title: Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus

abstract:
Like many viruses, Hepatitis C Virus (HCV) has a high nutation rate, which helps the virus adapt quickly, but mutations come with fitness costs. Fitness costs can be studied by different approaches, such as experimental or frequency-based approaches. The frequency-based approach is particularly useful to estimate in vivo fitness costs, but this approach works best with deep sequencing data from many hosts, are. In this study, we applied the frequency-based approach to a large dataset of 195 patients and estimated the fitness costs of mutations at 7957 sites along the HCV genome. We used beta regression and random forest models to better understand how different factors influenced fitness costs. Our results revealed that costs of nonsynonymous mutations were three times higher than those of synonymous mutations, and mutations at nucleotides A or T had higher costs than those at C or G. Genome location had a modest effect, with lower costs for mutations in HVR1 and higher costs for mutations in Core and NS5B. Resistance mutations were, on average, costlier than other mutations. Our results show that in vivo fitness costs of mutations can be virus specific, reinforcing the utility of constructing in vivo fitness cost maps of viral genomes.

Author SummaryUnderstanding how viruses evolve within patients is important for combatting viral diseases, yet studying viruses within patients is difficult. Laboratory experiments are often used to understand the evolution of viruses, in place of assessing the evolution in natural populations (patients), but the dynamics will be different. In this study, we aimed to understand the within-patient evolution of Hepatitis C virus, which is an RNA virus that replicates and mutates extremely quickly, by taking advantage of high-throughput next generation sequencing. Here, we describe the evolutionary patterns of Hepatitis C virus from 195 patients: We analyzed mutation frequencies and estimated how costly each mutation was. We also assessed what factors made a mutation more costly, including the costs associated with drug resistance mutations. We were able to create a genome-wide fitness map of within-patient mutations in Hepatitis C virus which proves that, with technological advances, we can deepen our understanding of within-patient viral evolution, which can contribute to develop better treatments and vaccines.


title: A Generative Approach toward Precision Antimicrobial Peptide Design

abstract: As the emergence of bacterial resistance is outpacing the development of new antibiotics, we must find cost-effective and innovative approaches to discover new antibacterial therapeutics. Antimicrobial peptides (AMPs) represent one promising solution to fill this void, since they generally undergo faster development, display rapid onsets of killing, and most importantly, show lower risks of induced resistance. Despite prior success in AMP design with physics- and/or knowledge-based approaches, an efficient approach to precisely design peptides with high activity and selectivity is still lacking. Toward this goal, we have invented a novel approach which utilizes a generative model to predict AMP-like sequences, followed by molecular modeling to rank the candidates. Thus, we can identify peptides with desirable sequences, structures, and potential specific interactions with bacterial membranes. For the proof of concept, we curated a dataset that comprises 500,000 non-AMP peptide sequences and nearly 8,000 labeled AMP sequences to train the generative model. For 12 generated peptides that are cationic and likely helical, we assessed the membrane binding propensity via extensive all-atom molecular simulations. The top six peptides were promoted for synthesis, chemical characterizations, and antibacterial assays, showing various inhibition to bacterial growth. Three peptides were validated with broad-spectrum antibacterial activity. In aggregate, the combination of AMP generator and sophisticated molecular modeling affords enhanced speed and accuracy in AMP design. Our approach and results demonstrate the viability of a generative approach to develop novel AMPs and to help contain the rise of antibiotic resistant microbes.

category: biophysics


title: Social information use shapes the coevolution of sociality and virulence

abstract: AO_SCPLOWBSTRACTC_SCPLOWSocial contacts can facilitate the spread of both survival-related information and infectious diseases, but little is known about how these processes combine to shape host and parasite evolution. Here, we use a theoretical model that captures both infection and information transmission processes to investigate how host sociality (contact effort) and parasite virulence (disease-associated mortality rate) (co)evolve. We show that selection for sociality (and in turn, virulence) depends on both the intrinsic costs and benefits of social information and infection as well as their relative prevalence in the population. Specifically, greater sociality and lower virulence evolve when the risk of infection is either low or high and social information is neither very common nor too rare. Lower sociality and higher virulence evolve when the prevalence patterns are reversed. When infection and social information are both at moderate levels in the population, the direction of selection depends on the relative costs and benefits of being infected or informed. We also show that sociality varies inversely with virulence, and that parasites may be unable to prevent runaway selection for higher contact efforts. Together, these findings provide new insights for our understanding of group living and how apparently opposing ecological processes can influence the evolution of sociality and virulence in a range of ways.

category: evolutionary biology


title: Parametric cognitive load reveals hidden costs in the neural processing of perfectly intelligible degraded speech

abstract:
Speech is often degraded by environmental noise or hearing impairment. People can compensate for degradation, but this requires cognitive effort. Previous research has identified frontotemporal networks involved in effortful perception, but materials in these works were also less intelligible, and so it is not clear whether activity reflected effort or intelligibility differences. We used functional magnetic resonance imaging to assess the degree to which spoken sentences were processed under distraction, and whether this depended on speech quality even when intelligibility of degraded speech was matched to that of clear speech (i.e., 100%). On each trial, participants either attended to a sentence, or to a concurrent multiple object tracking (MOT) task that imposed parametric cognitive load. Activity in bilateral anterior insula reflected task demands: during the MOT task, activity increased as cognitive load increased, and during speech listening, activity increased as speech became more degraded. In marked contrast, activity in bilateral anterior temporal cortex was speech-selective, and gated by attention when speech was degraded. In this region, performance of the MOT task with a trivial load blocked processing of degraded speech whereas processing of clear speech was unaffected. As load increased, responses to clear speech in these areas declined, consistent with reduced capacity to process it. This result dissociates cognitive control from speech processing: substantially less cognitive control is required to process clear speech than is required to understand even very mildly degraded, 100% intelligible, speech. Perceptual and control systems clearly interact dynamically during real-world speech comprehension.

Significance StatementSpeech is often perfectly intelligible even when degraded, e.g., by background sound, phone transmission, or hearing loss. How does degradation alter cognitive demands? Here, we use fMRI to demonstrate a novel and critical role for cognitive control in the processing of mildly degraded but perfectly intelligible speech. We compare speech that is matched for intelligibility but differs in putative control demands, dissociating cognitive control from speech processing. We also impose a parametric cognitive load during perception, dissociating processes that depend on tasks from those that depend on available capacity. Our findings distinguish between frontal and temporal contributions to speech perception and reveal a hidden cost to processing mildly degraded speech, underscoring the importance of cognitive control for everyday speech comprehension.

category: neuroscience


title: Interpretable multi-timescale models for predicting fMRI responses to continuous natural speech

abstract: Natural language contains information at multiple timescales. To understand how the human brain represents this information, one approach is to build encoding models that predict fMRI responses to natural language using representations extracted from neural network language models (LMs). However, these LM-derived representations do not explicitly separate information at different timescales, making it difficult to interpret the encoding models. In this work we construct interpretable multi-timescale representations by forcing individual units in an LSTM LM to integrate information over specific temporal scales. This allows us to explicitly and directly map the timescale of information encoded by each individual fMRI voxel. Further, the standard fMRI encoding procedure does not account for varying temporal properties in the encoding features. We modify the procedure so that it can capture both short- and long-timescale information. This approach outperforms other encoding models, particularly for voxels that represent long-timescale information. It also provides a finer-grained map of timescale information in the human language pathway. This serves as a framework for future work investigating temporal hierarchies across artificial and biological language systems.


title: The underlying mechanisms of improved balance after one and ten sessions of balance training in older adults

abstract:
Training improves balance control in older adults, but the time course and neural mechanisms underlying these improvements are unclear. We studied balance robustness and performance, H-reflex gains, paired reflex depression, and co-contraction duration in ankle muscles after one and ten training sessions in 22 older adults (+65yrs). Mediolateral balance robustness, time to balance loss in unipedal standing on a platform with decreasing rotational stiffness, improved (33%) after one session, with no further improvement after ten sessions. Balance performance, absolute mediolateral center of mass velocity, improved (18.75%) after one session in perturbed unipedal standing and (18.18%) after ten sessions in unperturbed unipedal standing. Co-contraction duration of soleus/tibialis anterior increased (16%) after ten sessions. H-reflex gain and paired reflex depression excitability did not change. H-reflex gains were lower, and soleus/tibialis anterior co-contraction duration was higher in participants with more robust balance after ten sessions, and co-contraction duration was higher in participants with better balance performance at several time-points. Changes in robustness and performance were uncorrelated with changes in co-contraction duration, H-reflex gain, or paired reflex depression. In older adults, balance robustness improved over a single session, while performance improved gradually over multiple sessions. Changes in co-contraction and excitability of ankle muscles were not exclusive causes of improved balance.

HighlightsO_LIBalance robustness and balance performance in perturbed unipedal standing was improved after one balance training session, with no further improvement after ten sessions.
C_LIO_LIBalance performance in unperturbed unipedal standing was improved after ten sessions
C_LIO_LIH-reflex and paired reflex depression did not change after training in unipedal or bipedal standing.
C_LIO_LICo-contraction duration of antagonistic ankle muscles increased after ten sessions in perturbed and unperturbed unipedal standing.
C_LIO_LIChanges in co-contraction duration and excitability of ankle muscles were not exclusive causes of improved balance.
C_LI


title: Spatial relations trigger visual binding of people

abstract: To navigate the social world, humans must represent social entities, and the relationships between those entities, starting with spatial relationships. Recent research suggests that two bodies are processed with particularly high efficiency in visual perception, when they are in a spatial positioning that cues interaction, i.e. close and face-to-face. Socially relevant spatial relations such as facingness may facilitate visual perception by triggering grouping of bodies into a new integrated percept, which would make the stimuli more visible and easier to process. We used electroencephalography and a frequency-tagging paradigm to measure a neural correlate of grouping (or visual binding), while female and male participants saw images of two bodies face-to-face or back-to-back. The two bodies in a dyad flickered at frequency F1 and F2, respectively, and appeared together at a third frequency Fd (dyad frequency). This stimulation should elicit a periodic neural response for each body at F1 and F2, and a third response at Fd, which would be larger for face-to-face (vs. back-to-back) bodies, if those stimuli yield additional integrative processing. Results showed that responses at F1 and F2 were higher for upright than for inverted bodies, demonstrating that our paradigm could capture neural activity associated with viewing bodies. Crucially, the response to dyads at Fd was larger for face-to-face (vs. back-to-back) dyads, suggesting integration mediated by grouping. We propose that spatial relations that recur in social interaction (i.e., facingness) promote binding of multiple bodies into a new representation. This mechanism can explain how the visual system contributes to integrating and transforming the representation of disconnected body-shapes into structured representations of social events.


title: Lung macrophages mediate helminth resistance through differential activation of recruited monocyte-derived alveolar macrophages and arginine depletion

abstract: Macrophages are known to mediate anti-helminth responses, but it remains uncertain which subsets are involved or how macrophages actually kill helminths. Here we show rapid monocyte recruitment to the lung after infection with the nematode parasite, Nippostrongylus brasiliensis. In this inflamed tissue microenvironment these monocytes differentiate into an alveolar-like macrophage (AM) phenotype, expressing both Siglec-F and CD11c, surround invading parasitic larvae and preferentially kill parasites in vitro. Monocyte-derived AMs (Mo-AMs) express type 2-associated markers and show distinct remodeling of the chromatin landscape relative to tissue-derived AMs. In particular, they express high amounts of Arg1 (arginase-1), which we demonstrate mediates helminth killing through L-arginine depletion. These studies indicate that recruited monocytes are selectively programmed in the pulmonary environment to express AM markers and an anti-helminth phenotype.

category: immunology


title: Individual small in-stream barriers contribute little to strong local population genetic structure five strictly aquatic macroinvertebrate taxa

abstract: Water flow in river networks is frequently regulated by man-made in-stream barriers. These obstacles can hinder dispersal of aquatic organisms and isolate populations leading to the loss of genetic diversity. Although millions of small in-stream barriers exist worldwide, such as weirs below 2 m or tunnels and pipes, their impact on the dispersal of macroinvertebrates with strictly aquatic life cycles is unclear. We therefore assessed the effects of such barriers on the population structure and effective dispersal of five macroinvertebrate species with strictly aquatic life cycles: the amphipod crustacean Gammarus fossarum (clade 11), three snail species of the Ancylus fluviatilis species complex and the flatworm Dugesia gonocephala. We studied populations at nine weirs and eight culverts (3 pipes, 5 tunnels), built 33-109 years ago, in the heavily fragmented catchment of the river Ruhr (Sauerland, Germany). To assess fragmentation and barrier effects, we generated genome-wide SNP data using ddRAD sequencing and evaluated clustering, differentiation between populations up- and downstream of each barrier and effective migration rates among sites and across barriers. Additionally, we applied population genomic simulations to assess expected differentiation patterns under different gene flow scenarios. Our data show that populations of all species are highly isolated at regional and local scales within few kilometres. While the regional population structure likely results from historical processes, the strong local differentiation suggests that contemporary dispersal barriers exist. However, we identified significant barrier effects only for pipes (for A. fluviatilis II and III) and few larger weirs (>1.3 m; for D. gonocephala). Therefore our data suggest that most small in-stream barriers can probably be overcome by all studied taxa frequently enough to prevent fragmentation. Thus, the barriers leading to population isolation after few kilometres still need to be identified. Specifically, it remains to be tested if the strong local differentiation is a result of a cumulative effect of small barriers, or if e.g. larger in-stream barriers, land use, chemical pollution, urbanisation, or a combination of these factors impede gene flow.

category: ecology


title: Integrative, multi-omics, analysis of blood samples improves model predictions: applications to cancer

abstract:
BackgroundCancer genomic studies often include data collected from several omics platforms. Each omics data source contributes to the understanding of the underlying biological process via source specific ("individual") patterns of variability. At the same time, statistical associations and potential interactions among the different data sources can reveal signals from common biological processes that might not be identified by single source analyses. These common patterns of variability are referred to as "shared" or "joint". In this work, we show how the use of joint and individual components can lead to better predictive models, and to a deeper understanding of the biological process at hand. We identify joint and individual contributions of DNA methylation, miRNA and mRNA expression collected from blood samples in a lung cancer case-control study nested within the Norwegian Women and Cancer (NOWAC) cohort study, and we use such components to build prediction models for case-control and metastatic status. To assess the quality of predictions, we compare models based on simultaneous, integrative analysis of multi-source omics data to a standard non-integrative analysis of each single omics dataset, and to penalized regression models. Additionally, we apply the proposed approach to a breast cancer dataset from The Cancer Genome Atlas.

ResultsOur results show how an integrative analysis that preserves both components of variation is more appropriate than standard multi-omics analyses that are not based on such a distinction. Both joint and individual components are shown to contribute to a better quality of model predictions, and facilitate the interpretation of the underlying biological processes in lung cancer development.

ConclusionIn the presence of multiple omics data sources, we recommend the use of data integration techniques that preserve the joint and individual components across the omics sources. We show how the inclusion of such components increases the quality of model predictions of clinical outcomes.

category: genomics


title: A likelihood-based deconvolution of bulk gene expression data using single-cell references

abstract: Direct comparison of bulk gene expression profiles is complicated by distinct cell type mixtures in each sample which obscure whether observed differences are actually due to changes in expression levels themselves or simply due to differing cell type compositions. Single-cell technology has made it possible to measure gene expression in individual cells, achieving higher resolution at the expense of increased noise. If carefully incorporated, such single-cell data can be used to deconvolve bulk samples to yield accurate estimates of the true cell type proportions, thus enabling one to disentangle the effects of differential expression and cell type mixtures. Here, we propose a generative model and a likelihood-based inference method that uses asymptotic statistical theory and a novel optimization procedure to perform deconvolution of bulk RNA-seq data to produce accurate cell type proportion estimates. We demonstrate the effectiveness of our method, called RNA-Sieve, across a diverse array of scenarios involving real data and discuss extensions made uniquely possible by our probabilistic framework, including a demonstration of well-calibrated confidence intervals.


title: Development and validation of nanobodies specifically targeting the oncogenic Phosphatase of Regenerating Liver-3 (PRL-3)

abstract: Phosphatase of Regenerating Liver-3 (PRL-3) is associated with cancer progression and metastasis in various solid tumors and leukemias. The mechanisms that drive PRL-3s oncogenic functions are not well understood, in part due to a lack of research tools available to study this protein. In particular, small molecules do not exhibit binding specificity for PRL-3 over highly homologous family members PRL-1 and PRL-2, and antibodies directed against PRL-3 are limited by assay type. We have begun to address these issues by developing alpaca-derived single domain antibodies, or nanobodies, targeting PRL-3 with a KD of 30-300 nM and no activity towards PRL-1 and PRL-2. Hydrogen deuterium exchange mass spectrometry (HDX-MS) and co-immunoprecipitation with a known PRL-3 substrate showed the nanobodies bind PRL-3 outside of the active site, meaning they can be used to study PRL-3 interaction with binding partners. The nanobodies were also specific to PRL-3 over other PRLs in immunoprecipitation and immunofluorescence experiments in human cancer cells that overexpressed the PRL family. We found that N-terminal tags on PRL-3, such as GFP and FLAG, changed PRL-3 localization compared to untagged protein, indicating that the nanobodies may provide new insights into PRL-3 trafficking and function. The anti-PRL-3 nanobodies represent an important expansion of the research tools available to study PRL-3 function and can be used to define the role of PRL-3 in cancer progression.

category: biochemistry


title: Axon Diameter Measurements using Diffusion MRI are Infeasible

abstract: The feasibility of non-invasive axonal diameter quantification with diffusion MRI is a strongly debated topic due to the neuroscientific potential of such information and its relevance for the axonal signal transmission speed. It has been shown that under ideal conditions, the minimal diameter producing detectable signal decay is bigger than most human axons in the brain, even using the strongest currently available MRI systems. We show that resolving the simplest situations including multiple diameters is unfeasible even with diameters much bigger than the diameter limit. Additionally, the recently proposed effective diameter resulting from fitting a single value over a distribution is almost exclusively influenced by the biggest axons. We show how impractical this metric is for comparing different distributions. Overall, axon diameters currently cannot be quantified by diffusion MRI in any relevant way.


title: Comparing Fecal, Saliva, and Chicha Microbiomes Between Mothers and Children in an Indigenous Ecuadorian Cohort

abstract: Recent research has elucidated many factors which play a role in the development and composition of human microbiomes. In this study we briefly examine the microbiomes of saliva and fecal samples from 71 indigenous individuals, and chicha samples from 28 single family households in a remote community in the Ecuadorian Amazon. Fecal and saliva samples were collected at two separate time points whereas chicha samples were collected at four time points, once each day of the fermentation process. In total 324 samples were collected: 113 saliva, 108 chicha, and 103 fecal. Microbial composition and diversity were assessed using shotgun metagenome sequence data. Chicha samples were found to be nearly entirely composed of the order Lactobacillales, accounting for 90.1% of the relative abundance. Saliva samples also contained a high relative abundance of Lactobacillales (31.9%) as well as being composed of Neisseriales (12.8%), Actinomycineae (8.7%), Bacteroidales (7.0%), Clostridiales (6.8%), Micrococcineae (6.5%), and Pasteurellales (6.0%). Fecal samples were largely composed of the three orders Clostridiales (33.7%), Bacteroidales (21.9%), and Bifidobacteriales (16.5%). Comparison of -diversity, as calculated by Shannons Diversity Index, in mothers and their offspring showed no significant difference between the two groups in either fecal or saliva samples. Comparison of {beta}-diversity in fecal and saliva samples, as calculated by the Bray-Curtis Dissimilarity measure, within household units and between differing households showed that members of the same household were significantly less dissimilar to each other than to members of other households in the community. Average microbiome composition for individuals within fecal and saliva samples was assessed to determine the impact of an individuals household on the composition of their microbiome. Household was determined to have a significant impact on both fecal and oral microbiome compositions.

category: microbiology


title: Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture

abstract: How complex actin network architectures arise and coexist in membrane-enclosed cell environment remains unknown. By encapsulating actin and crosslinking proteins -actinin and fascin in giant unilamellar vesicles (GUVs), we show that physical confinement and its size can lead to formation of complex actin structures, including rings and asters at GUV peripheries and centers. Strikingly, we find that the materials properties of the aster structures depend on the ratio of the relative concentrations of -actinin and fascin, and we demonstrate that this results from -actinin and fascin sorting into separate domains in the structures. We complement our experiments with molecular simulations that capture the spontaneous formation of competing network architectures; these provide a microscopic view of the dynamics and delineate the molecular features that promote sorting. We propose that the observed boundary-imposed effect on protein sorting is a general mechanism for creating emergent structures in biopolymer networks with multiple crosslinkers.


title: Arabidopsis inositol polyphosphate kinases regulate COP9 signalosome functions in phosphate-homeostasis

abstract:
Targeted protein degradation is essential for physiological development and adaptation to stress. Mammalian INOSITOL PENTAKISPHOSPHATE 2-KINASE (IP5K) and INOSITOL HEXAKISPHOSPHATE KINASE 1 (IP6K1) pair generates inositol polyphosphates (InsPs) to modulate association/dissociation equilibrium of Cullin RING Ubiquitin E3 ligases (CRLs) on the COP9 signalosome (CSN) platform. Deneddylase activity of the CSN5 subunit protects cullins from self-ubiquitination ensuring their functional continuity. In plants, similar regulations by InsP-kinases are not known. Here, we show conserved interactions of Arabidopsis thaliana INOSITOL PENTAKISPHOSPHATE 2-KINASE 1 (IPK1) and INOSITOL 1,3,4-TRISPHOSPHATE 5/6-KINASE 1 (ITPK1), counterparts of the above mammalian InsP-kinase pair, with selective CSN subunits. In ipk1 or itpk1 mutants, deneddylation deficiencies not only cause increased neddylated Cullin1 (CUL1Nedd8) pools more prone to degradation but also impair CSN5 entry/exit shuttles on the CSN holo-complex. Constitutive phosphate-starvation response (PSR), previously known for these mutants are suppressed by pharmacological inhibition of neddylation thus linking CSN-CRL functions to phosphate (Pi)-sensing. Similarly, in wild-type plants exposed to compounds that impair CSN5 deneddylase function affects its dynamics and mimic PSR properties of the mutants. We further show that under Pi-deprivation more CSN5 retentions on the CSN holo-complex and the resulting enhanced CUL1Nedd8 pools is essential for induction of downstream Pi-starvation inducible (PSI) genes. Overall, with our data we present InsP-kinase involvements in maintenance of Pi-homeostasis in plants via CRL-CSN(5) functional synergism.

SignificanceNeddylation modifications on Culling-RING E3 ligases (CRLs) while essential for their role in proteostasis, also threaten their own stability. Selective inositol polyphosphates (InsPs) aid the constitutive photomorphogenesis 9 signalosome (CSN) functions in protecting, deneddylating, and facilitating CRL recycling. Here we demonstrate that plant mutants deficient in these InsPs have disturbed CSN subunit partitioning, are deficient in deneddylase activity, and hyperaccumulate neddylated cullins that lead to constitutive phosphate-starvation response (PSR). Inhibition of CSN functions/consequences mirror the InsP mutant properties indicating pivotal involvement of CSN in phosphate homeostasis. These raises promising possibilities of targeted intervention on CSN functions for nutritional benefit of plants.

category: plant biology


title: Effects of various carbohydrates on the in vitro pollen germination of Vinca rosea and Cucumis melo var. utilissimus

abstract: Pollen germination is crucial for the process of plant development which strongly depends on the presence of carbohydrates as a primary source of energy. In this study, we analyzed the differential effects of four sugars with varying concentrations on the pollen germination of Vinca rosea Linn. and Cucumis melo var. utilissimus (Duth. & Fuller) using Brewbaker and Kwacks medium as germination medium and hanging drop method after an incubation period of 1 hour. Sucrose and glucose supported the pollen germination but galactose and fructose did not support and even considerably inhibited the pollen germination of Vinca rosea. However in pollen germination of Cucumis melo var. utilissimus, all the four sugars supported the pollen germination. The study suggests that 15% sucrose, for Vinca rosea, and 12% galactose, for Cucumis melo var. utilissimus, supports in achieving the highest pollen germination percentage when added to the pollen germination medium.


title: The mTORC1-mediated activation of ATF4 promotes protein and glutathione synthesis downstream of growth signals

abstract: The mechanistic target of rapamycin complex 1 (mTORC1) stimulates a coordinated anabolic program in response to growth-promoting signals. Paradoxically, recent studies indicate that mTORC1 can activate the adaptive stress-responsive transcription factor ATF4 through mechanisms distinct from its canonical induction by the integrated stress response (ISR). However, how ATF4 functions in response to these distinct modes of regulation and its broader role as a downstream target of mTORC1 are unknown. Therefore, we directly compared ATF4-dependent transcriptional changes induced upon activation of mTORC1 or the ISR. The mTORC1-ATF4 pathway stimulated the expression of only a subset of the ATF4 target genes stimulated by the ISR, including genes involved in amino acid uptake, synthesis, and tRNA charging. We demonstrate that ATF4 is a metabolic effector of mTORC1 involved in both its established role in promoting protein synthesis and in a previously unappreciated function for mTORC1 in stimulating cellular cystine uptake and glutathione synthesis.

category: cell biology


title: Longitudinal in vivo micro-CT-based approach allows spatio-temporal characterization of fracture healing patterns and assessment of biomaterials in mouse femur defect models

abstract:
Thorough preclinical evaluation of functionalized biomaterials for treatment of large bone defects is essential prior to clinical application. Using in vivo micro-computed tomography (micro-CT) and mouse femoral defect models with different defect sizes, we were able to detect spatio-temporal healing patterns indicative of physiological and impaired healing in three defect sub-volumes and the adjacent cortex. The time-lapsed in vivo micro-CT-based approach was then applied to evaluate the bone regeneration potential of functionalized biomaterials using collagen and BMP-2. Both collagen and BMP-2 treatment led to distinct changes in bone turnover in the different healing phases. Despite increased periosteal bone formation, 87.5% of the defects treated with collagen scaffolds resulted in non-unions. Additional BMP-2 application significantly accelerated the healing process and increased the union rate to 100%. This study further shows potential of time-lapsed in vivo micro-CT for capturing spatio-temporal deviations preceding non-union formation and how this can be prevented by application of functionalized biomaterials.

This study therefore supports the application of longitudinal in vivo micro-CT for discrimination of normal and disturbed healing patterns and for the spatio-temporal characterization of the bone regeneration capacity of functionalized biomaterials.

category: bioengineering


title: Combined analysis of the time-resolved transcriptome and proteome of plant pathogen Xanthomonas oryzae pv. oryzae

abstract: Xanthomonas oryzae pv. oryzae (Xoo) is a plant pathogen responsible for causing bacterial blight in rice. The immediate alterations in Xoo upon initial contact with rice are essential for pathogenesis. We studied time-resolved genome-wide gene expression in pathogenicity-activated Xoo cells at the transcriptome and proteome levels. The early response genes of Xoo include genes related to cell motility, inorganic ion transport, and effectors. The alteration of gene expression is initiated as early as few minutes after the initial interaction and changes with time. The time-resolved comparison of the transcriptome and proteome shows the differences between transcriptional and translational expression peaks in many genes, although the overall expression pattern of mRNAs and proteins is conserved. The discrepancy suggests an important role of translational regulation in Xoo at the early stages of pathogenesis. The gene expression analysis using time-resolved transcriptome and proteome provides unprecedented valuable information regarding Xoo pathogenesis.


title: Perceptual coupling and decoupling of the default mode network during mind-wandering and reading

abstract:
While reading, the mind can wander to unrelated autobiographical information, creating a perceptually-decoupled state detrimental to narrative comprehension. To understand how this mind-wandering state emerges, we asked whether retrieving autobiographical content necessitates functional disengagement from visual input. In Experiment 1, brain activity was recorded using functional magnetic resonance imaging (fMRI) in an experimental situation mimicking naturally occurring mind-wandering, allowing us to precisely delineate neural regions involved in memory and reading. Individuals read expository texts and ignored personally relevant autobiographical memories, as well as the opposite situation. Medial regions of the default mode network (DMN) were recruited during memory retrieval. In contrast, left temporal and lateral prefrontal regions of the DMN, as well as ventral visual cortex, were recruited when reading for comprehension. Experiment 2 used functional connectivity at rest to establish that (i) DMN regions linked to memory are more functionally decoupled from regions of ventral visual cortex than regions in the same network engaged when reading, and (ii) individuals reporting more mind-wandering and worse comprehension, while reading in the lab, showed increased functional decoupling between visually-connected DMN sites important for reading and a region of dorsal occipital cortex linked to autobiographical memory in Experiment 1. These data suggest we lose track of the narrative when our mind wanders because the generation of autobiographical mental content relies on cortical regions within the DMN which are functionally decoupled from ventral visual regions engaged during reading.

Significance statementWhen the mind wanders during reading, we lose track of information from the narrative. We hypothesised that poor comprehension occurs because retrieving autobiographical memories reduces the perceptual coupling necessary to understand written words. We show that default mode network (DMN) areas involved in reading are functionally more connected to ventral visual regions than DMN regions important for autobiographical memory. Furthermore, individuals who mind-wander more, and comprehend less, have weaker connectivity between visually-coupled DMN regions linked to reading and dorsal occipital areas linked to autobiographical memory. These data suggest that when our minds wander during reading, retrieval of personally-relevant information activates DMN regions that are functionally disconnected from visual input, creating a perceptually decoupled state detrimental to comprehension.


title: Sucrose transport and metabolism control carbon partitioning between stem and grain in rice

abstract:
The source-sink relationship is key to overall crop performance. Detailed understanding of the factors that determine source-sink dynamics is imperative for the balance of biomass and grain yield in crop plants. We investigated the differences in the source-sink relationship between a cultivated rice Oryza sativa cv. Nipponbare and a wild rice Oryza australiensis that show striking differences in biomass and grain yield. Oryza australiensis, accumulating higher biomass, not only showed higher photosynthesis per unit leaf area but also exported more sucrose from leaves than Nipponbare. However, grain features and sugar levels suggested limited sucrose mobilization to the grains in the wild rice due to vasculature and sucrose transporter functions. Low cell wall invertase activity and high sucrose synthase cleavage activity followed by higher expression of cellulose synthase genes in Oryza australiensis stem utilized photosynthates preferentially for the synthesis of structural carbohydrates, resulting in high biomass. In contrast, the source-sink relationship favored high grain yield in Nipponbare via accumulation of transitory starch in the stem, due to higher expression of starch biosynthetic genes, which is mobilized to panicles at the grain filling stage. Thus, vascular features, sucrose transport, and functions of sugar metabolic enzymes explained the differences in the source-sink relationship between Nipponbare and Oryza australiensis.

HighlightVascular features, sucrose transport, and sugar metabolic enzyme activity contribute to the differential source-sink relationship between the selected cultivated and wild rice that differ in biomass and grain yield.


title: Spatial modulation of hippocampal activity in freely moving macaques

abstract: The hippocampal formation is linked to spatial navigation, but there is little corroboration from freely-moving primates with concurrent monitoring of three-dimensional head and gaze stances. We recorded neurons and local field potentials across hippocampal regions in rhesus macaques during free foraging in an open environment while tracking their head and eye. Theta band activity was intermittently present at movement onset and modulated by saccades. Many cells were phase-locked to theta, with few showing theta phase precession. Most hippocampal neurons encoded a mixture of spatial variables beyond place fields and a negligible number showed prominent grid tuning. Spatial representations were dominated by facing location and allocentric direction, mostly in head, rather than gaze, coordinates. Importantly, eye movements strongly modulated neural activity in all regions. These findings reveal that the macaque hippocampal formation represents three-dimensional space using a multiplexed code, with head orientation and eye movement properties dominating over simple place and grid coding during free exploration.


title: Niche evolution of the Neotropical tree genus Otoba in the context of global biogeography of the nutmeg family, Myristicaceae

abstract:
AimPlant distributions are influenced by species ability to colonize new areas via long-distance dispersal and propensity to adapt to new environments via niche evolution. We use Otoba (Myristicaceae), an ecologically dominant tree genus found in low-to-mid elevation wet forests, as a system to understand the relative importance of these processes within the Neotropics, a region characterized by high species richness and a diversity of biomes.

LocationNeotropics and global

TaxonOtoba and entire Myristicaceae

MethodsWe resolve the first phylogeny of Otoba using targeted sequence capture phylogenomics. We pair this with the most densely sampled phylogeny of Myristicaceae to date, inferred using publicly available data. We then use phylogenetic comparative methods to infer biogeography and examine patterns of niche evolution.

ResultsMyristicaceae has an Old World origin, with a single expansion event into the Americas. Divergence dates, fossil evidence, and a notable lack of long-distance dispersal are consistent with a Boreotropical origin of Neotropical Myristicaceae. Mirroring the rarity of dispersal at the family level, Otobas biogeography is marked by few biogeographic events: two expansions into Central America from a South American ancestor and a single dispersal event across the Andes. This limited movement contrasts with rapid climatic niche evolution, typically occurring across geographically proximate habitats.

Main conclusionsContrasting with previous studies, long-distance dispersal does not need to be invoked to explain the pantropical distribution of Myristicaceae, nor the biogeography of Otoba. This likely results from the familys relatively large seeds that are dispersed by large-bodied vertebrates. Instead, rapid niche evolution in Otoba has facilitated its occurrence throughout mesic habitats of the northern Neotropics, including the Amazon rainforest and Andean montane forests. Otoba adds to a growing group of Neotropical plant clades in which climate adaptation following local migration is common, implying an important role of niche evolution in the assembly of the Neotropical flora.

Significance statementSpecies distributions across the climatically and topographically heterogenous Neotropics are explained by a combination of local adaptation and dispersal. The relative importance of these mechanisms is clade dependent. We find that niche evolution in geographically proximal habitats is much more common than long-distance dispersal to preadapted regions in the tree genus Otoba, which includes both hyperdominant Amazonian species and narrow Andean endemics. The lack of long-distance dispersal is likely due to Otobas large seeds. Our results add to a growing body of literature demonstrating a key role of labile niche evolution across steep environmental gradients in Neotropical plant biogeography.


title: The timing of human adaptation from Neanderthal introgression

abstract: Admixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of Neanderthal adaptive introgression. From these, we identify cases in which Neanderthal introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation and contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples.


title: Role of 5-HT2C receptors in zebrafish alarm reactions and post-exposure behavior

abstract:
Serotonin (5-HT) receptors have been implicated in responses to aversive stimuli in mammals and fish, but its precise role is still unknown. Moreover, since at least seven families of 5-HT receptors exist in vertebrates, the role of specific receptors is still debated. Aversive stimuli can be classified as indicators of proximal, distal, or potential threat, initiating responses that are appropriate for each of these threat levels. Responses to potential threat usually involve cautious exploration and increased alertness, while responses to distal and proximal threat involve a fight-flight-freeze reaction. We exposed adult zebrafish to a conspecific alarm substance (CAS) and observed behavior during (distal threat) and after (potential threat) exposure, and treated with the 5-HT2C receptor agonists MK-212 or WAY-161503 or with the antagonist RS-102221. The agonists blocked CAS-elicited defensive behavior (distal threat), but not post-exposure increases in defensive behavior (potential threat), suggesting inhibition of responses to distal threat. MK-212 blocked changes in freezing elicited by acute restraint stress, a model of proximal threat, while RS-102221 blocked changes in geotaxis elicited this stressor. We also found that RS-102221, a 5-HT2C receptor antagonist, produced small effect on behavior during and after exposure to CAS.

Preprint: https://www.biorxiv.org/content/10.1101/2020.10.04.324202; Data and scripts: https://github.com/lanec-unifesspa/5-HT-CAS/tree/master/data/5HT2C


title: 5-HT2C agonists and antagonists block different components of behavioral responses to potential, distal, and proximal threat in zebrafish


title: Peripheral kappa opioid receptor activation drives cold hypersensitivity in mice

abstract: Noxious cold sensation is commonly associated with peripheral neuropathies, however, there has been limited progress in understanding the mechanism of cold pain. Here we identify a role for kappa opioid receptors (KOR) in driving noxious cold hypersensitivity. First, we show that systemic activation of KOR by the agonist U50,488 (U50), increases the latency to jump and the number of jumps on a cold plate at 3{degrees}C, and that the KOR antagonist NorBNI attenuates U50-induced noxious cold hypersensitivity. However, the central administration of NorBNI does not block U50-induced noxious cold hypersensitivity, suggesting that peripheral KOR may modulate this effect. To directly test this, we use the peripherally-restricted KOR agonist, ff(nle)r-NH2 and also show selective activation of peripheral KOR causes noxious cold hypersensitivity. To begin to understand how peripheral KOR drive noxious cold hypersensitivity we investigated whether KOR interact with transient receptor potential ankyrin 1(TRPA1) channels, known to facilitate the perception of noxious cold, in dorsal root ganglion (DRG). Using fluorescent in situ hybridization, we show that KOR mRNA colocalizes with the transcripts for the cold-activated TRPA1 channels in DRG. We also show a potentiation in intracellular calcium release in DRG neurons during the simultaneous application of the TRPA1 agonist, mustard oil (MO), and a KOR agonist, U50, when compared to MO alone. Together our data suggest that peripheral KOR may induce noxious cold hypersensitivity through modulation of TRPA1 channels.


title: Joint evolution of mycorrhizal type, pollination, and seed dispersal mode in trees

abstract: Although tree diversity is fundamental to terrestrial ecosystems, the processes that generate it remain uncertain. Mycorrhizal type, pollination mode, and seed dispersal mode may be key drivers of tree diversity. We predicted that mycorrhizal symbiosis drove evolution of pollination and seed dispersal modes because arbuscular mycorrhizal (AM) associations would favour long-range seed or pollen dispersal owing to their negative plant-soil-feedback effects on conspecific individuals, and ectomycorrhizal (EcM) associations would favour short-range dispersal owing to their positive effects. We analysed evolutionary relationships among mycorrhizal type, seed dispersal mode, and pollination mode in 704 tree species and conducted a meta-analysis of the dispersal distances of the various seed dispersal and pollination modes. We found evidence of joint evolution of all three features. Most AM-associated trees had endozoochorous seed dispersal and biotic pollination and these dispersal modes had long dispersal distances, whereas most EcM-associated trees had anemochorous seed dispersal and wind pollination and these dispersal modes had relatively shorter dispersal distances. Overall, evolution of mycorrhizal type, seed dispersal mode, and pollination mode were linked, strongly suggesting that mycorrhizal symbiosis drives the evolution of seed and pollination modes and contributes to tree diversification.


title: Gene-rich X chromosomes implicate intragenomic conflict in the evolution of bizarre genetic systems

abstract:
Haplodiploidy and paternal genome elimination (HD/PGE) are common in invertebrates, having evolved at least two dozen times, all from male heterogamety (i.e., systems with X chromosomes). However, why X chromosomes are important for the evolution of HD/PGE remains debated. The Haploid Viability Hypothesis posits that X-linked genes promote the evolution of male haploidy by facilitating purging recessive deleterious mutations. The Intragenomic Conflict Hypothesis holds that conflict between genes drives genetic system turnover; under this model, X-linked genes could promote the evolution of male haploidy due to conflicts with autosomes over sex ratios and genetic transmission. We studied lineages where we can distinguish these hypotheses: species with germline PGE that retain an XX/X0 sex determination system (gPGE+X). Because evolving PGE in these cases involves changes in transmission without increases in male hemizygosity, a high degree of X linkage in these systems is predicted by the Intragenomic Conflict Hypothesis but not the Haploid Viability Hypothesis. To quantify the degree of X linkage, we sequenced and compared 7 gPGE+X species genomes with 11 related species with typical XX/XY or XX/X0 genetic systems, representing three transitions to gPGE. We find highly increased X linkage in both modern and ancestral genomes of gPGE+X species compared to non-gPGE relatives, and recover a significant positive correlation between percent X linkage and the evolution of gPGE. These are among the first empirical results suggesting a role for intragenomic conflict in the evolution of novel genetic systems like HD/PGE.

Significance StatementSex determination systems such as haplodiploidy, in which males gene transmission is haploid, are surprisingly common, however, the evolutionary paths to these systems are poorly understood. X chromosomes may play a particularly important role, either by increasing survival of males with only maternal genomes, or due to conflicts between X-chromosomal and autosomal genes. We studied X-chromosome gene richness in three arthropod lineages in which males are diploid as adults but only transmit their maternally-inherited haploid genome. We find that species with such atypical systems have far more X chromosomal genes than related diploid species. These results suggest that conflict between genetic elements within the genome drives the evolution of unusual sex determination systems.


title: CEP78 functions downstream of CEP350 to control biogenesis of primary cilia by negatively regulating CP110 levels

abstract: CEP78 is a centrosomal protein implicated in ciliogenesis and ciliary length control, and mutations in the CEP78 gene cause retinal cone-rod dystrophy associated with hearing loss. However, the mechanism by which CEP78 affects cilia formation is unknown. Based on a recently discovered disease-causing CEP78 p.L150S mutation, we identified the disease-relevant interactome of CEP78. We confirmed that CEP78 interacts with the EDD1-DYRK2-DDB1VPRBP E3 ubiquitin ligase complex, which is involved in CP110 ubiquitination and degradation, and identified a novel interaction between CEP78 and CEP350 that is weakened by the CEP78L150S mutation. We show that CEP350 promotes centrosomal recruitment and stability of CEP78, which in turn leads to centrosomal recruitment of EDD1. Consistently, cells lacking CEP78 display significantly increased cellular and centrosomal levels of CP110, and depletion of CP110 in CEP78-deficient cells restored ciliation frequency to normal. We propose that CEP78 functions downstream of CEP350 to promote ciliogenesis by negatively regulating CP110 levels via an EDD1-dependent mechanism.


title: Proteolytic activation of SARS-CoV-2 spike at the S1/S2 boundary: potential role of proteases beyond furin

abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses its spike (S) protein to mediate viral entry into host cells. Cleavage of the S protein at the S1/S2 and/or S2 site(s) is associated with viral entry, which can occur at either the cell plasma membrane (early pathway) or the endosomal membrane (late pathway), depending on the cell type. Previous studies show that SARS-CoV-2 has a unique insert at the S1/S2 site that can be cleaved by furin, which appears to expand viral tropism to cells with suitable protease and receptor expression. Here, we utilize viral pseudoparticles and protease inhibitors to study the impact of the S1/S2 cleavage on infectivity. Our results demonstrate that S1/S2 pre-cleavage is essential for early pathway entry into Calu-3 cells, a model lung epithelial cell line, but not for late pathway entry into Vero E6 cells, a model cell line. The S1/S2 cleavage was found to be processed by other proteases beyond furin. Using bioinformatic tools, we also analyze the presence of a furin S1/S2 site in related CoVs and offer thoughts on the origin of the insertion of the furin-like cleavage site in SARS-CoV-2.


title: Trait Anxiety Effects on Late Phase Threatening Speech Processing: Evidence from EEG

abstract:
The effects of threatening stimuli, including threatening language, on trait anxiety have been widely studied. However, whether anxiety levels have a direct effect on language processing has not been so consistently explored. The present study focuses on eventrelated potential (ERP) patterns resulting from electroencephalographic (EEG) measurement of participants (n = 36) brain activity while they perform a dichotic listening task. Participants anxiety level was measured via a behavioural inhibition system scale (BIS). Later, participants listened to dichotically paired sentences, one neutral and the other threatening, and indicated at which ear they heard the threatening stimulus. Threatening sentences expressed threat semantically-only, prosodically-only, or both combined (congruent threat). ERPs showed a late positivity, interpreted as a late positive complex (LPC). Results from Bayesian hierarchical models provided strong support for an association between LPC and BIS score. This was interpreted as an effect of trait anxiety on deliberation processes. We discuss two possible interpretations. On the one hand, verbal repetitive thinking, as associated with anxious rumination and worry, can be the mechanism disrupting late phase deliberation processes. Instantiated by inner speech, verbal repetitive thinking might be the vehicle of anxiety-related reappraisal and/or rehearsal. On the other hand, increased BIS could be simply affecting an extended evaluation stage as proposed by multistep models, maybe due to over-engagement with threat or to task-related effects.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/323642v3_ufig1.gif" ALT="Figure 1">
View larger version (45K):
org.highwire.dtl.DTLVardef@17ee4a7org.highwire.dtl.DTLVardef@1d5cb2eorg.highwire.dtl.DTLVardef@10e4121org.highwire.dtl.DTLVardef@d5ec6e_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Repetitive and Brief Occlusion of the Majority of the Vena Cava Flow Attenuates Pulmonary Arterial Hypertension and Improves IK+ of the Pulmonary Arterial Smooth Muscle Cells in Rat Models: a novel potential therapeutic strategy for PAH

abstract: By now, there are limited therapeutic approaches satisfactory for pulmonary arterial hypertension (PAH) treatment. In the present study, we established a novel rat model, repetitive and brief occlusion (RBO) of the majority of the right atrium venous blood flow in the conscious rats. Using this model, we found that the RBO treatment significantly improved the pulmonary hemodynamics with a lower pulmonary vascular resistance observed. The IK+ and big-conductance Ca2+-activated K+ (BK) channels were involved in the mechanism of the RBO treatment for PAH. Although the results are limited, the conclusion are solid and we believe this manuscript is valuable for all the researchers and clinical doctors who are interested in PAH.

category: pathology


title: A novel juxtamembrane basolateral targeting motif regulates TGF-β receptor signaling in Drosophila

abstract: In polarized epithelial cells, receptor-ligand interactions can be restricted by different spatial distributions of the two interacting components, giving rise to an underappreciated layer of regulatory complexity. We explored whether such regulation occurs in the Drosophila wing disc, an epithelial tissue that requires the TGF-{beta} family member Dpp for growth and patterning. Dpp protein has been observed in a gradient within the columnar cells of the disc, but also uniformly in the disc lumen, leading to the question of how graded signaling is achieved in the face of two distinctly localized pools. We find the Dpp type II receptor Punt, but not the type I receptor Tkv, is enriched at the basolateral membrane, and depleted at the junctions and apical surface. Wit, a second type II receptor, shows a markedly different behavior, with the protein detected on all membrane regions but enriched at the apical side. Mutational studies identified the BLT, a short juxtamembrane sequence required for basolateral targeting of Punt in both wing discs and mammalian MDCK cells, and that dominantly confers basolateral localization on an otherwise apical receptor. Rescue of punt mutants with transgenes altered in the targeting motif showed that flies expressing apicalized Punt due to the lack of a functional BLT displayed developmental defects, female sterility and significant lethality. We also show that apicalized Punt does not produce an ectopic signal, indicating that the apical pool of Dpp is not a significant signaling source even when presented with Punt. Finally, we present evidence that the BLT acts through polarized sorting machinery that differs between types of epithelia. This suggests a code whereby each epithelial cell type may differentially traffic common receptors to enable distinctive responses to spatially localized pools of extracellular ligands.


title: Force-dependent remodeling of cytoplasmic ZO-1 condensates contributes to cell-cell adhesion through enhancing tight junctions

abstract: Although the physiological importance of biomolecular condensates is widely recognized, how it is controlled in time and space during development is largely unknown. Here we show that a tight junction protein ZO-1 forms cytoplasmic condensates in the trophectoderm (TE) of the mouse embryo before E4.0. These disappear via dissolution, and ZO-1 accumulates at the cell junction as the blastocyst cavity grows and internal pressure on TE cells increases. In contrast, this dissolution was less evident in TE cells attached to the inner cell mass, as they receive weaker tensile forces. Furthermore, analyses using MDCK cells have demonstrated that the ZO-1 condensates are generated and maintained by liquid-liquid phase separation. Our study also highlights that the dynamics of these condensates depends on the physical environment via an interaction between ZO-1 and F-actin. We propose that the force-dependent regulation of ZO-1 condensation contributes to establishing robust cell-cell adhesion during early development.


title: Force-dependent remodeling of cytoplasmic ZO-1 condensates contributes to cell-cell adhesion


title: NAP-CNB: Bioinformatic pipeline to predict MHC-I-restricted T cell epitopes in mice

abstract: Lack of a dedicated integrated pipeline for neoantigen discovery in mice hinders cancer immunotherapy research. Novel sequential approaches through recurrent neural networks can improve the accuracy of T-cell epitope immunogenicity predictions in mice, and a simplified variant selection process can reduce operational requirements. We have developed a web server tool (NAP-CNB) for a full and automatic pipeline based on recurrent neural networks, to predict putative neoantigens from tumoral RNA sequencing reads. The developed software can estimate H-2 peptide ligands, with an AUC of 0.95, directly from tumor samples. As a proof-of-concept, we used the B16 melanoma model to test the systems predictive capabilities, and we report its putative neoantigens. NAP-CNB web server is freely available at http://biocomp.cnb.csic.es/NeoantigensApp/ with scripts and datasets accessible through the download section.

category: bioinformatics


title: CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer

abstract: MicroRNAs (miRNAs), which play critical roles in gene regulatory networks, have emerged as promising diagnostic and prognostic biomarkers for human cancer. In particular, circulating miRNAs that are secreted into circulation exist in remarkably stable forms, and have enormous potential to be leveraged as non-invasive biomarkers for early cancer detection. Novel and user-friendly tools are desperately needed to facilitate data mining of the vast amount of miRNA expression data from The Cancer Genome Atlas (TCGA) and large-scale circulating miRNA profiling studies. To fill this void, we developed CancerMIRNome, a comprehensive database for the interactive analysis and visualization of miRNA expression profiles based on 10,998 samples from 33 TCGA projects and 21,993 samples from 40 public circulating miRNome datasets. A series of cutting-edge bioinformatics tools and machine learning algorithms have been packaged in CancerMIRNome, allowing for the pan-cancer analysis of a miRNA of interest across multiple cancer types and the comprehensive analysis of miRNome profiles to identify dysregulated miRNAs and develop diagnostic or prognostic signatures. The data analysis and visualization modules will greatly facilitate the exploit of the valuable resources and promote translational application of miRNA biomarkers in cancer. The CancerMIRNome database is publicly available at http://bioinfo.jialab-ucr.org/CancerMIRNome.


title: A potential role for reinforcement learning in speech production

abstract: Reinforcement learning, the ability to change motor behavior based on external reward, has been suggested to play a critical role in early stages of speech motor development and is widely used in clinical rehabilitation for speech motor disorders. However, no current evidence exists that demonstrates the capability of reinforcement to drive changes in human speech behavior. Speech provides a unique test of the universality of reinforcement learning across motor domains: speech is a complex, high-dimensional motor task whose goals do not specify a task to be performed in the environment but ultimately must be self-generated by each speaker such that they are understood by those around them. Across four experiments, we examine whether reinforcement learning alone is sufficient to drive changes in speech behavior and parametrically test two features known to affect reinforcement learning in reaching: how informative the reinforcement signal is as well as the availability of sensory feedback about the outcomes of ones motor behavior. We show that learning does occur and is more likely when participants receive auditory feedback that gives an implicit target for production, even though they do not explicitly imitate that target. Contrary to results from upper limb control, masking feedback about movement outcomes has no effect on speech learning. Together, our results suggest a potential role for reinforcement learning in speech but that it likely operates differently than in other motor domains.


title: A meta-analysis of the effect of organic and mineral fertilizers on soil microbial diversity

abstract: Organic agriculture, employing manures or composts, has been proposed as a way of mitigating undesirable impacts of mineral fertilizer use. Of particular interest is the effect of fertilizer regime on soil microbes, which are key to nutrient cycling, plant health and soil structure. However, the effect of fertilizers on soil microbial diversity remains poorly understood. Since biological diversity is an important determinant of ecosystem function and a fundamental metric in community ecology, the effects of fertilizer regimes on soil microbial diversity are of theoretical and applied interest. Here, we conduct a meta-analysis of 37 studies reporting microbial diversity metrics in mineral fertilized (NPK), organically fertilized (ORG) and unfertilized control (CON) soils. Of these studies, 32 reported taxonomic diversity derived from sequencing, gradient gel electrophoresis, or RFLP. Functional diversity, derived from Biolog Ecoplate measures of carbon substrate metabolism, was reported in 8 studies, with 3 studies reporting both diversity metrics. Bacterial and archaeal diversity was reported in 28 taxonomic studies, and fungal diversity in 8 taxonomic studies. We found that functional diversity was 2.8 % greater in NPK compared with CON, 7.0 % greater in ORG vs CON, and 3.8 % greater in ORG vs NPK. Bacterial and archaeal taxonomic diversity was not significantly different between NPK and CON, but on average 2.9% greater in ORG vs CON, and 2.4 % greater in ORG vs. NPK. Fungal taxonomic diversity was not significantly different between any treatment pairs. There was very high residual heterogeneity in all meta-analyses of soil diversity, suggesting that a large amount of further research is required to fully understand the influence of fertilizer regimes on microbial diversity and ecosystem function.


title: A brief glimpse at a haptic target is sufficient for multisensory integration in reaching movements

abstract: Goal-directed aiming movements toward visuo-haptic targets (i.e., seen and handheld targets) are generally more precise than those toward visual only or haptic only targets. This multisensory advantage stems from a continuous inflow of haptic and visual target information during the movement planning and execution phases. However, in everyday life, multisensory movements often occur without the support of continuous visual information. Here we investigated whether and to what extent limiting visual information to the initial stage of the action still leads to a multisensory advantage. Participants were asked to reach a handheld target while vision was briefly provided during the movement planning phase (50 ms, 100 ms, 200 ms of vision before movement onset), or during the planning and early execution phases (400 ms of vision), or during the entire movement. Additional conditions were performed in which only haptic target information was provided, or, only vision was provided either briefly (50 ms, 100 ms, 200 ms, 400 ms) or throughout the entire movement. Results showed that 50 ms of vision before movement onset were sufficient to trigger a direction-specific visuo-haptic integration process that increased endpoint precision. We conclude that, when a continuous support of vision is not available, endpoint precision is determined by the less recent, but most reliable multisensory information rather than by the latest unisensory (haptic) inputs.


title: Model-based inference of neutralizing antibody avidities against influenza virus

abstract:
To assess the response to vaccination, quantity (concentration) and quality (avidity) of neutralizing antibodies are the most important parameters. Specifically, an increase in avidity indicates germinal center formation, which is required for establishing long-term protection. For influenza, the classical hemagglutination inhibition (HI) assay, however, quantifies a combination of both, and to separately determine avidity requires high experimental effort. We developed from first principles a biophysical model of hemagglutination inhibition to infer IgG antibody avidities from measured HI titers and IgG concentrations. The model accurately describes the relationship between neutralizing antibody concentration/avidity and HI titer, and explains quantitative aspects of the HI assay, such as robustness to pipetting errors and detection limit. We applied our model to infer avidities against the pandemic 2009 H1N1 influenza virus in vaccinated patients (n=45) after hematopoietic stem cell transplantation (HSCT) and validated our results with independent avidity measurements using an enzyme-linked immunosorbent assay with urea elution. Avidities inferred by the model correlated with experimentally determined avidities ({rho}=0.54, 95% CI=[0.31, 0.70], P<10-4). The model predicted that increases in IgG concentration mainly contribute to the observed HI titer increases in HSCT patients and that immunosuppressive treatment is associated with lower baseline avidities. Since our approach requires only easy-to-establish measurements as input, we anticipate that it will help to disentangle causes for poor vaccination outcomes also in larger patient populations. This study demonstrates that biophysical modelling can provide quantitative insights into agglutination assays and complement experimental measurements to refine antibody response analyses.

Author SummaryInfluenza vaccines are assessed based on the induced antibody response, where antibody quantity (concentration) and antibody binding strength (avidity) determine the potency to neutralize the virus. In addition, an increase in avidity indicates a successful germinal center reaction, which is required for establishing long-term protection. However, the hemagglutination inhibition (HI) assay - traditionally used to assess influenza vaccines - measures a combination of both antibody concentration and avidity, and to separately determine avidity requires high experimental effort. We developed a biophysical model of the HI assay, which enables the inference of antibody avidities from measured HI titers and antibody concentrations. We applied our approach to a vaccinated population of immunocompromised patients after blood stem cell transplantation and validated our results experimentally. The model predicted that vaccination induced an increase in avidity in only a few patients and that patients under immunosuppressive treatment show lower baseline avidities. Since our approach requires only easily measurable data as input, it can facilitate the investigation of vaccine responses in larger populations. This study demonstrates that biophysical modelling can complement experimental data and provide additional details on agglutination experiments and antibody responses.


title: Auto-inhibition of Cnn binding to γ-TuRCs prevents ectopic microtubule nucleation and cell division defects

abstract:
{gamma}-tubulin ring complexes ({gamma}-TuRCs) nucleate microtubules. They are recruited to centrosomes in dividing cells via binding to N-terminal CM1 domains within {gamma}-TuRC-tethering proteins, including Drosophila Cnn. Binding promotes microtubule nucleation and is restricted to centrosomes in dividing cells, but the mechanism regulating binding remains unknown. Here we identify an extreme N-terminal "CM1 auto-inhibition" (CAI) domain found specifically within the centrosomal isoform of Cnn (Cnn-C) that inhibits {gamma}-TuRC binding. Robust binding occurs after removal of the CAI domain or with the addition of phospho-mimetic mutations, suggesting that phosphorylation helps relieve inhibition. We show that regulation of Cnn binding to {gamma}-TuRCs is isoform-specific and that mis-regulation of binding can result in ectopic cytosolic microtubules and major defects during cell division. We also find that human CDK5RAP2 is auto-inhibited from binding {gamma}-TuRCs, suggesting conservation across species. Overall, our results shed light on how and why CM1 domain binding to {gamma}-TuRCs is regulated.

Summary (for the online JCB table of contents and alerts)We show that auto-inhibition regulates the binding between microtubule nucleating complexes and proteins that tether them to sites of microtubule nucleation. Failure to properly regulate this binding can lead to ectopic cytosolic microtubule nucleation and major defects during cell division.


title: A novel subset of follicular helper-like MAIT cells has capacity for B cell help and antibody production in the mucosa.

abstract:
Mucosal-associated invariant T (MAIT) cells are innate-like T lymphocytes that aid in protection against bacterial pathogens at mucosal surfaces via release of inflammatory cytokines and cytotoxic molecules. Recent evidence suggests MAIT cells are capable of providing B cell help. In this study, we describe a previously unreported population of CXCR5+ T follicular helper (Tfh)-like MAIT cells, MAITfh, that have the capacity to provide B cell help within mucosal lymphoid organs. MAITfh cells are preferentially located near germinal centers in human tonsils and express the classical Tfh-associated transcription factor, B-cell lymphoma 6 (BCL-6), co-stimulatory markers, inducible T cell costimulatory (ICOS) and programmed death receptor 1 (PD-1), and cytokines, interleukin (IL)-21. Furthermore, we demonstrate the ability of MAIT cells to provide B cell help in vivo following mucosal challenge with Vibrio cholerae. Specifically, we show that adoptive transfer of MAIT cells into {beta} T cell-deficient mice promoted B cell differentiation and increased serum V. cholerae-specific IgA responses. Our data demonstrate the capacity of MAIT cells to participate in adaptive immune responses, and suggest that MAIT cells may be potential targets for mucosal vaccines.

One Sentence SummaryWe identified and characterized a novel subset of T follicular helper-like MAIT (MAITfh) cells that has the capacity to provide B cell help, and show the sufficiency of MAIT cells to promote production of pathogen-specific IgA antibodies and B cell differentiation in mucosal challenge.


title: Stabilizing role of seed banks and the maintenance of bacterial diversity

abstract: Coexisting species often exhibit negative frequency dependence due to mechanisms that promote population growth and persistence when rare. These stabilizing mechanisms can maintain diversity through interspecific niche differences, but also through life-history strategies like dormancy that buffer populations in fluctuating environments. However, there are few tests demonstrating how seed banks contribute to long-term community dynamics and the maintenance of diversity. Using a multi-year, high-frequency time series of bacterial community data from a north temperate lake, we documented patterns consistent with stabilizing coexistence. Bacterial taxa exhibited differential responses to seasonal environmental conditions, while seed bank dynamics helped maintain diversity over winter. Strong negative frequency dependence in rare, but metabolically active, taxa suggested a role for biotic interactions in promoting coexistence. Together, our results provide field-based evidence that niche differences and seed banks contribute to recurring community dynamics and the long-term maintenance of diversity in nature.


title: Rapid suppression and sustained activation of distinct cortical regions for a delayed sensory-triggered motor response

abstract: The neuronal mechanisms generating a delayed motor response initiated by a sensory cue remain elusive. Here, we tracked the precise sequence of cortical activity in mice transforming a brief whisker stimulus into delayed licking using wide-field calcium imaging, multi-region high-density electrophysiology and time-resolved optogenetic manipulation. Rapid activity evoked by whisker deflection acquired two prominent features for task performance: i) an enhanced excitation of secondary whisker motor cortex, suggesting its important role connecting whisker sensory processing to lick motor planning, and ii) a transient reduction of activity in orofacial sensorimotor cortex, which contributed to suppressing premature licking. Subsequent widespread cortical activity during the delay period largely correlated with anticipatory movements, but when these were accounted for, a focal sustained activity remained in frontal cortex, which was causally essential for licking in the response period. Our results demonstrate key cortical nodes for motor plan generation and timely execution in delayed goal-directed licking.


title: Structural brain imaging predicts individual-level task activation maps using deep learning

abstract: Accurate individual functional mapping of task activations is a potential tool for biomarker discovery and is critically important for clinical care. While structural imaging does not directly map task activation, we hypothesized that structural imaging contains information that can accurately predict variations in task activation between individuals. To this end, we trained a convolutional neural network to use structural imaging (T1-weighted, T2-weighted, and diffusion tensor imaging) to predict 47 different functional MRI task activation volumes across seven task domains. The U-Net model was trained on 654 subjects and then subsequently tested on 122 unrelated subjects. The predicted activation maps correlated more strongly with their actual maps than with the maps of the other test subjects. An ablation study revealed that a model using the shape of the cortex alone or the shape of the subcortical matter alone was sufficient to predict individual-level differences in task activation maps, but a model using the shape of the whole brain resulted in markedly decreased performance. The ablation study also showed that the additional information provided by the T2-weighted and diffusion tensor imaging strengthened the predictions as compared to using the T1-weighted imaging alone. These results indicate that structural imaging contains information that is predictive of inter-subject variability in task activation mapping and cortical folding patterns as well as microstructural features may be a key component to linking brain structure to brain function.


title: Activation of the membrane-bound Nrf1 transcription factor by USP19, a ubiquitinspecific protease C-terminally tail-anchored in the endoplasmic reticulum

abstract: The membrane-bound transcription factor Nrf1 (i.e., encoded by Nfe2l1) is activated by sensing glucose deprivation, cholesterol excess, proteasomal inhibition and oxidative stress, and then mediates distinct signaling responses in order to maintain cellular homeostasis. Herein, we found that Nrf1 stability and transactivity are both enhanced by USP19, a ubiquitin-specific protease tail-anchored in the endoplasmic reticulum (ER) through its C-terminal transmembrane domain. Further experiments revealed that USP19 directly interacts with Nrf1 in proximity to the ER and topologically acts as a deubiquitinating enzyme to remove ubiquitin moieties from this protein, and hence allows it to circumvent the potential proteasomal degradation. Such USP19-mediated effect takes place only after Nrf1 is retrotranslocated by p97 out of ER membranes to dislocate the cytoplasmic side. Conversely, knockout of USP19 causes significant decreases in the Nrf1 abundance and its active isoform entering the nucleus, resulting in down-regulation of its target proteasomal subunits. This led to a modest reduction of USP19-/--derived tumor growth in xenograft mice, when compared with wild-type controls. Altogether, these demonstrate that USP19 serves as a novel mechanistic modulator of Nrf1, but not Nrf2, enabling Nrf1 to be rescued from putative ubiquitin-directed ER-associated degradation pathway. In turn, our additional experimental evidence has unraveled that transcriptional expression of endogenous USP19 and its promoter-driven reporter genes is differentially regulated by Nrf2, as well by Nrf1, at distinct layers within a complex hierarchical regulatory network.


title: North American fireflies host low bacterial diversity

abstract: Although there are numerous studies of firefly mating flashes, lantern bioluminescence, and anti-predation lucibufagin metabolites, almost nothing is known about their microbiome. We therefore used 16S rRNA community amplicon sequencing to characterize the gut and body microbiomes of four North American firefly taxa: Ellychnia corrusca, the Photuris versicolor species complex, Pyractomena borealis, and Pyropyga decipiens. These firefly microbiomes all have very low species diversity, often dominated by a single species, and each firefly type has a characteristic microbiome. Although the microbiomes of male and female fireflies did not differ from each other, Ph. versicolor gut and body microbiomes did, with their gut microbiomes being enriched in Pseudomonas and Acinetobacter. Ellychnia corrusca egg and adult microbiomes were unique except for a single egg microbiome that shared a community type with E. corrusca adults, which could suggest microbial transmission from mother to offspring. Mollicutes that had been previously isolated from fireflies were common in our firefly microbiomes. These results set the stage for further research concerning the function and transmission of these bacterial symbionts.


title: The guidance and adhesion protein FLRT2 dimerizes in cis via dual Small-X3-Small transmembrane motifs

abstract:
Fibronectin Leucine-rich Repeat Transmembrane (FLRT 1-3) proteins are a family of broadly expressed single-spanning transmembrane receptors that play key roles in development. Their extracellular domains mediate homotypic cell-cell adhesion and heterotypic protein interactions with other receptors to regulate cell adhesion and guidance. These in trans FLRT interactions determine the formation of signaling complexes of varying complexity and function. Whether FLRTs also interact at the surface of the same cell, in cis, remains unknown. Here, molecular dynamics simulations reveal two dimerization motifs in the FLRT2 transmembrane helix. Single particle tracking experiments show that these  Small-X3-Small motifs synergize with a third dimerization motif encoded in the extracellular domain to permit the cis association and co-diffusion patterns of FLRT2 receptors on cells. These results may point to a competitive switching mechanism between in cis and in trans interactions which suggests that homotypic FLRT interaction mirrors the functionalities of classic adhesion molecules.

FieldsStructural Biology and Biophysics / Computational Biology


title: In-depth analysis of proteomic and genomic fluctuations during the time course of human embryonic stem cells directed differentiation into beta cells.

abstract:
Pluripotent stem cells (PSC) endocrine differentiation at a large scale allows sampling of transcriptome and proteome with phosphoproteome (proteoform) at specific time points. We describe the dynamic time course of changes in cells undergoing directed beta-cell differentiation and show target proteins or previously unknown phosphorylation of critical proteins in pancreas development, NKX6-1, and Chromogranin A (CHGA). We describe fluctuations in the correlation between gene expression, protein abundance, and phosphorylation, which follow differentiation protocol perturbations of cell fates at all stages to identify proteoform profiles. Our computational modeling recognizes outliers on a phenomic landscape of endocrine differentiation, and we outline several new biological pathways involved. We have validated our proteomic data by analyzing two independent single-cell RNA sequencing datasets for in-vitro pancreatic islet productions using the same cell starting material and differentiation protocol and corroborating our findings for several proteins suggest as targets for future research.

Moreover, our single-cell analysis combined with proteoform data places new protein targets within the specific time point and at the specific pancreatic lineage of differentiating stem cells. We also suggest that non-correlating proteins abundances or new phosphorylation motifs of NKX6.1 and CHGA point to new signaling pathways that may play an essential role in beta-cell development. We present our findings for the research communitys use to improve endocrine differentiation protocols and developmental studies.


title: The role of cytosolic polyadenylation element binding protein 2 alternative splicing in hypoxia

abstract: HIF1 (Hypoxia-inducible Factor 1) is a transcription factor that plays a crucial role in the hypoxia stress response. However, chronic hypoxia exposure can cause irreversible physiological changes that can lead to pulmonary hypertension (PH), and the need for therapeutics to ameliorate these conditions is great and unmet. Previous studies in our lab have demonstrated that CPEB2 (cytoplasmic polyadenylation element binding protein 2) is a translational repressor of one of the HIF1 subunits: HIF1. Our lab demonstrated that the alternatively spliced CPEB2A isoform of CPEB2 is a repressor of translation, while the CPEB2B isoform is a translational activator of HIF1 during hypoxia, suggesting a major regulatory role for CPEB2 AS in the pulmonary hypoxic response. Although it is well established that during hypoxia, HIF1 levels are dramatically upregulated due to a decrease in the degradation of this factor, we propose that during chronic hypoxia, the expression of HIF1 is maintained via a translational mechanism, likely alongside a decrease in proteolytic degradation. In this study we demonstrate that depletion of the CPEB2B splice isoform has an inhibitory effect on the translation of nascent HIF1 protein during chronic hypoxia, but not the acute phase. We further demonstrate this pathway is dependent on the initiation factor eIF3H. Finally, we show data that indicate CPEB2A and CPEB2B bind differentially to cytoplasmic polyadenylation element consensus sequences depending on the surrounding sequence context. These findings are important since they provide evidence for the potential of CPEB2 to act as a therapeutic target for treating chronic hypoxia-related pulmonary diseases.


title: Stimulus-independent neural coding of event semantics: Evidence from cross-sentence fMRI decoding

abstract: Multivariate neuroimaging studies indicate that the brain represents word and object concepts in a format that readily generalises across stimuli. Here we investigated whether this was true for neural representations of simple events described using sentences. Participants viewed sentences describing four events in different ways. Multivariate classifiers were trained to discriminate the four events using a subset of sentences, allowing us to test generalisation to novel sentences. We found that neural patterns in a left-lateralised network of frontal, temporal and parietal regions discriminated events in a way that generalised successfully over changes in the syntactic and lexical properties of the sentences used to describe them. In contrast, decoding in visual areas was sentence-specific and failed to generalise to novel sentences. In the reverse analysis, we tested for decoding of syntactic and lexical structure, independent of the event being described. Regions displaying this coding were limited and largely fell outside the canonical semantic network. Our results indicate that a distributed neural network represents the meaning of event sentences in a way that is robust to changes in their structure and form. They suggest that the semantic system disregards the surface properties of stimuli in order to represent their underlying conceptual significance.


title: The landscape of metabolic pathway dependencies in cancer cell lines

abstract:
The metabolic reprogramming of cancer cells creates metabolic vulnerabilities that can be therapeutically targeted. However, our understanding of metabolic dependencies and the pathway crosstalk that creates these vulnerabilities in cancer cells remains incomplete. Here, by integrating gene expression data with genetic loss-of-function and pharmacological screening data from hundreds of cancer cell lines, we identified metabolic vulnerabilities at the level of pathways rather than individual genes. This approach revealed that metabolic pathway dependencies are highly context-specific such that cancer cells are vulnerable to inhibition of one metabolic pathway only when activity of another metabolic pathway is altered. Notably, we also found that the no single metabolic pathway was universally essential, suggesting that cancer cells are not invariably dependent on any metabolic pathway. In addition, we confirmed that cell culture medium is a major confounding factor for the analysis of metabolic pathway vulnerabilities. Nevertheless, we found robust associations between metabolic pathway activity and sensitivity to clinically approved drugs that were independent of cell culture medium. Lastly, we used parallel integration of pharmacological and genetic dependency data to confidently identify metabolic pathway vulnerabilities. Taken together, this study serves as a comprehensive characterization of the landscape of metabolic pathway vulnerabilities in cancer cell lines.

Author SummaryCancer cells rewire their metabolism, which creates targetable metabolic vulnerabilities. Previous analyses of metabolic vulnerabilities in cancer cells have been limited to the analysis of individual genes or metabolites. However, metabolic pathways exhibit significant cross talk and compensation for one another. We developed a computational method to answer the question: when a metabolic pathways activity is high, which other metabolic pathways become more essential or less essential? By integrating genetic screen data with drug response data from FDA approved drugs, we identified cancer cell line dependence on metabolic pathways as opposed to individual genes. For example, we found that identifying key regulators of metabolic pathways, such as the Pentose Phosphate Pathway, may serve as a biomarker to identify which patients may benefit from antifolate chemotherapies (e.g. methotrexate, 5-fluorouracil). The efforts outlined here serve as the first characterization of the landscape of metabolic pathway vulnerabilities in cancer cell lines. Our results demonstrate the benefit of analyzing dependencies on metabolic pathways as opposed to metabolic genes.

category: cancer biology


title: A novel female-specific circadian clock mechanism regulating metabolism

abstract: Circadian clocks enable organisms to predict and align their behaviors and physiologies to constant daily day-night environmental cycle. Because the ubiquitin ligase Siah2 has been identified as a potential regulator of circadian clock function in cultured cells, we have used Siah2-deficient mice to examine its function in vivo. Our experiments demonstrate a striking and unexpected sexually dimorphic effect of Siah2 deficiency on the regulation of rhythmically expressed genes. The absence of Siah2 in females, but not in males, altered the expression of core circadian clock genes and drastically remodeled the rhythmic hepatic transcriptome. Siah2 loss, only in females, increased the expression of 100s of genes selectively at mid-day, resulting in a >50% increase in the number of rhythmically expressed genes, and shifted the expression of 100s of other genes from a mid-night peak, to a mid-day peak. The combined result is a near inversion of overall rhythmicity in gene expression selectively in Siah2-deficient females. This dramatic reorganization created a substantial misalignment between rhythmic liver functions and feeding/behavioral rhythms, and consequently disrupted daily patterns of lipid/lipoprotein metabolism and metabolic responses to high-fat diet. Collectively, our results suggest that Siah2 is part of a female-specific circadian mechanism important for maintaining metabolic homeostasis and may play a key role in establishing sexual dimorphisms in metabolism, and broadly reveal that circadian clocks may drive rhythms using novel sex-specific transcriptional pathways.

category: physiology


title: Dimerization of a membrane transporter is driven by differential energetics of lipid solvation of dissociated and associated states

abstract:
Over two-thirds of integral membrane proteins of known structure assemble into oligomers. Yet, the forces that drive the association of these proteins remain to be delineated, as the lipid bilayer is a solvent environment that is both structurally and chemically complex. In this study we reveal how the lipid solvent defines the dimerization equilibrium of the CLC-ec1 Cl-/H+ antiporter. Integrating experimental and computational approaches, we show that monomers associate to avoid a thinned-membrane defect caused by their exposed dimerization interfaces. In this defect, lipids are strongly tilted and less densely packed than in the bulk, with a larger degree of entanglement between opposing leaflets and greater water penetration into the bilayer interior. Dimerization restores the membrane to a near-native state and therefore, appears to be driven by the larger free-energy cost of lipid solvation of the dissociated protomers. Supporting this theory, we demonstrate that addition of short-chain lipids strongly shifts the dimerization equilibrium towards the monomeric state, and show that the cause of this effect is that these lipids preferentially solvate the defect. Importantly, we show that this shift requires only minimal quantities of short-chain lipids, with no measurable impact on either the macroscopic physical state of the membrane or the proteins biological function. Based on these observations, we posit that free-energy differentials for local lipid solvation define membrane-protein association equilibria. With this, we argue that preferential lipid solvation is a plausible cellular mechanism for lipid regulation of oligomerization processes, as it can occur at low concentrations and does not require global changes in membrane properties.

IMPACT STATEMENTDifferences in the lipid solvation energetics of associated and dissociated states is a primary driving force for membrane protein oligomerization, presenting a molecular mechanism for lipid regulation in biology.


title: Haisu: Hierarchical Supervised Nonlinear Dimensionality Reduction

abstract:
We propose a novel strategy for incorporating hierarchical supervised label information into nonlinear dimensionality reduction techniques. Specifically, we extend t-SNE, UMAP, and PHATE to include known or predicted class labels and demonstrate the efficacy of our approach on multiple single-cell RNA sequencing datasets. Our approach, "Haisu," is applicable across domains and methods of nonlinear dimensionality reduction. In general, the mathematical effect of Haisu can be summarized as a variable perturbation of the high dimensional space in which the original data is observed. We thereby preserve the core characteristics of the visualization method and only change the manifold to respect known or assumed class labels when provided. Our strategy is designed to aid in the discovery and understanding of underlying patterns in a dataset that is heavily influenced by parent-child relationships. We show that using our approach can also help in semi-supervised settings where labels are known for only some datapoints (for instance when only a fraction of the cells is labeled). In summary, Haisu extends existing popular visualization methods to enable a user to incorporate known, relevant relationships via a user-defined hierarchical distancing factor.

Availabilitygithub.com/Cobanoglu-Lab/Haisu