly under increasing levels of climate change and other anthropogenic pressures. However, characterizing the connectivity among populations remains one of the greatest challenges for the effective conservation of an increasing number of endangered species. Achieving conservation targets requires an understanding of which seascape features influence dispersal and subsequent genetic structure. This is particularly challenging for adult-disperser species, and when distribution-wide sampling is difficult. Here, we developed a two-step modelling framework to investigate how seascape features drive the genetic connectivity of marine species without larval dispersal, to better guide the design of marine protected area networks and corridors. We applied this framework to the endangered grey reef shark, Carcharhinus amblyrhynchos, a reef-associated shark distributed across the tropical Indo-Pacific. In the first step, we developed a seascape genomic approach based on isolation-by-resistance models involving circuit theory applied to 515 shark samples, genotyped for 4,491 nuclear single-nucleotide polymorphisms, to explore which parameters drive their population genetic differentiation. We show that deep oceanic areas act as strong barriers to dispersal, while proximity to habitat facilitates dispersal. In the second step, we predicted the resulting genetic differentiation across the entire distribution range of the species, providing both local and global-scale conservation units for future management guidance. We found that grey reef shark populations are more fragmented than expected for such a mobile species, raising concerns about the resilience of isolated populations under high anthropogenic pressures. We recommend the use of this framework to identify barriers to gene flow and to help in the delineation of conservation units at different scales, together with its integration across multiple species when considering marine spatial planning.


title: Prevalent sex ratio bias in Caenorhabditis nematodes

abstract: Although equal sex ratio represents an equilibrium in evolutionary theory, cases of sex ratio bias are accumulating, mostly reported in single species. Here, we surveyed progeny sex ratios in 23 species of the nematode genus Caenorhabditis. In experiments where males and females had unlimited access to each other (unlimited mating), we found 15 species out of the 23 species had female(hermaphrodite)-biased sex ratios. Phylogenetic mapping indicates female-bias to represent the ancestral state, with the occurrence of seven independent transitions from female-bias to non-bias along the phylogeny. As sperm competition could underlie the female bias, we also assayed progeny sex ratios in an experiment where mating was limited to a few hours. Of the 15 species that showed female-biased ratios under unlimited mating, six species showed no sex ratio bias when mating was limited. This result is consistent with sperm competition whereby X-bearing sperm take precedence over nullo-X during fertilization, yielding more female progeny when sperm are unlimited but equal sex ratio when sperm are limited. The other nine species showed sex ratio bias in both experiments, but the day-by-day profiles suggest sperm competition may also play a role. Our study shows that sex ratio evolution within Caenorhabditis nematodes is dynamic and that sex ratio bias is common not only in parasites as previously found but also in free-living nematodes. Our results also suggest that sperm competition could be a mechanism underlying sex ratio bias.

category: evolutionary biology


title: Uterine-specific SIRT1 deficiency confers premature uterine aging and impairs invasion and spacing of blastocyst and stromal cell decidualization in mice.

abstract:
A distinct age-related alteration in the uterine environment has recently been identified as a prevalent cause of the reproductive decline in older female mice. However, the molecular mechanisms that underlie age-associated uterine adaptability to pregnancy are not known. Sirtuin 1 (SIRT1), a multifunctional NAD+-dependent deacetylase that regulates cell viability, senescence and inflammation during aging, is reduced in aged decidua. Thus, we hypothesize that SIRT1 plays a critical role in uterine adaptability to pregnancy and that uterine-specific ablation of Sirt1 gene accelerates premature uterine aging. Female mice with uterine ablation of Sirt1 gene using progesterone receptor Cre (PgrCre) exhibit subfertility and signs of premature uterine aging. These Sirt1-deficient mothers showed decreases in litter size from their 1st pregnancy and became sterile (25.1{+/-}2.5 weeks of age) after giving birth to the 3rd litter. We report that uterine-specific Sirt1 deficiency impairs invasion and spacing of blastocysts, and stromal cell decidualization, leading to abnormal placentation. We found that these problems traced back to the very early stages of hormonal priming of the uterus. During the window of receptivity, Sirt1 deficiency compromises uterine epithelial-stromal crosstalk, whereby estrogen (E2), progesterone (P4) and Indian hedgehog (IHH) signaling pathways are dysregulated, hampering stromal cell priming for decidualization. Uterine transcriptomic analyses also link these causes to perturbations of histone proteins and epigenetic modifiers, as well as adrenomedullin signaling, hyaluronic acid metabolism, and cell senescence. Strikingly, our results also identified genes with significant overlaps with the transcriptome of uteri from aged mice and transcriptomes related to master regulators of decidualization (e.g., Foxo1, Wnt4, Sox17, Bmp2, Egfr and Nr2f2). Our results also implicate accelerated deposition of aging-related fibrillar type I and III collagens in Sirt1-deficient uteri. Collectively, SIRT1 is an indispensable age-related regulator of invasion and spacing of blastocysts, as well as decidualization of stromal cells.

Author SummaryAdvanced maternal age (i.e., [≥]35 years old) is considered a significant risk factor for birth defects, including fetal growth restriction, stillbirth, preterm birth, and preeclampsia. Lifestyle factors such as tobacco smoke, alcohol usage and other environmental toxins are facilitators of premature reproductive aging. Thus, understanding the precise mechanisms by which female reproductive organs age is a prerequisite for ultimately developing counteracting therapies. Much attention has been focused on ovarian function and oocyte quality, but we provide evidence that severe placentation defects are a major cause of age-related reproductive decline, which results from an impaired decidual response by uterine stromal cells. This problem is due to a blunted progesterone (P4) responsiveness of the aging uterus, via its cognate receptor, PGR. In the present study, the uterine SIRT1 gene was deleted to advance understanding of the genetics of premature uterine aging in a mouse model of blunted PGR actions that is similar to physiological aging. Our results have informed as to molecular changes in response to blunting PGR actions in aging uteri that are unrelated to oocyte quality, and provide new insights into strategies for developing counteracting measures for pregnancy in females at an advanced reproductive age.

category: genetics


title: Recovering high-quality host genomes from gut metagenomic data through genotype imputation

abstract:
Metagenomic data sets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, if a reference panel is available, genotype imputation can be employed to reconstruct host genotypes and maximise the use of such a priori useless data. We tested the performance of a two-step strategy to input genotypes from four types of reference panels, comprised of deeply sequenced chickens to low-depth host genome (~2x coverage) data recovered from metagenomic samples of chicken intestines. The target chicken population was formed by two broiler breeds and the four reference panels employed were (i) an internal panel formed by population-specific individuals, (ii) an external panel created from a public database, (iii) a combined panel of the previous two, and (iv) a diverse panel including more distant populations. Imputation accuracy was high for all tested panels (concordance >0.90), although samples with coverage under 0.28x consistently showed the lowest accuracies. The best imputation performance was achieved by the combined panel due to the high number of imputed variants, including low-frequency ones. However, common population genetics parameters measured to characterise the chicken populations, including observed heterozygosity, nucleotide diversity, pairwise distances and kinship, were only minimally affected by panel choice, with all four panels yielding suitable results for host population characterization and comparison. Likewise, genome scans between the two studied broiler breeds using imputed data with each panel consistently identified the same sweep regions. In conclusion, we show that the applied imputation strategy enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitate the implementation of hologenomic approaches that jointly analyse host genomic and microbial metagenomic data.

Author summaryWe introduce and assess a methodological approach that enables recovering animal genomes from complex mixtures of metagenomic data, and thus expand the portfolio of analyses that can be conducted from samples such as faeces and gut contents. Metagenomic data sets of host-associated microbial communities often contain DNA of the host organism. The principal drawback to use this data for host genomic characterisation is the low percentage and quality of the host DNA. In order to leverage this data, we propose a two-step imputation method, to recover high-density of variants. We tested the pipeline in a chicken metagenomic dataset, validated imputation accuracy statistics, and studied common population genetics parameters to assess how these are affected by genotype imputation and choice of reference panel. Being able to analyse both domains from the same data set could considerably reduce sampling and laboratory efforts and resources, thereby yielding more sustainable practices for future studies that embrace a hologenomic approach that jointly analyses animal genomic and microbial metagenomic features.

category: genomics


title: A novel single-cell RNA-sequencing platform and its applicability connecting genotype to phenotype in ageing-disease

abstract: Advances in single cell multi-omics analysis such as the ability of a genotype to show phenotypic diversity lead to a comprehensive understanding of cellular events in human diseases. The cardinal feature to access this information is the technology used for single-cell isolation, barcoding, and sequencing. While numerous platforms have been reported for single-cell RNA-sequencing, technical enhancements are needed in terms of highly purified single cell selection, cell documentation or limitations in cell sizing and chemistry. In this study, we present a novel high-throughput platform using a full-length RNA-sequencing approach that offers substantial technical improvements of all parameters. We applied this platform to dermal fibroblasts derived from six patients with different segmental progeria syndromes and defined phenotype-associated pathway signatures and variant-associated expression modifiers. These results validate the applicability of our platform to highlight genotype-expression relationships for molecular phenotyping in ageing disorders.


title: Designing Biological Micro-Sensors with Chiral Nematic Liquid Crystal Droplets

abstract: Biosensing using liquid crystals has a tremendous potential by coupling the high degree of sensitivity of their alignment to their surroundings with clear optical feedback. Many existing set-ups use birefringence of nematic liquid crystals, which severely limits straightforward and frugal implementation into a sensing platform due to the sophisticated optical set-ups required. In this work, we instead utilize chiral nematic liquid crystal micro-droplets, which show strongly reflected structural colour, as sensing platforms for surface active agents. We systematically quantify the optical response of closely related biological amphiphiles and find unique optical signatures for each species. We detect signatures across a wide range of concentrations (from M to mM), with fast response times (from seconds to minutes). The striking optical response is a function of the adsorption of surfactants in a non-homogeneous manner and the topology of the liquid crystal orientation at the interface requiring a scattering, multidomain structure, which we observe to be different between molecules. We show lab-on-a-chip capability of our method by drying droplets in high-density two-dimensional arrays and simply hydrating the chip to detect dissolved analytes. Finally, we show proof-of-principle in vivo biosensing in the intestinal tracts of live zebrafish larvae, demonstrating CLC droplets show a clear and differential optical response between healthy and inflamed tissues. Our unique approach has great potential in developing on-site detection platforms and detecting biological amphiphiles in living organisms.

category: bioengineering


title: Comparison of brain activity while tasting of passion fruit juice sweetened with caloric and non-caloric sweeteners

abstract:
Sweetener type can influence sensory properties and consumers acceptance and preference for low-calorie products. An ideal sweetener does not exist, and each sweetener must be used in situations to which it is best suited. Aspartame and sucralose can be good substitutes for sucrose in passion fruit juice. Despite the interest in artificial sweeteners, little is known about how artificial sweeteners are processed in the human brain. Here, we evaluated brain signals of 11 healthy subjects when they tasted passion fruit juice equivalently sweetened with sucrose (9.4 g/100 g), sucralose (0.01593 g/100 g), or aspartame (0.05477 g/100 g). Electroencephalograms were recorded for two sites in the gustatory cortex (i.e., C3 and C4). Data with artifacts were disregarded, and the artifact-free data were used to feed a CNN. Our results indicated that the brain responses distinguish juice sweetened with different sweeteners with an average accuracy of 0.823.

Practical ApplicationsFinding sweeteners that best fit consumer preferences evolves understanding how the gustatory cortex processes sweeteners. Ideal equivalence will occur when the brain is no longer able to distinguish stimuli that are consciously perceived. This study presents a method of signal acquisition using a single channel and an open-source processing environment. This would allow, for example, to disregard the use of a commercial electroencephalograph and expand the studies in this area and offering to food industry additional tools in the development of products sweetened with non-caloric sweeteners.


title: Quantifying the effect of caloric and non-caloric sweeteners in the brain response using EEG and convolutional neural network


title: Pan-cancer in silico analysis of somatic mutations in G-protein coupled receptors: The effect of evolutionary conservation and natural variance

abstract:
G protein-coupled receptors (GPCRs) form the most frequently exploited drug target family, moreover they are often found mutated in cancer. Here we used an aggregated dataset of mutations found in cancer patient samples derived from the Genomic Data Commons and compared it to the natural human variance as exemplified by data from the 1000 Genomes project. While the location of these mutations across the protein domains did not differ significantly in the two datasets, a mutation enrichment was observed in cancer patients among conserved residues in GPCRs such as the "DRY" motif. We subsequently created a ranking of high scoring GPCRs, using a multi-objective approach (Pareto Front Ranking). The validity of our approach was confirmed by re-discovery of established cancer targets such as the LPA and mGlu receptor families, and we identified novel GPCRs that had not been directly linked to cancer before such as the P2Y Receptor 10 (P2RY10). As a proof of concept, we projected the structurally investigated mutations in the crystal structure of the C-C Chemokine (CCR) 5 receptor, one of the high-ranking GPCRs previously linked to cancer. Several positions were pinpointed that relate to either structural integrity or endogenous and synthetic ligand binding, providing a rationale to their mechanism of influence in cancer. In conclusion, this study identifies a list of GPCRs that are prioritized for experimental follow up characterization to elucidate their role in cancer. The computational approach here described can be adapted to investigate the roles in cancer of any protein family.

Author summaryDespite cancer being one of the most studied diseases due to its high mortality rate, one underexplored aspect is the association of certain protein families with tumor pathogenicity. We focused hereon the G protein-coupled receptorsfamily for three reasons. Firstly, it has been shown that this is the second most mutated class of proteins in cancer following kinases. Secondly, this family has been extensively studied resulting in a wide availability of experimental data for these proteins. Finally, more than 30 % of the drugs currently in the market targetitsmembers.For these receptors, weexplored the mutational landscape across cancer patients compared to healthy individuals. Our findings show the existence of cancer-related alteration patterns thatoccuratconserved positions. Additionally, we computationally ranked these G protein-coupled receptors on their importance in the pathogenesis of cancer based on multiple objectives. The result is a list of recommendations on where to focus next. These results suggest that there is room for repurposing existing therapies for cancer treatment while also highlighting the risk of potential interactions between cancer treatmentsand common drugs. All in all, we present a window of opportunity for new targeting strategies in oncology for G protein-coupled receptors.


title: MACA: Marker-based automatic cell-type annotation for single cell expression data

abstract:
SummaryAccurately identifying cell-types is a critical step in single-cell sequencing analyses. Here, we present marker-based automatic cell-type annotation (MACA), a new tool for annotating single-cell transcriptomics datasets. We developed MACA by testing 4 cell-type scoring methods with 2 public cell-marker databases as reference in 6 single-cell studies. MACA compares favorably to 4 existing marker-based cell-type annotation methods in terms of accuracy and speed. We show that MACA can annotate a large single-nuclei RNA-seq study in minutes on human hearts with ~290k cells. MACA scales easily to large datasets and can broadly help experts to annotate cell types in single-cell transcriptomics datasets, and we envision MACA provides a new opportunity for integration and standardization of cell-type annotation across multiple datasets.

Availability and implementationMACA is written in python and released under GNU General Public License v3.0. The source code is available at https://github.com/ImXman/MACA.

ContactYang Xu (yxu71@vols.utk.edu), Sikander Hayat (hayat221@gmail.com)


title: In silico analyses of maleidride biosynthetic gene clusters

abstract: Maleidrides are a family of structurally related fungal natural products, many of which possess diverse, potent bioactivities. Previous identification of several maleidride biosynthetic gene clusters, and subsequent experimental work, has determined the  core set of genes required to construct the characteristic medium-sized alicyclic ring with maleic anhydride moieties. Through genome mining, this work has used these core genes to discover ten entirely novel maleidride biosynthetic gene clusters, amongst both publicly available genomes, and encoded within the genome of the previously un-sequenced epiheveadride producer Wicklowia aquatica CBS125634. We have undertaken phylogenetic analyses and comparative bioinformatics on all known and putative maleidride biosynthetic gene clusters to gain further insights regarding these unique biosynthetic pathways.


title: On the use of facial and neck cooling to improve indoor occupant thermal comfort in warm conditions

abstract: Face and neck cooling has been found effective to improve thermal comfort during exercise in the heat despite the surface area of human face and neck regions accounts for only 5.5% of the entire body. Presently, very limited work in the literature has been reported on face and neck cooling to improve indoor thermal comfort. In this work, two energy-efficient wearable face and neck cooling fans were used to enhance occupants thermal comfort in two warm indoor conditions (30 & 32 {degrees}C). Local skin temperatures and perceptual responses while using those two wearable cooling fans were examined and compared. Results showed that both cooling fans could largely reduce local skin temperatures at the forehead, face and neck regions up to 2.1 {degrees}C. Local thermal sensation votes at the face and neck were decreased by 0.82-1.21 scale unit at two studied temperatures. Overall TSVs dropped by 1.03-1.14 and 1.34-1.66 scale unit at 30 and 32 {degrees}C temperatures, respectively. Both cooling fans could extend the acceptable HVAC temperature setpoint to 32.0 {degrees}C, resulting in an average energy saving of 45.7% as compared to the baseline HVAC setpoint of 24.5 {degrees}C. Further, the free-control cooling mode is recommended to occupants for further improving thermal comfort while using those two types of wearable cooling fans indoors. Lastly, it is concluded that those two wearable cooling fans could greatly improve thermal comfort and save HVAC energy despite some issues on dry eyes and dry lips associated with those wearable cooling fans were noted.

category: biophysics


title: Trimeric Photosystem I facilitates energy transfer from phycobilisomes in Synechocystis PCC 6803

abstract:
In cyanobacteria, phycobilisomes serve as peripheral light-harvesting complexes of the two photosystems, extending their antenna size and the wavelength range of photons available for photosynthesis. The abundance of phycobilisomes, the number of phycobiliproteins they contain, and their light-harvesting function are dynamically adjusted in response to the physiological conditions. Phycobilisomes are also thought to be involved in state transitions that maintain the excitation balance between the two photosystems. Unlike its eukaryotic counterpart, PSI is trimeric in many cyanobacterial species and the physiological significance of this is not well understood. Here we compared the composition and light-harvesting function of phycobilisomes in cells of Synechocystis sp. PCC 6803, which has primarily trimeric PSI, and the{Delta} psaL mutant unable to form trimers. We also investigated a mutant additionally lacking the PsaJ and PsaF subunits of PSI. Both strains with monomeric PSI accumulated significantly more allophycocyanin per chlorophyll, indicating higher abundance of phycobilisomes. On the other hand, a higher phycocyanin:allophycocyanin ratio in WT suggests larger phycobilisomes or the presence of APC-less phycobilisomes (CpcL-type), that are not assembled in cells with monomeric PSI. Steady-state and time-resolved fluorescence spectroscopy at room temperature and 77 K revealed that PSII receives more energy from the phycobilisomes at the expense of PSI in cells with monomeric PSI, regardless of the presence of PsaF. Taken together, these results show that the oligomeric state of PSI has an impact on the excitation energy flow in Synechocystis.

One-sentence summaryCyanobacterial mutants with monomeric PSI show changes in the composition and abundance of phycobilisomes and in the excitation energy transfer to PSII and PSI.


title: Trimeric Photosystem I facilitates energy transfer from phycobilisomes in Synechocystis sp. PCC 6803


title: Synonymous mutations can alter protein dimerization through localized interface misfolding involving self-entanglements

abstract:
Synonymous mutations in messenger RNAs (mRNAs) can reduce protein-protein binding affinities by more than half despite leaving the proteins amino acid sequence unaltered. Here, we use coarse-grain simulations of protein synthesis, ejection from the ribosome, post-translational dynamics, and dimerization to understand how synonymous mutations can influence the dimerization of the two E. coli homodimers oligoribonuclease and ribonuclease T. We synthesize each protein from its wildtype, fastest- and slowest-translating synonymous mRNAs and calculate the ensemble-average interaction energy between the resulting dimers. We find, similar to experiments with other dimers, that oligoribonucleases dimerization is altered by synonymous mutations. Relative to wildtype, the dimer interaction energy becomes 4% and 10% stronger, respectively, when translated from its fastest- and slowest-translating mRNAs. Ribonuclease T dimerization, however, is insensitive to synonymous mutations. The structural and kinetic origin of these changes are misfolded states containing non-covalent lasso-entanglements, many of which structurally perturb the dimer interface, whose probability of occurrence depends on translation speed. Translation of the fast- and slow-translating mRNAs of oligoribonuclease decreases the population of these misfolded states relative to wildtype. For ribonuclease T, however, these misfolded populations are insensitive to synonymous mutations. Entanglements cause altered dimerization energies for oligoribonuclease as there is a significant association (odds ratio: 50) between non-native self-entanglements and weak-binding dimer conformations. These conclusions are independent of model resolution, as entangled structures persist in long-time-scale all-atom simulations. Thus, non-native changes in entanglement is a mechanism through which oligomer structure and function can be altered.

SIGNIFICANCE STATEMENTSynonymous mutations affect a range of post-translational protein functions, including dimerization, without altering the amino acid sequence of the encoded protein. This suggests that proteins somehow retain a "memory" of their translation-elongation kinetics long after synthesis is complete. Here, we demonstrate that synonymous mutations can change the likelihood that nascent proteins misfold into self-entangled conformations. These self-entangled structures are similar to the native state but with key conformational perturbations that disrupt the dimer interface, reducing their ability to dimerize. Rearrangement of such self-entangled states to the native state is a slow process, offering a structural explanation for how translation-elongation kinetics can influence long-time-scale protein-protein binding affinities.


title: Eukaryotic CRFK cells motion characterized with atomic force microscopy

abstract: We performed a time-lapse imaging with Atomic Force Microscopy (AFM) of the motion of eukaryotic CRFK (Crandell-Rees Feline Kidney) cells adhered onto a glass surface and anchored to other cells in culture medium at 37{degrees}C. The main finding is a gradient in the spring constant of the actomyosin cortex along the cells axis. The rigidity increases at the rear of the cells during motion. This observation as well as a dramatic decrease of the volume suggests that cells may organize a dissymmetry in the skeleton network to expulse water and drive actively the rear edge.


title: Domestic pigs experimentally infected with Mycobacterium bovis and Mycobacterium tuberculosis exhibit different disease outcomes

abstract: Domestic pigs share many similarities with humans in their pulmonary anatomy, physiology, and immunology. Accordingly, pigs have been shown to be valuable models to study human tuberculosis (TB). Here we examined the outcome of disease in domestic pigs challenged via two different routes with either the human-adapted TB bacillus Mycobacterium tuberculosis or the zoonotic bovine TB bacillus M. bovis in head-to-head comparisons. We found that pigs challenged intravenously with M. bovis AF2122/97 exhibited severe morbidity and rapid onset of mortality, accompanied by higher tissue bacterial burden and necrosis compared to pigs challenged similarly with M. tb Erdman. Concordantly, pigs challenged with aerosolized M. bovis AF2122/97 exhibited reduced weight gain and more severe pathology than pigs challenged similarly with M. tb Erdman. Moreover, pigs aerosol-challenged with M. bovis AF2122/97 exhibited a spectrum of granulomatous lesions ranging from small well-contained granulomas to caseous-necrotic lesions mimicking active TB disease in humans. In contrast, pigs aerosol-challenged with M. tb Erdman exhibited arrested granuloma development. Irrespective of challenge dose and pathological outcome however, peripheral IFN-{gamma} responses were similar in both M. bovis AF2122/97 and M. tb Erdman challenged pigs. This study demonstrates domestic pigs can support infections with M. bovis and M. tb and develop pathology similar to what is observed in humans. And although M. bovis AF2122/97 appears to be more virulent than M. tb Erdman, both strains can be used to model TB in domestic pigs, depending on whether one wishes to recapitulate either acute and active TB or latent TB infections.


title: AT-752, a double prodrug of a guanosine nucleotide analog, inhibits yellow fever virus in a hamster model

abstract:
Yellow fever virus (YFV) is a zoonotic pathogen re-emerging in parts of the world, causing a viral hemorrhagic fever associated with high mortality rates. While an effective vaccine is available, having an effective antiviral against YFV is critical against unexpected outbreaks, or when vaccination is not recommended. We have previously identified AT-281, the free base of AT-752, an orally available double prodrug of a guanosine nucleotide analog, as a potent inhibitor of YFV in vitro, with a 50% effective concentration (EC50) of 0.31 M. In hamsters infected with YFV (Jimenez strain), viremia rose about 4 log10-fold and serum alanine aminotransferase (ALT) 2-fold compared to sham-infected animals. Treatment with 1000 mg/kg AT-752 for 7 days, initiated 4 h prior to viral challenge, reduced viremia to below the limit of detection by day 4 post infection (pi) and returned ALT to normal levels by day 6 pi. When treatment with AT-752 was initiated 2 days pi, the virus titer and ALT dropped >2 log10 and 53% by day 4 and 6 pi, respectively. In addition, at 21 days pi, 70 - 100% of the infected animals in the treatment groups survived compared to 0% of the untreated group (p<0.001). Moreover, in vivo formation of the active triphosphate metabolite AT-9010 was measured in the animal tissues, with the highest concentrations in liver and kidney, organs that are vulnerable to the virus. The demonstrated in vivo activity of AT-752 suggests that it is a promising compound for clinical development in the treatment of YFV infection.

Author summaryYellow fever virus (YFV) is transmitted by mosquitoes, and its infection can lead to a lethal viral hemorrhagic fever associated with liver damage. While an effective vaccine is available, in places where the vaccination rate is low, in the event of an unexpected outbreak, or where vaccination is not recommended individually, having an effective antiviral treatment is critical. We previously reported that the nucleotide analog prodrug AT-752 potently inhibited the YFV in cultured cells. Here we showed that in hamsters infected with YFV, oral treatment with 1000 mg/kg AT-752 for 7 days reduced the production of infectious virus particles in the blood, and decreased serum alanine aminotransferase, a marker of liver damage, to levels measured in uninfected animals. In addition, at 21 days after infection, 70 - 100% of the infected animals in the treatment groups survived compared to 0% in the untreated group. Moreover, the amount of the active metabolite formed from AT-752 was highest in the livers and kidneys of the treated animals, organs that are targeted by the virus. These results suggest that AT-752 is a promising compound to develop for the treatment of YFV infection.


title: Preservation of neural synchrony at peak alpha frequency via global synaptic scaling compensates for white matter structural decline over adult lifespan

abstract: We propose that preservation of functional integration, estimated from measures of neural synchrony, is a key neurocompensatory mechanism associated with healthy human ageing. To support this proposal, we demonstrate how phase-locking at peak alpha frequency from Magnetoencephalography (MEG) data is invariant over lifespan in a large cohort of human participants, aged 18-88 years. Using empirically derived connection topologies from diffusion tensor imaging (DTI) data, we create an in-silico model of whole-brain alpha dynamics. We show that enhancing inter-areal coupling can cancel the effect of increased axonal transmission delay associated with age-related degeneration of white matter tracts and thus, preserve neural synchrony. Together with analytical solutions for non-biological all-to-all connection scenarios, our model establishes the theoretical principles by which frequency slowing with age, frequently observed in the alpha band in diverse populations, can be viewed as an epiphenomenon of the underlying neurocompensatory mechanisms.

category: neuroscience


title: Temporal changes in resting state networks induced by propofol anesthesia.

abstract:
The cerebral cortical changes associated with propofol-induced unconsciousness remain unknown. While the anesthetic agent affects the entire cerebral cortices, there might be spatiotemporal differences in cortical changes. In particular, we hypothesized that there might be spatiotemporal differences in cortical changes with propofol-anesthesia. To address this hypothesis, we investigated power spectrum changes in electrocorticography (ECoG) signals obtained during the induction phase from awake state to unconsciousness. We found that, 1) the power increased in the range of frequencies < 46 Hz (delta to low gamma), and decreased in the range (62-150) Hz (high gamma), in global channels during the induction phase. 2) The power in the frontoparietal network (FPN), specifically the superior parietal lobule and prefrontal cortex, started to change early, but took a long time to completely change. However, the power in the default mode network (DMN) started to change late, but took a short time to completely change. 3) The power change ({Delta}Power) in the DMN was more conspicuous than that of the dorsal attention network (DAN) in high gamma frequency. Considering that the FPN is involved in communication with the external world and that DMN is involved in communication with self, loss of consciousness induced by general anesthesia results from first, disrupted communication between self and external world, and is then followed by disrupted communication within self, with decreased activity of the FPN, and later, attenuated activity of the DMN.

Significance StatementWe investigated the spatiotemporal changes of power spectrum in human electrocorticography (ECoG) during the induction phase from awake state to unconsciousness. We found that from delta to low gamma frequency, the power increased, while in high gamma frequency, the power decreased over all channels. The power in the frontoparietal network (FPN) preferentially changed, then the power in the DMN changed later. The power in DMN decreased more than those in other RSNs in high gamma frequency. Loss of consciousness induced by general anesthesia results from first, disrupted communication between self and external world, followed by disrupted communication within self, with decreased activity of the FPN, and later, attenuated activity of the DMN.