title: A simple and viable approach to estimate population trends

abstract: Changes in population abundances over time are of central concern for environmental conservation and the understanding of population dynamics. The standard slope estimator has restricting assumptions and lacks a constant range, which makes its interpretation less intuitive. Herein, more robust measures of trend. It is based on proportional difference and can be used for data on various scale types. If it is applied to ranks it yields the correlation coefficient. Related measures of association are described that assess the relationship between species, including a rank-order correlation that is sensitive to top ranks and a correlation for continuous data that is more robust than the correlation coefficient. All proposed measures have a range between -1 and +1. Furthermore, they can provide a common ground for evaluating trend strength and strength of association for populations undergoing very different dynamics.


title: Role of MULE activities in the positive selection of sweet orange cultivars

abstract: Sweet orange (SWO) mainly propagates asexually and has a higher bud sport selection frequency than most other citrus species1. Many cultivar groups have been subjected to artificial selections for tens to hundreds of years2. The reasons for the high bud sport selection frequency and how positive selections impact the mutation activities in SWO are not well understood. Here, we find two highly active Mutator-like transposable element families (CiMULE1 and CiMULE2) with novel insertion loci in most SWO accessions, and their transposition activities in SWO are up to over 100-fold higher than in SWOs two parental species. Almost all SWO cultivars could be distinguished based on their insertion loci, and three to eight tag insertions are found for each cultivar group. Many insertions have putatively altered cultivar traits, including several biallelic pairs. Multiple SWO lineages with high transposition activities of CiMULE1 or CiMULE2 have been selected independently. CiMULE1 and CiMULE2 have played an important role in SWO breeding. And artificial selections led to the significant increase of their activities in SWO within tens to hundreds of years, which in turn accelerated bud sport selection dramatically. CiMULE1 and CiMULE2 may function as accelerators in adaptative evolution in citrus.

category: genetics


title: Epigenetic changes associated with hyperglycaemia exposure in the longitudinal D.E.S.I.R. cohort.

abstract:
AimUnderstanding DNA methylation dynamics associated with progressive hyperglycaemia exposure could provide early diagnostic biomarkers and an avenue for delaying type 2 diabetes (T2D) disease. We aimed to identify DNA methylation changes during a 6-year period associated with early hyperglycaemia exposure using the longitudinal D.E.S.I.R. cohort.

MethodsWe selected individuals with progressive hyperglycaemia exposure based on T2D diagnostic criteria: 27 with long-term exposure, 34 with short-term exposure and 34 normoglycaemic controls. DNA from blood at inclusion and at the 6-years visit was subjected to methylation analysis using 850K methylation-EPIC arrays. A linear mixed model was used to perform an epigenome-wide association study (EWAS) and identify methylated changes associated with hyperglycaemia exposure during 6-year time-period.

ResultsWe did not identify differentially methylated sites that reached FDR-significance in our cohort. Based on EWAS, we focused our analysis on methylation sites that had a constant effect during the 6-years across the hyperglycaemia groups compared to controls and found the most statistically significant site was the reported cg19693031 probe (TXNIP). We also performed an EWAS with HbA1c, using the inclusion and the 6-years methylation data and did not identify any FDR-significant CpGs.

ConclusionsOur study reveals that DNA methylation changes are not robustly associated with hyperglycaemia exposure or HbA1c during a short-term period, however, our top loci indicate potential interest and should be replicated in larger cohorts.

category: genomics


title: Single-cell RNA-sequencing analysis reveals the molecular mechanism of subchondral bone cell heterogeneity in the development of osteoarthritis

abstract: The cellular composition and underlying spatiotemporal transformation processes of subchondral bone in osteoarthritis (OA) remain unknown. Herein, various cell subsets from tibial plateau of OA patients are identified, and the mechanism of subchondral microstructure alteration is elaborated using single-cell RNA sequencing technique. We identified two novel endothelial cell (EC) populations characterized by either exosome synthesis and inflammation response, or vascular function and angiogenesis. Three osteoblast (OB) subtypes are introduced, separately related to vascularization, matrix manufacturing and matrix mineralization. The distinct roles and functions of these novel phenotypes in OA development are further discussed, as well as interaction network between these subpopulations. The variation tendency of each population is testified in a DMM mouse model. The identification of cell types demonstrates a novel taxonomy and mechanism for ECs and OBs inside subchondral bone area, provides new insights into the physiological and pathological behaviors of subchondral bone in OA pathogenesis.

category: pathology


title: The effect of auditory stimulation on the nonlinear dynamics of heart rate: the impact of emotional valence and arousal.

abstract:
BackgroundAlthough it is known that sound exposure evokes changes in autonomic activity, the effects of noise and music on the nonlinear behavior of heart rate fluctuations remain poorly understood and controversial. This study aims to assess the influence of sound subjective emotional valence and arousal on the nonlinear characteristics of the autonomic nervous system during passive listening.

MethodsIn this study, forty-two subjects listened to four sounds: (1) white noise, (2) road traffic noise, (3) excitatory music, and (4) a lullaby. The experiment consisted of two consecutive sessions: five minutes of rest, followed by five minutes of listening. RR intervals were recorded during both sessions. The following linear and nonlinear heart rate variability indices were computed: SDNN, RMSSD, F, HF, approximate (ApEn) and sample entropy (SampEn), correlation dimension (D2), Poincare plot indices (SD1, SD2), fractal scaling exponents (alpha1, alpha2), and recurrence plot indices (Lmean, Lmax, DET, LAM, Vmax, TT, ShanEn).

ResultsExcitatory music was associated with significant decrease in SDNN and RMSSD, diminished HF, and a substantial reduction in LF. Excitatory music exposure induced significant increases in DET, SD1 and SD2, but changes in DFA, SampEn, and D2 were nonsignificant. Traffic noise, white noise, and the lullaby did not cause significant changes in the measures of heart rate variability.

ConclusionPresentation of music evoking strong negative emotions elicits a prominent decrease in respiratory sinus arrhythmia. Poincare plot and recurrence plot measures possess high sensitivity to high arousal and unpleasant music. Contrary to previous studies, we did not find the effects of relaxing music on heart rate variability.

category: physiology


title: Liguleless narrow and narrow odd dwarf act in overlapping pathways to regulate maize development & physiology

abstract: narrow odd dwarf (nod) and Liguleless narrow (Lgn) are pleiotropic maize mutants that both encode plasma membrane proteins, cause similar developmental patterning defects, and constitutively induce stress signaling pathways. To investigate how these mutants coordinate maize development and physiology, we screened for protein interactors of NOD by affinity purification. LGN was identified by this screen as a strong candidate interactor, and we confirmed the NOD-LGN molecular interaction through orthogonal experiments. We further demonstrated that LGN, a receptor-like kinase, can phosphorylate NOD in vitro, hinting that they could act in intersecting signal transduction pathways. To test this hypothesis, we generated Lgn-R;nod mutants in two backgrounds (B73 and A619) and found that these mutations enhance each other, causing more severe developmental defects than either single mutation on its own, with phenotypes including very narrow leaves, increased tillering, and failure of the main shoot. Transcriptomic and metabolomic analyses of the single and double mutants in the two genetic backgrounds revealed widespread induction of pathogen defense genes and a shift in resource allocation away from primary metabolism in favor of specialized metabolism. These effects were similar in each single mutant and heightened in the double mutant, leading us to conclude that NOD and LGN act cumulatively in overlapping signaling pathways to coordinate growth-defense tradeoffs in maize.

category: plant biology


title: Hybrid conferences: opportunities, challenges and ways forward

abstract: Hybrid conferences are in-person events that are also accessible online. This type of meeting format was rare pre-COVID-19 but started to become more common recently given the asynchronous global progression of the pandemic and the uneven access and distribution of vaccines that led to a large proportion of participants being unable to attend international conferences in person. Here we report the organization of a middle-sized (581 participants: 159 onsite, 422 online) international hybrid conference that took place in France in September 2021. We highlight particular organizational challenges inherent to this relatively new type of meeting format. Furthermore, we surveyed both in-person and online participants to better understand their conference experience and to propose improvements based on the feedback received. Finally, we compare the advantages and disadvantages of three types of conferences (onsite-only, online-only and hybrid) and suggest that hybrid events should be favored in the future because they offer the most flexibility to participants. We conclude by proposing suggestions and ways forward to maximize accessibility and inclusivity of hybrid conferences.

category: scientific communication and education


title: Treatment response prediction: Is model selection unreliable?

abstract: Quantitative modelling has become an essential part of the drug development pipeline. In particular, pharmacokinetic and pharmacodynamic models are used to predict treatment responses in order to optimise clinical trials and assess the safety and efficacy of dosing regimens across patients. It is therefore crucial that treatment response predictions are reliable. However, the data available to fit models are often limited, which can leave considerable uncertainty about the best model to use. Common practice is to select the model that is most consistent with the observed data based on the Akaike information criterion (AIC). Another popular approach is to average the predictions across the subset of models consistent with the data. In this article, we argue that both approaches can lead to unreliable predictions, as treatment responses typically display nonlinear dynamics, so models can be consistent with the observed dynamics, whilst predicting incorrect treatment responses. This is especially the case when predicting treatment responses for either times or dosing regimens that go beyond the observed dynamics. Across a range of experiments on both real laboratory data and synthetically derived data on Neisseria gonorrhoeae response to ciprofloxacin, we show that probabilistic averaging of models results in more reliable treatment response predictions.

category: systems biology


title: The effect of type and context of sensorimotor information on corticospinal excitability

abstract:
During skilled hand-object interactions, the human sensorimotor system generates predictive motor commands based on visual information and sensorimotor memories established from previous experience. Here we investigated whether predictive force scaling could be adapted to context-dependent information that is not always explicitly available. We probed the effect of motor prediction mechanisms on corticospinal excitability (CSE) with transcranial magnetic stimulation (TMS). In experiment 1, participants performed a continuous force tracking task by squeezing a manipulandum. We varied the type of visual information for predicting motor output by displaying either the actual target force curve participants had to match (sinusoidal curve condition) or the visual error between the required and exerted force (horizontal line condition). CSE was modulated by the rate of change of forces (speed) in both conditions. Force direction changes further modulated CSE but in the sinusoidal curve condition only. These findings indicate that the corticospinal output mainly reflects the ongoing motor command, but can also be modulated by less explicit contextual information. In experiment 2, we tested whether participants could accurately predict the required force scaling in a standard random weight object lifting task, which also included series of small weight increments. Results showed that participants were unable to generate accurate force predictions by extrapolating weight from the implicit series, which failed to modulate CSE, unsurprisingly. Altogether, these findings suggest that corticospinal output is modulated based on context-dependent information when mediated by explicit visual cues, but not when sensorimotor cues are presented in an implicit manner.

HighlightsO_LIVisual cues and sensorimotor experience are key for hand-object interactions
C_LIO_LIWe investigated the underlying corticospinal excitability (CSE) changes
C_LIO_LIVisual cues improved motor performance and modulated CSE
C_LIO_LICSE was partly modulated by less explicit information
C_LIO_LIImplicit information did not improve motor performance and nor modulate CSE
C_LI

category: neuroscience


title: Unsupervised approach to decomposing neural tuning variability

abstract: Neural representation is often described by the tuning curves of individual neurons with respect to certain stimulus variables. Despite this tradition, it has become increasingly clear that neural tuning can vary substantially in accordance with a collection of internal and external factors. A challenge we are facing is the lack of appropriate methods to accurately capture trial-to-trial tuning variability directly from the noisy neural responses. Here we introduce an unsupervised statistical approach, Poisson functional principal component analysis (Pf-PCA), which identifies different sources of systematic tuning fluctuations, moreover encompassing several current models (e.g.,multiplicative gain models) as special cases. Applying this method to neural data recorded from macaque primary visual cortex- a paradigmatic case for which the tuning curve approach has been scientific essential- we discovered a novel simple relationship governing the variability of orientation tuning, which unifies different types of gain changes proposed previously. By decomposing the neural tuning variability into interpretable components, our method enables discovery of new structure of the neural code, capturing the influence of the stimulus drive and internal states simultaneously.


title: Target-agnostic discovery of Rett Syndrome therapeutics by coupling computational network analysis and CRISPR-enabled in vivo disease modeling

abstract: It is difficult to develop effective treatments for neurodevelopmental genetic disorders, such as Rett syndrome, which are caused by a single gene mutation but trigger changes in numerous other genes, and thereby also severely impair functions of organs beyond the central nervous system (CNS). This challenge is further complicated by the lack of sufficiently broad and biologically relevant drug screens, and the inherent complexity in identifying clinically relevant targets responsible for diverse phenotypes. Here, we combined human gene regulatory network-based computational drug prediction with in vivo screening in a population-level diversity, CRISPR-edited, Xenopus laevis tadpole model of Rett syndrome to carry out target-agnostic drug discovery, which rapidly led to the identification of the FDA-approved drug vorinostat as a potential repurposing candidate. Vorinostat broadly improved both CNS and non-CNS (e.g., gastrointestinal, respiratory, inflammatory) abnormalities in a pre-clinical mouse model of Rett syndrome. This is the first Rett syndrome treatment to demonstrate pre-clinical efficacy across multiple organ systems when dosed after the onset of symptoms, and network analysis revealed a putative therapeutic mechanism for its cross-organ normalizing effects based on its impact on acetylation metabolism and post-translational modifications of microtubules.


title: Long-distance axon growth ability of corticospinal neurons is lost in a segmentally-distinct manner.

abstract:
The neonatal central nervous system (CNS) in mammals is known to support greater regeneration than the adult CNS. Established models of neonatal CNS injuries cause significant disruption to the microenvironments needed for axon growth and guidance. This limits their ability to investigate long-distance axon growth ability. We established a novel microsurgical approach to transect developing corticospinal neuron (CSN) axons, without producing an overt spinal lesion and investigated long-distance growth ability of the developing corticospinal tract (CST) in neonatal mice. We identified, rather surprisingly, that this ability is not equivalently lost at distinct spinal levels. At postnatal day 4 (P4), while this ability is robustly maintained at thoracic T11, it is completely abolished at cervical C2. We further identify that thoraco-lumbar-projecting CSN lose growth ability at cervical C2 even while extending axons to thoraco-lumbar segments. Further, long-distance regrowth is possible even when CSN axons are displaced from their "normal" location in the dorsal funiculus to the dorsolateral funiculus, where only a minority of the CST normally traverses. The differential loss of long-distance growth at distinct spinal levels does not appear to be due to segmental differences in astrocytic or microglial activation. Our results suggest that the initial control over long-distance axon growth is differentially governed across the length of an axon by context-specific mechanisms.

HighlightsLong-distance axon growth ability is not lost equally across the entire length of a developing axon.

Corticospinal tract (CST) axonal regenerative ability in the cervical spinal cord is lost even during the period of CST growth to thoracic and lumbar segments.

The segmentally distinct loss of long-distance CST regeneration during development is not due to segmental differences in astrocytic or microglial activation.


title: SARS-CoV-2 spike proteins uptake mediated by lipid raft ganglioside GM1 in human cerebrovascular cells

abstract: While there is clinical evidence of neurological manifestation in coronavirus disease-19, its unclear whether this is due to differential severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uptake from blood by cells of the cerebrovasculature. SARS-CoV-2 and its spike protein (SP) interact with the endothelium but the roles of extracellular peptidase domain on angiotensin converting enzyme 2 receptors (ACE2) and ACE2 independent pathways (such as glycans) are not fully elucidated. In addition, for SARS-CoV-2 to enter the brain parenchyma from blood it has to cross several cell types, including the endothelium, pericytes and vascular smooth muscle. Since SARS-CoV-2 interacts with host cells via it SP at the entry point of it life cycle, we used fluorescently labelled SP (SP-555) (wild type and mutants) to model viral behaviour, in vitro, for these cell types (endothelial, pericytes and vascular smooth muscle) to explore pathways of viral entry into brain from blood. There was differential SP uptake by these cell types. The endothelial cells had the least uptake, which may limit SP uptake into brain from blood. Uptake was mediated by ACE2, but it was dependent on SP interaction with ganglioside GM1 in the lipid raft. Mutation sites, N501Yand E484K and D614G, as seen in variants of interest, were differentially taken up by these cell types. There was greater uptake but neutralization with anti-ACE2 and anti-GM1antibodies was less effective. Our data suggested that GM1/lipid raft is an important entry point of SARS-CoV-2 into these cells since inhibition of SP uptake with both anti-ACE2 and anti-GM1 together was similar to that with only anti-GM1, and both ACE2 and GM1 are within the lipid raft region of plasma membrane. Thus, GM1 is a potential SARS-CoV-2 and therapeutic target at the cerebrovasculature.


title: Discovering dynamical models of human behavior

abstract: Response time (RT) data collected from cognitive tasks are a cornerstone of psychology and neuroscience research, yet existing models of these data either make strong assumptions about the data generating process or are limited to modeling single trials. We introduce task-DyVA, a deep learning framework in which expressive dynamical systems are trained to reproduce sequences of RTs observed in data from individual human subjects. Models fitted to a large task-switching dataset captured subject-specific behavioral differences with high temporal precision, including task-switching costs. Through perturbation experiments and analyses of the models latent dynamics, we find support for a rational account of switch costs in terms of a stability-flexibility tradeoff. Thus, our framework can be used to discover interpretable cognitive theories that explain how the brain dynamically gives rise to behavior.


title: A passive computational marker for individual differences in non-reinforced learning

abstract: Although research about preference formation and modification has classically focused on the role of external reinforcements, there is also increasing evidence for a key role of non-externally reinforced cognitive mechanisms such as attention and memory in preference modification. In a novel paradigm for behavioral change called the Cue-Approach training (CAT) task, preferences are modified via the mere association of images of stimuli with a neutral cue and a rapid motor response, without external reinforcements. The procedures efficacy has been replicated across dozens of studies, and the net behavioral change was linked with increased activity in a frontal value-based decision-making brain region during the post-training probe choice phase. However, the cognitive mechanisms during the training phase itself have not been elucidated. Based on the structure of the task alongside recent findings of the involvement of striatal and supplementary motor regions during training, we hypothesized that a motor-related learning process could be a prospective candidate. To test this hypothesis, we developed a computational model of the motor response pattern during training in a large corpus of data collected from 864 participants across 29 different CAT experiments. Using Bayesian modeling of the meta-analysis data, we developed a computational marker for individualized learning in the training task, which was found to be associated with the preference modification effect in the subsequent probe task, both at the participant-level as well as in the more granular individual-item level. Following the conclusions of the meta-analysis, in two additional experiments (a pilot study and a larger preregistered replication study) we aimed to affect learning efficacy by manipulating the training procedure difficulty. As hypothesized and preregistered, training difficulty was captured by the new computational marker identified on the previously collected samples. Manipulation of the training difficulty also resulted in a differential preference modification effect, suggesting a causal relationship between the motor learning captured by the computational model and the post-training behavioral change effect. Our work highlights a novel non-reinforced preference modification pathway, suggesting that attention and motor learning are linked to preference formation, and provides a computational framework to identify individualized training markers which could predict future behavioral change effects.


title: Task feedback suggests a post-perceptual locus of serial dependence

abstract: Decisions across a range of perceptual tasks are known to be biased toward stimuli and choices from the past. So-called serial dependence is thought to be an adaptive low-level mechanism that promotes perceptual stability across visual inputs. However, recent studies suggest post-perceptual mechanisms may instead contribute to serially-biased responses, calling into question the locus of serial dependence and the nature of integration of past and present sensory inputs. Here, we uncover decisional contributions to serial dependence that account for the majority, if not all of the bias. We measured serial dependence in a 3D motion extrapolation task where uncertainty in the sensory information varied from trial to trial. Furthermore, visual and auditory response feedback were provided to a subset of participants on every trial. We found that responses were significantly more biased toward the previously reported motion direction rather than the previously presented direction, with larger biases on trials with greater uncertainty in the sensory input. Critically, response feedback was associated with an abolishment of bias toward the previously presented direction, and a significant reduction of bias toward the previously reported direction. These results provide clear evidence for a post-perceptual locus of serial dependence and support the role of serial dependence as a behavioral strategy to overcome sensory uncertainty.


title: Immune and Clotting Dysfunction Detected in Saliva and Blood Plasma after COVID-19.

abstract: A growing number of studies indicate that coronavirus disease 2019 (COVID-19) is associated with inflammatory sequelae, but molecular signatures governing the normal vs. pathologic convalescence process have not been well-delineated. We characterized global immune and proteome responses in matched plasma and saliva samples obtained from COVID-19 patients collected between 4-6 weeks after initial clinical symptoms resolved. Convalescent subjects showed robust IgA and IgG responses and positive antibody correlations between matched saliva and plasma samples. However, global shotgun proteomics revealed persistent inflammatory patterns in convalescent samples including dysfunction of salivary innate immune cells and clotting factors in plasma (e.g., fibrinogen and antithrombin), with positive correlations to acute COVID-19 disease severity. Saliva samples were characterized by higher concentrations of IgA, and proteomics showed altered pathways that correlated positively with IgA levels. Our study positions saliva as a viable fluid to monitor immunity beyond plasma to document COVID-19 immune, inflammatory, and coagulation-related sequelae.

category: immunology


title: Persistent Immune and Clotting Dysfunction Detected in Saliva and Blood Plasma after COVID-19


title: Computational exploration of bio-remediation solution for mixed plastic waste

abstract: The plastic materials are recalcitrant in the open environment, surviving longer without complete remediation. The current disposal methods of used plastic material are not efficient; consequently, plastic wastes are infiltrating the natural resources of the biosphere. A sustaining solution for plastic waste is either recycling or making it part of the earths biogeochemical cycle. We have collected, manually mined, and analyzed the previous reports on plastic biodegradation. Our results demonstrate that the biodegradation pattern of plastics follows the chemical classification of plastic types. Based on clustering analysis, the distant plastic types are grouped into two broad categories of plastic types, C-C (non-hydrolyzable) and C-X (hydrolyzable). The genus enrichment analysis suggests that Pseudomonas and Bacillus from bacteria and Aspergillus and Penicillium from fungal are potential genera for bioremediation of mixed plastic waste. Overall results have pointed towards a possible solution of mixed plastic waste either in a circular economy or open remediation. The meta-analysis of the reports revealed a historical inclination of biodegradation studies towards C-X type of plastic; however, the C-C class is dominated in overall plastic production. An interactive web portal of reports is hosted at plasticbiodegradation.com for easy access by other researchers for future studies

category: microbiology


title: SARS-CoV-2 Omicron spike H655Y mutation is responsible for enhancement of the endosomal entry pathway and reduction of cell surface entry pathway

abstract:
The SARS-CoV-2 Omicron variant reportedly displays decreased usage of the cell surface entry pathway mediated by the host transmembrane protease, serine 2 (TMPRSS2) and increased usage of the endosomal entry pathway mediated by cathepsin B/L. These differences result in different cell tropisms and low fusogenicity from other SARS-CoV-2 variants. Recent studies have revealed that host metalloproteases are also involved in cell surface entry and fusogenic activity of SARS-CoV-2, independent of TMPRSS2. However, the involvement of metalloproteinase-mediated cell entry and fusogenicity in Omicron infections has not been investigated. Here, we report that Omicron infection is less sensitive to the metalloproteinase inhibitor marimastat, like the TMPRSS2 inhibitor nafamostat, and is more sensitive to the cathepsin B/L inhibitor E-64d than infections with wild-type SARS-CoV-2 and other variants. The findings indicate that Omicron preferentially utilizes the endosomal pathway rather than cell surface pathways for entry. Moreover, the Omicron variant also displays poor syncytia formation mediated by metalloproteinases, even when the S cleavage status mediated by fusion-like proteases is unchanged. Intriguingly, the pseudovirus assay showed that a single mutation, H655Y, of the Omicron spike (S) is responsible for the preferential entry pathway usage without affecting the S cleavage status. These findings suggest that the Omicron variant has altered entry properties and fusogenicity, probably through the H655Y mutation in its S protein, leading to modulations of tissue and cell tropism, and reduced pathogenicity.

Author summaryRecent studies have suggested that the SARS-CoV-2 Omicron variant displays altered cell tropism and fusogenicity, in addition to immune escape. However, comprehensive analyses of the usage of viral entry pathways in Omicron variant have not been performed. Here, we used protease inhibitors to block each viral entry pathway mediated by the three host proteases (cathepsin B/L, TMPRSS2, and metalloproteinases) in various cell types. The results clearly indicated that Omicron exhibits enhanced cathepsin B/L-dependent endosome entry and reduced metalloproteinase-dependent and TMPRSS2-dependent cell surface entry. Furthermore, the H655Y mutation of Omicron S determines the relative usage of the three entry pathways without affecting S cleavage by the host furin-like proteases. Comparative data among SARS-CoV-2 variants, including Omicron, may clarify the biological and pathological phenotypes of Omicron but increase the understanding of disease progression in infections with other SARS-CoV-2 variants.


title: High neutralizing antibody levels against SARS-CoV-2 Omicron after UB-612 booster vaccination

abstract: The highly transmissible Omicron variant has caused high rates of breakthrough infections among vaccinated and convalescent individuals. Here, we demonstrate that a booster dose of UB-612 vaccine candidate delivered 7-9 months after primary vaccination increases neutralizing antibody levels by 131-, 61- and 49-fold against ancestral SARS-CoV-2, Omicron BA.1 and BA.2 variants, respectively. Based on the RBD protein binding antibody responses, we estimated a ~95% efficacy against symptomatic COVID-19 caused by the ancestral strain after a UB-612 booster. Our results support UB-612 vaccine as a potent booster against current and emerging SARS-CoV-2 variants.


title: CMLD-2 Attenuates Myofibroblast Activation and Bleomycin-Induced Pulmonary Fibrosis in Mice through Antagonizing ELAVL1-Mediated Osteopontin mRNA Stabilization

abstract:
BackgroundFibroblast-myofibroblasts transition (FMT) is one of the hallmark cellular processes in pulmonary fibrosis. This study is to investigate the effects of CMLD-2 in FMT and pulmonary fibrosis, which antagonizes HuR, a supposedly key regulatory RNA binding protein (RBP).

MethodsHuR or other deferentially expressed RBPs during TGF-{beta}1-induced FMT were analyzed by transcriptomic methods, and further validated in vitro or in fibrotic lung specimens. The effects of HuR overexpression, down-regulation or inhibition by an antagonist CMLD-2 were analyzed in FMT or bleomycin-induced experimental lung fibrosis. HuR-targeting RNA and their interactions were analyzed by CLIP-seq.

ResultsHuR, hnRNPA1, hnRNPE1, TIA1 and TFRC were significantly up-regulated, while ESRP1, ESRP2 and TTP were significantly down-regulated. Cytoplasmic expression of HuR was activated in IPF lung tissue and rat lungs of bleomycin-induced fibrosis. HuR overexpression induced -SMA and collagen I expression, increased the proliferation and migration capacities of fibroblasts with or without the stimulation of TGF-{beta}1. HuR knockdown by shRNA inhibited the proliferation, transition, collagen production and migration properties in fibroblasts or in TGF-{beta}1-stimulated myofibroblasts. Combinative analysis of RNA-seq and CLIP-seq data revealed major HuR binding motifs and several HuR-bound, differentially expressed mRNAs in FMT, specifically SPP1 mRNA encoding osteopontin. HuR-mediated SPP1 mRNA stabilization was further validated by RIP-PCR and half-life analysis using SPP1 mutant transcripts. Inhibiting HuR using CMLD-2 attenuated SPP1/osteopontin expression, TGF-{beta}1-induced FMT in vitro and bleomycin-induced pulmonary fibrosis in mice. Nuclear-cytoplasmic shuttle of HuR was activated in TGF-{beta}1-induced FMT, which was inhibited by p38MAPK (SB203580) or PKC (Go-6976) inhibition, but not associated with phosphorylation of HuR.

ConclusionsFibroblast-myofibroblast transition is activated by HuR-SPP1 mRNA interactions, and CMLD-2 is potentiated to be a therapeutic agent targeting HuR for fibroblast-myofibroblast transition and pulmonary fibrosis.

category: molecular biology


title: Stem cells partner with matrix remodeling cells during regeneration

abstract: Regeneration of missing or damaged tissue requires the concerted activities of both pre-existing and newly generated cells. While previous studies identified regeneration-induced gene expression programs in tissues and single cells1-6, emerging spatial transcriptomic methods can place these programs into their organismal context at near cellular resolution7-11. Here we report a spatial transcriptomic atlas of whole-body regeneration and identify changes in gene expression patterning and tissue architecture during regeneration. We produced spatially resolved RNA-seq data from regenerating tail fragments of the free-living planarian Schmidtea mediterranea. Comparison of fragments 6 and 48 hours after amputation revealed time-dependent changes in gene expression patterns and cellular associations. Notable examples include re-localization of agat-1+ epidermal cells from lateral edges to both lateral and anterior edges and the discovery of wound-induced association of stem cells with cells expressing the matrix remodeling gene matrix metalloproteinase-1. Our results thoroughly detail changes in gene expression patterns and uncover interactions between stem cells and their microenvironment, demonstrating the unique ability of unbiased spatial profiling methods to reveal the biology of regeneration.

category: developmental biology


title: SER: an R package to compute environmental regime over a certain time period

abstract:
O_LIEnvironmental regime (or environmental legacy or historical legacy) is the environmental dynamic characteristics over a given (either long or short) time period, such as frequency of mean or extreme events and rate of change, which might be masked by using only contemporary variables.
C_LIO_LIWe present SER, an R package for estimating environmental regimes for different environmental variables. Using the data included in the package, several examples are shown.
C_LIO_LISER is suitable for any types of environmental variables e.g., nutrient concentration, light, dissolved oxygen. In addition, by changing the argument "days_bf", it is possible to compute environmental regimes in any interested time period, such as days, months or years.
C_LIO_LIOur case study showed that inclusion of environmental regimes dramatically increased the explained variation of temporal {beta}-diversity and its components. Environmental regimes, particularly in a given time period, are expected to advance the "environment - community" relationships in ecological studies. In addition, they can be implemented in other subjects, e.g., social science, socioeconomics, epidemiology, with important applied implications.
C_LI

category: ecology


title: Exploring links between climatic predictability and the evolution of within- and transgenerational plasticity

abstract: In variable environments, phenotypic plasticity can increase fitness by providing tight environment-phenotype matching. However, adaptive plasticity is expected to evolve only when the future selective environment can be predicted based on the prevailing conditions. That is, the juvenile environment should be predictive of the adult environment (within-generation plasticity) or the parental environment should be predictive of the offspring environment (transgenerational plasticity). Here, we test links between environmental predictability and evolution of adaptive plasticity by combining time series analyses and a common garden experiment using temperature as a stressor in a temperate butterfly (Melitaea cinxia). Time series analyses revealed that across season fluctuations in temperature over 48 years is overall predictable. However, within the growing season, temperature fluctuations showed high heterogeneity across years with low autocorrelations and timing of temperature peaks were asynchronous. Most life-history traits showed strong within-generation plasticity for temperature and traits such as body size and growth rate broke the temperature-size rule. Evidence for transgenerational plasticity, however, was weak and detected for only two traits each in an adaptive and non-adaptive direction. We suggest that low predictability of temperature fluctuations within the growing season likely disfavours the evolution of adaptive transgenerational plasticity but instead favours strong within-generation plasticity.

category: evolutionary biology


title: A genome-wide mutational constraint map quantified from variation in 76,156 human genomes

abstract: The depletion of disruptive variation caused by purifying natural selection (constraint) has been widely used to investigate protein-coding genes underlying human disorders, but attempts to assess constraint for non-protein-coding regions have proven more difficult. Here we aggregate, process, and release a dataset of 76,156 human genomes from the Genome Aggregation Database (gnomAD), the largest public open-access human genome reference dataset, and use this dataset to build a mutational constraint map for the whole genome. We present a refined mutational model that incorporates local sequence context and regional genomic features to detect depletions of variation across the genome. As expected, proteincoding sequences overall are under stronger constraint than non-coding regions. Within the noncoding genome, constrained regions are enriched for regulatory elements and variants implicated in complex human diseases and traits, facilitating the triangulation of biological annotation, disease association, and natural selection to non-coding DNA analysis. More constrained regulatory elements tend to regulate more constrained genes, while non-coding constraint captures additional functional information underrecognized by gene constraint metrics. We demonstrate that this genome-wide constraint map provides an effective approach for characterizing the non-coding genome and improving the identification and interpretation of functional human genetic variation.


title: Multiple forward scattering reduces the measured scattering coefficient of whole blood in visible-light optical coherence tomography

abstract: Optical properties of blood encode oxygen-dependent information. Noninvasive optical detection of these properties is increasingly desirable to extract biomarkers for tissue health. Recently, visible-light optical coherence tomography (vis-OCT) demonstrated retinal oxygen saturation (sO2) measurements using the depth-resolved spectrum of blood. Such measurements rely on differences between the absorption and scattering coefficients of oxygenated and deoxygenated blood. However, there is still broad disagreement, both theoretically and experimentally, on how vis-OCT measures bloods scattering coefficient. Incorrect assumptions of bloods optical properties can add additional uncertainties or biases into vis-OCTs sO2 model. Using Monte Carlo simulation of a retinal vessel, we determined that vis-OCT almost exclusively detects multiple-scattered photons in blood. Meanwhile, photons mostly forward scatter in blood within the visible spectral range, allowing photons to maintain ballistic paths and penetrate deeply, leading to a reduction in the measured scattering coefficient. We defined a scattering scaling factor (SSF) to account for such a reduction and found that SSF varied with measurement conditions, such as numerical aperture, depth resolution, and depth selection. We further experimentally validated SSF in ex vivo blood phantoms pre-set sO2 levels and in the human retina, both of which agreed well with our simulation.

category: bioengineering


title: In-silico method for predicting infectious strains of Influenza A virus from its genome and protein sequences

abstract:
Influenza A is a contagious viral disease responsible for four pandemics in the past and a major public health concern. Being zoonotic in nature, the virus can cross the species barrier and transmit from wild aquatic bird reservoirs to humans via intermediate hosts. Virus gradually undergoes host adaptive mutations in their genome and proteins, resulting in different strain s/vari ants which might spread virus from avians/mammals to humans. In this study, we have developed an in-silico models to identify infectious strains of Influenza A virus, which has the potential of getting transmitted to humans, from its whole genome/proteins. Firstly, machine learning based models were developed for predicting infectious strains using composition of 15 proteins of virus. Random Forest based model of protein Hemagglutinin, achieved maximum AUC 0.98 on validation data using dipeptide composition. Secondly, we obtained maximum AUC of 0.99 on validation dataset using one-hot-encoding features of each protein of virus. Thirdly, models build on DNA composition of whole genome of Influenza A, achieved maximum AUC 0.98 on validation dataset. Finally, a web-based service, named "FluSPred"(https://webs.iiitd.edu.in/raghava/fluspred/) has been developed which incorporate best 16 models (15 proteins and one based on genome) for prediction of infectious strains of virus. In addition, we provided standalone software for the prediction and scanning of infectious strains at large-scale (e.g., metagenomics) from genomic/proteomic data. We anticipate this tool will help researchers in prioritize high-risk viral strains of novel influenza virus possesses the capability to spread human to human, thereby being useful for pandemic preparedness and disease surveillance.

Key PointsO_LIInfluenza A is a contagious viral disease responsible for four pandemics.
C_LIO_LIVirus can cross species barrier and infect human beings.
C_LIO_LIIn silico models developed for predicting human infectious strains of virus.
C_LIO_LIModels developed were build using 15 proteins and whole genome datasets.
C_LIO_LIWebserver and standalone package for predicting and scanning of high-risk viral strains.
C_LI

category: bioinformatics


title: Syrah, a Slide-seqV2 pipeline augmentation

abstract: Spatial transcriptomic techniques such as Slide-seqV2 uncover novel relationships and interactions between cell types by coupling gene expression and spatial data. Here we discuss two unexpected sources of error in Slide-seqV2 data, one physical and one computational. To address this we present an analysis pipeline augmentation, Syrah, which corrects for these errors and show that it improves both data quantity and quality over the standard pipeline alone or in combination with additional sequencing.


title: Exploiting deep transfer learning for the prediction of functional noncoding variants using genomic sequence

abstract:
MotivationThough genome-wide association studies have identified tens of thousands of variants associated with complex traits and most of them fall within the noncoding regions, they may not the causal ones. The development of high-throughput functional assays leads to the discovery of experimental validated noncoding functional variants. However, these validated variants are rare due to technical difficulty and financial cost. The small sample size of validated variants makes it less reliable to develop a supervised machine learning model for achieving a whole genome-wide prediction of noncoding causal variants.

ResultsWe will exploit a deep transfer learning model, which is based on convolutional neural network, to improve the prediction for functional noncoding variants. To address the challenge of small sample size, the transfer learning model leverages both large-scale generic functional noncoding variants to improve the learning of low-level features and context-specific functional noncoding variants to learn high-level features toward the contextspecific prediction task. By evaluating the deep transfer learning model on three MPRA datasets and 16 GWAS datasets, we demonstrate that the proposed model outperforms deep learning models without pretraining or retraining. In addition, the deep transfer learning model outperforms 18 existing computational methods in both MPRA and GWAS datasets.

Availabilityhttps://github.com/lichen-lab/TLVar

Supplementary InformationSupplementary data are available at Bioinformatics online.

Contactchen61@iu.edu


title: Stability and expression of SARS-CoV-2 spike-protein mutations

abstract: Protein fold stability likely plays a role in SARS-CoV-2 S-protein evolution, together with ACE2 binding and antibody evasion. While few thermodynamic stability data are available for S-protein mutants, many systematic experimental data exist for their expression. In this paper, we explore whether such expression levels relate to the thermodynamic stability of the mutants. We studied mutation-induced SARS-CoV-2 S-protein fold stability, as computed by three very distinct methods and eight different protein structures to account for method- and structure-dependencies. For all methods and structures used (24 comparisons), computed stability changes correlate significantly (99% confidence level) with experimental yeast expression from the literature, such that higher expression is associated with relatively higher fold stability. Also significant, albeit weaker, correlations were seen for ACE2 binding. The effect of thermodynamic fold stability may be direct or a correlate of amino acid or site properties, notably the solvent exposure of the site. Correlation between computed stability and experimental expression and ACE2 binding suggests that functional properties of the SARS-CoV-2 S-protein mutant space are largely determined by a few simple features, due to underlying correlations. Our study lends promise to the development of computational tools that may ideally aid in understanding and predicting SARS-CoV-2 S-protein evolution.

category: biophysics


title: Short-term and bystander effects of radiation on murine submandibular glands

abstract:
Many patients treated for head and neck cancers experience salivary gland hypofunction due to radiation damage. Understanding the mechanisms of cellular damage induced by radiation treatment is important in order to design methods of radioprotection. In addition, it is crucial to recognize the indirect effects of IR and the systemic responses that may alter saliva secretion. In this study, radiation was delivered to murine submandibular glands (SMG) bilaterally, using a 137Cs gamma ray irradiator, or unilaterally, using a small animal radiation research platform (SARRP). Analysis at 3, 24 and 48 hours showed dynamic changes in mRNA levels and protein abundance in SMG irradiated bilaterally. Unilateral irradiation using the SARRP caused similar changes in the irradiated SMG, as well as significant off-target, bystander effects in the non-irradiated contralateral SMG.

Summary statementRapid changes in gene expression occur in irradiated salivary glands within hours of irradiation, and in non-irradiated contralateral glands, due to bystander effects.

category: cancer biology


title: Robust and durable prophylactic protection conferred by RNA interference in preclinical models of SARS-CoV-2

abstract: RNA interference is a natural antiviral mechanism that could be harnessed to combat SARS-CoV-2 infection by targeting and destroying the viral genome. We screened lipophilic small-interfering RNA (siRNA) conjugates targeting highly conserved regions of the SARS-CoV-2 genome and identified leads targeting outside of the spike-encoding region capable of achieving [≥]3-log viral reduction. Serial passaging studies demonstrated that a two-siRNA combination prevented development of resistance compared to a single-siRNA approach. A two-siRNA combination delivered intranasally protected Syrian hamsters from weight loss and lung pathology by viral infection upon prophylactic administration but not following onset of infection. Together, the data support potential utility of RNAi as a prophylactic approach to limit SARS-CoV-2 infection that may help combat emergent variants, complement existing interventions, or protect populations where vaccines are less effective. Most importantly, this strategy has implications for developing medicines that may be valuable in protecting against future coronavirus pandemics.

category: pharmacology and toxicology


title: Pyrroloquinoline Quinone inhibits PCSK9, augments LDLR recycling and enhances the effect of atorvastatin

abstract:
High fat diet intake or statin therapy are known to increase the expression of PCSK9, a key factor involved in the lipid metabolism. Inhibition of PCSK9 is a potential novel strategy for treatment of CVD. Aim of the present study is to investigate the effect of PQQ and atorvastatin on PCSK9 expression in high fat, 10% fructose diet (HFFD) fed rats. Rats received HFFD for 10 weeks followed by treatment of 5 weeks with ATS 10 or 20 mg/kg, PQQ 10 or 20 mg/kg, p.o. per se or in combinations. The effect of the treatments on serum lipid profile, transaminases and PCSK9 concentrations was estimated. Hepatic expressions of PCSK9 and LDLR were quantified by real time quantitative Polymerase chain reaction (RT-qPCR) and western blotting analysis. Compared with the positive control, rats receiving PQQ and ATS showed significant decrease in serum levels of triglycerides, total cholesterol, LDL, VLDL, non-HDL and atherogenic index. Further, drug treatment resulted in decreased serum ALT and AST levels (P < 0.0001). PQQ in combination with atorvastatin reduced serum PCSK9 levels (P < 0.0001) while downregulating the hepatic expression of PCSK9 (P < 0.0001) and increasing the expression of LDL-R (P < 0.001) and rescuing its degradation. PQQ along with atorvastatin prevented the LDLR degradation that was induced in the HFFD fed rats by decreasing PCSK9 expression. The results support an improvement in cholesterol management by adding PQQ to statin treatment.

Graphical abstract

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title: Glucagon Receptor Signaling at White Adipose Tissue Does Not Regulate Lipolysis

abstract:
ObjectiveAlthough the physiologic role of glucagon receptor signaling in the liver is well defined, the impact of glucagon receptor (Gcgr) signaling at white adipose tissue (WAT) continues to be debated. While numerous studies propose glucagon stimulates WAT lipolysis, we lack evidence that physiological concentrations of glucagon regulate WAT lipolysis. Glucagon receptor antagonists are proposed as a treatment to lower blood glucose in people with type 2 diabetes, yet concerns on how these treatments may affect lipid homeostasis have led to questions regarding the potential safety and efficacy of such therapeutics. Tight regulation of adipose tissue lipolysis is critical for whole body lipid homeostasis. In turn, we used WAT Gcgr knockout mice to determine if glucagon regulates lipolysis at WAT in the mouse.

MethodsWe assessed the effects of fasting and acute exogenous glucagon administration in wildtype C57BL/6J and Gcgr Adipocyte+/+ vs GcgrAdipocyte-/- mice. Using an ex vivo lipolysis protocol, we further examined the direct effects of glucagon on physiologically (fasted) and pharmacologically stimulated lipolysis.

ResultsAdipocyte Gcgr expression did not affect fasting induced lipolysis or hepatic lipid accumulation in lean or diet induced obese (DIO) mice. Acute glucagon administration did not affect serum non-esterified fatty acids (NEFA), leptin, or adiponectin concentration, but did increase serum glucose and FGF21, regardless of genotype. Glucagon did not affect ex vivo lipolysis in explants from either Gcgr Adipocyte+/+ or GcgrAdipocyte-/- mice. Gcgr expression did not affect fasting-induced or isoproterenol-stimulated lipolysis from WAT explants. Moreover, glucagon receptor signaling at WAT does not affect body weight or glucose homeostasis in lean or DIO mice.

ConclusionsWe have established that glucagon does not regulate WAT lipolysis, either directly or indirectly. Unlike the crucial role of hepatic glucagon receptor signaling in maintaining glucose and lipid homeostasis, we observed no metabolic consequence of WAT glucagon receptor deletion.


title: Stroke disconnectome decodes reading networks

abstract: Cognitive functional neuroimaging has been around for over 30 years and has shed light on the brain areas relevant for reading. However, new methodological developments enable mapping the interaction between functional imaging and the underlying white matter networks. In this study, we used such a novel method, called the disconnectome, to decode the reading circuitry in the brain. We used the resulting disconnection patterns to predict the typical lesion that would lead to reading deficits after brain damage. Our results suggest that white matter connections critical for reading include fronto-parietal U-shaped fibres and the vertical occipital fasciculus (VOF). The lesion most predictive of a reading deficit would impinge on the left inferior parietal and the three temporal and occipital gyri. This novel framework can systematically be applied to bridge the gap between the neuropathology of language and cognitive neuroscience.


title: The neural code behind real-world recognition abilities

abstract: We recorded a large dataset of high-density electroencephalographic signals and used a combination of behavioural tests and machine learning to characterise the brain computations covarying with face recognition in individuals with extraordinary abilities. We show that individual face recognition ability can be accurately decoded from brain activity in an extended temporal interval for face and non-face objects. We demonstrate that this decoding is supported by perceptual and semantic brain computations.


title: Reversible edema following electric drilling of macaque craniotomy

abstract: In-vivo electrophysiology requires direct access to brain tissue, necessitating the development and refinement of surgical procedures and techniques that promote the health and well-being of the animal subjects. Here, we report a series of findings noted on structural magnetic resonance imaging (MRI) scans in monkeys with MRI-compatible implants following small craniotomies that provide access for intracranial electrophysiology. We found distinct brain regions exhibiting hyperintensities in T2-weighted scans that were prominent underneath the sites at which craniotomies had been performed. We interpreted these hyperintensities as edema of the neural tissue and found that they were predominantly present following electric drilling, but not when manual, hand-operated drills were used. Further, the anomalies subsided within 2-3 weeks following surgery. Our report highlights the utility of MRI-compatible implants that promote clinical examination of the animals brain, sometimes revealing findings that may go unnoticed when incompatible implants are used. We show replicable differences in outcome when using electric vs. mechanical devices, both ubiquitous in the field. If electric drills are used, our report cautions electrophysiological recordings from tissue directly underneath the craniotomy for the first 2-3 weeks following the procedure due to putative edema.


title: Novel method for reliably measuring spontaneous postsynaptic potentials/currents in whole-cell patch clamp recordings in the central nervous system

abstract:
In chemical synapses of the central nervous system (CNS) an information unit is transmitted via the presynaptic release of a neurotransmitter vesicle, a quantum, eliciting a postsynaptic membrane electric response of a certain amplitude, a quantal size. This key determinant of neural computation has not been reliably measured due to the nature of synaptic communication and technical limitations of electrophysiological recordings in the CNS. Measuring amplitudes of spontaneous postsynaptic currents (sPSCs) or potentials (sPSPs) at the cell soma potentially offers a technically straight forward way to estimate the quantal size as these miniature responses (minis) are ellicited by the spontaneous release of a single neurotransmitter vesicle. However, somatically recorded minis are massively attenuated and, for the most part, are indistinguishable from background noise fluctuations. For them to be accurately estimated, a revised method would have to isolate the noise component. As the first step in devising such a method, we developed and described a novel sPSP/sPSC detection algorithm as part of our quantal analysis software called  minis. We tested the performance of the algorithm in detecting real and simulated minis in rat cortical slice whole-cell recordings and compared it to other most commonly used similar detection algorithms in the field of the synaptic function research. This benchmarking analysis revealed superior detection performance by our algorithm. The release version of the algorithm also offers great flexibility as it can be controlled through graphical and programming interfaces making it suitable for the needs of most individual researchers studying the central synapse function.

Significance statementBeing able to measure accurately the electrical size of synapses in the brain is critical for understanding neural computations. Offering a novel algorithm for measuring properties of spontaneous synaptic signalling is an important first step in doing so. By its qualities of being transparent and objectively evaluated, this algorithm sets an important methodological standard for comparative assessment of other popular algorithms in the field of the synaptic function research. Because of its superior performance and flexibility, the algorithm also offers a technological improvement greatly useful to individual researchers in the field. Finally, its evaluation process highlighted common methodological pitfalls surrounding the spontaneous synaptic signalling research that hopefully could reduce their future impact.


title: Plant Virus Database: a resource for exploring the diversity of plant viruses and their interactions with hosts

abstract: Plant viruses cause huge damage to commercial crops, yet the studies towards plant viruses are limited and the diversity of plant viruses are under-estimated yet. This study built an up-to-date atlas of plant viruses by computationally identifying viruses from the RNA-seq data in the One Thousand Plant Transcriptomes Initiative (1KP) and by integrating plant viruses from public databases, and further built the Plant Virus Database (PVD, freely available at http://47.90.94.155/PlantVirusBase/#/home) to store and organize these viruses. The PVD contained 3,206 virus species and 9,604 virus-plant host interactions which were more than twice that reported in previous plant virus databases. The plant viruses were observed to infect only a few plant hosts and vice versa. Analysis and comparison of the viromes in the Monocots and Eudicots, and those in the plants in tropical and temperate regions showed significant differences in the virome composition. Finally, several factors including the viral group (DNA and RNA viruses), enveloped or not, and the transmission mode of viruses, were found to have no or weak associations with the host range of plant viruses. Overall, the study not only provides a valuable resource for further studies of plant viruses, but also deepens our understanding towards the genetic diversity of plant viruses and the virus-host interactions.


title: Vaginal microbiome-host interactions modeled in a human vagina-on-a-chip

abstract:
BackgroundA dominance of non-iners Lactobacillus species in the vaginal microbiome is optimal and strongly associated with gynecological and obstetric health, while the presence of diverse obligate or facultative anaerobic bacteria and a paucity in Lactobacillus species, similar to communities found in bacterial vaginosis (BV), is considered non-optimal and associated with adverse health outcomes. Various therapeutic strategies are being explored to modulate the composition of the vaginal microbiome; however, there is no human model that faithfully reproduces the vaginal epithelial microenvironment for preclinical validation of potential therapeutics or testing hypotheses about vaginal epithelium-microbiome interactions.

ResultsHere, we describe an organ-on-a-chip (Organ Chip) microfluidic culture model of the human vaginal mucosa (Vagina Chip) that is lined by hormone-sensitive, primary vaginal epithelium interfaced with underlying stromal fibroblasts, which sustains a low physiological oxygen concentration in the epithelial lumen. We show that the Vagina Chip can be used to assess colonization by optimal L. crispatus consortia as well as non-optimal Gardnerella vaginalis-containing consortia, and to measure associated host innate immune responses. Co-culture of the L. crispatus consortia was accompanied by maintenance of epithelial cell viability, accumulation of D- and L-lactic acid, maintenance of a physiologically relevant low pH, and down regulation of proinflammatory cytokines. In contrast, co-culture of G. vaginalis-containing consortia in the Vagina Chip resulted in epithelial cell injury, a rise in pH, and upregulation of proinflammatory cytokines.

ConclusionThis study demonstrates the potential of applying human Organ Chip technology to create a preclinical model of the human vaginal mucosa that can be used to better understand interactions between the vaginal microbiome and host tissues, as well as to evaluate the safety and efficacy of live biotherapeutics products.


title: Genome mining, phylogenetic, and functional analysis of arsenic (As) resistance operons in Bacillus strains, isolated from As-rich hot spring microbial mats

abstract: The geothermal zone of Araro, Mexico, is located within the trans-Mexican volcanic belt, an area with numerous arsenic (As)-rich hot springs. In this study, the draft genome sequence of two endemic Bacillus strains (ZAP17 and ZAP62) from Araro microbial mat hot springs was determined, which were able to grow on arsenate (up to 64 mM) and arsenite (up to 32 mM). Phylogenetic analysis based on 16S rRNA and gyrB sequences, as well as genome sequence analysis based on average nucleotide identity (>96%) and digital DNA-DNA hybridization (>70%), indicated that these strains belong to the Bacillus paralicheniformis ZAP17 and Bacillus altitudinis ZAP62. Furthermore, through genome mining, it was identified two arsenic resistance operons, arsRBC, and arsRBCDA in both strains as potential determinants of arsenic (As) resistance. Predicted ArsA (arsenial pump-driving ATPase), ArsB (Arsenical efflux pump protein), ArsC (Arsenate reductase), ArsD (Arsenical efflux pump protein) and ArsR (Metalloregulator/ars operon repressor) proteins, clearly grouped with their respective clades corresponding to other characterized bacterial species, mainly Firmicutes. To further evaluate the functionality of the ars operons in ZAP17 and ZAP62 strains, our results showed that arsRBC and arsRBCDA genes were expressed in the presence of arsenite (III). Finally, the presence of ars operons in the genome of Bacillus species residing in As-rich environments, such as the Araro hot springs, might be a potential mechanism to survive under such harsh conditions, as well as to design sustainable bioremediation strategies.


title: Regulation of EGF-stimulated activation of the PI-3K/AKT pathway by exocyst-mediated exocytosis

abstract: The phosphoinositide-3 kinase (PI-3K)/AKT cell survival pathway is an important pathway activated by EGFR signaling. Here we show, that in addition to previously described critical components of this pathway, i.e., the docking protein Gab1, the PI-3K/AKT pathway in epithelial cells is regulated by the exocyst complex, which is a vesicle tether that is essential for exocytosis. Using live-cell imaging, we demonstrate that PI(3,4,5)P3 levels fluctuate at the membrane on a minutes time scale and that these fluctuations are associated with local PI(3,4,5)P3 increases at sites where recycling vesicles undergo exocytic fusion. Supporting a role for exocytosis in PI(3,4,5)P3 generation, acute promotion of exocytosis by optogenetically driving exocyst-mediated vesicle tethering upregulates PI(3,4,5)P3 production and AKT activation. Conversely, acute inhibition of exocytosis using Endosidin2, a small-molecule inhibitor of the exocyst subunit Exo70, impairs PI(3,4,5)P3 production and AKT activation induced by EGF stimulation of epithelial cells. Moreover, prolonged inhibition of EGF signaling by EGFR tyrosine kinase inhibitors results in spontaneous reactivation of AKT without a concomitant relief of EGFR inhibition. However, this reactivation can be negated by acutely inhibiting the exocyst. These experiments demonstrate that exocyst-mediated exocytosis - by regulating PI(3,4,5)P3 levels at the plasma membrane - subserves activation of the PI-3K/AKT pathway by EGFR in epithelial cells.

category: cell biology


title: BIN1/Amphiphysin 2 and ezrin drive filopodia-like structures in myoblasts

abstract: Amphiphysin 2 (BIN1) is a membrane and actin remodeling protein mutated both in congenital and adult centronuclear myopathies. The BIN1 muscle-specific isoform finely tunes muscle regeneration in adulthood and regulates myoblast fusion. However, the underlying molecular mechanisms are unknown. Here, we report that BIN1 is required for myoblast fusion and participates in the formation of filopodia-like structures at myoblasts intercellular junctions. BIN1 bundles actin in vitro and regulates the membrane-to-cortex attachment, two key processes required for myoblast fusion. We identified ezrin as a new BIN1 partner and showed that BIN1 promotes ezrin association to PI(4,5)P2 at the membrane cortex. Our results establish BIN1 and ezrin as key players at the early stages of myoblast fusion for the formation of long-lived filopodia-like structures.


title: Lipolysis of bone marrow adipocytes is required to fuel bone and the marrow niche during energy deficits

abstract: To investigate roles for bone marrow adipocyte (BMAd) lipolysis in bone homeostasis, we created a BMAd-specific Cre mouse model in which we knocked out adipose triglyceride lipase (ATGL, Pnpla2). BMAd-Pnpla2-/- mice have impaired BMAd lipolysis, and increased size and number of BMAds at baseline. Although energy from BMAd lipid stores is largely dispensable when mice are fed ad libitum, BMAd lipolysis is necessary to maintain myelopoiesis and bone mass under caloric restriction. BMAd-specific Pnpla2 deficiency compounds the effects of caloric restriction on loss of trabecular bone, likely due to impaired osteoblast expression of collagen genes and reduced osteoid synthesis. RNA sequencing analysis of bone marrow adipose tissue reveals that caloric restriction induces dramatic elevations in extracellular matrix organization and skeletal development genes, and energy from BMAd is required for these adaptations. BMAd-derived energy supply is also required for bone regeneration upon injury, and maintenance of bone mass with cold exposure.


title: A conformational switch in clathrin light chain regulates lattice structure and endocytosis at the plasma membrane of mammalian cells.

abstract: The conformations of endocytic proteins and their interactions are key regulators of clathrin-mediated endocytosis. Three clathrin light chains (CLC), along with three clathrin heavy chains, assemble to form single clathrin triskelia that link into a geometric lattice that curves to drive endocytosis. Conformational changes in CLC have been shown to regulate triskelia assembly in solution, yet the nature of these structural changes, and their effects on lattice growth, curvature, and endocytosis in cells are unclear. Here, we develop a correlative fluorescence resonance energy transfer (FRET) and platinum replica electron microscopy method, named FRET-CLEM. With FRET-CLEM, we measure conformational changes in proteins at thousands of individual morphologically distinct clathrin-coated structures across cell membranes. We find that the N-terminus of CLC moves away from the plasma membrane and triskelia vertex as lattices curve. Preventing this conformational switch with acute chemical tools inside cells increased clathrin structure sizes and inhibited endocytosis. Therefore, a specific conformational switch in CLC regulates lattice curvature and endocytosis in mammalian cells.


title: The non-catalytic role of DNA polymerase epsilon in replication initiation in human cells

abstract: DNA polymerase epsilon in an essential enzyme, responsible for the synthesis of the leading strand during DNA replication. Deficiencies and mutations in DNA polymerase epsilon catalytic subunit (POLE1) cause severe developmental abnormalities and cancers. Paradoxically, the non-catalytic C-terminal domain of yeast polymerase epsilon catalytic subunit (Pol2) is sufficient for cell survival. The non-catalytic essential function of Pol2 in yeast has been associated with its role in the assembly of the replicative helicase CMG. However, the understanding of POLE1 functions in DNA replication initiation in human cells is falling behind. In this study we use an auxin-inducible degron system to study the effect of POLE1 depletion on replication initiation in human cells. Surprisingly, in the absence of POLE1, human cells were able to assemble CMG helicase and initiate DNA synthesis that failed shortly after. Expression of POLE1 C-terminal non-catalytic domain was enough to rescue replication initiation and support slow, but processive DNA synthesis, which was dependent on the POLE1-POLE2 interaction. We propose a model where in human cells POLE1/POLE2 are not essential for CMG assembly, but are required during later steps of replication initiation. Our study provides some insights into the role of DNA polymerase epsilon in replication initiation in human cells.


title: Ultrabithorax modifies a regulatory network of genes essential for butterfly eyespot development in a wing sector-specific manner

abstract: Nymphalid butterfly species often have a different number of eyespots in forewings and hindwings but how the hindwing identity gene, Ultrabithorax (Ubx), drives this asymmetry, is not fully understood. It is also unclear why eyespot serial homologs originated initially only in hindwings. To address these questions, we examined a three-gene regulatory network (GRN) for eyespot development in the hindwings of Bicyclus anynana butterflies, and compared it to the same network previously described for forewings. We also examined how Ubx interacted with each of these three eyespot-essential genes. We found similar genetic interactions between the three genes in fore and hindwings, but we discovered three regulatory differences: Antennapedia (Antp) merely enhances spalt (sal) expression in the eyespot foci in hindwings but is not essential for sal activation, as in forewings; Ubx up- regulates Antp in all hindwing eyespot foci but represses Antp outside these wing regions and; Ubx is regulating sal expression in a wing-sector specific manner, i.e., it does not affect sal expression in the wing sectors that contain eyespots in both fore and hindwings, but it positively regulates sal expression in the sectors that have hindwing-specific eyespots. These results suggest that Ubx, or its downstream targets, might have paid a role in the origin of eyespots, restricted initially to hindwings, via the positive regulation of sal, an essential gene for eyespot development. We propose that Antp got co-opted into the eyespot GRN at a later stage by coming under Ubx regulation. This Hox gene redundancy, together with a novel positive feedback loop between sal and Antp, might have allowed Antp to functionally replace Ubx in forewings and lead to the origin of forewing eyespots. Outside the eyespot focal regions, we discovered that Ubx is up-regulated by Distal-less along the wing margin. We propose a model for how the regulatory connections between these genes might have evolved to produce wing- and sector-specific variation in eyespot number.


title: The dynamics of speciation in the gall-forming aphid Geoica spp. within and among Pistacia host tree species

abstract:
Trees of the genus Pistacia serve as obligate hosts for gall-forming aphids (Hemiptera, Aphididae, Fordini). Each aphid species induces a characteristic gall on a single Pistacia host species. The genus Geoica (Fordini) induce similar spherical closed galls on the lower side of the leaflets midvein, on different Pistacia species. Two species of Pistacia trees that harbor Geoica galls grow naturally in Israel: P. palaestina and P. atlantica. We analyzed the phylogeny and the genetic structure of the Geoica species complex in Israel, and assessed the genetic differentiation and the level of host plant specificity of the aphids between P. atlantica and P. palaestina. We found that the splitting of the genus between P. atlantica and P. palaestina is estimated to have occurred 24-25 Ma (the Oligocene/Miocene boundary). Five different haplotypes suggesting five different species have been further speciating among Geoica spp., galling on P. atlantica, and an additional three species, on P. palaestina.

Accession Numbers (COI sequences)MW452548 - Pp-Q-7d-Gamla - Haplotype-VI
MW452549 - Pp-Q-10b-Gamla - Haplotype-VII
MW452550 - Pp-A-1a-Mezar - Haplotype-VII
MW452551 - Pp-S-6c-Sasa - Haplotype-VI
MW452552 - Pp-New Hermon-2-5 - Haplotype-VIII
MW452553 - Pa-Q-10a-II Gamla - Haplotype-IV
MW452554 - Pa-Q-5d Gamla - Haplotype-II
MW452555 - Pa-A-2f Mezar - Haplotype-IV
MW452556 - Pa-E-13 Anafa - Haplotype-III
MW452557 - Pa-K-10a Adolam - Haplotype-IV
MW452558 - Pa-K-3a Adolam - Haplotype-II
MW452559 - Pa-N-2a Nizana - Haplotype-I
MW452560 - Pa-Z-1-3 Hazeva - Haplotype-I
MW452561 - Pa-SL-3-3 Jordan-Sela - Haplotype-V

category: genetics


title: slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes

abstract: One of the goals of population genetics is to understand how evolutionary forces shape patterns of genetic variation over time. However, because populations evolve across both time and space, most evolutionary processes also have an important spatial component, acting through phenomena such as isolation by distance, local mate choice, or uneven distribution of resources. This spatial dimension is often neglected, partly due to the lack of tools specifically designed for building and evaluating complex spatio-temporal population genetic models. To address this methodological gap, we present a new framework for simulating spatially-explicit genomic data, implemented in a new R package called slendr (www.slendr.net), which leverages a SLiM simulation back end bundled with the package. With this framework, the users can programmatically and visually encode spatial population ranges and their temporal dynamics (i.e., population displacements, expansions, and contractions) either on real Earth landscapes or on abstract custom maps, and schedule splits and gene flow events between populations using a straightforward declarative language. Additionally, slendr can simulate data from traditional, non-spatial models, either with SLiM or using an alternative built-in coalescent msprime back end. Together with its R-idiomatic interface to the tskit library for tree sequence processing and analysis, slendr opens up the possibility of performing efficient, reproducible simulations of spatio-temporal genomic data entirely within the R environment, leveraging its wealth of libraries for geospatial data analysis, statistics, and visualization. Here, we present the design of the slendr R package and demonstrate its features on several practical example workflows.

category: genomics


title: Identification of BAHD acyltransferases associated with acylinositol biosynthesis in Solanum quitoense (naranjilla)

abstract: Plants make a variety of specialized metabolites that can mediate interactions with animals, microbes and competitor plants. Understanding how plants synthesize these compounds enables studies of their biological roles by manipulating their synthesis in vivo as well as producing them in vitro. Acylsugars are a group of protective metabolites that accumulate in the trichomes of many Solanaceae family plants. Acylinositol biosynthesis is of interest because it appears to be restricted to a subgroup of species within the Solanum genus. Previous work characterized a triacylinositol acetyltransferase involved in acylinositol biosynthesis in the Andean fruit plant Solanum quitoense (lulo or naranjillo). We characterized three additional S. quitoense trichome expressed enzymes, and found that virus induced gene silencing of each caused changes in acylinositol accumulation. Surprisingly, the in vitro triacylinositol products of these enzymes are distinct from those that accumulate in planta. These enzymes, nonetheless, provide an opportunities to test the biological impact and properties of these triacylinositols in vitro.

category: plant biology


title: Sleep Deprivation Induces Acute Dissociation via Altered EEG Rhythms Expression and Connectivity.

abstract:
The fragmented sleep, fragmented mind hypothesis has associated sleep disturbances and dissociative states in subjects with dissociative traits, as supported by neurophysiological theories of consciousness stating that altered states might result from an altered functional interaction among brain modules due to inefficient sleep processes.

Irrespective of dissociative traits, it is conceivable that a labile sleep-wake cycle might fuel dissociative states such as derealization, depersonalization, and dissociative amnesia.

To verify whether acute sleep loss can prompt dissociative states and to identify possible psychophysiological correlates, we evaluated dissociative experiences (by means of Phenomenology of Consciousness Inventory and Clinician Administered Dissociative State Scale) and resting state EEG features (band-wise spectral content and phase synchronization) after total sleep deprivation.

After deprivation, participants reported increased perception of altered state of consciousness and dissociative experiences, and a decreased perception of cognitive control. Analyzing the psychophysiological correlates of dissociative states following deprivation, we observed the following results: the higher the prefrontal theta spectral content, the higher the depersonalization state and the lower the self-awareness; the higher the intensity of the dissociative experiences, the higher the synchronization increase in alpha, beta, and gamma bands; the higher the decrease of higher-order functions, the higher the synchronization in the aforementioned bands.

Thus, acute sleep deprivation appears to fuel dissociative experiences by establishing a state of consciousness promoted by a higher large-scale synchronization at high frequencies.


title: Lipid Accumulation Induced by APOE4 Impairs Microglial Surveillance of Neuronal-Network Activity

abstract:
Apolipoprotein E4 (APOE4) is the greatest known genetic risk factor for developing late- onset Alzheimers disease and its expression in microglia is associated with pro- inflammatory states. How the interaction of APOE4 microglia with neurons differs from microglia expressing the disease-neutral allele APOE3 is currently unknown. Here, we employ CRISPR-edited induced pluripotent stem cells (iPSCs) to dissect the impact of APOE4 in neuron-microglia communication. Our results reveal that APOE4 induces a distinct metabolic program in microglia that is marked by the accumulation of intracellular neutral lipid stores through impaired lipid catabolism. Importantly, this altered lipid-accumulated state shifts microglia away from homeostatic surveillance and renders APOE4 microglia weakly responsive to neuronal activity. By examining the transcriptional signatures of APOE3 versus APOE4 microglia before and after exposure to neuronal conditioned media, we further established that neuronal soluble cues differentially induce a lipogenic program in APOE4 microglia that exacerbates pro- inflammatory signals. Pharmacological blockade of lipogenesis in APOE4 microglia is sufficient to diminish intracellular lipid accumulation and restore microglial homeostasis. Remarkably, unlike APOE3 microglia that support neuronal network activity, co-culture of APOE4 microglia with neurons disrupts the coordinated activity of neuronal ensembles. We identified that through decreased uptake of extracellular fatty acids and lipoproteins, APOE4 microglia disrupts the net flux of lipids which results in decreased neuronal activity via the potentiation of the lipid-gated K+ channel, GIRK3. These findings suggest that neurological diseases that exhibit abnormal neuronal network-level disturbances may in part be triggered by impairment in lipid homeostasis in non-neuronal cells, underscoring a novel therapeutic route to restore circuit function in the diseased brain.

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title: Investigating the "two-hit hypothesis": effects of prenatal maternal immune activation and adolescent cannabis use on neurodevelopment in mice

abstract:
BackgroundPrenatal exposure to maternal immune activation (MIA) and chronic adolescent cannabis use are both risk factors for neuropsychiatric disorders. However, exposure to a single risk factor may not result in major mental illness, indicating that multiple exposures may be required for illness onset. Here, we examine whether combined exposure to prenatal MIA and adolescent delta-9-tetrahydrocannabinol (THC), the main psychoactive component of cannabis, lead to enduring neuroanatomical and behavioural changes in adulthood.

MethodsMice were prenatally exposed to viral mimetic, poly I:C (5mg/kg), or vehicle at gestational day (GD)9, and postnatally exposed to chronic THC (5mg/kg, intraperitoneal) or vehicle during adolescence (postnatal day [PND]28-45). Longitudinal magnetic resonance imaging (MRI) was performed pre-treatment, PND25, post-treatment, PND50, and in adulthood, PND85, followed by behavioural tests for anxiety-like, social, and sensorimotor gating. Postmortem assessment of cannabinoid (CB)1 and 2 receptor expressing cells was performed in altered regions identified by MRI (anterior cingulate and somatosensory cortices, striatum, and hippocampus).

ResultsSubtle deviations in neurodevelopmental trajectory and subthreshold anxiety-like behaviours were observed in mice exposed to both risk factors. Sex-dependent effects were observed in patterns of shared brain-behaviour covariation, indicative of potential sex differences in response to MIA and THC. Density of CB1 and CB2 receptor positive cells was significantly decreased in all mice exposed to MIA, THC, or both.

ConclusionsThese findings suggest that there may be a cumulative effect of risk factor exposure on gross neuroanatomical development, and that the endocannabinoid system may be sensitive to both prenatal MIA, adolescent THC, or the combination.


title: Multisensory integration in neurons of the medial pulvinar of macaque monkey

abstract: The pulvinar is a heterogeneous thalamic nucleus, which is well developed in primates. One of its subdivisions, the medial pulvinar, is connected to many cortical areas, including the visual, auditory and somatosensory cortices, as well as with multisensory areas and premotor areas. However, except for the visual modality, little is known about its sensory functions. A hypothesis is that, as a region of convergence of information from different sensory modalities, the medial pulvinar plays a role in multisensory integration. To test this hypothesis, two macaque monkeys were trained to a fixation task and the responses of single-units to visual, auditory and auditory-visual stimuli were examined. Analysis revealed auditory, visual and multisensory neurons in the medial pulvinar. It also revealed multisensory integration in this structure, mainly subadditive and suppressive. These findings show that the medial pulvinar is involved in multisensory integration.


title: A conserved mechanism regulates reversible amyloids via pH-sensing regions

abstract: Amyloids were long viewed as irreversible, pathological aggregates, often associated with neurodegenerative diseases1. However, recent insights challenge this view, providing evidence that reversible amyloids can form upon stress conditions and fulfil crucial cellular functions2. Yet, the molecular mechanisms regulating functional amyloids and the differences to their pathological counterparts remain poorly understood. Here we investigate the conserved principles of amyloid reversibility by studying the essential metabolic enzyme pyruvate kinase (PK) in yeast and human cells. We demonstrate that PK forms stress-dependent reversible amyloids through a pH-sensitive amyloid core. Stress- induced cytosolic acidification promotes aggregate formation via protonation of specific glutamate (in yeast) or histidine (in human) residues within the amyloid core. Our work thus unravels a conserved and potentially widespread mechanism underlying amyloid functionality and reversibility, fine-tuned to the respective physiological cellular pH range.


title: Sexual selection moderates heat stress response in males and females

abstract: A widespread effect of climate change is the displacement of organisms from their thermal optima. The associated thermal stress imposed by climate change has been argued to have a particularly strong impact on male reproduction but evidence for this postulated sex-specific stress response is equivocal. One important factor that may explain intra- and interspecific variation in stress responses is sexual selection, which is predicted to magnify negative effects of stress. Nevertheless, empirical studies exploring the interplay of sexual selection and heat stress are still scarce. We tested experimentally for an interaction between sexual selection and thermal stress in the red flour beetle Tribolium castaneum by contrasting heat responses in male and female reproductive success between setups of enforced monogamy versus polygamy. We found that polygamy magnifies detrimental effects of heat stress in males but relaxes the observed negative effects in females. Our results suggest that sexual selection can reverse sex differences in thermal sensitivity, and may therefore alter sex-specific selection on alleles associated with heat tolerance. We argue that these findings have important implications for predicting the role of sexual selection for the adaptation to current global warming and increased frequency of extreme climatic events.


title: Transcriptomic response to ISAV infection in the gills, head kidney and spleen of resistant and susceptible Atlantic salmon

abstract:
BackgroundInfectious Salmonid Anaemia virus (ISAV) is an orthomyxovirus responsible of large losses in Atlantic salmon (Salmo salar) aquaculture. Current available treatments and vaccines are not fully effective, and therefore selective breeding to produce ISAV-resistant strains of Atlantic salmon (Salmo salar) is a high priority for the industry. Genomic selection and potentially genome editing can be applied to enhance the disease resistance of aquaculture stocks, and both approaches can benefit from increased knowledge on the genomic mechanisms of resistance to ISAV. To improve our understanding of the mechanisms underlying resistance to ISAV in Atlantic salmon we performed a transcriptomic study in ISAV-infected salmon with contrasting levels of resistance to this virus.

ResultsThree different tissues (gills, head kidney and spleen) were collected on 12 resistant and 12 susceptible fish at three timepoints (pre-challenge, 7 and 14 days post infection) and RNA sequenced. The transcriptomes of Infected and non-infected fish and of resistant and susceptible fish were compared at each timepoint. The results show that the responses to ISAV are organ-specific; an important response to the infection was observed in the head kidney, with up-regulation of immune processes such as interferon and NLR pathways, while in gills and spleen the response was more moderate. In addition to immune related genes our results suggest that other processes such as ubiquitination or ribosomal processing are important during early infection to ISAV. Moreover, the comparison between resistant and susceptible have also highlighted some interesting genes related to ubiquitination, intracellular transport or the inflammasome.

ConclusionsAtlantic salmon infection by ISAV revealed an organ-specific response, implying differential function during the infection. An early immune response was observed in the head kidney, while gills and spleen showed modest responses in comparison. Comparison between resistance and susceptible samples have highlighted genes of interest for further studies, for instance those related to ubiquitination or the inflammasome.


title: Use of Fe3O4 nanoparticles in reactor co-digestion of residues from 1G2G ethanol biorefinery: microbiological routes and operational aspects

abstract: The co-digestion of residues from the sugarcane industry has already proven to be a highly attractive process for biogas production through anaerobic digestion (AD). The use of residues such as vinasse (1G) filter cake (1G) and deacetylation liquor (2G) in operation in a continuous CSTR reactor showed a possibility of integration of 1G and 2G ethanol biorefineries through AD in previous work by our research group. The use of nanoparticles (NP) is a favorable way to optimize AD processes, as these additives serve as a means of introducing nutrients into the process in a more assertive way from the point of view of distribution and interaction with microorganisms. In this context, the present work proposed the optimization of the co-digestion of vinasse, filter cake, and deacetylation liquor in a continuous reactor through the addition of Fe3O4 NP, by the purpose of comparison results with the operation of the same substrates and the same condition but without NP. Initially, tests were carried out in batches with different concentrations of NPs, to evaluate the best concentration to be added in the continuous reactor. A concentration of 5 mg L-1 was chosen, and it was added to each increase in organic rate load (ORL) used in the process. CH4 production reached maximum values of 2.8 {+/-} 0.1 NLCH4 gVS-1 and organic matter removal 71 {+/-} 0.9%, in phase VI, with ORL of 5.5 gVS L-1 day-1. This production was 90% higher than the reactor co-digestion operation without the presence of NP. Furthermore, according to the results of pH, alkalinity, it can be concluded that the methanogenesis stabilized at 60 days of operation, being 30 days before when there was no NP added. The development of AD was stable, with low variations in the oxidation-reduction potential (ORP) and with stable organic acid (OA) concentrations, indicating the possibility of route propionic acid to produce CH4. The main methanogenic Archeae found was Methanoculleus, indicating that the predominant metabolic route was that of syntrophic acetate oxidation (SAO) coupled with hydrogenotrophic methanogenesis. The use of Fe3O4 NP managed to improve the AD operation of residues from the 1G2G ethanol production industry and did not modify the microbial community present, only stimulated their growth.


title: Implicit versus explicit timing - separate or shared mechanisms?

abstract: AO_SCPLOWBSTRACTC_SCPLOWTime implicitly shapes cognition, but time is also explicitly represented, for instance in the form of durations. Parsimoniously, the brain could use the same mechanisms for implicit and explicit timing. Yet, the evidence has been equivocal, revealing both joint versus separate signatures of timing. Here, we directly compared implicit and explicit timing using magnetoencephalography, whose temporal resolution allows investigating the different stages of the timing processes. Implicit temporal predictability was induced in an auditory paradigm by a manipulation of the foreperiod. Participants received two consecutive task instructions: discriminate pitch (indirect measure of implicit timing) or duration (direct measure of explicit timing). The results show that the human brain efficiently extracts implicit temporal statistics of sensory environments, to enhance the behavioral and neural responses to auditory stimuli, but that those temporal predictions did not improve explicit timing. In both tasks, attentional orienting in time during predictive foreperiods was indexed by an increase in alpha power over visual and parietal areas. Furthermore, pre-target induced beta power in sensorimotor and parietal areas increased during implicit compared to explicit timing, in line with the suggested role for beta oscillations in temporal prediction. Interestingly, no distinct neural dynamics emerged when participants explicitly paid attention to time, compared to implicit timing. Our work thus indicates that implicit timing shapes the behavioral and sensory response in an automatic way, and is reflected in oscillatory neural dynamics, while the translation of implicit temporal statistics to explicit durations remains somewhat inconclusive, possibly due to the more abstract nature of this task.


title: Toxoplasma gondii ROP1 subverts murine and human innate immune restriction

abstract: Toxoplasma gondii is an intracellular parasite that can infect many different host species and is a cause of significant human morbidity worldwide. T. gondii secretes a diverse array of effector proteins into the host cell which are critical for infection; however, the vast majority of these secreted proteins are uncharacterised. Here, we carried out a pooled CRISPR knockout screen in the T. gondii Prugniaud strain in vivo to identify secreted proteins that contribute to parasite immune evasion in the host. We identify 22 putative virulence factors and demonstrate that ROP1, the first-identified rhoptry protein of T. gondii, has a previously unrecognised role in parasite resistance to interferon gamma-mediated innate immune restriction. This function is conserved in the highly virulent RH strain of T. gondii and contributes to parasite growth in both murine and human macrophages. While ROP1 affects the morphology of rhoptries, from where the protein is secreted, it does not affect rhoptry secretion. ROP1 interacts with the host cell protein C1QBP, which appears to facilitate parasite immune evasion. In summary, we identify 22 secreted proteins which contribute to parasite growth in vivo and show that ROP1 is an important and previously overlooked effector in counteracting both murine and human innate immunity.


title: Phase separation of hnRNP A1 upon specific RNA-binding observed by magnetic resonance

abstract: Interaction of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) with specific single-stranded RNA and its relation to liquid-liquid phase separation were investigated in vitro by magnetic resonance based on site-directed spin labelling. An ensemble model of free hnRNP A1 in the absence of RNA was derived from distance distributions between spin labelled sites and small angle X-ray scattering. This model revealed a compact state of the low-complexity domain and interaction of this domain with the RNA recognition motifs. Paramagnetic relaxation enhancement NMR spectroscopy confirmed this interaction. The addition of RNA to dispersed solutions of hnRNP A1 induced phase separation, observed by formation of liquid droplets. The phase separation depended on the RNA concentration and sequence, with continuous wave EPR spectroscopy showing that local protein dynamics is affected by point mutations in the RNA sequence. We propose that an interplay of sequence-specific RNA binding and phase transition serves as a regulatory mechanism for RNA segregation in the stress response of cells.