title: Potent but transient immunosuppression of T-cells is a general feature of erythroid progenitor cells

abstract:
CD71+ erythroid cells (CECs) have been recently recognized in both neonates and cancer patients as potent immunoregulatory cells. Here, we show that in mice early-stage CECs expand in anemia, have high levels of arginase 2 (ARG2) and reactive oxygen species (ROS). In the spleens of anemic mice, CECs expansion-induced L-arginine depletion suppresses T-cell responses. In humans with anemia, CECs expand and express ARG1 and ARG2 that suppress T-cells IFN-{gamma} production. Moreover, bone marrow CECs from healthy human donors suppress T-cells proliferation. CECs differentiated from peripheral blood mononuclear cells potently suppress T-cell activation, proliferation, and IFN-{gamma} production in an ARG- and ROS-dependent manner. These effects are the most prominent for early-stage CECs (CD71highCD235adim cells). The suppressive properties disappear during erythroid differentiation as more differentiated CECs and mature erythrocytes lack significant immunoregulatory properties. Our studies provide a novel insight into the role of CECs in the immune response regulation.

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title: Potent but transient immunosuppression of T-cells is a general feature of CD71+ erythroid cells

category: immunology


title: Loss of C3aR induces immune infiltration and inflammatory microbiota in a novel spontaneous model of colon cancer

abstract:
Several lines of evidence suggest that inflammation plays a pivotal role in the development and progression of colorectal cancer (CRC) and can be unleashed by the loss of innate immunosurveillance. The complement system is a well characterized first line of defense against pathogens and a central component of the immune response. Emerging evidence suggests that complement anaphylatoxin C3a produced upon complement activation and acting via its receptor (C3aR) may play a role in intestinal homeostasis. However, to date, it is unknown whether and how the C3a/C3aR axis can affect CRC. By mining publicly available datasets, we found that CpG island methylation of c3ar1 occurs in CRC patients and is associated with significant downregulation of C3aR. By reverse-translating this finding we were able to shift in APCMin/+ mice the tumorigenesis from the small intestine to the colon therefore generating a novel mouse model, which more closely mirrors the CRC in humans. Transcriptomic analysis on colorectal polyps from our newly developed genetic mouse model revealed a significant increase in innate and adaptive immune signatures in absence of C3aR. Furthermore, loss of C3aR significantly impacted the fecal and tumor-associated microbiota and supported the blooming of pro-inflammatory bacterial species as confirmed by experiments of fecal microbiota transplantation.

Future studies will elucidate whether loss of C3aR can be exploited as a biomarker for sub-groups of CRC and whether the C3a/C3aR axis may be exploited for the generation of more effective therapeutic interventions.


title: Xanthomonas transcriptome inside cauliflower hydathodes reveals bacterial virulencestrategies and physiological adaptation at early infection stages

abstract: Xanthomonas campestris pv. campestris (Xcc) bacterium is a seed-transmitted vascular pathogen causing black rot disease on cultivated and wild Brassicaceae. Xcc enters the plant tissues preferentially via hydathodes which are organs localized at leaf margins. In order to decipher both physiological and virulence strategies deployed by Xcc during early stages of infection, the transcriptomic profile of Xcc was analyzed three days after entry into cauliflower hydathodes. Despite the absence of visible plant tissue alterations and a bacterial biotrophic lifestyle, 18% of Xcc genes undergo a transcriptional reprogramming, including a striking repression of chemotaxis and motility functions. Xcc full repertoire of virulence factors was not yet activated but the expression of the 95-gene HrpG regulon, including genes coding for the type three secretion machinery important for suppression of plant immunity, was induced. The expression of genes involved in metabolic adaptations such as catabolism of plant compounds, transport functions, sulfur and phosphate metabolism was upregulated while limited stress responses were observed three days post infection. These transcriptomic observations give information about the nutritional and stress status of bacteria during the early biotrophic infection stages and help to decipher the adaptive strategy of Xcc to the hydathode environment.

category: microbiology


title: (p)ppGpp inhibits 70S ribosome formation in Staphylococcus aureus by impeding GTPase-ribosome interactions

abstract: During nutrient limitation, bacteria produce the alarmones (p)ppGpp as effectors of the stress signalling network termed the stringent response. Screening for (p)ppGpp-binding targets within Staphylococcus aureus identified four ribosome-associated GTPases (RA-GTPases), RsgA, RbgA, Era and HflX, each of which are cofactors in ribosome assembly, where they cycle between the ON (GTP-bound) and OFF (GDP-bound) states. Entry into the OFF-state from the ON-state occurs upon hydrolysis of GTP, with GTPase activity increasing substantially upon ribosome association. When bound to (p)ppGpp, GTPase activity is inhibited, reducing 70S ribosome assembly. Here, we sought to determine how (p)ppGpp impacts RA-GTPase-ribosome interactions by examining the affinity and kinetics of binding between RA-GTPases and ribosomes in various nucleotide-bound states. We show that RA-GTPases preferentially bind to 5'-diphosphate-containing nucleotides GDP and ppGpp over GTP, which is likely exploited as a regulatory mechanism within the cell. Binding to (p)ppGpp reduces stable association of RA-GTPases to ribosomal subunits compared to the GTP-bound state both in vitro and within bacterial cells by inducing the OFF-state conformation. We propose that in this conformation, the G2/switch I loop adopts a conformation incompatible with ribosome association. Altogether, we highlight (p)ppGpp-mediated inhibition of RA-GTPases as a major mechanism of stringent response-mediated growth control.


title: The molecular basis of coupling between poly(A)-tail length and translational efficiency

abstract: In animal oocytes and early embryos, mRNA poly(A)-tail length strongly influences translational efficiency (TE), but later in development this coupling between tail length and TE disappears. Here, we elucidate how this coupling is first established and why it disappears. Overexpressing cytoplasmic poly(A)-binding protein (PABPC) in frog oocytes specifically improved translation of short-tailed mRNAs, thereby diminishing coupling between tail length and TE. Thus, coupling requires limiting PABPC, implying that in coupled systems longer-tail mRNAs better compete for limiting PABPC. In addition to expressing excess PABPC, post-embryonic cells had two other properties that prevented strong coupling: terminal-uridylation-dependent destabilization of mRNAs lacking bound PABPC, and a regulatory regime wherein PABPC contributes minimally to TE. Thus, these results revealed three fundamental mechanistic requirements for coupling and defined the context-dependent functions for PABPC, in which this protein promotes TE but not mRNA stability in coupled systems and mRNA stability but not TE in uncoupled systems.

category: molecular biology


title: Interaction Between Phosphoinositide 3-Kinase and the VDAC2 Channel Tethers Endosomes to Mitochondria and Promotes Endosome Maturation

abstract:
Intracellular organelles of mammalian cells communicate with each other during various cellular processes. The functions and molecular mechanisms of such interorganelle association remain largely unclear, however. We here identified voltage-dependent anion channel 2 (VDAC2), a mitochondrial outer membrane protein, as a binding partner of phosphoinositide 3-kinase (PI3K), a regulator of clathrin-independent endocytosis downstream of the small GTPase Ras. VDAC2 was found to tether endosomes positive for the Ras-PI3K complex to mitochondria in response to cell stimulation with epidermal growth factor and to promote clathrin-independent endocytosis as well as endosome maturation at membrane contact sites. With a newly developed optogenetics system to induce mitochondrion-endosome association, we found that, in addition to its structural role in such association, the pore function of VDAC2 is also required for the promotion of endosome maturation. Our findings thus uncover a previously unappreciated role of mitochondrion-endosome association in the regulation of endocytosis and endosome maturation.

HighlightsO_LIThe mitochondrial protein VDAC2 binds PI3K and tethers endosomes to mitochondria
C_LIO_LIVDAC2 promotes clathrin-independent endocytosis
C_LIO_LIVDAC2-PI3K interaction induces acidification of endosomes associated with mitochondria
C_LIO_LIThe pore function of VDAC2 also contributes to endosome maturation at contact sites
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category: cell biology


title: Characterization of the nanomechanical properties of the fission yeast (Schizosaccharomyces pombe) cell surface by atomic force microscopy

abstract: Variations in cell wall composition and biomechanical properties can contribute to the cellular plasticity required during complex processes such as polarized growth and elongation in microbial cells. This study utilizes atomic force microscopy (AFM) to map the cell surface topography of fission yeast, Schizosaccharomyces pombe, at regions of active polarized growth and to characterize the biophysical properties within these regions under physiological, hydrated conditions. High-resolution images acquired from AFM topographic scanning reveal decreased surface roughness at actively growing cell poles. Force extension curves acquired by nanoindentation probing with AFM cantilever tips under low applied force revealed increased cell wall elasticity and decreased cellular stiffness (cellular spring constant) at cell poles (17 {+/-} 4 mN/m) relative to the main body of the cell that is not undergoing growth and expansion (44 {+/-} 10 mN/m). These findings suggest that the increased elasticity and decreased stiffness at regions undergoing polarized growth at fission yeast cell poles provide the plasticity necessary for cellular extension. This is the first direct biophysical characterization of the S. pombe cell surface by AFM, and it provides a foundation for future investigation of how the surface topography and local nanomechanical properties vary during different cellular processes.


title: Universal DNA methylation age across mammalian tissues

abstract: Aging is often perceived as a degenerative process caused by random accrual of cellular damage over time. In spite of this, age can be accurately estimated by epigenetic clocks based on DNA methylation profiles from almost any tissue of the body. Since such pan-tissue epigenetic clocks have been successfully developed for several different species, it is difficult to ignore the likelihood that a defined and shared mechanism instead, underlies the aging process. To address this, we generated 10,000 methylation arrays, each profiling up to 37,000 cytosines in highly-conserved stretches of DNA, from over 59 tissue-types derived from 128 mammalian species. From these, we identified and characterized specific cytosines, whose methylation levels change with age across mammalian species. Genes associated with these cytosines are greatly enriched in mammalian developmental processes and implicated in age-associated diseases. From the methylation profiles of these age-related cytosines, we successfully constructed three highly accurate universal mammalian clocks for eutherians, and one universal clock for marsupials. The universal clocks for eutherians are similarly accurate for estimating ages (r>0.96) of any mammalian species and tissue with a single mathematical formula. Collectively, these new observations support the notion that aging is indeed evolutionarily conserved and coupled to developmental processes across all mammalian species - a notion that was long-debated without the benefit of this new and compelling evidence.

category: developmental biology


title: Bazooka/Par3 cooperates with Sanpodo for the assembly of Notch signaling clusters following asymmetric division of Drosophila sensory organ precursor cells

abstract: In multiple cell lineages, Delta-Notch signaling regulates cell fate decisions owing to unidirectional signaling between daughter cells. In Drosophila pupal sensory organ lineage, Notch regulates pIIa/pIIb fate decision at cytokinesis. Notch and Delta that localize apically and basally at the pIIa-pIIb interface, are expressed at low levels and their residence time at the plasma membrane is in the order of the minute. How Delta can effectively interact with Notch to trigger signaling from a large plasma membrane remains poorly understood. Here, we report that the signaling interface possesses a unique apicobasal polarity with Par3/Bazooka localizing in the form of nano-clusters at the apical and basal level. Notch is preferentially targeted to the pIIa-pIIb interface where it co-clusters with Bazooka and the Notch cofactor Sanpodo. Clusters whose assembly relies on Bazooka and Sanpodo activities, are also positive for Neuralized, the E3 ligase required for Delta-activity. We propose that the nano-clusters act as snap buttons at the new pIIa-pIIb interface to allow efficient intra-lineage signaling.


title: THE UNAPPARENT EFFECT OF CLIMATE FORCING ON URBAN AMOEBIASIS IN MEXICO CITY

abstract: AO_SCPLOWBSTRACTC_SCPLOWDespite advances in the provision of sanitation infrastructure in cities, diarrheal-related illnesses continue to be a global burden. In cities of the developing world, explanations for the persistence of diarrheal-related diseases revolve around the role of sanitation, poverty, and individual behavior. Less is known about the role of climate in forcing the inter-annual variability of transmission. We quantified the contribution of rainfall to the transmission of a diarrhoeal disease caused by the protozoan Entamoeba histolytica. We formulated a process-based model of the population dynamics of Entamoeba histolytica in 6 municipalities of Mexico City, and we reconstructed the interannual variability of the observed cases of amebiasis between 2005 and 2012. Using inference methods for non-linear systems, we estimated that 10% of the susceptible individuals were infected in early 2005 and 90% of those infections were causally related to the exposure to the environmental stage of the pathogen after rainfall events. The magnitude of these results underscores the importance of considering the interaction between climate forcing and water management as ecological determinants of health in megacities.

category: ecology


title: Long-term changes in the breeding biology of a New Zealand bellbird population suggest plasticity in life-history responses to ecological restoration

abstract: Ecological restoration projects provide excellent opportunities to study how animals adapt their life-history strategies in response to changeable environments. A fundamental way animals can optimise reproductive success in changing conditions is trading-off aspects of their breeding system. The New Zealand bellbird (Anthornis melanura) has had a long-term presence on the small restoration island, Tiritiri Matangi Island (Tiri), spanning the islands degraded agricultural past to its current extensively restored state. We studied the breeding biology of this bellbird population to assess how their reproductive life-history strategies have responded over time to the restoration on Tiri. We compared the current breeding data (2012-2016) of the bellbirds with data from between 2001-2010 (including Baillie, 2011, Cope, 2007), and from 1977-1978 (Anderson and Craig, 2003), prior to the islands restoration. We also explored associations between abiotic/biotic factors and bellbird reproductive success for the most recent period (2012-2016). Our main finding was that clutch size significantly declined over time from a mean of 3.6 to 2.4 eggs per nest and this decline correlated with increasing population density. This is consistent with a density dependent effect, although further data are required to empirically test this conclusion. Overall, the earliest spring laying dates were in late August and the latest extended to January, with all chicks fledged by the end of February. Nest success was 47% (range 40 - 54%) across 2012-2016, falling within a similar range as previous studies. We found little effect of year, weather, parental age or morphometrics on reproductive success. We observed directional change in patterns of parental investment between 1977-1978 and 2012-2016; in 2012-2016, parents persisted with raising single broods rather than abandoning and re-nesting to raise larger broods. These results suggest that the bellbirds life-history traits are plastic in response to local conditions which provides an advantage when repopulating a regenerating or changing habitat.


title: Resonance in physiologically structured population models

abstract: Ecologists have long sought to understand how the dynamics of natural populations are affected by the environmental variation those populations experience. A transfer function is a useful tool for this purpose, as it uses linearization theory to show how the frequency spectrum of the fluctuations in a populations abundance relates to the frequency spectrum of environmental variation. Here, we show how to derive and to compute the transfer function for a continuous-time model of a population that is structured by a continuous individual-level state variable such as size. To illustrate, we derive, compute, and analyze the transfer function for a size-structured population model of stony corals with open recruitment, parameterized for a common Indo-Pacific coral species complex. This analysis identifies a sharp multi-decade resonance driven by space competition between existing coral colonies and incoming recruits. The resonant frequency is most strongly determined by the rate at which colonies grow, and the potential for resonant oscillations is greatest when colony growth is only weakly density-dependent. While these resonant oscillations are unlikely to be a predominant dynamical feature of degraded reefs, they suggest dynamical possibilities for marine invertebrates in more pristine waters. The size-structured model that we analyze is a leading example of a broader class of physiologically structured population models, and the methods we present should apply to a wide variety of models in this class.


title: Spatial pattern analysis of line-segment data in ecology

abstract:
O_LIThe spatial analysis of linear features (lines and curves) is a challenging and rarely attempted problem in ecology. Existing methods are typically expressed in abstract mathematical formalism, making it difficult to assess their relevance and transferability into an ecological setting. A set of concrete and accessible tools is needed.
C_LIO_LIWe develop a new method to analyse the spatial patterning of line-segment data. It is based on a generalisation of Ripleys K-function and includes an analogue of the transformed L-function, together with estimators and theoretical expectation values. We introduce a class of line-segment processes, related to the Boolean model, which we use in conjunction with Monte-Carlo methods and information criteria to generate and compare candidate models. We demonstrate the utility of our method using fallen tree (dead log) data collected from two one-hectare Australian tall eucalypt forest plots.
C_LIO_LIComparing six line-segment models, we find for both plots that the distribution of fallen logs is best explained by plot-level spatial heterogeneity. The use of non-uniform distributions to model dead-log orientation on the forest floor improves model performance in one of the two sites. Our case study highlights the challenges of model comparison in spatial-pattern analysis, where Monte-Carlo approaches based on the discrepancy of simulated summary functions can generate a different ranking of models than that of information criteria.
C_LIO_LIThese methods are of a general nature and are applicable to any line-segment data. In the context of forest ecology, the integration of fallen logs as linear structural features in a landscape with the point locations of living trees, and a quantification of their interactions, will yield new insights into the functional and structural role of tree fall in forest communities and their enduring post-mortem ecological legacy as spatially distributed decomposing logs.
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title: Fundamental identifiability limits in molecular epidemiology

abstract: Viral phylogenies provide crucial information on the spread of infectious diseases, and many studies fit mathematical models to phylogenetic data to estimate epidemiological parameters such as the effective reproduction ratio (Re) over time. Such phylodynamic inferences often complement or even substitute for conventional surveillance data, particularly when sampling is poor or delayed. It remains generally unknown, however, how robust phylodynamic epidemiological inferences are, especially when there is uncertainty regarding pathogen prevalence and sampling intensity. Here we use recently developed mathematical techniques to fully characterize the information that can possibly be extracted from serially collected viral phylogenetic data, in the context of the commonly used birth-death-sampling model. We show that for any candidate epidemiological scenario, there exist a myriad of alternative, markedly different and yet plausible "congruent" scenarios that cannot be distinguished using phylogenetic data alone, no matter how large the dataset. In the absence of strong constraints or rate priors across the entire study period, neither maximum-likelihood fitting nor Bayesian inference can reliably reconstruct the true epidemiological dynamics from phylogenetic data alone; rather, estimators can only converge to the "congruence class" of the true dynamics. We propose concrete and feasible strategies for making more robust epidemiological inferences from viral phylogenetic data.

category: evolutionary biology


title: Loss of cysteine rich domain was critical for evolution of heterodimerization in Toll proteins.

abstract:
Toll proteins play roles in immunity/development which have largely remained conserved. However, there are differences in Toll biology as mammalian TLRs recognise pathogen associated molecular patterns (PAMPs) but not their invertebrate homologues. The reason for the same is not known. One critical molecular difference is absence of Cysteine Rich Domain (CRD) in vertebrate Tolls and their presence in invertebrates. Interestingly, in Drosophila, all Toll proteins have CRD except Toll9. This provided us the appropriate model to investigate significance of loss of CRD in Toll evolution. CRDs nudge protein dimerization by forming disulphide bonds hence we asked if they did same in Drosophila Toll-proteins. We tested if, Toll-1(which forms homodimer) can heterodimerize with Toll-9. We found that wildtype Toll-1 didnt interact with Toll9 however; when CRD of Toll1 was deleted/mutated it formed heterodimer with Toll9. This indicates that presence of CRD limits Toll proteins to form homodimer and thus its loss was a critical event which pushed Toll proteins towards heterodimerization. We further show that Drosophila Toll9 can directly bind dsRNA, a PAMP. Interestingly, dsRNA affinity for toll-9 monomer was twice as that for the dimer, which can be attributed to CRD loss. Thus, we show that loss of CRD was a major step in Toll evolution as it resulted in functional diversity and was a first step towards heterodimer formation. Therefore, we propose that CRD loss was under positive selection and also that heterodimerization of Toll-proteins is an evolved property.

One line summaryLoss of Cysteine Rich Domain in Drosophila Toll9 and recognition of dsRNA.


title: The impact of antigenic escape on the evolution of virulence

abstract: Understanding the evolutionary drivers determining the transmission rate and virulence of pathogens remains an important challenge for evolutionary theory with clear implications to the control of human, agricultural and wildlife infectious disease. Although disease is often very dynamic, classical theory examines the long-term outcome of evolution at equilibrium and, in simple models, typically predicts that R0 is maximized. For example, immune escape may lead to complex disease dynamics including repeated epidemics, fluctuating selection and diversification. Here we model the impact of antigenic drift and escape on the evolution of virulence and show analytically that these non-equilibrium dynamics select for more acute pathogens with higher virulence. Specifically, under antigenic drift and when partial cross immunity leads to antigenic escape, our analysis predicts the long-term maximization of the intrinsic growth rate of the parasite resulting in more acute and virulent pathogens than those predicted by classic R0 maximization. Furthermore, it follows that these pathogens will have a lower R0 leading to implications for epidemic, endemic behavior and control. Our analysis predicts both the timings and outcomes of antigenic shifts leading to repeated epidemics and predicts the increase in variation in both antigenicity and virulence before antigenic escape. There is considerable variation in the degree of antigenic escape that occurs across pathogens and our results may help to explain the difference in virulence between related pathogens most clearly seen in the human A, B and C influenzas. More generally our results show the importance of examining the evolutionary consequences of non-equilibrium dynamics.


title: Simultaneous single cell measurements of intranuclear proteins and gene expression

abstract: Identifying gene regulatory targets of nuclear proteins in tissues remains a challenge. Here we describe intranuclear Cellular Indexing of Transcriptomes and Epitopes (inCITE-seq), a scalable method for measuring multiplexed intranuclear protein levels and the transcriptome in parallel in thousands of cells, enabling joint analysis of TF levels and gene expression in vivo. We apply inCITE-seq to characterize cell state-related changes upon pharmacological induction of neuronal activity in the mouse brain. Modeling gene expression as a linear combination of quantitative protein levels revealed the genome-wide effect of each TF and recovered known targets. Cell type-specific genes associated with each TF were co-expressed as distinct modules that each corresponded to positive or negative TF levels, showing that our approach can disentangle relative contributions of TFs to gene expression and add interpretability to gene networks. InCITE-seq can illuminate how combinations of nuclear proteins shape gene expression in native tissue contexts, with direct applications to solid or frozen tissues and clinical specimens.

category: genomics


title: Splenic denervation attenuates repeated social defeat stress-induced T-lymphocyte inflammation

abstract:
BackgroundPost-traumatic stress disorder (PTSD) is a devastating psychological disorder that significantly increases the risk for inflammatory diseases. While the exact etiology of this predisposition remains unclear, PTSD canonically increases overall sympathetic tone resulting in increased norepinephrine (NE) outflow. Previously, we demonstrated that exogenous NE alters mitochondrial superoxide in T-lymphocytes to produce a pro-inflammatory T-helper 17 (TH17) phenotype. Therefore, we hypothesized sympathetic-driven neuroimmune interactions could mediate psychological trauma-induced T-lymphocyte inflammation.

MethodsRepeated social defeat stress (RSDS) is a preclinical murine model that recapitulates the behavioral, autonomic, and inflammatory aspects of PTSD. Targeted splenic denervation (Dnx) was performed to deduce the contribution of splenic sympathetic nerves to RSDS-induced inflammation. Eighty-five C57BL/6J mice underwent Dnx or sham-operation, followed by RSDS or control paradigms. Animals were assessed for behavioral, autonomic, inflammatory, and redox profiles.

ResultsDnx did not alter the antisocial or anxiety-like behavior induced by RSDS. In circulation, RSDS Dnx animals exhibited diminished levels of T-lymphocyte-specific cytokines (IL-2, IL-17A, and IL-22) compared to intact animals, whereas other non-specific inflammatory cytokines (e.g., IL-6, TNF-, and IL-10) were unaffected by Dnx. Importantly, Dnx specifically ameliorated the increases in RSDS-induced T-lymphocyte mitochondrial superoxide, TH17 polarization, and pro-inflammatory gene expression with minimal impact to non-T-lymphocyte immune populations.

ConclusionsOverall, our data suggest that sympathetic nerves regulate RSDS-induced splenic T-lymphocyte inflammation, but play a minimal role in the behavioral and non-T-lymphocyte inflammatory phenotypes induced by this psychological trauma paradigm.

category: animal behavior and cognition


title: Enhancing top-down proteomics of brain tissue with FAIMS

abstract: Proteomic investigations of Alzheimers and Parkinsons disease have provided valuable insights into neurodegenerative disorders. Thus far, these investigations have largely been restricted to bottom-up approaches, hindering the degree to which one can characterize a proteins "intact" state. Top-down proteomics (TDP) overcomes this limitation, however it is typically limited to observing only the most abundant proteoforms and of a relatively small size. Therefore, offline fractionation techniques are commonly used to reduce sample complexity, limiting throughput. A higher throughput alternative is online fractionation, such as gas phase high-field asymmetric waveform ion mobility spectrometry (FAIMS). Utilizing a high complexity sample derived from Alzheimers disease brain tissue, we describe how the addition of FAIMS to TDP can robustly improve the depth of proteome coverage. For example, implementation of FAIMS at -50 compensation voltage (CV) more than doubled the mean number of non-redundant proteoforms observed (1,833 {+/-} 17, n = 3), compared to without (754 {+/-} 35 proteoforms). We also found FAIMS can influence the transmission of proteoforms and their charge envelopes based on their size. Importantly, FAIMS enabled the identification of intact amyloid beta (A{beta}) proteoforms, including the aggregation-prone A{beta}1-42 variant which is strongly linked to Alzheimers disease.

category: biochemistry


title: A nexus of intrinsic dynamics underlies translocase priming

abstract: The cytoplasmic ATPase SecA and the membrane-embedded SecYEG channel assemble to form the functional Sec translocase. How this interaction primes and catalytically activates the translocase remains unclear. We now show that priming exploits a sophisticated nexus of intrinsic dynamics in SecA. Using atomistic simulations, single molecule FRET and hydrogen/deuterium exchange mass spectrometry we reveal multiple distributed dynamic islands that cross-talk with domain and quaternary motions. These dynamic elements are highly conserved and essential for function. Central to the nexus is a slender Stem through which, motions in the helicase ATPase domain of SecA biases how the preprotein binding domain rotates between open-closed clamping states. Multi-tier dynamics are enabled by an H-bonded framework covering most of the SecA structure and allowing conformational alterations with minimal energy inputs. As a result, dimerization, the channel and nucleotides select pre-existing conformations, and alter local dynamics to restrict or promote catalytic activity and clamp motions. These events prime the translocase for high affinity reception of non-folded preprotein clients. Such dynamics nexuses are likely universal and essential in multi-liganded protein machines.


title: Quantifying nanotherapeutics penetration using hydrogel based microsystem as a new 3D in-vitro platform

abstract:
The huge gap between 2D in vitro assays used for drug screening, and the in vivo 3D-physiological environment hampered reliable predictions for the route and accumulation of nanotherapeutics in vivo. For such nanotherapeutics, Multi-Cellular Tumour Spheroids (MCTS) is emerging as a good alternative in vitro model. However, the classical approaches to produce MCTS suffer from low yield, slow process, difficulties in MCTS manipulation and compatibility with high-magnification fluorescent optical microscopy. On the other hand, spheroid-on-chip set-ups developed so far require a microfluidic practical knowledge difficult to transfer to a cell biology laboratory.

We present here a simple yet highly flexible 3D-model microsystem consisting of agarose-based microwells. Fully compatible with the multi-well plates format conventionally used in cell biology, our simple process enables the formation of hundreds of reproducible spheroids in a single pipetting. Immunostaining and fluorescent imaging including live high-resolution optical microscopy can be performed in-situ, with no manipulation of spheroids.

As a proof-of-principle of the relevance of such in vitro platform for nanotherapeutics evaluation, this study investigates the kinetic and localization of nanoparticles within colorectal cancer MCTS cells (HCT-116). The nanoparticles chosen are sub-5 nm ultrasmall nanoparticles made of polysiloxane and gadolinium chelates that can be visualized in MRI (AGuIX(R), currently implicated in clinical trials as effective radiosensitizers for radiotherapy) and confocal microscopy after addition of Cy 5.5. We show that the amount of AGuIX(R) nanoparticles within cells is largely different in 2D and 3D. Using our flexible agarose-based microsystems, we are able to resolve spatially and temporally the penetration and distribution of AGuIX(R) nanoparticles within MCTS. The nanoparticles are first found in both extracellular and intracellular space of MCTS. While the extracellular part is washed away after few days, we evidenced intracellular localisation of AGuIX(R), mainly within lysosomes compartment, but also occasionally within mitochondria. Our agarose-based microsystem appears hence as a promising 3D in vitro user-friendly platform for investigation of nanotherapeutics transport, ahead of in vivo studies.

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category: bioengineering


title: Immunoengineered Nanobead System for the Isolation and Detection of Circulating Tumor Cells

abstract: Highly efficient capture and detection of circulating tumor cells (CTCs) remain elusive mainly because of their extremely low concentration in the peripheral blood of patients. Herein, we present an approach for the simultaneous capturing, isolation, and detection of CTCs using an immuno-fluorescent magnetic nanobead system (iFMNS) coated with a monoclonal anti-EpCAM antibody. The developed antibody nanobead system allows magnetic isolation and fluorescent-based quantification of CTCs. The expression of EpCAM on the surface of captured CTCs could be directly visualized without additional immune-fluorescent labeling. Our approach is shown to result in a 70 - 95% capture efficiency of CTCs, and 95% of the captured cells remain viable. Using our approach, the isolated cells could be directly used for culture, reverse transcription-polymerase chain reaction (RT-PCR), and immunocytochemistry (ICC) identification. We applied iFMNS for testing CTCs in peripheral blood samples from a lung cancer patient, which suggested that this approach would be a promising tool for CTCs enrichment and detection in one step.


title: Combined Enhanced Biological Phosphorus Removal (EBPR) and Nitrite Accumulation for Treating High-strength Wastewater

abstract: The enhanced biological phosphorus removal (EBPR) has been widely applied in treating domestic wastewater, while the performance on high-strength P wastewater is less investigated and the feasibility of coupling with short-cut nitrogen removal process remains unknown. This study first achieved the simultaneous high-efficient P removal and stable nitrite accumulation in one sequencing batch reactor for treating the synthetic digested manure wastewater. The average effluent P could be down to 0.8 {+/-} 1.0 mg P/L and the P removal efficiency was 99.5 {+/-} 0.8%. Candidatus Accumulibacter was the dominant polyphosphate accumulating organism (PAO) with the relative abundance of 14.2-33.1% in the reactor. Examination of the micro-diversity of Candidatus Accumulibacter using 16s rRNA gene-based oligotyping analysis revealed one unique Accumulibacter oligotype that different from the conventional system, which accounted for 64.2-87.9% of the total Accumulibacter abundance. The presence of high-abundant glycogen accumulating organisms (GAO) (15.6-40.3%, Defluviicoccus and Candidatus Competibacter) did not deteriorate the EBPR performance. Moreover, nitrite accumulation happened in the system with the effluent nitrite up to 20.4 {+/-} 6.4 mg N/L and the nitrite accumulation ratio was nearly 100% maintained for 140 days (420 cycles). Nitrosomonas was the dominant ammonia-oxidizing bacteria with relative abundance of 0.3-2.4% while nitrite-oxidizing bacteria were almost undetected (<0.1%). The introduction of extended anaerobic phase and high volatile fatty acid concentrations were proposed to be the potential selector forces to promote partial nitrification. This is the first study that combined EBPR with nitrite-accumulation for digested manure wastewater treatment, and it provided new sights in strategies to combine the EBPR and short-cut nitrogen removal via nitrite to achieve simultaneous nitrogen and phosphorus removal.


title: miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline

abstract: MicroRNAs and tRFs are classes of small non-coding RNAs, known for their roles in translational regulation of genes. Advances in next-generation sequencing (NGS) have enabled high-throughput small RNA-seq studies, which require robust alignment pipelines. Our laboratory previously developed miRge and miRge2.0, as flexible tools to process sequencing data for annotation of miRNAs and other small-RNA species and further predict novel miRNAs using a support vector machine approach. Although, miRge2.0 is a leading analysis tool in terms of speed with unique quantifying and annotation features, it has a few limitations. We present miRge3.0 which provides additional features along with compatibility to newer versions of Cutadapt and Python. The revisions of the tool include the ability to process Unique Molecular Identifiers (UMIs) to account for PCR duplicates while quantifying miRNAs in the datasets and an accurate GFF3 formatted isomiR tool. miRge3.0 also has speed improvements benchmarked to miRge2.0, Chimira and sRNAbench. Finally, miRge3.0 output integrates into other packages for a streamlined analysis process and provides a cross-platform Graphical User Interface (GUI). In conclusion miRge3.0 is our 3rd generation small RNA-seq aligner with improvements in speed, versatility, and functionality over earlier iterations.

category: bioinformatics


title: DBPOM: a comprehensive database of pharmaco-omics for cancer precision medicine

abstract: During the course of cancer treatment, both efficacy and the adverse effects of drugs on patients should be taken into account. Although some public databases and modeling frameworks have been developed through studies on drug response, the negative effects of drugs are always neglected. Furthermore, most of them only considered the ramifications of the drug on the cell line, but the effects on the patient still require a huge amount of work to integrate data from various databases and calculations, especially in relation to precision treatment. In order to address these issues, we developed the DBPOM (http://www.dbpom.net/, a comprehensive database of pharmaco-omics for cancer precision medicine), which explores various drugs efficacy levels by calculating their potency in reverse, or enhancing cancer-associated gene expression changes. When compared with existing databases, the DBPOM could estimate the effectiveness of a drug on individual patients through the mapping of various cell lines to each person according to their genetic mutation similarities. The DBPOM is an easy-to-use and one-stop database for clinicians and drug researchers to search and analyze the overall effect of a drug or a drug combination on cancer patients as well as the biological functions that they target. We anticipate that DBPOM will become an important resource and analysis platform for drug development, drug mechanism studies and the discovery of new therapies.


title: UniverSC: a flexible cross-platform single-cell data processing pipeline

abstract: Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.


title: Ectopic FVIII expression and misfolding in hepatocytes as a potential cause of human hepatocellular carcinoma

abstract:
Clotting factor VIII (FVIII) is the protein deficient in the bleeding disorder hemophilia A (HA). FVIII is a 330 kDa glycoprotein with a domain structure of A1-A2-B-A3-C1-C2. The B domain is dispensable for activity but in vivo hepatocyte transfection with B domain deleted (BDD) DNA vector resulted in FVIII misfolding, endoplasmic reticulum (ER) stress, and apoptosis in murine hepatocytes. In addition, mice exposed to transient ER stress through expression of a different misfolded protein and then fed a diet (HFD) for 9 months developed hepatocellular carcinoma (HCC). Therefore, we tested whether ectopic expression of BDD followed by HFD feeding may also cause HCC. Here we compared two FVIII variants with different folding efficiencies in the ER upon expression in hepatocytes in mice: 1) BDD; and 2) N6 which retains 226 amino acids from the B domain with 6 N-linked glycans that does not significantly aggregate or cause hepatocyte apoptosis. We directed transient expression of BDD or N6 from a DNA vector in hepatocytes of 6-week-old mice. One week later, mice were fed 60% HFD for 65 weeks. Remarkably, 100% of mice that received BDD vector developed liver tumors, whereas only 58% of mice that received N6 vector and none of the mice that received empty vector developed liver tumors. The findings suggest that increased protein misfolding in the ER can predispose to HCC in the context of a HFD. They also raise attention regarding the safety of ectopic expression of BDD in hepatocytes during FVIII gene therapy in humans.

Key pointsExpression of BDD FVIII in murine hepatocytes in vivo causes accumulation of misfolded FVIII aggregates in the endoplasmic reticulum.

Hepatocyte BDD expression with subsequent high-fat diet induces liver tumors that are reduced upon expression of a well-folded FVIII variant.

category: cancer biology


title: Lipophilic Nanocrystal Prodrug-Release Defines the Extended Pharmacokinetic Profiles of a Year-Long Cabotegravir

abstract: A single, once every eight-week cabotegravir (CAB) long-acting parenteral is more effective than daily oral emtricitabine and tenofovir disoproxil fumarate in preventing human immunodeficiency virus type one (HIV-1) transmission. Extending CAB dosing to a yearly injectable can advance efforts leading to the elimination of viral transmission. The current submission adds rigor, reproducibility and mechanistic insights for the extended apparent half-life of a yearlong antiretroviral injectable. Pharmacokinetic (PK) profiles of a nanoformulated fatty acid ester CAB prodrug (named NM2CAB) were affirmed at two academic and one contract research laboratory. PK profiles showed plasma CAB levels at or above the protein-adjusted 90% inhibitory concentration for up to one year after a single dose. Measures of drug biodistribution demonstrated sustained native drug at the muscle injection site and in lymphoid tissues (spleen and lymph nodes). The results paralleled NM2CAB uptake and retention in human macrophages. NM2CAB nanocrystals were stable in blood, tissue and liver homogenates. The long apparent drug half-life followed pH-dependent slow prodrug release in weeks from the nanocrystal. In contrast, solubilized prodrug was hydrolyzed in hours in plasma and tissues recorded from multiple mammalian species at basic pH. No measurable toxicities were recorded. These results, taken together, affirm the pharmacological mechanistic properties of a year-long nanoformulated CAB prodrug supporting the established protocol design for formulation safety, rigor and reproducibility.

category: pharmacology and toxicology


title: Sodium channel Nav1.2-L1342P variant displaying complex biophysical properties renders hyperexcitability of cortical neurons derived fromhuman iPSCs

abstract: With the wide adoption of whole-exome sequencing in children having seizures, an increasing number of SCN2A variants has been revealed as possible genetic causes of epilepsy. Voltage-gated sodium channel Nav1.2, encoded by gene SCN2A, is strongly expressed in the pyramidal excitatory neurons and supports action potential firing. One recurrent SCN2A variant is L1342P, which was identified in multiple patients with early-onset encephalopathy and intractable seizures. Our biophysical analysis and computational modeling predicted gain-of-function features of this epilepsy-associated Nav1.2 variant. However, the mechanism underlying L1342P mediated seizures and the pharmacogenetics of this variant in human neurons remain unknown. To understand the core phenotypes of the L1342P variant in human neurons, we took advantage of a reference human induced pluripotent stem cell (hiPSC) line, in which L1342P was engineered by CRISPR/Cas9 mediated genome-editing. Using patch-clamping and micro-electrode array (MEA) recording, we found that the cortical neurons derived from hiPSCs carrying heterozygous L1342P variant presented significantly increased intrinsic excitability, higher sodium current density, and enhanced bursting and synchronous network firing, showing clear hyperexcitability phenotypes. Interestingly, the L1342P neuronal culture displayed a degree of resistance to the anti-seizure medication (phenytoin), which likely recapitulated aspects of clinical observation of patients carrying the L1342P variant. In contrast, phrixotoxin-3 (PTx3), a Nav1.2 isoform-specific blocker, was able to potently alleviate spontaneous and chemical-induced hyperexcitability of neurons carrying the L1342P variant. Our results reveal a possible pathogenic underpinning of Nav1.2-L1342P mediated epileptic seizures, and demonstrate the utility of genome-edited hiPSCs as an in vitro platform to advance personalized phenotyping and drug discovery.

category: physiology


category: neuroscience


title: Untargeted metabolomic analyses reveal the diversity and plasticity of the specialized metabolome in seeds of different Camelina sativa varieties

abstract:
Despite the essential role of Specialized Metabolites (SMs) in the interaction of plants with the environment, studying the ability of crop seeds to produce these protective compounds has been neglected. Furthermore, seeds produce a myriad of SMs providing an interesting model to investigate their diversity and plasticity. Camelina sativa gained a lot of interest in the past few years as rustic oil seed crop. A characterization of seed SM landscapes in six camelina genotypes grown in the field and harvested during five growing seasons has been undertaken in this work. This allowed a comprehensive annotation of seed SMs combining analyses that cluster SMs based on their chemical structures and co-accumulation patterns. These data showed broad effects of the environment on the stimulation of the seed-specialized metabolome. Among well annotated compounds, flavonols were identified as the metabolic class characterised by high plasticity, revealing significant variable accumulation according to the year and/or the genotype. Lastly, a deeper characterisation of primary metabolites and lipids in two selected genotypes has been performed. We showed that, in addition to flavonols, alkaloids and glucosinolates displayed a higher phenotypic plasticity with respect to most of the primary metabolites, including some sugars and major storage compounds such as fatty acids, proteins and most lipid classes (e.g. DAG, TAG), but similar plasticity compared to free aminoacids and carboxylic acids. This work highlighted major and unexplored effects of the environment on the seed specialized metabolome demonstrating that seeds exhibit a dynamic and plastic metabolism, with an impact on seed quality.

Significance statementSeeds produce a myriad of Specialized Metabolites (SMs) with an essential role in the interaction of plants with the environment. We characterized SM landscapes, primary metabolites and lipid composition in the seeds of camelina genotypes grown in the open field in five consecutive growing seasons. Our results showed the predominant effect of the environment on the regulation of the seed - specialized metabolome, with a potential impact on seed quality of camelina that may also occur in other oilseed crops.

category: plant biology


title: Untargeted metabolomic analyses reveal the diversity and plasticity of the specialized metabolome in seeds of different Camelina sativa genotypes


title: Identifying neuron subtype-specific metabolic network changes in single cell transcriptomics of Alzheimer's Disease using perturb-Met

abstract: Metabolic aberrations are a prominent feature of Alzheimers Disease (AD). Different neuronal subtypes have selective vulnerability in AD. Despite the recent advance of single cell and single nucleus RNA-seq of AD brains, genome-scale metabolic network changes in neuronal subtypes have not been systematically studied with detail. To bridge this knowledge gap, I developed a computational method called perturb-Met that can uncover transcriptional dysregulation centered at hundreds of metabolites in a metabolic network. perturb-Met successfully recapitulated known glycolysis, cholesterol, and other metabolic defects in APOE4-neurons and microglia, many of which are missed by current methods. Applying perturb-Met on AD snRNA-seq data, I revealed that the four neuronal subtypes in the entorhinal cortex shows subtype-specific metabolic changes, namely mitochondrial complex I metabolism, ganglioside metabolism, galactose and heparan sulfate metabolism, as well as glucose and lipid metabolism, respectively. perturb-Met also revealed significant changes in protein glycosylation in the neuron subtype specifically found in AD brains. These subtype-specific metabolic changes may potentially underlie their selective vulnerability in AD. perturb-Met is a valuable tool to discover potential metabolic network changes in many other single cell or bulk transcriptomic studies.

category: systems biology


title: ΔFBA: Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data

abstract: Genome-scale metabolic models (GEMs) provide a powerful framework for simulating the entire set of biochemical reactions occurring in a cell. Constraint-based modeling tools like flux balance analysis (FBA) developed for the purposes of predicting metabolic flux distribution using GEMs face considerable difficulties in estimating metabolic flux alterations between experimental conditions. Particularly, the most appropriate metabolic objective for FBA is not always obvious, likely context-specific, and not necessarily the same between conditions. Here, we propose a new method, called {Delta}FBA (deltaFBA), that employs constraint-based modeling, in combination with differential gene expression data, to evaluate changes in the intracellular flux distribution between two conditions. Notably, {Delta}FBA does not require specifying the cellular objective to produce the flux change predictions. We showcased the performance of {Delta}FBA through several case studies involving the prediction of metabolic alterations caused by genetic and environmental perturbations in Escherichia coli and caused by Type-2 diabetes in human muscle.


title: Drosophila local search emerges from iterative odometry of consecutive run lengths.

abstract: The ability to keep track of ones location in space is a critical behavior for animals navigating to and from a salient location, and its computational basis is now beginning to be unraveled. Here, we tracked flies in a ring-shaped channel as they executed bouts of search triggered by optogenetic activation of sugar receptors. Unlike experiments in open field arenas, which produce highly tortuous search trajectories, our geometrically constrained paradigm enabled us to monitor flies decisions to move toward or away from the fictive food. Our results suggest that flies use path integration to remember the location of a food site even after it has disappeared, and that flies can remember the location of a former food site even after walking around the arena one or more times. To determine the behavioral algorithms underlying Drosophila search, we developed multiple state transition models and found that flies likely accomplish path integration by combining odometry and compass navigation to keep track of their position relative to the fictive food. Our results indicate that whereas flies re-zero their path integrator at food when only one feeding site is present, they adjust their path integrator to a central location between sites when experiencing food at two or more locations. Together, this work provides a simple experimental paradigm and theoretical framework to advance investigations of the neural basis of path integration.


title: Drosophila re-zero their path integrator at the center of a fictive food patch


title: SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma

abstract: SARS-CoV-2 501Y.V2 (B.1.351), a novel lineage of coronavirus causing COVID-19, contains substitutions in two immunodominant domains of the spike protein. Here, we show that pseudovirus expressing 501Y.V2 spike protein completely escapes three classes of therapeutically relevant antibodies. This pseudovirus also exhibits substantial to complete escape from neutralization, but not binding, by convalescent plasma. These data highlight the prospect of reinfection with antigenically distinct variants and foreshadows reduced efficacy of spike-based vaccines.

category: immunology


title: ACVR1R206H increases osteogenic/ECM gene expression and impairs myofiber formation in human skeletal muscle stem cells

abstract: Abnormalities in skeletal muscle repair lead to poor function and complications such as scarring or heterotopic ossification (HO). Here, we use fibrodysplasia ossificans progressiva (FOP), a disease of progressive HO caused by ACVR1R206H (Activin receptor type-1 receptor) mutation, to elucidate how ACVR1 affects skeletal muscle repair. Rare and unique primary FOP human muscle stem cells (Hu-MuSCs) isolated from cadaveric skeletal muscle demonstrated increased ECM marker expression, and showed skeletal muscle-specific impaired engraftment and regeneration ability. Human induced pluripotent stem cell (iPSC)-derived muscle stem/progenitor cells (iMPCs) Single cell transcriptome analyses from FOP also revealed unusually increased ECM and osteogenic marker expression compared to control iMPCs. These results show that iMPCs can recapitulate many aspects of Hu-MuSCs for detailed in vitro study, that ACVR1 is a key regulator of Hu-MuSC function and skeletal muscle repair; and that ACVR1 activation in iMPCs or Hu-MuSCs contributes to HO by changing the local tissue environment.


title: Single-cell trajectory inference guided enhancement of thyroidmaturation in vitro using TGF-beta inhibition

abstract: The thyroid gland regulates metabolism and growth via secretion of thyroid hormones by thyroid follicular cells (TFCs). Loss of TFCs, by cellular dysfunction, autoimmune destruction or surgical resection, underlies hypothyroidism. Recovery of thyroid hormone levels by transplantation of mature TFCs derived from stem cells in vitro holds great therapeutic promise. However, the utilization of in vitro derived tissue for regenerative medicine is restricted by the efficiency of differentiation protocols to generate mature organoids. Here, to improve the differentiation efficiency for thyroid organoids, we utilized single-cell RNA-Seq to chart the molecular steps undertaken by individual cells during the in vitro transformation of mouse embryonic stem cells to TFCs. Our single-cell atlas of mouse organoid systematically and comprehensively identifies, for the first time, the cell types generated during production of thyroid organoids. Using pseudotime analysis, we identify TGF-beta and planar-cell polarity (PCP) pathways as regulators of thyroid maturation in vitro. Using pharmacological manipulation of TGF-beta pathway, we improve the level of thyroid maturation, in particular the induction of Nis expression. This in turn, leads to an enhancement of iodide organification in vitro, suggesting functional improvement of the thyroid organoid. Our study highlights the potential of single-cell molecular characterization in understanding and improving thyroid maturation and paves the way for identification of therapeutic targets against thyroid disorders.


title: Highly accurate barcode and UMI error correction using dual nucleotide dimer blocks allows direct single-cell nanopore transcriptome sequencing

abstract: Droplet-based single-cell sequencing techniques have provided unprecedented insight into cellular heterogeneities within tissues. However, these approaches only allow for the measurement of the distal parts of a transcript following short-read sequencing. Therefore, splicing and sequence diversity information is lost for the majority of the transcript. The application of long-read Nanopore sequencing to droplet-based methods is challenging because of the low base-calling accuracy currently associated with Nanopore sequencing. Although several approaches that use additional short-read sequencing to error-correct the barcode and UMI sequences have been developed, these techniques are limited by the requirement to sequence a library using both short- and long-read sequencing. Here we introduce a novel approach termed single-cell Barcode UMI Correction sequencing (scBUC-seq) to efficiently error-correct barcode and UMI oligonucleotide sequences synthesized by using blocks of dimeric nucleotides. The method can be applied to correct either short-read or long-read sequencing, thereby allowing users to recover more reads per cell and permits direct single-cell Nanopore sequencing for the first time. We illustrate our method by using species-mixing experiments to evaluate barcode assignment accuracy and evaluate differential isoform usage and fusion transcripts using myeloma and sarcoma cell line models.


title: Comparative and Stability Study of Glucose Concentrations Measured in Sodium Fluoride and Serum Separator tubes

abstract:
IntroductionSodium fluoride/potassium oxalate (NaF/KOx) tubes were once regarded as the gold-standard tubes for glucose analysis. Even though their ineffectiveness in immediately inhibiting glycolysis has been reported in several studies especially in the first 1-4hours, they are still used in our clinical Biochemistry laboratory for glucose measurement. However in its absence, only SSTs are employed for glucose measurement.

AimTo determine whether SSTs can replace NaF/KOx tubes for laboratory-based measurement of blood glucose and to assess the stability of glucose concentrations for 3 days period

MethodsDuring the study period (1 March to 11 April, 2015), a total of 50 paired samples collected separately in NaF/KOx tubes and SSTs from healthy adult participants in the Gambia Adults Reference Intervals Study (GARIS) project were used as the project sample size. The samples were analysed within 2hours, and at 24hours, 42hours and 72hours time-points following blood collection and separation using Vitros 350 dry chemistry analyser. The GARIS samples were treated as clinical samples.

ResultsThere was no significant difference in the mean glucose concentrations between the two tubes (Mean difference= 0.06mmol/L; P=0.38) recorded in the different time-points. Using growth trajectory and mixed effects model, the study data showed no significant change in the glucose concentrations (p=0.25) for three days period.

ConclusionsThe study confirms that SSTs can produce similar glucose results when employed in the absence of NaF/KOx tubes. Besides, the glucose concentrations were stable in both tubes for three days when the samples were separated within two hours and refrigerated in 2-8{degrees}C.


title: Development and validation of an LC-MS/MS method for determination of B vitamins and some its derivatives in whole blood

abstract:
Obligate symbiotic bacteria associated with the insects feeding exclusively on vertebrate blood are supposed to complement B vitamins presumably lacking in their diet, vertebrate blood. Recent genomic analyses revealed considerable differences in biosynthetic capacities across different symbionts, indicating that levels of B vitamins vary across different vertebrate hosts. However, a rigorous determination of B vitamins content in blood of various vertebrates has not yet been approached. A reliable analytical method focused on B vitamin complex in blood and hemolymph can provide valuable informative background and understanding of general principles of insect symbiosis.

In this work chromatographic separation of a mixture of eight B vitamins (B1 - thiamine, B2 - riboflavin, B3 - niacin, B5 - pantothenic acid, B6 - pyridoxine, B7 - biotin, B9 - folic acid and B12 - cyanocobalamine), four B vitamin derivatives (B3 - niacinamide, B6 - pyridoxal-5-phosphate, B6 - 4-pyridoxic acid and B9 - tetrahydrofolic acid) and 3 stable isotope labelled internal standards (B3 - niacin-13C6, B5 - pantothenic acid (di-{beta}-alanine-13C6,15N2) and B7 - biotin-(ring-6,6-d2)) on C30 column was developed. Detection was carried out using dual-pressure linear ion trap mass spectrometer in FullScan MS/MS and SIM mode. Matching internal standards with analytes was done according to the results of linearity, accuracy and precision. Except for vitamin B9 (tetrahydrofolic acid) instrument quantitation limits of all analytes were ranging from 0.42 to 5.0 g/L, correlation coefficients from 0.9997 to 1.0000 and QC coefficients from 0.53 to 3.2 %.

Optimization of whole blood sample preparation step was focused especially on evaluation of two types of protein-precipitation agents: trichloroacetic acid and zinc sulphate in methanol. Samples of whole blood prepared in six independent replicates were spiked at 10 g/L and 100 g/L level. The best results were obtained for zinc sulphate in methanol, but only nine analytes (B1 - thiamine, B2 - riboflavin, B3 - niacin, B3 - niacinamide, B5 - pantothenic acid, B6 - pyridoxine, B6 - 4-pyridoxic acid, B7 - biotin and B12 - cyanocobalamine) were successfully validated. Accuracy of the procedure using this protein-precipitating agent was ranging from 89 to 120 %, precision from 0.5 to 13 % and process efficiency from 65 to 108 %.

HighlightsO_LILC-MS/MS method for quantitation of eight B vitamins and four B vitamin derivatives was developed.
C_LIO_LIDeproteinization agents trichloroacetic acid and ZnSO4/methanol were tested for protein precipitation of whole blood.
C_LIO_LIAccuracy, precision and process efficiency were evaluated.
C_LIO_LISuccessful method validation for seven B vitamins and two B vitamin derivatives in whole blood.
C_LI


title: 2-kupl: mapping-free variant detection from DNA-seq data of matched samples

abstract: The detection of genome variants, including point mutations, indels and structural variants, is a fundamental and challenging computational problem. We address here the problem of variant detection between two deep-sequencing (DNA-seq) samples, such as two human samples from an individual patient, or two samples from distinct bacterial strains. The preferred strategy in such a case is to align each sample to a common reference genome, collect all variants and compare these variants between samples. Such mapping-based protocols have several limitations. DNA sequences with large indels, aggregated mutations and structural variants are hard to map to the reference. Furthermore, DNA sequences cannot be mapped reliably to genomic low complexity regions and repeats. Herein, we introduce 2-kupl, a k-mer based, mapping-free protocol to detect variants between two DNA-seq samples. On simulated and actual data, 2-kupl achieves a higher precision than other mapping-free protocols. Applying 2-kupl to prostate cancer whole exome data, we identify a number of candidate variants in hard-to-map regions and propose potential novel recurrent variants in this disease.


title: Impact of an alpha helix and a cysteine-cysteine disulfide bond on the resistance of bacterial adhesion pili to stress

abstract:
Escherichia coli express adhesion pili that mediate attachment to host cell surfaces that are exposed to body fluids in the urinary and gastrointestinal tracts. Pilin subunits are organized into helical polymers, with a tip adhesin for specific host binding. Pili can elastically unwind when exposed to fluid flow force, reducing the adhesin load, thereby facilitating sustained attachment. Here we investigate biophysical and structural differences of pili commonly expressed on bacteria that inhabit the urinary and intestinal tracts. Optical tweezers measurements reveal that Class 1 pili of uropathogenic E. coli (UPEC), as well as Class 1b of enterotoxigenic E. coli (ETEC), undergo an additional conformational change beyond pilus unwinding, providing significantly more elasticity to their structure than ETEC Class 5 pili. Looking comprehensively at structural and steered molecular dynamics simulation data, we find this difference in Class 1 pili subunit behavior originates from an -helical motif that can unfold when exposed to force. A disulfide bond cross-linking {beta}-strands in Class 1 pili stabilizes subunits, allowing them to tolerate higher forces than Class 5 pili that lack this covalent bond. We suggest that these extra contributions to pilus resiliency are relevant for the UPEC niche since resident bacteria are exposed to stronger, more transient shear forces compared to those experienced by ETEC bacteria in the mucosa of the intestinal tract. Interestingly, Class 1b ETEC pili include the same structural features seen in UPEC pili, while requiring lower unwinding forces that are more similar to those of Class 5 ETEC pili.

Significance StatementAdhesion pili are often essential virulence factors for attachment of pathogenic bacteria in specific environmental niches. We provide mechanistic details of structural differences impacting the biophysical properties of pili found on bacteria in the urinary and intestinal tracts. We see that pili from urinary tract bacteria are composed of subunits optimized for their microenvironment. First, they can tolerate higher forces than intestinal pili due to a disulfide bond that limits subunit unfolding. Second, their greater flexibility is due to an -helical motif that can unfold, absorbing force that could otherwise lead to bacteria detachment. Our work provides insight into the central role of pilus structural and biophysical properties for the sustained bacterial adherence necessary to initiate disease.

category: biophysics


title: Introducing Novel Molecular-based Method for Quantification of Homologous Recombination Efficiency

abstract:
BackgroundHomologous recombination (HR) pathway is a DNA double-stranded breaks repair pathway well-known for its high level of accuracy. Low HR pathway efficiency clinically known as homologous recombination deficiency (HRD) was identified in some cancers such as breast and ovarian cancers and studies have reported the sensitivity of HRD cancer cells to DNA repair inhibitors such as Olaparib. However, current techniques including immunofluorescence-based technique are qualitative-based, hence lack sensitivity to determine the functionality of HR pathway. Additionally, some of the techniques including gene expression arrays require expression study of wide range genes involve in HR pathway, which is not cost-effective. The aim of the study is to optimise a PCR-based assay (Norgens Homologous Recombination kit) that can be employed to quantitate HR efficiency in cells, which accurately reflects the functional status of HR pathway.

Methods and FindingsThe kit has two test plasmids (dl-1 and dl-2) with partial deletions in the LacZ gene and the plasmids are generated from modification of pUC19. HR-proficient (HeLa and AsPC-1) and HR-deficient (CAPAN-1 cells) cancer cell lines were transfected with the two plasmids to generate functional LacZ gene (i.e. recombinant product). The recombinant product was quantified by real-time PCR. Although recombinant product was generated in all the cell lines, our real-time PCR demonstrated a high quantity of recombinant product in HeLa cell line whilst low quantity in CAPAN-1 and AsPC-1 cell lines. The quantity of recombinant product generated and quantified reflects HR pathway efficiency.

ConclusionOverall, the results have provided some evidence that the PCR-based kit can be suitably employed for quantification of HR efficiency provided appropriate transfection method and reagent are used. However, further study is required to confirm HR efficiency status of AsPC-1 cells to ascertain the low HR efficiency detected by the kit in these cells.


title: Defining the cell surface proteomic landscape of multiple myeloma reveals immunotherapeutic strategies and biomarkers of drug resistance

abstract: The myeloma cell surface proteome ("surfaceome") not only determines tumor interaction with the microenvironment but serves as an emerging arena for therapeutic development. Here, we use glycoprotein capture proteomics to first define surface markers most-enriched on myeloma when compared to B-cell malignancy models, revealing unexpected biological signatures unique to malignant plasma cells. We next integrate our proteomic dataset with existing transcriptome databases, nominating CCR10 and TXNDC11 as possible monotherapeutic targets and CD48 as a promising co-target for increasing avidity of BCMA-directed cellular therapies. We further identify potential biomarkers of resistance to both proteasome inhibitors and lenalidomide including changes in CD53, EVI2B, CD10, and CD33. Comparison of short-term treatment with chronic resistance delineates large differences in surface proteome profile under each type of drug exposure. Finally, we develop a miniaturized version of the surface proteomics protocol and present the first surface proteomic profile of a primary myeloma patient plasma cell sample. Our dataset provides a unique resource to advance the biological, therapeutic, and diagnostic understanding of myeloma.


title: Effect of Leaf Aqueous Extract of Manilkara hexandra on Digestive and Glucose Metabolic Enzymes, and Serum Glucose Level in Labeo rohita Fingerlings

abstract: Manilkara hexandra (Roxb.) Dubard (common name Khirni, family: Sapotaceae) is an evergreen traditionally used medicinal plant. The present study aimed to see the effects of leaf aqueous extract of M. hexandra (LAEMH) on digestive and glucose metabolic enzyme action and serum glucose level in rohu, Labeo rohita, fingerlings. Experimental fish were fed a basal diet (Group I), and diets supplemented with LAEMH at 300 mg (Group II) and 600 mg (Group III) kg-1body weight. A significant reduction in serum glucose was noticed in the treated groups when compared with the control group. The reduced amylase activity was noticed in the treated fingerlings in a dose-dependent manner. However, lipase and protease activities didnt differ significantly among the experimental groups. Reduced serum glucose level might be correlated with the decline in the activity of digestive amylase in fish. Group II (3.35{+/-}0.19 U) and Group III (3.49{+/-}0.13 U) were recorded with reduced glucose-6-phosphatase activities than the control group (4.4{+/-}0.39 U). Moreover, the study revealed a decline in fructose-1,6-phosphatase activities in the treated groups in comparison to the control group. The decline in the activities of the metabolic enzymes might be associated with the non-availability of glucose owing to reduced activity of the digestive amylase in the treated groups. In conclusion, the present study established the hypoglycaemic effect of the leaf aqueous extract of M. hexandra in a fish model.


title: Leaf Aqueous Extract of Manilkara hexandra influenced Glucose Metabolism in fish: An observation with Labeo rohita Fingerlings as model organism


title: Adipocyte deletion of the RNA binding protein HuR induces cardiac hypertrophy and fibrosis

abstract:
Adipose tissue continues to gain appreciation for its broad role as an endocrine organ, and disruptions in adipose tissue homeostasis plays a central role in cardiovascular physiology. We have previously shown that expression of the RNA binding protein HuR in adipose tissue mediates energy expenditure, but the potential cardiovascular impacts of this finding have not been explored. We show here that adipose tissue-specific deletion of HuR (Adipo-HuR-/-) is sufficient to induce the spontaneous development of cardiac hypertrophy and fibrosis. Hearts from Adipo-HuR-/- mice have increased left ventricular (LV) ejection fraction, rate of pressure generation, and LV posterior wall thickness that is accompanied by an increase in LV/body weight ratio and hypertrophic gene expression. Furthermore, Adipo-HuR-/- hearts display increased fibrosis by picrosirius red staining and periostin expression. To identify underlying mechanisms, we applied both RNA-seq and weighted gene co-expression network analysis (WGCNA) to define HuR-dependent changes in gene expression as well as significant relationships between adipose tissue gene expression and LV mass. RNA-seq results demonstrate a significant increase in pro-inflammatory gene expression in the subcutaneous white adipose tissue (scWAT) from Adipo-HuR-/- mice that is accompanied by an increase in serum levels of both TNF- and IL-6. WGCNA identified a significant enrichment in inflammation, apoptosis/cell death, and vesicle-mediated transport genes among those whose expression most significantly associated with CVD in Adipo-HuR-/-. In conclusion, we demonstrate that the loss of HuR expression in adipose tissue promotes the development of cardiac hypertrophy and fibrosis, potentially through modulation of inflammation and vesicle-mediated transport in scWAT.

NEW AND NOTEWORTHYThis work demonstrates the spontaneous development of cardiac hypertrophy and fibrosis upon adipose tissue-specific deletion of the RNA binding protein HuR that appears to be mechanistically driven by HuR-dependent changes in inflammatory and extracellular vesicle transport mediating genes in the subcutaneous white adipose tissue. These results suggest that loss of HuR expression in adipose tissue in obesity, as demonstrated in mouse and humans by our group and others, may contribute to obesity-mediated CVD.


title: Extinction of the Thylacine

abstract: Like the Dodo and Passenger Pigeon before it, the predatory marsupial Thylacine (Thylacinus cynocephalus), or  Tasmanian tiger, has become an iconic symbol of human-caused extinction. The last captive animal died in 1936, but even today reports of the Thylacines possible ongoing survival in remote regions of Tasmania are newsworthy and capture the publics imagination. Extirpated from mainland Australia in the mid-Holocene, the large island of Tasmania became the species final stronghold. Following European settlement in the 1800s, the Thylacine was heavily persecuted and pushed to the margins of its range, although many sightings were reported thereafter--even well beyond the 1930s. To gain a new depth of insight into the extinction of the Thylacine, we assembled an exhaustive database of 1,237 observational records from Tasmania (from 1910 onwards), quantified their uncertainty, and charted the patterns these revealed. We also developed a new method to visualize the species 20th-century spatio-temporal dynamics, to map potential post-bounty refugia and pinpoint the most-likely location of the final persisting subpopulation. A direct reading of the high-quality records (confirmed kills and captures, in combination with sightings by past Thylacine hunters and trappers, wildlife professionals and experienced bushmen) implies a most-likely extinction date within four decades following the last capture (i.e., 1940s to 1970s). However, uncertainty modelling of the entire sighting record, where each observation is assigned a probability and the whole dataset is then subject to a sensitivity analysis, suggests that extinction might have been as recent as the late 1980s to early 2000s, with a small chance of persistence in the remote south-western wilderness areas. Beyond the intrinsically fascinating problem of reconstructing the final fate of the Thylacine, the new spatio-temporal mapping of extirpation developed herein would also be useful for conservation prioritization and search efforts for other rare taxa of uncertain status.

category: zoology


title: Resolving when (and where) the Thylacine went extinct


title: Pest control strategies after first signs of invasive black rat: case study in the Community of Madrid

abstract:
Rodents are animals that provoke special concern in the rural and urban areas as may cause potential damage in facilities and infrastructures as well as social alarm. The control of rodent populations is based on prevention and on what it has been called an "Integrated Pest Management" strategy. The most important species affected by this strategy are brown rat (Rattus norvegicus), black rat (Rattus rattus L.) and mouse (Mus musculus). In the present work, our original objective was to monitor changes in status or range of rodent species in the Community of Madrid (Spain). We conducted in coordination with the professional organization of Pest Control Operators "ANECPLA" a procedure designed to obtain faecal samples in locations with rodenticide treatment. Determination of pest specie was based on cytochrome b (cytb) sequences and phylogenetic analysis. We received samples from a variety of locations in which a rodenticide treatment was applied due to infestation or to citizen notice. While we recorded a number of data about the distribution of brown rat the presence of black rat was unexpectedly discovered. The detection of this species implies changes in pest control strategies to improve the results in the application of rodenticides available in the market.

Key MessageRodent pest control is a key issue but little is known about Spanish populations. We aimed to know how many rat species there are in Central Spain, specifically in the Community of Madrid. We found for the first time the presence of black rat and a new wild strain of brown rat in this area. These findings have change the strategies of rodent treatment and stresses the importance of population studies for a better control.


title: VEGF-A/VEGFR-1: a painful astrocyte-mediated signaling blocked by the anti-VEGFR-1 mAb D16F7

abstract: Chemotherapy-induced neuropathic pain is a clinically relevant adverse effect of several anticancer drugs leading to dose reduction or therapy discontinuation. The lack of knowledge about the mechanisms of neuropathy development and pain chronicization makes chemotherapy-induced neuropathic pain treatment an unmet medical need. In this context, the vascular endothelial growth factor A (VEGF-A) has emerged as a neurotoxicity biomarker in a model of chemotherapy-induced neuropathy, and its decrease has been related to pain relief. Aim of this study was to clarify the VEGF-A-dependent pain signaling in the CNS for individuating new targeted therapeutic approaches. In mice, the intrathecal infusion of VEGF-A induced a dose-dependent noxious hypersensitivity mediated by the VEGF receptor 1 (VEGFR-1) as demonstrated by pharmacological and genetic tools. In electrophysiological study, VEGF-A stimulated the spinal nociceptive neurons activity through VEGFR-1. In the dorsal horn of the spinal cord, VEGF-A increased in astrocytes of animals affected by neuropathy suggesting this cell population as a source of the potent pain mediator. Accordingly, the selective knockdown of astrocytic VEGF-A, by shRNAmir, blocked the development of oxaliplatin-induced neuropathic pain. Besides, the anti-VEGFR-1 mAb D16F7 (previously described as anticancer) effectively relieved neuropathic pain induced by chemotherapeutic agents. In conclusion, astrocyte-released VEGF-A is a new player in the complex neuron-glia network that oversees physiological and pathological pain and D16F7 mAb rises as a potent pain killer strategy.


title: Function-structure Coupling：White matter fMRI hyper-activation associates with structural integrity reductions in schizophrenia

abstract:
BackgroundWhite matter (WM) microstructure deficit may be an underlying factor in the brain dysconnectivity hypothesis of schizophrenia using diffusion tensor imaging (DTI). However, WM dysfunction is unclear in schizophrenia. This study aimed to investigate the association between structural deficits and functional disturbances in major WM tracts in schizophrenia.

MethodsUsing functional magnetic resonance imaging (fMRI) and DTI, we developed the skeleton-based white matter functional analysis, which could achieve voxel-wise function-structure coupling by projecting the fMRI signals onto a skeleton in WM. We measured the fractional anisotropy (FA) and WM low-frequency oscillation activation and their couplings in ninety-three schizophrenia patients and 122 healthy controls (HCs). An independent open database (62 schizophrenia patients and 71 HCs) was used to test the reproducibility. Finally, associations between WM activations and five behaviour assessment categories (cognition, emotion, motor, personality and sensory) were examined.

ResultsThis study revealed a reversed pattern of structure and function in frontotemporal tracts, as follows. (1) WM hyper-activation was associated with reduced FA in schizophrenia. (2) The function-structure association was positive in healthy controls but negative in schizophrenia patients. Furthermore, function-structure dissociation was exacerbated by long illness duration and severe negative symptoms. (3) WM activations were significantly related to cognition and emotion.

ConclusionsThis study indicated function-structure dys-coupling, with higher functional activation and reduced structural integration in frontotemporal WM, which may reflect a potential mechanism in WM neuropathologic processing of schizophrenia.


title: Neuroprotective derivatives of tacrine that target NMDA receptor and acetyl cholinesterase - Design, synthesis and biological evaluation

abstract: The complex and multifactorial nature of neuropsychiatric diseases demands multi-target drugs that can intervene with various sub-pathologies underlying disease progression. Targeting the impairments in cholinergic and glutamatergic neurotransmissions with small molecules has been suggested as one of the potential disease-modifying approaches for Alzheimers disease (AD). Tacrine, apotent inhibitor of acetylcholinesterase (AChE) is the first FDA approved drug for the treatment of AD. Tacrine is also a low affinity antagonist of N-methyl-D-aspartate receptor (NMDAR). However, tacrine was withdrawn from its clinical use later due to its hepato-toxicity. With an aim to develop novel high affinity multi-target directed ligands (MTDLs) against AChE and NMDAR, with reduced hepatotoxicity, we performed in silico structure-based modifications on tacrine, chemical synthesis of the derivatives and in vitro validation of their activities. Nineteen such derivatives showed inhibition with IC50 values in the range of 18.53{+/-}2.09 to 184.09{+/-}19.23 nM against AChE and 0.27{+/-}0.05 to 38.84{+/-}9.64 M against NMDAR. Some of the selected compounds also protected rat primary cortical neurons from glutamate induced excitotoxicity. Two of the tacrine derived MTDLs, 201 and 208 exhibited in vivo efficacy in rats by protecting against behavioral impairment induced by administration of the excitotoxic agent, monosodium glutamate. Additionally, several of these synthesized compounds also exhibited promising inhibitory activities against butyrylcholinesterase and {beta}-secretase. Given the therapeutic potential of MTDLs in disease-modifying therapy, our studies revealed several promising MTDLs of which 201 appears to be a potential candidate for immediate preclinical and clinical evaluations.


title: Neutralization of SARS-CoV-2 lineage B.1.1.7 pseudovirus by BNT162b2 vaccine-elicited human sera

abstract: Recently, a new SARS-CoV-2 lineage called B.1.1.7 has emerged in the United Kingdom that was reported to spread more efficiently than other strains. This variant has an unusually large number of mutations with 10 amino acid changes in the spike protein, raising concerns that its recognition by neutralizing antibodies may be affected. Here, we investigated SARS-CoV-2-S pseudoviruses bearing either the Wuhan reference strain or the B.1.1.7 lineage spike protein with sera of 16 participants in a previously reported trial with the mRNA-based COVID-19 vaccine BNT162b2. The immune sera had equivalent neutralizing titers to both variants. These data, together with the combined immunity involving humoral and cellular effectors induced by this vaccine, make it unlikely that the B.1.1.7 lineage will escape BNT162b2-mediated protection.


title: mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants

abstract: To date severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected over 100 million individuals resulting in over two million deaths. Many vaccines are being deployed to prevent coronavirus disease 2019 (COVID-19) including two novel mRNA-based vaccines1,2. These vaccines elicit neutralizing antibodies and appear to be safe and effective, but the precise nature of the elicited antibodies is not known3-6. Here we report on the antibody and memory B cell responses in a cohort of 20 volunteers who received either the Moderna (mRNA-1273) or Pfizer-BioNTech (BNT162b2) vaccines. Consistent with prior reports, 8 weeks after the second vaccine injection volunteers showed high levels of IgM, and IgG anti-SARS-CoV-2 spike protein (S) and receptor binding domain (RBD) binding titers3,5,6. Moreover, the plasma neutralizing activity, and the relative numbers of RBD-specific memory B cells were equivalent to individuals who recovered from natural infection7,8. However, activity against SARS-CoV-2 variants encoding E484K or N501Y or the K417N:E484K:N501Y combination was reduced by a small but significant margin. Consistent with these findings, vaccine-elicited monoclonal antibodies (mAbs) potently neutralize SARS-CoV-2, targeting a number of different RBD epitopes in common with mAbs isolated from infected donors. Structural analyses of mAbs complexed with S trimer suggest that vaccine- and virus-encoded S adopts similar conformations to induce equivalent anti-RBD antibodies. However, neutralization by 14 of the 17 most potent mAbs tested was reduced or abolished by either K417N, or E484K, or N501Y mutations. Notably, the same mutations were selected when recombinant vesicular stomatitis virus (rVSV)/SARS-CoV-2 S was cultured in the presence of the vaccine elicited mAbs. Taken together the results suggest that the monoclonal antibodies in clinical use should be tested against newly arising variants, and that mRNA vaccines may need to be updated periodically to avoid potential loss of clinical efficacy.


title: Rapid protection from COVID-19 in nonhuman primates vaccinated intramuscularly but not intranasally with a single dose of a recombinant vaccine

abstract:
The ongoing pandemic of Coronavirus disease 2019 (COVID-19) continues to exert a significant burden on health care systems worldwide. With limited treatments available, vaccination remains an effective strategy to counter transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent discussions concerning vaccination strategies have focused on identifying vaccine platforms, number of doses, route of administration, and time to reach peak immunity against SARS-CoV-2. Here, we generated a single dose, fast-acting vesicular stomatitis virus-based vaccine derived from the licensed Ebola virus (EBOV) vaccine rVSV-ZEBOV, expressing the SARS-CoV-2 spike protein and the EBOV glycoprotein (VSV-SARS2-EBOV). Rhesus macaques vaccinated intramuscularly (IM) with a single dose of VSV-SARS2-EBOV were protected within 10 days and did not show signs of COVID-19 pneumonia. In contrast, intranasal (IN) vaccination resulted in limited immunogenicity and enhanced COVID-19 pneumonia compared to control animals. While IM and IN vaccination both induced neutralizing antibody titers, only IM vaccination resulted in a significant cellular immune response. RNA sequencing data bolstered these results by revealing robust activation of the innate and adaptive immune transcriptional signatures in the lungs of IM-vaccinated animals only. Overall, the data demonstrates that VSV-SARS2-EBOV is a potent single-dose COVID-19 vaccine candidate that offers rapid protection based on the protective efficacy observed in our study.

One sentence summaryVSV vaccine protects NHPs from COVID-19 in 10 days

category: microbiology


title: Native-like SARS-CoV-2 spike glycoprotein expressed by ChAdOx1 nCoV-19/AZD1222 vaccine

abstract: Vaccine development against the SARS-CoV-2 virus focuses on the principal target of the neutralizing immune response, the spike (S) glycoprotein. Adenovirus-vectored vaccines offer an effective platform for the delivery of viral antigen, but it is important for the generation of neutralizing antibodies that they produce appropriately processed and assembled viral antigen that mimics that observed on the SARS-CoV-2 virus. Here, we describe the structure, conformation and glycosylation of the S protein derived from the adenovirus-vectored ChAdOx1 nCoV-19/AZD1222 vaccine. We demonstrate native-like post-translational processing and assembly, and reveal the expression of S proteins on the surface of cells adopting the trimeric prefusion conformation. The data presented here confirms the use of ChAdOx1 adenovirus vectors as a leading platform technology for SARS-CoV-2 vaccines.


title: Transcriptomic analysis reveals niche gene expression effects of beta-hydroxybutyrate in primary myotubes

abstract: Various forms of fasting, including time-restricted feeding, alternate day fasting, and periodic fasting have shown promise in clinical and pre-clinical studies to normalize body weight, improve metabolic health, and protect against disease. Recent studies suggest that {beta}-hydroxybutyrate ({beta}OHB), a characteristic ketone body of the fasted metabolic state, acts as a potential signaling molecule mediating the beneficial effects of the various forms of fasting, potentially by acting as a histone deacetylase inhibitor. In the first part we investigated whether {beta}OHB, in comparison to the well-established histone deacetylase inhibitor butyrate, influences cellular differentiation in vitro. In C2C12 myotubes, 3T3-L1 adipocytes, and THP-1 monocytes, millimolar concentrations of {beta}OHB did not alter differentiation, as determined by gene expression and histological assessment, whereas equimolar concentrations of butyrate potently impaired differentiation in all cell types. RNA-sequencing revealed that unlike butyrate, {beta}OHB minimally impacted gene expression in adipocytes, macrophages, and hepatocytes. However, in myocytes, {beta}OHB upregulated genes involved in the TCA cycle and oxidative phosphorylation, while downregulating genes belonging to cytokine and chemokine signal transduction. Overall, our data do not support the notion that {beta}OHB serves as a powerful signaling molecule regulating gene expression in adipocytes, macrophages and hepatocytes, but suggest that {beta}OHB may act as a niche signaling molecule in muscle.

category: molecular biology


title: Packing the Standard Genetic Code in its box: 3-dimensional late Crick wobble

abstract: Minimally-evolved codes are constructed with randomly chosen Standard Genetic Code (SGC) triplets, and completed with completely random triplet assignments. Such "genetic codes" have not evolved, but retain SGC qualities. Retained qualities are inescapable, part of the logic of code evolution. For example, sensitivity of coding to arbitrary assignments, which must be <{approx} 10%, is intrinsic. Such sensitivity comes from elementary combinatorial properties of coding, and constrains any SGC evolution hypothesis. Similarly, evolution of last-evolved functions is difficult, due to late kinetic phenomena, likely common across codes. Census of minimally-evolved code assignments shows that shape and size of wobble domains controls packing into a coding table, strongly shifting accuracy of codon assignments. Access to the SGC therefore requires a plausible pathway to limited randomness, avoiding difficult completion while packing a highly ordered, degenerate code into a fixed three-dimensional space. Late Crick wobble in a 3-dimensional genetic code assembled by lateral transfer satisfies these varied, simultaneous requirements. By allowing parallel evolution of SGC domains, it can yield shortened evolution to SGC-level order, and allow the code to arise in smaller populations. It effectively yields full codes. Less obviously, it unifies well-studied sources for order in amino acid coding, including a stereochemical minority of triplet-amino acid associations. Finally, fusion of its intermediates into the definitive SGC is credible, mirroring broadly-accepted later cellular evolution.


category: evolutionary biology


title: Diel transcriptional pattern contributes to functional and taxonomic diversity in supraglacial microbial communities

abstract: Despite the harsh environmental conditions, glacier surfaces host metabolically active bacterial communities, especially in cryoconite holes, small ponds filled with melting water and with a fine-grained sediment at the bottom. We investigated the daily changes in transcript profiles of the microbial community of a cryoconite hole on an Alpine glacier. Using a metatranscriptomic shotgun sequencing, we observed different level of expression of the main carbon and energy metabolisms along the day. Oxygenic and anoxygenic photosynthesis peaked their activity at the sunrise and sunset, respectively, and showed an inhibition at midday, in response to high solar radiation. Carbon fixation genes were expressed all day long with the lowest coverage at night. Different microbial populations were responsible for this metabolic function along the day. Cyanobacteria and Algae were the most active primary producers at the sunrise and the sunset, whereas at night and at noon chemosynthetic proteobacteria, likely hydrogen oxidisers, were most active. Furthermore, the observed temporal cascade of transcript peaks of photosynthesis and respiration recalls those occurring in both coastal and open waters in ocean, thus supporting the hypothesis that conserved temporally phased biotic interactions are ubiquitous among aquatic communities worldwide.

category: ecology


title: Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions

abstract: SARS-CoV-2 has emerged as a major threat to global public health, resulting in global societal and economic disruptions. Here, we investigate the intramolecular and intermolecular RNA interactions of wildtype (WT) and a mutant ({Delta}382) SARS-CoV-2 virus in cells using high throughput structure probing on Illumina and Nanopore platforms. We identified twelve potentially functional structural elements within the SARS-CoV-2 genome, observed that identical sequences can fold into divergent structures on different subgenomic RNAs, and that WT and {Delta}382 virus genomes can fold differently. Proximity ligation sequencing experiments identified hundreds of intramolecular and intermolecular pair-wise interactions within the virus genome and between virus and host RNAs. SARS-CoV-2 binds strongly to mitochondrial and small nucleolar RNAs and is extensively 2-O-methylated. 2-O-methylation sites in the virus genome are enriched in the untranslated regions and are associated with increased pair-wise interactions. SARS-CoV-2 infection results in a global decrease of 2-O-methylation sites on host mRNAs, suggesting that binding to snoRNAs could be a pro-viral mechanism to sequester methylation machinery from host RNAs towards the virus genome. Collectively, these studies deepen our understanding of the molecular basis of SARS-CoV-2 pathogenicity, cellular factors important during infection and provide a platform for targeted therapy.

category: genomics