title: Stochastic dynamics of social patch foraging decisions

abstract: Animals typically forage in groups. Social foraging can help animals avoid predation and decrease their uncertainty about the richness of food resources. Despite this, theoretical mechanistic models of patch foraging have overwhelmingly focused on the behavior of single foragers. In this study, we develop a mechanistic model that accounts for the behavior of individuals foraging together and departing food patches following an evidence accumulation process. Each individuals belief about patch quality is represented by a stochastically accumulating variable which is coupled to others belief to represent the transfer of information. We consider a cohesive group, and model information sharing by considering both intermittent pulsatile coupling (only communicate decision to leave) and continuous diffusive coupling (communicate throughout the evidence accumulation process). We find that foraging efficiency under pulsatile coupling has a stronger dependence on the coupling strength parameter compared to diffusive. Despite employing minimal information transfer, pulsatile coupling can still provide similar or higher foraging efficiency compared to diffusive coupling. Conversely, since diffusive coupling is more robust to parameter choices, it performs better when individuals have heterogeneous departure criteria and social information weighting. Efficiency is measured by a reward rate function that balances the amount of energy accumulated against the time spent in a patch, computed by solving an ordered first passage time problem for the patch departures of each individual. Using synthetic data we show that we can distinguish between the two modes of communication and identify the model parameters. Our model establishes a social patch foraging framework to parse and identify deliberative decision strategies, to distinguish different forms of social communication, and to allow model fitting to real world animal behavior data.

category: animal behavior and cognition


title: pkgndep: a tool for analyzing dependency heaviness of R packages

abstract:
SummaryNumerous R packages have been developed for bioinformatics analysis in the last decade and dependencies among packages have become critical issues to consider. In this work, we proposed a new metric named dependency heaviness that measures the number of unique dependencies that a parent brings to a package, and we proposed possible solutions for reducing the complexity of dependencies by optimizing the use of heavy parents. We implemented the metric in a new R package pkgndep which provides an intuitive way for dependency heaviness analysis. Based on pkgndep, we additionally performed a global analysis of dependency heaviness on CRAN and Bioconductor ecosystems and we revealed top packages that have significant contributions of high dependency heaviness to their child packages.

Availability and implementationThe package pkgndep and documentations are freely available from the Comprehensive R Archive Network (CRAN) https://cran.r-project.org/package=pkgndep. The dependency heaviness analysis for all 21,741 CRAN and Bioconductor packages retrieved on 2021-10-28 are available at https://pkgndep.github.io/.

category: bioinformatics


title: pkgndep: a tool for heaviness analysis on R package dependencies


title: Stress-induced phase separation of ERES components into Sec bodies precedes ER exit inhibition in mammalian cells.

abstract: Phase separation of ER-exit-sites (ERES) components into membraneless compartments, the Sec bodies, occurs in Drosophila cells upon specific cellular stressors, i.e., salt stress and amino acid starvation, and their formation is linked to the inhibition of the early secretory pathway. Here, we show Sec bodies also form in secretory mammalian INS-1 cells upon the same stress. These reversible and membraneless structures are positive for ERES components, including both isoforms of Sec16 (A and B) and COPII subunits. We find that Sec16A, but not Sec16B, is a driver for Sec body formation. We show that the coalescence of ERES components into Sec bodies occurs by fusion, in line with their liquid-droplet properties. Lastly, we demonstrate that stress-induced ER-exit inhibition is a consequence of the significant coalescence of Sec16A into Sec bodies, leading to its depletion from ERES that become non-functional. Stress relief causes an immediate dissolution of Sec bodies and the concomitant restoration of protein exit from the ER. We propose a model in which dynamic conversion between ERES and Sec body assembly, driven by Sec16A, regulates protein exit from the ER during stress and upon stress relief in mammalian cells, thus providing a conserved pro-survival mechanism in response to stress.

category: cell biology


title: Environmental contributions to the evolution of trait differences in Geum triflorum: implications for restoration

abstract:
Premise of the StudyUnderstanding how environment influences the distribution of trait variation across a species range has important implications for seed transfer during restoration. Heritable genetic differences associated with environment could impact fitness when transferred into new environments. Here, we test the degree to which the environment shapes the evolution and distribution of genetic effects for traits important to adaptation.

MethodsIn a common garden experiment, we quantified trait differentiation for populations of Geum triflorum sourced from three distinct ecoregions and evaluated the ability of climate to predict trait variation. Populations were sourced from alvar ecoregions which experience predictable extremes in seasonal water availability and the prairie ecoregion which exhibits unpredictable changes in water availability.

Key ResultsPlants sourced from alvar ecoregions exhibited smaller but more numerous stomata and greater intrinsic water use efficiency relative to prairie plant populations supporting the evolution of ecotypic differences. Estimates of standing genetic variance and heritable genetic variation for quantitative traits suggest alvar populations have greater adaptive potential. However, reduced evolvability suggest all populations of G. triflorum may have limited capacity to evolve in response to environmental change.

ConclusionsThese results point towards the importance of understanding the role of environment in shaping the distribution and evolution of genetic differences across seed populations and how these data may inform recommendations for seed transfer across novel environments and our expectations of populations adaptive potential.

category: evolutionary biology


title: Generation and validation of an anti-human PANK3 mouse monoclonal antibody

abstract: Coenzyme A (CoA) is an essential co-factor at the intersection of diverse metabolic pathways. Cellular CoA biosynthesis is regulated at the first committed step-- phosphorylation of pantothenic acid--catalyzed by pantothenate kinases (PANK1,2,3 in humans, PANK3 being the most highly expressed). Despite the critical importance of CoA in metabolism, the differential roles of PANK isoforms remain poorly understood. Our investigations of PANK proteins as precision oncology collateral lethality targets (PANK1 is co-deleted as part of the PTEN locus in some highly aggressive cancers) were severely hindered by a dearth of commercial antibodies that can reliably detect endogenous PANK3. While we successfully validated commercial antibodies for PANK1 and PANK2 using CRISPR knockout cell lines, we found no commercial antibody that could detect endogenous PANK3. We therefore set out to generate a mouse monoclonal antibody against human PANK3 protein. We demonstrate that clone (Clone MDA-299-62A) can reliably detect endogenous PANK3 protein in cancer cell lines, with band-specificity confirmed by CRISPR PANK3 knockout cell lines. Sub-cellular fractionation indicates that PANK3 is overwhelmingly cytosolic and expressed broadly across cancer cell lines. PANK3 monoclonal antibody MDA-299-62A should prove a valuable tool for researchers investigating this understudied family of metabolic enzymes in health and disease.

category: biochemistry


title: High-Resolution Tandem Mass Spectrometry Indicates Rubisco Activase is Associated with PS I-LHC I-LHC II Membranes

abstract: During proteomic investigations examining the mobile LHC II chlorophyll antenna complex associated with Photosystem I (PS I), we identified, with very high confidence, the association of Rubisco Activase with PS I-LHC I-LHC II membranes. Using very rigorous criteria (p-values [≤] 10-5), a total of fifty-three high-quality Rubisco Activase peptides were identified by high resolution tandem mass spectrometry in two biological replicates, each digested with either trypsin or chymotrypsin, independently. Using these criteria, and searching the entire spinach proteome, only proteins previously known to be associated with PS I (the PS I subunits PsaD and PsaL, Lhca1-4, Lhcb1-3), the monomeric Lhcb proteins, Lhcb4-6 (which will be discussed elsewhere), and Rubisco Activase were identified. The presence of Rubisco Activase closely associated with PS I has important implications with respect to the activation of this enzyme and, consequently, the Calvin cycle by PS I, which will be discussed.


title: Substrate Binding and Inhibition of the Anion Exchanger 1 Transporter

abstract: Anion Exchanger 1 (AE1, SLC4A1) is the primary bicarbonate (HCO3-) transporter expressed in erythrocyte membranes where it mediates transport of CO2 between lungs and other tissues via import/export of bicarbonate. It is also a key regulator of erythrocyte structure and antigenic recognition. Previous biochemical studies, and a low-resolution crystal structure of the transmembrane domain have provided initial insight into AE1 structure and function. However, key questions remain regarding substrate binding and transport as well as the mechanism of inhibition. The orientation of the intracellular domain as well as the localization of lipid and sterol binding sites also remain enigmatic. We herein present seven novel high resolution cryo-EM structures of the full length human transporter in the apo, bicarbonate-bound, and several inhibitor-bound states combined with uptake- and computational studies. To our knowledge, these studies represent the first full length human, and substrate bound, SLC4 transporter structure. Our results reveal important molecular details about substrate binding and transport, as well as the diverse mechanisms of AE1 inhibition by both research chemicals and prescription drugs. We also provide novel insights into the full-length transporter architecture, identify the conformational space of the Diego blood antigen system and elucidate multiple lipid and sterol binding sites.


title: Two-pore channel blockade by phosphoinositide kinase inhibitors YM201636 and PI-103 determined by a histidine residue near pore-entrance

abstract: Human two-pore channels (TPCs) are endolysosomal cation channels and play an important role in NAADP-evoked Ca2+ release and endomembrane dynamics. TPCs are activated by PI(3,5)P2, which is synthesized by PIKfyve. Here, we found that YM201636, a widely used PIKfyve inhibitor, potently inhibits PI(3,5)P2-induced human TPC2 channel Na+ currents in a dose-dependent manner with an IC50 of 0.16 M. YM201636 also effectively inhibits the currents of a constitutively open TPC2 mutant channel, whereas it exerts no effect when applied in the channels closed state. A YM201636 analog, PI-103, an inhibitor of PI3K and mTOR, also inhibits human TPC2 with an IC50 of 0.64 M. Substitution of the pore-constriction residues Leu690, Leu694 and Tyr312 by Ala reduced the effectiveness of YM201636 and PI-103 in channel inhibition. Interestingly, a His699 residue located near the cytosolic pore entrance is a key determinant for the TPC2 channels sensitivity to YM201636 and PI-103, whose substitution with a Phe in the human TPC1 largely accounts for the channels loss of inhibition by YM201636. Molecular dynamic simulation and docking analysis of YM201636s binding to TPC2 indicated that His699 can interact with the inhibitor and facilitate the channel-blockade at the cytosolic end of the pore. We conclude that YM201636 and PI-103 directly block the TPC2s open-state channel pore at the cytosolic entrance where the His699 is a key determinant for the blockers access to the pore. These findings identify two new potent TPC2 channel blockers, reveal a channel pore entrance blockade mechanism, and provide a new protein target in interpreting the pharmacological effects of these two widely used phosphoinositide kinase inhibitors.


title: Single Cell Proteomics Using a Trapped Ion Mobility Time-of-Flight Mass Spectrometer Provides Insight into the Post-translational Modification Landscape of Individual Human Cells

abstract:
Single cell proteomics is a powerful tool with potential for markedly enhancing understanding of cellular processes. Previously reported single cell proteomics innovations employ Orbitrap mass spectrometers. In this study we describe the development, optimization, and application of multiplexed single cell proteomics to the analysis of human-derived cells using trapped ion mobility time-of-flight mass spectrometry. This method, denoted as pasefRiQ is an advance as it allows accurate peptide quantification as demonstrated by a two-proteome standard model, with little variation in accuracy in samples at picogram peptide concentrations. When employing a peptide carrier channel to boost protein sequence coverage, we obtain over 40,000 tandem mass spectra in 30 minutes, providing unprecedented sequence coverage of each identified protein. Using NCI-H-358 cells, which are a human bronchioalveolar carcinoma and KRASG12C model cell line, we demonstrate that the level of coverage achieved using this method enables the quantification of up to 1,255 proteins per cell and the detection of multiple classes of post-translational modifications in single cells. Further, when the cells were treated with AMG510, a KRASG12C covalent inhibitor, pasefRiQ revealed cell-to-cell variability in the impact of the drug on the NCI-H-358 proteome. In fact, when examining proteins that changed in protein abundance in response to AMG510 we can identify those that are disproportionately increased or decreased in a small number of cells relative to the total population of cells that were cultured and treated simultaneously. These results suggest single cell proteomics through pasefRiQ can provide powerful insight for cellular and drug mechanism studies.

SummaryThis work describes the establishment of a single cell proteomics method using a time-of-flight mass spectrometer. Through this approach, we demonstrate the confident identification of post-translational modifications in single human-derived cells. Additionally, using a KRASG12C covalent inhibitor as a model compound we show that this method can be used to understand pharmacological responses of single human-derived cultured cells.


title: Selection of Synthetic Proteins to Modulate the Human Frataxin Function

abstract: Frataxin is a kinetic activator of the mitochondrial supercomplex for iron-sulfur cluster assembly. Low frataxin expression or a decrease in its functionality results in Friedreichs Ataxia (FRDA). With the aim of creating new molecular tools to study this metabolic pathway, and ultimately, to explore new therapeutic strategies, we have investigated the possibility of obtaining small proteins exhibiting a high affinity for frataxin. In this study, we applied the ribosome display approach, using human frataxin as the target. We focused on Affi_224, one of the proteins that we were able to select after five selection rounds. We have studied the interaction between both proteins and discussed some applications of this specific molecular tutor, concerning the modulation of supercomplex activity. Affi_224 and frataxin showed a KD value in the nanomolar range, as judged by surface plasmon resonance analysis. Most likely, it binds to the frataxin acidic ridge, as suggested by the analysis of chemical shift perturbations (NMR) and computational simulations. Affi_224 was able to increase Cys NFS1 desulfurase activation exerted by the FRDA frataxin variant G130V. Our results suggest quaternary addition may be a new tool to modulate frataxin function in vivo. Nevertheless, more functional experiments under physiological conditions should be carried out to evaluate Affi_224 effectiveness in FRDA cell models.


title: Cryo-EM structures reveal ubiquinone-10 binding to mitochondrial complex I and conformational transitions associated with Q-site occupancy

abstract: Mitochondrial complex I is a central metabolic enzyme that uses the reducing potential of NADH to reduce ubiquinone-10 (Q10) and drive four protons across the inner mitochondrial membrane, powering oxidative phosphorylation. Although many complex I structures are now available, structures of Q10-bound states have remained elusive. Here, we reconstitute mammalian complex I into phospholipid nanodiscs with exogenous Q10. Using cryo-EM, we reveal a Q10 molecule occupying the full length of the Q-binding site in the  active (ready-to-go) resting state (plus a matching substrate-free structure) and apply molecular dynamics simulations to propose how the charge states of key residues influence the Q10 binding pose. By comparing ligand-bound and ligand-free forms of the  deactive resting state (that require reactivating to catalyse), we begin to define how substrate binding restructures the deactive Q-binding site, providing insights into its physiological and mechanistic relevance.


title: Live visualization of cytosolic and endoplasmic reticulum redox potential in zebrafish embryos reveals region-specific differences

abstract: Redox homeostasis is an integral part of many cellular processes and its perturbation is associated with conditions such as diabetes, aging, and neurodegenerative disorders. Redox homeostasis or redox potential in organelles is maintained within a particular range to facilitate the organelle specific cellular redox reactions. Previous studies using yeast, cell systems, and nematodes have demonstrated the Endoplasmic Reticulum (ER) has a more oxidizing environment while the cytosol exhibits a reducing redox potential. However, we know very little about redox state of ER in the vertebrate systems. We created transgenic zebrafish (Danio rerio) lines with roGFP sensors targeted to the cytosol and ER for studying physiological redox potential at the systems level. In the process, we characterized the ER-targeting signal sequence in D. rerio for the first time. Measurements of the redox state in live embryos found that the ER and cytosol exhibit deviations from the expected range in different regions of the developing embryos. The ER is more reducing than expected in certain tissues, and cytosol has oxidizing regions at par with the ER in other parts of the embryo. This was particularly true for the brain which showed the heterogeneity of redox state in both the ER and the cytosol. These differences became even more evident in a transgenic line expressing the more sensitive roGFPiE variant. Thus, live monitoring of redox potential across the developing zebrafish embryos revealed interesting regions of redox heterogeneity at the organism level.


title: Expansion and differentiation of ex vivo cultured erythroblasts in scalable stirred bioreactors

abstract: Transfusion of donor-derived red blood cells (RBCs) is the most common form of cell therapy. Production of transfusion-ready cultured RBCs (cRBCs) is a promising replacement for the current fully donor-dependent therapy. However, very large number of cells are required for transfusion. Here we scale-up cRBC production from static cultures to 0.5 L stirred tank bioreactors, and identify the effect of operating conditions on the efficiency of the process. Oxygen requirement of proliferating erythroblasts (0.55-2.01 pg/cell/h) required sparging of air to maintain the dissolved oxygen concentration at the tested setpoint (2.88 mg O2/L). Erythroblasts could be cultured at dissolved oxygen concentrations as low as 0.7 O2 mg/mL without negative impact on proliferation, viability or differentiation dynamics. Stirring speeds of up to 600 rpm supported erythroblast proliferation, while 1800 rpm led to a transient halt in growth and accelerated differentiation followed by a recovery after 5 days of culture. Erythroblasts could also be differentiated in bioreactors, with final enucleation levels and hemoglobin content similar to parallel cultures under static conditions. After defining optimal mixing and aeration strategies, erythroblast proliferation cultures were successfully scaled up to 3 L bioreactors.

category: bioengineering


title: RNA velocity unraveled

abstract: We perform a thorough analysis of RNA velocity methods, with a view towards understanding the suitability of the various assumptions underlying popular implementations. In addition to providing a self-contained exposition of the underlying mathematics, we undertake simulations and perform controlled experiments on biological datasets to assess workflow sensitivity to parameter choices and underlying biology. Finally, we argue for a more rigorous approach to RNA velocity, and present a framework for Markovian analysis that points to directions for improvement and mitigation of current problems.

category: biophysics


title: Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins

abstract: For intrinsically disordered proteins (IDPs), a pressing question is how sequence codes for function. Dynamics serves as a crucial link, reminiscent of the role of structure in sequence-function relations of structured proteins. To define general rules governing sequence-dependent backbone dynamics, we carried out long molecular dynamics simulations of eight IDPs. Blocks of residues exhibiting large amplitudes in slow dynamics are rigidified by local inter-residue interactions or secondary structures. A long region or an entire IDP can be slowed down by long-range contacts or secondary- structure packing. On the other hand, glycines promote fast dynamics and either demarcate rigid blocks or facilitate multiple modes of local and long-range inter-residue interactions. The sequence-dependent backbone dynamics endows IDPs with versatile response to binding partners, with some blocks recalcitrant while others readily adapting to intermolecular interactions.


title: Differences in Ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts

abstract: The stability of RNA increases as the charge density of the alkali metal cations increases. The molecular mechanism for the stability does not exist. To fill this gap, we performed all-atom molecular dynamics (MD) pulling simulations to dissect the microscopic origin of this phenomenon. We first established that the free energy landscape obtained in the simulations is in excellent agreement with the single-molecule optical tweezer experiments. The origin of the stronger stability in Na+ compared to K+ is found to be due to the differences in the charge-density related binding modes. The smaller hydrated Na+ ion preferentially binds to the highly charged phosphates. In contrast, the larger K+ ions interact with the major grooves. As a result, the electrostatic repulsion between the phosphate groups is reduced more effectively by Na+ ions. Because the proposed mechanism is generic, we predict that the same conclusions are valid for divalent alkaline earth metal cations.


title: The Role of Glycocalyx Steric Effects on Viral Endocytosis

abstract: Understanding the mechanisms of viral entry is key to aiding the development of effective anti-viral treatments. In this work, we produce a simple thermodynamic model of viral entry, which is able to predict the differences between viruses. We also show that the glycocalyx, which is often neglected in studies of cell-entry, plays a key role, and the density and structure of the glycocalyx can determine whether or not a virus can enter the cell. We further find that co-receptors play not only a signalling role, but an important thermodynamic role in viral entry. We then show that this model can be used to calculate the cell-entry probabilities of a given virus, which can shine a light on the clinical observations associated with a virus.


title: Kinase Suppressor of Ras 2 regulates small-cell lung carcinoma tumor propagating cells

abstract: Tumor propagating cells (TPCs) make up a small proportion of tumor cells responsible for self-renewal and long-term propagation of small-cell lung carcinoma (SCLC) tumors. Here, we show that Kinase Suppressor of Ras 2 (KSR2) is an important regulator of the self-renewing and clonogenic properties of SCLC cells. KSR2 is a molecular scaffold which promotes Raf/MEK/ERK signaling and AMPK signaling in SCLC. KSR2 is preferentially expressed in the ASCL1 subtype of SCLC tumors as well as the pulmonary neuroendocrine cells from which the SCLC tumors arise. The expression of KSR2 in SCLC and pulmonary neuroendocrine cells was previously unrecognized and serves as a novel model for understanding the role of KSR2-dependent signaling in normal and malignant tissues. Disruption of KSR2 in SCLC-A cell lines significantly reduces colony forming ability of TPCs in vitro and tumor initiating capacity in vivo. These data indicate that the expression of KSR2 is an essential driver of SCLC-A tumor propagating cell function, and therefore may play a role in SCLC tumor initiation. These findings shed light on a key distinct protein responsible for regulation in ASCL1 subtype SCLC tumors, and a potential subtype specific therapeutic target.

category: cancer biology


title: Molecular signature of RV cardiac remodeling associated with Polymerase Gamma mutation

abstract: Aging is associated with metabolic dysfunction and metabolic dysfunction accelerates the course of aging. This is well illustrated by aging-like phenotypes displayed in the Polymerase Gamma mutant mouse. Here, a key residue of the mitochondrial DNA polymerase is mutated (D257A) which hinders proof reading capacity, resulting in mitochondrial DNA mutation and instability. Given known cardiac phenotypes in the POLG mutant mouse, we sought to characterize the course of cardiac dysfunction in the POLG mutant to guide future intervention studies. Including both male and female animals allowed interrogation of sex-specific responses to severe metabolic dysfunction. We also conducted RNA-seq analysis on cardiac right ventricles to broadly identify mechanisms engaged by severe metabolic dysfunction that are associated with RV pathology. Several interesting sex differences were noted. Specifically, female POLG mutants died earlier than male POLG mutants and LV chamber diameters were impacted earlier in females than males. Moreover, male POLG mutants showed LV wall thinning while female POLG mutant LV walls were thicker. Both males and females displayed significant RV hypertrophy. Finally, RNA-seq analysis of the RV tissue indicated that POLG mutation significantly impacted canonical pathways associated with inflammation, fibrosis, and heart failure. Comparison of this RNA-seq dataset with other publically available datasets highlight 1) strong conservation among downregulated genes in models of accelerated cardiac aging, 2) the potential involvement of the mitochondrial unfolded protein response in the POLG mutant, and 3) the ability of zinc dependent HDAC inhibition to rescue the expression of genes downregulated in accelerated cardiac aging.

category: pathology


title: Knockout of Sorbs2 in Cardiomyocytes Leads to Dilated Cardiomyopathy in Mice

abstract:
2.RationaleSorbs2 is a cardiomyocyte-enriched, cytoskeletal adaptor protein, and given some evidence for its dysregulated expression in failing hearts, there is growing interest in understanding its roles in cardiac biology and disease. While Sorbs2 global knockout mice display lethal cardiomyopathy with severe arrhythmias, the underlying mechanisms remain unclear, and whether this results from intrinsic loss of Sorbs2 in cardiomyocytes is unknown, as Sorbs2 is also well-expressed in the nervous system and vasculature. In addition, the potential relevance of Sorbs2 in human cardiomyopathy remains underexplored.

ObjectiveTo characterize the effects and potential underlying mechanisms of cardiomyocyte- specific deletion of Sorbs2 on cardiac structure and function in mice, and to further examine Sorbs2 dysregulation in failing hearts and explore potential links between Sorbs2 genetic variations and human cardiovascular disease phenotypes.

Methods and ResultsWe report that myocardial Sorbs2 expression is consistently upregulated in humans with ischemic and idiopathic cardiomyopathies, and in experimental animal models of heart failure (HF). We generated mice with cardiomyocyte-specific loss of Sorbs2 (Sorbs2-cKO) and found early atrial and ventricular conduction abnormalities, despite unaltered expression of primary action potential ion channels and gap junction proteins. At mid-life, Sorbs2-cKO mice exhibit impaired cardiac contractility with cardiomyofibers failing to maintain adequate mechanical tension. As a result, these mice develop progressive diastolic and systolic dysfunction, enlarged cardiac chambers, and die with congestive HF at approximately one year of age. Comprehensive survey of potential underlying mechanisms revealed that Sorbs2-cKO hearts exhibit defective microtubule polymerization and compensatory upregulation of structural proteins desmin, vinculin, and tubulins. Finally, consistent with our observations in mice, we identified suggestive links between Sorbs2 genetic variants and related human cardiac phenotypes, including conduction abnormalities, atrial enlargement, and dilated cardiomyopathy.

ConclusionsOur studies show that Sorbs2 is essential for maintaining cytoskeletal structural integrity in cardiomyocytes likely through strengthening the interactions between microtubules and other structural proteins at crosslink sites. Overall, this study provides key insights into the critical role for Sorbs2 in cardiomyocytes and likely other cell types in maintaining normal cardiac structure and function and highlights its potential clinical relevance.

category: physiology


title: Gain-of-function, focal segmental glomerulosclerosis Trpc6 mutation minimally affects susceptibility to renal injury in several mouse models.

abstract: Mutations in TRPC6 are a cause of autosomal dominant focal segmental glomerulosclerosis in humans. Many of these mutations are known to have a gain-of-function effect on the non-specific cation channel function of TRPC6. In vitro studies have suggested these mutations affect several signaling pathways, but in vivo studies have largely compared wild-type and Trpc6-deficient rodents. We developed mice carrying a gain-of-function Trpc6 mutation encoding an E896K amino acid change, corresponding to a known FSGS mutation in TRPC6. Homozygous mutant Trpc6 animals have no appreciable renal pathology, and do not develop albuminuria until very advanced age. The Trpc6E896K mutation does not impart susceptibility to PAN nephrosis. The animals show a slight delay in recovery from the albumin overload model. In response to chronic angiotensin II infusion, Trpc6E896K/E896K mice have slightly greater albuminuria initially compared to wild-type animals, an effect that is lost at later time points, and a statistically non-significant trend toward more glomerular injury. This phenotype is nearly opposite to that of Trpc6-deficient animals previously described. The Trpc6 mutation does not appreciably impact renal interstitial fibrosis in response to either angiotensin II infusion, or folate-induced kidney injury. TRPC6 protein and TRPC6-agonist induced calcium influx could not be detected in glomeruli. In sum, these findings suggest that a gain-of-function Trpc6 mutation confers only a mild susceptibility to glomerular injury in the mouse.


title: Functional characterization of Atlantic salmon (Salmo salar L.) PepT2 transporters

abstract:
The high-affinity/low-capacity system Slc15a2 (PepT2) is responsible for the reuptake of di/tripeptides from the renal proximal tubule, but it also operates in many other tissues/organs. Information regarding PepT2 in teleost fish is limited and to date functional data are available from the zebrafish (Danio rerio) only. Here, we report the identification of two slc15a2 genes in the Atlantic salmon (Salmo salar) genome, namely slc15a2a and slc15a2b. The two encoded PepT2 proteins share 87% identity and resemble both structurally and functionally to the canonical vertebrate PepT2 system. The mRNA tissue distribution analyses reveal a widespread distribution of slc15a2a transcripts, being more abundant in the brain and gills, while slc15a2b transcripts are mainly expressed in kidney and distal part of gastrointestinal tract. The function of the two transporters was investigated by heterologous expression in Xenopus laevis oocytes and two- electrode voltage-clamp recordings of transport and presteady-state currents. Both PepT2a and PepT2b in the presence of Gly-Gln elicit pH-dependent and Na+ independent inward currents. The biophysical and kinetic analysis of the recorded currents defined the transport properties, confirming that the two Atlantic salmon PepT2 proteins behave as high-affinity/low-capacity transporters. The recent structures and the previous kinetic schemes of rat and human PepT2 qualitatively account for the characteristics of the two Atlantic salmon proteins. This study is the first to report on the functional expression of two PepT2-type transporters that operate in the same vertebrate organism as a result of (a) gene duplication process(es).

Key points summaryO_LITwo slc15a2-type genes, slc15a2a and slc15a2b coding for PepT2-type peptide transporters were found in the Atlantic salmon.
C_LIO_LIslc15a2a transcripts, widely distributed in the fish tissues, are abundant in brain and gills, while slc15a2b transcripts are mainly expressed in kidney and distal gastrointestinal tract.
C_LIO_LIAmino acids involved in vertebrate Slc15 transport function are conserved in PepT2a and PepT2b proteins.
C_LIO_LIDetailed kinetic analysis indicates that both PepT2a and PepT2b operate as high-affinity transporters.
C_LIO_LIThe kinetic schemes and structures proposed for the mammalian models of PepT2 are suitable to explain the function of the two Atlantic salmon transporters.
C_LI


title: Conifer leaves have a peroxisomal oxidative decarboxylation path in the photorespiratory pathway

abstract:
The photorespiratory pathway consists of enzymes operating in chloroplasts, mitochondria, and peroxisomes. Conifer leaves lack one of them, chloroplastic Gln synthetase, which questioned the current belief that the photorespiratory mechanism is identical between angiosperm C3 species and conifers. A photorespiratory-metabolite analysis of the leaves of 13 conifer and 14 angiosperm tree species revealed significant differences in the mean metabolite concentrations between the two taxonomic groups: the glycerate content on chlorophyll basis in conifer leaves was <1/10 that detected in angiosperm leaves, whereas the glycolate content was 1.6 times higher in conifer leaves. Glycerate is produced from Ser through an intermediate, hydroxypyruvate. To investigate the lower glycerate levels observed in conifer leaves, we performed experiments of 13C-labeled Ser feeding to the detached shoots of a conifer (Cryptomeria japonica) via the transpiration stream, and compared the labeling patterns of photorespiratory metabolites with those of an angiosperm (Populus nigra). Glycerate was most labeled in P. nigra, whereas glycolate was more labeled than glycerate in C. japonica. The photorespiration pathway involves H2O2-scavenging and H2O2-generating enzymes, catalase (CAT) and glycolate oxidase (GLO), respectively, which are the peroxisomal targeting enzymes in angiosperms. In contrast, database analyses of the peroxisomal targeting signal motifs and analyses of the peroxisomal fractions isolated from C. japonica leaves indicated that the conifer peroxisomes were not a major localization of CAT. These results suggest that the conifer photorespiration pathway has a bypass from Ser to glycolate via the decarboxylation of hydroxypyruvate, because of an imbalance between CAT and GLO activities in peroxisomes.

One sentence summaryConifer peroxisome is not a major localization of catalase and yields a unique oxidative decarboxylation path in the photorespiratory pathway.

category: plant biology


title: Genomic characterization of a wild-like tomato accession found in Arizona; a northward migration story

abstract:
Tomato domestication history has been revealed to be a highly complex story. A major contributor to this complexity is an evolutionary intermediate group (Solanum lycopersicum var. cerasiforme (Alef.) Voss; SLC) between the domesticated tomato (Solanum lycopersicum var. lycopersicum L.; SLL) and its wild relative (Solanum pimpinellifolium L.; SP). SLC includes accessions with a broad spectrum of genomic and phenotypic characteristics. Some of the SLC accessions were previously hypothesized to be spreading northward from South America into Mesoamerica and that migration probably entailed reversal to wild-like phenotypes such as smaller fruits. Prior to this study, the northernmost confirmed extension of the SLC was limited to northern Mexico.

In this study, we employed genomic methods to investigate the origin of a wild-like tomato found in a garden in Scottsdale Arizona, USA. The so-called "Arizona tomato" featured a vigorous growth habit and carried small fruits weighing 2-3 grams. Our phylogenomic analyses revealed the identity of the Arizona tomato as a member of the Mexican SLC population (SLC MEX). To our knowledge, this is the first report of an SLC accession, confirmed using genomics, growing spontaneously in Arizona. This finding could have implications for conservation biology as well as agriculture.


title: Synthetic memory circuits for programmable cell reconfiguration in plants

abstract: Plant biotechnology predominantly relies on a restricted set of genetic parts with limited capability to customize spatiotemporal and conditional expression patterns. Synthetic gene circuits have the ability to integrate multiple customizable input signals through a processing unit constructed from biological parts, to produce a predictable and programmable output. Here, we present a suite of functional recombinase-based gene circuits for use in plants. We first established a range of key gene circuit components compatible with plant cell functionality. We then used these to develop a range of operational logic gates using the identify function (activation) and negation function (repression) in Arabidopsis protoplasts and in vivo, demonstrating their utility for programmable manipulation of transcriptional activity in a complex multicellular organism. Through utilization of genetic recombination these circuits create stable long-term changes in expression and recording of past stimuli. This highly-compact programmable gene circuit platform provides new capabilities for engineering sophisticated transcriptional programs and previously unrealised traits into plants.

category: synthetic biology


title: Non-destructive chemical sensing within bulk soil using 1000 biosensors per gram of matrix

abstract: Gene expression can be monitored in hard-to-image environmental materials using gas-reporting biosensors, but these outputs have only been applied in autoclaved matrices that are hydrated with rich medium. To better understand the compatibility of indicator gas reporting with environmental samples, we evaluated how matrix hydration affects the gas signal of an engineered microbe added to a sieved soil. A gas-reporting microbe presented a gas signal in a forest soil (Alfisol) when hydrated to an environmentally-relevant osmotic pressure. When the gas signal was concentrated prior to analysis, a biosensor titer of 103 cells/gram soil produced a significant signal when soil was supplemented with halides. A signal was also observed without halide amendment, but a higher cell titer (106 cells/gram soil) was required. A sugar-regulated gas biosensor was able to report with a similar level of sensitivity when added to an unsterilized soil matrix, illustrating how gas concentration enables biosensing within a soil containing environmental microbes. These results establish conditions where engineered microbes can report on gene expression in living environmental matrices with minimal perturbation, using biosensor titers that are orders of magnitude lower than the number of cells typically observed in a gram of soil.


title: A critique of common methods for comparing the scaling of vertical force production in flying insects

abstract: Maximum vertical force production (Fvert) is an integral measure of flight performance that generally scales with size. Numerous methods of measuring Fvert and body size exist, but few studies have compared how these methods affect the conclusions of scaling analyses. We compared two common techniques for measuring Fvert in bumblebees (Bombus impatiens) and mason bees (Osmia lignaria), and examined Fvert scaling using five size metrics. Fvert results were similar with incremental or asymptotic load-lifting, but scaling analyses were sensitive to the size metric used. Analyses based on some size metrics indicated similar scaling exponents and coefficients between species, whereas other metrics indicated different coefficients. Furthermore, Fvert showed isometry with body lengths and fed and starved masses, but negative allometry with dry mass. We conclude that Fvert can be measured using either incremental or asymptotic loading but choosing a size metric for scaling studies requires careful consideration.

category: zoology


title: Predatory mites, a green pesticide, and an Entomopathogenic compound: A proposed IPM tactic based on pest species diversity indices and population dynamics

abstract: The study was aimed to conduct the population dynamics and diversity indices for three major pest species in order to design an IPM protocol in two experimental sites (Om Saber, Beheira Governorate 30{degrees}2950.6"N, 30{degrees}4618.8"E), and (Kom Oshim, Fayoum Governorate 29{degrees}3440.9"N, 30{degrees}5538.3"E). The resulted data showed statistically significant fluctuation, population dynamics, abundance, distribution, and diversity indices of the two-spotted spider mite (TSSM) Tetranychus urticae Koch (Acari: Tetranychidae), the silver leaf whitefly Bemisia tabaci Genn. (Hemiptera: Aleyrodidae), and the onion thrips Thrips tabaci Lindman (Thysanoptera: Thripidae) which recorded on four plant species belonging to Brassicaceae (Siberian (Russian) kale Brassica napus var. pabularia L. and Italian (Tuscan) kale Brassica oleracea var. palmifolia), and Lamiaceae (Spearmint Mentha spicata L. and Saudi Mint Mentha longifolia L.). The proposed IPM program consisted of predatory mites; Phytoseiulus persimilis Athias-Henriot, Amblyseius swirskii Athias-Henriot, and Cydnoseius negevi (Swirski & Amitai) (Acari: Phytoseiidae), a green pesticide, and an entomopathogenic compound. It was concluded that abiotic and biotic factors together help in explaining why various pest species build their communities rapidly and increase their parameters that become above the EIL. Such factors are hypothesized to affect the plant-arthropod, predator-herbivore, predator-predator, and tri-trophic interactions. And it recommends the application of such protocol should consider the timing of tacking an action and merging tactics together to get the maximum efficiency.


title: Biogeography and Validation of species limits in Caribbean Red Bats (Vespertilionidae: Lasiurus)

abstract: AO_SCPLOWBSTRACTC_SCPLOWDefining species limits using an integrative framework is crucial for biodiversity assessments and to maintain taxonomic stability. These approaches are robust and can be useful to also validate the status of species that are uncommon and underrepresented in biological collections. We examined the species limits and validated the taxonomic status of the Minor Red Bat (Lasiurus minor), an uncommon species originally described from four specimens. Our approach consisted of three independent lines of evidence combining genetic and phenotypic data. Phylogenetic analyses confirmed the uniqueness of L. minor compared to three other geographically and closely related Red Bat species. Furthermore, coalescent species delimitation supported the four Red Bat species hypothesis. Linear phenotypic analyses demonstrated that L. minor is distinct from other Red Bats despite a morphological continuum. Finally, we reassessed the diagnosability of characters used to describe L. minor using an objective shape analysis approach, which emphasized the support for this taxon. Based on our findings, while identification in the field could still pose a challenge, there is strong support to recognize L. minor. This study settles a longstanding taxonomic question and provides evidence to better understand Caribbean biodiversity.


title: Shisa7-dependent regulation of GABAA receptor single-channel gating kinetics

abstract: GABAA receptors (GABAARs) mediate the majority of fast inhibitory transmission throughout the brain. Although it is widely known that pore-forming subunits critically determine receptor function, it is unclear whether their single-channel properties are modulated by GABAAR-associated transmembrane proteins. We previously identified Shisa7 as a GABAAR auxiliary subunit that modulates the trafficking, pharmacology, and kinetic properties of these receptors. In particular, Shisa7 accelerates receptor deactivation; however, the underlying mechanisms by which Shisa7 controls GABAAR kinetics have yet to be determined. Here we have performed single-channel recordings and find that while Shisa7 does not change channel slope conductance, it reduces the frequency of openings. Importantly, Shisa7 modulates GABAAR gating by decreasing the duration and open probability (Po) within bursts. Kinetic analysis of dwell times, activation modeling, and macroscopic simulations indicate that Shisa7 accelerates GABAAR deactivation by governing the time spent between close and open states during gating. Together, our data provide a mechanistic basis for how Shisa7 controls GABAAR gating kinetics and reveal for the first time that GABAAR single-channel properties can be modulated by an auxiliary subunit. These findings shed light on processes that shape the temporal dynamics of GABAergic transmission.

category: neuroscience


title: Defective mitochondrial-lysosomal axis promotes extracellular vesicles release of mitochondrial components in Huntington's Disease

abstract:
Mitochondrial and autophagy dysfunction are mechanisms proposed to be involved in the pathogenesis of several neurodegenerative diseases. Huntingtons disease (HD) is a progressive neurodegenerative disorder associated with mutant Huntingtin-induced abnormalities in neuronal mitochondrial dynamics and quality control. Former studies suggest that the removal of defective mitochondria may be compromised in HD. The mitochondrial quality control is a complex, well-orchestrated pathway that can be compromised through mitophagy dysregulation or impairment in the mitochondrial-lysosomal axis. Another mitochondrial stress response is the generation of mitochondrial-derived vesicles that fuse with the endolysosomal system and form multivesicular bodies that are extruded from cells as extracellular vesicles (EVs).

In this study, we comprehensively characterized the mitochondrial and autophagy alterations in premanifest and manifest HD patients and performed a proteomic and genomic EVs profile. We observed that manifest HD patients exhibit mitochondrial and autophagy impairment associated with enhanced EVs release. Further, we detected mitochondrial components in EVs released by HD cells and in neuron-derived EVs. The EV-associated mtDNA copies were elevated in manifest HD patients suggesting to be an alternative pathway for secretion of reactive mitochondrial components. This study provides a novel framework connecting EVs enhanced release of mitochondrial components to mitochondrial and lysosomal dysfunction in HD.


title: The zinc finger transcription factor Sall1 is required for the early developmental transition of microglia in mouse embryos

abstract: Microglia play many critical roles in neural development. Recent single-cell RNA-sequencing studies have found diversity of microglia both across different stages and within the same stage in the developing brain. However, how such diversity is controlled during development is poorly understood. In this study, we first found the expression of the macrophage mannose receptor CD206 in early-stage embryonic microglia on mouse brain sections. This expression showed a sharp decline between E12.5 and E13.5 across the central nervous system. We next tested the roles of the microglia-expressed zinc finger transcription factor SALL1 in this early transition of gene expression. By deleting Sall1 specifically in microglia, we found that many microglia continued to express CD206 when it is normally downregulated. In addition, the mutant microglia continued to show less ramified morphology in comparison with controls even into postnatal stages. Thus, SALL1 is required for early microglia to transition into a more mature status during development.


title: Enhanced Sodium Channel Inactivation by Temperature and FHF2 Deficiency Blocks Heat Nociception

abstract: Transient voltage-gated sodium currents are essential for the initiation and conduction of action potentials in neurons and cardiomyocytes. The amplitude and duration of sodium currents are tuned by intracellular fibroblast growth factor homologous factors (FHFs/iFGFs) that associate with the cytoplasmic tails of voltage-gated sodium channels (Navs), and genetic ablation of Fhf genes disturbs neurological and cardiac functions. Amongst reported phenotypes, Fhf2null mice undergo lethal hyperthermia-induced cardiac conduction block attributable to the combined effects of FHF2 deficiency and elevated temperature on the cardiac sodium channel (Nav1.5) inactivation rate. Fhf2null mice also display a lack of heat nociception, while retaining other somatosensory capabilities. Here we employ electrophysiological and computational methods to show that the heat nociception deficit can be explained by the combined effects of elevated temperature and FHF2 deficiency on the inactivation gating of sodium channels Nav1.7 and Nav1.8 expressed in dorsal root ganglion C-fibers. Hence, neurological and cardiac heat-associated deficits in Fhf2null mice derive from shared impacts of FHF deficiency and temperature towards Nav inactivation gating kinetics in distinct tissues.


title: Cerebral organoids for modeling of HSV-1-induced-multiscale neuropathology associated with Alzheimers disease and phenotypic rescue

abstract:
Herpes simplex virus type I (HSV-1) infection is a potential risk factor involved in the pathogenesis of Alzheimers disease (AD) and contributes to the AD viral hypothesis. However, further understanding of the neuropathological effects of the HSV-1 infection is hampered by the limitations of existing infection models due to the distinct differences between human brains and other mammalians brains. Here we generated cerebral organoid models derived from pluripotent stem cells to investigate the HSV-induced pathogenesis associated with AD and the role of antiviral drugs in the phenotypic rescue. Our results identified that the HSV-1-infected cerebral organoids recapitulated multiscale neuropathology pertaining to the onset and progression of AD across the genetic, cellular, and tissue levels, including the multicellular A{beta} deposition, dysregulated endogenous AD mediators, reactive gliosis, neuroinflammation, and neural loss. Furthermore, we identified that two antiviral drugs, namely Ribavirin (RBV) and Valacyclovir (VCV), inhibited HSV-1 replication and rescued the neuropathological phenotypes associated with AD in the HSV-1-infected cerebral organoids, implying their therapeutic potential to slow down the progression of AD. Our study provides a high-fidelity human-relevant in-vitro HSV-1 infection model to reconstitute the multiscale neuropathological features associated with AD and discover therapeutic drug candidates relevant to the AD viral hypothesis.

IMPORTANCEAD is a progressive neurodegenerative disorder characterized by neuronal death, brain atrophy, and cognitive impairment. HSV-1 is a neurotropic double-stranded DNA virus resulting in long-term neurological sequelae in adults.

There is accumulating evidence indicating that AD may be associated with HSV-1 infections. In this study, we generated human-physiologically related cerebral organoids derived from human embryonic stem cells (hESCs) to investigate the influence of HSV-1 infection on the neuropathology associated with AD. We found that the HSV-1-infected cerebral organoids could model typical neuropathological features associated with AD. Additionally, we discovered that both RBV and VCV significantly rescued the HSV-1-induced pathological phenotypes associated with AD. These findings may open new avenues of consideration related to HSV-1 infection and AD. Furthermore, the contribution of these antiviral drugs to AD linked to HSV-1 infection will provide new clues to potential new therapies.


title: Mentalizing in economic games is associated with enhanced activation and connectivity in left temporoparietal junction

abstract: Studies in Social Neuroeconomics have consistently reported activation in social cognition regions during interactive economic games suggesting mentalizing during economic choice. It remains important to test the involvement of neural activity associated with mentalizing in an economic games context within the same sample of participants performing the same task. We designed a novel version of the classic false-belief task in which participants observed interactions between agents in the ultimatum and trust games and were subsequently asked to infer the agents beliefs. We compared activation patterns during the economic-games false-belief task to those during the classic false-belief task using conjunction analyses. We find significant overlap in left TPJ, and dmPFC, as well as temporal pole during two task phases: belief formation and belief inference. Moreover, gPPI analyses show that during belief formation right TPJ is a target of both left TPJ and right temporal pole (TP) seed regions, while during belief inferences all seed regions show interconnectivity with each other. These results indicate that across different task types and phases, mentalizing is associated with activation and connectivity across central nodes of the social cognition network. Importantly, this is the case in the context of the novel economic-games and classic false-belief tasks.


title: Mentalizing in an economic games context is associated with enhanced activation and connectivity in left temporoparietal junction


title: Neurodevelopmental Patterns of Early Postnatal White Matter Maturation Represent Distinct Underlying Microstructure and Histology

abstract: During the early postnatal period, cerebral white matter undergoes rapid maturation through a complex series of interrelated cellular and histogenetic processes. Accurately quantifying these processes is important for improving understanding of early brain development, developmental abnormalities related to prematurity, and neurodevelopmental diseases. Past efforts have used magnetic resonance imaging (MRI) to track these developmental processes in vivo. However, most previous studies have relied on single imaging modality data and have often been limited by small samples and analytics that do not evaluate complex multivariate imaging patterns. Here, we applied an advanced unsupervised multivariate pattern analysis technique, non-negative matrix factorization (NMF), to T2w/T1w signal ratio maps from a large cohort of newborns (Developing Human Connectome Project [dHCP], n=342), revealing patterns of synchronous white matter maturation. These patterns showed divergent age-related maturational trajectories and differential susceptibility to premature birth, which were replicated in an independent large sample of newborns (Early Life Adversity, Biological Embedding, and Risk for Developmental Precursors of Mental Disorders [eLABE], n=239). Furthermore, we showed that T2w/T1w signal variations in white matter maturational patterns are explained by differential contributions of white matter microstructure indices (i.e., free water content and neurite density index) derived from neurite orientation dispersion and density imaging (NODDI) modeling of diffusion-weighted MRI. Finally, we demonstrated how white matter maturation patterns relate to distinct histological features by comparing our findings with postmortem late fetal/early postnatal brain tissue staining. Together, these results delineate a novel MRI representation of white matter microstructural and histological reorganization during the early postnatal development.


title: The Drosophila chemokine-like Orion bridges phosphatidylserine and Draper in phagocytosis of neurons

abstract: Phagocytic clearance of degenerating neurons is triggered by "eat-me" signals exposed on the neuronal surface. The conserved neuronal eat-me signal phosphatidylserine (PS) and the engulfment receptor Draper (Drpr) mediate phagocytosis of degenerating neurons in Drosophila. However, how PS is recognized by Drpr-expressing phagocytes in vivo remains poorly understood. Using multiple models of dendrite degeneration, we show that the Drosophila chemokine-like protein Orion is a PS-binding protein responsible for detecting PS exposure on neurons; it is supplied cell-non-autonomously to coat PS-exposing dendrites and to bridge interactions between PS and Drpr, thus enabling phagocytosis. As a result, the accumulation of Orion on neurons and on phagocytes produces opposite outcomes by potentiating and suppressing phagocytosis, respectively. Moreover, the Orion dosage is a key determinant of the sensitivity of phagocytes to PS exposed on neurons. Lastly, mutagenesis analyses show that the sequence motifs shared between Orion and human immunomodulatory proteins are important for Orion secretion and binding to PS. Thus, our results uncover a missing link in PS-mediated phagocytosis in Drosophila and imply conserved mechanisms of phagocytosis of neurons.


title: Alpha-Amylase increases predict a freezing-like response and cortical alpha oscillations

abstract: Individual differences in the reactivity of the sympathetic nervous system in response to stressful situations are thought to be an important predictor for psychological well-being and the focus of current scientific investigations. Here, we explored whether increased sympathetic nervous activity (SNA) was associated with reduced alpha power and with increased freezing-like behaviour (i.e., body sway) while watching threatening stimuli, reflecting enhanced attention. Salivary alpha-amylase (sAA) was used as a proxy for sympathetic nervous activity, which is elevated in stressful situations. A passive viewing task with affective pictures (unpleasant, neutral, pleasant) was carried out, and pre- and post- task sAA samples were taken. Oscillatory brain activity in the EEG and body sway were assessed simultaneously during the task. The results point to an increase in sAA being associated with reduced alpha power decrease to the unpleasant compared to the neutral pictures as well as increased freezing-like behaviour (i.e., reduction in body sway for unpleasant versus neutral pictures). It appears that an increase in SNA is linked to less attentional valence differentiation. Furthermore, our study corroborates findings from the animal literature in that the SNA increase is linked to a freezing-like response.


title: Prediction error processing speeds up in presence of multisensory contexts

abstract:
Prediction errors in the brain are indexed by two event related potentials - MMN and P300 which are elicited whenever there is a violation of regularity in occurrence of a repetitive stimulus. While, MMN reflects the brains ability to perform automatic comparisons between consecutive stimuli and provides an electrophysiological index of sensory error detection, P300 is associated with cognitive processes such as attention and memory. Till date, there has been extensive research on the roles of MMN and P300 individually, because of their potential to be used as clinical markers of consciousness and attention, respectively. However, the relationship between these two ERPs, in context of prediction error propagation is an open question. Secondly, whether these events represent modality specific or modality independent information processing needs to be tested in unisensory and multisensory environments. Our EEG study on 22 healthy human volunteers shows that multisensory prediction errors are temporally facilitated by the constituent unisensory modality that has shorter processing latencies at any stage of prediction error processing. Employing source localization using individual participants MRI scan, our study reveals that the corresponding ERP generators underlying the temporal hierarchy of prediction mismatch signals in the brain transition from being modality sensitive to modality independent across both unisensory and multisensory contexts. Such knowledge can be of immense value in clinical research for determining the stages of various treatments in aging, schizophrenia and depression, and their efficacy on cognitive function.

Significance statementFailure of an expected event to occur needs to reinforce the internal model of environment in the brain thus, forming a key ingredient of any predictive coding framework. Just the way it does for human learning, the analysis of prediction errors can help guide machine learning in artificial intelligence by minimizing the error feedback. In order to facilitate such studies, it is important to first empirically establish how these prediction errors are processed in the human brain and how differently are they processed across various modalities because the environment around us is essentially multisensory in nature. Our electroencephalography study captures this precisely, both temporally and spatially.


title: The sialidase NEU3 promotes pulmonary fibrosis in mice

abstract: Sialic acid is often the distal sugar on glycoconjugates, and sialidases are enzymes that remove this sugar. In fibrotic lesions in human and mouse lungs, there is extensive desialylation of glycoconjugates, and upregulation of sialidases including the extracellular sialidase NEU3. In the bleomycin model of pulmonary fibrosis, mice lacking NEU3 (Neu3-/-) showed strongly attenuated bleomycin-induced weight loss, lung damage, inflammation, upregulation of TGF-{beta}1, and fibrosis. This indicates that NEU3 is necessary for the full spectrum of bleomycin-induced pulmonary fibrosis. To determine if NEU3 is sufficient for fibrosis, mice not treated with bleomycin were treated with recombinant murine NEU3 or inactive NEU3. Aspiration of NEU3 caused inflammation and fibrosis in the lungs, while inactive NEU3 caused inflammation but not fibrosis. Mice were also treated with NEU3 starting 10 days after bleomycin. In male but not female mice, NEU3 increased inflammation and fibrosis. Inactive NEU3 did not enhance bleomycin-induced lung fibrosis. These results suggest that NEU3 is sufficient to induce fibrosis in the lungs, and that this effect is mediated by NEU3s enzymic activity.

category: immunology


title: Multidimensional single-cell analysis identifies a role of CD2-CD58 interactions for clinical antitumor T cell responses

abstract:
The in vivo persistence of adoptively transferred T cells is predictive of anti-tumor response. Identifying functional properties of infused T cells that lead to in vivo persistence and tumor eradication has remained elusive. We profiled CD19-specific CAR T cells that comprise the infusion products used to treat large B cell lymphomas using high-throughput single-cell technologies based on Timelapse Imaging Microscopy In Nanowell Grids (TIMING) that integrates killing, cytokine secretion, and transcriptional profiling. Our results show that the directional migration of CD19-specific CAR T cells is correlated with polyfunctionality. We identified that CD2 on T cells is associated with directional migration and that the interaction between CD2 on T cells and CD58 on lymphoma cells accelerates killing and serial killing. Consistent with this, we observed elevated CD58 expression on pre-treatment tumor samples in patients with relapsed or refractory large B cell lymphomas treated with CD19-specific CAR T cell therapy was associated with complete clinical response and survival. These results highlight the importance of studying dynamic T-cell tumor cell interactions in identifying optimal antitumor responses.

KEY POINTS- Profiling patient infusion products revealed that polyfunctional CAR T cells show directional migration, which is associated with higher CD2 expression
- The ligand for CD2, CD58 is expressed at higher levels in the tumors of lymphoma patients who respond better to CAR T cell treatment


title: Vaccine-elicitation of cross-group neutralizing protective antibodies to influenza A viruses

abstract: Current influenza vaccines predominantly induce immunity to the hypervariable viral hemagglutinin (HA) head, requiring frequent vaccine reformulation. Conversely, antigenic sites on the conserved HA stem are subdominant and harbor a supersite which is targeted by broadly neutralizing antibodies (bnAbs), making it a prime target for universal vaccines. Here, we show that co-immunization of two stem immunogens derived from influenza A group 1 and 2 HAs elicits cross-group protective immunity and neutralizing antibody responses in mice, ferrets, and nonhuman primates (NHPs). Immunized mice were protected from multiple group 1 and 2 viruses, and all animal models showed broad serum neutralizing activity. A bnAb isolated from an immunized NHP broadly neutralized and conferred protection from viruses including H5N1 and H7N9. Genetic and structural analyses revealed a remarkable convergent evolution between macaque and human bnAbs, illustrating the biophysical constraints for acquiring immunoglobulins with cross-group specificity. Co-immunization of stem immunogens elicits not only group-specific protective immunity, but also cross-group bnAb responses, and represents a step towards broadly protective influenza vaccines.


title: Loss of RNase J leads to multi-drug tolerance and accumulation of highly structured mRNA fragments in Mycobacterium tuberculosis

abstract: Despite the existence of well-characterized, canonical mutations that confer high-level drug resistance to Mycobacterium tuberculosis (Mtb), there is evidence that drug resistance mechanisms are more complex than simple acquisition of such mutations. Recent studies have shown that Mtb can acquire non-canonical resistance-associated mutations that confer survival advantages in the presence of certain drugs, likely acting as stepping-stones for acquisition of high-level resistance. Rv2752c/rnj, encoding RNase J, is disproportionately mutated in drug-resistant clinical Mtb isolates. Here we show that deletion of rnj confers increased tolerance to lethal concentrations of several drugs. RNAseq revealed that RNase J affects expression of a subset of genes enriched for PE/PPE genes and stable RNAs and is key for proper 23S rRNA maturation. Gene expression differences implicated two sRNAs and ppe50-ppe51 as important contributors to the drug tolerance phenotype. In addition, we found that in the absence of RNase J, many short RNA fragments accumulate because they are degraded at slower rates. We show that the accumulated transcript fragments are targets of RNase J and are characterized by strong secondary structure and high G+C content, indicating that RNase J has a rate-limiting role in degradation of highly structured RNAs. Taken together, our results demonstrate that RNase J indirectly affects drug tolerance, as well as reveal the endogenous roles of RNase J in mycobacterial RNA metabolism.

category: microbiology


title: Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by multi-omic analysis

abstract:
BackgroundAlterations of the gut microbiome have been linked to multiple chronic diseases. However, the drivers of such changes remain largely unknown. The oral cavity acts as a major route of exposure to exogenous factors including pathogens, and processes therein may affect the communities in the subsequent compartments of the gastrointestinal tract. Here, we perform strain-resolved, integrated multi-omic analyses of saliva and stool samples collected from eight families with multiple cases of type 1 diabetes mellitus (T1DM).

ResultsWe identified distinct oral microbiota mostly reflecting competition between streptococcal species. More specifically, we found a decreased abundance of the commensal Streptococcus salivarius in the oral cavity of T1DM individuals, which is linked to its apparent competition with the pathobiont Streptococcus mutans. The decrease in S. salivarius in the oral cavity was also associated with its decrease in the gut as well as higher abundances in facultative anaerobes including Enterobacteria. In addition, we found evidence of gut inflammation in T1DM as reflected in the expression profiles of the Enterobacteria as well as in the human gut proteome. Finally, we were able to follow transmitted strain-variants from the oral cavity to the gut at the metagenomic, metatranscriptomic and metaproteomic levels, highlighting not only the transfer, but also the activity of the transmitted taxa along the gastrointestinal tract.

ConclusionsAlterations of the oral microbiome in the context of T1DM impact the microbial communities in the lower gut, in particular through the reduction of "oral-to-gut" transfer of Streptococcus salivarius. Our results indicate that the observed oral-cavity-driven gut microbiome changes may contribute towards the inflammatory processes involved in T1DM. Through the integration of multi-omic analyses, we resolve strain-variant "mouth-to-gut" transfer in a disease context.


title: Metagenomic and Metabolomic Analyses Reveal Synergistic Effects of Fecal Microbiota Transplantation and Anti-PD-1 Therapy on Treating Colorectal Cancer

abstract: Anti-PD-1 immunotherapy has saved numerous lives of cancer patients; however, it only exerts efficacy in 10-15% of patients with colorectal cancer. Fecal microbiota transplantation (FMT) is a potential approach to improving the efficacy of anti-PD-1 therapy, whereas the detailed mechanisms and the applicability of this combination therapy remain unclear. In this study, we evaluated the synergistic effect of FMT with anti-PD-1 in curing colorectal tumor-bearing mice using a multi-omics approach. Mice treated with the combination therapy showed superior survival rate and tumor control, compared to the mice received anti-PD-1 therapy or FMT alone. Metagenomic analysis showed that composition of gut microbiota in tumor-bearing mice treated with anti-PD-1 therapy was remarkably altered through receiving FMT. Particularly, Bacteroides genus, including FMT-increased B. thetaiotaomicron, B. fragilis, and FMT-decreased B. ovatus might contribute to the enhanced efficacy of anti-PD-1 therapy. Furthermore, metabolomic analysis upon mouse plasma revealed several potential metabolites that upregulated after FMT, including punicic acid and aspirin, might promote the response to anti-PD-1 therapy via their immunomodulatory functions. This work broadens our understanding of the mechanism by which FMT improves the efficacy of anti-PD-1 therapy, which may contribute to the development of novel microbiota-based anti-cancer therapies.


title: Metagenomes of Red Sea subpopulations challenge the use of morphology and marker genes to assess Trichodesmium diversity

abstract:
The bloom forming Trichodesmium are filamentous cyanobacteria of key interest due to their ability to fix carbon and nitrogen within an oligotrophic marine environment. Trichodesmium blooms typically comprise a complex assemblage of subpopulations and colony-morphologies that are predicted to exhibit distinct ecological lifestyles. Here, we assessed the poorly studied diversity of Trichodesmium in the Red Sea, based on metagenome-assembled genomes (MAGs) and hetR gene-based phylotyping.

We assembled four non-redundant MAGs from morphologically distinct Trichodesmium colonies (tufts, dense and thin puffs). T. thiebautii (puffs) and T. erythraeum (tufts) were the dominant species within these morphotypes. While subspecies diversity is present for both T. thiebautii and T. erythraeum, a single T. thiebautii genotype comprised both thin and dense puff morphotypes, and we therefore hypothesize that the phenotypic variation between these morphologies is likely attributed to gene regulation. Additionally, we found the rare non-diazotrophic clade IV and V genotypes, related to T. nobis and T. miru respectively, that likely occurred as single filaments. HetR gene phylogeny indicates that the genotype in clade IV could represent the species T. contortum.

We further show that hetR phylotyping can overestimate the taxonomic diversity of Trichodesmium, as two copies of the hetR gene were present within T. thiebautii genomes, one of which misidentified this lineage as T. aureum. Taken together, our results highlight the importance of re-assessing Trichodesmium taxonomy while showing the ability of genomics to capture the complex diversity and distribution of Trichodesmium populations.


title: Shrimp vaccination with insect-adapted yellow head virus (YHV) extends survival upon YHV challenge

abstract: This short paper on yellow head virus Type1 (YHV-1) describes preliminary research worthy of further study. YHV-1 disease outbreaks can cause severe mortality in the cultivated shrimp Penaeus (Penaeus) monodon and Penaeus (Litopenaeus) vannamei. No practical preventative treatment such as vaccination has been reported. However, it has been shown that C6/36 mosquito cell cultures can adapt to YHV-1 and become persistently immunopositive for the virus after 30 split-cell passages or more. Shrimp injection with homogenates from low passages caused yellow head disease (YHD) but from high passages did not, even though injection resulted in immunopositive hemocytes in the injected shrimp. This suggested YHV-1 attenuation during insect cell passaging and the possibility of using cell homogenates as a vaccine to protect shrimp against virulent YHV-1. To test this hypothesis, we injected shrimp with 30th passage homogenates to test for protection against YHD upon subsequent challenge with virulent YHV-1. Results confirmed earlier work that hemocytes of the infected shrimp became both reverse transcriptase PCR positive and immunopositive for YHV-1 but exhibited no mortality. Similarly, there was no mortality in the control group injected with homogenate from YHV-1 negative insect cells. When subsequently challenged with YHV-1, shrimp in the positive control group injected with homogenate from naive insect cells gave 100 percent mortality within 7 days post challenge while total mortality in the group injected with YHV-1 homogenate did not occur until day 9 post challenge. Kaplan-Meier log-rank survival analysis revealed that survival curves for the two groups were significantly different (p<0.001) and that the mean survival time for the test group (6.5 days) was significantly longer than that in the positive control group (5.4 days). The results confirmed that shrimp injection with YHV-1 immunopositive insect-cell homogenate gave transient resistance to YHV infection and that further research into the possible use of insect cell lines to produce shrimp antiviral vaccines is warranted.


title: The evolution of colistin resistance increases bacterial resistance to host antimicrobial peptides and virulence

abstract: Antimicrobial peptides (AMPs) offer a promising solution to the antibiotic resistance crisis. However, an unresolved serious concern is that the evolution of resistance to therapeutic AMPs may generate cross-resistance to host AMPs, compromising a cornerstone of the innate immune response. We systematically tested this hypothesis using globally disseminated mobile colistin resistance (MCR) that has been selected by the use of colistin in agriculture and medicine. Here we show that MCR provides a selective advantage to E. coli in the presence of key AMPs from humans and agricultural animals by increasing AMP resistance. Moreover, MCR promotes bacterial growth in human serum and increases virulence in a Galleria mellonella infection model. Our study shows how the anthropogenic use of AMPs can drive the accidental evolution of resistance to the innate immune system of humans and animals. These findings have major implications for the design and use of therapeutic AMPs and they suggest that MCR will be difficult to eradicate, even if colistin use is withdrawn.


title: Discovery of Flaviviridae-derived endogenous viral elements in shrew genomes provide novel insights into Pestivirus ancient history

abstract: As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large dataset of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members, including major human pathogens such as Zika, dengue, or hepatitis C viruses. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.


title: Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functioning CopA in Environmental Microbiomes

abstract: Exploring natural diversity of functional genes/proteins from environmental DNA (eDNA) in a high-throughput fashion remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 88 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits. Manual curation of 1214 hits of high-confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually 175 novel copA sequences of high-quality were discovered. Phylogenetic analysis showed that almost all of these putative CopA proteins are distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli ({Delta}copA). Growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake. One recombinant harboring copA-like 15 (copAL15) successfully restored Cu resistance of host with a substantially enhanced Cu uptake. Two novel copA genes were fused with the gfp gene and expressed in E. coli for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.


title: Fitness costs of pfhrp2 and pfhrp3 deletions underlying diagnostic evasion in malaria parasites

abstract:
BackgroundRapid diagnostic tests based on detection of histidine rich proteins (HRP) are widely used for malaria diagnosis, but parasites carrying pfhrp deletions can evade detection and are increasing in frequency in some countries. Models aim to predict conditions under which pfhrp2 and/or pfhrp3 deletions will increase, but a key parameter - the fitness cost of deletions - is unknown

MethodsWe removed pfhrp2 and/or pfhrp3 from a Malawian parasite clone using CRISPR/Cas9 and measured fitness costs by conducting pairwise competition experiments.

ResultsWe observed significant fitness costs of 0.087 {+/-} 0.008 (1 s.e.) per asexual cycle for pfhrp2 deletion and 0.113 {+/-} 0.008 (1 s.e.) for the pfhrp2/3 double deletion, relative to the unedited progenitor parasite. The results demonstrate [~]10% reduced survival of parasites bearing deletions of these loci.

ConclusionsPrior modelling suggested that diagnostic selection may drive increased frequency of pfhrp2 and pfhrp3 deletions when fitness costs are [≤]10%. Our laboratory competition experiments are consistent with costs of pfhrp2/3 deletions lying at this critical tipping point. These results may inform future modelling efforts and help us to understand why pfhrp2/3 deletions are increasing in some locations (Ethiopia/Eritrea) but not in others (Mekong region).


title: Bacterial outer-membrane polysaccharide export (OPX) proteins occupy three structural classes with selective β-barrel porin requirements for polymer secretion

abstract: Secretion of high-molecular-weight polysaccharides across the bacterial envelope is ubiquitous as it enhances prokaryotic survival in (a)biotic settings. Such polymers are often assembled by Wzx/Wzy- or ABC transporter-dependent schemes that implicate outer-membrane (OM) polysaccharide export (OPX) proteins in polymer translocation to the cell surface. In the social predatory bacterium Myxococcus xanthus, exopolysaccharide (EPS)-pathway WzaX, major spore coat (MASC)-pathway WzaS, and biosurfactant polysaccharide-pathway WzaB were herein found to be truncated OPX homologues of Escherichia coli Wza lacking OM-spanning -helices. Comparative genomics across all bacteria, complemented with cryo-electron tomography cell- envelope analyses, revealed WzaX/S/B architecture to be the most common amongst three defined OPX-protein structural classes independent of periplasmic thickness. Fold-recognition and deep- learning analyses revealed the conserved M. xanthus proteins MXAN_7418/3226/1916 (encoded adjacent to WzaX/S/B) to be integral OM {beta}-barrels, with structural homology to the poly-N-acetyl-D- glucosamine synthase-dependent pathway porin PgaA. Such porins were identified in bacteria near numerous genes for all three OPX-protein classes. Interior MXAN_7418/3226/1916 {beta}-barrel electrostatics were found to match known properties of their associated polymers. With MXAN_3226 essential for MASC export, and MXAN_7418 absence shown herein to compromise EPS translocation, these data support a novel secretion paradigm for Wzx/Wzy-dependent pathways in which those containing an OPX component that cannot span the OM instead utilize a {beta}-barrel porin to mediate polysaccharide transport across the OM.


title: Why FIT and bHLH Ib interdependently regulate Fe-uptake

abstract: FIT (FER-LIKE IRON DEFICIENCY- INDUCED TRANSCRIPTION FACTOR) and four bHLH Ib transcription factors (TFs) bHLH38, bHLH39, bHLH100 and bHLH101, are the master regulators of Fe uptake genes, and they interact with each other to activate the Fe uptake systems. However, it remains unclear why FIT and bHLH Ib depend on each other to regulate the Fe deficiency response. By analyzing Fe deficiency phenotypes and Fe uptake genes, we found that the quadruple bhlh4x mutants (bhlh38 bhlh39 bhlh100 bhlh101) mimic the fit mutant. Subcellular localization analyses indicate that bHLH38 and bHLH39 are preferentially expressed in the cytoplasm whereas bHLH100 and bHLH101 in the nucleus. Transcriptome data show that the genes involved in Fe signaling pathway show the same expression trends in bhlh4x and fit. Genetic analyses suggest that FIT and bHLH Ib depend each other to regulate the Fe deficiency response. Further biochemical assays indicate that bHLH Ib TFs possess the DNA binding ability and FIT has the transcription activation ability. This work concludes that FIT and bHLH Ib form a functional transcription complex in which bHLH Ib is responsible for target recognition and FIT for transcription activation, explaining why FIT and bHLH Ib interdependently regulate Fe uptake.

category: molecular biology


title: Relevance study of vector competence and insecticide resistance in Aedes aegypti laboratory lines

abstract:
The urban mosquito species Aedes aegypti is the main vector of arboviruses worldwide. Mosquito control with insecticides is the most prevalent method for preventing transmission in the absence of effective vaccines and available treatments; however, the extensive use of insecticides has led to the development of resistance in mosquito populations throughout the world, and the number of epidemics caused by arboviruses has increased.

Three mosquito lines with different resistance profiles to deltamethrin were isolated in French Guiana, including one with the I1016 knock-down resistant allele. Significant differences were observed in the cumulative proportion of mosquitoes with a disseminated chikungunya virus infection over time. In addition, certain genes (CYP6BB2, CYP6N12, GST2, trypsin) were variably overexpressed in the midgut at 7 days after an infectious blood meal in these three lines. Therefore, detoxification enzymes and kdr mutations may contribute to an enhanced midgut barrier and reduced dissemination rate.

Our work shows that vector competence for chikungunya virus varied between Ae. aegypti laboratory lines with different deltamethrin-resistance profiles. More accurate verification of the functional association between insecticide resistance and vector competence remains to be demonstrated.

ImportanceThree Ae. aegypti lines, isolated from the same collection site, underwent different insecticide selection pressures against deltamethrin under laboratory conditions. As a result, they developed different resistant profiles. In this study, when these lines were fed an artificial infectious blood meal containing chikungunya virus, all three lines including the reference strain showed a high infection rate. There was no statistical difference in infection rate found; however, the dissemination rate of the virus from midgut to head were significantly different. A higher resistance level detected by the WHO test was correlated with a lower viral dissemination rate for each strain. This study presented evidence that the insecticide selection pressure or the existence of insecticide resistance could lead to differences in viral dissemination or even transmission in mosquito populations. We hope that our study can give more insights into understanding the roles of mosquito insecticide resistance on viral transmission.


title: Improved Predictions Of MHC-Peptide Binding Using Protein Language Models

abstract: AO_SCPLOWBSTRACTC_SCPLOWMajor histocompatibility complex (MHC) molecules bind to peptides from exogenous antigens, and present them on the surface of cells, allowing the immune system (T cells) to detect them. Elucidating the process of this presentation is essential for regulation and potential manipulation of the cellular immune system [1]. Predicting whether a given peptide will bind to the MHC is an important step in the above process, motivating the introduction of many computational approaches. NetMHCPan [2], a pan-specific model predicting binding of peptides to any MHC molecule, is one of the most widely used methods which focuses on solving this binary classification problem using a shallow neural network. The successful results of AI methods, especially Natural Language Processing (NLP-based) pretrained models in various applications including protein structure determination, motivated us to explore their use in this problem as well. Specifically, we considered fine-tuning these large deep learning models using as dataset the peptide-MHC sequences. Using standard metrics in this area, and the same training and test sets, we show that our model outperforms NetMHCpan4.1 which has been shown to outperform all other earlier methods [2].


title: Polymorphic ribonucleoprotein folding as a basis for translational regulation

abstract:
The widely occurring bacterial RNA chaperone Hfq is a key factor in the post-transcriptional control of hundreds of genes in Pseudomonas aeruginosa. How this broadly acting protein can contribute to the regulation requirements of so many different genes remains puzzling. Here, we describe the structures of higher-order assemblies formed on control regions of different P. aeruginosa target mRNAs by Hfq and its partner protein Crc. Our results show that these assemblies have mRNA-specific quaternary architectures resulting from the combination of multivalent protein-protein interfaces and recognition of patterns in the RNA sequence. The structural polymorphism of the ribonucleoprotein assemblies enables selective translational repression of many different target mRNAs. This system suggests how highly complex regulatory pathways can evolve and be rewired with a simple economy of proteinogenic components.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/480102v1_ufig1.gif" ALT="Figure 1">
View larger version (34K):
org.highwire.dtl.DTLVardef@1b34242org.highwire.dtl.DTLVardef@1c31071org.highwire.dtl.DTLVardef@16c8750org.highwire.dtl.DTLVardef@27ca3c_HPS_FORMAT_FIGEXP  M_FIG C_FIG The RNA chaperone Hfq, in conjunction with the co-repressor Crc, forms higher order assemblies on nascent mRNAs. These complexes impact on translation of hundreds of transcripts in the pathogen Pseudomonas aeruginosa. Assemblies with different quaternary structures result from the interactions of the proteins with sequence motifs and structural elements in different mRNA targets, as well as from a repertoire of protein-to-protein interfaces. In this way, the combination of RNA sequence and two proteins can generate the diversity required to regulate many genes. It is proposed that the multi-step assembly process is highly cooperative and most likely competes kinetically with translation initiation to silence the targeted transcripts.


title: Cross-modality Synthesis of EM Time Series and Live Fluorescence Imaging

abstract:
Analyses across imaging modalities allow the integration of complementary spatiotemporal information about brain development, structure and function. However, systematic atlasing across modalities is limited by challenges to effective image alignment. We combine highly spatially resolved electron microscopy (EM) and highly temporally resolved time-lapse fluorescence microscopy (FM) to examine the emergence of a complex nervous system in C. elegans embryogenesis. We generate an EM pseudo time series at four classic developmental stages and create a landmark-based co-optimization algorithm for cross-modality image alignment, which handles developmental heterochrony among datasets to achieve accurate single-cell level alignment. Synthesis based on the EM series and time-lapse FM series carrying different cell-specific markers reveals critical dynamic behaviors across scales of identifiable individual cells in the emergence of the primary neuropil, the nerve ring, as well as a major sensory organ, the amphid. Our study paves the way for systematic cross-modality analysis in C. elegans and demonstrates a powerful approach that may be applied broadly.

HighlightsO_LIAn EM time series to examine the emergence of an entire nervous system
C_LIO_LIA landmark-based co-optimization algorithm for cross modality image alignment in the presence of developmental heterochrony
C_LIO_LIIntegration of EM and fluorescence series reveals cell behaviors at high spatial and temporal resolution
C_LIO_LISystematic single-cell annotation of EM data enables efficient navigation and targeted re-imaging
C_LI

category: developmental biology


title: Speciation in Nearctic oak gall wasps is frequently correlated with changes in host plant, host organ, or both.

abstract: Quantifying the frequency of shifts to new host plants within diverse clades of specialist herbivorous insects is critically important to understand whether and how host shifts contribute to the origin of species. Oak gall wasps (Hymenoptera: Cynipidae: Cynipini) comprise a tribe of ~1000 species of phytophagous insects that induce gall formation on various organs of trees in the family Fagacae, -- primarily the oaks (genus Quercus; ~435 sp). The association of oak gall wasps with oaks is ancient (~50 my), and most oak species are galled by one or more gall wasp species. Despite the diversity of both gall wasp species and their plant associations, previous phylogenetic work has not identified a strong signal of host plant shifting among oak gall wasps. However, most emphasis has been on the Western Palearctic and not the Nearctic where both oaks and oak gall wasps are considerably more species rich and where oaks are more phylogenetically diverse. We collected 86 species of Nearctic oak gall wasps from 10 of the 14 major clades of Nearctic oaks and sequenced >1000 Ultra Conserved Elements (UCEs) and flanking sequences to infer wasp phylogenies. We assessed the relationships of Nearctic gall wasps to one another and, by leveraging previously published UCE data, to the Palearctic fauna. We then used phylogenies to infer historical patterns of shifts among host tree species and tree organs. Our results indicate that oak gall wasps have moved between the Palearctic and Nearctic at least four times, that some Palearctic clades have their proximate origin in the Nearctic, and that gall wasps have shifted within and between oak tree sections, subsections, and organs considerably more often than the analysis of previous data have suggested. Given that host shifts have been demonstrated to drive reproductive isolation between host-associated populations in other phytophagous insects, our analyses of Nearctic gall wasps suggest that host shifts are key drivers of speciation in this clade, especially in hotspots of oak diversity. Though formal assessment of this hypothesis requires further study, two putatively oligophagous gall wasp species in our dataset show signals of host-associated genetic differentiation unconfounded by geographic distance, suggestive of barriers to gene flow associated with the use of alternative host plants.


title: Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates

abstract:
HIV-1 is a rapidly evolving virus able to evade host immunity through rapid adaptation during chronic infection. The HIV-1 group M has diversified since its zoonosis into several subtypes at a rate of the order of 10-3 changes per site per year. This rate varies between different parts of the genome and its inference is sensitive to the time scale and diversity spanned by the sequence data used. Higher rates are estimated on short time scales and particularly for within-host evolution, while rate estimates spanning decades or the entire HIV-1 pandemic tend to be lower. The underlying causes of this difference are not well understood.

We investigate here the role of rapid reversions toward a preferred evolutionary sequence state on multiple time scales. We show that within-host reversion mutations are under positive selection and contribute substantially to sequence turnover, especially at conserved sites. We then use the rates of reversions and non-reversions estimated from longitudinal within-host data to parametrize a phylogenetic sequence evolution model. Sequence simulation of this model on HIV-1 phylogenies reproduces diversity and apparent evolutionary rates of HIV-1 in gag and pol, suggesting that a tendency to rapidly revert to a consensus-like state can explain much of the time dependence of evolutionary rate estimates in HIV-1.


title: Strength of stabilizing selection on the amino-acid sequence is associated with the amount of non-additive variance in gene expression.

abstract: The distinction between the additive and non-additive components of genetic trait variance has long been known to be crucial for predicting the potential of a population to respond to selection. Yet we know surprisingly little about the genomic and evolutionary factors that influence non-additive genetic variance in natural populations. Here, we use a quantitative genetic breeding design to delineate the additive and non-additive components of expression variance of 17,657 gene transcripts in the outcrossing plant Arabidopsis lyrata. We find that most of the genetic variance in gene expression is from non-additive variance. Transcripts showing the highest levels of non-additive variance tend to be longer, clustered in larger groups of co-expressed genes, and enriched in functions related to cellular differentiation or to the epigenetic reprogramming of gene expression. Furthermore, we find that genes with the most non-additive variation not only display a markedly lower rate of synonymous variation, they are also exposed to stronger stabilizing selective forces than genes with high additive variance. To the best of our knowledge, this study is the first to show that stabilizing selection on amino-acid sequences is associated with a decrease in a populations potential for adaptation of gene expression levels.

category: genetics