title: DNA replication stress stratifies prognosis and enables exploitable therapeutic vulnerabilities of HBV-associated hepatocellular carcinoma: an in silico strategy towards precision oncology

abstract:
BackgroundHepatitis B virus (HBV), the main risk factor for hepatocellular carcinoma (HCC) development, integrates into the host genome, causing genetic instability, which may trigger malignancies to exhibit chronic DNA replication stress, providing exploitable therapeutic vulnerabilities. Therefore, customizing prognostication approach and expanding therapeutic options are of great clinical significance to HBV-associated HCCs.

MethodsA robust machine-learning framework was designed to develop a DNA replication stress-related prognostic index (PIRS) based on 606 retrospectively collected HBV-associated HCC cases. Molecular profiles and drug response of HCC cell lines were leveraged to predict therapeutic targets and agents for patients with high mortality risk.

ResultsCompared with established population-based predictors, PIRS manifested superior performance for prognostic prediction in HBV-associated HCCs. Lower PIRS tightly associated with higher expression of HBV oncoproteins, activated immune/metabolism pathways and higher likelihood of responding to immunotherapy; while higher PIRS showed co-occurrence manner with elevated Ki-67 progression marker and cancer stemness, and significantly enriched in DNA replication stress, cell cycle pathways, chromatin remodeling regulons, and presented an  immune-cold phenotype with unfavorable clinical outcome. Through large-scale in silico drug screening, four potential therapeutic targets (TOP2A, PRMT1, CSNK1D, and PPIH) and five agents including three topoisomerase inhibitors (teniposide, doxorubicin, and epirubicin) and two CDK inhibitors (JNJ-7706621 and PHA-793887) were identified for patients with high PIRS.

ConclusionsOverall, PIRS holds potential to improve the population-based therapeutic strategies in HCC and sheds new insight to the clinical management for those HBV carriers; current analytic framework provides a roadmap for the rational clinical development of personalized treatment.


title: Spectrum graph-based de-novo sequencing algorithm MaxNovo achieves high peptide identification rates in collisional dissociation MS/MS spectra

abstract: We describe MaxNovo, a novel spectrum graph-based peptide de-novo sequencing algorithm integrated into the MaxQuant software. It identifies complete sequences of peptides as well as sequence tags that are incomplete at one or both of the peptide termini. MaxNovo searches for the highest-scoring path in a directed acyclic graph representing the MS/MS spectrum with peaks as nodes and edges as potential sequence constituents consisting of single amino acids or pairs. The raw score is a sum of node and edge weights, plus several reward scores, for instance, for complementary ions or protease compatibility. For search-engine identified peptides, it correlates well with the Andromeda search engine score. We use a particular score normalization and the score difference between the first and second-best solution to define a combined score that integrates all available information. To evaluate its performance, we use a human cell line dataset and take as ground truth all Andromeda-identified MS/MS spectra with an Andromeda score of at least 100. MaxNovo outperforms other software in particular in the high-sensitivity range of precision-coverage plots. We also identify incomplete sequence tags and study their statistical properties. Next, we apply MaxNovo to ion mobility-coupled time of flight data. Here we achieve excellent performance as well, except for potential swaps of the two amino acids closest to the C-terminus, which are not well resolved due to the low end of the mass range in MS/MS spectra in this dataset. We demonstrate the applicability of MaxNovo to palaeoproteomics samples with a Late Pleistocene hominin proteome dataset that was generated using three proteases. Interestingly, we did not use any machine learning in the construction of MaxNovo, but implemented expert domain knowledge directly in the definition of the score. Yet, it performs as good as or better than the leading deep learning-based algorithm.

category: bioinformatics


title: Quantifying the Effect of Anti-cancer Compound (Piperlongumine) on Cancer Cells Using Single-Cell Force Spectroscopy

abstract: Natural compounds have shown a great potential in anti-cancer research by tumor growth inhibition and anti-metastatic properties. Piperlongumine (PL) is a natural compound derived from pepper species that has been demonstrated to have anti-cancer effect on HeLa cells. Here we focus on understanding the mechanical properties of HeLa cells under PL treatment, using Atomic Force Microscopy (AFM) based single-cell manipulation technique. We used AFM to pull single HeLa cells and acquired the force-distance curves that presented stepwise patterns. We analyzed the step force (SF) and observed that cells treated with PL exhibit higher force compared to control cells. This SF increase was also observed in experiments performed on substrates of different stiffness. Therefore, analyzing SF, it is possible to investigate the effect of PL on the mechanical properties of the HeLa cells. The understanding of the PL action on HeLa cells mechanical properties may help in the development of effective therapeutic drugs against cancers.

category: biophysics


title: GENETICALLY-DETERMINED MYB INSUFFICIENCY DIRECTLYIMPACTS ON PROTEOSTASIS IN HEMATOPOIETIC STEM CELLSPREDISPOSING TO AGE-RELATED MYELOID NEOPLASIA

abstract: The Myb transcription factor plays critical roles in normal and malignant hematopoiesis. Acquired genetic dysregulation of Myb, which plays a central role in hematopoietic stem cell (HSC) gene regulation, is involved in the etiology of a number of leukemias. Also, inherited non-coding variants of the Myb gene are a factor in susceptibility to many hematological conditions, including myeloproliferative neoplasms (MPN), but the mechanisms by which variations in Myb levels predispose to disease, including age-dependency in disease occurrence, are completely unknown. Here, we address these key points by showing that Myb insufficiency in mice leads in later life to MPN, myelodysplasia, and leukemia, mirroring the age profile of equivalent human diseases. This age-dependence is intrinsic to HSC, involving progressive accumulation of subtle changes. Interestingly, and linking to previous studies showing the importance of proteostasis to the maintenance of normal HSC, we observed altered proteosomal activity in young Myb-insufficient mice and later elevated ribosome activity. We propose that these alterations collectively cause an imbalance in proteostasis, potentially creating a cellular milieu favoring disease initiation by driver mutations.

category: cancer biology


title: MYB insufficiency disrupts proteostasis in hematopoietic stem cells leading to age-related neoplasia


title: Reprogramming the neuroblastoma epigenome with a mitochondrial uncoupler

abstract: Dysregulated DNA methylation is associated with poor prognosis in cancer patients, promoting tumorigenesis and therapeutic resistance1. DNA methyltransferase inhibitors (DNMTi) reduce DNA methylation and promote cancer cell differentiation, with two DNMTi already approved for cancer treatment2. However, these drugs rely on cell division to dilute existing methylation, thus the  demethylation effects are achieved in a passive manner, limiting their application in slow-proliferating tumor cells. In this study we use a mitochondrial uncoupler, niclosamide ethanolamine (NEN), to actively achieve global DNA demethylation. NEN treatment promotes DNA demethylation by activating electron transport chain (ETC) to produce -ketoglutarate (-KG), a substrate for the DNA demethylase TET. In addition, NEN inhibits reductive carboxylation, a key metabolic pathway to support growth of cancer cells with defective mitochondria or under hypoxia. Importantly, NEN treatment reduces 2-hydroxyglutarate (2-HG) generation and blocks DNA hypermethylation under hypoxia. Together, these metabolic reprogramming effects of NEN actively alter the global DNA methylation landscape and promote neuroblastoma differentiation. These results not only support Warburgs original hypothesis that inhibition of ETC causes cell de-differentiation and tumorigenesis, but also suggest that mitochondrial uncoupling is an effective metabolic and epigenetic intervention that remodels the tumor epigenome for better prognosis.


title: SYS-Mut: Decoding the Functional Significance of Rare Somatic Mutations in Cancer

abstract: Current tailored-therapy efforts in cancer are largely focused on a small number of highly recurrently-mutated driver genes but therapeutic targeting of these oncogenes remains challenging. On the other hand, the vast number of genes mutated infrequently across cancers have received less attention, in part, due to a lack of understanding of their biologic significance. Here we present SYS-Mut, a systems biology platform that can robustly infer the biologic consequences of somatic mutations by integrating routine multi-omic profiles in primary tumors. We established the accuracy of SYS-Mut by recapitulating the functional impact of known driver genes in PanCancer datasets. Subsequent application of SYS-Mut on low-frequency gene mutations in Head and Neck Cancers (HNSC), followed by molecular and pharmacogenetic validation, revealed the lipidogenic network as a novel therapeutic vulnerability in aggressive HNSC. SYS-Mut is thus a robust scalable framework that enables discovery of new targetable avenues in cancer.


title: Machine Learning prediction of cardiac resynchronisation therapy response from combination of clinical and model-driven data

abstract:
AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSUp to 30%-50% of chronic heart failure patients who underwent cardiac resynchronization therapy (CRT) do not respond to the treatment. Therefore, patient stratification for CRT and optimization of CRT device settings remain a challenge.

ObjectiveThe main goal of our study is to develop a predictive model of CRT outcome using a combination of clinical data recorded in patients before CRT and simulations of the response to biventricular (BiV) pacing in personalized computational models of the cardiac electrophysiology.

Materials and MethodsRetrospective data from 57 patients who underwent CRT device implantation was utilized. Positive response to CRT was defined by a 10% increase in the left ventricular ejection fraction in a year after implantation. For each patient, an anatomical model of the heart and torso was reconstructed from MRI and CT images and tailored to ECG recorded in the participant. The models were used to compute ventricular activation time, ECG duration and electrical dyssynchrony indices during intrinsic rhythm and BiV pacing from active poles of leads. For building a predictive model of CRT response, we used clinical data recorded before CRT device implantation together with model-derived biomarkers of ventricular excitation in the left bundle branch block mode of activation and under BiV stimulation. Several Machine Learning (ML) classifiers and feature selection algorithms were tested on the hybrid dataset, and the quality of predictors was assessed using the area under receiver operating curve (ROC AUC). The classifiers on the hybrid data were compared with ML models built on clinical data only.

ResultsThe best ML classifier utilizing a hybrid set of clinical and model-driven data demonstrated ROC AUC of 0.82, an accuracy of 0.82, sensitivity of 0.85, and specificity of 0.78, improving quality over that of ML predictors built on clinical data from much larger datasets. Distance from the LV pacing site to the post-infarction zone and ventricular activation characteristics under BiV pacing were shown as the most relevant model-driven features for CRT response classification.

ConclusionOur results suggest that combination of clinical and model-driven data increases the accuracy of classification models for CRT outcomes.

category: physiology


title: Two engineered AAV capsid variants for efficient transduction of human cortical neurons directly converted from iPSC

abstract: Recombinant adeno-associated virus (AAV) is the most widely used vector for gene therapy in clinical trials. To increase transduction efficiency and specificity, novel engineered AAV variants with modified capsid sequences are evaluated in human cell cultures and non-human primates. In the present study, we tested two novel AAV capsid variants, AAV2-NNPTPSR and AAV9-NVVRSSS, in human cortical neurons, which were directly converted from human induced pluripotent stem cells and cocultured with rat primary astrocytes. AAV2-NNPTPSR variant efficiently transduced both induced human cortical glutamatergic neurons and induced human cortical GABAergic interneurons. By contrast, AAV9-NVVRSSS variant transduced both induced human cortical neurons and cocultured rat primary astrocytes. High viral titers (1x10E5 viral genomes per cell) caused a significant decrease in viability of induced human cortical neurons. Low viral titers (1x10E4 viral genomes per cell) lead to a significant increase in the neuronal activity marker c-Fos in transduced human neurons following treatment with a potassium channel blocker, which may indicate functional alterations induced by viral transduction and/or transgene expression.

category: neuroscience


title: Fast wavefront shaping for two-photon brain imaging with large field of view correction

abstract: Introduction paragraphIn-vivo optical imaging with diffraction-limited resolution deep inside scattering biological tissues is obtained by non-linear fluorescence microscopy1. Active compensation of tissue-induced aberrations and light scattering through adaptive wavefront correction2,3 further extends depth penetration by restoring high resolution at large depth. However, at large depths those corrections are only valid over a very limited field of view within the angular memory effect4. To overcome this limitation, we introduce an acousto-optic light modulation technique for fluorescence imaging with simultaneous wavefront correction at pixel scan speed. Biaxial wavefront corrections are first learned by adaptive optimization at multiple locations in the image field. During image acquisition, the learned corrections are then switched on-the-fly according to the position of the excitation focus during the raster scan. The proposed microscope is applied to in-vivo transcranial neuron imaging and demonstrates correction of skull-induced aberrations and scattering across large fields of view at 40 kHz data acquisition speed.


title: Involvement of Brn3a-positive spinal dorsal horn neurons in the transmission of visceral pain in inflammatory bowel disease model mice

abstract: Spinal dorsal horn plays crucial roles in the transmission and processing of somatosensory information. Although spinal neural circuits which process several distinct types of cutaneous sensation have been extensively studied, those responsible for visceral pain transmission remain poorly understood. In the present study, we analyzed the dextran sodium sulfate (DSS)-induced inflammatory bowel disease (IBD) model mice to characterize the spinal dorsal horn neurons involved in visceral pain transmission. DSS-treated mice exhibited increased abdominal licking behavior, suggestive of experiencing visceral pain. Immunostaining of c-fos, a marker indicating neuronal activity, demonstrated that numerous c-fos-positive cells were found bilaterally in the lumbosacral spinal dorsal horn, and their distribution was particularly abundant in the shallow dorsal horn. Neurochemical characterization of these neurons revealed that the percentage of the POU transcription factor Brn3a-positive neurons among the c-fos-positive neurons in the shallow dorsal horn was 30-40% in DSS-treated mice, which was significantly higher than that in the somatic pain model mice. We further demonstrated by neuronal tracing that within the shallow dorsal horn, Brn3a-positive neurons are represented more highly in spino-solitary projection neurons than in spino-parabrachial projection ones. These results raised the possibility that Brn3a-positive spinal dorsal horn neurons make a large contribution to visceral pain transmission, and part of which was mediated through spino-solitary pathway.


title: In vivo characterization and application of a novel potassium channel-based optogenetic silencer in the healthy and epileptic mouse hippocampus

abstract:
The performance of available optogenetic inhibitors remains insufficient due to low light sensitivity, short-lasting photocurrents, and unintended changes in ion distributions. To overcome these limitations, a novel potassium channel-based optogenetic silencer was developed and successfully applied in various in vitro and acute in vivo settings (Bernal Sierra et al., 2018). This tool, a two-component construct called PACK, comprises a photoactivated adenylyl cyclase (bPAC) and a cAMP-dependent potassium channel (SthK). Here, we examined the long-term inhibitory action and side effects of the PACK construct in healthy and epileptic adult male mice. We targeted hippocampal CA1 pyramidal cells using a viral vector and enabled illumination of these neurons via an implanted optic fiber. Local field potential (LFP) recordings from the CA1 of freely moving mice revealed significantly reduced neuronal activity during 50-minute intermittent illumination, especially in the beta and gamma frequency ranges. Adversely, PACK expression in healthy mice induced chronic astrogliosis, dispersion of pyramidal cells, and generalized seizures. These side effects were independent of the light application and were also present in mice expressing bPAC without the potassium channel. Additionally, light-activation of bPAC alone increased neuronal activity, presumably via enhanced cAMP signaling. In chronically epileptic mice, the dark activity of bPAC/PACK in CA1 prevented the spread of spontaneous epileptiform activity from the seizure focus to the contralateral bPAC/PACK-expressing hippocampus. Taken together, the PACK tool is a potent optogenetic inhibitor but requires refinement of its light-sensitive domain to avoid unexpected physiological changes.

Significance statementOptogenetics allows precise manipulation of neuronal activity via genetically encoded light-sensitive proteins. Unfortunately, available optogenetic inhibitors are not suitable for prolonged use. The newly developed two-component potassium channel-based optogenetic inhibitor, PACK, has been identified as a potent silencer of neurons in various acute experiments. Here, we characterized the PACK construct in freely behaving healthy and epileptic mice. We targeted the PACK silencer specifically to CA1 pyramidal neurons, where illumination with short light pulses at low frequencies reliably reduced neuronal activity. In chronically epileptic mice, PACK prevented the spread of epileptiform activity from the seizure focus to the contralateral PACK-expressing hippocampus. The major disadvantage of the PACK silencer is its light-sensitive domain, the bPAC adenylyl cyclase, which may induce side effects.


title: Hierarchical Timescales in the Neocortex: Mathematical Mechanism and Biological Insights

abstract:
A cardinal feature of the neocortex is the progressive increase of the spatial receptive fields along the cortical hierarchy. Recently, theoretical and experimental findings have shown that the temporal response windows also gradually enlarge, so that early sensory neural circuits operate on short-time scales whereas higher association areas are capable of integrating information over a long period of time. While an increased receptive field is accounted for by spatial summation of inputs from neurons in an upstream area, the emergence of timescale hierarchy cannot be readily explained, especially given the dense inter-areal cortical connectivity known in modern connectome. To uncover the required neurobiological properties, we carried out a rigorous analysis of an anatomically-based large-scale cortex model of macaque monkeys. Using a perturbation method, we show that the segregation of disparate timescales is defined in terms of the localization of eigenvectors of the connectivity matrix, which depends on three circuit properties: (1) a macroscopic gradient of synaptic excitation, (2) distinct electrophysiological properties between excitatory and inhibitory neuronal populations, and (3) a detailed balance between long-range excitatory inputs and local inhibitory inputs for each area-to-area pathway. Our work thus provides a quantitative understanding of the mechanism underlying the emergence of timescale hierarchy in large-scale primate cortical networks.

Significance StatementIn the neocortex, while early sensory areas encode and process external inputs rapidly, higher association areas are endowed with slow dynamics suitable for accumulating information over time. Such a hierarchy of temporal response windows along the cortical hierarchy naturally emerges in a model of multi-areal primate cortex. This finding raises the question of why diverse temporal modes are not mixed in roughly the same way across the whole cortex, despite high connection density and an abundance of feedback loops. We investigate this question by mathematically analyzing the anatomically-based network model of macaque cortex, and show that three general principles of synaptic excitation and inhibition are crucial for timescale segregation in a hierarchy, a functionally important characteristic of the cortex.


title: Effects of acute and repeated administration of the selective M4 PAM VU0152099 on cocaine vs. food choice in male rats

abstract: AO_SCPLOWBSTRACTC_SCPLOWLigands that stimulate muscarinic acetylcholine receptors 1 and 4 (M1, M4) have shown promising effects as putative pharmacotherapy for cocaine use disorder in rodent assays. We have previously shown reductions in cocaine effects with acute M4 stimulation, as well as long-lasting, delayed, reductions in cocaine taking and cocaine seeking with combined M1/M4 receptor stimulation or with M1 stimulation alone. M4 stimulation opposes dopaminergic signaling acutely, but direct dopamine receptor antagonists have proved unhelpful in managing cocaine use disorder because they lose efficacy with long-term administration. It is therefore critical to determine whether M4 approaches themselves can remain effective with repeated or chronic dosing. We assessed the effects of repeated administration of the M4 positive allosteric modulator (PAM) VU0152099 in rats trained to choose between intravenous cocaine and a liquid food reinforcer, to obtain quantitative measurement of whether M4 stimulation could produce delayed and lasting reduction in cocaine taking. VU0152099 produced progressively augmenting suppression of cocaine choice and cocaine intake, but produced neither rebound nor lasting effects after treatment ended. To compare and contrast effects of M1 vs. M4 stimulation, we tested whether the M4 PAM VU0152100 suppressed cocaine self-administration in mice lacking CalDAG-GEFI signaling factor, required for M1-mediated suppression of cocaine self-administration. CalDAG-GEFI ablation had no effect on M4-mediated suppression of cocaine self-administration. These findings support the potential usefulness of M4 PAMs as pharmacotherapy to manage cocaine use disorder, alone or in combination with M1-selective ligands, and show that M1 and M4 stimulation modulate cocaine-taking behavior by distinct mechanisms.


title: Electrical impulse characterization along actin filaments in pathological conditions

abstract: We present an interactive Mathematica notebook that characterizes the electrical impulses along actin filaments in both muscle and non-muscle cells for a wide range of physiological and pathological conditions. The program is based on a multi-scale (atomic [->] monomer [->] filament) approach capable of accounting for the atomistic details of a protein molecular structure, its biological environment, and their impact on the travel distance, velocity, and attenuation of monovalent ionic wave packets propagating along microfilaments. The interactive component allows investigators to conduct original research by choosing the experimental conditions (intracellular Vs in vitro), nucleotide state (ATP Vs ADP), actin isoform (alpha, gamma, beta, and muscle or non-muscle cell), as well as, a conformation model that covers a variety of mutants and wild-type (the control) actin filament. The simplicity of the theoretical formulation and the high performance of the Mathematica software enable the analysis of multiple conditions without computational restrictions. These studies may provide an unprecedented molecular understanding of why and how age, inheritance, and disease conditions induce dysfunctions in the biophysical mechanisms underlying the propagation of electrical signals along actin filaments.


title: Sex-specific divergent maturational trajectories in the post-natal rat basolateral amygdala

abstract: The basolateral amygdala (BLA), the part of the amygdala complex involved in the transduction of perceptual stimuli into emotion, undergoes profound reorganization at adolescence in rodents and humans. How cellular and synaptic plasticity evolve throughout postnatal development in both sexes is only partially understood. We used a cross-sectional approach to compare the morphology, neuronal, and synaptic properties of BLA neurons in rats of both sexes at adolescence and adulthood. While BLA pyramidal neurons from rats of both sexes displayed similar current-voltage relationships, rheobases, and resting potentials during pubescence, differences in these parameters emerged between sexes at adulthood: BLA neurons were more excitable in males than females. During pubescence, BLA neuron excitability was highest in females and unchanged in males; male action potentials were smaller and shorter than females and fast afterhyperpolarizations were larger in males. During post-natal maturation, no difference in spine density was observed between groups or sexes but spine length increased and decreased in females and males, respectively. A reduction in spine head diameter and volume was observed exclusively in females. Basic synaptic properties also displayed sex-specific maturational differences. Stimulus-response relationships and maximal fEPSP amplitudes where higher in male adolescents compared with adults but were similar in females of both ages. Spontaneous excitatory postsynaptic currents mediated by AMPA receptors were smaller in BLA neurons from adolescent female compared with their adult counterparts but were unchanged in males. These differences did not directly convert into changes in overall synaptic strength estimated from the AMPA/NMDA ratio, which was smaller in adolescent females. Finally, the developmental courses of long-term potentiation and depression (LTP, LTD) were sexually dimorphic. LTP was similarly present during the adolescent period in males and females but was not apparent at adulthood in females. In contrast, LTD followed an opposite development: present in adolescent females and expressed in both sexes at adulthood. These data reveal divergent maturational trajectories in the BLA of male and female rats and suggest cellular substrates to the BLA linked sex-specific behaviors at adolescence and adulthood.


title: Global Mapping of Mouse CSF Flow via HEAP-METRIC Phase-contrast MRI

abstract: Roles of Cerebrospinal fluid (CSF) in brain waste clearance and homeostasis has been increasingly recognized, thus measuring its flow dynamics could provide important information about its function and perturbance. While phase-contrast MRI can be used for non-invasive flow mapping, so far its mapping of low velocity flow (such as mouse brain CSF) is not possible. Here we developed a novel generalized Hadamard encoding based multi-band acceleration scheme dubbed HEAP-METRIC (Hadamard Encoding APproach of Multi-band Excitation for short TR Imaging aCcelerating), and with significantly increased SNR per time, HEAP-METRIC phase-contrast MRI achieved fast and accurate mapping of slow (~102 micron/s) flow. Utilizing this novel method, we revealed a heterogeneous global pattern of CSF flow in the awake mouse brain with a averaged flow of ~200 micron/s, and further found isoflurane anesthesia reduced CSF flow that was accompanied by reduction of glymphatic function. Therefore, we developed the novel HEAP-METRIC phase-contrast MRI for mapping low velocity flow, and demonstrated its capability for global mapping of mouse CSF flow and its potential alterations related to various physiological or pathological conditions.


title: Supervised Phenotype Discovery from Multimodal Brain Imaging

abstract: Data-driven discovery of image-derived phenotypes (IDPs) from large-scale multimodal brain imaging data has enormous potential for neuroscientific and clinical research by linking IDPs to subjects demographic, behavioural, clinical and cognitive measures (i.e., non-imaging derived phenotypes or nIDPs). However, current approaches are primarily based on unsupervised approaches, without use of information in nIDPs. In this paper, we proposed Supervised BigFLICA (SuperBigFLICA), a semi-supervised, multimodal, and multi-task fusion approach for IDP discovery, which simultaneously integrates information from multiple imaging modalities as well as multiple nIDPs. SuperBigFLICA is computationally efficient and largely bypasses the need for parameter tuning. Using the UK Biobank brain imaging dataset with around 40,000 subjects and 47 modalities, along with more than 17,000 nIDPs, we showed that SuperBigFLICA enhances the prediction power of nIDPs, bench-marked against IDPs derived by conventional expert-knowledge and unsupervised-learning approaches (with average nIDP prediction accuracy improvements of up to 46%). It also enables learning of generic imaging features that can predict new nIDPs. Further empirical analysis of the SuperBigFLICA algorithm demonstrates its robustness in different prediction tasks and the ability to derive biologically meaningful IDPs in predicting health outcomes and cognitive nIDPs, such as fluid intelligence and hypertension scores.


title: Batch Effects are Causal Effects: Applications in Human Connectomics

abstract: Batch effects, undesirable sources of variance across multiple experiments, present a substantial hurdle for scientific and clinical discoveries. Specifically, the presence of batch effects can create both spurious discoveries and hide veridical signals, contributing to the ongoing reproducibility crisis. Typical approaches to dealing with batch effects conceptualize  batches as an associational effect, rather than a causal effect, despite the fact that the sources of variance that comprise the batch - potentially including experimental design and population demographics - causally impact downstream inferences. We therefore cast batch effects as a causal problem rather than an associational problem. This reformulation enables us to make explicit the assumptions and limitations of existing approaches for dealing with batch effects. We therefore develop causal batch effect strategies--Causal DO_SCPLOWCORRC_SCPLOW for discovery of batch effects and Causal ComBat for mitigating batch effects - which build upon existing statistical associational methods by incorporating modern causal inference techniques. We apply these strategies to a large mega-study of human connectomes assembled by the Consortium for Reliability and Reproducibility, consisting of 24 batches including over 1700 individuals to illustrate that existing approaches create more spurious discoveries (false positives) and miss more veridical signals (true positives) than our proposed approaches. Our work therefore introduces a conceptual framing, as well as open source code, for combining multiple distinct datasets to increase confidence in claims of scientific and clinical discoveries.


title: Where is all the nonlinearity: flexible nonlinear modeling of behaviorally relevant neural dynamics using recurrent neural networks

abstract: Understanding the dynamical transformation of neural activity to behavior requires modeling this transformation while both dissecting its potential nonlinearities and dissociating and preserving its nonlinear behaviorally relevant neural dynamics, which remain unaddressed. We present RNN PSID, a nonlinear dynamic modeling method that enables flexible dissection of nonlinearities, dissociation and preferential learning of neural dynamics relevant to specific behaviors, and causal decoding. We first validate RNN PSID in simulations and then use it to investigate nonlinearities in monkey spiking and LFP activity across four tasks and different brain regions. Nonlinear RNN PSID successfully dissociated and preserved nonlinear behaviorally relevant dynamics, thus outperforming linear and non-preferential nonlinear learning methods in behavior decoding while reaching similar neural prediction. Strikingly, dissecting the nonlinearities with RNN PSID revealed that consistently across all tasks, summarizing the nonlinearity only in the mapping from the latent dynamics to behavior was largely sufficient for predicting behavior and neural activity. RNN PSID provides a novel tool to reveal new characteristics of nonlinear neural dynamics underlying behavior.


title: Smoothness discriminates physical from motor imagery practice of arm-reaching movements.

abstract: Physical practice (PP) and motor imagery practice (MP) lead to the execution of fast and accurate arm movements. However, there is currently no information about the influence of MP on movement smoothness, nor about which performance parameters best discriminate these practices. In the current study, we assessed motor performances with an arm pointing task with constrained precision before and after PP (n= 15), MP (n= 15), or no practice (n= 15). We analyzed gains between Pre- and Post-Test for five performance parameters: movement duration, mean and maximal velocities, total displacements, and the number of velocity peaks characterizing movement smoothness. The results showed an improvement of performance after PP and MP for all parameters, except for total displacements. The gains for movement duration, and mean and maximal velocities were statistically higher after PP and MP than after no practice, and comparable between practices. However, motor gains for the number of velocity peaks were higher after PP than MP, suggesting that movements were smoother after PP than after MP. A discriminant analysis also identified the number of velocity peaks as the most relevant parameter that differentiated PP from MP. The current results provide evidence that PP and MP specifically modulate movement smoothness during arm reaching tasks. This difference may rely on online corrections through sensory feedback integration, available during PP but not during MP.


title: Strategy-dependent effects of working-memory limitations on human perceptual decision-making

abstract: Deliberative decisions based on an accumulation of evidence over time depend on working memory, and working memory has limitations, but how these limitations affect deliberative decision-making is not understood. We used human psychophysics to assess the impact of working-memory limitations on the fidelity of a continuous decision variable. Participants decided the average location of multiple visual targets. This computed, continuous decision variable degraded with time and capacity in a manner that depended critically on the strategy used to form the decision variable. This dependence reflected whether the decision variable was computed either: 1) immediately upon observing the evidence, and thus stored as a single value in memory; or 2) at the time of the report, and thus stored as multiple values in memory. These results provide important constraints on how the brain computes and maintains temporally dynamic decision variables.


title: Metformin in nucleus accumbens core reduces cue-induced cocaine seeking in male and female rats

abstract: This study investigated the potential therapeutic effects of the FDA-approved drug metformin on cue-induced reinstatement of cocaine seeking. Metformin (dimethyl-biguanide) is a first-line treatment for type II diabetes that, among other mechanisms, is involved in the activation of adenosine monophosphate activated protein kinase (AMPK). Cocaine self-administration and extinction is associated with decreased levels of phosphorylated AMPK within the nucleus accumbens core (NAcore). Previously it was shown that increasing AMPK activity in the NAcore decreased cue-induced reinstatement of cocaine seeking. Decreasing AMPK activity produced the opposite effect. The goal of the present study was to determine if metformin in the NAcore reduces cue-induced cocaine seeking in adult male and female Sprague Dawley rats. Rats were trained to self-administer cocaine followed by extinction prior to cue-induced reinstatement trials. Metformin microinjected in the NAcore attenuated cue-induced reinstatement in male and female rats. Importantly, metformins effects on cocaine seeking were not due to a general depression of spontaneous locomotor activity. In female rats, metformins effects did generalize to a reduction in cue-induced reinstatement of sucrose seeking. These data support a potential role for metformin as a pharmacotherapy for cocaine use disorder, but warrant caution given the potential for metformins effects to generalize to a natural reward in female rats.


title: Feed-forward inhibition fine-tunes response timing in auditory-vocal interactions

abstract: The ability to regulate vocal timing is a fundamental aspect of communicative interactions for many species, including conversational speech among humans, yet little is known about the neural circuitry that regulates the input-dependent timing of vocal replies. Exploring this topic in the zebra finch premotor area HVC, we identify feed-forward inhibition as a key regulator of vocal response timing. Based on a spiking network model informed by behavioral and electrophysiological data from communicating zebra finches, we predicted that two different patterns of inhibition regulate vocal-motor responses. In one scenario, the strength of production-related premotor inhibition translates into plasticity in vocal response delays. In the other scenario, fast transient interneuron activity in response to auditory input results in the suppression of call production while a call is heard, thereby reducing acoustic overlap between callers. Extracellular recordings in HVC during the listening phase confirm the presence of auditory-evoked response patterns in putative inhibitory interneurons, along with corresponding signatures of auditory-evoked activity suppression. The proposed model provides a parsimonious framework to explain how auditory-vocal transformations can give rise to vocal turn-taking and highlights multiple roles of local inhibition for behavioral modulation at different time scales.


title: Hippocampal astroglial hypertrophy in mice subjected to early life maternal deprivation

abstract: Early-life stress (ELS), including chronic deprivation of maternal care, exerts persistent life-long effects on animal physiology and behavior, and is associated with several neurodevelopmental disorders. Long-lasting changes in neuronal plasticity and electrophysiology are documented extensively in the animal models of ELS. However, the role of astroglia in the lasting effects of ELS remains elusive. Astrocytes are intricately involved in the regulation of synaptic physiology and behavior. Moreover, astrocytes play a major role in the innate and adaptive immune responses in the central nervous system (CNS). The role of immune responses and neuroinflammation in the altered brain development and persistent adverse effects of ELS are beginning to be explored. Innate immune response in the CNS is characterized by a phenomenon called astrogliosis, a process in which astrocytes undergo hypertrophy, along with changes in gene expression and function. While the immune activation and neuroinflammatory changes concomitant with ELS, or in juveniles and young adults have been reported, it is unclear whether mice subjected to ELS exhibit astrogliosis-like alterations well into late-adulthood. Here, we subjected mice to maternal separation from postnatal day 2 to day 22 and performed comprehensive morphometric analysis of hippocampal astrocytes during late-adulthood. We found that the astrocytes in the stratum radiatum region of the CA1 hippocampal subfield from maternally separated mice exhibit significant hypertrophy as late as 8 months of age, revealing the crucial changes in astrocytes that manifest long after the cessation of ELS. This study highlights the persistence of neuroinflammatory changes in mice exposed to ELS.


title: Information dynamics in neuronal networks of macaque cerebral cortex reflect cognitive state and behavior.

abstract:
One of the essential functions biological neural networks is the processing of information. This comprises processing sensory information to perceive the environment, up to processing motor information to interact with the environment. Due to methodological concerns, it has been historically unclear how information processing changes during different cognitive or behavioral states, and to what extent information is processed within or between the network of neurons in different brain areas. In this study, we leverage recent advances in the calculation of information dynamics to explore neural-level processing within and between the fronto-parietal areas AIP, F5 and M1 during a delayed grasping task performed by three macaque monkeys. While information processing was high within all areas during all cognitive and behavioral states of the task, inter-areal processing varied widely: during visuo-motor transformation, AIP and F5 formed a reciprocally connected processing unit, while no processing was present between areas during the memory period. Movement execution was processed globally across all areas with a predominance of processing in the feedback direction. Additionally, the fine-scale network structure re-configured at the neuron-level in response to different grasping conditions, despite of no differences in the overall amount of information present. These results suggest that areas dynamically form higher-order processing units according to the cognitive or behavioral demand, and that the information processing network is hierarchically organized at the neuron-level, with the coarse network structure determining the behavioral state and finer changes reflecting different conditions.

Significance StatementWhat does it mean to say that the brain "processes information?" Scientists often discuss the brain in terms of information processing - animals take in information from their environment through their senses, and use it to make decisions about how to act in the world. In this work, we use a mathematical framework called information theory to explore how signals from the environment influence brain activity, and how brain activity in turn informs on behaviors. We found that different brain regions processed information in dynamic and flexible ways, with signals flowing up and down the hierarchy of sensory-motor depending on the demands of the moment. This shows how "computation" in the brain can reflect complex behaviors and cognitive states.


title: Information processing dynamics in neural networks of macaque cerebral cortex reflect cognitive state and behavior.


title: IL-10 receptor blockade delivered simultaneous with BCG vaccination sustains long term protection against Mycobacterium tuberculosis infection in mice

abstract: Mycobacterium bovis bacillus Calmette-Guerin (BCG) immunization still remains the best vaccination strategy available to control the development of active tuberculosis (TB). Protection afforded by BCG vaccination gradually wanes over time and while booster strategies have promise, they remain under development. An alternative approach is to improve BCG efficacy through host-directed therapy. Building upon prior knowledge that blockade of interleukin-10 receptor 1 (IL-10R1) during early Mycobacterium tuberculosis (M.tb) infection improves and extends control of M.tb infection in mice, we employed a combined anti-IL-10R1/BCG vaccine strategy. A subcutaneous, single vaccination of BCG/IL10-R1 increased the numbers of CD4+ and CD8+ central memory T cells, and reduced TH1 and TH17 cytokine levels in the lung for up to 7 weeks post vaccination. Subsequent M.tb challenge in mice showed both an early (4 week) and sustained long-term (47 week) control of infection, which was associated with increased survival. In contrast, protection of BCG/saline vaccinated mice waned 8 weeks post M.tb infection. Our findings demonstrate that a single and simultaneous vaccination with BCG/IL10-R1 sustains long-term protection, identifying a promising approach to enhance and extend the current BCG mediated protection against TB.

category: immunology


title: Distinct inflammatory and transcriptomic profiles in dominant versus subordinate males in mouse social hierarchies

abstract:
Social status is a critical factor determining health outcomes in human and nonhuman social species. In social hierarchies with reproductive skew, individuals compete to monopolize resources and increase mating opportunities. This can come at a significant energetic cost leading to trade-offs between different physiological systems. Particularly, changes in energetic investment in the immune system can have significant short and long-term effects on fitness and health. We have previously found that dominant alpha male mice living in social hierarchies have increased metabolic demands related to territorial defense. In this study, we tested the hypothesis that high-ranking male mice favor energetically inexpensive adaptive immunity, while subordinate mice show higher investment in innate immunity. We housed 12 groups of 10 outbred CD-1 male mice in a social housing system. All formed linear social hierarchies and subordinate mice had higher concentrations of plasma corticosterone (CORT) than alpha males. This difference was heightened in highly despotic hierarchies. Using flow cytometry, we found that dominant status was associated with a significant shift in immunophenotypes towards favoring adaptive versus innate immunity. Using Tag-Seq to profile hepatic and splenic transcriptomes of alpha and subordinate males, we identified genes that regulate metabolic and immune defense pathways that are associated with status and/or CORT concentration. In the liver, dominant animals showed an up-regulation of specific genes involved in major urinary production and catabolic processes, whereas subordinate animals showed an up-regulation of genes promoting biosynthetic processes, wound healing, and proinflammatory responses. In spleen, subordinate mice showed up-regulation of genes facilitating oxidative phosphorylation and DNA repair and CORT was negatively associated with genes involved in lymphocyte proliferation and activation. Together, our findings suggest that dominant and subordinate animals adaptively shift energy investment in immune functioning and gene expression to match their contextual energetic demands.

HighlightsO_LIImmunity is shaped by stress and energetic pressures associated with social status
C_LIO_LIDominant and subordinate mice favor adaptive and innate immunity, respectively
C_LIO_LIDominants increase expression of genes involved in energy production
C_LIO_LIWound healing and DNA repair genes are upregulated in subordinates
C_LIO_LIGenes related to maintaining and signaling social status are upregulated in dominants
C_LI


title: Evidence of structural rearrangements and variability in pESI(like) megaplasmids of S.Infantis by resolving the pESI-like-blaCTX-M-1 positive variant.

abstract:
The increasing prevalence of pESI(like)-positive, multidrug-resistant (MDR) S. Infantis in Europe is a cause of major concern. As previously demonstrated, the pESI(like) megaplasmid is not only a carrier of antimicrobial resistant (AMR) genes (at least tet, dfr and sul genes), but also harbours several virulence factors and toxin/antitoxin systems that enhance its persistence in the S. Infantis host.

In this study, five pESI(like) plasmids were long-read sequenced using Oxford Nanopore Technology (ONT) and their complete sequences were resolved. Comparison of the structure and gene content of the five sequenced plasmids, and further comparison with previously published pESI(like) sequences, indicated that although the sequence of pESI(like) remains almost identical, its structure is composed of regions inserted or transposed after different events.

The results obtained in this study are essential to better understand the plasticity and the evolution of the pESI(like) megaplasmid, and therefore to better address risk management options and policy decisions to fight against AMR and MDR in Salmonella and other food-borne pathogens.

category: microbiology


title: Aphid transmission of a Potexvirus, Foxtail mosaic virus, in the presence of the Potyvirus helper component proteinase

abstract: To establish successful infections, plant viruses compete with the host plants for limited resources and thus alter the physiological state of the plants. After successful infection, insect vectors are required for the transmission of some plant viruses to the next host plant. One of the largest groups of plant viruses, the potyvirus, can be transmitted by aphids. During transmission, the potyvirus protein helper component proteinase (HC-Pro) binds to the yet-to-be-defined aphid receptor on the stylet, as well as to the virus particles through the Asp-Ala-Gly (DAG) motif of the viral coat protein. Previously it was determined that a naturally occurring DAG motif in the non-aphid transmissible potexvirus, Potato aucuba mosaic potexvirus (PAMV), is functional when the HC-Pro is provided through co-infection with a potyvirus. Further, the DAG motif of PAMV can be successfully transferred to another non-aphid transmissible potexvirus, Potato virus X (PVX), to convey aphid transmission capabilities. We expand on this previous work by demonstrating, the DAG motif from two different potyviruses, Sugarcane mosaic virus and Turnip mosaic virus, as well as the DAG motif from the previous potexvirus PAMV, can be added to another non-aphid transmissible potexvirus, Foxtail mosaic virus (FoMV), to make it aphid transmissible. Transmission efficiency varied from less than 10% to over 80% depending on the DAG motif and host plant used in transmission, suggesting not all DAG motifs are equal for engineering aphid transmission. The underlying mechanisms mediating this variation still need to be explored.


title: Kinetic tracking of Plasmodium falciparum antigen presentation reveals determinants of protein export and membrane insertion

abstract: Intracellular malaria parasites export many proteins into their host cell, inserting several into the erythrocyte plasma membrane to enable interactions with their external environment. While static techniques have identified some surface-exposed proteins, other candidates have eluded definitive localization and membrane topology determination. Moreover, both export kinetics and the mechanisms of membrane insertion remain largely unexplored. We introduce Reporter of Insertion and Surface Exposure (RISE), a method for continuous nondestructive tracking of antigen exposure on infected cells. RISE utilizes a small 11 aa NanoLuc fragment inserted into a target protein and detects surface exposure through high-affinity complementation. We tracked insertion of CLAG3, a malaria parasite protein linked to nutrient uptake, throughout the P. falciparum cycle in human erythrocytes. Our approach also revealed key determinants of trafficking and surface exposure. Removal of a C-terminal transmembrane domain aborted export. Unexpectedly, certain increases in the exposed reporter size improved surface exposure by up to 50-fold, revealing that both size and charge of the extracellular epitope influence membrane insertion. Insertion of parasite proteins at the host cell surface and antigen accessibility is regulated by multiple factors, enabling intracellular parasite survival and immune evasion under a broad range of conditions.


title: Legionella pneumophila regulates host cell motility by targeting Phldb2 with a 14-3-3ζ-dependent protease effector

abstract: The cytoskeleton network of eukaryotic cells is essential for diverse cellular processes, including vesicle trafficking, cell motility and immunity, thus is a common target for bacterial virulence factors. A number of effectors from the bacterial pathogen Legionella pneumophila have been shown to modulate the function of host actin cytoskeleton to construct the Legionella-containing vacuole (LCV) permissive for its intracellular replication. In this study, we identified the Dot/Icm effector Lem8 (Lpg1290) as a protease that interferes with host motility. We show that the protease activity of Lem8 is catalyzed by a Cys-His-Asp motif known to be associated with diverse biochemical activities. Intriguingly, we found that Lem8 interacts with the host regulatory protein 14-3-3{zeta}, which activates its protease activity. Furthermore, Lem8 undergoes self-cleavage in a process that requires 14-3-3{zeta}. We identified the PH domain-containing protein Phldb2 involved in cell migration as a target of Lem8 and demonstrate that Lem8 plays a role in the inhibition of host cell migration. Our results reveal a novel mechanism of inhibiting host cell motility by L. pneumophila for its virulence.


title: Iron promotes Slc7a11-deficient valvular interstitial cell osteogenic differentiation: A possible mechanism by which ferroptosis participates in intraleaflet hemorrhage-induced calcification.

abstract:
BackgroundCalcific aortic valve disease (CAVD) is the most frequent pathogeny of aortic valve replacement in developed countries. Iron deposits are found in the intraleaflet hemorrhage (IH) areas of calcific aortic valves. Ferroptosis is a form of regulated cell death that involves metabolic dysfunction resulting from iron overload-dependent excessive lipid peroxidation. In this research, we attempted to clarify the role of ferroptosis in CAVD.

MethodsThe level of ferroptosis in tissue and valvular interstitial cells (VICs) was assessed by the contents of 4-HNE, NADPH, ROS, and GSH, lipid peroxidation and mitochondrial morphology. The levels of calcification, iron accumulation and Slc7a11 expression in surgical aortic valve specimens were detected by Alizarin red or Von Kossa, Perls blue and immunohistochemical staining. The osteogenic differentiation of VICs was assessed by PCR and western blot analyses. Furthermore, RNA sequencing was used to detect potential differentially expressed genes between normal and osteogenic medium-treated (OM-treated) VICs.

ResultsOur experiments demonstrated that ferroptosis occurred in the IH areas of calcific aortic valves. We also found that Slc7a11 was expressed at low levels in OM-treated VICs and IH areas. Finally, we demonstrated that iron promoted Slc7a11-deficient VICs osteogenic differentiation by aggravating ferroptosis in vitro.

ConclusionIn conclusion, iron promotes Slc7a11-deficient VIC osteogenic differentiation by aggravating ferroptosis in vitro, thereby accelerating the progression of aortic valve calcification.

StatementStatements and opinions expressed in the articles and communications herein are those of the author(s) and not necessarily those of the Editor(s), Society, or publisher, and the Editor(s), Society, and publisher disclaim any responsibility or liability for such material.

Brief SummaryIn this work, two novel notions have been proposed. First, we reported that ferroptosis participated in the progression of CAVD. Second, this is the first cytology experiment of valvular interstitial cells (VICs) to clarify the mechanism by which intraleaflet hemorrhage aggravates calve calcification. This research provides new ideas and targets for alleviating the progression of CAVD, especially in patients who have calcified aortic valves without severe stenosis.

category: molecular biology


title: Unscheduled DNA replication in G1 causes genome instability through head-to-tail replication fork collisions

abstract: DNA replicates once per cell cycle. Interfering with the regulation of DNA replication initiation generates genome instability through over-replication and has been linked to early stages of cancer development. Here, we engineered genetic systems in budding yeast to induce unscheduled replication in the G1-phase of the cell cycle. Unscheduled G1 replication initiated at canonical S-phase origins across the genome. We quantified differences in replisomes in G1- and S-phase and identified firing factors, polymerase , and histone supply as factors that limit replication outside S-phase. G1 replication per se did not trigger cellular checkpoints. Subsequent replication during S-phase, however, resulted in over-replication and led to chromosome breaks via head-to-tail replication fork collisions that are marked by chromosome-wide, strand-biased occurrence of RPA-bound single-stranded DNA. Low-level, sporadic induction of G1 replication induced an identical response, indicating findings from synthetic systems are applicable to naturally occurring scenarios of unscheduled replication initiation by G1/S deregulation.


title: Fibroadipogenic Progenitors contribute to microvascular repair during skeletal muscle regeneration

abstract: Skeletal muscle injury results in a disruption of the muscle bed vascular network. A local source of vascular progenitors during muscle regeneration has not been clearly identified. Fibroadipogenic progenitors (FAPs) are required for proper regeneration, however they can also directly contribute to fibrotic and fatty infiltration in response to chronic muscle injury and muscle disease. We show here that acute muscle injury leads to hypoxia and glucose deprivation, triggering FAP proliferation and differentiation into endothelial cells in vitro and in vivo. In response to glucose deprivation, FAPs down regulate fibrotic and fat associated genes and acquire an endothelial cell fate, which is dependent upon mTORC2-HIF2-eNOS pathway. These findings bring new insights into the mechanisms of vascular regeneration during muscle regeneration and define a highly plastic resident progenitor population that responds to oxygen/glucose-deprivation induced cell stress by promoting an endothelial cell fate.

category: cell biology


title: A comparison between time-constrained counts and line transects as methods to estimate butterfly diversity in tropical habitats

abstract: Long-term species monitoring programmes have revealed catastrophic insect population declines and disruption of biological communities that are contributing to biodiversity loss. Such discoveries have been possible because of standardised methods, such as line transects, of counting butterflies and other insects. However, line transects are not feasible in many tropical and mountainous habitats, so alternative methods must be explored. To tackle this issue, we devised time-constrained (30-min) counts and compared butterfly diversity as estimated through this method with that estimated through line transects in three tropical habitats in India (evergreen forest, dry deciduous forest and an urban woodland). We tested the efficacy of the two methods to sample species richness and abundance, as well as numbers of rare, endemic and specialist butterflies. We observed greater species richness, and more species of habitat specialists and endemics per sample in time-constrained counts in evergreen forest, but not in the other two habitats. Thus, time-constrained counts were more efficient at detecting species in the species-rich evergreen habitat. Apart from this difference, the two sampling methods captured similar levels of species richness and other measures of diversity. Our study thus shows that time-constrained counts is a suitable if not a superior alternative to line transects to conduct butterfly diversity surveys and population monitoring in complex tropical landscapes. Due to methodological flexibility and simplicity, this method may be particularly useful to study the impacts of climate change, habitat fragmentation and land use practices on butterfly conservation in populous and tech-ready tropical countries using citizen science frameworks.

category: ecology


title: A comparison between time-constrained counts and line transects as methods to estimate butterfly diversity and monitor populations in tropical habitats


title: Spatial modeling of extinct Southeast Asian Hobbit Homo floresiensis habitat suitability based on its diet availability and climatic parameters as a proxy

abstract: The discovery of a new prehistoric species of the genus Homo remains a significant matter of intense interest. One of significant discovery recently is the Homo floresiensis, representing a small-bodied and small-brained hominin, excavated, and found in Liang Bua Cave in Flores Island, East Nusa Tenggara, Indonesia. This species height was only about 106 cm (36") and the weight was 30-40 kg (66-86 lbs). H. floresiensis was known consumed extant murine rodents as its diets as this was evidence found in Liang Bua Cave. Then this study aims to model the H. floresiensis suitable habitat using maximum entropy method and 2 extant murine rodents, Rattus exulans and R. rattus as a proxy. The results show that the most suitable habitats for H. floresiensis indicated by suitable habitat values close to 1 were concentrated in the central of Flores Island that was overlapped with mountainous areas with elevation ranging from 1500 to 2000 m. These suitable habitats were also overlapped with dense vegetation covers, volcanic rock, and Kiro rock formation. Climatic parameters that limit the distributions of H. floresiensis were annual mean temperature, isothermality, minimum temperature of coldest period, and precipitation seasonality. Parts of Flores Island with the low temperature below 20 {degrees}C were favorable for H. floresiensis while an increase in isothermality limits the H. floresiensis distributions.


title: Machine learning techniques to derive bioclimatic classifications for Colombia

abstract: Bioclimatic classifications seek to divide a study region into geographic areas with similar bioclimatic characteristics. In this study we proposed two bioclimatic classifications for Colombia using machine learning techniques. We firstly characterized the precipitation space of Colombia using principal component analysis. Based on Lang classification, we then projected all background sites in the precipitation space with their corresponding categories. We sequentially fit logistic regression models to reclassify all background sites in the precipitation space with six redefined Lang categories. New categories were the used to define a new modified Lang and Caldas-Lang classifications.


title: Comparing trait syndromes between Taiwanese subtropical terrestrial and epiphytic ferns and lycophytes at the species and community level

abstract:
O_LIWhile functional trait-trait and trait-environment relationships are well studied in angiosperms, it is less clear if similar relationships, such as the leaf economics spectrum (LES), hold for ferns and lycophytes. Similarly, studies exploring potential differences in trait-trait and trait-environment relationships between terrestrial and epiphytic fern communities in a given ecosystem are largely lacking.
C_LIO_LIWe measured nine leaf traits for 76 terrestrial and 43 epiphytic fern and lycophyte species across 59 vegetation plots along an elevation gradient in the subtropical forest of Northern Taiwan. We explored trait-trait and trait-environment relationships at both the species- and community level for both species groups.
C_LIO_LIEpiphytes differed from terrestrial ferns and lycophytes in species- and community-level trait values, mainly reflecting responses to higher drought and nutrient stress. The angiosperm LES was reflected in the trait-trait correlations of terrestrial ferns, but not of epiphytes. This suggests that epiphytic trait patterns are mainly shaped by water, rather than nutrient availability. Trait-environment relationships were nonetheless more-or-less similar for several drought-related traits across both species groups.
C_LIO_LIThis study illustrates that ferns and lycophyte trait patterns are not equivalent for epiphytic and terrestrial species or communities, and should not be extrapolated across species groups or between the species- and community-level.
C_LI


title: Novel insights on obligate symbiont lifestyle and adaptation to chemosynthetic environment as revealed by the giant tubeworm genome

abstract: The mutualism between the giant tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has been extensively researched over the past 40 years. However, the lack of the host whole genome information has impeded the full comprehension of the genotype/phenotype interface in Riftia. Here we described the high-quality draft genome of Riftia, its complete mitogenome, and tissue-specific transcriptomic data. The Riftia genome presents signs of reductive evolution, with gene family contractions exceeding expansions. Expanded gene families are related to sulphur metabolism, detoxification, anti-oxidative stress, oxygen transport, immune system, and lysosomal digestion, reflecting evolutionary adaptations to the vent environment and endosymbiosis. Despite the derived body plan, the developmental gene repertoire in the gutless tubeworm is extremely conserved with the presence of a near intact and complete Hox cluster. Gene expression analyses establishes that the trophosome is a multi-functional organ marked by intracellular digestion of endosymbionts, storage of excretory products and haematopoietic functions. Overall, the plume and gonad tissues both in contact to the environment harbour highly expressed genes involved with cell cycle, programmed cell death, and immunity indicating a high cell turnover and defence mechanisms against pathogens. We posit that the innate immune system plays a more prominent role into the establishment of the symbiosis during the infection in the larval stage, rather than maintaining the symbiostasis in the trophosome. This genome bridges four decades of physiological research in Riftia, whilst simultaneously provides new insights into the development, whole organism functions and evolution in the giant tubeworm.

category: evolutionary biology


title: Ecological constraints on highly evolvable olfactory receptor genes and morphology

abstract:
While evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with constant exposure to a changing odorant landscape; detecting adaptation amidst extensive chemosensory diversity is an open challenge. Phyllostomid bats, an ecologically diverse clade that evolved plant-visiting from an insectivorous ancestor, suggest the evolution of novel food detection mechanisms is a key innovation: phyllostomids behaviorally rely strongly on olfaction, while echolocation is supplemental. If this is true, exceptional variation in underlying olfactory genes and phenotypes may have preceded dietary diversification. We compared olfactory receptor (OR) genes sequenced from olfactory epithelium transcriptomes and olfactory epithelium surface area of bats with differing diets. Surprisingly, although OR evolution rates were quite variable and generally high, they are largely independent of diet. Olfactory epithelial surface area, however, is relatively larger in plant-visiting bats and there is an inverse relationship between OR evolution rates and surface area. Relatively larger surface areas suggest greater reliance on olfactory detection and stronger constraint on maintaining an already diverse OR repertoire. Instead of the typical case in which specialization and elaboration is coupled with rapid diversification of associated genes, here the relevant genes are already evolving so quickly that increased reliance on smell has led to stabilizing selection, presumably to maintain the ability to consistently discriminate among specific odorants -- a potential ecological constraint on sensory evolution.

Significance StatementThe evolutionary relationship between genes and morphology is complex to decipher, and macroevolutionary trends are often measured independently; this is especially challenging to quantify in unstable genomic regions or hypervariable traits. Odorant cues are detected by proteins encoded by the largest and fasted-evolving gene family in the mammalian genome and expressed in epithelia distributed on elaborate bony structures in the nose, posing a challenge to quantification. Yet, the direct interaction of the olfactory system with environmental signals strongly suggest that selection shapes its immense diversity. In neotropical bats, where reliance on plant-visiting evolved from an insectivorous ancestor, we discovered clear dietary differences amongst species, but only after considering morphological and molecular data simultaneously, emphasizing the power of a coupled analysis.


title: 'Lose-to-gain' adaptation to genome decayin the structure of the smallest eukaryotic ribosomes

abstract: AO_SCPLOWBSTRACTC_SCPLOWThe evolution of microbial parasites involves the interplay of two opposing forces. On the one hand, the pressure to survive drives parasites to improve through Darwinian natural selection. On the other, frequent genetic drifts result in genome decay, an evolutionary process in which an ever-increasing burden of deleterious mutations leads to gene loss and gradual genome reduction. Here, seeking to understand how this interplay occurs at the scale of individual macromolecules, we describe cryo-EM and evolutionary analyses of ribosomes from Encephalitozoon cuniculi, a eukaryote with one of the most reduced genomes in nature. We show that E. cuniculi ribosomes, the smallest eukaryotic cytoplasmic ribosomes to be structurally characterized, employ unparalleled structural innovations that allow extreme rRNA reduction without loss of ribosome integrity. These innovations include the evolution of previously unknown rRNA features such as molten rRNA linkers and bulgeless rRNA. Furthermore, we show that E. cuniculi ribosomes withstand the loss of rRNA and protein segments by evolving a unique ability to effectively trap small molecules and use them as ribosomal building-blocks and structural mimics of degenerated rRNA and protein segments. Overall, our work reveals a recurrent evolutionary pattern, which we term "lose-to-gain" evolution, where it is only through the loss of rRNA and protein segments that E. cuniculi ribosomes evolve their major innovations. Our study shows that the molecular structures of intracellular parasites long viewed as reduced, degenerated, and suffering from various debilitating mutations instead possess an array of systematically overlooked and extraordinary structural features. These features allow them to not only adapt to molecular reduction but evolve new activities that parasites can possibly use to their advantage.


title: Genome-wide analysis illustrates the effect of polyploidization in Phragmites australis

abstract: Polyploidization is a common event in plant evolution, and it plays an important role in plant speciation and adaptation. To address the role of polyploidization in grass diversification, we studied Phragmites australis, a species with intraspecific variation of chromosome numbers ranging from 2n=36 to 144. A combined analysis of genome structure, phylogeny and population genetics were used to study the evolution of P. australis. Whole-genome sequencing of three representative lineages revealed the allopolyploid origin of the species, with subgenome divergence dating back to approximately 29 million years ago, and the genomes showed hallmarks of relaxed selection associated with asexual propagation. Genome-wide analysis of 88 individuals from different populations around the world using restriction site associated DNA sequencing (RAD-seq) identified seven main intraspecific lineages with extensive genetic admixture. Each lineage was characterized by a distinct ploidy level, mostly tetraploid or octoploid, suggesting several polyploid events. Furthermore, we observed octoploid and hexaploid lineages at contact zones in Romania, Hungary and South Africa, suggestively due to genomic conflicts in allotetraploid parental lineages. Polyploidy may have evolved as a strategy to escape from the evolutionary dead-end of asexual propagation and the resulting decrease in genomic plasticity.


title: Genome-wide analysis tracks the emergence of intraspecific polyploids in Phragmites australis


title: Parallel evolution of phage resistance - virulence trade - offs during in vitro and nasal Pseudomonas aeruginosa phage treatment

abstract: With rising antibiotic resistance, there has been increasing interest in treating pathogenic bacteria with bacteriophages (phage therapy). One limitation of phage therapy is the ease at which bacteria can evolve resistance. Negative effects of resistance may be mitigated when resistance results in reduced bacterial growth and virulence, or when phage coevolve to overcome resistance. Resistance evolution and its consequences are contingent on the bacteria-phage combination and their environmental context, making therapeutic outcomes hard to predict. One solution might be to conduct "in vitro evolutionary simulations" using bacteria-phage combinations from the therapeutic context. Overall, our aim was to investigate parallels between in vitro experiments and in vivo dynamics in a human participant. Evolutionary dynamics were similar, with high levels of resistance evolving quickly with limited evidence of phage evolution. Resistant bacteria - evolved in vitro and in vivo - had lower virulence. In vivo, this was linked to lower growth rates of resistant isolates, whereas in vitro phage resistant isolates evolved greater biofilm production. Population sequencing suggests resistance resulted from selection on de novo mutations rather than sorting of existing variants. These results highlight the speed at which phage resistance can evolve in vivo, and in vitro experiments may give useful insights for clinical evolutionary outcomes.


title: Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats

abstract:
In the largest DNA-based study of domestic cat to date, 11,036 individuals (10,419 pedigreed cats from 91 breeds and breed types and 617 non-pedigreed cats) were genotyped via commercial panel testing, elucidating the distribution and frequency of known genetic variants associated with blood type, disease and physical traits across cat breeds. Blood group determining variants, which are relevant clinically and in cat breeding, were genotyped to assess the across breed distribution of blood types A, B and AB. Extensive panel testing identified 13 disease-associated variants in 48 breeds or breed types for which the variant had not previously been observed, strengthening the argument for panel testing across populations. The study also indicates that multiple breed clubs have effectively used DNA testing to reduce disease-associated genetic variants within certain pedigreed cat populations. Appearance-associated genetic variation in all cats is also discussed. Additionally, we combined genotypic data with phenotype information and clinical documentation, actively conducted owner and veterinarian interviews, and recruited cats for clinical examination to investigate the causality of a number of tested variants across different breed backgrounds. Lastly, genome-wide informative SNP heterozygosity levels were calculated to obtain a comparable measure of the genetic diversity in different cat breeds.

This study represents the first comprehensive exploration of informative Mendelian variants in felines by screening over 10,000 domestic cats. The results qualitatively contribute to the understanding of feline variant heritage and genetic diversity and demonstrate the clinical utility and importance of such information in supporting breeding programs and the research community. The work also highlights the crucial commitment of pedigreed cat breeders and registries in supporting the establishment of large genomic databases that when combined with phenotype information can advance scientific understanding and provide insights that can be applied to improve the health and welfare of cats.

category: genetics


title: Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties

abstract: Knowledge about crops genetic diversity is essential to promote effective use and conservation of their genetic resources, because genetic diversity enables farmers to adapt their crops to specific needs and is the raw material for breeding efforts. Currently, manioc (Manihot esculenta ssp. esculenta) is one of the most important food crops in the world and has the potential to help achieve food security in the context of on-going climate changes. In this study we assessed the patterns of genome-wide diversity of traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of Sao Paulo. We used single nucleotide polymorphisms to evaluate the organization of genetic diversity and to identify selective signatures contrasting varieties from different biomes with samples of maniocs wild relative M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses. This presumed adaptive variation might have been important for the initial domestication and for the crops diversification in response to cultivation in different environments. The neutral variation revealed high levels of genetic diversity within groups of varieties from different biomes and low to moderate genetic divergence among biomes. These results reflect the complexity of maniocs biology and its evolutionary dynamics under traditional cultivation. Our results exemplify how the smallholder practices contribute to the conservation of maniocs genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.


title: Geometrical Study of Virus RNA Sequences

abstract: In this contribution, some applications of the earlier developed fast algorithm of calculating coordinates of single nucleotides and RNA fragments are considered to create multi-scale geometrical models of RNAs and their mutations. The algorithm allows to plot single nucleotides and RNAs fragments on one figure and to track the RNA mutations of any level visually and numerically using interpolation formulas and point-to-point estimates of coordinates of ATG starting triplets and single nucleotides. The performed study of many samples of SARS CoV-2 viruses shows perturbations of ATG starting triplet coordinates in the vicinity of orf1ab gene end only.

category: genomics


title: Comparative genomics of three Colletotrichum scovillei strains and genetic analysis revealed genes involved in fungal growth and virulence on chili pepper

abstract:
Colletotrichum scovillei is a virulent pathogen and the dominant species causing anthracnose of chili pepper in many Asian countries. Three strains of this pathogen, Coll-524, Coll-153 and Coll-365, show varied virulence on chili pepper fruit. Among the three strains, Coll-365 showed significant defects in growth and virulence. To decipher the genetic variations among these strains and identify genes contributing to growth and virulence, in this study, comparative genomic analysis and gene transformation to verify gene function were applied. The genomes of the three strains were sequenced and Coll-524 had 1.3% and 1.5% more genes than Coll-153 and Coll-365, respectively. Compared to Coll-524 and Coll-153, Coll-365 had numerous gene losses including 33 effector genes that are distributed in different scaffolds and a cluster of 14 genes in a 34-kb genomic fragment. Through gene transformation, three genes in the 34-kb fragment were identified to have functions in growth and/or virulence of C. scovillei. Gene 15019 encoding a protein related to phospholipase A2-activating protein enhanced the growth of Coll-365. A combination of 15019 with one transcription factor gene 15022 and one C6 zinc finger domain-containing protein gene 15029 was found to enhance the pathogenicity of Coll-365. Introduction of gene 15215, which encodes a LysM domain-containing protein, into Coll-365 caused a reduction in the germination rate of Coll-365. In conclusion, the higher virulent strain Coll-524 had more genes and encoded more pathogenicity related proteins and transposable elements than the other two strains, which may contribute to the high virulence of Coll-524. In addition, the absence of the 34-kb fragment plays a critical role in the defects of growth and virulence of strain Coll-365.

Author SummaryColletotrichum scovillei is a highly virulent and dominant pathogen causing anthracnose of chili that leads to significant economic loss in chili production in many Asia countries. In this study we focus on finding the gene differences of three C. scovillei strains with different pathogenicity in chili pepper infection and verifying the function of some genes in the lowest virulence strain. We sequenced them and did gene annotation and genome comparison. We setup a simple mathematical method to identify gene variations between strong and weak virulence strains. Our results show that the lowest virulence strain has less pathogenicity-related genes. We also found that the absence of 14 genes in a compact genomic fragment was part of the reason of growth and virulence defect of the lowest virulence strain. We identified four genes that play roles on fungal growth and/or virulence on chili pepper. We also found a group of effector genes that specifically appear in species collected form infected chili in C. acutatum species complex. Our research provides detailed information for why the three strains have different virulence on chili pepper.


title: HLA class II mediates type 1 diabetes risk by anti-insulin repertoire selection

abstract: Type 1 diabetes (T1D) is a common autoimmune disorder characterized by the destruction of insulin-secreting pancreatic {beta} cells [1], in which polymorphism of the human leukocyte antigen (HLA) class II region is the major genetic risk factor [2, 3, 4]. However, how variation in class II molecules alters T1D risk remains a longstanding question. Here we show how T1D risk due to HLA class II haplotype combinations [5] correlates with the frequency of negatively charged sequences in the CDR3{beta} region of CD4+ T cell receptor (TCR) repertoires purified from peripheral blood. These sequences are known to be common in receptors that bind insulin B:9-23 [6], the primary autoantigen in T1D. We also show the same effect in circulating activated CD4+ T cells from newly-diagnosed T1D cases, and in islet-infiltrating T cells from patients with active T1D. Furthermore, we demonstrate that the proportion of insulin-reactive CD4+ T cells present in islets is predicted by the frequency of these negatively charged CDR3{beta} amino acid sequences. Our results suggest diagnostic uses of T cell repertoire profiling in early detection of insulin autoimmunity, and inform ongoing efforts to improve tolerance induction to insulin and prevention of T1D [7].


title: Biochemical characterization of a human septin octamer

abstract:
1Septins are part of the cytoskeleton and polymerize into non-polar filaments of heteromeric hexamers or octamers. They belong to the class of P-loop GTPases but the roles of GTP binding and hydrolysis on filament formation and dynamics are not well understood.

The basic human septin building block is the septin rod, a hetero-octamer composed of SEPT2, SEPT6, SEPT7, and SEPT9 with a stoichiometry of 2:2:2:2 (2-7-6-9-9-6-7-2).

Septin rods polymerize by end-to-end and lateral joining into linear filaments and higher ordered structures such as rings, sheets, and gauzes.

We purified a recombinant human septin octamer from E. coli for in vitro experimentation that is able to polymerize into filaments. We could show that the C-terminal region of the central SEPT9 subunit contributes to filament formation and that the human septin rod decreases the rate of in vitro actin polymerization.

We provide further first kinetic data on the nucleotide uptake- and exchange properties of human hexameric and octameric septin rods. We could show that nucleotide uptake prior to hydrolysis is a dynamic process and that a bound nucleotide is exchangeable. However, the hydrolyzed {gamma}-phosphate is not released from the native protein complex. We consequently propose that GTP hydrolysis in human septins does not follow the typical mechanism known from other small GTPases.

category: biochemistry


title: Prider - multiplexed primer design using linearly scaling approximation of set coverage

abstract:
Designing oligonucleotide primers and probes is one of the key steps of various laboratory experiments such as multiplexed PCR or digital multiplexed ligation assays. When designing primers and probes to complex, heterogeneous DNA data sets, an optimization problem arises where the smallest number of oligonucleotides covering the largest diversity of the input dataset needs to be identified. Tools that provide this optimization in an efficient manner for large input data are currently lacking.

Here we present Prider, an R package for designing primers and probes with a nearly optimal coverage for complex and large sequence sets. Prider initially prepares a full primer coverage of the input sequences, the complexity of which is subsequently reduced by removing components of high redundancy or narrow coverage. The primers from the resulting near-optimal coverage are easily accessible as data frames and their coverage across the input sequences can be visualized as heatmaps using Priders plotting function. Prider scales linearly to increasing sequence data and therefore permits efficient design of primers to large and highly diverse DNA datasets.

Prider is available on GitHub under the permissive BSD-3-clause license:

https://github.com/manutamminen/prider


title: Design and Computational Analysis of a Chimeric Avian Influenza Antigen: A Yeast-displayed, Universal and Cross-protective Vaccine Candidate

abstract:
BackgroundA cross-protective avian influenza vaccine candidate can be designed by using a preserved antigen against mutation in various subtypes of influenza. M2e peptide sequence has remained remarkably unchanged in influenza type A isolated since 1918.

MethodsA consensus sequence of M2e peptide was obtained from 31 sequences of H5N8, H5N1, H9N2 and H7N9 subtypes of avian influenza virus isolated from 7 avian species in 5 Asian countries. A partial sequence of flagellin was considered as an adjuvant. Subsequently, two chimeric antigens were designed to be virtually cloned and expressed using PYD1 vector and EBY100 yeast strain. The stability and conformational features of these two antigens were assessed through molecular dynamic (MD) simulations. The detectability of vaccine candidates by a specific monoclonal antibody (MAb148) were estimated through docking studies.

ResultsIn spite of significant compactness and stability of the first candidate in comparison with the second design, it was less detectable by MAb148. Contrary to the first chimeric antigen, Van der Waals, electrostatic and binding energies of the interaction of the second antigen with MAb148 were significantly closer to the positive control. It is shown that epitopes of the second chimeric antigen could be correctly located in the specific pocket of CDR region of MAb148.

ConclusionThe second chimeric antigen could be considered as a yeast-displayed avian influenza vaccine candidate due to the capability of provoking humoral immunity and innate immune system by M2e and flagellin respectively.


title: Quantifying Intratumor Heterogeneity by Key Genes Selected Using Concrete Autoencoder

abstract: The tumor cell population in a cancer tissue has distinct molecular characteristics and exhibits different phenotypes, thus, resulting in different subpopulations. This phenomenon is known as Intratumor Heterogeneity (ITH), which is a major contributor in drug resistance, poor prognosis, etc. Therefore, quantifying the levels of ITH in cancer patients is essential and there are many algorithms which do so in different ways, using different types of omics data. DEPTH (Deviating gene Expression Profiling Tumor Heterogeneity) is the latest algorithm that uses transcriptomic data to evaluate the ITH score. It shows promising performance, has strong similarity with six other algorithms, and has advantage over two algorithms that uses same type of data (tITH, sITH). However, it has a major drawback that it uses expression values of all the genes ([~]20K genes) in quantifying ITH levels. We hypothesize that a subset of key genes is sufficient to quantify the ITH level for a tumor. To prove our hypothesis, we developed a deep learning-based computational framework using unsupervised Concrete Autoencoder (CAE) to select a set of cancer-specific key genes that can be used to evaluate the ITH score. For experiment, we used gene expression profile data of tumor cohorts of breast, kidney and lung cancer from TCGA repository. We selected three sets of key genes, each set related to breast, kidney, and lung tumor cohorts, using multi-run CAE. For the three cancers stated and three molecular subtypes of lung cancer, we calculated ITH level using all genes and key genes selected by CAE and performed a side-by-side comparison. It was found that similar conclusions can be reached for survival and prognostic outcomes based on ITH scores derived from all genes and the sets of key genes. Additionally, for subtypes of lung cancer, the comparative distribution of ITH scores derived from all genes and key genes remains similar. Based on these observations, it can be stated that, a subset of key genes, instead of all genes, is sufficient for ITH quantification. Our results also showed that many of the key genes are prognostically significant, which can be used as possible therapeutic targets.


title: Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution

abstract: Interpretation of non-coding genome remains an unsolved challenge in human genetics due to impracticality of exhaustively annotate biochemically active elements in all conditions. Deep learning based computational approaches emerge recently to help interpretating non-coding regions. Here we present LOGO (Language of Genome), a self-attention based contextualized pre-trained language model containing only 2 self-attention layers with 1 million parameters as a substantially light architecture that applies self-supervision techniques to learn bidirectional representations of unlabeled human reference genome. LOGO is then fine-tuned for sequence labelling task, and further extended to variant prioritization task via a special input encoding scheme of alternative alleles followed by adding a convolutional module. Experiments show that LOGO achieves 15% absolute improvement for promoter identification and up to 4.5% absolute improvement for enhancer-promoter interaction prediction. LOGO exhibits state-of-the-art multi-task predictive power on thousands of chromatin features with only 3% parameterization benchmarking against fully supervised model, DeepSEA and 1% parameterization against a recent BERT-based language model for human genome. For allelic-effect prediction, locality introduced by one dimensional convolution shows improved sensitivity and specificity for prioritizing non-coding variants associated with human diseases. In addition, we apply LOGO to interpret type 2 diabetes (T2D) GWAS signals and infer underlying regulatory mechanisms. We make a conceptual analogy between natural language and human genome and demonstrate LOGO is an accurate, fast, scalable, and robust framework to interpret non-coding regions for global sequence labeling as well as for variant prioritization at base-resolution.


title: Exploring Intuitive Approaches to Protein Conformation Clustering Using Regions of High Structural Variance

abstract:
This paper presents a method to find structurally high variance segments of the different conformations of a single protein and uses clusters them using different distance metrics and interpretation of coordinate and angle data presented by three different methods: root mean squared derivation RMSD, t-distributed Stochastic Neighbor Embedding (t-SNE) based map, and dihedral-based clustering. The methods were applied on the human cylin-dependent kinase 2 (CDK2) protein, code P24941 uniprot using a series of python scripts and clustering packages. We test our methods on the data of the CDK2 protein as it is a highly researched protein, with practical applications of clustering in cancer research, crucial in the regulation of the cell-cycle, and has a sizeable amount of experimental data collected on the confirmation structures.

While using the distance based root mean squared deviation RMSD provides data of structure to structure dissimilarity between different conformations, a simple RMSD matrix lacks to ability to describe the subsequence-wise in shape and absolute position which could be the main identifying elements for a proteins conformation and state. To make up for this loss we explore an intuitive and more flexible method, able to accept multiple high structural variance segments, which takes coordinate based data, through a series of maps and with the help of t-SNE, and maps each segment as a feature in the clustering matrix. This method, however, would require additional testing on other proteins and modifications to verify its consistency and test its robustness.

In the end we explore the pros and cons of the three methods applied on the high structural variance regions. Despite the randomness factor by the t-SNE used in mapping the coordinates to lower dimensions, the coordinate-based approach consistently performed better than the RSMD and dihedral based methods in clustering the three groups of the CDK2 protein kinase. We also found that analyzing only the substructures identified by the high variance detection algorithm consistently provided more distinct clusters with higher multi-class F1 scores.


title: PIPENN: Protein Interface Prediction with an Ensemble of Neural Nets

abstract:
MotivationProtein interactions play an essential role in many biological and cellular processes, such as protein-protein interaction (PPI) in signaling pathways, binding to DNA in transcription, and binding to small molecules in receptor activation or enzymatic activity. Experimental identification of protein binding interface residues is a time-consuming, costly, and challenging task. Several machine learning and other computational approaches exist which predict such interface residues. Here we explore if Deep Learning (DL) can be used effectively for this prediction task, and which learning strategies and architectures may be most efficient. We introduce seven DL architectures that are applied to eleven independent test sets, focused on the residues involved in PPI interfaces and in binding RNA/DNA and small molecule ligands.

ResultsWe constructed a large data set dubbed BioDL, comprising protein-protein interaction data from the PDB and protein-ligand interactions (DNA, RNA and small molecules) from the BioLip database. Additionally, we reused our existing curated homo- and heteromeric PPI data sets. We performed several experiments to assess the impact of different data features, spatial forms, encoding schemes, network initializations, loss functions, regularization mechanisms, and activation functions on the performance of the predictors. Benchmarking the resulting DL models with an independent test set (ZK448) shows no single DL architecture performs best on all instances, but that an ensemble of DL architectures consistently achieves peak prediction performance. Our PIPENNs ensemble predictor outperforms current state-of-the-art sequence-based protein interface predictors on all interaction types, achieving AUCs of 0.718 (protein-protein), 0.823 (protein-nucleotide) and 0.842 (protein- small molecule) respectively.

AvailabilitySource code and data sets at https://github.com/ibivu/pipenn/

Contactr.haydarlou@vu.nl


title: Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data

abstract: Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost, exemplified by well over a half of million ONT SARS-COV-2 datasets. Tracking low frequency intra-host variants has provided important insights with respect to elucidating within host viral population dynamics and transmission. However, given the higher error rate of ONT, accurate identification of intra-host variants with low allele frequencies remains an open challenge with no viable solutions available. In response to this need, we present Variabel, a novel approach and first method designed for rescuing low frequency intra-host variants from ONT data alone. We evaluated Variabel on both within patient and across patient paired Illumina and ONT datasets; our results show that Variabel can accurately identify low frequency variants below 0.5 allele frequency, outperforming existing state-of-the-art ONT variant callers for this task. Variabel is open-source and available for download at: www.gitlab.com/treangenlab/variabel.