title: Long-term molecular turnover of actin stress fibers revealed by advection-reaction analysis in fluorescence recovery after photobleaching

abstract: Fluorescence recovery after photobleaching (FRAP) is a versatile technique to evaluate the intracellular molecular exchange called turnover. Physicochemical models of FRAP typically consider the molecular diffusion and chemical reaction that simultaneously occur on a time scale of seconds to minutes. Particularly for long-term measurements, however, an advection effect can no longer be ignored, which transports the proteins in specific directions within the cells and accordingly shifts the spatial distribution of the local chemical equilibrium. Nevertheless, existing FRAP models have not considered the spatial shift, and as such, the turnover rate is often analyzed without considering the spatiotemporally updated chemical equilibrium. Here we develop a new FRAP model aimed at long-term measurements to quantitatively determine the two distinct effects of the advection and chemical reaction, i.e., the different major sources of the change in fluorescence intensity. To validate this approach, we carried out FRAP experiments on actin in stress fibers over a time period of more than 900 s, and the advection rate was shown to be comparable in magnitude to the chemical dissociation rate. We further found that the actin-myosin interaction and actin polymerization differently affect the advection and chemical dissociation. Our results thus suggest that the distinction between the two effects is indispensable to extract the intrinsic chemical properties of the actin cytoskeleton from the observations of complicated turnover in cells.


title: Urocortin 3 in the posterodorsal medial amygdala mediates psychosocial stress-induced suppression of LH pulsatility in female mice

abstract: Exposure to psychosocial stress disrupts reproductive function and interferes with pulsatile luteinising hormone (LH) secretion in mammals. The posterodorsal sub-nucleus of the medial amygdala (MePD) is part of the limbic brain and is an upstream modulator of the reproductive axis as well as stress and anxiety states. Corticotropin releasing factor type-2 receptors (CRFR2) are activated in the presence of psychosocial stress together with an increased expression of the CRFR2 ligand Urocortin3 (Ucn3) in MePD of rodents. We investigate whether Ucn3 signalling in the MePD is involved in mediating the suppressive effect of psychosocial stress exposure on LH pulsatility. Firstly, we administered Ucn3 into the MePD and monitored the effect on pulsatile LH secretion in ovariectomised mice. Next, we delivered Astressin2B, a highly selective CRFR2 antagonist, intra-MePD in the presence of predator odor, 2,4,5-Trimethylthiazole (TMT) and examined the effect on LH pulses. Subsequently, we virally infected ovariectomised Ucn3-cre-tdTomato mice with inhibitory DREADDs targeting the MePD Ucn3 neurons while exposing the mice to TMT or restraint stress and examined the effect on LH pulsatility as well as corticosterone (CORT) release. Administration of Ucn3 into the MePD dose-dependently inhibited pulsatile LH secretion and intra-MePD administration of Astressin2B blocked the suppressive effect TMT on LH pulsatility. Additionally, DREADDs inhibition of MePD Ucn3 neurons blocked TMT and restraint stress-induced inhibition of LH pulses as well as CORT release in the presence of TMT. These results demonstrate for the first time that Ucn3 neurons in the MePD mediate psychosocial stress-induced suppression of the GnRH pulse generator and psychosocial stress-induced CORT secretion. Ucn3 signalling in the MePD plays a fundamental role in modulating the hypothalamic-pituitary-ganadal and hypothalamic-pituitary-adrenal axes, and this brain locus may represent a nodal centre in the crosstalk between the reproductive and stress axes.

category: physiology


title: Developmental plasticity in visual cortex is necessary for normal visuomotor integration and visuomotor skill learning

abstract:
The experience of coupling between motor output and visual feedback is necessary for the development of visuomotor skills and shapes visuomotor integration in visual cortex. Whether these experience-dependent changes involve plasticity in visual cortex remains unclear. Here, we probed the role of NMDA receptor-dependent plasticity in mouse primary visual cortex (V1) during visuomotor development. Using a conditional knockout of NMDA receptors and a photoactivatable inhibitor of CaMKII, we locally perturbed plasticity in V1 during first visual experience, recorded neuronal activity in V1, and tested the mice in a visuomotor task. We found that perturbing plasticity before, but not after, first visuomotor experience reduces responses to unpredictable stimuli, diminishes the suppression of predictable feedback in V1, and impairs visuomotor skill learning later in life. Our results demonstrate that plasticity in the local V1 circuit during early life is critical for shaping visuomotor integration.

*** Dear reader, please note this manuscript is formatted in a standard submission format, and all statistical information is provided in Table S1. ***

O_TBL View this table:
org.highwire.dtl.DTLVardef@4a9283org.highwire.dtl.DTLVardef@1d903beorg.highwire.dtl.DTLVardef@84b2f8org.highwire.dtl.DTLVardef@1d4c5org.highwire.dtl.DTLVardef@37d9b8_HPS_FORMAT_FIGEXP  M_TBL O_FLOATNOTable S1.C_FLOATNO O_TABLECAPTIONStatistics All values are rounded to two significant decimals, except values smaller than 10-5. The tests used, were two-sample independent t-test (t-test 2), one sample t-test (t-test 1), or a bootstrap estimate of the 95% confidence interval (CI).

C_TABLECAPTION C_TBL

category: neuroscience


title: UNIGEMS: plasmids and parts to facilitate teaching on assembly, gene expression control and logic in E. coli

abstract: Synthetic biology is as an excellent vehicle for education, as it enables creative combination of engineering and molecular biology approaches for quantitative characterisations of the assembled constructs. However, there is a limited number of resources available for such applications in the educational context, where straightforward setup, easily measurable phenotypes and extensibility are of particular importance. To expand the availability of education-friendly resources to teach synthetic biology and genetic engineering, we developed Unigems, a set of 10 plasmids that enable out-of-the-box investigations of principles of gene expression control, as well as more complex designs a biological logic gate. The system uses a common high-copy plasmid backbone and a common set of primers to enable Gibson-assembly of PCR-generated or synthesised parts into a target vector. It currently has two reporter genes with either two constitutive (high- or low-level) or two inducible (lactose- or arabinose-) promoters, as well as a single-plasmid implementation of an AND logic gate. The Unigems system has already been employed in undergraduate teaching settings, during outreach events and for training of iGEM teams. All plasmids have been deposited in Addgene.

category: synthetic biology


title: Lipid droplets protect human β cells from lipotoxic-induced stress and cell identity changes

abstract: Free fatty acids (FFAs) are often stored in lipid droplet (LD) depots for eventual metabolic and/or synthetic use in many cell types, such a muscle, liver, and fat. In pancreatic islets, overt LD accumulation was detected in humans but not mice. LD buildup in islets was principally observed after roughly 11 years of age, increasing throughout adulthood under physiologic conditions, and also enriched in type 2 diabetes. To obtain insight into the role of LDs in human islet {beta} cell function, the levels of a key LD structural protein, perilipin2 (PLIN2), were manipulated by lentiviral-mediated knock-down (KD) or over-expression (OE) in EndoC{beta}H2-Cre cells, a human cell line with adult islet {beta}-like properties. Glucose stimulated insulin secretion was blunted in PLIN2KD cells and improved in PLIN2OE cells. An unbiased transcriptomic analysis revealed that limiting LD formation induced effectors of endoplasmic reticulum (ER) stress that compromised the expression of critical {beta} cell function and identity genes. These changes were aggravated by exogenous treatment with FFAs toxic to islet {beta} cells, and essentially reversed by PLIN2OE or using the ER stress inhibitor, tauroursodeoxycholic acid. These results strongly suggest that LDs are essential for adult human islet {beta} cell activity by preserving FFA homeostasis.

category: cell biology


title: A tripartite cytolytic toxin formed by Vibrio cholerae proteins with flagellum-facilitated secretion

abstract:
The protein MakA was discovered as a motility-associated secreted toxin from Vibrio cholerae, Here, we show that MakA is part of a gene cluster encoding four additional proteins: MakB, MakC, MakD and MakE. The MakA, MakB and MakE proteins were readily detected in culture supernatants of wild type V. cholerae whereas secretion was very much reduced from a flagellum deficient mutant. Crystal structures of MakA, MakB and MakE revealed structural relationship to a superfamily of bacterial pore-forming proteins. Cloning and expression of MakA/B/E in Escherichia coli resulted in toxicity of the bacteria towards Caenorhabditis elegans used as a predatory organism model. None of these Mak proteins alone or in pairwise combinations were cytolytic but an equimolar mixture of MakA, MakB and MakE acted as a tripartite cytolytic toxin in vitro causing lysis of erythrocytes and cytotoxicity on cultured human colon carcinoma cells. Formation of oligomeric complexes on liposomes was observed by electron microscopy. Oligomer interaction with membranes was initiated by MakA membrane binding followed by MakB and MakE joining in formation of a pore structure. A predicted membrane insertion domain of MakA was shown by site-directed mutagenesis to be essential for toxicity towards C. elegans. Bioinformatic analyses revealed that the makCDBAE gene cluster is present as a novel genomic island in the vast majority of sequenced genomes of V. cholerae and the fish pathogen V. anguillarum. We suggest that the hitherto unrecognized cytolytic MakA/B/E toxin can contribute to Vibrionaceae fitness and virulence potential in different host environments and organisms.

Significance StatementVibrio cholerae, responsible for outbreaks and pandemics of cholera disease, is a highly motile organism by virtue of a single flagellum. We describe that the flagellum facilitates the secretion of three V. cholerae proteins encoded by a hitherto unrecognized novel genomic island. The proteins MakA/B/E can form a tripartite cytolytic toxin that lyses erythrocytes and is cytotoxic to cultured human cells. A structural basis for the Mak protein cytolytic activity was obtained by X-ray crystallography. Flagellum-facilitated secretion, remarkably ensuring spatially co-ordinated delivery of Mak proteins, revealed a new role for the V. cholerae flagellum considered of particular significance for the bacterial environmental persistence. Our findings will pave the way for the development of new diagnostics and therapeutic strategies against pathogenic Vibrionaceae.

category: biochemistry


title: 3D structure and in situ arrangements of CatSper channel in the sperm flagellum

abstract: The sperm calcium channel CatSper plays a central role in successful fertilization as a primary Ca2+ gateway into the sperm flagellum. However, CatSpers complex subunit composition has impeded its reconstitution in vitro and structural elucidation. Here, we applied cryo-electron tomography to visualize the macromolecular organization of the native CatSper channel complex in intact mammalian sperm, as well as identified three additional CatSper-associated proteins. The repeating CatSper units form long zigzag-rows in four nanodomains along the flagella. In both mouse and human sperm, each CatSper repeat consists of a tetrameric pore complex. Murine CatSper contains an additional outwardly directed wing-structure connected to the tetrameric channel. The majority of the extracellular domains form a canopy above each pore-forming channel that interconnects to a zigzag-shaped roof. The intracellular domains link two neighboring channel complexes to a diagonal array. The loss of this intracellular link in Efcab9-/- sperm distorts the longitudinally aligned zigzag pattern and compromises flagellar movement. This work offers unique insights into the mechanisms underlying the assembly and transport of the CatSper complex to generate the nanodomains and provides a long-sought structural basis for understanding CatSper function in the regulation of sperm motility.

category: biophysics


title: Selectively expressing SARS-CoV-2 Spike protein S1 subunit in cardiomyocytes induces cardiac hypertrophy in mice.

abstract: Cardiac injury is common in hospitalized COVID-19 patients and portends poorer prognosis and higher mortality. To better understand how SARS-CoV-2 (CoV-2) damages the heart, it is critical to elucidate the biology of CoV-2 encoded proteins, each of which may play multiple pathological roles. For example, CoV-2 Spike glycoprotein (CoV-2-S) not only engages ACE2 to mediate virus infection, but also directly impairs endothelial function and can trigger innate immune responses in cultured murine macrophages. Here we tested the hypothesis that CoV-2-S damages the heart by activating cardiomyocyte (CM) innate immune responses. HCoV-NL63 is another human coronavirus with a Spike protein (NL63-S) that also engages ACE2 for virus entry but is known to only cause moderate respiratory symptoms. We found that CoV-2-S and not NL63-S interacted with Toll-like receptor 4 (TLR4), a crucial pattern recognition receptor that responsible for detecting pathogen and initiating innate immune responses. Our data show that the S1 subunit of CoV-2-S (CoV-2-S1) interacts with the extracellular leucine rich repeats-containing domain of TLR4 and activates NF-kB. To investigate the possible pathological role of CoV-2-S1 in the heart, we generated a construct that expresses membrane-localized CoV-2-S1 (S1-TM). AAV9-mediated, selective expression of the S1-TM in CMs caused heart dysfunction, induced hypertrophic remodeling, and elicited cardiac inflammation. Since CoV-2-S does not interact with murine ACE2, our study presents a novel ACE2-independent pathological role of CoV-2-S, and suggests that the circulating CoV-2-S1 is a TLR4-recognizable alarmin that may harm the CMs by triggering their innate immune responses.

category: pathology


title: Localization of planteose hydrolysis during seed germination of Orobanche minor

abstract:
Root parasitic weeds of the Orobanchaceae, such as witchweeds (Striga spp.) and broomrapes (Orobanche and Phelipanche spp.), cause serious losses in agriculture worldwide. No practical method to control these parasitic weeds has been developed to date. Understanding the characteristic physiological processes in the life cycles of root parasitic weeds is particularly important to identify specific targets for growth modulators. In our previous study, planteose metabolism was revealed to be activated soon after the perception of strigolactones in germinating seeds of O. minor. Nojirimycin inhibited planteose metabolism and impeded seed germination of O. minor, indicating that planteose metabolism is a possible target for root parasitic weed control. In the present study, we investigated the distribution of planteose in dry seeds of O. minor by matrix-assisted laser desorption/ionization-mass spectrometry imaging. Planteose was detected in tissues surrounding--but not within--the embryo, supporting its suggested role as a storage carbohydrate. Biochemical assays and molecular characterization of an -galactosidase family member, OmAGAL2, indicated the enzyme is involved in planteose hydrolysis in the apoplast around the embryo after the perception of strigolactones to provide the embryo with essential hexoses for germination. These results indicated that OmAGAL2 is a potential molecular target for root parasitic weed control.

HighlightPlanteose accumulated in tissues surrounding the embryo in Orobanche minor dry seeds and was indicated to be hydrolyzed in the apoplast around the embryo by -galactosidase during germination.

category: plant biology


title: Distinct Processing of Sensory Prediction Error and Task Error during Motor Learning

abstract:
Implicit motor recalibration allows us to flexibly move in novel and changing environments. Conventionally, implicit recalibration is thought to be driven by errors in predicting the sensory outcome of movement (i.e., sensory prediction errors). However, recent studies have shown that implicit recalibration is also influenced by errors in achieving the movement goal (i.e., task errors). Exactly how sensory prediction errors and task errors interact to drive implicit recalibration and, in particular, whether task errors alone might be sufficient to drive implicit recalibration remain unknown. To test this, we induced task errors in the absence of sensory prediction errors by displacing the target mid-movement. We found that task errors alone failed to induce implicit recalibration. In additional experiments, we simultaneously varied the size of sensory prediction errors and task errors. We found that implicit recalibration driven by sensory prediction errors could be continuously modulated by task errors, revealing an unappreciated dependency between these two sources of error. Moreover, implicit recalibration was attenuated when the target was simply flickered in its original location, even though this manipulation did not affect task error - an effect likely attributed to attention being directed away from the feedback cursor. Taken as a whole, the results were accounted for by a computational model in which sensory prediction errors and task errors, modulated by attention, interact to determine the extent of implicit recalibration.

Authors summaryWhat information does the brain use to maintain precise calibration of the sensorimotor system? Using a reaching task paired with computational modeling, we find that movements are implicitly recalibrated by errors in predicting both the sensory outcome of movement (i.e., sensory prediction errors) as well as errors in achieving the movement goal (i.e., task errors). Even though task errors alone do not elicit implicit recalibration, they nonetheless modulate implicit recalibration when sensory prediction error is present. The results elucidate an unappreciated interaction between these two sources of error in driving implicit recalibration.


title: Interactions between sensory prediction error and task error during implicit motor learning


title: Gaze-Related Activity in Primate Frontal Cortex Predicts and Mitigates Spatial Uncertainty

abstract: A remarkable feature of primate behavior is the ability to predict future events based on past experience and current sensory cues. To understand how the brain plans movements in the presence of unstable cues, we recorded gaze-related activity in the frontal cortex of two monkeys engaged in a quasi-predictable cue-conflict task. Animals were trained to look toward remembered visual targets in the presence of a landmark that shifted with fixed amplitude but randomized direction. As simulated by a probabilistic model based on known physiology/behavior, gaze end points assumed a circular distribution around the target, mirroring the possible directions of the landmark shift. This predictive strategy was reflected in frontal cortex activity (especially supplementary eye fields), which anticipated future gaze distributions before the actual landmark shift. In general, these results implicate prefrontal cortex in the predictive integration of environmental cues and their learned statistical properties to mitigate spatial uncertainty.


title: An IRF4-MYC-mTORC1 integrated pathway controls cell growth and the proliferative capacity of activated B cells during B cell differentiation in vivo

abstract: Cell division is an essential component of B cell differentiation to antibody-secreting plasma cells, with critical reprogramming occurring during the initial stages of B cell activation. However, a complete understanding of the factors that coordinate early reprogramming events in vivo remain to be determined. In this study, we examined the initial reprogramming by IRF4 in activated B cells using an adoptive transfer system and mice with a B cell-specific deletion of IRF4. IRF4-deficient B cells responding to influenza, NP-Ficoll and LPS divided, but stalled during the proliferative response. Gene expression profiling of IRF4-deficient B cells at discrete divisions revealed IRF4 was critical for inducing MYC target genes, oxidative phosphorylation, and glycolysis. Moreover, IRF4-deficient B cells maintained an inflammatory gene expression signature. Complementary chromatin accessibility analyses established a hierarchy of IRF4 activity and identified networks of dysregulated transcription factor families in IRF4-deficient B cells, including E-box binding bHLH family members. Indeed, B cells lacking IRF4 failed to fully induce Myc after stimulation and displayed aberrant cell cycle distribution. Furthermore, IRF4-deficient B cells showed reduced mTORC1 activity and failed to initiate the B cell-activation unfolded protein response and grow in cell size. Myc overexpression in IRF4-deficient was sufficient to overcome the cell growth defect. Together, these data reveal an IRF4-MYC-mTORC1 relationship critical for controlling cell growth and the proliferative response during B cell differentiation.

category: immunology


title: Microbiome diversity and host immune functions may define the fate of sponge holobionts under future ocean conditions

abstract: The sponge-associated microbial community contributes to the overall health and adaptive capacity of the sponge holobiont. This community is regulated by the environment, as well as the immune system of the host. However, little is known about the effect of environmental stress on the regulation of host immune functions and how this may, in turn, affect sponge-microbe interactions. In this study, we compared the microbiomes and immune repertoire of two sponge species, the demosponge, Neopetrosia compacta and the calcareous sponge, Leucetta chagosensis, under varying levels of acidification and warming stress. Neopetrosia compacta harbors a diverse bacterial assemblage and possesses a rich repertoire of scavenger receptors while L. chagosensis has a less diverse microbiome and an expanded range of pattern recognition receptors and proteins with immunological domains. Upon exposure to warming and acidification, the microbiome and host transcriptome of N. compacta remained stable, which correlated with high survival. In contrast, the bacterial community of L. chagosensis exhibited drastic restructuring and widespread downregulation of host immune-related pathways, which accompanied tissue necrosis and mortality. Differences in microbiome diversity and immunological repertoire of diverse sponge groups highlight the central role of host-microbe interactions in predicting the fate of sponges under future ocean conditions.

category: microbiology


title: RPRD Proteins Control Transcription in Human Cells

abstract: The regulation of transcription is an essential process that allows the cell to respond to various internal and external signals. RNA Polymerase II (Pol II) activity is controlled by a number of factors which bind to the C-terminal domain (CTD) of its largest subunit, RPB1, and stimulate or suppress RNA synthesis. Here, we demonstrate that CTD-interacting proteins, RPRD2, RPRD1B and RPRD1A act as negative regulators of transcription and their levels inversely correlate with the accumulation of nascent and newly transcribed RNA in human cells. We show that the RPRD proteins form mutually exclusive complexes with Pol II to coordinate their roles in transcriptional control. Our data indicate that RPRD2 exerts the most substantial impact on transcription and has the potential to alter key biological processes including the cellular stress response and cell growth.

category: molecular biology


title: Single molecule studies reveal branched pathways for activator-dependent pre-initiation complex assembly

abstract:
RNA polymerase II (Pol II) transcription reconstituted from purified factors suggests pre-initiation complexes (PICs) can assemble by sequential incorporation of factors at the TATA box. However, these basal transcription reactions are generally independent of activators and co-activators. To study PIC assembly under more realistic conditions, we used single-molecule microscopy to visualize factor dynamics during activator-dependent reactions in nuclear extracts. Surprisingly, Pol II, TFIIF, and TFIIE can pre-assemble on enhancer-bound activators before loading into PICs, and multiple Pol II complexes can bind simultaneously to create a localized cluster. Unlike TFIIF and TFIIE, TFIIH binding is singular and dependent on the basal promoter. Activator-tethered factors exhibit dwell times on the order of seconds. In contrast, PICs can persist on the order of minutes in the absence of nucleotide triphosphates, although TFIIE remains unexpectedly dynamic even after TFIIH incorporation. Our kinetic measurements lead to a new branched model for activator-dependent PIC assembly.

HIGHLIGHTSSingle molecule microscopy reveals unexpected dynamics of RNA Pol II and GTFs

Multiple Pol IIs cluster on UAS/enhancer-bound activators before binding the core promoter

Pol II, TFIIF, and TFIIE, but not TFIIH, can pre-assemble at the UAS/enhancer

Activators increase the rates of Pol II and GTF association with DNA

eTOC BlurbSingle-molecule microscopy experiments by Baek et al. show that RNA polymerase II and basal transcription factors TFIIF and TFIIE preassemble on UAS/enhancer-bound activators, poised for loading into initiation complexes with TFIIH at the core promoter. Transcription activators kinetically enhance factor recruitment, creating a localized cluster of polymerases at the UAS/enhancer.


title: Single molecule studies reveal branched pathways for activator-dependent assembly of RNA polymerase II pre-initiation complexes


title: The novel Rab5 effector FERRY links early endosomes with the translation machinery

abstract: Local translation is vital to polarized cells such as neurons and requires a precise and robust distribution of different mRNAs and the translation machinery across the entire cell. The underlying mechanisms are poorly understood and important players are still to be identified. Here, we discovered a novel Rab5 effector complex which leads to mental retardation when genetically disrupted. The Five-subunit Endosomal Rab5 and RNA/ribosome intermediarY, FERRY complex localizes to early endosomes and associates with the translation machinery and a subset of mRNAs including mRNAs for mitochondrial proteins. It directly interacts with mRNA, thereby exhibiting different binding efficacies. Deletion of FERRY subunits reduces the endosomal localization of transcripts, indicating a role in mRNA distribution. Accordingly, FERRY-positive early endosomes harboring mRNA encoding mitochondrial proteins were observed in close proximity to mitochondria in neurons. Therefore, the FERRY complex plays a role for mRNA localization by linking early endosomes with the translation machinery.


title: easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application

abstract: Large-scale ecological sampling can be difficult and costly, especially for organisms that are too small to be easily identified in a natural environment by eye. Typically, these microscopic floral and fauna are sampled by collecting substrates from nature and then separating organisms from substrates in the laboratory. In many cases, diverse organisms can be identified to the species-level using molecular barcodes. To facilitate large-scale ecological sampling of microscopic organisms, we used a geographic data-collection platform for mobile devices called Fulcrum that streamlines the organization of geospatial sampling data, substrate photographs, and environmental data at natural sampling sites. These sampling data are then linked to organism isolation data from the laboratory. Here, we describe the easyFulcrum R package, which can be used to clean, process, and visualize ecological field sampling and isolation data exported from the Fulcrum mobile application. We developed this package for wild nematode sampling, but it is extensible to other organisms. The advantages of using Fulcrum combined with easyFulcrum are (1) the elimination of transcription errors by replacing manual data entry and/or spreadsheets with a mobile application, (2) the ability to clean, process, and visualize sampling data using a standardized set of functions in the R software environment, and (3) the ability to join disparate data to each other, including environmental data from the field and the molecularly defined identities of individual specimens isolated from samples.

category: ecology


title: Intranasal oxytocin reduces pre-courtship aggression and increases paternal response in California mice (Peromyscus californicus)

abstract:
Oxytocin (OXT) is a neuropeptide that can facilitate prosocial behavior and decrease social stress and anxiety. We investigated whether acute pulses of intranasal (IN) OXT influenced social behavior during social challenges that are likely to occur throughout the lifespan of a wild mouse. To test this, we examined the acute effects of IN OXT in the male California mouse (Peromyscus californicus), a monogamous, biparental, and territorial rodent, using a within-subjects longitudinal design. Social challenges included a pre-courtship male-female encounter conducted during the initial aggressive and not the following affiliative phase of courtship, same-sex resident intruder test, and parental care test, with each test and dose separated by at least two weeks. Males were treated with intranasal infusions of 0.8 IU/kg OXT or saline controls 5-min before each behavioral test, receiving a total of three treatments of either IN OXT or saline control. We predicted that IN OXT would 1) decrease aggression and increase affiliation during the pre-courtship aggression phase, 2) increase aggression during resident intruder paradigms and 3) increase paternal care and vocalizations during a paternal care test. As predicted, during pre-courtship aggression with a novel female, IN OXT males displayed less contact aggression than control males, although with no change in affiliative behavior. However, post-pairing, during the resident intruder test, IN OXT males did not differ from control males in contact aggression. During the paternal care test, IN OXT males were quicker to approach their pups than control males but did not differ in vocalizations produced, unlike our previous research demonstrating an effect on vocalizations in females. In summary, during pre-courtship aggression and the paternal care test, IN OXT promoted prosocial approach; however, during the resident intruder test IN OXT did not alter social approach. These data suggest that IN OXT promotes prosocial approach specifically in social contexts that can lead to affiliation.

HIGHLIGHTSO_LIIN OXT attenuates male aggression during pre-courtship encounters
C_LIO_LIIN OXT does not attenuate male aggression during resident intruder encounters
C_LIO_LIIN OXT increases paternal responsiveness during a paternal care challenge
C_LIO_LIIN OXT in fathers does not influence total paternal care or vocalizations
C_LI

GRAPHICAL ABSTRACT

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category: animal behavior and cognition


title: G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from {tau}RAMD Simulations

abstract:
There is a growing appreciation of the importance of drug-target binding kinetics for lead optimization. For G protein-coupled receptors (GPCRs), which mediate signaling over a wide range of timescales, the drug dissociation rate is often a better predictor of in vivo efficacy than binding affinity, although it is more challenging to compute. Here, we assess the ability of the {tau}-Random Acceleration Molecular Dynamics ({tau}RAMD) approach to reproduce relative residence times and reveal dissociation mechanisms and the effects of allosteric modulation for two important membrane-embedded drug targets: the {beta}2-adrenergic receptor and the muscarinic acetylcholine receptor M2. The dissociation mechanisms observed in the relatively short RAMD simulations (in which molecular dynamics (MD) simulations are performed using an additional force with an adaptively assigned random orientation applied to the ligand) are in general agreement with much more computationally intensive conventional MD and metadynamics simulations. Remarkably, although decreasing the magnitude of the random force generally reduces the number of egress routes observed, the ranking of ligands by dissociation rate is hardly affected and agrees well with experiment. The simulations also reproduce changes in residence time due to allosteric modulation and reveal associated changes in ligand dissociation pathways.

TABLE OF CONTENTS GRAPHIC

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title: G Protein-Coupled Receptor-Ligand Dissociation Rates and Mechanisms from {tau}RAMD Simulations


title: A hemifused complex is the hub in a network of pathways to membrane fusion

abstract:
Membrane fusion is a critical step for many essential processes, from neurotransmission to fertilization. For over 40 years protein-free fusion driven by calcium or other cationic species has provided a simplified model of biological fusion, but the mechanisms remain poorly understood. Cation-mediated membrane fusion and permeation are essential in their own right to drug delivery strategies based on cell-penetrating peptides or cation-bearing lipid nanoparticles. Experimental studies suggest calcium drives anionic membranes to a hemifused intermediate which constitutes a hub in a network of pathways, but the pathway selection mechanism is unknown. Here we develop a mathematical model that identifies the network hub as a highly dynamical hemifusion complex. Multivalent cations drive expansion of this high tension hemifusion interface between interacting vesicles during a brief transient. The fate of this interface determines the outcome, either fusion, dead-end hemifusion or vesicle lysis. The model reproduces the unexplained finding that calcium-driven fusion of vesicles with planar membranes typically stalls at hemifusion, and we show the equilibrated hemifused state is a novel lens-shaped complex. Thus, membrane fusion kinetics follow a stochastic trajectory within a network of pathways, with outcome weightings set by a hemifused complex intermediate.

SignificanceCells use multicomponent machineries to fuse membranes for neurotransmitter and hormone release and other fundamental processes. Protein-free fusion using calcium or other multivalent cationic fusogens has long been studied as a simplifying model. Cation-mediated membrane fusion or permeation are key events for a number of current drug delivery strategies. However, the mechanisms determining outcomes are unknown. Here we develop a mathematical model that identifies a dynamic hemifusion complex as the decision hub that stochastically sets the outcome in a network of pathways. Cations transiently grow a high tension hemifusion interface between membrane-enclosed compartments, whose fate governs whether fusion, dead-end hemifusion or vesicle lysis occurs. The model provides a systematic framework to predict outcomes of cationic fusogen-mediated interactions between membrane-enclosed compartments.


title: Large-Scale Intrinsic Functional Brain Organization Emerges from Three Canonical Spatiotemporal Patterns

abstract: Resting-state functional MRI has yielded many, seemingly disparate insights into large-scale organization of the human brain. Representations of the brains large-scale organization can be divided into two broad categories - zero-lag representations of functional connectivity structure and time-lag representations of traveling wave or propagation structure. Here we sought to unify multiple observed phenomena in these two categories by applying concepts from the study of standing (zero-lag) and traveling (time-lag) waves. Using simulated data, we first described the behavior of zero-lag and time-lag analyses applied to spatiotemporal patterns with varying degrees of standing and traveling wave patterns. We then identified three low-frequency spatiotemporal patterns in empirical resting-state fMRI signals, composed of a mixture of standing and traveling wave dynamics, that describe both the zero-lag and time-lag structure of these signals. We showed that a wide range of previously observed empirical phenomena, including functional connectivity gradients, the task-positive/task-negative pattern, the global signal, time-lag propagation patterns, the quasiperiodic pattern, and the functional connectome network structure are manifestations of these three spatiotemporal patterns. These patterns account for much of the global spatial structure that underlies functional connectivity analyses, and therefore impact how we interpret everything derived from resting-state fMRI data from functional networks to graphs.


title: A Parsimonious Description of Global Functional Brain Organization in Three Spatiotemporal Patterns


title: Large-scale neural recordings with single-cell resolution in human cortex using high-density Neuropixels probes

abstract: Recent advances in multi-electrode array technology have made it possible to monitor large neuronal ensembles at cellular resolution. In humans, however, current approaches either restrict recordings to only a few neurons per penetrating electrode or combine the signals of thousands of neurons in local field potential (LFP) recordings. Here, we describe a new probe variant and set of techniques which enable simultaneous recording from over 200 well-isolated cortical single units in human participants during intraoperative neurosurgical procedures using silicon Neuropixels probes. We characterized a diversity of extracellular waveforms with eight separable single unit classes, with differing firing rates, positions along the length of the linear electrode array, spatial spread of the waveform, and modulation by LFP events such as inter-ictal discharges and burst suppression. While some additional challenges remain in creating a turn-key recording system, high-density silicon arrays provide a path for studying human-specific cognitive processes and their dysfunction at unprecedented spatiotemporal resolution.


title: A Machine Learning-Enabled Pipeline for Large-Scale Virtual Drug Screening

abstract:
Virtual screening is receiving renewed attention in drug discovery, but progress is hampered by challenges on two fronts: handling the ever increasing sizes of libraries of drug-like compounds, and separating true positives from false positives. Here we developed a machine learning-enabled pipeline for large-scale virtual screening that promises breakthroughs on both fronts. By clustering compounds according to molecular properties and limited docking against a drug target, the full library was trimmed by 10-fold; the remaining compounds were then screened individually by docking; and finally a dense neural network was trained to classify the hits into true and false positives. As illustration, we screened for inhibitors against RPN11, the deubiquitinase subunit of the proteasome and a drug target for breast cancer.

TOC Graphic O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY


title: Population inter-connectivity over the past 120,000 years explains distribution and diversity of Central African hunter-gatherers

abstract: The evolutionary history of African hunter-gatherers holds key insights into modern human diversity. Here we combine ethnographic and genetic data on Central African hunter-gatherers (CAHG) to show that their current distribution and density is explained by ecology rather than by a displacement to marginal habitats due to recent farming expansions, as commonly assumed. We also predict hunter-gatherer presence across Central Africa over the past 120,000 years using paleoclimatic reconstructions, which were statistically validated by dated archaeological sites. Finally, we show that genomic estimates of separation times between CAHG groups match our ecological estimates of periods favouring population splits, and that recoveries of connectivity would have facilitated subsequent gene-flow. Our results reveal that CAHG stem from a deep history of partially connected populations. This form of sociality allowed the coexistence of relatively large effective population sizes and local differentiation, with important implications for the evolution of genetic and cultural diversity in Homo sapiens.

category: evolutionary biology


title: The ADP-glucose pyrophosphorylase from Melainabacteria: a comparative study between photosynthetic and non-photosynthetic bacterial sources

abstract: Until recently, all members of the cyanobacterial phylum were considered capable of performing oxygenic photosynthesis. This view has been questioned after the discovery of a group of presumed non-photosynthetic cyanobacteria named Melainabacteria. Using metagenomic data, we identified sequences encoding putative ADP-glucose pyrophosphorylase (EC 2.7.7.27, ADP-GlcPPase) from free-living and intestinal Melainabacteria. These genes were de novo synthesized and overexpressed in Escherichia coli. The purified recombinant proteins from the free-living and the intestinal Melainabacteria showed ADP-GlcPPase activity, with Vmax values of 2.3 and 7.1 U/mg, respectively. Both enzymes had similar affinities towards ATP (S0.5 [~]0.3 mM) although the one from the intestinal source displayed a 6-fold higher affinity for glucose-1P. Both recombinant ADP-GlcPPases were sensitive to allosteric activation by glucose-6P (A0.5 [~]0.3 mM), and to inhibition by Pi and ADP (I0.5 between 0.2 to 3 mM). Interestingly, the enzymes from Melainabacteria were insensitive to 3-phosphoglycerate, which is the principal activator of ADP-GlcPPases from photosynthetic cyanobacteria. To the best of our knowledge, this is the first biochemical characterization of an active enzyme from Melainabacteria, offering further data to discussions regarding their phylogenetic position. This work contributes to a better understanding regarding the evolution of allosteric mechanisms in ADP-GlcPPases, an essential enzyme for the synthesis of glycogen in prokaryotes and starch in plants.


title: The EXO70B2 exocyst subunit contributes to papillae and encasement formation in anti-fungal defence in Arabidopsis

abstract:
In the reaction to non-adapted Blumeria graminis f. sp. hordei (Bg), Arabidopsis thaliana leaf epidermal cells deposit cell wall reinforcements called papillae or seal fungal haustoria in encasements, both of which involve intensive exocytosis. A plant syntaxin SYP121/PEN1 has been found to be of key importance for the timely formation of papillae, and the vesicle tethering complex exocyst subunit EXO70B2 has been found to contribute to their morphology. Here, we identify a specific role for the EXO70B2-containing exocyst complex in the papillae membrane domains important for the callose deposition and GFP-SYP121 delivery to the focal attack sites, as well as its contribution to encasement formation. The mRuby2-EXO70B2 co-localises with the exocyst core subunit SEC6 and GFP-SYP121 in the membrane domain of papillae, and both proteins have the capacity to directly interact. The exo70B2/syp121 double mutant has a reduced number of papillae and haustorial encasements in response to Bg, indicating an additive role of the exocyst in SYP121 coordinated non-host resistance. In summary, we report cooperation between the plant exocyst and a SNARE protein in penetration resistance against non-adapted fungal pathogens.

HighlightThe exocyst complex containing EXO70B2 subunit has specific role in papilla and encasement formation, implemented in coordination with the pathway regulated by the SYP121 SNARE complex in defence.


title: Meiotic cell cycle progression requires adaptation to a constitutive DNA damage signal

abstract: Meiotic chromosome segregation relies on synapsis and crossover recombination between homologous chromosomes. These processes require multiple steps that are coordinated by the meiotic cell cycle and monitored by surveillance mechanisms. In the nematode Caenorhabditis elegans, CHK-2 kinase is activated at meiotic entry; its activity is essential for homologous synapsis and DSB formation. CHK-2 is normally inactivated at mid-prophase, but how this occurs has not been established. Defects in synapsis or establishment of crossover intermediates delay meiotic progression by prolonging the activity of CHK-2. We report that CHK-2 is necessary and sufficient to inhibit crossover designation. We further find that CHK-2 is inactivated at mid-prophase by a pathway that mediates DNA damage checkpoint adaptation in proliferating human cells: Polo-like kinases, particularly PLK-2, phosphorylate and inhibit CHK-2 in response to formation of crossover intermediates. These findings help to illuminate the mechanisms of crossover assurance and meiotic cell cycle control.


title: Land Use and Endemic Avian Biodiversity on Nusa Penida

abstract:
Understanding anthropogenic alterations to land use and their effects can inform conservation efforts in tropical biodiversity hotspots. In 2004 the Indonesian Palau Penida Archipelago, off the coast of Bali, was established as an unofficial bird reserve; however, studies of the islands land use and avian biodiversity were never conducted and have not been monitored. I surveyed birds across 32 transects in land use categories designated: agriculture, deforested, developed, and forest. Forest transects presented the greatest endemic species richness, but overall, Shannon diversity different significantly among land use categories, particularly forested and deforested. ANOVA indicated exotic bird density was significantly higher than endemic bird density across all transects. Birds serve as a common biodiversity barometer and this study can serve to inform land use management decisions on the Archipelago and throughout reserves and protected areas throughout the tropics.

RingkasanMemahami perubahan antropogenik untuk penggunaan lahan dan dampaknya dapat menginformasikan upaya konservasi di hotspot keanekaragaman hayati tropis. Pada tahun 2004 Kepulauan Palau Penida Indonesia, di lepas pantai Bali, didirikan sebagai cagar burung tidak resmi; Namun, studi tentang penggunaan lahan pulau-pulau dan keanekaragaman hayati burung tidak pernah dilakukan dan belum dipantau. Saya mensurvei burung di 32 transek dalam kategori penggunaan lahan yang ditunjuk: pertanian, gundul, dikembangkan, dan hutan. Transek hutan menunjukkan kekayaan spesies endemik terbesar, tetapi secara keseluruhan, keanekaragaman Shannon berbeda secara signifikan di antara kategori penggunaan lahan, terutama yang berhutan dan digunduli. ANOVA menunjukkan kepadatan burung eksotis secara signifikan lebih tinggi daripada kepadatan burung endemik di semua transek. Burung berfungsi sebagai barometer keanekaragaman hayati yang umum dan studi ini dapat berfungsi untuk menginformasikan keputusan pengelolaan penggunaan lahan di Kepulauan Indonesia dan di seluruh cagar dan kawasan lindung di seluruh daerah tropis.


title: Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers

abstract: Human papillomavirus (HPV) causes 5% of all cancers and frequently integrates into host chromosomes, but the impacts of integration in tumorigenesis remain unclear. Analysis of 105 HPV-positive oropharyngeal cancers by whole genome sequencing detects viral integration in 77%, revealing five statistically significant integration hotspots near genes that regulate epithelial stem cell maintenance (i.e. SOX2, TP63, FGFR, MYC) and immune evasion (i.e. CD274). Somatic hyperamplification is enriched 16-fold near HPV integrants, and the extent of focal host genomic instability increases with local density of HPV integrants. Genes expressed at extreme outlier levels are increased 86-fold within +/- 150 kb of integrants. Across 95% of tumors with integration, host gene transcription is disrupted via intragenic integrants, chimeric transcription, outlier expression, gene breaking and/or de novo expression of noncoding or imprinted genes. We conclude that HPV integration contributes substantively to cancer development by causing extensive disruption of host genome structure and gene expression.

category: genomics


title: The gravitation-driven stress-reduced urothelial barrier in toad bladder urothelium

abstract:
The urinary bladder urothelial are highly specialized epithelia that protect the underlying tissues from mechanical stress and seal them from the overlying fluid space. To better understand the maintaining permeability induced electrical potential roles played by urothelial in the bladder, we established a protocol of gravitation stress in toad urothelial, observed the transmembrane potential difference variation.

MethodThe toad urothelial were mounted in a using chamber which the chamber was separated to two solution spaces, and stable with 0.9% saline solution. The electrodes were settled on the surface of each side of the preparation, serosal side definite as cathode. The using chamber was settled in the centrifugal rotor and under 300 rpm rotation to obtain a vertically +4G gravitation on serosal chamber 5min.

Resulta transient transmembrane potential difference increasing was observed after adding CaCl2 (3% solution) in serosal chamber. The amplitude increasing phase included a rapid and a slowly ascending phase. In gravitation stressed urothelial preparation, CaCl2 induced transient phase was significantly increased, furthermore the secondary slowly ascending phase was much more amplified on its amplitude axis and significantly prolonged on the time scale than that evoked in control preparations. The evoked total amplitude increasing were 10 times higher than that in control.

ConclusionThe urinary bladder epithelial layer has a structure which regulates ion permeability as a barrier. The tight junction plays an important role as the intercellular coupling in the apical side of the epithelial cell. On the other hand, it is known that the ion channel exists on the epithelial cell membrane and regulates the physiological process. The gravitation stress weakened the tight junction. The transmembrane potential difference was enhanced both on its amplitude and prolonged time. The gravitation stress induced hyperpolarization that evoked by CaCl2 is one kind of Cl- transfer from serosal chamber in which high Ca2+ in the urothelial basal membrane activated the calcium-activated chloride channels. This outwardly rectifying chloride channel induced hyperpolarization can be blocked by Nppb.


title: Dominant Effect Of Host Genetics On Skin Microbiota Composition In Homeostasis And Wound Healing

abstract: Animal microbiota have complex interactions with hosts and environment that determines its composition. Yet the ability of hosts to determine their microbiota composition is less well studied. In this study, to investigate the role host genetics in determining skin microbiota, we used 30 different mouse strains from the recombinant inbred panel, the Collaborative Cross. Murine skin microbiota composition was strongly dependent on murine strain with > 50% of the variation explained by murine strain. In particular, a quantitative trait locus on chromosome 4 associates both with Staphylococcus abundance and principal-component multi-trait analyses. Additionally, excisional wound associated changes in microbiota composition were not uniform across mouse strains and were host-specific, the genetic background accounting for about 40% of the variation in microbiota. Genetic background also had the highest effect on the healing speed of wounds accounting for over 50% of the variation while mouse age and microbiota composition change accounted only for 20% and 5% of the healing speed despite reaching statistical significance. In conclusion, host genetics has a significant impact on the skin microbiota composition during both homeostasis and wound healing. These findings have long reaching implications in our understanding of associations between microbiota dysbiosis and disease.

category: systems biology


title: Determinants of Murine Skin Microbiota Composition in Homeostasis and Wound Healing


title: Systematic evaluation of genome-wide metabolic landscapes in lactic acid bacteria reveals diet-induced and strain-specific probiotic idiosyncrasies

abstract: Lactic acid bacteria (LAB) naturally occur in animal and plant niches and are well-known to elicit several health benefits in humans. Yet, how they adapt their functional metabolic landscapes to diverse nutrient environments and synthesize relevant bioactive compounds remain unexplored across genera, species and strains. Hence, presented herein is a systematic framework for comprehensively characterizing the genome-wide metabolisms of six representative LAB by combining multi-omics data with in silico modeling. We analyse the differences in their growth and cellular fitness, biosynthetic capability of health-relevant compounds, i.e., postbiotics, and probable interactions with 15 common gut microbiota under 11 virtual dietary regimes, and show such attributes are diet- and species-specific. Particularly, some LAB exhibit a desirable balance between synthesis of beneficial postbiotic compounds, positive interactions with beneficial gut commensals, and the ability to colonize and persist in gut environment. We also observe that "high fat-low carb" diets likely lead to detrimental outcomes in most LAB. Our results clearly highlight that probiotics are not "one size fits all" commodities and need to be formulated in a personalised manner for their use as dietary supplements and live biotherapeutics. Overall, the proposed framework will systematize the probiotic administration and could also widen the strain repertoire.


title: EEG-based neurofeedback with network components extraction: data-driven approach by multilayer ICA extension and simultaneous EEG-fMRI measurements

abstract:
Several studies have reported advanced treatments for depressive symptoms, such as real-time neurofeedback (NF) with functional MRI (fMRI) and/or electroencephalogram (EEG). NF focusing on a regularization of brain activity associated with the amygdala or functional connectivity (FC) between the executive control network (ECN) and default mode network (DMN) has been applied to reduce depressive symptoms. However, it is practically difficult to install the fMRI-NF system and to consistently provide treatment, because of high cost. Additionally, no practical signal processing techniques have been developed extracting FC-related features from EEG signals, particularly when no physical forward models are available. In this regard, stacked pooling and linear components estimation (SPLICE), recently proposed as a multilayer extension of independent component analysis (ICA) and related independent subspace analysis (ISA), can be a promising alternative. The resting-state EEG network features can be correlated with fMRI network activity corresponding to the DMN or ECN. This may enable the modulation of the target FC-related features in EEG-based NF.

In this study, we developed a real-time EEG NF system for improving depressive symptoms by using the SPLICE. Utilizing information from the fMRI biomarkers, we evaluated our paradigm for effectiveness with regard to upregulation of the dorsolateral prefrontal cortex /middle frontal gyrus or downregulation of the precuneus/posterior cingulate cortex. We conducted an NF experiment in participants with subclinical depression; the participants were divided into the NF group (n=8) and the sham group (n=9). We found a significant reduction and a large effect size in the rumination response scale (RRS) score (reflection) in the NF group, compared to the sham group.

However, we did not find a significant relationship between the training score and difference in symptoms. This suggests that increased controllability of the EEG signals did not directly reduce the RRS reflection score. This could be due to various reasons such as improper feature extraction, individual differences, and the targeted brain regions. In this paper, we also discuss the possible ways to modify our NF protocol including the design of the experiment, sample size, and online processing. We then discuss way to improve the NF training, based on our results.


title: EEG-based neurofeedback with network components extraction: a data-driven approach by multilayer ICA extension and simultaneous EEG-fMRI measurements


title: Opioid antagonism reduces wanting by strengthening frontostriatal connectivity

abstract: Goal-directed behavior depends on both motivational ("wanting") and hedonic ("liking") dimensions of rewards. Previous animal and human research linked wanting and liking to anatomically and neurochemically distinct brain mechanisms, but it remains unknown as to how the different brain regions and neurotransmitter systems interact in processing distinct reward dimensions. Here, we assessed how pharmacological manipulations of opioid and dopamine receptor activation modulate the neural processing of wanting and liking in humans in a randomized, placebo-controlled, double-blind clinical trial. Blocking opioid receptor activation with naltrexone selectively reduced wanting of rewards, which on a neural level was reflected by stronger coupling between dorsolateral prefrontal cortex and the striatum under naltrexone compared with placebo. Our findings thus provide insights into how opioid receptors mediate frontostriatal gating of specifically motivational, not hedonic, aspects of rewards.


title: RiboTRIBE: Monitoring Translation with ADAR-meditated RNA Editing

abstract: RNA translation is tightly regulated to ensure proper protein expression in cells and tissues. Translation is often assayed with biochemical assays such as ribosome profiling and TRAP, which are effective in many contexts. These assays are however not ideal with limiting amounts of biological material when it can be difficult or even impossible to make an extract with sufficient signal or sufficient signal:noise. Because of our interest in translational regulation within the few Drosophila adult circadian neurons, we fused the ADAR catalytic domain (ADARcd) to several small subunit ribosomal proteins and assayed mRNA editing in Drosophila S2 cells. The strategy is named RiboTRIBE and is analogous to a recently published APOBEC-based method. The list of RiboTRIBE-edited transcripts overlaps well with ribosome profiling targets, especially with more highly ranked targets. There is also an enriched number of editing sites in ribosome-associated mRNA comparing to total mRNA, indicating that editing occurs preferentially on polyribosome-associated transcripts. The use of cycloheximide to freeze translating ribosomes causes a substantial increase in the number of RiboTRIBE targets, which is decreased by pretreating cells with the chain terminating drug puromycin. NOTE: Additional experiments performed after first submitting this manuscript to BioRxiv estimate that less than 5% of Rps28b-ADAR is ribosome-associated. This is because the vast majority of the fusion protein sediments at the top of a polyribosome gradient. We therefore suggest that most editing reported in the manuscript is not catalyzed by ribosome-associated ADAR (10/2/2021).


title: Emergence of border-ownership by large-scale consistency and long-range interactions: Neuro-computational model to reflect global configurations

abstract: The visual system performs remarkably well to perceive depth order of surfaces without stereo disparity, indicating the importance of figure-ground organization based on pictorial cues. To understand how figure-ground organization emerges, it is essential to investigate how the global configuration of an image is reflected. In the past, many neuro- computational models developed to reproduce figure-ground organization implemented algorithms to give a bias to convex areas. However, in certain conditions, a convex area can be perceived as a hole and a non-convex area as figural. This occurs when the surface properties of the convex area are consistent with the background and, hence, are grouped together in our perception. We argue that large-scale consistency of surface properties is reflected in the border-ownership computation. We developed a model, called DISC2, that first analyzes relationships between two border-ownership signals of all possible combinations in the image. It then enhances signals if they satisfy the following conditions: 1. the two signals fit to a convex configuration, and 2. the surface properties at the locations of the two signals are consistent. The strength of the enhancement decays with distance between the signals. The model gives extremely robust responses to various images with complexities both in shape and depth order. Furthermore, we developed an advanced version of the model ("augmented model") where the global computation above interacts with local computation of curvilinearity, which further enhanced the robust nature of the model. The results suggest the involvement of similar computational processes in the brain for figure-ground organization.


title: Deposition chamber technology as building blocks for a standardized brain-on-chip framework

abstract: In vitro modeling of human brain connectomes is key to explore the structure-function relationship of the central nervous system. The comprehension of this intricate relationship will serve to better study the pathological mechanisms of neurodegeneration, and hence to perform improved drug screenings for complex neurological disorders, such as Alzheimers and Parkinsons diseases. However, currently used in vitro modeling technologies lack potential to mimic physiologically relevant neural structures, because they are unable to represent the concurrent interconnectivity between myriad subtypes of neurons across multiple brain regions. Here, we present an innovative microfluidic design that allows the controlled and uniform deposition of various specialized neuronal populations within unique plating chambers of variable size and shape. By applying our design, we offer novel neuro-engineered microfluidic platforms, so called neurofluidic devices, which can be strategically used as organ-on-a-chip platforms for neuroscience research. Through the fine tuning of the hydrodynamic resistance and the cell deposition rate, the number of neurons seeded in each plating chamber can be tailored from a thousand up to a million, creating multi-nodal circuits that represent connectomes existing within the intact brain. These advances provide essential enhancements to in vitro platforms in the quest accurately model the brain for the investigation of human neurodegenerative diseases.

category: bioengineering


title: Assessing the utility of CASP14 models for molecular replacement

abstract: The assessment of CASP models for utility in molecular replacement is a measure of their use in a valuable real-world application. In CASP7, the metric for molecular replacement assessment involved full likelihood-based molecular replacement searches; however, this restricted the assessable targets to crystal structures with only one copy of the target in the asymmetric unit, and to those where the search found the correct pose. In CASP10, full molecular replacement searches were replaced by likelihood-based rigid-body refinement of models superimposed on the target using the LGA algorithm, with the metric being the refined likelihood (LLG) score. This enabled multi-copy targets and very poor models to be evaluated, but a significant further issue remained: the requirement of diffraction data for assessment. We introduce here the relative-expected-LLG (reLLG), which is independent of diffraction data. This reLLG is also independent of any crystal form, and can be calculated regardless of the source of the target, be it X-ray, NMR or cryo-EM. We calibrate the reLLG against the LLG for targets in CASP14, showing that it is a robust measure of both model and group ranking. Like the LLG, the reLLG shows that accurate coordinate error estimates add substantial value to predicted models. We find that refinement by CASP groups can often convert an inadequate initial model into a successful MR search model. Consistent with findings from others, we show that the AlphaFold2 models are sufficiently good, and reliably so, to surpass other current model generation strategies for attempting molecular replacement phasing.

category: bioinformatics


title: MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping

abstract:
Phylogenetic tree confidence is often estimated from a multiple sequence alignment (MSA) using the Felsenstein bootstrap heuristic. However, this does not account for systematic errors in the MSA, which may cause substantial bias to the inferred phylogeny. Here, I describe the MSA ensemble bootstrap, a new procedure which generates a set of replicate MSAs by varying parameters such as gap penalties and substitution scores. Such an ensemble is called diagnostic if the typical distance between MSAs is comparable to the error rate. Confidence in a prediction derived from an MSA, e.g. a monophyletic clade, is expressed as the fraction of the ensemble where the prediction is reproduced. This approach is implemented in MUSCLE by modifying the Probcons algorithm, which is based on a hidden Markov model (HMM). An ensemble is generated by perturbing HMM parameters and permuting the guide tree. Ensembles generated by this method are shown to be diagnostic on the Balibase benchmark. To enable scaling to large datasets, divide-and-conquer heuristics are introduced. A new benchmark (Balifam) is described with 36 sets of 10000+ proteins. On Balifam, ensembles generated by MUSCLE are shown to align an average of 59% of columns correctly, 13% better than Clustal-omega (52% correct) and 26% better than MAFFT (47% correct). The ensemble bootstrap is applied to a previously published tree of RNA viruses, showing that the high reported Felsenstein bootstrap confidence of Ribovirus phylum branching order is an artifact of systematic MSA errors.

Data availabilityMuscle source code https://github.com/rcedgar/muscle.

Balifam benchmark https://github.com/rcedgar/balifam.

Qscore source code https://github.com/rcedgar/qscore.

Palmscan source code https://github.com/rcedgar/palmscan.


title: Reliable in silico ranking of engineered therapeutic TCR binding affinities using MMPBSA and MMGBSA calculations.

abstract: Accurate and efficient in silico ranking of protein-protein binding affinities is useful for protein design with applications in biological therapeutics. One popular approach to rank binding affinities is to apply the molecular mechanics Poisson Boltzmann/generalized Born surface area (MMPB/GBSA) method to molecular dynamics trajectories. Here, we identify protocols that enable the reliable evaluation of T-cell receptor (TCR) variants binding to their target, peptide-human leukocyte antigens (pHLAs). We suggest different protocols for variant sets with few ([≤]4) or many mutations, with entropy corrections important for the latter. We demonstrate how potential outliers could be identified in advance and that just 5-10 replicas of short (4 ns) MD simulations may be sufficient for reproducible and accurate ranking of TCR variants. The protocols developed here can be applied towards in silico screening during the optimization of therapeutic TCRs, potentially reducing both the cost and time taken for biologic development.


title: Reliable  in silico  ranking of engineered therapeutic TCR binding affinities with MMPBSA and MMGBSA.


title: Structural mechanism of calcium-mediated hormone recognition and Gβ interaction by the human melanocortin-1 receptor

abstract: Melanocortins are peptide hormones critical for stress response, energy homeostasis, inflammation, and skin pigmentation. Their functions are mediated by five G protein-coupled receptors (MC1R to MC5R), predominately through the stimulatory G protein (Gs). MC1R, the founding member of melanocortin receptors, is mainly expressed in melanocytes and is involved in melanogenesis. Dysfunction of MC1R is associated with the development of melanoma and skin cancer. Here we present three cryo-electron microscopy structures of the MC1R-Gs complexes bound to endogenous hormone -MSH, a marketed drug afamelanotide, and a synthetic agonist SHU9119. These structures reveal the orthosteric binding pocket for the conserved HFRW motif among melanocortins and the crucial role of calcium ion in ligand binding. They also demonstrate the basis of differential activities among different ligands. In addition, unexpected interactions between MC1R and the G{beta} subunit were discovered from these structures. Together, our results provide a conserved mechanism of calcium-mediated ligand recognition, specific mode of G protein coupling, and a universal activation pathway of melanocortin receptors.


title: Reprogramming and redifferentiation of mucosal-associated invariant T cells reveals tumor inhibitory activity

abstract: Mucosal-associated invariant T (MAIT) cells belong to a family of innate-like T cells that bridge innate and adaptive immunities. Although MAIT cells have been implicated in tumor immunity, it currently remains unclear whether they function as tumor promoting or inhibitory cells. Therefore, we herein used induced pluripotent cell (iPSC) technology to investigate this issue. Murine MAIT cells were reprogrammed into iPSCs and redifferentiated towards MAIT-like cells (m-reMAIT cells). m-reMAIT cells were activated by an agonist and MR1-tetramer, a reagent to detect MAIT cells, in the presence and absence of antigen-presenting cells. This activation accompanied protein tyrosine phosphorylation and the production of T helper (Th)1-, Th2-, and Th17-cytokines and inflammatory chemokines. Upon adoptive transfer, m-reMAIT cells migrated to different organs with maturation in mice. Furthermore, m-reMAIT cells prolonged mouse survival upon tumor inoculation through the NK cell-mediated reinforcement of cytolytic activity. Collectively, the present results demonstrated the utility and role of m-reMAIT cells in tumor immunity, and will contribute to insights into the function of MAIT cells in immunity.

category: cancer biology


title: Ectopic expression of KRASG12D and p53R167H in porcine mammary epithelial cells results in transformation and tumorigenesis

abstract: We describe our initial studies in the development of an orthotopic, genetically-defined, large animal model of breast cancer, using immunocompetent pigs. Primary mammary epithelial cells were isolated from the porcine gland. Primary mammary cells were immortalized with hTERT, and then transformed cell lines were generated from these immortalized cells with oncogenic KRAS and dominant negative p53. The transformed cell lines outperformed the primary cells in terms proliferation, population doubling time, soft agar growth, 2D migration, and Matrigel invasion. Three transformed cell lines were selected based on in vitro performance, and were able to grow tumors when injected subcutaneously in nude mice, with undifferentiated morphology. Tumorigenic porcine mammary cell lines were generated in this report.


title: The cardiac STAT3 intercalated disc specific expression in tail suspension rat

abstract:
BackgroundThe cardiovascular system is significantly agitated by loss of gravity. In microgravity, the body fluids shift toward the thoracic cavity, induced the heart becomes more spherical. This further increased the cardiac preload with an increasing of transmural central venous pressure, affects the right heart ventricles to tolerating the enhanced preload on the right ventricular wall.

MethodIn this study we investigated the rat right ventricle remodeling in simulating persistent microgravity by using tail-suspension model, examined the remolding of the heart and the specific STAT3 expression in right heart myocardium.

ResultThe results indicated that microgravity induced heart remodeling included a significant increasing of the ventricular weight in the left. However, the right ventricle was not increased significantly in the microgravity simulation rats. The histological study demonstrated that the outstanding development on right ventricular wall which included the gap junction remodeling and STAT3 signaling protein specific accumulation in the right ventricles.

ConclusionThe results existed that the right cardiac ventricle has a distinctive remodeling process during microgravity simulation which was not the muscular hypertrophy and relative weight increasing, but manifested the STAT3 accumulation and the electrical gap junction remodeling. The effect of microgravity induced right ventricle remodeling and the STAT3 specific accumulation can be used for multi-purpose research.

category: physiology


title: Comparative plastomics of Amaryllidaceae: Inverted repeat expansion and the degradation of the ndh genes in Strumaria truncata Jacq.

abstract: Amaryllidaceae is a widespread and distinctive plant family contributing both food and ornamental plants. Here we present an initial survey of plastomes across the family and report on both structural rearrangements and gene losses. Most plastomes in the family are of similar gene arrangement and content however some taxa have shown gains in plastome length while in several taxa there is evidence of gene loss. Strumaria truncata shows a substantial loss of ndh family genes while three other taxa show loss of cemA, which has been reported only rarely. Our sparse sampling of the family has detected sufficient variation to suggest further sampling across the family could be a rich source of new information on plastome variation and evolution.


title: A genotype independent DMP-HI system in dicot crops

abstract: Doubled haploid (DH) technology is used to obtain homozygous lines in a single generation, which significantly accelerates the crop breeding trajectory. Traditionally, in vitro culture is used to generate DHs, but is limited by species and genotype recalcitrance. In vivo haploid induction (HI) through seed is been widely and efficiently used in maize and was recently extended to several monocot crops. However, a similar generic and efficient HI system is still lacking in dicot crops. Here we show that genotype-independent in vivo HI can be triggered by mutation of DMP genes in tomato, rapeseed and tobacco with HI rates of ~1.9%, 2.4% and 1.2%, respectively. The DMP-HI system offers a robust DH technology to facilitate variety improvement in these crops. The success of this approach and the conservation of DMP genes paves the way for a generic and efficient genotype-independent HI system in other dicot crops.


title: Luminosity thresholds of colored surfaces are determined by their heuristic upper-limit luminances in the visual system

abstract: We typically have a fairly good idea whether a given object is self-luminous or illuminated, but it is not fully understood how we make this judgement. This study aimed to identify determinants of the luminosity threshold, a luminance level at which a surface begins to appear self-luminous. We specifically tested a hypothesis that our visual system knows the maximum luminance level that a surface can reach under the physical constraint that a surface cannot reflect more light than any incident light and applies this prior to determine the luminosity thresholds. Observers were presented with a 2-degree circular test field surrounded by numerous overlapping colored circles and luminosity thresholds were measured as a function of (i) the chromaticity of the test field, (ii) the shape of surrounding color distribution and (iii) the color of the illuminant of the surrounding colors. We found that the luminosity thresholds peaked around the chromaticity of test illuminants and decreased as the purity of the test chromaticity increased. However, the loci of luminosity thresholds across chromaticities were nearly invariant to the shape of the surrounding color distribution and generally resembled the loci drawn from theoretical upper-limit luminances and upper-limit luminance boundaries of real objects. These trends were particularly evident for illuminants on the black-body locus and did not hold well under atypical illuminants such as magenta or green. These results support the idea that our visual system empirically internalizes the gamut of surface colors under natural illuminants and a given object appears self-luminous when its luminance exceeds this internalized upper-limit luminance.

category: neuroscience


title: Luminosity thresholds of colored surfaces are determined by their upper-limit luminances empirically internalized in the visual system


title: The neurocomputational architecture of explore-exploit decision making

abstract: Humans and other animals often make the difficult decision to try new options (exploration) and forego immediate rewards (exploitation). Novelty-seeking is an adaptive solution to this explore-exploit dilemma, but our understanding of the neural computations supporting novelty-seeking in humans is limited. Here, we presented the same explore-exploit decision making task to monkeys and humans and found evidence that the computational basis for novelty-seeking is conserved across primate species. Critically, through computational model-based decomposition of event-related functional magnetic resonance imaging (fMRI) in humans, these findings reveal a previously unidentified cortico-subcortical architecture mediating explore-exploit behavior in humans.


title: Changes in dynamic transitions between integrated and segregated states underlie visual hallucinations in Parkinson's disease

abstract:
BackgroundVisual hallucinations in Parkinsons disease (PD) are transient, suggesting a change in dynamic brain states. However, the causes underlying these dynamic brain changes are not known.

MethodsFocusing on fundamental network properties of integration and segregation, we used rsfMRI to examine alterations in temporal dynamics in PD patients with hallucinations (n=16) compared to those without hallucinations (n=75) and a group of normal controls (n=32). We used network control theory to examine how structural connectivity guides transitions between functional states. We then studied the brain regions most involved in these state transitions, and examined corresponding neurotransmitter density profiles and receptor gene expression in health.

ResultsThere were significantly altered temporal dynamics in PD with hallucinations, with an increased proportion of time spent in the Segregated state compared to non-hallucinators and controls; less between-state transitions; and increased dwell time in the Segregated state. The energy cost needed to transition from integrated-to-segregated state was lower in PD-hallucinators compared to non-hallucinators. This was primarily driven by subcortical and transmodal cortical brain regions, including the thalamus and default mode network regions. The regional energy needed to transition from integrated-to-segregated state was significantly correlated with regional neurotransmitter density and gene expression profiles for serotoninergic (including 5HT2A), GABAergic, noradrenergic and cholinergic but not dopaminergic density profiles.

ConclusionsWe describe the patterns of temporal functional dynamics in PD-hallucinations, and link these with neurotransmitter systems involved in early sensory and complex visual processing. Our findings provide mechanistic insights into visual hallucinations in PD and highlighting potential therapeutic targets.


title: Quantification of RNA Polymerase I transcriptional attenuation at the active VSG expression site in Trypanosoma brucei

abstract: The cell surface of the extracellular pathogen Trypanosoma brucei consists of a dense coat of variant surface glycoprotein (VSG), which enables the parasite to evade the immune system of the vertebrate host. Only one VSG gene from a large repertoire is expressed from a so-called bloodstream form expression site (BES) at a given timepoint. There are several BES in every parasite but only one is transcriptionally active. Other BES are silenced by transcriptional attenuation. Periodic activation of a previously-silenced BES results in differential VSG transcription and escape from the immune response. A process called antigenic variation. In contrast to gene transcription in other eukaryotes, the BES is transcribed by RNA polymerase I (Pol I). It was proposed that this highly-processive polymerase is needed to provide a sufficiently high transcription rate at the VSG gene. Surprisingly, we discovered a position-dependent Pol I activity and attenuation of transcriptional elongation also at the active BES. Transcription rates at the VSG gene appear to be comparable to Pol II-mediated transcription of house-keeping genes. Although these findings are in contradiction to the long-standing concept of continuously high transcription rates at the active BES in Trypanosoma brucei, they are complementary to recent groundbreaking findings about transcriptional regulation of VSG genes.


title: Altered effective connectivity from the posterior insula to the amygdala mediates the relationship between psychopathic traits and concern with the Harm foundation

abstract: Psychopathic traits have been demonstrated to be associated with different types of morality; however, the neuropsychological mechanism underlying the relationship between psychopathic traits and morality remains unclear. Our study examined the effective connectivity (EC) of psychopathic traits-related brain regions and its association to concern with different moral foundations by combining behavioral measures with resting-state fMRI. We administered the Levenson Self-Report Psychopathy Scale (LSRP) and Moral Foundation Questionnaire (MFQ) to 78 college students after resting-state fMRI scanning. Our results showed that total and primary psychopathic traits score predicted concern with the Harm foundation. The EC from the posterior insula to the amygdala was negatively correlated with psychopathic traits and positively with concern with the Harm foundation. Altered posterior insula-amygdala EC partially mediated the relationship between psychopathic traits and concern with the Harm foundation. Our findings indicated that individuals with elevated psychopathic traits may have atypical processes in recognizing and integrating bodily state information into emotional responses, leading to less concern for harm-related morality. The study deepened our understanding of the neuropsychological mechanism underlying the relationship between psychopathic traits and morality and may have implications for the prevention of higher psychopathic traits individuals from committing serious transgressions.


title: Differential ubiquitination as an effective strategy employed by Blood-Brain Barrier for prevention of bacterial transcytosis

abstract:
The protective mechanisms of blood-brain barrier (BBB) prohibiting entry of blood borne pathogens and toxins into the central nervous system (CNS) is critical for maintenance of homeostasis in the brain. These include various forms of intracellular defence mechanisms which are vital to block bacterial transcytosis, the major route of trafficking adopted by meningeal pathogens to transit into the CNS. However, mechanistic details of the defence mechanisms and their exploitation to prevent bacterial meningitis remain unexplored. In this study, we established that brain endothelium driven ubiquitination acts as a major intracellular defence mechanism for clearance of S. pneumoniae, a critical neurotropic pathogen, during its transit through BBB. Our findings suggest that brain endothelium employs differential ubiquitination with either K48 or K63-Ub chain topologies as an effective strategy to target SPN towards diverse killing pathways. While K63-Ub decoration triggers autophagic killing, K48-Ub directs pneumococcus exclusively to the proteasome machinery. Indeed, time lapse fluorescence imaging involving proteasomal marker LMP2 revealed that in BBB, majority of the ubiquitinated SPN were cleared by proteasome. Fittingly, pharmacological inhibition of proteasome and autophagy pathway not only led to exclusive accumulation of K48-Ub and K63-Ub marked SPN, respectively, but also triggered significant increment in intracellular SPN burden. Moreover, genetic impairment of formation of either K48 or K63-Ub chain topology demonstrated that though both chain types play important roles in disposal of intracellular SPN, K48-Ub chains and subsequent proteasomal degradation has more pronounced contribution towards ubiquitinated SPN killing in brain endothelium. Collectively, these observations for the first time illustrated a pivotal role of differential ubiquitination in orchestrating a symphony of intracellular defence mechanisms blocking pathogen trafficking into the brain which could be further exploited to prevent bacterial CNS infections.

IMPORTANCEAmong the different cellular barriers present in the human body, Blood-Brain Barrier (BBB) is unique as it not only provides structural integrity but also protects the central nervous system (CNS) from pathogen invasion. In recent past, ubiquitination, which is known to be involved in protein quality control and cellular homeostasis, has been proven to be critically involved in pathogen clearance. In this study, employing S. pneumoniae as a model CNS pathogen, we wanted to decipher the critical contribution of ubiquitination in protective mechanism of BBB while tackling bacterial entry into the CNS. Our results suggest, that BBB deploys differential ubiquitination as an effective strategy to prevent neurotropic bacterial trafficking into the brain. By portraying a comprehensive picture of ubiquitin coat on SPN, we figured out that different ubiquitin chain topologies formed on the pneumococcus dictated the selection of downstream degradative pathways, namely, autophagy and proteasomal machinery. Amongst these, contribution of proteasomal system in clearance of pneumococcus was found to be more pronounced. Overall our study revealed how BBB deploys differential ubiquitination as a strategy to trigger autophagy and proteasomal system, which work in tandem to ensure brains identity as an immunologically sterile site.


title: Oxidative stress is a potential cost of synchronous nesting in olive ridley sea turtles

abstract: Olive ridley sea turtles, Lepidochelys olivacea, exhibit a polymorphic reproductive behaviour nesting in solitary or in mass aggregations termed "arribadas", where thousands of turtles nest at once. Arribadas may provide fitness benefits including mate finding during nearshore aggregations and predator satiation at the time of hatching, but the potential costs of arribada nesting remain understudied. To explore the potential trade-offs of the fitness benefits associated with arribada nesting, we collected blood from olive ridley turtles nesting in arribada and solitary. We measured reproductive and metabolic hormones (progesterone, estradiol, testosterone, thyroxine, and triiodothyronine), triglycerides (TG), non-esterified fatty acids (NEFA) and markers of oxidative damage (4-hydroxynonenal, malondialdehyde, protein carbonyls, and nitrotyrosine). Arribada nesters were bigger and had higher levels of progesterone than solitary nesters. Similarly, thyroid hormones were higher in individuals nesting in arribada than in solitary nesters, while TG and NEFA were positively correlated in arribada but not in solitary nesters. Nesting in arribada was associated with increased lipid peroxidation and protein carbonyls compared to solitary nesting. These results suggest that nesting in arribada is potentially more energetically expensive than nesting solitarily, and that oxidative stress may be a trade-off of the fitness benefits associated with arribada nesting.


abstract:
BackgroundClosing the loop between brain activity and behavior is one of the most active areas of development in neuroscience. There is particular interest in developing closed-loop control of neural oscillations. Many studies report correlations between oscillations and functional processes. Oscillation-informed closed-loop experiments might determine whether these relationships are causal and would provide important mechanistic insights which may lead to new therapeutic tools. These closed-loop perturbations require accurate estimates of oscillatory phase and amplitude, which are challenging to compute in real time.

New MethodWe developed an easy to implement, fast and accurate Toolkit for Oscillatory Real-time Tracking and Estimation (TORTE). TORTE operates with the open-source Open Ephys GUI (OEGUI) system, making it immediately compatible with a wide range of acquisition systems and experimental preparations.

ResultsTORTE efficiently extracts oscillatory phase and amplitude from a target signal and includes a variety of options to trigger closed-loop perturbations. Implementing these tools into existing experiments is easy and adds minimal latency to existing protocols.

Comparison with Existing MethodsMost labs use in-house lab-specific approaches, limiting replication and extension of their experiments by other groups. Accuracy of the extracted analytic signal and accuracy of oscillation-informed perturbations with TORTE match presented results by these groups. However, TORTE provides access to these tools in a flexible, easy to use toolkit without requiring proprietary software.

ConclusionWe hope that that the availability of a high-quality, open-source, and broadly applicable toolkit will increase the number of labs able to perform oscillatory closed-loop experiments, and will improve the replicability of protocols and data across labs.

HighlightsO_LITORTE provides a toolkit to investigate closed loop oscillation-informed experiments.
C_LIO_LIThe toolkit is versatile and open-source promoting replicability across scientists.
C_LIO_LIThe analytic signal algorithm within TORTE preforms equally to existing algorithms.
C_LI


title: Toolkit for Oscillatory Real-time Tracking and Estimation (TORTE)


title: Adaptation of Drosophila larva foraging in response to changes in food distribution

abstract: When foraging, animals combine internal cues and sensory input from their environment to guide sequences of behavioral actions. Drosophila larva executes crawls, turns, and pauses to explore the substrate and find food sources. This exploration has to be flexible in the face of changes in the quality of food so that larvae feed in patches with favorable food and look for another source when the current location does not fulfill their nutritional needs. But which behavioral elements adapt, and what triggers those changes remain elusive. Using experiments and modeling, we investigate the foraging behavior of larvae in homogeneous environments with different food types and in environments where the food sources are patchy. Our work indicates that the speed of larval crawling and frequency of pauses is modulated by the food quality. Interestingly, we found that the genetic dimorphism in the foraging gene influences the exploratory behavior only when larvae crawl on yeast patches. While in a homogeneous substrate larvae maintain a turning bias in a specific orientation, in a patchy substrate larvae orient themselves towards the food when the patch border is reached. Therefore, by adapting different elements in their foraging behavior, larvae either increase the time inside nutritious food patches or continue exploring the substrate in less nutritious environments.


title: Deamidation of the human eye lens protein γS-crystallin accelerates oxidative aging

abstract:
Cataract disease, a clouding of the eye lens due to precipitation of lens proteins, affects millions of people every year worldwide. The proteins that comprise the lens, the crystallins, show extensive post-translational modifications (PTMs) in aged and cataractous lenses, most commonly deamidation and oxidation. Although surface-exposed glutamines and asparagines show the highest rates of deamidation, multiple modifications can accumulate over time in these long-lived proteins, even for buried residues. Both deamidation and oxidation have been shown to promote crystallin aggregation in vitro; however, it is not clear precisely how these modified crystallins contribute to insolubilization. Here, we report six novel crystal structures of a major human lens protein, {gamma}S-crystallin ({gamma}S): one of the wild-type in a monomeric state, and five of deamidated {gamma}S variants, ranging from three to nine deamidation sites, after varying degrees of sample aging. Consistent with previous work that focused on single-to triple-site deamidation, the deamidation mutations do not appear to drastically change the fold of {gamma}S; however, increasing deamidation leads to accelerated oxidation and disulfide bond formation. Successive addition of deamidated sites progressively destabilized protein structure as evaluated by differential scanning fluorimetry. Light scattering showed the deamidated variants display an increased propensity for aggregation compared to the wild-type protein. The results suggest the deamidated variants are useful as models for accelerated aging; the structural changes observed over time provide support for redox activity of {gamma}S-crystallin in the human lens.

HighlightsO_LINovel structures of cataract-associated variants of human eye lens protein {gamma}S-crystallin reported
C_LIO_LIIncreasing deamidation of {gamma}S-crystallin decreases stability and affects aggregation propensity
C_LIO_LIOverall fold of {gamma}S-crystallin maintained among deamidated and disulfide-bonded variants
C_LIO_LIDeamidated {gamma}S variants form disulfide bonds more rapidly than wild-type {gamma}S
C_LIO_LIPotential functional advantage of disulfide bonding in the CXCXC motif proposed
C_LI

category: biochemistry


title: SARS-CoV-2 activates ER stress and Unfolded protein response

abstract: Coronavirus disease-2019 (COVID-19) pandemic caused by the SARS-CoV-2 coronavirus infection is a major global public health concern affecting millions of people worldwide. The scientific community has joint efforts to provide effective and rapid solutions to this disease. Knowing the molecular, transmission and clinical features of this disease is of paramount importance to develop effective therapeutic and diagnostic tools. Here, we provide evidence that SARS-CoV-2 hijacks the glycosylation biosynthetic, ER-stress and UPR machineries for viral replication using a time-resolved (0-48 hours post infection, hpi) total, membrane as well as glycoproteome mapping and orthogonal validation. We found that SARS-CoV-2 induces ER stress and UPR is observed in Vero and Calu-3 cell lines with activation of the PERK-eIF2-ATF4-CHOP signaling pathway. ER-associated protein upregulation was detected in lung biopsies of COVID-19 patients and associated with survival. At later time points, cell death mechanisms are triggered. The data show that ER stress and UPR pathways are required for SARS-CoV-2 infection, therefore representing a potential target to develop/implement anti-CoVID-19 drugs.


title: Transcriptomic Analysis of the Innate Immune Response to in vitro Transfection of Plasmid DNA

abstract: The innate immune response to cytosolic DNA is intended to protect the host from viral infections, but it can also inhibit the delivery and expression of therapeutic transgenes in gene and cell therapies. The goal of this work was to use mRNA-sequencing to reveal correlations between the transfection efficiencies of four cell types (PC-3, Jurkat, HEK-293T, and primary CD3+ T cells) and their innate immune responses to nonviral gene delivery. Overall, the highest transfection efficiency was observed in HEK-293T cells (87%), which upregulated only 142 genes with no known anti-viral functions. Lipofection upregulated a much larger number (n = 1,057) of cytokine-stimulated genes (CSGs) in PC-3 cells, which also exhibited a significantly lower transfection efficiency. However, the addition of serum during Lipofection and electroporation significantly increased transfection efficiencies and decreased the number of upregulated genes in PC-3 cells. Finally, while Lipofection of Jurkat and Primary T cells only upregulated a few genes, several anti-viral CSGs that were absent in HEK and upregulated in PC-3 cells were observed to be constitutively expressed in T cells, which may explain their relatively low Lipofection efficiencies (8-21%). Indeed, overexpression of one such CSG (IFI16) significantly decreased transfection efficiency in HEK cells to 33%.