title: Oncogenic RAS instructs morphological transformation of human epithelia via differential tissue mechanics.

abstract: The RAS proto-oncogene is a critical regulator of cell state, morphology and mechanics, and plays a key role in cancer progression. Here, by using a human epithelial model in vitro, we ask how morpho-mechanical changes driven by oncogenic RAS activation at the level of individual cells are collectively integrated to drive changes in tissue behaviour. We found that the uniform oncogenic expression of HRAS.V12 in confined epithelial monolayers causes reproducible changes in the structure and organization of the tissue, which acquires a transitory bilayered morphology. RAS-driven bilayering associates with reproducible layer-specific differences in cell-cell contractility and cell-matrix forces. These drive the initially flat tissues to form three-dimensional structures mimicking some of the behaviours seen in human cancers. Our findings establish a physical mechanism of cellular collectives through which uniform expression of RAS can be interpreted differently in different places of the same tissue to regulate its physiological and pathological morphology.


title: A conserved regulatory module regulates receptor kinase signaling in immunity and development

abstract: Ligand recognition by cell-surface receptors underlies development and immunity in both animals and plants. Modulating receptor signaling is critical for appropriate cellular responses but the mechanisms ensuring this are poorly understood. Here, we show that signaling by plant receptors for pathogen-associated molecular patterns (PAMPs) in immunity and CLAVATA3/EMBRYO SURROUNDING REGION-RELATED peptides (CLEp) in development employ a similar regulatory module. In the absence of ligand, signaling is dampened through association with specific type-2C protein phosphatases (PP2Cs). Upon activation, PAMP and CLEp receptors phosphorylate divergent cytosolic kinases, which, in turn, phosphorylate the phosphatases, thereby promoting their release from the receptor complexes. Our work reveals a regulatory circuit shared between immune and developmental receptor signaling, which may have broader important implications for plant receptor kinase-mediated signaling in general.

category: plant biology


title: Plants export 2-monopalmitin and supply both fatty acyl and glyceryl moieties to arbuscular mycorrhizal fungi

abstract: Arbuscular mycorrhizal fungi (AMF) rely on their host plants to provide them with fatty acids (FA), but the precise form(s) in which they are supplied is still unclear. Here we show that ectopic expression of the transcription factor REQUIRED FOR ARBUSCULAR MYCORRHIZATION 1 (RAM1) can drive secretion of 2-monoacylglycerols (2MGs) from Medicago truncatula roots and that their main FA moiety is palmitic acid, although myristic acid and stearic acid were also detected. RAM1-dependent 2MG secretion requires the acyl-acyl carrier protein thioesterase FATM, the glycerol-3-phosphate (G3P) acyltransferase RAM2 and the ATP binding cassette transporter STR. Furthermore, 14C glycerol labelling experiments using mycorrhizal M. truncatula roots that are deficient in glycerol kinase, FAD-dependent G3P dehydrogenase and the G3P acyltransferase RAM2 suggest that most of the glyceryl moieties in Rhizophagus irregularis storage lipids are provided by their host plant through the 2MG pathway. Taken together, our data support the hypothesis that the plant exports 2MGs across the peri-arbuscular membrane in mycorrhizal roots and that the AMF receive and utilise both the FA and glyceryl moieties to make their storage lipids.


title: Conductivity of the phloem in Mangifera indica L.

abstract:
Mangifera indica is the fifth most consumed fruit worldwide, and the most important in tropical regions, but its anatomy is quite unexplored. Previous studies examined the effect of chemicals on the xylem structure in the stems of mango, but the anatomy of the phloem has remained elusive, leaving the long distance transport of photo assimilates understudied.

In this work, we used a combination of fluorescence and electron microscopy to evaluate in detail the structure of the sieve tube elements composing the phloem tissue in the tapering branches of mango trees. We then used this information to better understand the hydraulic conductivity of the sieve tubes following current models of fluid transport in trees.

Our results revealed that the anatomy of the phloem in the stems changes from current year branches, where it was protected by pericyclic fibers, to older ones, where the lack of fibers was concomitant with laticiferous canals embedded in the phloem tissue. Callose was present in the sieve plates, but also in the walls of the phloem conduits, making them discernible from other phloem cells in fresh sections. A scaling geometry of the sieve tube elements, including the number of sieve areas and the pore size across tapering branches resulted in an exponential conductivity from current year branches to the base of the tree.

Our measurements of the phloem in mango fit with measurements of the phloem architecture in the stems of forest woody species, and imply that, despite agronomic pruning practices, the sieve conduits of the phloem scale with the tapering branches. As a result, the pipe model theory applied to the continuous tubing system of the phloem appears as a good approach to understand the "long distance" hydraulic transport of photoassimilates in fruit trees.


title: The intrinsic chaperone network of Arabidopsis stem cells confers protection against proteotoxic stress

abstract: The biological purpose of plant stem cells is to maintain themselves while providing new pools of differentiated cells that form organs and rejuvenate or replace damaged tissues1-3. Protein homeostasis, or proteostasis, is required for cell function and viability4-7. However, the link between proteostasis and plant stem cell identity remains unknown. In contrast to their differentiated counterparts, we find that root stem cells can prevent the accumulation of aggregated proteins even under proteotoxic stress conditions such as heat stress or proteasome inhibition. Notably, root stem cells exhibit enhanced expression of distinct chaperones that maintain proteome integrity. Particularly, intrinsic high levels of the TRiC/CCT chaperonin determine stem cell maintenance and their remarkable ability to suppress protein aggregation. Overexpression of CCT8, a key activator of TRiC/CCT assembly8, is sufficient to ameliorate protein aggregation in differentiated cells and confer resistance to proteotoxic stress in plants. Taken together, our results indicate that enhanced proteostasis mechanisms in stem cells could be an important requirement for plants to persist under extreme environmental conditions and reach extreme long ages. Thus, proteostasis of stem cells could provide insights to design and breed plants tolerant to environmental challenges caused by the climate change.


title: Piriformospora indica employs hosts putrescine for growth promotion in plants

abstract: Growth promotion by endosymbiont Piriformospora indica has been observed in various plants; however, specific functional metabolites involved in P. indica mediated growth promotion are unknown. A GC-MS based untargeted metabolite analysis was used to identify Solanum lycopersicum metabolites altered during P. indica mediated growth promotion. Metabolomic analysis showed primary metabolites altered and specifically putrescine to be maximally induced in roots during the interaction. P. indica induced putrescine biosynthetic gene SlADC1 in S. lycopersicum and acts via arginine decarboxylase (ADC) mediated pathway. P. indica did not promote growth in Sladc-VIGS (virus induced gene silencing of SlADC gene) lines of S. lycopersicum and when the ADC enzyme was inhibited with an inhibitor, DL--(Difluoromethyl) arginine. In Arabidopsis adc knock-out mutants, P. indica do not promote growth and this response was rescued upon exogenous application of putrescine. Putrescine promoted growth by elevation of auxin (indole-3-acetic acid) and gibberellin (GA4, GA7) levels in S. lycopersicum. Putrescine is also important for P. indica hyphal growth indicating that it is co-adapted by both host and microbe. Hence, we conclude that putrescine is an essential metabolite and its biosynthesis in plants is crucial for P. indica mediated growth promotion and fungal growth.


title: Transcripts repressed at the stop of phloem unloading highlight the energy efficiency of sugar import in the ripening V. vinifera fruit.

abstract: Transcriptomic changes at the cessation of sugar accumulation in the pericarp of Vitis vinifera were addressed on single berries re-synchronized according to their individual growth patterns. The net rates of water, sugars and K+ accumulation inferred from individual growth and solute concentration confirmed that these inflows stopped simultaneously in the ripe berry, while the small amount of malic acid remaining at this stage was still being oxidized at low rate. Re-synchronized individual berries displayed negligible variations in gene expression among triplicates. RNA-Seq studies revealed sharp reprogramming of cell wall enzymes and structural proteins at the stop of phloem unloading, associated with an 80% repression of multiple sugar transporters and aquaporins on the plasma or tonoplast membranes, with the noticeable exception of H+/sugar symporters, that were rather weakly and constitutively expressed. This was verified in three genotypes placed in contrasted thermo-hydric conditions. The prevalence of SWEET suggests that electrogenic transporters would play a minor role on the plasma membranes of SE/CC complex and the one of the flesh, while sucrose/H+ exchangers dominate on its tonoplast. Cis-regulatory elements present in their promoters allowed to sort these transporters in different groups, also including specific TIPs and PIPs paralogs, and cohorts of cell wall related genes. Together with simple thermodynamic considerations, these results lead to propose that H+/sugar exchangers at the tonoplast, associated with a considerably acidic vacuolar pH, may exhaust cytosolic sugars in the flesh and alleviate the need for supplementary energization of sugar transport at the plasma membrane.


title: Transcripts switched off at the stop of phloem unloading highlight the energy efficiency of sugar import in the ripening V. vinifera fruit.


title: Immune phase transition under steroid treatment

abstract: The steroid hormone, Glucocorticoid (GC) is a well-known immunosuppressant that controls T cell-mediated adaptive immune response. In this work, we have developed a minimal kinetic network model of T-cell regulation connecting relevant experimental and clinical studies to quantitatively understand the long-term effects of GC on pro-inflammatory T-cell (Tpro) and anti-inflammatory T-cell (Tanti) dynamics. Due to the antagonistic relation between these two types of T-cells, their long-term steady-state population ratio helps us to characterize three classified immune-regulations: (i) weak ([Tpro]>[Tanti]); (ii) strong ([Tpro]<[Tanti]), and (iii) moderate ([Tpro] [~] [Tanti]); holding the characteristic bistability). In addition to the differences in their long-term steady-state outcome, each immune-regulation shows distinct dynamical phases. In the pre-steady, a characteristic intermediate stationary phase is observed to develop only in the moderate regulation regime. In the medicinal field, the resting time in this stationary phase is distinguished as a clinical latent period. GC dose-dependent steady-state analysis shows an optimal level of GC to drive a phase-transition from the weak/auto-immune prone to the moderate regulation regime. Subsequently, the pre-steady state clinical latent period tends to diverge near that optimal GC level where [Tpro]: [Tanti] is highly balanced. The GC-optimized elongated stationary phase explains the rationale behind the requirement of long-term immune diagnostics, especially when long-term GC-based chemotherapeutics and other immunosuppressive drugs are administrated. Moreover, our study reveals GC sensitivity of clinical latent period which might serve as an early warning signal in the diagnosis of different immune phases and determining immune phase-wise steroid treatment.

category: systems biology


title: Architecture of the Neuro-Glia-Vascular System

abstract:
Astrocytes connect the vasculature to neurons and mediate the supply of nutrients and biochemicals. They also remove metabolites from the neurons and extracellular environment. They are involved in a growing number of physiological and pathophysiological processes. Understanding the biophysical, physiological, and molecular interactions in this neuro-glia-vascular ensemble (NGV) and how they support brain function is severely restricted by the lack of detailed cytoarchitecture. To address this problem, we used data from multiple sources to create a data-driven digital reconstruction of the NGV at micrometer anatomical resolution. We reconstructed 0.2 mm3 of rat somatosensory cortical tissue with approximately 16000 morphologically detailed neurons, its microvasculature, and approximately 2500 morphologically detailed protoplasmic astrocytes. The consistency of the reconstruction with a wide array of experimental measurements allows novel predictions of the numbers and locations of astrocytes and astrocytic processes that support different types of neurons. This allows anatomical reconstruction of the spatial microdomains of astrocytes and their overlapping regions. The number and locations of end-feet connecting each astrocyte to the vasculature can be determined as well as the extent to which they cover the microvasculature. The structural analysis of the NGV circuit showed that astrocytic shape and numbers are constrained by vasculatures spatial occupancy and their functional role to form NGV connections. The digital reconstruction of the NGV is a resource that will enable a better understanding of the anatomical principles and geometric constraints which govern how astrocytes support brain function.

Table of contentsO_ST_ABSMain pointsC_ST_ABSO_LIThe Blue Brain Project digitally reconstructs a part of neocortical Neuro-Glia-Vascular organization
C_LIO_LIInterdependencies and topological methods allow dense in silico reconstruction from sparse experimental data
C_LIO_LIThe polarized role of protoplasmic astrocytes constrains their shapes and numbers
C_LI

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category: neuroscience


title: Associations between lower limb isometric torque, isokinetic torque, and explosive force with phases of reactive stepping in young, healthy adults

abstract: Reactive stepping is one of the only strategies that can lead to successful stabilization following a large challenge to balance. Improving function of specific muscles associated with reactive stepping may improve features of reactive balance control. Accordingly, this study aimed to determine the relationship between lower limb muscle strength and explosive force with force plate-derived timing measures of reactive stepping. Nineteen young, healthy adults (27.6 {+/-} 3.0 years of age; 10 women: 9 men) responded to 6 perturbations (~13-15% of body weight) using an anterior lean-and-release system (causing a forward fall), where they were instructed to recover balance in as few steps as possible. Foot-off, swing, and restabilization times were estimated from force plates. Peak isokinetic torque, isometric torque, and explosive force of the knee extensors/flexors and plantar/dorsiflexors were measured using isokinetic dynamometry. Correlations were run based on a priori hypotheses and corrected for the number of comparisons (Bonferroni) for each variable. Knee extensor explosive force was negatively correlated with swing time (r = -0.582, p = 0.009). Knee flexor peak isometric torque also showed a negative association with restabilization time (r = -0.459, p = 0.048), however this was not statistically significant after correcting for multiple comparisons. There was no significant relationship between foot-off time and knee or plantar flexor explosive force (p > 0.025). These findings suggest that there may be utility to identifying specific aspects of reactive step timing when studying the relationship between muscle strength and reactive balance control. Exercise training aimed at improving falls risk should consider targeting specific aspects of muscle strength depending on specific deficits in reactive stepping.


title: Assessment of Flourishing Levels of Individuals by Using Resting State fNIRS with Different Functional Connectivity Measures

abstract: Flourishing is an important criterion to assess wellbeing, however, controversies remain, particularly around assessing it with self-report measures. Due to this reason, to be able to understand the underlying neural mechanisms of well-being, researchers often utilize neuroimaging techniques. However, rather than individual answers, previous neuroimaging studies using statistical approaches provided an answer in average sense. To overcome these problems, we applied machine learning techniques to discriminate 43 highly flourishing from regular flourishing individuals by using a publicly available resting state functional near infrared spectroscopy (rs-fNIRS) dataset to get an answer in individual level. We utilized both Pearsons correlation (CC) and Dynamic Time Warping (DTW) algorithm to estimate functional connectivity from rs-fNIRS data on temporo-parieto-occipital region as input to nine different machine learning algorithms. Our results revealed that by utilizing oxyhemoglobin concentration change with Pearsons correlation (CC - {Delta}HbO) and deoxy hemoglobin concentration change with dynamic time warping (DTW - {Delta}Hb), we could be able to classify flourishing individuals with 90 % accuracy with AUC 0.90 and 0.93 using nearest neighbor and Radial Basis Kernel Support Vector Machine. This finding suggests that temporo-parieto-occipital regional based resting state connectivity might be a potential biomarker to identify the levels of flourishing and using both connectivity measures might allow us to find different potential biomarkers.


title: Fibrillar Aβ causes profound microglial metabolic perturbations in a novel APP knock-in mouse model

abstract:
Microglial dysfunction is believed to play a pathogenic role in Alzheimers disease (AD). Here, we characterize the amyloid-{beta} related pathology and microglial responses in an engineered APP knock-in mouse model of familial AD. This model recapitulates key pathological features of AD such as a progressive accumulation of parenchymal amyloid plaques and vascular amyloid deposits, altered glial responses and neurodegeneration. Leveraging multi-omics approaches, we found lipid accumulation and an exacerbated disease-associated transcriptomic response in methoxy-X04-positive, phagocytic microglia. Together, these findings highlight the potential of this novel, open-access mouse model to investigate AD pathogenesis and demonstrate that fibrillar A{beta} triggers lipid dysregulation and immuno-metabolic perturbations in phagocytic microglia.

HighlightsO_LINovel open-access APP KI mouse model shows salient AD pathological features
C_LIO_LIDeep phenotyping of sorted microglia reveals profound lipidomic perturbations in line with Alois Alzheimers original descriptions of glial adipose inclusions
C_LIO_LIImmunometabolic perturbations are exacerbated in microglia accumulating fibrillar A{beta}
C_LI


title: Neisseria gonorrhoeae subverts formin-dependent actin polymerization to colonize human macrophages

abstract: Dynamic reorganization of the actin cytoskeleton dictates plasma membrane morphology and is frequently subverted by bacterial pathogens for entry and colonization of host cells. The human-adapted bacterial pathogen Neisseria gonorrhoeae can colonize and replicate when cultured with human macrophages, however the basic understanding of how this process occurs is incomplete. N. gonorrhoeae is the etiological agent of the sexually transmitted disease gonorrhea and tissue resident macrophages are present in the urogenital mucosa which is colonized by the bacteria. We uncovered that when gonococci colonize macrophages they can establish an intracellular or a cell surface-associated niche that support bacterial replication independently. Unlike other intracellular bacterial pathogens, which enter host cells as single bacterium, establish an intracellular niche and then replicate, gonococci invade human macrophages as a colony. Individual diplococci are rapidly phagocytosed by macrophages and transported to lysosomes for degradation. However, we found that surface-associated gonococcal colonies of various sizes can invade macrophages by triggering actin skeleton rearrangement resulting in plasma membrane invaginations that slowly engulf the colony. The resulting intracellular membrane-bound organelle supports robust bacterial replication. The gonococci-occupied vacuoles evaded fusion with the endosomal compartment and were enveloped by a network of actin filaments. We demonstrate that gonococcal colonies invade macrophages via a process mechanistically distinct from phagocytosis that is regulated by the actin nucleating factor FMNL3. Our work provides insights into the gonococci life-cycle in association with human macrophages and defines key host determinants for macrophage colonization.

category: microbiology


title: Type 2 Diabetes Modifies Skeletal Muscle Gene Expression Response to Gastric Bypass Surgery

abstract:
Roux-en-Y gastric bypass (RYGB) is an effective treatment for type 2 diabetes mellitus (T2DM) which can result in remission of clinical symptoms, yet mechanisms for improved skeletal muscle health are poorly understood. We sought to define the impact of existing T2DM on RYGB-induced muscle transcriptome changes.

MethodsVastus lateralis biopsy transcriptomes were generated pre- and 1-yr post-RYGB in black adult females with (T2D; n = 5, age=51{+/-}6 yr, BMI=53.0{+/-}5.8 kg/m2) and without (CON; n = 7,43{+/-}6 yr,51.0{+/-}9.2 kg/m2) T2DM. Insulin, glucose, and HOMA-IR were measured in blood at the same time points. ANCOVA detected differentially expressed genes (p< 0.01, Fold change<|1.2|), which were used to identify enriched biological pathways.

ResultsPre-RYGB, 95 probes were downregulated with T2D including subunits of mitochondrial complex I. Post-RYGB, the T2D group had normalized gene expression when compared to their non-diabetic counterparts with only 3 probes remaining significantly different. In the T2D, we identified 52 probes upregulated from pre- to post-RYGB, including NDFUB7 and NDFUA1.

ConclusionBlack females with T2DM show extensive down regulation of genes across aerobic metabolism pathways prior to RYGB, which resolves 1 year post-RYGB and is related to improvements in clinical markers. These data support efficacy of RYGB for improving skeletal muscle health, especially in patients with T2DM.

category: molecular biology


title: A conserved machinery underlies the synthesis of a chitosan layer in the Candida chlamydospore cell wall

abstract:
The polysaccharide chitosan is found in the cell wall of specific cell types in a variety of fungal species where it contributes to stress resistance, or in pathogenic fungi, virulence. Under certain growth conditions, the pathogenic yeast Candida dubliniensis forms a cell type termed a chlamydosospore, which has an additional internal layer in its cell wall as compared to hyphal or yeast cell types. We report that this internal layer of the chlamydospore wall is rich in chitosan. The ascospore wall of Saccharomyces cerevisiae also has a distinct chitosan layer. As in S. cerevisiae, formation of the chitosan layer in the C. dubliniensis wall requires the chitin synthase CHS3 and the chitin deacetylase CDA2. In addition, three lipid droplet-localized proteins Rrt8, Srt1, and Mum3, identified in S. cerevisiae as important for chitosan layer assembly in the ascospore wall, are required for the formation of the chitosan layer of the chlamydospore wall in C. dubliniensis. These results reveal that a conserved machinery is required for the synthesis of a distinct chitosan layer in the walls of these two yeasts and may be generally important for incorporation of chitosan into fungal walls.

ImportanceThe cell wall is the interface between the fungal cell and its environment and disruption of cell wall assembly is an effective strategy for antifungal therapies. Therefore, a detailed understanding of how cell walls form is critical to identify potential drug targets and develop therapeutic strategies. This work shows that a set of genes required for assembly of a chitosan layer in the cell wall of S. cerevisiae is also necessary for chitosan formation in a different cell type in a different yeast, C. dubliniensis. Because chitosan incorporation into the cell wall can be important for virulence, the conservation of this pathway suggests possible new targets for antifungals aimed at disrupting cell wall function.

category: cell biology


abstract: Gonadal sex determination is controlled by the support cells of testes and ovaries. In testes, the epigenetic mechanism that maintains cellular memory to suppress female sexual differentiation remains unknown. Here, we show that Polycomb suppresses a female gene regulatory network in Sertoli cells, the specific support cells for postnatal testes. Through genetic ablation, we removed Polycomb repressive complex 1 (PRC1) from embryonic Sertoli cells after sex determination. PRC1-depleted postnatal Sertoli cells exhibited defective proliferation and cell death, leading to the degeneration of adult testes. In adult Sertoli cells, PRC1 suppressed the specific, critical genes required for granulosa cells, the support cells of ovaries, thereby inactivating the female gene regulatory network. The underlying chromatin of female genes was coated with Polycomb-mediated repressive modifications: PRC1-mediated H2AK119ub and PRC2-mediated H3K27me3. Taken together, we identify a critical mechanism centered on Polycomb that maintains the male fate in adult testes.

category: developmental biology


title: Polycomb suppresses a female gene regulatory network in Sertoli cells


title: Polycomb suppresses a female gene regulatory network to ensure testicular differentiation


title: Expanding the marine range of the endangered black-capped petrel (Pterodroma hasitata): Occurrence in the northern Gulf of Mexico and conservation implications

abstract: The black-capped petrel (Pterodroma hasitata) is an endangered seabird endemic to the western north Atlantic. Although estimated at ~ 1,000 breeding pairs, only ~ 100 nests have been located at two sites in Haiti and three sites in the Dominican Republic. At sea, the species primarily occupies waters of the western Gulf Stream in the Atlantic and the Caribbean Sea. Due to limited data, there is currently not a consensus on the marine range of the species. There are several maps in use for the marine range of the species and these differ with respect to the north, south, and eastward extent of the range. None of these maps, however, includes the Gulf of Mexico. Here, we report on observations of black-capped petrels during two vessel-based survey efforts throughout the northern Gulf of Mexico from July 2010 - July 2011, and from April 2017 - September 2019. During the 558 days and 54.7 km of surveys from both efforts we tallied 40 black-capped petrels. Most observations occurred in the eastern Gulf, although birds were observed over much of the east-west and north-south footprint of the survey area. Predictive models indicated that habitat suitability for black-capped petrels was highest in areas associated with dynamic waters of the Loop Current, similar to habitat used along the western edge of the Gulf Stream in the western north Atlantic. We suggest that the range for black-capped petrels be modified to include the entire northern Gulf of Mexico although distribution may be more clumped in the eastern Gulf and patchier elsewhere. It remains unclear, however, which nesting areas are linked to the Gulf of Mexico.

category: ecology


title: Breeding seasonality generates reproductive trade-offs in a long-lived mammal

abstract:
The evolutionary benefits of reproductive seasonality are usually measured by a single fitness component, namely offspring survival to nutritional independence (Bronson, 2009). Yet different fitness components may be maximised by dissimilar birth timings. This may generate fitness trade-offs that could be critical to understanding variation in reproductive timing across individuals, populations and species. Here, we use long-term demographic and behavioural data from wild chacma baboons (Papio ursinus) living in a seasonal environment to test the adaptive significance of seasonal variation in birth frequencies. Like humans, baboons are eclectic omnivores, give birth every 1-3 years to a single offspring that develops slowly, and typically breed year-round. We identify two distinct optimal birth timings in the annual cycle, located 4-months apart, which maximize offspring survival or minimize maternal interbirth intervals (IBIs), by respectively matching the annual food peak with late or early weaning. Observed births are the most frequent between these optima, supporting an adaptive trade-off between current and future reproduction. Furthermore, infants born closer to the optimal timing favouring maternal IBIs (instead of offspring survival) throw more tantrums, a typical manifestation of mother-offspring conflict (Maestripieri, 2002). Maternal trade-offs over birth timing, which extend into mother-offspring conflict after birth, may commonly occur in long-lived species where development from birth to independence spans multiple seasons. Such trade-offs may substantially weaken the benefits of seasonal reproduction, and our findings therefore open new avenues to understanding the evolution of breeding phenology in long-lived animals, including humans.

SIGNIFICANCE STATEMENTWhy some species breed seasonally and others do not remain unclear. The fitness consequences of birth timing have traditionally been measured on offspring survival, ignoring other fitness components. We investigated the effects of birth timing on two fitness components in wild baboons, who breed year-round despite living in a seasonal savannah. Birth timing generates a trade-off between offspring survival and future maternal reproductive pace, meaning that mothers cannot maximize both. When birth timing favours maternal reproductive pace (instead of offspring survival), behavioural manifestations of mother-offspring conflict around weaning are intense. These results open new avenues to understand the evolution of reproductive timings in long-lived animals including humans, where such reproductive trade-offs may commonly weaken the intensity of reproductive seasonality.

category: evolutionary biology


title: Self-organization and information transfer in Antarctic krill swarms

abstract: Antarctic krill swarms are one of the largest known animal aggregations. However, despite being the keystone species of the Southern Ocean, little is known about how swarms are formed and maintained, and we lack a detailed understanding of the local interactions between individuals that provide the basis for these swarms. Here we analyzed the trajectories of captive, wild-caught krill in 3D to determine individual level interaction rules and quantify patterns of information flow. Our results suggest krill operate a novel form of collective organization, with measures of information flow and individual movement adjustments expressed most strongly in the vertical dimension, a finding not seen in other swarming species. In addition, local directional alignment with near neighbors, and strong regulation of both direction and speed relative to the positions of groupmates suggest social factors are vital to the formation and maintenance of swarms. This research represents a first step in understanding the fundamentally important swarming behavior of krill.

category: animal behavior and cognition


title: High-speed large-scale 4D activities mapping of moving C. elegans by deep-learning-enabled light-field microscopy on a chip

abstract: We report a novel fusion of microfluidics and light-field microscopy, to achieve high-speed 4D (space + time) imaging of moving C. elegans on a chip. Our approach combines automatic chip-based worm loading / compartmentalization / flushing / reloading with instantaneous deep-learning light-field imaging of moving worm. Taken together, we realized intoto image-based screening of wild-type and uncoordinated-type worms at a volume rate of 33 Hz, with sustained observation of 1 minute per worm, and overall throughput of 42 worms per hour. With quickly yielding over 80000 image volumes that four-dimensionally visualize the dynamics of all the worms, we can quantitatively analyse their behaviours as well as the neural activities, and correlate the phenotypes with the neuron functions. The different types of worms can be readily identified as a result of the high-throughput activity mapping. Our approach shows great potential for various lab-on-a-chip biological studies, such as embryo sorting and cell growth assays.

category: bioengineering


title: freqpcr: interval estimation of population allele frequency based on quantitative PCR ΔΔCq measures from bulk samples

abstract: PCR techniques, both quantitative (qPCR) and non-quantitative, have been used to estimate allele frequency in a population. However, the labor required to sample numerous individuals, and subsequently handle each sample, makes quantification of rare mutations, including pesticide resistance genes at the early stages of resistance development, challenging. Meanwhile, pooling DNA from multiple individuals as a "bulk sample" may reduce handling costs. The qPCR output for a bulk sample, however, contains uncertainty owing to variations in DNA yields from each individual, in addition to measurement errors. In this study, we developed a statistical model for the interval estimation of allele frequency using {Delta}{Delta}Cq-based qPCR analyses of multiple bulk samples collected from a population. We assumed a gamma distribution as the individual DNA yield and developed an R package for parameter estimation, which was verified with real DNA samples from acaricide-resistant spider mites, as well as a numerical simulation. Our model resulted in unbiased point estimates of the allele frequency compared with simple averaging of the {Delta}{Delta}Cq values, while their confidence intervals suggest that collecting and pooling additional samples from individuals may produce higher precision than individual PCR tests with moderate sample sizes.

category: bioinformatics


title: freqpcr: estimation of population allele frequency using qPCR ΔΔCq measures from bulk samples


title: Simulating freely-diffusing single-molecule FRET data with consideration of protein conformational dynamics

abstract:
Single molecule Forster resonance energy transfer experiments have added a great deal to the understanding of conformational states of biologically important molecules. While great progress has been made in studying structural dynamics of biomolecular systems, much is still unknown for systems with conformational heterogeneity particularly those with high flexibility. For instance, with currently available techniques, it is difficult to work with intrinsically disordered proteins, particularly when freely diffusing smFRET experiments are used. Simulated smFRET data allows for the control of the underlying process that generates the data to examine if a given smFRET data analysis technique can detect these underlying differences. Here, we extend the PyBroMo software that simulates freely diffusing smFRET data to include a distribution of inter-dye distances generated using Langevin dynamics in order to model proteins with conformational flexibility within a given state. We compare standard analysis techniques for smFRET data to validate the new module relative to the base PyBroMo software and observe qualitative agreement in the results of standard analysis for the two timestamp generation methods. The Langevin dynamics module provides a framework for generating timestamp data with an known underlying heterogeneity of inter-dye distances that will be necessary for the development of new analysis techniques that study flexible proteins or other biomolecular systems.

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category: biophysics


title: An integrated comparative physiology and molecular approach pinpoints mediators of breath-hold capacity in dolphins

abstract: Ischemic events, such as ischemic heart disease and ischemic stroke, are the number one cause of death globally. Ischemia prevents blood, carrying essential nutrients and oxygen, from reaching tissues and organ systems, leading to cell and tissue death, and eventual organ failure. While humans are relatively intolerant to these ischemic events, other species, such as marine mammals, have evolved remarkable tolerance to chronic ischemia/reperfusion during diving. Here we capitalized on the unique adaptations of bottlenose dolphins (Tursiops truncatus) as a comparative model of ischemic stress and hypoxia tolerance to identify molecular features associated with breath-holding. Using RNA-Seq we observed time-dependent upregulation of the arachidonate 5-lipoxygenase (ALOX5) gene during breath-holding. Consistent with the RNA-Seq data, we also observed increased ALOX5 enzymatic activity in the serum of dolphins undergoing breath holds. ALOX5 has previously been shown to be activated during hypoxia in rodent models, and its metabolites, leukotrienes, induce vasoconstriction. The upregulation of ALOX5 occurred within the estimated aerobic dive limit of the species, suggesting that ALOX5 enzymatic activity may promote tolerance to ischemic stress through sustained vasoconstriction in dolphins during diving. These observations pinpoint a potential molecular mechanism by which dolphins, and perhaps other marine mammals, have adapted to the prolonged breath-holds associated with diving.

category: physiology


title: Inactivated rabies virus vectored SARS-CoV-2 vaccine prevents disease in a Syrian hamster model.

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent coronavirus that has caused a worldwide pandemic. Although human disease is often asymptomatic, some develop severe illnesses such as pneumonia, respiratory failure, and death. There is an urgent need for a vaccine to prevent its rapid spread as asymptomatic infections accounting for up to 40% of transmission events. Here we further evaluated an inactivated rabies vectored SARS-CoV-2 S1 vaccine CORAVAX in a Syrian hamster model. CORAVAX adjuvanted with MPLA-AddaVax, a TRL4 agonist, induced high levels of neutralizing antibodies and generated a strong Th1-biased immune response. Vaccinated hamsters were protected from weight loss and viral replication in the lungs and nasal turbinates three days after challenge with SARS-CoV-2. CORAVAX also prevented lung disease, as indicated by the significant reduction in lung pathology. This study highlights CORAVAX as a safe, immunogenic, and efficacious vaccine that warrants further assessment in human trials.


title: Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

abstract: Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified a viral load threshold that minimizes false positives. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.


title: Young domestic chicks spontaneously represent the absence of objects

abstract: Absence is a notion that is usually captured by language-related concepts like zero or negation. Whether non-linguistic creatures encode similar thoughts is an open question, as everyday behavior marked by absence (of food, of social partners) can be explained solely by expecting presence somewhere else. We investigated 8-day-old chicks looking behavior in response to events violating expectations about the presence or absence of an object. We found different behavioral responses to violations of presence and absence, suggesting distinct underlying mechanisms. Importantly, chicks displayed an avian signature of novelty detection to violations of absence, namely a sex-dependent left-eye-bias. Follow-up experiments excluded accounts that would explain this bias by perceptual mismatch or by representing the object at different locations. These results suggest that the ability to spontaneously form thoughts about the absence of objects likely belongs to the initial cognitive repertoire of vertebrate species.


title: Wild-captive contrasts in non-vocal communicative repertoires and functional specificity in orang-utans

abstract: The creation of novel communicative acts is an essential element of human language. Although some research suggests the presence of this ability in great apes, this claim remains controversial. Here, we use orang-utans (Pongo spp.) to systematically assess the effect of the wild-captive contrast on the repertoire size of communicative acts. We find that individual communicative repertoires are significantly larger in captive compared to wild settings, irrespective of species, age-sex class or sampling effort. Twenty percent of the orang-utan repertoire in captivity were not observed in the wild. In Sumatran orang-utans, the more sociable species, functional specificity was also higher in captive versus wild settings. We thus conclude that orang-utans, when exposed to a more sociable and terrestrial lifestyle, have the behavioural plasticity to invent new communicative behaviours that are highly functionally specific. This productive capacity by great apes is a major prerequisite for the evolution of language and seems to be ancestral in the hominid lineage.


title: Coevolutionary Analysis and Perturbation-Based Network Modeling of the SARS-CoV-2 Spike Protein Complexes with Antibodies: Binding-Induced Control of Dynamics, Allosteric Interactions and Signaling

abstract: The structural and biochemical studies of the SARS-CoV-2 spike glycoproteins and complexes with highly potent antibodies have revealed multiple conformation-dependent epitopes highlighting the link between conformational plasticity of spike proteins and capacity for eliciting specific binding and broad neutralization responses. In this study, we used coevolutionary analysis, molecular simulations, and perturbation-based hierarchical network modeling of the SARS-CoV-2 S complexes with H014, S309, S2M11 and S2E12 antibodies targeting distinct epitopes to explore molecular mechanisms underlying binding-induced modulation of dynamics, stability and allosteric signaling in the spike protein trimers. The results of this study revealed key regulatory centers that can govern allosteric interactions and communications in the SARS-CoV-2 spike proteins. Through coevolutionary analysis of the SARS-CoV-2 spike proteins, we identified highly coevolving hotspots and functional clusters forming coevolutionary networks. The results revealed significant coevolutionary couplings between functional regions separated by the medium-range distances which may help to facilitate a functional cross-talk between distant allosteric regions in the SARS-CoV-2 spike complexes with antibodies. We also discovered a potential mechanism by which antibody-specific targeting of coevolutionary centers can allow for efficient modulation of allosteric interactions and signal propagation between remote functional regions. Using a hierarchical network modeling and perturbation-response scanning analysis, we demonstrated that binding of antibodies could leverage direct contacts with coevolutionary hotspots to allosterically restore and enhance couplings between spatially separated functional regions, thereby protecting the spike apparatus from membrane fusion. The results of this study also suggested that antibody binding can induce a switch from a moderately cooperative population-shift mechanism, governing structural changes of the ligand-free SARS-CoV-2 spike protein, to antibody-induced highly cooperative mechanism that can better withstand mutations in the functional regions without significant deleterious consequences for protein function. This study provides a novel insight into allosteric regulatory mechanisms of SARS-CoV-2 S proteins, showing that antibodies can modulate allosteric interactions and signaling of spike proteins, providing a plausible strategy for therapeutic intervention by targeting specific hotspots of allosteric interactions in the SARS-CoV-2 proteins.


title: DNA methylation of PGC-1α is associated with elevated mtDNA copy number and altered urinary metabolites in Autism Spectrum Disorder

abstract:
BackgroundAutism Spectrum Disorder (ASD) is a complex disorder that is underpinned by numerous dysregulated biological pathways, including canonical mitochondrial pathways. Epigenetic mechanisms contribute to this dysregulation and DNA methylation is an important factor in the aetiology of ASD. We examined the relationship between DNA methylation of peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1), an essential transcriptional regulator of mitochondrial homeostasis, and mitochondrial dysfunction in an ASD cohort of South African children.

ResultsUsing targeted Next Generation bisulfite sequencing, we found 12 highly variable CpG sites in PGC-1 that were significantly differentially methylated (p<0.05) between ASD (n = 55) and controls (n = 44). In ASD, eight CpG sites were hypermethylated in the PGC-1 promotor with a putative binding site for CAMP response binding element 1 (CREB1) spanning one of these CpG sites (p = 1 x 10-6). Mitochondrial DNA (mtDNA) copy number, a marker of mitochondrial function, was elevated (p = 0.002) in ASD compared to controls and correlated significantly with DNA methylation at the PGC-1 promoter. There was a positive correlation between methylation at PGC-1 at CpG#1 and mtDNA copy number (Spearmans r = 0.2, n = 49, p = 0.04) in ASD, but a negative correlation between methylation at PGC-1 at CpG#4 promoter and mtDNA copy number in controls (Spearmans r = -0.4, n = 42, p = 0.045). While there was no relationship between mtDNA deletions and PGC-1 methylation in ASD, mtDNA deletions correlated negatively with methylation at PGC-1 at CpG#4 (Spearmans r = -0.4, n = 42, p = 0.032) in controls. Furthermore, levels of urinary organic acids associated with mitochondrial dysfunction correlated significantly (p<0.05) with DNA methylation at PGC-1 CpG#1 and mtDNA copy number in ASD (n= 20) and controls (n= 13) with many of these metabolites involved in altered redox homeostasis and neuroendocrinology.

ConclusionsThese data show an association between PGC-1 promoter methylation, elevated mtDNA copy number and metabolomic evidence of mitochondrial dysfunction in ASD. This highlights an unexplored link between DNA methylation and mitochondrial dysfunction in ASD.


title: Neutralizing and protective human monoclonal antibodies recognizing the N-terminaldomain of the SARS-CoV-2 spike protein

abstract: Most human monoclonal antibodies (mAbs) neutralizing SARS-CoV-2 recognize the spike (S) protein receptor-binding domain and block virus interactions with the cellular receptor angiotensin-converting enzyme 2. We describe a panel of human mAbs binding to diverse epitopes on the N-terminal domain (NTD) of S protein from SARS-CoV-2 convalescent donors and found a minority of these possessed neutralizing activity. Two mAbs (COV2-2676 and COV2-2489) inhibited infection of authentic SARS-CoV-2 and recombinant VSV/SARS-CoV-2 viruses. We mapped their binding epitopes by alanine-scanning mutagenesis and selection of functional SARS-CoV-2 S neutralization escape variants. Mechanistic studies showed that these antibodies neutralize in part by inhibiting a post-attachment step in the infection cycle. COV2-2676 and COV2-2489 offered protection either as prophylaxis or therapy, and Fc effector functions were required for optimal protection. Thus, natural infection induces a subset of potent NTD-specific mAbs that leverage neutralizing and Fc-mediated activities to protect against SARS-CoV-2 infection using multiple functional attributes.

category: immunology


title: Increased elastase sensitivity and decreased intramolecular interactions in the more transmissible SARS-CoV-2 variants' spike protein

abstract:
Two SARS-CoV-2 variants showing increased transmissibility relative to the Wuhan virus have recently been identified. Although neither variant causes more severe illness or increased risk of death, the faster spread of the virus is a major threat. Using computational tools, we found that the new SARS-CoV-2 variants may acquire an increased transmissibility by increasing the propensity of its spike protein to expose the receptor binding domain. This information leads to the identification of potential treatments to avert the imminent threat of these more transmittable SARS-CoV-2 variants.

TeaserThe more infective SARS-CoV-2 variants may expose its Achilles Heel - an opportunity to reduce their spreading.


title: Evaluation of the effects of SARS-CoV-2 genetic mutations on diagnostic RT-PCR assays

abstract:
Several mutant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging. Mismatch(es) in primer/probe binding regions would decrease the detection sensitivity of the PCR test, thereby affecting the results of clinical testing. In this study, we conducted an in silico survey on SARS-CoV-2 sequence variability within the binding regions of primer/probe published by the Japan National Institute of Infectious Diseases (NIID) and Centers for Disease Control and Prevention (CDC). In silico analysis revealed the presence of mutations in the primer/probe binding regions. We performed RT-PCR assays using synthetic RNAs containing the mutations and showed that some mutations significantly decreased the detection sensitivity of the RT-PCR assays.

Our results highlight the importance of genomic monitoring of SARS-CoV-2 and evaluating the effects of mismatches on PCR testing sensitivity.


title: Use Of Canine Olfactory Detection For COVID-19 Testing Study On U.A.E. Trained Detection Dog Sensitivity

abstract:
This study aimed to evaluate the sensitivity of 21 dogs belonging to different United Arab Emirates (UAE) Ministry of Interior (MOI), trained for COVID-19 olfactory detection.

The study involved 17 explosives detection dogs, two cadaver detection dogs and two dogs with no previous detection training. Training lasted two weeks before starting the validation protocol. Sequential five and seven-cone line-ups were used with axillary sweat samples from symptomatic COVID-19 individuals (SARS-CoV-2 PCR positive) and from asymptomatic COVID-19 negative individuals (SARS-CoV-2 PCR negative). A total of 1368 trials were performed during validation, including 151 positive and 110 negative samples. Each line-up had one positive sample and at least one negative sample. The dog had to mark the positive sample, randomly positioned behind one of the cones. The dog, handler and data recorder were blinded to the positive sample location.

The calculated overall sensitivities were between 71% and 79% for three dogs, between83% and 87% for three other dogs, and equal to or higher than 90% for the remaining 15 dogs (more than two thirds of the 21 dogs).

After calculating the overall sensitivity for each dog using all line-ups, "matched" sensitivities were calculated only including line-ups containing COVID-19 positive and negative samples strictly comparable on confounding factors such as diabetes, anosmia, asthma, fever, body pain, diarrhoea, sex, hospital, method of sweat collection and sampling duration. Most of the time, the sensitivities increased after matching.

Pandemic conditions in the U.A.E., associated with the desire to use dogs as an efficient mass-pretesting tool has already led to the operational deployment of the study dogs.

Future studies will focus on comparatives fields-test results including the impact of the main COVID-19 comorbidities and other respiratory tract infections.


title: Generation and characterization of a laforin nanobody inhibitor

abstract: Mutations in the gene encoding the glycogen phosphatase laforin result in the fatal childhood epilepsy Lafora disease (LD). A cellular hallmark of LD is cytoplasmic, hyper-phosphorylated, glycogen-like aggregates called Lafora bodies (LBs) that form in nearly all tissues and drive disease progression. Additional tools are needed to define the cellular function of laforin, understand the pathological role of laforin in LD, and determine the role of glycogen phosphate in glycogen metabolism. We present the generation and characterization of laforin nanobodies. We identify multiple classes of specific laforin-binding nanobodies and determine their binding epitopes using hydrogen deuterium exchange (HDX) mass spectrometry. Further, one family of nanobodies is identified that serves as an inhibitor of laforin catalytic activity. The laforin nanobodies are an important set of tools that open new avenues to define unresolved questions.

category: biochemistry


title: Inhibition of microglial GBA hampers the microglia-mediated anti-oxidant and protective response in neurons

abstract:
Homozygotic mutations in the GBA gene cause Gauchers disease, moreover, both patients and heterozygotic carriers have been associated with 20- to 30-fold increased risk of developing Parkinsons disease. In homozygosis, these mutations impair the activity of {beta}-glucocerebrosidase, the enzyme encoded by GBA, and generate a lysosomal disorder in macrophages, which changes morphology towards an engorged phenotype, considered the hallmark of Gauchers disease. In the brain, most of the pathological effects caused by GBA mutations have been attributed to the {beta}-glucocerebrosidase deficit in neurons, while a microglial phenotype for these mutations has never been reported. Here, we applied the bioluminescence imaging technology, immunohistochemical and gene expression analysis to investigate the consequences of microglial {beta}-glucocerebrosidase inhibition in the brain of reporter mice, in primary neuron/microglia co-cultures and in cell lines. Our data demonstrate the existence of a novel mechanism by which microglia sustain the antioxidant/detoxifying response mediated by the nuclear factor erythroid 2-related factor 2 in neurons. The central role played by microglia in this neuronal response in vivo was proven by pharmacological depletion of the lineage in the brain, while co-cultures experiments provided insight on the nature of this cell-to-cell communication showing that this mechanism requires a direct microglia-to-neuron contact supported by functional actin structures. Pharmacological inhibition of microglial {beta}-glucocerebrosidase was proven to induce morphological changes, turn on an anti-inflammatory/repairing pathway and hinder the microglia ability to activate the anti-oxidant/detoxifying response, thus increasing the neuronal susceptibility to neurotoxins.

Altogether, our data suggest that microglial {beta}-glucocerebrosidase inhibition impairs microglia-to-neuron communication increasing the sensitivity of neurons to oxidative or toxic insults, thus providing a possible mechanism for the increased risk of neurodegeneration observed in carriers of GBA mutations.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/427380v1_ufig1.gif" ALT="Figure 1">
View larger version (60K):
org.highwire.dtl.DTLVardef@15c2c3corg.highwire.dtl.DTLVardef@5c4e34org.highwire.dtl.DTLVardef@12718dorg.highwire.dtl.DTLVardef@dcfeca_HPS_FORMAT_FIGEXP  M_FIG C_FIG In BriefMicroglia, through actin-dependent structures, contact neurons and induce a detoxification response by increasing the NFE2L2 signalling pathway. Inhibition of GCase activity by CBE treatment produces a morpho-functional change in microglia cells hampering the neuroprotective microglia-neuron communication thus inducing a phenotype in dopaminergic neurons characterized by increased susceptibility to oxidative stress or toxic insults.


title: Modeling Brain Connectivity Dynamics in Functional Magnetic Resonance Imaging via Particle Filtering

abstract: Interest in the studying of functional connections in the brain has grown considerably in the last decades, as many studies have pointed out that these interactions can play a role as markers of neurological diseases. Most studies in this field treat the brain network as a system of connections stationary in time, but dynamic features of brain connectivity can provide useful information, both on physiology and pathological conditions of the brain. In this paper, we propose the application of a computational methodology, named Particle Filter (PF), to study non-stationarities in brain connectivity in functional Magnetic Resonance Imaging (fMRI). The PF algorithm estimates time-varying hidden parameters of a first-order linear time-varying Vector Autoregressive model (VAR) through a Sequential Monte Carlo strategy. On simulated time series, the PF approach effectively detected and enabled to follow time-varying hidden parameters and it captured causal relationships among signals. The method was also applied to real fMRI data, acquired in presence of periodic tactile or visual stimulations, in different sessions. On these data, the PF estimates were consistent with current knowledge on brain functioning. Most importantly, the approach enabled to detect statistically significant modulations in the cause-effect relationship between brain areas, which correlated with the underlying visual stimulation pattern presented during the acquisition.


title: RIPK1 activates distinct gasdermins in macrophages and neutrophils upon pathogen blockade of innate immune signalling

abstract: Injection of effector proteins to block host innate immune signalling is a common strategy used by many pathogenic organisms to establish an infection. Pathogenic Yersinia species for example inject the acetyltransferase YopJ into target cells to inhibit NF-{kappa}B and MAPK signalling. To counteract this, detection of YopJ activity in myeloid cells promotes the assembly of a RIPK1-caspase-8 death-inducing platform that confers antibacterial defence. While recent studies revealed that caspase-8 cleaves the pore-forming protein, gasdermin D (GSDMD) to trigger pyroptosis in macrophages, whether RIPK1 activates additional substrates downstream of caspase-8 to promote host defence is unclear. Here, we report that the related gasdermin family member gasdermin E (GSDME) is activated upon detection of YopJ activity in a RIPK1 kinase-dependent manner. Specifically, GSDME promotes neutrophil pyroptosis and IL-1{beta} release, which is critical for anti-Yersinia defence. During in vivo infection, IL-1{beta} neutralisation increases bacterial burden in wild type but not Gsdme-deficient mice. Thus, our study establishes GSDME as an important mediator that counteracts pathogen blockade of innate immune signalling.


title: PEBP regulates balance between apoptosis and autophagy, enabling coexistence of arbovirus and insect vector

abstract:
Apoptosis and autophagy are two most prominent forms of programmed cell deaths (PCD) that have been implicated in antiviral immunity in vertebrate and plant hosts. Arboviruses are able to coexist with its arthropod vectors by coordinating the PCD immunity, but the regulatory mechanism involved is largely unknown. We found that the coat protein (CP) of an insect-borne plant virus TYLCV directly interacted with a phosphatidylethanolamine-binding protein (PEBP) of its insect vector whitefly to negatively influence the MAPK signaling cascade. As a result, the apoptosis was activated in whitefly which increased viral loading. Simultaneously, the PEBP4-CP interaction liberated ATG8, the hallmark of autophagy initiation, and eliminates arbovirus. Furthermore, apoptosis-promoted virus loading was compromised by agonist-induced autophagy, but autophagy-associated suppression on virus loading was unaffected by apoptosis agonist or inhibitor, suggesting that virus loading was predominantly determined by autophagy rather than by apoptosis. Our results demonstrated that maintaining a mild immune response by coordinating apoptosis and autophagy processes presumably could facilitate coexistence of the arbovirus and its insect vector. Taken together, immune homeostasis shaped by two types of PCD may facilitate the arbovirus preservation within the insect vector.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/427364v1_ufig1.gif" ALT="Figure 1">
View larger version (41K):
org.highwire.dtl.DTLVardef@a1e3baorg.highwire.dtl.DTLVardef@6ddc26org.highwire.dtl.DTLVardef@906b04org.highwire.dtl.DTLVardef@161db14_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIInteraction between whitefly PEBP4 and TYLCV CP suppresses phosphorylation of MAPK cascade, activating apoptosis
C_LIO_LITYLCV CP liberates PEBP4-bound ATG8, resulting in lipidation of ATG8 and initiation of autophagy.
C_LIO_LIPEBP4 balances apoptosis and autophagy in viruliferous whitefly to optimize virus loading without obvious fitness cost.
C_LI


title: ATGs ubiquitination is required for circumsporozoite protein to subvert host innate immunity against malaria liver stage

abstract: Although exoerythrocytic forms (EEFs) of liver stage malaria parasite in parasitophorous vacuole (PV) encountered with robust host innate immunity, EEFs can still survive and successfully complete infection of hepatocytes, and the underlying mechanism is largely unknown. Here, we showed that sporozoite circumsporozoite protein (CSP) translocated from the parasitophorous vacuole into the hepatocyte cytoplasm significantly inhibited the killing of exo-erythrocytic forms (EEFs) by interferon-gamma (IFN-{gamma}). Attenuation of IFN-{gamma}-mediated killing of EEFs by CSP was dependent on its ability to reduce the levels of autophagy-related genes (ATGs) in hepatocytes. The ATGs downregulation occurred through its enhanced ubiquitination mediated by E3 ligase NEDD4, an enzyme that was upregulated by CSP when it translocated from the cytoplasm into the nucleus of hepatocytes via its nuclear localization signal (NLS) domain. Thus, we have revealed an unrecognized role of CSP in subverting host innate immunity and shed new light for a prophylaxis strategy against liver-stage infection.


title: The abaI/abaR quorum sensing system effects pathogenicity in Acinetobacter baumannii

abstract:
Acinetobacter baumannii is a Gram-negative pathogen that has emerged as one of the most troublesome pathogens for health care institutions globally. Bacterial quorum sensing (QS) is a process of cell-to-cell communication that relies on the production, secretion and detection of autoinducer (AI) signals to share information about cell density and regulate gene expression accordingly. In this study, we performed a comprehensive set of experiments show that deletion of quorum sensing genes showed differences in growth characteristics, morphology, biofilm formation and virulence, and increased susceptibility to some antimicrobials and exhibited motility defects. RNA-seq analysis indicated that genes involved in various aspects of energy production and conversion, Valine, leucine and isoleucine degradation and lipid transport and metabolism showed different expression.

IMPORTANCEPrevious studies on bacterial quorum sensing mainly focused on biofilm formation and motility and antibiotic resistance. In this study, we focused on detecting the role of the abaI/abaR QS system in the virulence of A. baumannii. Our work provides a new insight into abaI/abaR quorum sensing system effects pathogenicity in A. baumannii. We propose that targeting the AHL synthase enzyme abaI could provide an effective strategy for attenuating virulence. On the contrary, interdicting the autoinducer synthase-receptor abaR elicits unpredictable consequences, which may lead to enhanced bacterial virulence.


title: Extreme C-to-A Hypermutation at a Site of Cytosine-N4 Methylation

abstract:
Methylation of cytosine in DNA at position C5 increases the rate of C[->]T mutations in bacteria and eukaryotes. Methylation at the N4 position, employed by some restriction-modification systems, is not known to increase the mutation rate. Here I report that a Salmonella enterica Type III restriction-modification system that includes a cytosine-N4 methyltransferase causes an enormous increase in the rate of mutation of the methylated cytosines, which occur at the overlined C in the motif [Formula]. Mutations consist mainly of C[->]A transversions, the rate of which is increased ~500-fold by the restriction-modification system. The rate of C[->]T transitions is also increased, and somewhat exceeds that at C5-methylated cytosines in Dcm sites. Two other Salmonella N4 methyltransferases investigated do not have such dramatic effects, although in one case there is a modest increase in C[->]A mutations along with an increase in C[->]T mutations. Sensitivity of the C[->]A rate to orientation with respect to both DNA replication and transcription is higher at hypermutable sites than at other cytosines, suggesting a fundamental mechanistic difference between hypermutation and ordinary mutation.

IMPORTANCEMutation produces the raw material for adaptive evolution, but also imposes a burden because most mutations are deleterious. The rate of mutation at a particular site is affected by a variety of factors. In both prokaryotes and eukaryotes, methylation of C at the C5 position, a naturally-occurring DNA modification, greatly increases the rate of C[->]T mutation. A distinct C modification that occurs in prokaryotes, methylation at N4, is not known to increase mutation rate. Here I report that a bacterial restriction-modification system, found in some Salmonella, increases the rate of C[->]A mutation by a factor of 500 at sites that it methylates at N4. This rate increase is much greater than that caused by C5 methylation. Although fewer than one in 1600 positions analyzed are methylation sites, over 10% of all mutations occur at these sites. Like other examples of extremely high mutation rate, whether naturally-occurring or the result of laboratory mutation, this phenomenon may shed light on the mechanism of mutation in general.


title: Recombination facilitates adaptive evolution in rhizobial soil bacteria

abstract:
Homologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations and by readily creating new combinations of beneficial alleles. Here, we investigate how the proportion of amino acid substitutions fixed by adaptive evolution () depends on the recombination rate in bacteria. We analyze 3086 core protein-coding sequences from 196 genomes belonging to five closely-related species of the genus Rhizobium. These genes are found in all species and do not display any signs of introgression between species. We estimate  using the site frequency spectrum (SFS) and divergence data for all pairs of species. We evaluate the impact of recombination within each species by dividing genes into three equally sized recombination classes based on their average level of intragenic linkage disequilibrium. We find that  varies from 0.07 to 0.39 across species and is positively correlated with the level of recombination. This is both due to a higher estimated rate of adaptive evolution and a lower estimated rate of non-adaptive evolution, suggesting that recombination both increases the fixation probability of advantageous variants and decreases the probability of fixation of deleterious variants. Our results demonstrate that homologous recombination facilitates adaptive evolution measured by  in the core genome of prokaryote species in agreement with studies in eukaryotes.

Significance statementWhether intraspecific homologous recombination has a net beneficial or detrimental effect on adaptive evolution is largely unexplored in natural bacterial populations. We address this question by evaluating polymorphism and divergence data across the core genomes of 196 bacterial sequences--belonging to five closely related species of the genus Rhizobium. We show that the proportion of amino acid changes fixed due to adaptive evolution () increases with an increased recombination rate. This correlation is observed both in the interspecies and intraspecific comparisons. By using a population genetics approach our results demonstrate that homologous recombination directly impacts the efficacy of natural selection in the core genome of prokaryotes, as previously reported in eukaryotes.


title: Codominance of two symbiont genera within the same coral host is associated with elevated symbiont productivity and lower host susceptibility to thermal stress

abstract: In recent years, as sea surface temperature increases, many coral species that used to harbor symbionts of the genus Cladocopium have become colonized with the thermally tolerant genus, Durusdinium. Here, we asked how the symbionts of one genus react to the presence of another symbiont genus within the same coral host, and what effect this interaction has on the host. We used previously published transcriptomic data from Acropora hyacinthus corals hosting Cladocopium and/or Durusdinium symbionts and looked at gene expression in all three symbiotic partners depending on the relative proportion of the two symbiont genera within the same host. We find that both Cladocopium and Durusdinium change their expression the most when their proportions within the host are nearly equal (the state that we call "codominance"): both genera elevate expression of photosynthesis and ribosomal genes, suggesting increase in photosynthesis and growth (i.e. higher productivity). At the same time, the coral host also elevates production of ribosomes suggesting faster cellular growth, and, when heated, shows less pronounced stress response. These results can be explained in two alternative ways. One explanation is that increased competition between codominant symbionts switches them to the higher productivity mode, which benefits the host, making it more resilient to stress. Alternatively, the symbionts elevated productivity might be not the cause but the consequence of the host being particularly healthy. Under this explanation, rapid growth of the healthy host creates new space, lowering the symbioints competition and thus promoting their growth, which allows for codominance to happen where one genus would otherwise outcompete another. The latter explanation is supported by the fact that codominance is associated with lower symbiont densities, assessed as relative proportions of symbiont reads in the data. Irrespective of the causation direction, the presence of mixed symbiont communities could potentially be used as an instant indicator of coral well-being, which would be a useful tool for coral conservation and restoration.


title: Biochemical and Structural Characterization of Two Cif-Like Epoxide Hydrolases from Burkholderia cenocepacia

abstract: Epoxide hydrolases catalyze the conversion of epoxides to vicinal diols in a range of cellular processes such as signaling, detoxification, and virulence. These enzymes typically utilize a pair of tyrosine residues to orient the substrate epoxide ring in the active site and stabilize the hydrolysis intermediate. A new subclass of epoxide hydrolases that utilize a histidine in place of one of the tyrosines was established with the discovery of the CFTR Inhibitory Factor (Cif) from Pseudomonas aeruginosa. Although the presence of such Cif-like epoxide hydrolases was predicted in other opportunistic pathogens based on sequence analyses, only Cif and its homologue aCif from Acinetobacter nosocomialis have been characterized. Here we report the biochemical and structural characteristics of Cfl1 and Cfl2, two Cif-like epoxide hydrolases from Burkholderia cenocepacia. Cfl1 is able to hydrolyze xenobiotic as well as biological epoxides that might be encountered in the environment or during infection. In contrast, Cfl2 shows very low activity against a diverse set of epoxides. The crystal structures of the two proteins reveal quaternary structures that build on the well-known dimeric assembly of the /{beta} hydrolase domain, but broaden our understanding of the structural diversity encoded in novel oligomer interfaces. Analysis of the interfaces reveals both similarities and key differences in sequence conservation between the two assemblies, and between the canonical dimer and the novel oligomer interfaces of each assembly. Finally, we discuss the effects of these higher-order assemblies on the intra-monomer flexibility of Cfl1 and Cfl2 and their possible roles in regulating enzymatic activity.


title: Enrichment of Zα domains at cytoplasmic stress granules is due to their innate ability to bind nucleic acids

abstract: Z domains are a subfamily of winged Helix-Turn-Helix (wHTH) domains found exclusively in proteins involved in the nucleic acids sensory pathway of vertebrate innate immune system and host evasion by viral pathogens. Interestingly, they are the only known protein domains that recognise the left-handed helical conformation of both dsDNA and dsRNA, known as Z-DNA and Z-RNA. Previously, it has been demonstrated that ADAR1 and ZBP1, two proteins possessing the Z domains, localize to cytosolic stress granules. It was further speculated that such localization is principally mediated by Z domains. To characterize and better understand such distinct and specific localization, we characterised the in vivo interactions and localization pattern for the amino terminal region of human DAI harbouring two Z domains (Z{beta}DAI). Using immunoprecipitation and mass spectrometry, we identified several interacting partners that were components of the complex formed by Z domains and RNAs. Differential interacting partners to wild-type Z, relative to mutant proteins, demonstrated that most of the physiologically relevant interactions are mediated by the nucleic acid binding ability of the Z{beta}. Further, we also show enrichment of selected complex components in cytoplasmic stress granules under conditions of stress. This ability is mostly lost in the mutants of Z{beta}DAI (Z{beta}DAI 4xmut) that lack nucleic-acid binding ability. Thus, we posit that the mechanism for the translocation of Z domain-containing proteins to stress granules is mainly mediated by the nucleic acid binding ability of their Z domains. Finally, we demonstrate that FUS and PSF/p54nrb, two RNA binding proteins with established roles in stress granules, interact with Z, which provides strong evidence for a role of these proteins in the innate immune system.


title: Microarray screening reveals a non-conventional SUMO-binding mode linked to DNA repair by non-homologous end-joining

abstract: SUMOylation is critical for a plethora of cellular signalling pathways including the repair of DNA double-strand breaks (DSBs). If misrepaired, DSBs can lead to cancer, neurodegeneration, immunodeficiency and premature ageing. Based on systematic proteome microarray screening combined with widely applicable carbene footprinting and high-resolution structural profiling, we define two non-conventional SUMO2-binding modules on XRCC4, a DNA repair protein important for DSB repair by non-homologous end-joining (NHEJ). Mechanistically, interaction of SUMO2 with XRCC4 is incompatible with XRCC4 binding to at least two other NHEJ proteins - XLF and DNA ligase 4 (LIG4). These findings are consistent with SUMO2 interactions of XRCC4 acting as backup pathways at different stages of NHEJ, in the absence of these factors or their dysfunctioning. Such scenarios are not only relevant for carcinogenesis, but also for the design of precision anti-cancer medicines and the optimisation of CRISPR/Cas9-based gene editing. This work reveals insights into topology-specific SUMO recognition and its potential for modulating DSB repair by NHEJ. Moreover, it provides a rich resource on binary SUMO receptors that can be exploited for uncovering regulatory layers in a wide array of cellular processes.


title: In silico analysis and cluster validation of potential breast cancer nsSNPs of serological tumor marker CA27.29

abstract:
Background & ObjectivesCA27.29 is a breast cancer-associated glycoprotein. Many genetic variations caused by non-synonymous nucleotide polymorphisms (nsSNPs) are known to affect the functionality of the CA27.29 protein.

MethodsIn the present manuscript, an in silico analysis of the genetic variations in CA27.29 was done to observe functional nsSNPs that possibly alter its stability. Among 2205 SNPs identified from the publically available SNP database (dbSNP), 213 (9.66%) synonymous SNPs, 24 (1.09%) non-synonymous SNPs, and 1351 (61.27%) noncoding intronic SNPs were observed. The function predictability tools SIFT, Provean and Polyphen2 were used to uncover variations in the analyzed nsSNPs and their functionality.

ResultsA total of 16, 20 and 10 non-synonymous SNPs (nsSNPs) were predicted to be damaging or deleterious by SIFT, Polyphen, and Provean tools respectively. Intriguingly, 9 nsSNPs were predicted to be damaging by all the three tools used while 4 nsSNPs were predicted to be damaging by SIFT and Polyphen tools. The substitutions C/G->T and G->A/T were observed to be dominant in the analyzed nsSNPs that probably have damaging role to CA27.29 glycoprotein. Moreover, the validation of results using ClinVar tool revealed that all the analyzed possibly, probably and highly damaging nsSNPs are yet to be reported and studied. Besides this, we found Global minor allele frequency (Global MAF) for only 11 nsSNPs, the values of which were observed to be <0.1% that further confirmed the novelty of the analyzed variants.

Interpretation & ConclusionsAmong the analyzed nsSNPs, 3 nsSNPs rs145691584, rs148332231 and rs191544901 were found to be located in 3UTR region of CA27.29 gene that were assumed to have the possible functional roles in altering the protein stability. The present study is useful to gain useful insights into the genetic variations in nsSNPs that may playing a critical role in determining the susceptibility to breast cancer.


title: DevKidCC allows for robust classification and direct comparisons of kidney organoid datasets

abstract: Kidney organoids provide a valuable resource to understand kidney development and disease. Clustering algorithms and marker genes fail to accurately and robustly classify cellular identity between human pluripotent stem cell (hPSC)-derived organoid datasets. Here we present a new method able to accurately classify kidney cell subtypes, a hierarchical machine learning model trained using comprehensive reference data from single cell RNA-sequencing of human fetal kidney (HFK). We demonstrate the tools (DevKidCC) performance by application to all published kidney organoid datasets and a novel dataset. DevKidCC is available on Github and can be used on any kidney single cell RNA-sequence data.


title: Alignment of biomedical data repositories with open, FAIR, citable and trustworthy principles

abstract: Increasing attention is being paid to the operation of biomedical data repositories in light of efforts to improve how scientific data is handled and made available for the long term. Multiple groups have produced recommendations for functions that biomedical repositories should support, with many using requirements of the FAIR data principles as guidelines. However, FAIR is but one set of principles that has arisen out of the open science community. They are joined by principles governing open science, data citation and trustworthiness, all of which are important aspects for biomedical data repositories to support. Together, these define a framework for data repositories that we call OFCT: Open, FAIR, Citable and Trustworthy. Here we developed an instrument using the open source PolicyModels toolkit that attempts to operationalize key aspects of OFCT principles and piloted the instrument by evaluating eight biomedical community repositories listed by the NIDDK Information Network (dkNET.org). Repositories included both specialist repositories that focused on a particular data type or domain, in this case diabetes and metabolomics, and generalist repositories that accept all data types and domains. The goal of this work was both to obtain a sense of how much the design of current biomedical data repositories align with these principles and to augment the dkNET listing with additional information that may be important to investigators trying to choose a repository, e.g., does the repository fully support data citation? The evaluation was performed from March to November 2020 through inspection of documentation and interaction with the sites by the authors. Overall, although there was little explicit acknowledgement of any of the OFCT principles in our sample, the majority of repositories provided at least some support for their tenets.

category: scientific communication and education


title: A tool for assessing alignment of biomedical data repositories with open, FAIR, citation and trustworthy principles


title: Luminal nutrients activate distinct patterns in submucosal and myenteric neurons in the mouse small intestine

abstract: Nutrient signals sensed by enteroendocrine cells are conveyed to the enteric nervous system (ENS) to initiate intestinal reflexes. We addressed whether there are specific enteric pathways dedicated to detecting different luminal nutrients. Calcium imaging was performed on intact jejunal preparations from Wnt1-cre;R26R-GCaMP3 and Villin-cre;R26R-GCaMP3 mice which express a fluorescent calcium indicator in their ENS or intestinal epithelium, respectively. Glucose, acetate, and L-phenylalanine were perfused onto the mucosa whilst imaging underlying enteric neurons. Nutrient transport or diffusion across the mucosa was mimicked by applying nutrients onto sensory nerve endings in a villus, or onto myenteric ganglia. The nutrients perfused onto the mucosa each elicited Ca2+ transients in submucosal neurons and in distinct patterns of myenteric neurons. Notably, the neurochemical subtypes of myenteric neurons that responded differed between the nutrients, while submucosal responders were predominantly cholinergic. Nutrients applied into villi or onto ganglia did not elicit specific neuronal responses but did stimulate Ca2+ signaling in the mucosal epithelium. These data suggest that nutrients are first detected at the level of the epithelium and that the ENS is capable of discriminating between different compositions of luminal content. Furthermore, our data show that responses to mucosal stimulation are primarily in the myenteric plexus and submucosal neurons respond secondarily.


title: Itaconate and derivatives reduce interferon responses and inflammation in influenza A infection

abstract: Itaconate has recently emerged as a metabolite with immunomodulatory properties. We evaluated effects of endogenous itaconate and exogenous itaconate, dimethyl-, and 4-octyl-itaconate on host responses to influenza A virus infection. Infection induced ACOD1 (the enzyme catalyzing itaconate synthesis) mRNA in monocytes and macrophages, which correlated with viral replication and was abrogated by itaconate treatment. Pulmonary inflammation and weight loss were greater in Acod1-/- than wild-type mice, and ectopic synthesis of itaconate in human epithelial cells reduced infection-induced inflammation. The compounds induced different recruitment programs in infected human macrophages, and transcriptome profiling revealed that they reversed infection-triggered interferon responses and modulated inflammation in cell lines, PBMC, and lung tissue. Single-cell RNA sequencing of PBMC revealed that infection induced ACOD1 exclusively in monocytes, whereas treatment silenced IFN-responses in monocytes, lymphocytes, and NK cells. Viral replication did not increase under treatment despite the dramatically repressed IFN responses, but 4-octyl itaconate inhibited viral transcription in PBMC. The results reveal dramatic reprogramming of host responses by itaconate and derivatives and their potential as adjunct treatments for hyperinflammation in viral infection.


title: Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection


title: Adaptive laboratory evolution triggers pathogen-dependent broad-spectrum antimicrobial potency in Streptomyces

abstract: In the present study, adaptive laboratory evolution was used to stimulate antibiotic production in a weak antibiotic-producing Streptomyces strain JB140. The seven different competition experiments utilized three serial passages (three cycles of adaptation-selection of 15 days each) of a weak antibiotic-producing Streptomyces strain (wild-type) against one (biculture) or two (triculture) or three (quadriculture) target pathogens. This resulted in the evolution of a weak antibiotic-producing strain into the seven unique mutant phenotypes that acquired the ability to constitutively exhibit increased antimicrobial activity against bacterial pathogens. The mutant not only effectively inhibited the growth of the tested pathogens but also observed to produce antimicrobial against multidrug-resistant (MDR) E. coli. Intriguingly, the highest antimicrobial activity was registered with the Streptomyces mutants that were adaptively evolved against the three pathogens (quadriculture competition). In contrast to the adaptively evolved mutants, a weak antimicrobial activity was detected in the un-evolved, wild-type Streptomyces. To get molecular evidence of evolution, RAPD profiles of the wild-type Streptomyces and its evolved mutants were compared that revealed significant polymorphism among them. These results demonstrated that competition-based adaptive laboratory evolution method can constitute a platform for evolutionary engineering to select improved phenotypes (mutants) with increased production of antibiotics against targeted pathogens.


title: Helarchaeota and Co-occurring Sulfate-Reducing Bacteria in Subseafloor Sediments from the Costa Rica Margin

abstract: Deep sediments host many archaeal lineages, including those of the Asgard superphylum that may depend on/require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin. Our molecular analyses revealed three new metagenome-assembled genomes (MAGs) affiliating with Helarchaeota, each of which has three variants of the methyl-CoM reductase-like (MCR-like) complex that may enable them to oxidize short-chain alkanes anaerobically. These Helarchaeota have no multi-heme cytochromes (MHCs) but have Group 3b and Group 3c [NiFe] hydrogenases, and formate dehydrogenase, and therefore could transfer the reducing equivalents generated from alkane oxidation to external partners via the transfer of these substances. We also recovered five MAGs of SRB affiliated with the class of Desulfobacteria, two of which showed relative abundances (represented by genome coverages) positively correlated with those of the three Helarchaeota. Genome analysis suggested that these SRB bacteria have the capacity of H2 and formate utilizations and may facilitate electron transfers from other organisms by means of these reduced substances. Our findings suggest that Helarchaeota may metabolize synergistically with SRB in marine anoxic sediments, and exert an important influence on the carbon cycle by mitigating the hydrocarbon emission from sediments to the overlying ocean.


title: GRP78 binds SARS-CoV-2 Spike protein and ACE2 and GRP78 depleting antibody blocks viral entry and infection in vitro

abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the current COVID-19 global pandemic, utilizes the host receptor angiotensin-converting enzyme 2 (ACE2) for viral entry. However, other host factors may also play major roles in viral infection. Here we report that the stress-inducible molecular chaperone GRP78 can form a complex with the SARS-CoV-2 Spike protein and ACE2 intracellularly and on the cell surface, and that the substrate binding domain of GRP78 is critical for this function. Knock-down of GRP78 by siRNA dramatically reduced cell surface ACE2 expression. Treatment of lung epithelial cells with a humanized monoclonal antibody (hMAb159), selected for its ability to cause GRP78 endocytosis and its safe clinical profile in preclinical models, reduces cell surface ACE2 expression, SARS-CoV-2 Spike-driven viral entry, and significantly inhibits SARS-CoV-2 infection in vitro. Our data suggest that GRP78 is an important host auxiliary factor for SARS-CoV-2 entry and infection and a potential target to combat this novel pathogen and other viruses that utilize GRP78.


title: Genome recombination-mediated tRNA up-regulation conducts general antibiotic resistance of bacteria at early stage

abstract: Bacterial antibiotic resistance sets a great challenge to human health. It seems that the bacteria can spontaneously evolve resistance against any antibiotic within short time without the horizontal transfer of heterologous genes and before accumulating drug-resistant mutations. We have shown that the tRNA-mediated translational regulation counteracts the reactive oxygen species in bacteria. In this study, we demonstrated that isolated and subcultured Escherichia coli elevated its tRNAs under antibiotic stress to rapidly provide antibiotic resistance, especially at the early stage, before upregulating the efflux pump and evolving resistance mutations. The DNA recombination system repaired the antibiotic-induced DNA breakage in the genome, causing numerous structural variations. These structural variations are overrepresented near the tRNA genes, which indicated the cause of tRNA up-regulation. The strains knocking out the recombination system could not up-regulate tRNAs, and coincidently, they could hardly evolve antibiotic resistance in multiple antibiotics, respectively. With these results, we proposed a multi-stage model of bacterial antibiotic resistance in an isolated scenario: the early stage (recombination - tRNA up-regulation - translational regulation); the medium stage (up-regulation of efflux pump); the late stage (resistance mutations). These results also indicated that the bacterial DNA recombination system and tRNA could be targeted to retard the bacterial spontaneous drug resistance.


title: The power of dying slowly - persistence as unintentional dormancy

abstract:
Persistence is a state of bacterial dormancy where cells with low metabolic activity and growth rates are phenotypically tolerant to antibiotics and other cytotoxic substances. Given its obvious advantage to bacteria, several researchers have been looking for the genetic mechanism behind persistence. However, other authors argue that there is no such mechanism and that persistence results from inadvertent cell errors. In this case, the persistent population should decay according to a power-law with a particular exponent of -2. Studying persisters decay is, therefore, a valuable way to understand persistence. Here we simulated the fate of susceptible cells in laboratory experiments in the context of indirect resistance. Eventually, under indirect resistance, detoxifying drug-resistant cells save the persister cells that leave the dormant state and resume growth. The simulations presented here show that, by assuming a power-law decline, the exponent is close to -2, which is the expected value if persistence results from unintentional errors. Whether persisters are cells in a moribund state or, on the contrary, result from a genetic program, should impact the research of anti-persistent drugs.

Author SummaryPersistence, a form of bacterial dormancy, was discovered in the early days of the antibiotic era. Thanks to dormancy, these cells often evade antibiotic therapy and the immune system. However, despite its clinical importance, this phenotypes nature is still under debate. Arguably, the prevailing view is that persistence is an evolved (selected for) bet-hedging mechanism to survive in the presence of cytotoxic agents such as antibiotics. In that case, the persister population should decay exponentially, although at a much slower pace than the non-persister population. A few authors recently advanced an alternative hypothesis: bacterial persistence results from many malfunctions and cell division errors. In this case, persistent populations should decay according to a power-law with exponent of -2, that is, according to 1/t2. Here we simulated the fate of susceptible bacterial cells in the presence of bactericidal antibiotics in the context of indirect resistance based on laboratory experiments performed earlier. By showing that the dynamics of persister cells is consistent with 1/t2, our results corroborate the hypothesis that the phenomenon of bacterial persistence is an accidental consequence of inadvertent cell problems and errors. If confirmed, this conclusion should impact the research strategies of anti-persistent drugs.

O_QD"The following day, no one died. This fact, being absolutely contrary to lifes rules, provoked enormous and, in the circumstances, perfectly justifiable anxiety in peoples minds, for we have only to consider that in the entire forty volumes of universal history there is no mention, not even one exemplary case, of such a phenomenon ever having occurred..."

Death with interruptions

Jose Saramago (2005)

Nobel Prize for Literature 1998

C_QD


title: The Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster

abstract:
An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and its impact on host physiology. This research can be confounded by poorly-understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multi-way interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the Drosophila gut microbiome (from single taxa to the five-member community of Acetobacter and Lactobacillus species) under three nutrient regimes. We show that the metabolic function of Drosophila gut bacteria is dynamic, influenced by community composition and responsive to dietary modulation. Furthermore, we show that ecological interactions such as competition and mutualism identified from the growth patterns of gut bacteria are underlain by a diversity of metabolic interactions, and show that the bacteria tend to compete for amino acids and B vitamins more frequently than for carbon sources. Our results reveal that in addition to fermentation products such as acetate, intermediates of the tricarboxylic acid (TCA) cycle including 2-oxoglutarate and succinate are produced at high flux and cross-fed between bacterial taxa suggesting important roles for TCA cycle intermediates in modulating Drosophila gut microbe interactions and the potential to influence host traits. These metabolic models provide specific predictions of the patterns of ecological and metabolic interactions among gut bacteria under different nutrient regimes, with potentially important consequences for overall community metabolic function and nutritional interactions with the host.

IMPORTANCEDrosophila is an important model for microbiome research partly because of the low complexity of its mostly culturable gut microbiota. Our current understanding of how Drosophila interacts with its gut microbes and how these interactions influence host traits derives almost entirely from empirical studies that focus on individual microbial taxa or classes of metabolites. These studies have failed to capture fully the complexity of metabolic interactions that occur between host and microbe. To overcome this limitation, we reconstructed and analyzed 31 metabolic models for every combination of the five principal bacterial taxa in the gut microbiome of Drosophila. This revealed that metabolic interactions between between Drosophila gut bacterial taxa are highly dynamic and influenced by co-occurring bacteria and nutrient availability. Our results generate testable hypothesis about among-microbe ecological interactions in the Drosophila gut and the diversity of metabolites available to influence host traits.