TOXIFY: a deep learning approach to classify animal venom proteins

In the era of Next-Generation Sequencing and shotgun proteomics, the sequences of animal toxigenic proteins are being generated at rates exceeding the pace of traditional means for empirical toxicity verification. To facilitate the automation of toxin identification from protein sequences, we trained Recurrent Neural Networks with Gated Recurrent Units on publicly available datasets. The resulting models are available via the novel software package TOXIFY, allowing users to infer the probability of a given protein sequence being a venom protein. TOXIFY is more than 20X faster and uses over an order of magnitude less memory than previously published methods. Additionally, TOXIFY is more accurate, precise, and sensitive at classifying venom proteins

Expression of mitochondrial branched-chain aminotransferase and α-keto-acid dehydrogenase in rat brain: implications for neurotransmitter metabolism

In the brain, metabolism of the essential branched chain amino acids (BCAAs) leucine, isoleucine, and valine, is regulated in part by protein synthesis requirements. Excess BCAAs are catabolized or excreted. The first step in BCAA catabolism is catalyzed by the branched chain aminotransferase (BCAT) isozymes, mitochondrial BCATm and cytosolic BCATc. A product of this reaction, glutamate, is the major excitatory neurotransmitter and precursor of the major inhibitory neurotransmitter γ-aminobutyric acid (GABA). The BCATs are thought to participate in a α-keto-acid nitrogen shuttle that provides nitrogen for synthesis of glutamate from α-ketoglutarate. The branched-chain α-keto acid dehydrogenase enzyme complex (BCKDC) catalyzes the second, irreversible step in BCAA metabolism, which is oxidative decarboxylation of the branched-chain α-keto acid (BCKA) products of the BCAT reaction. Maple Syrup Urine Disease (MSUD) results from genetic defects in BCKDC, which leads to accumulation of toxic levels of BCAAs and BCKAs that result in brain swelling. Immunolocalization of BCATm and BCKDC in rats revealed that BCATm is present in astrocytes in white matter and in neuropil, while BCKDC is expressed only in neurons. BCATm appears uniformly distributed in astrocyte cell bodies throughout the brain. The segregation of BCATm to astrocytes and BCKDC to neurons provides further support for the existence of a BCAA-dependent glial-neuronal nitrogen shuttle since the data show that BCKAs produced by glial BCATm must be exported to neurons. Additionally, the neuronal localization of BCKDC suggests that MSUD is a neuronal defect involving insufficient oxidation of BCKAs, with secondary effects extending beyond the neuron

Measuring the Cosmic Equation of State with Counts of Galaxies

The classical dN/dz test allows the determination of fundamental cosmological parameters from the evolution of the cosmic volume element. This test is applied by measuring the redshift distribution of a tracer whose evolution in number density is known. In the past, ordinary galaxies have been used as such a tracer; however, in the absence of a complete theory of galaxy formation, that method is fraught with difficulties. In this paper, we propose studying instead the evolution of the apparent abundance of dark matter halos as a function of their circular velocity, observable via the linewidths or rotation speeds of visible galaxies. Upcoming redshift surveys will allow the linewidth distribution of galaxies to be determined at both z~1 and the present day. In the course of studying this test, we have devised a rapid, improved semi-analytic method for calculating the circular velocity distribution of dark halos based upon the analytic mass function of Sheth et al. (1999) and the formation time distribution of Lacey & Cole (1993). We find that if selection effects are well-controlled and minimal external constraints are applied, the planned DEEP Redshift Survey should allow the measurement of the cosmic equation-of-state parameter w to 10% (as little as 3% if Omega_m has been well-determined from other observations). This type of test has the potential also to provide a constraint on any evolution of w such as that predicted by ``tracker'' models.Comment: 4 pages plus 3 embedded figures; version approved by Ap. J. Letters. A greatly improved error analysis has been added, along with a figure showing complementarity to other cosmological test

Glucose-6-phosphate reduces calcium accumulation in rat brain endoplasmic reticulum

Brain cells expend large amounts of energy sequestering calcium (Ca2+), while loss of Ca2+ compartmentalization leads to cell damage or death. Upon cell entry, glucose is converted to glucose-6-phosphate (G6P), a parent substrate to several metabolic major pathways, including glycolysis. In several tissues, G6P alters the ability of the endoplasmic reticulum (ER) to sequester Ca2+. This led to the hypothesis that G6P regulates Ca2+ accumulation by acting as an endogenous ligand for sarco-endoplasmic reticulum calcium ATPase (SERCA). Whole brain ER microsomes were pooled from adult male Sprague-Dawley rats. Using radio-isotopic assays, 45Ca2+ accumulation was quantified following incubation with increasing amounts of G6P, in the presence or absence of thapsigargin, a potent SERCA inhibitor. To qualitatively assess SERCA activity, the simultaneous release of inorganic phosphate (Pi) coupled with Ca2+ accumulation was quantified. Addition of G6P significantly and decreased Ca2+ accumulation in a dose-dependent fashion (1–10 mM). The reduction in Ca2+ accumulation was not significantly different that seen with addition of thapsigargin. Addition of glucose-1-phosphate or fructose-6-phosphate, or other glucose metabolic pathway intermediates, had no effect on Ca2+ accumulation. Further, the release of Pi was markedly decreased, indicating G6P-mediated SERCA inhibition as the responsible mechanism for reduced Ca2+ uptake. Simultaneous addition of thapsigargin and G6P did decrease inorganic phosphate in comparison to either treatment alone, which suggests that the two treatments have different mechanisms of action. Therefore, G6P may be a novel, endogenous regulator of SERCA activity. Additionally, pathological conditions observed during disease states that disrupt glucose homeostasis, may be attributable to Ca2+ dystasis caused by altered G6P regulation of SERCA activity

Severity of Depression Predicts Remission Rates Using Transcranial Magnetic Stimulation

Background: Multiple factors likely impact response and remission rates in the treatment of depression with repetitive transcranial magnetic stimulation (rTMS). Notably the role of symptom severity in outcomes with rTMS is poorly understood.Objective/Hypothesis: This study investigated the predictors of achieving remission in patients suffering from depression who receive ≥3 rTMS treatments per week. Methods: Available data on 41 patients treated at Walter Reed National Military Medical Center from 2009 to 2014 were included for analysis. Patients received a range of pulse sequences from 3,000 to 5,000 with left sided or bilateral coil placement. Primary outcome measures were total score on the Patient Health Questionnaire (PHQ-9) or the Quick Inventory of Depressive Symptomatology—Self Rated (QIDS-SR). Remission was defined as a total score less than five, and response was defined as a 50% decrease in the total score on both outcome metrics. Outcomes in patients diagnosed as suffering from mild or moderate depression were compared to those suffering from severe depression. Results: Of the 41 patients receiving treatment, 16 reached remission by the end of treatment. Remission rate was associated with the initial severity of depression, with patients with mild or moderate depression reaching remission at a significantly higher rate than those with severe depression. Total number of rTMS sessions or length of treatment were not predictors of remission. Conclusion: Patients with a baseline level of depression characterized as mild or moderate had significantly better outcomes following rTMS compared to patients with severe depression

The cytokine temporal profile in rat cortex after controlled cortical impact

Cerebral inflammatory responses may initiate secondary cascades following traumatic brain injury (TBI). Changes in the expression of both cytokines and chemokines may activate, regulate, and recruit innate and adaptive immune cells associated with secondary degeneration, as well as alter a host of other cellular processes. In this study, we quantified the temporal expression of a large set of inflammatory mediators in rat cortical tissue after brain injury. Following a controlled cortical impact (CCI) on young adult male rats, cortical and hippocampal tissue of the injured hemisphere and matching contralateral material was harvested at early (4, 12, and 24 hours) and extended (3 and 7 days) time points post-procedure. Naïve rats that received only anesthesia were used as controls. Processed brain homogenates were assayed for chemokine and cytokine levels utilizing an electrochemiluminescence-based multiplex ELISA platform. The temporal profile of cortical tissue samples revealed a multi-phasic injury response following brain injury. CXCL1, IFN-γ, TNF-α levels significantly peaked at four hours post-injury compared to levels found in naïve or contralateral tissue. CXCL1, IFN-γ, and TNF-α levels were then observed to decrease at least 3-fold by 12 hours post-injury. IL-1β, IL-4, and IL-13 levels were also significantly elevated at four hours post-injury although their expression did not decrease more than 3-fold for up to 24 hours post-injury. Additionally, IL-1β and IL-4 levels displayed a biphasic temporal profile in response to injury, which may suggest their involvement in adaptive immune responses. Interestingly, peak levels of CCL2 and CCL20 were not observed until after four hours post-injury. CCL2 levels in injured cortical tissue were significantly higher than peak levels of any other inflammatory mediator measured, thus suggesting a possible use as a biomarker. Fully elucidating chemokine and cytokine signaling properties after brain injury may provide increased insight into a number of secondary cascade events that are initiated or regulated by inflammatory responses

Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock

Whole-genome sequencing has provided fundamental insights into infectious disease epidemiology, but has rarely been used for examining transmission dynamics of a bacterial pathogen in wildlife. In the Greater Yellowstone Ecosystem (GYE), outbreaks of brucellosis have increased in cattle along with rising seroprevalence in elk. Here we use a genomic approach to examine Brucella abortus evolution, cross-species transmission and spatial spread in the GYE. We find that brucellosis was introduced into wildlife in this region at least five times. The diffusion rate varies among Brucella lineages (∼3 to 8 km per year) and over time. We also estimate 12 host transitions from bison to elk, and 5 from elk to bison. Our results support the notion that free-ranging elk are currently a self-sustaining brucellosis reservoir and the source of livestock infections, and that control measures in bison are unlikely to affect the dynamics of unrelated strains circulating in nearby elk populations

ESAT-6 Secretion-Independent Impact of ESX-1 Genes espF and espG1 on Virulence of Mycobacterium tuberculosis

Background. The pathogenesis of Mycobacterium tuberculosis largely depends on the secretion of the 6-kD early secreted antigenic target ESAT-6 (EsxA) and the 10-kD culture filtrate protein CFP-10 (EsxB) via the ESX-1/typeVII secretion system. Although gene products from the core RD1 region have been shown to be deeply implicated in this process, less is known about proteins encoded further upstream in the 5′ region of the ESX-1 cluster, such as the ESX-1 secretion-associated proteins (Esps) EspF or EspG1. Methods. To elucidate the role of EspF/G1, whose orthologs in Mycobacterium marinum and Mycobacterium smegmatis are reportedly involved in EsxA/B secretion, we constructed 3 M. tuberculosis knockout strains deleted for espF, espG1 or the segment corresponding to the combined RD1bcg-RD1mic region of bacille Calmette-Guérin (BCG) and Mycobacterium microti, which also contains espF and espG1. Results. Analysis of these strains revealed that, unlike observations with the model organisms M. smegmatis or M. marinum, disruption of espF and espG1 in M. tuberculosis did not impact the secretion and T cell recognition of EsxA/B but still caused severe attenuation. Conclusions. The separation of the 2 ESX-1-connected phenotypes (ie, EsxA/B secretion and virulence) indicates that EsxA/B secretion is not the only readout for a functional ESX-1 system and suggests that other processes involving EspF/G1 also play important roles in ESX-1-mediated pathogenicit

Spatial and Temporal Variations of Microplastics within Humboldt Bay, California

This study aimed to quantify microplastic (MP) concentration and analyze the spatial and temporal variabilities of the concentrations during the tidal cycle in Humboldt Bay, California. To get an approximation of MP concentration, both water and sediment samples were taken at five different stations, twice during one tidal cycle. Sampling was conducted during two different cruises, on the 19th and 21st of September 2020. The samples were processed in the lab using a density separation procedure and filtration. MP concentrations in the different samples were determined using an average optical microscopy count. Comparison of the water column MP concentrations during ebb and flood tides shows higher concentrations during flood tide, 49.0 particles/L ± 32.37 (flood) vs 34.4 particles/L ± 16.32 (ebb), indicating that MPs are brought into Humboldt Bay from the ocean. The comparison of the MP concentrations during lower energy and higher energy conditions indicates that concentrations in the water column were elevated when there was greater tidal kinetic energy, approximated by the covariance of the measured velocity in North Bay Channel. This result was assumed to be caused by the strong tidal currents stirring up both sediments and the settled MPs into the water column. Due to lower tidal kinetic energy on the sediment sampling cruise day, we could not confirm that assumption. Water samples indicated that MPs are heterogeneously distributed in the bay, with higher concentrations found near the Entrance Channel and lower concentrations found further north in the bay. Sediment samples also indicate a heterogeneous distribution of MPs in the bay, with the lowest concentrations near the Entrance Channel, 15 particles/kg, where high tidal currents inhibit settling of particles