title: An updated framework to account for inter-individual variability when quantifying phenotypic variation

abstract:
O_LIIn trait-based ecology, phenotypic variation (PVar) is often quantified with measures that express average differences between populations standardized in the range 0-1. A major problem with these measures is that they disregard the within-population trait variability. In addition, most of these measures cannot be decomposed across scales. This can alter their interpretation, thus limiting their applicability.
C_LIO_LITo overcome these problems, we propose a new measure, the Phenotypic Dissimilarity Index (PhD) that is insensitive to the within-population interindividual trait variability. Likewise, PhD can be used to quantify PVar between individuals in a population while accounting for the PVar within individuals.
C_LIO_LIUsing simulated and real data, we showed that PhD index correctly quantifies PVar when the within-population trait variability is not negligible, as in many ecological studies. By accounting for within-population trait variability, the PhD index generally provides a more parsimonious quantification of PVar across an environmental gradient compared to other estimators.
C_LIO_LITraits sampled within a species have an inherent variability. Accounting for such variability is essential to understand species phenotypic responses to environmental cues. As such, the PhD index will provide ecologists with an asset to reliably quantify and compare PVar within and between species across environmental gradients at different scales. We also provide an R function to calculate the PhD index.
C_LI

category: ecology


title: Uncertainty and precaution in hunting wolves twice in a year

abstract: When humanity confronts the risk of extinction of species, many people invoke precautions, especially in the face of uncertainty. Although precautionary approaches are value judgments, the optimal design and effect of precautions or lack thereof are scientific questions. We investigated Wisconsin gray wolves Canis lupus facing a second wolf-hunt in November 2021 and use three legal thresholds as the societal value judgments about precautions: (1) the 1999 population goal, 350 wolves, (2) the threshold for statutory listing under the state threatened and endangered species act, 250 wolves; and (3) state extirpation <2 wolves. This allows us to explore the quantitative relationship between precaution and uncertainty. Working from estimates of the size wolf population in April 2021 and reproduction to November, we constructed a simple linear model with uninformative priors for the period April 2021-April 2022 including an uncertain wolf-hunt in November 2021. Our first result is that the state government under-counted wolf deaths in the year preceding both wolf-hunts. We recommend better scientific analysis be used when setting wolf-hunt quotas. We find official recommendations for a quota for the November 2021 wolf-hunt risk undesirable outcomes. Even a quota of zero has a 13% chance of crossing threshold 1. Therefore, a zero death toll would be precautionary. Proponents for high quotas bear the burden of proof that their estimates are accurate, precise, and reproducible. We discuss why our approach is transferable to non-wolves. We show how scientists have the tools and concepts for quantifying and explaining the probabilities of crossing thresholds set by laws or other social norms. We recommend that scientists grapple with data gaps by explaining what the uncertainty means for policy and the public including the consequences of being wrong.


title: SARS-CoV-2 infects human adipose tissue and elicits an inflammatory response consistent with severe COVID-19

abstract:
The COVID-19 pandemic, caused by the viral pathogen SARS-CoV-2, has taken the lives of millions of individuals around the world. Obesity is associated with adverse COVID-19 outcomes, but the underlying mechanism is unknown. In this report, we demonstrate that human adipose tissue from multiple depots is permissive to SARS-CoV-2 infection and that infection elicits an inflammatory response, including the secretion of known inflammatory mediators of severe COVID-19. We identify two cellular targets of SARS-CoV-2 infection in adipose tissue: mature adipocytes and adipose tissue macrophages. Adipose tissue macrophage infection is largely restricted to a highly inflammatory subpopulation of macrophages, present at baseline, that is further activated in response to SARS-CoV-2 infection. Preadipocytes, while not infected, adopt a proinflammatory phenotype. We further demonstrate that SARS-CoV-2 RNA is detectable in adipocytes in COVID-19 autopsy cases and is associated with an inflammatory infiltrate. Collectively, our findings indicate that adipose tissue supports SARS-CoV-2 infection and pathogenic inflammation and may explain the link between obesity and severe COVID-19.

One sentence summaryOur work provides the first in vivo evidence of SARS-CoV-2 infection in human adipose tissue and describes the associated inflammation.

category: immunology


title: Diverse northern Asian and Jomon-related genetic structure discovered among socially complex Three Kingdoms period Gaya region Koreans

abstract:
The genetic history of prehistoric and protohistoric Korean populations is not well understood due to the lack of ancient Korean genomes. Here, we report the first paleogenomic data from Korea; eight shotgun-sequenced genomes (0.7x[~]6.1x coverage) from two archeological sites in Gimhae: Yuha-ri shell mound and Daesung-dong tumuli, the most important funerary complex of the Gaya confederacy. All eight individuals are from the Korean Three Kingdoms period (4th-7th century CE), during which there is archaeological evidence of extensive trade connections with both northern (modern-day China) and eastern (modern-day Japan) kingdoms. All genomes are best modeled as an admixture between a northern-Chinese Iron Age genetic source and a Japanese-Jomon-related ancestry. The proportion of Jomon-related ancestry suggests the presence of two genetic groups within the population. The observed substructure indicates diversity among the Gaya population that is not related to either social status or sex.

Teaser1,700-year-old genomes reveal the genetic diversity of ancient Koreans in the Gimhae region.

category: evolutionary biology


title: Humans, machines, and language: A deep alignment in underlying computational styles?

abstract: The emergence of artificial neural networks (ANNs) that seem capable of emulating the remarkable human capacity for language has raised fundamental questions about complex cognition in humans and machines. This debate has taken place, however, in the context of limited empirical evidence about how the internal operations of ANNs relate to dynamic processes in the human brain as listeners understand language. Using Representational Similarity Analysis, we conducted a set of in-depth comparisons between these two types of systems, focusing on a core aspect of human language - the building of a structured and meaningful interpretation as each word in a sentence is heard in sequence. We extracted incremental structural measures of unfolding sentences from a deep language ANN and tested these against the spatiotemporally resolved brain activity recorded by electro/magnetoencephalography when human participants were listening to the same sentences. These uniquely neurocomputationally specific comparisons revealed strong behavioral and neural alignments between humans and ANNs in the use of multi-dimensional probabilistic constraints to build word-by-word structural interpretations, suggesting important commonalities in basic computational strategies for finding structure in time.

category: neuroscience


title: Finding structure in time: Humans, machines, and language


title: Integrative multi-omics analyses reveal multi-modal FOXG1 functions acting on epigenetic processes and in concert with NEUROD1 to regulate synaptogenesis in the mouse hippocampus

abstract:
BackgroundFOXG1 has important functions for neuronal differentiation and balances excitatory/inhibitory network activity. Mutations in the human FOXG1 gene cause a rare neurodevelopmental disorder, FOXG1-syndrome, which manifests differing phenotypes, including severe cognitive dysfunction, microencephaly, social withdrawal, and communication and memory deficits. Changes at the molecular level underlying these functional abnormalities upon FOXG1 haploinsufficiency are largely unexplored, in human patients as well as in animals modelling the debilitating disease.

MethodsWe present multi-omics data and explore comprehensively how FOXG1 impacts neuronal maturation at the chromatin level in the adult mouse hippocampus. We used RNA-, ATAC- and ChIP-sequencing of primary hippocampal neurons and co-immunoprecipitation to explore various levels of epigenetic changes and transcription factor networks acting to alter neuronal differentiation upon reduction of FOXG1.

ResultsWe provide the first comprehensive multi-omics data set exploring FOXG1 presence at the chromatin and identifying the consequences of reduced FOXG1 expression in primary hippocampal neurons. Analyzing the multi-omics data, our study reveals that FOXG1 uses various different ways to regulate transcription at the chromatin level. On a genome-wide level, FOXG1 (i) both represses and activates transcription, (ii) binds mainly to enhancer regions, and (iii) bidirectionally alters the epigenetic landscape in regard to levels of H3K27ac, H3K4me3, and chromatin accessibility. Genes affected by the chromatin alterations upon FOXG1 reduction impact synaptogenesis and axonogenesis. This finding emphasizes the importance of FOXG1 to integrate and coordinate transcription of genes necessary for proper neuronal function by acting on a genome-wide level. Interestingly, FOXG1 acts through histone deacetylases (HDACs) and inhibition of HDACs partly rescued transcriptional alterations observed upon FOXG1 reduction. On a more detailed level of analysis, we show that FOXG1 (iv) operates synergistically with NEUROD1. Interestingly, we could not detect a clear hierarchy of these two key transcription factors, but instead provide first evidence that they act in highly concerted and orchestrated manner to control neuronal differentiation.

ConclusionsThis integrative and multi-omics view of changes upon FOXG1 reduction reveals an unprecedented multimodality of FOXG1 functions converging on neuronal maturation, fueling novel therapeutic options based on epigenetic drugs to alleviate, at least in part, neuronal dysfunctions.


title: General dimensions of human brain morphometry inferred from genome-wide association data

abstract: Understanding the neurodegenerative mechanisms underlying cognitive declines in the general population may facilitate early detection of adverse health outcomes in late life. We develop Genomic Principal Components Analysis (genomic PCA) to elucidate the complex biological connections between macroscopic brain organisation, ageing, and cognitive ability. A genetic principal component (PC) representing dimensions of shared genetic architecture in brain morphometry across the whole brain accounted for 40% of the genetic variance across 83 individual brain regions. Genomic PCs corresponding to more specific canonical brain networks of interest accounted for 47-65% of the genetic variance in the corresponding brain regions. These genomic PCs were negatively associated with a measure of brain age (rg = -0.34) and the loadings of individual brain regions on the whole brain genomic PC corresponded to sensitivity of the corresponding region to age (r = -0.27). We identified positive genetic associations between the genomic PCs of brain morphometry and a general factor of cognitive ability (rg = 0.17-0.21 for different networks). Genomic PCA allowed us to model structural covariance within brain networks at the level of their underlying genetic architecture. We identified substantial genetic overlap between brain morphometry, ageing, and cognitive ability.

category: genetics


title: Development of Permanent Artificial Bowel Replacement Substrates

abstract:
Short bowel syndrome (SDS) is a malabsorption disorder caused by loss of function of the small intestine, either by trauma or innately. Current treatment options include parenteral nutrition (PN) or allograft transplants. Long term PN dependence can lead to complications due to line infections and toxicity from the formula itself. A lack of healthy donors results in long waiting lists and high mortality rates. With allograft transplants, long-term graft and patient survival rates are poor (48% and 39% respectively at 5 years); graft loss occurs due to rejection (48%), thrombosis (28%), sepsis (12%); main causes of death are due to bacterial infection (94%) and rejection. Costs associated with PN annually per patient approximate to {pound}40,000, whereas one allograft procedure costs approximately {pound}80,000; not including intervention due to complications.

Interest in developing an off-the-shelf bioengineered alternative have been expressed. Autologous transplants could be a more beneficial route to improving survival rates, enabling the transplant of patients healthy cells back to them. We describe here the development of a synthetic poly(ethylene terephthalate) scaffold using electrospinning, which showed excellent physical and chemical characteristics; high surface area:volume ratio, high mechanical strength, high porosity, and the ability to be chemically/physically functionalised without losing integrity in structure and physical properties. The cost of electrospinning is far lower in comparison to the current available treatment options, potentially providing a stable, off-the-shelf, ready-to-culture product as the need arises for applications in tissue engineered small intestine (TESI), or 3D models for small bowel research.

category: bioengineering


title: A Biodegradable, Tacrolimus-releasing Nerve Wrap Promotes Peripheral Nerve Regeneration

abstract: Axonal regeneration following nerve repair is slow and often incomplete, resulting in poor functional recovery and sometimes lifelong disability. Yet, there are no FDA-approved therapies available to promote nerve regeneration. Tacrolimus accelerates axonal regeneration, but systemic side-effects presently outweigh its potential benefits for peripheral nerve surgery. We have developed a biodegradable drug delivery system for the sustained local release of tacrolimus at the nerve repair site, with suitable properties for large-scale manufacturing and clinical application, aiming to promote axonal regeneration and functional recovery with minimal systemic drug exposure. Tacrolimus is encapsulated in polycarbonate-urethane nanofibers and electrospun to generate an implantable nerve wrap that releases therapeutic doses of bioactive tacrolimus over 31 days. Size and drug loading are adjustable for applications in small and large caliber nerves, and the wrap degrades within 120 days into biocompatible byproducts. Tacrolimus released from the nerve wrap promotes axon elongation in vitro and accelerates nerve regeneration and functional recovery in preclinical nerve repair models while systemic drug exposure is reduced by 80% compared to systemic delivery. Given its surgical suitability and preclinical efficacy and safety, this system may provide a readily translatable approach to support axonal regeneration and recovery in patients undergoing nerve surgery.


title: A data-informed mean-field approach to mapping of cortical parameter landscapes

abstract:
Constraining the many biological parameters that govern cortical dynamics is computa-tionally and conceptually difficult because of the curse of dimensionality. This paper addresses these challenges by proposing (1) a novel data-informed mean-field (MF) approach to efficiently map the parameter space of network models; and (2) an organizing principle for studying parameter space that enables the extraction biologically meaningful relations from this high-dimensional data. We illustrate these ideas using a large-scale network model of the Macaque primary visual cortex. Of the 10-20 model parameters, we identify 7 that are especially poorly constrained, and use the MF algorithm in (1) to discover the firing rate contours in this 7D parameter cube. Defining a "biologically plausible" region to consist of parameters that exhibit spontaneous Excitatory and Inhibitory firing rates compatible with experimental values, we find that this region is a slightly thickened codimension-1 submanifold. An implication of this finding is that while plausible regimes depend sensitively on parameters, they are also robust and flexible provided one compensates appropriately when parameters are varied. Our organizing principle for conceptualizing parameter dependence is to focus on certain 2D parameter planes that govern lateral inhibition: Intersecting these planes with the biologically plausible region leads to very simple geometric structures which, when suitably scaled, have a universal character independent of where the intersections are taken. In addition to elucidating the geometry of the plausible region, this invariance suggests useful approximate scaling relations. Our study offers, for the first time, a complete characterization of the set of all biologically plausible parameters for a detailed cortical model, which has been out of reach due to the high dimensionality of parameter space.

Author SummaryCortical circuits are characterized by a high degree of structural and dynamical complexity, and this biological reality is reflected in the large number of parameters in even semi-realistic cortical models. A fundamental task of computational neuroscience is to understand how these parameters govern network dynamics. While some neuronal parameters can be measured in vivo, many remain poorly constrained due to limitations of available experimental techniques. Computational models can address this problem by relating difficult-to-measure parameters to observable quantities, but to do so one must overcome two challenges: (1) the computational expense of mapping a high dimensional parameter space, and (2) extracting biological insights from such a map. This study aims to address these challenges in the following ways: First, we propose a parsimonious data-informed algorithm that efficiently predicts spontaneous cortical activity, thereby speeding up the mapping of parameter landscapes. Second, we show that lateral inhibition provides a basis for conceptualizing cortical parameter space, enabling us to begin to make sense of its geometric structure and attendant scaling relations. We illustrate our approach on a biologically realistic model of the monkey primary visual cortex.


title: Tension-driven multi-scale self-organisation in human iPSC-derived muscle fibers

abstract: Human muscle is a hierarchically organised tissue with its contractile cells called myofibers packed into large myofiber bundles. Each myofiber contains periodic myofibrils built by hundreds of contractile sarcomeres that generate large mechanical forces. To better understand the mechanisms that coordinate human muscle morphogenesis from tissue to molecular scales, we adopted a simple in vitro system using induced pluripotent stem cell-derived human myogenic precursors. When grown on an unrestricted two-dimensional substrate, developing myofibers spontaneously align and self-organise into higher-order myofiber bundles, which grow and consolidate to stable sizes. Following a transcriptional boost of sarcomeric components, myofibrils assemble into chains of periodic sarcomeres that emerge across the entire myofiber. By directly probing tension we found that tension build-up precedes sarcomere assembly and increases within each assembling myofibril. Furthermore, we found that myofiber ends stably attach to other myofibers using integrin-based attachments and thus myofiber bundling coincides with stable myofiber bundle attachment in vitro. A failure in stable myofiber attachment results in a collapse of the myofibrils. Overall, our results strongly suggest that mechanical tension across sarcomeric components as well as between differentiating myofibers is key to coordinate the multi-scale self-organisation of muscle morphogenesis.

category: developmental biology


title: Infants' attention to eyes is an independent, heritable trait predicting later verbal competence

abstract: From birth, infants orient preferentially to faces, and when looking at the face, they attend primarily to eyes and mouth - two areas that convey different types of information. Here, in a sample of 535 5-month-old infant twins, we assessed eye (relative to mouth) preference in early infancy. Eye preference was independent from all other concurrent traits measured, and had a moderate-to-high contribution from genetic influences (A = .57; 95% CI: .45, .66). Preference for eyes over mouth at 5 months predicted higher parent ratings of verbal competence in toddlerhood, but did not predict autistic traits. These results suggest that variation in eye looking reflects a type of biological niche picking emerging before infants can select their environments by other means (crawling or walking).


title: Single injection of very mild dose BOTOX in the vastus lateralis improves testicular spermatogenesis and sperm motility in ageing experimental mice

abstract: Acetylcholine (ACh), a key neurochemical messenger that plays key roles in neuroplasticity and muscle contraction. While ACh is important for the physiological function of the testis, abnormal levels of ACh cause testicular atrophy and male infertility. BOTOX is a therapeutic form of the botulinum neurotoxin that blocks the excessive release of ACh at the neuromuscular junction. Previously, repeated intracremasteric injections and slight overdose of BOTOX have been reported to induce adverse effects in the testicular parameter of experimental rodents. However, a mild dose of BOTOX is highly beneficial against skin ageing, neurological deficits, overactive urinary bladder problems, testicular pain and erectile dysfunctions. Considering the facts, the possible therapeutic benefit of BOTOX on the testis might be achieved via its minimal dose and indirect mode of action rather than repeated high quantity in the local supply. Therefore, we revisited the effect of BOTOX but with a trace amount injected into the vastus lateralis of the thigh muscle, and analyzed histological parameters of testis and quality of semen in ageing experimental mice. Experimental animals injected with 1 U/kg bodyweight of BOTOX showed enhanced spermatogenesis in associations with increased activities of key antioxidants in the testis, leading to increased total sperm count and motility. This study signifies that a mild intramuscular dose of BOTOX can be considered as a potential treatment strategy to manage and prevent male infertility.

category: pharmacology and toxicology


title: Comparing adaptive coding of reward in bipolar I disorder and schizophrenia

abstract:
BackgroundDeficits in neural processing of reward have been described in both bipolar disorder (BD) and schizophrenia (SZ), but it remains unclear to what extent these deficits are caused by similar mechanisms. Efficient reward processing relies on adaptive coding which allows representing large input spans by limited neuronal encoding ranges. Deficits in adaptive coding of reward have previously been observed across the SZ spectrum and correlated with total symptom severity. In the present work we sought to establish whether adaptive coding is similarly affected in patients with BD.

Methods25 patients with BD, 27 patients with SZ and 25 healthy controls performed a variant of the Monetary Incentive Delay task during functional magnetic resonance imaging in two reward range conditions.

ResultsAdaptive coding was impaired in BD and SZ in the posterior part of the right caudate. In contrast, BD did not show impaired adaptive coding in the anterior caudate and right precentral gyrus/insula, where SZ showed deficits compared to healthy controls.

ConclusionsBD patients show adaptive coding deficits, that are similar to those observed in SZ in the right posterior caudate. Adaptive coding in BD appeared more preserved as compared to SZ participants especially in the more anterior part of the right caudate and to a lesser extent also in the right precentral gyrus. Thus, dysfunctional adaptive coding could constitute a fundamental deficit in severe mental illnesses that extends beyond the schizophrenia spectrum.


title: Neural basis of learning to perceive speech through touch using an acoustic-to-vibrotactile speech sensory substitution

abstract:
The goal of sensory substitution is to convey the information transduced by one sensory system through a novel sensory modality. One example is vibrotactile (VT) speech, for which acoustic speech is transformed into vibrotactile patterns. Despite an almost century-long history of studying vibrotactile speech, there has been no study of the neural bases of VT speech learning. We here trained hearing adult participants to recognize VT speech syllables. Using fMRI, we showed that both somatosensory (left post-central gyrus) and auditory (right temporal lobe) regions acquire selectivity for VT speech stimuli following training. The right planum temporale in particular was selective for both VT and auditory speech. EEG source-estimated activity revealed temporal dynamics consistent with direct, low-latency engagement of right temporal lobe following activation of the left post-central gyrus. Our results suggest that VT speech learning achieves integration with the auditory speech system by "piggybacking" onto corresponding auditory speech representations.

Significance statementIn sensory substitution, the information conveyed by one sensory system is used to replace the function of another. Blind individuals, for example, can learn to use a visual-to-acoustic sensory substitution device to navigate the world. We tested the hypothesis that sensory substitution can more generally occur in typical individuals, by exploiting the existence of multi-sensory convergence areas in the brain. We trained hearing participants to recognize speech syllables presented as vibrotactile stimulation patterns. Using fMRI and EEG, we show that vibrotactile speech learning integrates with the auditory speech system by "piggybacking" onto corresponding auditory speech representations. These results suggest that the human brain can bootstrap new senses by leveraging one sensory system to process information normally processed by another.


title: The challenges of independence: ontogeny of at-sea behaviour in a long-lived seabird

abstract: The transition to independent foraging represents an important developmental stage in the life cycle of most vertebrate animals. Juveniles differ from adults in various life history traits and tend to survive less well than adults in most long-lived animals. Several hypotheses have been proposed to explain higher mortality including that of inadequate/inferior foraging skills compared to adults, young naive individuals combining lack of experience and physical immaturity. Thus a change in behaviour, resulting in an improvement of skills acquired from growing experience, is expected to occur during a period of learning through the immaturity phase. Very few studies have investigated the ontogeny of foraging behaviour over long periods of time, particularly in long-lived pelagic seabirds, due to the difficulty of obtaining individual tracking data over several years. We investigated the foraging behaviour, through activity patterns, during the successive life stages of the endangered Amsterdam albatross by using miniaturized activity loggers on naive juveniles, immatures and adults. Juvenile naive birds during their first month at sea after leaving their colony exhibited lower foraging effort (greater proportion of time spent sitting on water, higher duration and more numerous bouts on water, and lower duration and less numerous flying bouts). Juveniles reached similar activity values to those of immatures and adults as early as the 2nd-3rd months since independence, suggesting a progressive improvement of foraging performances during the first two months since fledging. We found support for the body-size hypothesis with respect to sex differences in activity parameters according to time elapsed since departure from the colony and month of the year, consistent with the important sexual dimorphism in the Amsterdam albatross. Whatever the life stage considered, activity parameters exhibited temporal variability reflecting the modulation of foraging behaviour possibly linked to both extrinsic (i.e. environmental conditions such as variability in food resources or in wind) and intrinsic (i.e. energetic demands linked to plumage renew during moult) factors.


title: Hyaluronan and Elastin-Like Protein (HELP) Gels Significantly Improve Cargo Retention in the Myocardium

abstract: Heart disease is the leading cause of death globally, and delivery of therapeutic cargo (e.g. cells, proteins, drugs) through direct injection into the myocardium is a promising clinical intervention. However, retention of deliverables to the contracting myocardium is low, with as much as 60 - 90% of payload being lost within 24 hours. Commercially-available injectable hydrogels, including Matrigel, have been hypothesized to increase payload retention, but have not yielded significant improvements in quantified analyses. Here, we assess a recombinant hydrogel composed of chemically modified hyaluronan and elastin-like protein (HELP) as an alternative injectable carrier to increase cargo retention. HELP is crosslinked using dynamic covalent bonds, and tuning the hyaluronan chemistry significantly alters hydrogel mechanical properties including stiffness, stress-relaxation rate, and ease of injectability through a needle or catheter. These materials can be injected even after complete crosslinking, extending the time window for surgical delivery. We show that HELP gels significantly improve in vivo retention of microsphere cargo compared to Matrigel, both 1 day and 7 days post-injection directly into the rat myocardium. These data suggest that HELP gels may assist with the clinical translation of therapeutic cargo designed for delivery into the contracting myocardium by preventing acute cargo loss.


title: The role of extracellular matrix biomolecules on endometrial epithelial cell attachment and cytokeratin 18 expression on gelatin hydrogels

abstract: The endometrium undergoes profound changes in tissue architecture and composition, both during the menstrual cycle as well as in the context of pregnancy. Dynamic remodeling processes of the endometrial extracellular matrix (ECM) are a major element of endometrial homeostasis, including changes across the menstrual cycle. A critical element of this tissue microenvironment is the endometrial basement membrane, a specialized layer of proteins that separates the endometrial epithelium from the underlying endometrial ECM. Bioengineering models of the endometrial microenvironment that present an appropriate endometrial ECM and basement membrane may provide an improved environment to study endometrial epithelial cell (EEC) function. Here, we exploit a tiered approach using two-dimensional high throughput microarrays and three-dimensional gelatin hydrogels to define patterns of EEC attachment and cytokeratin 18 (CK18) expression in response to combinations of endometrial basement membrane proteins. We identify combinations (collagen IV + tenascin C; collagen I + collagen III; hyaluronic acid + tenascin C; collagen V; collagen V + hyaluronic acid; collagen III; collagen I) that facilitate increased EEC attachment, increased CK18 intensity, or both. We also identify significant EEC mediated remodeling of the GelMA matrix environment via analysis of nascent protein deposition. Together, we report efforts to tailor the localization of basement membrane-associated proteins and proteoglycans in order to investigate tissue engineered models of the endometrial microenvironment.


title: Plant structural and nutritional responses to drought differ among common pasture species

abstract: In the face of a changing climate, research indicates that more frequent and severe drought conditions are critical problems that will constrain production of high-quality forage and influence the performance of grazing animals in the future. In addition, the duration of drought and potential trade-offs between plant morphology and nutritional composition may influence plant drought adaptation strategies across pasture species, and the consequences for forage quality are not well understood. Here we present the results of a study investigating the effects of drought on biomass productivity, dead material, leaf:stem biomass allocation and nutritional composition (whole-plant and tissue-specific) across nine diverse pasture species. For this, we conducted a field experiment exposing species to a 6-month period of simulated severe drought (60% rainfall reduction during winter and spring) and samples were collected at multiple harvests. We found that drought had different, harvest-specific effects on plant biomass structure and nutritional composition among pasture species. The severity of drought impacts on productivity, but not on nutritional quality, increased with drought duration. In general, drought strongly reduced productivity, increased the percentage of dead material and had mixed effects (increases, decreases and no effect) on leaf:stem ratio and concentrations of crude protein, non-structural carbohydrates, neutral detergent fibre and lignin. Changes in plant-level nutritional quality were driven by simultaneous changes in both leaf and stem tissues for most, but not all, species. Our findings may be especially helpful for selection of adapted species/cultivars that could minimize potential drought risks on forage, thereby optimising pasture performance under future drought scenarios.

category: plant biology


title: Bronco T (Shirisadi kasaya), a polyherbal formulation ameliorates LPS induced septicemia in rats

abstract: Septicemia is a life-threatening state, leading to multi-organ failure, ARDS and death. So, efforts are being made to identify novel therapies. Here, Bronco T (BT), a polyherbal formulation developed in 1984 for treating asthma, has been repurposed against septicemia induced ALI. The LPS (3mg/kg BW) was injected intraperitoneally before 24 hours, of surgery to assess the cardiorespiratory parameters, blood PaO2/FiO2, pulmonary water content and histological changes in the lungs. The pentoxifylline (PTX) (25 mg/kg b.w.) was used as the positive control. The PTX was given one hour before LPS and BT was given 3 hours (orally in different doses of 3, 1.5 and 0.75 gm/kg BW) to maintain the Cmax of the drug. The LPS treated group showed significant bradypnea, bradycardia and low heart rate frequency as observed, through elongated peaks (RR) and (MAP) respectively and finally death after 95 minutes of LPS injection. The PTX and BT (3gm/kg) pretreatment significantly prevented these changes (dose-dependent in the BT group). The survival was maintained up to 190 min after LPS. The Pentoxifylline showed a better response (75%) than Bronco T (72%). In both the treatments, a significant decrease in pulmonary water content and minimal neutrophil infiltration and intact alveoli-capillary membrane was seen in the transverse section (T.S) of the lungs. Conclusion: Significant improvement was noted in survival time, lesser tissue damage and better lung physiology by treating with Bronco T in LPS induced septicemia.


title: State-of-the-art EEG artifact removal evaluation

abstract:
ObjectElectroencephalography (EEG) signals suffer from a low signal-to-noise ratio and are very susceptible to muscular, ambient noise, and other artifacts. Many artifact removal algorithms have been proposed to address this problem. However, the evaluation of these algorithms is conventionally too indirect (e.g., black-box comparisons of brain-computer interface performance before and after removal) because it is unclear which part of the signal represents raw EEG and which is noise. This project objectively benchmarks popular artifact removal algorithms and evaluates the fundamental Independent Component Analysis (ICA) approach thanks to a unique dataset where EEG is recorded simultaneously with other physiological signals-facial electromyography (EMG), accelerometers, and gyroscope-while ten subjects perform several repetitions of common artifact-inflicting tasks (blinking, speaking, etc.).

ApproachI have compared the correlation between EEG signals and the artifact-representing channels before and after applying an artifact removal algorithm across the different artifact-inflicting tasks. The extent to which an artifact removal method can reduce this correlation objectively quantifies its effectiveness for the different artifacts. In the same direction, I have determined to what extent ICA successfully detects artefactual components in EEG by comparing the corresponding correlations for independent components that are labelled as artifacts with those labeled as EEG.

Main resultThe FORCe was found to be the most effective and generic artifact removal method, cleaning almost 40% of artifacts. ICA is shown to be able to isolate almost 70% of artefactual components.

SignificanceThis work alleviates the problem of unreliable evaluation of EEG artifact removal frameworks and provides the first reliable benchmark for the most popular algorithms in this literature.


title: Integrating melt-electrowriting and inkjet bioprinting for engineering structurally organized articular cartilage

abstract: Successful cartilage engineering requires the generation of biological grafts mimicking the structure, composition and mechanical behaviour of the native tissue. Here melt-electrowriting (MEW) was used to produce arrays of polymeric structures whose function was to orient the growth of cellular aggregates spontaneously generated within these structures, and to provide tensile reinforcement to the resulting tissues. Inkjeting was used to deposit defined numbers of cells into MEW structures, which self-assembled into an organized array of spheroids within hours, ultimately generating a hybrid tissue that was hyaline-like in composition. Structurally, the engineered cartilage mimicked the histotypical organization observed in skeletally immature synovial joints. This biofabrication framework was then used to generate scaled-up (50mm x 50mm) cartilage implants containing over 3,500 cellular aggregates in under 15 minutes. After 8 weeks in culture, a 50-fold increase in the compressive properties of these MEW reinforced tissues were observed, while the tensile properties were still dominated by the polymer network, resulting in a composite construct demonstrating tension-compression nonlinearity mimetic of the native tissue. Helium ion microscopy further demonstrated the development of an arcading collagen network within the engineered tissue. This hybrid bioprinting strategy provides a versatile and scalable approach to engineer cartilage biomimetic grafts for biological joint resurfacing.


title: Fitness tracking reveals task-specific associations between memory, mental health, and exercise

abstract: Physical exercise can benefit both physical and mental well-being. Different forms of exercise (i.e., aerobic versus anaerobic; running versus walking, swimming, or yoga; high-intensity interval training versus endurance workouts; etc.) impact physical fitness in different ways. For example, running may substantially impact leg and heart strength but only moderately impact arm strength. We hypothesized that the mental benefits of exercise might be similarly differentiated. We focused specifically on how different forms of exercise might related to different aspects of memory and mental health. To test our hypothesis, we collected (in aggregate) roughly a centurys worth of fitness data. We then asked participants to fill out surveys asking them to self-report on different aspects of their mental health. We also asked participants to engage in a battery of memory tasks that tested their short and long term episodic, semantic, and spatial memory performance. We found that participants with similar exercise habits and fitness profiles tended to also exhibit similar mental health and task performance profiles. These effects were task-specific in that different exercise patterns or fitness characteristics varied with different aspects of memory, on different tasks.


title: A 6-CpG Validated Methylation Risk Score Model for Metabolic Syndrome: The HyperGEN and GOLDN Studies

abstract: There has been great interest in genetic risk prediction using risk scores in recent years, however, the utility of scores developed in European populations and later applied to non-European populations has not been successful. In this study, we used cross-sectional data from the Hypertension Genetic Epidemiology Network (HyperGEN, N=614 African Americans (AA)) and the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN, N=995 European Americans (EA)), to create a methylation risk score (MRS) for metabolic syndrome (MetS), demonstrating the utility of MRS across race groups. To demonstrate this, we first selected cytosine-guanine dinucleotides (CpG) sites measured on Illumina Methyl450 arrays previously reported to be significantly associated with MetS and/or component conditions (CPT1A cg00574958, PHOSPHO1 cg02650017, ABCG1 cg06500161, SREBF1 cg11024682, SOCS3 cg18181703, TXNIP cg19693031). Second, we calculated the parameter estimates for the 6 CpGs in the HyperGEN data and used the beta estimates as weights to construct a MRS in HyperGEN, which was validated in GOLDN. We performed association analyses using a logistic mixed model to test the association between the MRS and MetS adjusting for covariates. Results showed the MRS was significantly associated with MetS in both populations. In summary, a MRS for MetS was a strong predictor for the condition across two ethnic groups suggesting MRS may be useful to examine metabolic disease risk or related complications across ethnic groups.


title: Establishing CREATE: Lessons learned in setting up a training environment for early-career researchers in respiratory medicine

abstract:
BackgroundThe purpose of the National Health and Medical Research Council Centre of Research Excellence in Pulmonary Fibrosis (CRE-PF) is to improve and extend the lives of patients living with pulmonary fibrosis through the development of a comprehensive and integrated program of basic and clinical research and education across Australia. A key objective of the CRE-PF was establishment of a unique national training scheme, CREATE, for early-career researchers (ECRs) in respiratory research. CREATE ECRs are broadly drawn from two main fields of researchers: clinicians and scientists, where clinicians tend to be involved in part-time translational research and scientists are involved in broad scientific research including laboratory or genetic research, health economics or population research.

MethodsWe describe the CREATE Program which, with limited budget and the assistance of key organisations, has provided funding opportunities (scholarships, fellowships, prizes, travel and collaboration grants), professional development (mentoring program, symposia, presentation opportunities and on-line training) and fostered a connected, supportive research community for respiratory ECRs.

ResultsThe CREATE program has successfully fostered the development of the supported researchers, contributing substantially to the future of pulmonary fibrosis research in Australia. During the life of the program the CRE-PF has offered 10 PhD scholarships and five postdoctoral fellowships, awarded 13 travel grants and three grants to promote collaboration between ECRs from different institutes. A mentoring program has been established and CREATE Symposia have been held in association with key meetings. During COVID-19 restrictions, a series of virtual research meetings has offered 12 CREATE ECRs from seven universities the opportunity to present their research to a national audience.

CREATE research-related achievements are impressive, including over 80 first-author publications by ECRs, and many conference presentations. Contributions to the research community, measured by committee membership, is also strong.

ConclusionsIn spite of a very limited budget, wide geographic distribution of participants and the multi-disciplinary nature of the cohort, we have succeeded in providing a unique, supportive academic development environment for CREATE ECRs. Lessons learned in the process of developing this program include the importance of leveraging funding, being flexible, building networks and seeking and responding to ECR input.

category: scientific communication and education


title: SPARClink: an interactive tool to visualize the impact of the SPARC program

abstract: The NIH SPARC program seeks to accelerate the development of therapeutic devices that modulate electrical activity in nerves to improve organ function. SPARC-funded researchers are generating rich datasets from neuromodulation research that are curated and shared according to FAIR (Findable, Accessible, Interoperable, and Reusable) guidelines and are accessible to the public on the SPARC data portal. Keeping track of the utilization of these datasets within the larger research community is a feature that will benefit data generating researchers in showcasing the impact of their SPARC outcomes. This will also allow the SPARC program to display the impact of the FAIR data curation and sharing practices that have been implemented. This manuscript provides the methods and outcomes of SPARClink, our web tool for visualizing the impact of SPARC, which won the 2nd prize at the 2021 SPARC FAIR Codeathon. With SPARClink, we built a system that automatically and continuously finds new published SPARC scientific outputs (datasets, publications, protocols) and the external resources referring to them. SPARC datasets and protocols are queried using publicly accessible REST APIs (provided by Pennsieve and Protocols.io) and stored in a publicly accessible database. Citation information for these resources is retrieved using the NIH reporter API and NCBI Entrez system. A novel knowledge-graph-based structure was created to visualize the results of these queries and showcase the impact that the FAIR data principles can have on the research landscape when they are adopted by a consortium.

category: bioinformatics


title: UHRF1, NSUN2, and NEIL1 were Detected as Clinical Biomarker Candidates in Prostate Adenocarcinoma with Potential Roles in Disease Pathogenesis

abstract: Prostate cancer (PCa) is the most commonly diagnosed cancer in men. Expanding evidence suggests a significant association between cancer progression and RNA modifications. However, our knowledge of the link between m5C and hm5C pathways with PCa is limited. Therefore, we aimed to explore the diagnostic and prognostic values of m5C and hm5C regulators in PCa. In this study, genetic alterations in m5C and hm5C regulators were identified using publicly available databases. Differentially expressed genes in these pathways between tumor and nontumor samples, correlation among m5C and hm5C pathway members, and prognostic value of the regulators were evaluated. Furthermore, enrichment of gene ontology (GO) terms and KEGG pathways was carried out. Obtained results unveiled the mRNA level differences as the key genetic alterations for m5C and hm5C regulators between tumor and nontumor samples. UHRF1, TET3, and NEIL1 were significantly upregulated in tumor samples compared to nontumor ones, whereas EGR1 was significantly downregulated. UHRF1, DNMT1, NSUN2, NSUN4, C1orf77, C3orf37, WDR77, NEIL1, and TDG genes were identified as candidate prognostic markers of overall survival. The upregulated genes in patient samples with genetic alterations in m5C and hm5C pathways enriched cell cycle-related processes. In summary, our findings suggest that the m5C and hm5C regulators might play a role in PRAD development by activation of proliferation, and the UHRF1, NSUN2, and NEIL1 genes have the potential to be utilized as clinical biomarkers.


title: Cloud-enabled Fiji for reproducible, integrated and modular image processing

abstract: Modern biomedical image analyses workflows contain multiple computational processing tasks giving rise to problems in reproducibility. In addition, image datasets can span both spatial and temporal dimensions, with additional channels for fluorescence and other data, resulting in datasets that are too large to be processed locally on a laptop. For omics analyses, software containers have been shown to enhance reproducibility, facilitate installation and provide access to scalable computational resources on the cloud. However, most image analyses contain steps that are graphical and interactive, features that are not supported by most omics execution engines. We present the containerized and cloud-enabled Biodepot-workflow-builder platform that supports graphics from software containers and has been extended for image analyses. We demonstrate the potential of our modular approach with multi-step workflows that incorporate the popular and open-source Fiji suite for image processing. One of our examples integrates fully interactive Fiji macros with Jupyter notebooks. Our second example illustrates how the complicated cloud setup of an computationally intensive process such as stitching 3D digital pathology datasets using BigStitcher can be automated and simplified. In both examples, users can leverage a form-based graphical interface to execute multi-step workflows with a single click, using the provided sample data and preset input parameters. Alternatively, users can interactively modify the image processing steps in the workflow, apply the workflows to their own data, change the input parameters and macros. By providing interactive graphics support to software containers, our modular platform supports reproducible image analysis workflows, simplified access to cloud resources for analysis of large datasets, and integrated workflows across imaging, genomics and transcriptomics data.


title: A computational model of direction selectivity in Macaque V1 cortex based on dynamic differences between ON and OFF pathways

abstract:
This paper is about neural mechanisms of direction selectivity (DS) in Macaque primary visual cortex, V1. DS arises in V1 layer 4C which receives afferent input from the Magnocellular division of the Lateral Geniculate Nucleus (LGN). LGN itself, however, is not direction-selective. To understand the mechanisms of DS, we built a new computational model (DSV1) of 4C. DSV1 is a realistic, large-scale mechanistic model that simulates many V1 properties: orientation selectivity, spatial and temporal tuning, contrast response, and DS. In the model, DS is initiated by the dynamic difference of OFF and ON Magnocellular cell activity that excites the models layer 4C the recurrent network has no intra-cortical direction-specific connections. In experiments - and in DSV1 -- most 4C Simple cells were highly direction-selective but few 4C Complex cells had high DS. Furthermore, the preferred directions of the models direction-selective Simple cells were invariant with spatial and temporal frequency, in this way emulating the experimental data. The distribution of DS across the models population of cells was very close to that found in experiments. Analyzing DSV1, we found that the dynamic interaction of feedforward and intra-cortical synaptic currents led to cortical enhancement of DS for a majority of cells. In view of the strong quantitative agreement between DS in data and in model simulations, the neural mechanisms of DS in DSV1 may be indicative of those in the real visual cortex.

Significance StatementMotion perception is a vital part of our visual experience of the world. In monkeys, whose vision resembles that of humans, the neural computation of the direction of a moving target starts in the primary visual cortex, V1, in layer 4C that receives input from the eye through the Lateral Geniculate Nucleus (LGN). How Direction-Selectivity (DS) is generated in layer 4C is an outstanding unsolved problem in theoretical neuroscience. In this paper, we offer a solution based on plausible biological mechanisms: We present a new large-scale circuit model in which DS originates from slightly different LGN ON/OFF response time-courses and is enhanced in cortex without the need for direction-specific intra-cortical connections. The models DS is in quantitative agreement with experiments.


title: Identification and assessment of the antibacterial activity of ZnO nanoparticles produced by Vigna mungo and Rhizobacteria.

abstract: 1.ABSTRACTSZnO nanoparticles have received a lot of interest in recent years due to their unusual features. Antimicrobial properties of ZnO NPs However, the qualities of nanoparticles are determined by their size and form, making them suitable for a variety of applications. The current work looks at the synthesis, characterization, and antibacterial activity of ZnO NPs produced by Vigna Mungo and Rhizobacteria. Rhizobacteria isolated from V. mungo root nodule were morphologically, biochemically, and molecularly examined and identified as Rhizobium sp. strain and Bacillus flexus strain. The GC-MS analysis of methanol leaf extract of V. mungo was performed to detect and identify bioactive chemicals, and this indicated phytol as an antibacterial agent, while Squalene and Alpha - tocopherol had antioxidant and anti-tumour properties. Agar well diffusion experiment was used to determine the antibacterial properties of ZnO nanoparticles and Vigna Mungo leaf extract. This approach is widely documented, and standard zones of inhibition for sensitive and resistant values have been defined. The results demonstrated that both methanol extract and zinc oxide nanoparticles have strong antibacterial efficacy against the majority of the pathogens examined.

category: microbiology


title: Identification and assessment of the antibacterial activity of Vigna mungo and Rhizobacteria.


title: Conjugative transfer of naturally occurring plasmids in Mycolicibacterium sp.

abstract: Conjugation is considered the main horizontal gene transfer (HGT) mechanism in bacterial adaptation and evolution. In the Mycobacteriaceae family, Mycolicibacterium smegmatis has been used as the model organism for the conjugative transfer of hybrid plasmids. However, the natural conjugation process in any bacteria would involve the transfer of naturally occurring plasmids. Currently, there is a gap in this regard in relation to this abundant environmental genus of Mycobacteriaceae. Here, we performed conjugation experiments between wild Mycolicibacterium sp. strains involving naturally occurring plasmids (sizes of 21 and 274 kb), and interestingly, evidence of conjugative transfer was obtained. Thus, it is likely that conjugation occurs in Mycolicibacterium in the natural environment, representing a source of diversification and evolution in this genus of bacteria.


title: Double-check the zebrafish 18s rRNA qPCR primers: they may be wrong

abstract: A widely used qPCR primer for zebrafish gene rna18s (18s rRNA, or 18s), with the sequence of 5-TCGCtaGTtGGCATCGTTTAtG-3, is found to be incorrect. Initially designed for rainbow trout (Oncorhynchus mykiss) rna18s, the primer has four different nucleotides from the zebrafish sequence 5-TCGCGGGTCGGCATCGTTTACG-3 (indicated in bold/underlined, lowercase letters for rainbow trout and uppercase letters for zebrafish). Since its first use in zebrafish in 2006, this mismatched primer has been clearly stated to be used in at least 50 publications and may have affected hundreds or more in publications citing them. For a sensitive, quantitative method as qPCR, this error must be corrected as soon as possible in the zebrafish community by using rna18s primer sets with accurate sequences, such as those summarized and newly designed in this article.

category: molecular biology


title: Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch

abstract: RNA folds cotranscriptionally to traverse out-of-equilibrium intermediate structures that are important for RNA function in the context of gene regulation. To investigate this process, here we study the structure and function of the Bacillus subtilis yxjA purine riboswitch, a transcriptional riboswitch that downregulates a nucleoside transporter in response to binding guanine. Although the aptamer and expression platform domain sequences of the yxjA riboswitch do not completely overlap, we hypothesized that a strand exchange process triggers its structural switching in response to ligand binding. In vivo fluorescence assays, structural chemical probing data, and experimentally informed secondary structure modeling suggest the presence of a nascent intermediate central helix. The formation of this central helix in the absence of ligand appears to compete with both the aptamers P1 helix and the expression platforms transcriptional terminator. All-atom molecular dynamics simulations support the hypothesis that ligand binding stabilizes the aptamer P1 helix against central helix strand invasion, thus allowing the terminator to form. These results present a potential model mechanism to explain how ligand binding can induce downstream conformational changes by influencing local strand displacement processes of intermediate folds that could be at play in multiple riboswitch classes.

category: biochemistry


title: Cancer malignancy is correlated with up-regulation of PCYT2-mediated glycerol phosphate modification of α-dystroglycan

abstract: The dystrophin-glycoprotein complex connects the cytoskeleton with base membrane components such as laminin through unique O-glycans displayed on -dystroglycan (-DG). Genetic impairment of elongation of these glycans causes congenital muscular dystrophies. We previously identified that glycerol phosphate (GroP) can cap the core part of the -DG O-glycans and terminate their further elongation. This study examined the possible roles of the GroP modification in cancer malignancy, focusing on colorectal cancer. We found that the GroP modification critically depends on PCYT2, which serves as CDP-Gro synthase. Furthermore, we identified a significant positive correlation between cancer progression and GroP modification, which also correlated positively with PCYT2 expression. Moreover, we demonstrate that GroP modification promotes the migration of cancer cells. Based on these findings, we propose that the GroP modification by PCYT2 disrupts the glycan-mediated cell adhesion to the extracellular matrix and thereby enhances cancer metastasis. Thus, the present study suggests the possibility of novel approaches for cancer treatment by targeting the PCYT2-mediated GroP modification.


title: EXTENDED TUDOR-DOMAINS of the piRNA BIOGENESIS PATHWAY HAVE RNA-SPECIFIC NUCLEASE ACTIVITY

abstract: piRNAs are essential for transposon repression and protecting the germline from deleterious mutations. piRNA biogenesis comprises a primary and secondary pathway, and involves PIWI clade argonaute proteins and ancillary factors. Secondary piRNA biogenesis is tightly coupled to transposon repression. It requires processing of the 3 end of pre-piRNA during an amplification loop by an as yet unidentified endonuclease. Here, using crystallography, and biochemical assays, we discover that the Drosophila Qin protein, which is a critical member of the core amplification complex, has endonuclease activity. Qin contains five extended Tudor domains, which had been proposed to recognize methylated ligands. Instead, we show that these domains act as RNA-specific nucleases. This supports a role for Qin in the 3 end processing of Ago3-bound pre-piRNAs. Extended Tudor domains are frequent in piRNA-processing proteins, suggesting that the uncovered nuclease activity of this protein fold may be key to understanding the piRNA biogenesis.


title: Identification of the Park Grass Experiment soil metaproteome

abstract:
The Park Grass Experiment, is an international reference soil with an impressive repository of temperate grassland (meta)data, however, it still lacks documentation of its soil metaproteome. The identification of these proteins is crucial to our understanding of soil ecology and their role in major biogeochemical processes. However, protein extraction can be fraught with technical difficulties including co-extraction of humic material and lack of a compatible databases to identify proteins. To address these issues, we used two compatible soil protein extraction techniques on Park Grass soil, one that removed humic material, namely a modified freeze-dry, heat/thaw/phenol/chloroform (HTPC) method and another which co-extracted humic material, namely an established surfactant method. Proteins were identified by matching mass spectra against a tailored Park Grass metagenome database. We identified a broad range of proteins from Park Grass soil, mainly in "protein metabolism", "membrane transport", "carbohydrate metabolism", "respiration" and "ribosome associated" categories, enabling reconstitution of specific processes active in grassland soil. The soil microbiome was dominated by Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes at phyla level and Bradyrhizobium, Rhizobium, Acidobacteria, Streptomyces and Pseudolabrys at genus level. Further functional enrichment analysis enabled us to identify many proteins in regulatory and signalling networks of key biogeochemical cycles such as the nitrogen cycle. The combined extraction methods connected previous Park Grass metadata with the metaproteome, biogeochemistry and soil ecology. This could provide a base on which future targeted studies of important soil processes and their regulation can be built.

HighlightsO_LIParallel protein extraction methods identified 1266 proteins from Park Grass soil
C_LIO_LIProteome was enriched in ribosomal and respiration proteins for the surfactant extraction method and nitrogen associated proteins for the modified phenol/chloroform method
C_LIO_LIIdentification of regulatory and signalling proteins in key biogeochemical cycles
C_LIO_LILinks metaproteome to microbiome, biogeochemical cycles and Park Grass metadata
C_LIO_LIProvides baseline for future targeted studies
C_LI


title: Spinning sugars in antigen biosynthesis: a direct study of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases

abstract: The sugars streptose and dihydrohydroxystreptose (DHHS) are unique to the bacteria Streptomyces griseus and Coxiella burnetii respectively. Streptose forms the central moiety of the antibiotic streptomycin, whilst DHHS is found in the O-antigen of the zoonotic pathogen C. burnetii. Biosynthesis of these sugars has been proposed to follow a similar path to that of TDP-rhamnose, catalysed by the enzymes RmlA/RmlB/RmlC/RmlD. Streptose and DHHS biosynthesis unusually require a ring contraction step that might be performed by the orthologues of RmlC or RmlD. Genome sequencing of S. griseus and C. burnetii proposed the StrM and CBU1838 proteins respectively as RmlC orthologues. Here, we demonstrate through both coupled and direct observation studies that both enzymes can perform the RmlC 3,5 double epimerisation activity; and that this activity supports TDP-rhamnose biosynthesis in vivo. We demonstrate that proton exchange is faster at the 3 position than the 5 position, in contrast to a previously studied orthologue. We solved the crystal structures of CBU1838 and StrM in complex with TDP and show that they form an active site highly similar to previously characterised enzymes. These results further support the hypothesis that streptose and DHHS are biosynthesised using the TDP pathway and are consistent with the ring contraction step being performed on a double epimerised substrate, most likely by the RmlD paralogue. This work will support the determination of the full pathways for streptose and DHHS biosynthesis.


title: Optimization of growth and electrosynthesis of PolyHydroxyAlcanoates by the thermophilic bacterium Kyrpidia spormannii

abstract:
The electrosynthesis of valuable compounds by biofilms on electrodes is being intensively studied since few years. However, so far, the actual biofilms growing on cathodes produce mainly small and relatively inexpensive compounds such as acetate or ethanol. Recently, a novel Knallgas bacterium, Kyrpidia spormannii EA-1 has been described to grow on cathodes under thermophilic and microaerophilic conditions, producing significant amounts of PolyHydroxyAlkanoates (PHAs). These PHA are promising sustainable bioplastic polymers with the potential to replace petroleum-derived plastics in a variety of applications. However, the effect of culture conditions and electrode properties on the growth of K. spormannii EA-1 biofilms and PHA production is still unclear.

In this study, we report on the optimization of growth and PHA production in liquid culture and on the cathode of a Microbial Electrosynthesis System. Optimization of the preculture allows to obtain high cell density of up to 8.5 Log10 cells{middle dot}ml-1 in 48h, decreasing the time necessary by a factor of 2.5. With respect to cathodic biofilm formation, this study was focused on the optimization of three main operating parameters, which are the applied cathode potential, buffer pH, and the oxygen concentration in the feed gas. Maximum biofilm formation and PHA production was observed at an applied potential of -844mV vs. SCE, pH 6.5, O2 saturation of 2.5%. The PHA concentration in the biofilm reached a maximum of {approx}26.8 g{middle dot}cm-2 after optimization, but at 2.9% the coulombic efficiency remains relatively low. We expect that further nutrient limitation will allow the accumulation of more PHA, based on a dense biofilm growth. In conclusion, these findings take microbial electrosynthesis of PHA a step forward towards practical implementation.


title: BET Bromodomain Inhibitors Target the NEUROD1-subtype SCLC by Blocking NEUROD1 Transactivation

abstract: SCLC is a recalcitrant malignancy with a dismal prognosis. Four molecular subtypes of SCLC have been named, each associated with one master transcription factor (ASCL1, NEUROD1, POU2F3, or YAP1). Much is still unknown about NEUROD1s function and transactivation in this malignancy. Herein we report that knockout of NEUROD1 triggered SCLC to evolve into a YAP1 subtype. Through an integrated analysis of RNA-seq and ChIP-seq, we found NEUROD1 regulates neural-related genes by binding to gene promoters and distal enhancers. NEUROD1 physically interacts with BET bromodomain proteins and recruits them to actively transcribed genes. Inhibition of BET bromodomain proteins blocks NEUROD1 transactivation and suppresses SCLC growth. We identified LSAMP as one of the NEUROD1-target genes that mediate SCLCs sensitivity to BET bromodomain inhibitors. Our findings suggest that targeting transcriptional coactivators could be a new approach to block master transcription factors in SCLC to enable precision therapy.

category: cancer biology


title: The SKBR3 Cell-Membrane Proteome: Role in Aberrant Cancer Cell Proliferation and Resource for Precision Medicine Applications

abstract: The plasma membrane proteome resides at the interface between the extra- and intra-cellular environment and through its various roles in signal transduction, immune recognition, nutrient transport, and cell-cell and cell-matrix interactions plays an absolutely critical role in determining the fate of a cell. Our work was aimed at exploring the landscape of the cancer cell-membrane proteome responsible for sustaining uncontrolled cell proliferation, and its intrinsic resources for enabling detection and therapeutic interventions. SKBR3/HER2+ breast cancer cells were used as a model system and mass spectrometry for characterizing the proteome. The number of identified cell-membrane proteins exceeded 2,000, with ~1,300 being matched by two or more unique peptides. Classification in four major categories, i.e., proteins with receptor or enzymatic activity, CD antigens, transporters, and cell adhesion proteins, uncovered overlapping roles in biological processes that drive cell growth, apoptosis, differentiation, immune response, adhesion and migration, as well as capabilities for signaling crosstalk and alternate pathways for proliferation. The large number of tumor markers (>50) and putative drug targets (>100) exposed a vast potential for yet unexplored detection and targeting opportunities, whereas the presence of 15 antigen immunological markers enabled an assessment of epithelial, mesenchymal or stemness characteristics. Serum-starved cells displayed altered processes related to mitochondrial OXPHOS/ATP synthesis, protein folding and localization, while serum-treated cells exhibited attributes that support tissue invasion and metastasis. Altogether, our findings advance the understanding of the biological triggers that sustain aberrant cancer cell proliferation, survival and development of resistance to therapeutic drugs, and reveal the vast innate opportunities for guiding immunological profiling and precision medicine applications aimed at target selection or drug discovery.


title: The establishment of multiple knockout mutants of Colletotrichum orbiculare by CRISPR/Cas9 and Cre/loxP systems

abstract: Phytopathogenic fungi belonging to the Colletotrichum genus cause devastating damage for many plant species. Among them, Colletotrichum orbiculare is employed as a model fungus to analyze molecular aspects of plant-fungus interactions. Although gene disruption via homologous recombination (HR) was established for C. orbiculare, this approach is laborious due to its low efficiency. Here we developed methods to efficiently generate multiple knockout mutants of C. orbiculare. We first found that CRISPR/Cas9 system massively promoted gene-targeting efficiency. By transiently introducing a CRISPR/Cas9 vector, more than 90 % of obtained transformants were knockout mutants. Furthermore, we optimized a self-excision Cre/loxP marker recycling system for C. orbiculare because limited availability of desired selective markers hampers sequential gene disruption. In this system, integrated selective marker is removable from the genome via Cre recombinase driven by a xylose-inducible promoter, enabling reuse of the same selective marker for the next transformation. Using our CRISPR/Cas9 and Cre/loxP systems, we attempted to identify functional sugar transporters in C. orbiculare. Multiple disruptions of putative quinate transporter genes restrict fungal growth on media containing quinate as a sole carbon source, confirming their functionality as quinate transporters. Our analyses revealed that quinate acquisition is dispensable during fungal infection because this mutant displayed normal virulence to host plants. In addition, we successfully built mutations of 17 cellobiose transporter genes in a strain. From the data of knockout mutants established in this study, we inferred that repetitive rounds of gene disruption using CRISPR/Cas9 and Cre/loxP systems do not cause negative effects for fungal virulence and growth. Therefore, these systems will be powerful tools to perform systematic gene targeting approach for C. orbiculare.


title: Autotaxin may play a Critical Role between the Genetic Risk Factors and Pathogenesis of SLE in Plasmacytoid Dendritic Cells

abstract:
BackgroundThe importance of autotaxin, an enzyme that catalyzes lysophospholipid production, has recently been recognized in various diseases, including cancer and autoimmune diseases. Herein, we examined the role of autotaxin in systemic lupus erythematosus (SLE), utilizing data from ImmuNexUT, a comprehensive database consisting of transcriptome data and expression quantitative trait locus (eQTL) data of immune cells from patients with immune-mediated disorders.

MethodsSerum autotaxin concentrations in patients with SLE and healthy controls (HCs) were compared. The transcriptome data of patients with SLE and age-and sex-matched HCs were obtained from ImmuNexUT. The expression of ENPP2, the gene encoding autotaxin, was examined in peripheral blood immune cells. Next, weighted gene correlation network analysis (WGCNA) was performed to identify genes with expression patterns similar to ENPP2. The ImmuNexUT eQTL database and public epigenomic databases were used to infer the relationship between autotaxin and pathogenesis of SLE.

ResultsAutotaxin levels were elevated in the serum of patients with SLE compared to HCs. Furthermore, the expression of ENPP2 was higher in plasmacytoid dendritic cells (pDCs) than in other immune cell subsets, and its expression was elevated in pDCs of patients with SLE compared to HCs. In WGCNA, ENPP2 belonged to a module that correlated with disease activity. This module was enriched in interferon-associated genes and included genes whose expression was influenced by single-nucleotide polymorphisms associated with SLE, suggesting that it is a key module connecting genetic risk factors of SLE with disease pathogenesis. Analysis utilizing the ImmuNexUT eQTL database and public epigenomic databases suggested that the increased expression of ENPP2 in pDCs from patients with SLE may be caused by increased expression of interferon-associated genes and increased binding of STAT3 complexes to the regulatory region of ENPP2.

ConclusionsAutotaxin may play a critical role in connecting genetic risk factors of SLE to disease pathogenesis in pDCs.


title: Autotaxin is a Potential Link between Genetic Risk Factors and Pathogenesis of Systematic Lupus Erythematosus in Plasmacytoid Dendritic Cells


title: Gut microbiota analyses of Saudi populations for type 2 diabetes-related phenotypes reveals significant association

abstract:
Large-scale gut microbiome sequencing has revealed key links between microbiome dysfunction and metabolic diseases such as T2D. To date, these efforts have largely focused on Western populations, with few studies assessing T2D microbiota associations in Middle Eastern communities where T2D prevalence is now over 20%. We analyzed the composition of stool 16S rRNA from 461 T2D and 119 non-T2Dparticipants from the Eastern Province of Saudi Arabia. We quantified the abundance of microbial communities to examine any significant differences between subpopulations of samples based on diabetes status and glucose level. We observed overall positive enrichment within diabetics compared to healthy individuals and amongst diabetic participants; those with high glucose levels exhibited slightly more positive enrichment compared to those at lower risk of fasting hyperglycemia. In particular, the genus Firmicutes was upregulated in diabetic participants compared to non-diabetic participants, and T2D was associated with an elevated Firmicutes/Bacteroidetes ratio, consistent with previous findings. Based on diabetes status and glucose levels of Saudi participants, relatively stable differences in stool composition were perceived by differential abundance and alpha diversity measures.

Author summaryThe rates of Type 2 diabetes (T2D) in Saudi Arabia have risen dramatically in the last several decades due to socio-economic changes resulting in changes in dietary and sedentary lifestyles. This emergence has grown more rapidly and affects larger proportions of the population with estimates of T2D prevalence impacting 25% of the population. There is a paucity of microbiome data from Middle Eastern populations, and previous studies have been conducted on small sample sizes. Here we report on the first-ever characterization of gut microbiota T2D versus non-T2D and largest microbiome study ever conducted in a Middle Eastern country. The datasets from this study are important to create a regional reference T2D-microbiome catalogue which will propel the understanding of regional gut flora which are associated with T2D development. Based on T2D status and quantified glucose levels of Middle Eastern participants, relatively stable differences in stool composition were observed by differential abundance and alpha diversity measures. Comparing overlapping and varying patterns in gut microbiota with other studies is critical to assessing novel treatment options in light of a rapidly growing T2D health epidemic.


title: A MademoiseLLE domain binding platform links the key RNA transporter to endosomes

abstract: Spatiotemporal expression can be achieved by transport and translation of mRNAs at defined subcellular sites. An emerging mechanism mediating mRNA trafficking is microtubule- dependent co-transport on shuttling endosomes. Although progress has been made in identifying various components of the endosomal mRNA transport machinery, a mechanistic understanding of how these RNA-binding proteins are connected to endosomes is still lacking. Here, we demonstrate that a flexible MademoiseLLE (MLLE) domain platform within RNA- binding protein Rrm4 of Ustilago maydis is crucial for endosomal attachment. Our structure/function analysis uncovered three MLLE domains at the C-terminus of Rrm4 with a functionally defined hierarchy. MLLE3 recognises two PAM2-like sequences of the adaptor protein Upa1 and is essential for endosomal shuttling of Rrm4. MLLE1 and MLLE2 are most likely accessory domains exhibiting a variable binding mode for interaction with currently unknown partners. Thus, endosomal attachment of the mRNA transporter is orchestrated by a sophisticated MLLE domain binding platform.


title: Systematic identification of molecular mediators underlying sensing of Staphylococcus aureus by Pseudomonas aeruginosa

abstract: Bacteria typically exist in dynamic, multispecies communities where polymicrobial interactions influence fitness. Elucidating the molecular mechanisms underlying these interactions is critical for understanding and modulating bacterial behavior in natural environments. While bacterial responses to foreign species are frequently characterized at the molecular and phenotypic level, the exogenous molecules that elicit these responses are understudied. Here we outline a systematic strategy based on transcriptomics combined with genetic and biochemical screens of promoter-reporters to identify the molecules from one species that are sensed by another. We utilized this method to study interactions between the pathogens Pseudomonas aeruginosa and Staphylococcus aureus that are frequently found in co-infections. We discovered that P. aeruginosa senses diverse staphylococcal exoproducts including the metallophore staphylopine, intermediate metabolites citrate and acetoin, and multiple molecules that modulate its iron starvation response. Further, we show that staphylopine inhibits biofilm formation and that P. aeruginosa can utilize citrate and acetoin for growth, revealing that these interactions have both antagonistic and beneficial effects. Our screening approach thus identified multiple S. aureus secreted molecules that are sensed by P. aeruginosa and affect its physiology, demonstrating the efficacy of this approach, and yielding new insight into the molecular basis of interactions between these two species.


title: Substrate preferences, phylogenetic and biochemical properties of proteolytic bacteria present in the digestive tract of Nile tilapia

abstract: Vertebrate intestine appears an excellent source of proteolytic bacteria for industrial and probiotic use. We therefore aimed obtaining the gut-associated proteolytic species of Nile tilapia. Weve isolated twenty six bacterial strains from its intestinal tract, seven of which showed exoprotease activity with the formation of clear halos on skim milk. Their depolymerization ability was further assessed on three distinct proteins including casein, gelatin and albumin. All the isolates could successfully hydrolyze the three substrates indicating relatively broad specificity of their secreted proteases. Molecular taxonomy and phylogeny of the proteolytic isolates were determined based on their 16S rRNA gene barcoding which suggested that the seven strains belong to three phyla viz. Firmicutes, Proteobacteria and Actinobacteria, distributed across the genera Priestia, Citrobacter, Pseudomonas, Stenotrophomonas, Burkholderia, Providencia and Micrococcus. The isolates were further characterized by a comprehensive study of their morphological, cultural, cellular and biochemical properties which were consistent with the phylogenetic annotations. To reveal their proteolytic capacity alongside substrate preferences, enzyme-production was determined by the diffusion assay. The Pseudomonas, Stenotrophomonas and Micrococcus isolates appeared most promising with maximum protease production on casein, gelatin and albumin media respectively. Our findings present valuable insights into the phylogenetic and biochemical properties of gut-associated proteolytic strains of Nile tilapia.


title: Plasmodium falciparum vacuolar pyrophosphatase 1 for ring stage development and its transition to trophozoite

abstract: The malaria parasite relies on anaerobic glycolysis for energy supply when growing inside RBCs as its mitochondrion does not produce ATP. The ring stage lasts [~] 22 hours and is traditionally thought to be metabolically quiescent. However, recent studies show that the ring stage is active for several energy-costly processes including gene transcription/translation, protein export, and movement inside the RBC. It has remained unclear if a low glycolytic flux can meet the energy demand of the ring stage. Here we show that the metabolic by-product, pyrophosphate, is a critical energy source for the development of the ring stage and its transition to the trophozoite stage. During early phases of the asexual development, the parasite utilizes Plasmodium falciparum vacuolar pyrophosphatase 1 (PfVP1), an ancient pyrophosphate-driven proton pump, to pump protons across the parasite plasma membrane to maintain the membrane potential and cytosolic pH. Conditional deletion of PfVP1 leads to delayed ring stage development and a complete blockage of the ring-to-trophozoite transition, which can be partially rescued by Arabidopsis thaliana vacuolar pyrophosphatase 1, but not by the soluble pyrophosphatase from Saccharomyces cerevisiae. Proton-pumping pyrophosphatases are absent in humans, which highlights the possibility of developing highly selective VP1 inhibitors against the malaria parasite.


title: Malaria parasites utilize pyrophosphate to fuel an essential proton pump in the ring stage and the transition to trophozoite stage


title: Clarifying intercellular signalling in yeast: Saccharomyces cerevisiae does not undergo a quorum sensing-dependent switch to filamentous growth

abstract:
Saccharomyces cerevisiae can alter its morphology to a filamentous form associated with unipolar budding in response to environmental stressors. Induction of filamentous growth is suggested under nitrogen deficiency in response to alcoholic signalling molecules through a quorum sensing mechanism. To investigate this claim, we analysed the budding pattern of S. cerevisiae cells over time under low nitrogen while concurrently measuring cell density and extracellular metabolite concentration. We found that the proportion of cells displaying unipolar budding increased between local cell densities of 4.8x106 and 5.3x107 cells/ml. However, the observed increase in unipolar budding could not be reproduced when cells were prepared at the critical cell density and in conditioned media. Removing the nutrient restriction by growth under high nitrogen conditions also resulted in an increase in unipolar budding between local cell densities of 5.2x106 and 8.2x107 cells/ml, but there were differences in metabolite concentration compared to the low nitrogen conditions. This suggests that neither cell density, metabolite concentration, nor nitrogen deficiency were necessary or sufficient to increase the proportion of unipolar budding cells. It is therefore unlikely that quorum sensing is the mechanism controlling the switch to filamentous growth in S. cerevisiae. Only a high concentration of the putative signalling molecule, 2-phenylethanol resulted in an increase in unipolar budding, but this concentration was not physiologically relevant. We suggest that the compound 2-phenylethanol acts through a toxicity mechanism, rather than quorum sensing, to induce filamentous growth.

IMPORTANCEInvestigating dimorphism in the model organism Saccharomyces cerevisiae has been instrumental in understanding the signalling pathways that control hyphal growth and virulence in human pathogenic fungi. Quorum sensing was proposed to signal morphogenesis in S. cerevisiae populations. This mechanism requires the switch to filamentous growth to occur at a critical quorum sensing molecule concentration corresponding to a critical cell density. However, evidence for this mechanism is sparse and limited by the use of non-physiologically relevant concentrations of signalling metabolites. Our study designed a methodology to address this gap and may be applied to further studies of dimorphism in other types of yeasts. A significant implication of our findings is that morphogenesis does not occur in S. cerevisiae via a quorum sensing mechanism, and this important definition needs to be corrected. Mechanistic studies to understand dimorphism in yeasts, by considering metabolite concentrations, will further shed light onto this important cellular behaviour.


title: Decoding the transcriptome of denervated muscle at single-nucleus resolution

abstract:
BackgroundSkeletal muscle exhibits remarkable plasticity under both physiological and pathological conditions. One major manifestation of this plasticity is muscle atrophy that is an adaptive response to catabolic stimuli. Since the heterogeneous transcriptome responses to catabolism in different types of muscle cells are not fully characterized, we applied single-nucleus RNA sequencing (snRNA-seq) to unveil muscle atrophy related transcriptional changes at single nucleus resolution.

MethodsUsing a sciatic denervation mouse model of muscle atrophy, snRNA-seq was performed to generate single-nucleus transcriptional profiles of the gastrocnemius muscle from normal and denervated mice. Various bioinformatics analyses, including unsupervised clustering, functional enrichment analysis, trajectory analysis, regulon inference, metabolic signature characterization and cell-cell communication prediction, were applied to illustrate the transcriptome changes of the individual cell types.

ResultsA total of 29,539 muscle nuclei (normal vs denervation: 15,739 vs 13, 800) were classified into 13 nuclear types according to the known cell markers. Among these, the type IIb myonuclei were further divided into two subgroups, which we designated as type IIb1 and type IIb2 myonuclei. In response to denervation, the proportion of type IIb2 myonuclei increased sharply (78.12% vs 38.45%, p <0.05). Concomitantly, trajectory analysis revealed that denervated type IIb2 myonuclei clearly deviated away from the normal type IIb2 myonuclei, indicating that this subgroup underwent robust transcriptional reprogramming upon denervation. Signature genes in denervated type IIb2 myonuclei included Runx1, Gadd45a, Igfn1, Robo2, Dlg2, and Sh3d19 (p <0.001). The gene regulatory network analysis captured a group of atrophy-related regulons (Foxo3, Runx1, Elk4, Bhlhe40) whose activities were enhanced (p <0.01), especially in the type IIb2 myonuclei. The metabolic landscape in the myonuclei showed that most of the metabolic pathways were downregulated by denervation (p <0.001), while some of the metabolic signaling, such as glutathione metabolism, was specifically activated in the denervated type IIb2 myonulei. We also investigated the transcriptomic alterations in the type I myofibers, muscle stem cells, fibro-adipogenic progenitors, macrophages, endothelial cells and pericytes and characterized their signature responses to denervation. By predicting the cell-cell interactions, we observed that the communications between myofibers and muscle resident cells were diminished by denervation.

ConclusionOur results define the myonuclear transition, metabolic remodeling and gene regulation networks reprogramming associated with denervation-induced muscle atrophy and illustrate the molecular basis of the heterogeneity and plasticity of muscle cells in response to catabolism. These results provide a useful resource for exploring the molecular mechanism of muscle atrophy.


title: Molecular identification of rhizobacterial isolates from Prosopis limensis and their effect on the growth of Raphanus sativus under salt stress

abstract: Soil salinity negatively affects the development of agricultural crops. The utilization of plant growth-promoting rhizobacteria is a biotechnological alternative to mitigate this problem. Rhizobacteria were isolated from the roots and rhizosphere of Prosopis limensis Bentham "carob" to identify them and determine their potential as plant growth-promoters under salt stress. First, ACC deaminase activity was determined in Dworkin & Foster (DF) minimum medium with 3.0 mM ACC as a source of nitrogen; besides, tolerance to sodium chloride was determined in Nutrient Broth (NB) supplemented with 10% NaCI. Then, bacteria displaying ACC deaminase activity and a 10% NaCI tolerance were selected, identified through genomic analysis targeting the 16s rRNA gene, and inoculated into Raphanus sativus L. "radish" seeds to determine the effect on germination percentage under salt stress (80 mM NaCI) and, also on indole production and phosphate solubilization. Isolates were also utilized to evaluate their effect on the growth of radish in saline soils. Genomic analysis showed two bacterial isolates from the genus Pseudomonas and one from the genus Bordetella: Isolate MW604823 was identified as Pseudomonas sp.; isolate MW604824, as Pseudomonas hunanensis; and isolate MW604826 as Bordetella muralis. Thee isolates demonstrated ACC deaminase activity and tolerance to 10% NaCI. Inoculation of the isolates on radish seeds increased germination percentage compared to the control. The isolates displayed in vitro indole production and phosphate solubilization capacity. Moreover, the isolates promoted the growth of radish under salt stress conditions, increasing, leave number, root number, aerial, and root biomass, demonstrating their potential as a biofertilizers.


title: Dissecting the Roles of the Tuberin Protein in the Subcellular Localization of the G2/M Cyclin, Cyclin B1

abstract: Tuberin is a major component of the protein regulatory complex known as the Tuberous Sclerosis Complex and plays a crucial role in cell cycle progression and protein synthesis. Mutations in the Tuberin gene, TSC2, lead to the formation of benign tumors in many organ systems and causes the Tuberous Sclerosis Complex disorder. Genotypes ranging from point mutations to large deletions in the TSC2 gene have been clinically characterized with a wide range of phenotypes from skin tumors to large brain tumors. Our current work investigates the molecular mechanisms behind Tuberin and its ability to regulate the cell cycle through its binding to the G2/M cyclin, Cyclin B1. After creating an early stop codon in a critical region of the Tuberin, our results show the in vitro phenotype that occurs from a truncated Tuberin protein. Herein we demonstrate that this clinically relevant truncated form of Tuberin promotes an increased nuclear accumulation of Cyclin B1 and a subsequent increase in cell proliferation supporting the phenotypic data seen in the clinic with Tuberous Sclerosis Complex patients showing deletions within the TSC2 gene. This data provides an insight into some of the functional and molecular consequences of truncated proteins that are seen in clinical patients.

category: cell biology


title: Homosalate boosts the release of tumor-derived Extracellular Vesicles with anti-anoikis properties

abstract: Eukaryotic cells, including cancer cells, secrete highly heterogeneous populations of extracellular vesicles (EVs). EVs could have different subcellular origin, composition and functional properties, but tools to distinguish between EV subtypes are scarce. Here, we tagged CD63- or CD9-positive EVs secreted by triple negative breast cancer cells with Nanoluciferase enzyme, to set-up a miniaturized method to quantify secretion of these two EV subtypes directly in the supernatant of cells. We performed a cell-based high-content screening to identify clinically-approved drugs able to affect EV secretion. One of the identified hits is Homosalate, an anti-inflammatory drug found in sunscreens which robustly increased EVs release. Comparing EVs induced by Homosalate with those induced by Bafilomycin A1, we discovered that: 1) the two drugs act on EVs generated in distinct subcellular compartments and 2) EVs released upon treatment with Homosalate, but not with Bafilomycin A1, conferred anti-anoikis properties to another recipient tumor cell line. In conclusion, we identified a new drug modifying EV release and demonstrated that under influence of different drugs, triple negative breast cancer cells release EV subpopulations from different subcellular origins harboring distinct functional properties.


title: Biochemical propensity mapping for structural and functional anatomy of importin α IBB domain

abstract: Importin  has been described as a nuclear protein transport receptor that enables proteins synthesized in the cytoplasm to translocate into the nucleus. Besides its function in nuclear transport, an increasing number of studies have examined its non-nuclear transport functions. In both nuclear transport and non-nuclear transport, a functional domain called the IBB domain (importin {beta} binding domain) plays a key role in regulating importin  behavior, and is a common interacting domain for multiple binding partners. However, it is not yet fully understood how the IBB domain interacts with multiple binding partners, which leads to the switching of importin  function. In this study, we have distinguished the location and propensities of amino acids important for each function of the importin  IBB domain by mapping the biochemical/physicochemical propensities of evolutionarily conserved amino acids of the IBB domain onto the structure associated with each function. We found important residues that are universally conserved for IBB functions across organisms and families, in addition to those previously known, as well as residues that are presumed to be responsible for the differences in complex-forming ability between families and for functional switching.


title: MiR-30a-5p alters epidermal terminal differentiation during aging by regulating BNIP3L/NIX-dependent mitophagy

abstract: Chronological aging is characterized by an alteration of the genes regulatory network. In human skin, epidermal keratinocytes fail to differentiate properly with aging, leading to the weakening of the epidermal function. MiR-30a is particularly overexpressed with epidermal aging, but the downstream molecular mechanisms are still uncovered. The aim of this study was to decipher the effects of miR-30a overexpression in the human epidermis, with a focus on keratinocyte differentiation. We formally identified the mitophagy receptor BNIP3L as a direct target of miR-30a. Using a 3D organotypic model of reconstructed human epidermis overexpressing miR-30a, we observed a strong reduction of BNIP3L expression in the granular layer. In human epidermal sections of skin biopsies from donors of different ages, we observed a similar pattern of BNIP3L decrease with aging. Moreover, human primary keratinocytes undergoing differentiation in vitro also showed a decreased expression of BNIP3L with age, together with a retention of mitochondria. Moreover, aging is associated with altered mitochondrial metabolism in primary keratinocytes, including decreased ATP-linked respiration. Thus, miR-30a is a negative regulator of programmed mitophagy during keratinocytes terminal differentiation, impairing epidermal homeostasis with aging.