title: Coiled coils 9-to-5: Rational de novo design of α-helical barrels with tunable oligomeric states

abstract: The rational design of linear peptides that assemble controllably and predictably in water is challenging. Sequences must encode unique target structures and avoid alternative states. However, the stabilizing and discriminating non-covalent forces available are weak in water. Nonetheless, for -helical coiled-coil assemblies considerable progress has been made in rational de novo design. In these, sequence repeats of nominally hydrophobic (h) and polar (p) residues, hpphppp, direct the assembly of amphipathic helices into dimeric to tetrameric bundles. Expanding this pattern to hpphhph can produce larger -helical barrels. Here, we show that pentamers to nonamers are achieved simply by varying the residue at one of these h sites. In L/I-K-E-I-A-x-Z repeats, decreasing the size of Z from threonine to serine to alanine to glycine gives progressively larger oligomers. X-ray crystal structures of the resulting -helical barrels rationalize this: side chains at Z point directly into the helical interfaces, and smaller residues allow closer helix contacts and larger assemblies.


title: A Large-Scale Brain Network Mechanism for Increased Seizure Propensity in Alzheimer's Disease

abstract:
People with Alzheimers disease (AD) are 6-10 times more likely to develop seizures than the healthy aging population. Leading hypotheses largely consider increased excitability of local cortical tissue as primarily responsible for increased seizure prevalence in AD. However, both local dynamics and large-scale brain network structure are believed to be crucial for determining seizure likelihood and phenotype. In this study, we combine computational modelling with electrophysiological data to demonstrate a potential large-scale brain network mechanism for increased seizure propensity in people with AD. EEG was recorded from 21 people with probable AD and 26 healthy controls. At the time of EEG acquisition, all participants were free from seizures. Whole brain functional connectivity derived from source-reconstructed EEG recordings was used to build subject-specific brain network models of seizure transitions using an approach previously validated on participants with epilepsy vs controls. As cortical tissue excitability was increased in the simulations, network models of AD simulations were more likely to transition into seizures than simulations from healthy controls. Our results suggest an increased group-level probability of developing seizures at a future time for AD participants. We subsequently used the model to assess seizure propensity of different regions across the cortex. We found the most important regions for seizure generation were those typically burdened by amyloid-beta at the early stages of AD, as previously reported by in-vivo and post-mortem staging of amyloid plaques. These included cingulate, medial temporal, and orbital regions. Analysis of these spatial distributions also give potential insight into mechanisms of increased susceptibility to generalized (as opposed to focal) seizures in AD vs controls. This research suggests avenues for future studies testing patients with seizures, e.g. co-morbid AD/epilepsy patients, and comparisons with PET and MRI scans to relate regional seizure propensity with amyloid/tau pathology and cortical atrophy.

Author summaryPeople with Alzheimers disease (AD) are more likely to develop seizures than cognitively healthy people. In this study, we aimed to understand whether whole-brain network structure is related to this increased seizure likelihood. We used electroencephalography (EEG) to estimate brain networks from people with AD and healthy controls. We subsequently inserted these networks into a model brain and simulated disease progression by increasing the excitability of brain tissue. We found the simulated AD brains were more likely to develop seizures than the simulated control brains. No participants had seizures when we collected data, so our results suggest an increased probability of developing seizures at a future time for AD participants. Therefore functional brain network structure may play a role in increased seizure likelihood in AD. We also used the model to examine which brain regions were most important for generating seizures, and found that the seizure-generating regions corresponded to those typically affected in early AD. Our results also provide a potential explanation for why people with AD are more likely to have generalized seizures (i.e. seizures involving the whole brain, as opposed to  focal seizures which only involve certain areas) than the general population with epilepsy.

category: neuroscience


title: Pupillometry signatures of sustained attention and working memory

abstract: There exists an intricate relationship between attention and working memory. Recent work has further established that attention and working memory fluctuate synchronously, by tightly interleaving sustained attention and working memory tasks. This work has raised many open questions about physiological signatures underlying these behavioral fluctuations. Across two experiments, we explore pupil dynamics using real-time triggering in conjunction with an interleaved sustained attention and working memory task. In Experiment 1, we use behavioral real-time triggering and replicate recent findings from our lab (deBettencourt et al., 2019) that sustained attention fluctuates concurrently with the number of items maintained in working memory. Furthermore, highly attentive moments, detected via behavior, also exhibited larger pupil sizes. In Experiment 2, we develop a novel real-time pupil triggering technique to track pupil size fluctuations in real time and trigger working memory probes. We reveal that this pupil triggering procedure elicits differences in sustained attention, as indexed by response time. These experiments reflect methodological advances in real-time triggering and further characterize an important biomarker of sustained attention.


title: Phosphoproteomics reveals new insights into the role of PknG during the persistence of pathogenic mycobacteria in host macrophages

abstract:
Pathogenic mycobacteria, such as Mycobacterium tuberculosis, modulate the host immune system to evade clearance and promote long-term persistence, resulting in disease progression or latent infection. Understanding the mechanisms pathogenic mycobacteria use to escape elimination by the host immune system is critical to better understanding the molecular mechanisms of mycobacterial infection. Protein kinase G (PknG) in pathogenic mycobacteria has been shown to play an important role in avoiding clearance by macrophages through blocking phagosome-lysosome fusion; however, the exact mechanism is not completely understood. Here, to further investigate the role of mycobacterial PknG during early events of macrophage infection, RAW 264.7 macrophage cell lines were infected with M. bovis BCG wild-type and PknG knock-out mutant strains. After proteolysis, phosphopeptides were enriched via TiO2 columns and subjected to LC-MS/MS to identify differentially phosphorylated peptides between the wild-type and PknG mutant infected macrophages. A total of 1401 phosphosites on 914 unique proteins were identified. Following phosphoproteome normalisation and differential expression analysis, a total of 149 phosphosites were differentially phosphorylated in the wild-type infected RAW 264.7 macrophages versus the PknG knock-out mutant. A subset of 95 phosphosites was differentially up-regulated in the presence of PknG. Functional analysis of our data revealed that PknG kinase activity reprograms normal macrophage function through interfering with host cytoskeletal organisation, spliceosomal machinery, translational initiation, and programmed cell death. Differentially phosphorylated proteins in this study serve as a foundation for further validation and PknG host substrate assignment.

ImportanceTuberculosis (TB) remains one of the leading causes of death from infection worldwide, due to the ability of Mycobacterium tuberculosis (Mtb) to survive and replicate within the host, establishing reservoirs of live bacteria that promote persistence and recurrence of disease. Understanding the mechanisms that Mtb uses to evade the host immune system is thus a major goal in the TB field. Protein kinase G is thought to play an important role in Mtb avoiding clearance by the host through disruption of macrophage function, but the underlying molecular mechanisms of this are not well understood. Here, our new phosphoproteomic data reveals that mycobacterial PknG substantially reprograms normal macrophage function through extensive PknG-mediated post-translational control of critical host cellular processes. These novel findings therefore considerably increase our knowledge of mycobacterial pathogenicity, including specific host cellular pathways that might be re-activatable through host-directed therapy, thereby restoring macrophage ability to eliminate Mtb.

category: molecular biology


title: Mining metagenomes for natural product biosynthetic gene clusters: unlocking new potential with ultrafast techniques

abstract: Microorganisms produce an immense variety of natural products through the expression of Biosynthetic Gene Clusters (BGCs): physically clustered genes that encode the enzymes of a specialized metabolic pathway. These natural products cover a wide range of chemical classes (e.g., aminoglycosides, lantibiotics, nonribosomal peptides, oligosaccharides, polyketides, terpenes) that are highly valuable for industrial and medical applications1. Metagenomics, as a culture-independent approach, has greatly enhanced our ability to survey the functional potential of microorganisms and is growing in popularity for the mining of BGCs. However, to effectively exploit metagenomic data to this end, it will be crucial to more efficiently identify these genomic elements in highly complex and ever-increasing volumes of data2. Here, we address this challenge by developing the ultrafast Biosynthetic Gene cluster MEtagenomic eXploration toolbox (BiG-MEx). BiG-MEx rapidly identifies a broad range of BGC protein domains, assess their diversity and novelty, and predicts the abundance profile of natural product BGC classes in metagenomic data. We show the advantages of BiG-MEx compared to standard BGC-mining approaches, and use it to explore the BGC domain and class composition of samples in the TARA Oceans3 and Human Microbiome Project datasets4. In these analyses, we demonstrate BiG-MExs applicability to study the distribution, diversity, and ecological roles of BGCs in metagenomic data, and guide the exploration of natural products with clinical applications.

category: bioinformatics


title: Is Vaccination a Viable Method to Control Johnes Disease Caused by Mycobacterium avium subsp. paratuberculosis? Data from 12 Million Ovine Vaccinations and 7.6 Million Carcass Examinations in New South Wales, Australia from 1999-2009

abstract:
BackgroundMycobacterium avium subsp. paratuberculosis (MAP) causes Johnes disease (or paratuberculosis), a chronic wasting disease of ruminants and other animals resulting from granulomatous enteritis. There are increasing concerns that MAP is zoonotic. The prevalence of Johnes disease is increasing worldwide. In an attempt to control an epidemic of ovine Johnes disease (OJD) in New South Wales (NSW), a government/industry sponsored voluntary vaccination/on-farm management program commenced in 2000. We report herein an observational study of changes in disease prevalence as vaccination progressed, based on abattoir surveillance data for OJD from 1999 to 2009. We also discuss the epidemiological, policy, regulatory, research, economic and sociological elements that contributed to the development of a mature control program, whose aim was to halt the epidemic spread of OJD in a naive sheep population.

MethodsNSW was divided into areas of "High" (HPA), "Medium" (MPA) and "Low" (LPA) OJD prevalence. A killed whole cell vaccine (Gudair(R)) was administered to sheep from 2000 to 2009. Trained examiners evaluated the viscera of adult sheep carcasses at slaughter for gross evidence of OJD. MAP infection was confirmed by histopathology.

Principal findingsFrom 2000-2009, 12 million vaccine doses were administered in NSW (91%; 10.9 million in the HPA). Many of the vaccinated flocks were suffering > 5% annual mortality in adult sheep, with some individual flocks with 10-15% losses attributable to OJD. A total of 7.6 million carcasses were examined (38%; 2.9 million from the HPA). Overall, 16% of slaughter consignments (sheep consigned to the abattoir from a single vendor) were positive for OJD, of which 94% were from the HPA. In the HPA, the percentage of animals with lesions attributable to OJD at slaughter fell progressively from 2.4% (10,406/432,860) at commencement of vaccination in 2000 to 0.8% (1,573/189,564) by 2009. Herd immunity from vaccination in the HPA was estimated at 70% by 2009. This coincided with a progressive decrease in reports of clinical disease and mortalities in vaccinated flocks.

SignificanceWe show a decrease in the prevalence of lesions attributable to OJD in NSW concomitant with initiation of voluntary vaccination, on-farm management plans, abattoir monitoring and feedback of animal prevalence data to sheep producers. We conclude that a target of [≤] 1% regional prevalence of OJD affected sheep at slaughter is achievable using these interventions.

category: immunology


title: Is Vaccination a Viable Method to Control Johne's Disease Caused by Mycobacterium avium subsp. paratuberculosis? Data from 12 Million Ovine Vaccinations and 7.6 Million Carcass Examinations in New South Wales, Australia from 1999-2009


title: {-}Multivariable Association Discovery in Population-scale Meta-omics Studies

abstract: It is challenging to associate features such as human health outcomes, diet, environmental conditions, or other metadata to microbial community measurements, due in part to their quantitative properties. Microbiome multi-omics are typically noisy, sparse (zero-inflated), high-dimensional, extremely non-normal, and often in the form of count or compositional measurements. Here we introduce an optimized combination of novel and established methodology to assess multivariable association of microbial community features with complex metadata in population-scale observational studies. Our approach, MaAsLin 2 (Microbiome Multivariable Associations with Linear Models), uses general linear models to accommodate a wide variety of modern epidemiological studies, including cross-sectional and longitudinal designs, as well as a variety of data types (e.g. counts and relative abundances) with or without covariates and repeated measurements. To construct this method, we conducted a large-scale evaluation of a broad range of scenarios under which straightforward identification of meta-omics associations can be challenging. These simulation studies reveal that MaAsLin 2s linear model preserves statistical power in the presence of repeated measures and multiple covariates, while accounting for the nuances of meta-omics features and controlling false discovery. We also applied MaAsLin 2 to a microbial multi-omics dataset from the Integrative Human Microbiome (HMP2) project which, in addition to reproducing established results, revealed a unique, integrated landscape of inflammatory bowel disease (IBD) across multiple time points and omics profiles.

category: microbiology


title: Evolution of Phenotypic Plasticity under Host-Parasite Interactions

abstract:
Robustness and plasticity are essential features that allow biological systems to cope with complex and variable environments. Through the evolution of a given environment, the former, the insensitivity of phenotypes, is expected to increase, whereas the latter, the changeability of phenotypes, tends to diminish. However, in nature, plasticity is preserved to a certain degree. One possible cause for this is environmental variation, with one of the most important "environmental " factors being inter-species interactions. As a first step toward investigating phenotypic plasticity in response to an ecological interaction, we present the study of a simple two-species system consisting of hosts and parasites. Hosts are expected to evolve to achieve a phenotype that optimizes fitness and increases the robustness of the corresponding phenotype by reducing phenotypic fluctuations. Conversely, plasticity evolves in order to avoid certain phenotypes being attacked by parasites. By simulating evolution using the host gene-expression dynamics model, we analyze the evolution of genotype-phenotype mapping. If the interaction is weak, the fittest phenotype of the host evolves to reduce phenotypic variances. In contrast, if a sufficient degree of interaction occurs, the phenotypic variances of hosts increase to escape parasite attacks. For the latter case, we found two strategies: if the noise in the stochastic gene expression is below a certain threshold, the phenotypic variance increases via genetic diversification, whereas above the threshold, it is increased due to noise-induced phenotypic plasticity. We examine how the increase in the phenotypic variances due to parasite interactions influences the growth rate of a single host, and observed a trade-off between the two. Our results help elucidate the roles played by noise and genetic mutations in the evolution of phenotypic plasticity and robustness in response to host-parasite interactions.

Author summaryPlasticity and phenotypic variability induced by internal or external perturbations are common features of biological systems. However, certain environmental conditions initiate evolution to increase fitness and, in such cases, phenotypic variability is not advantageous, as has been demonstrated by previous laboratory and computer experiments. As a possible origin for such plasticity, we investigated the role of host-parasite interactions, such as those between bacteria and phages. Different parasite types attack hosts of certain phenotypes. Through numerical simulations of the evolution of host genotype-phenotype mapping, we found that, if the interaction is sufficiently strong, hosts increase phenotypic plasticity by increasing phenotypic fluctuations. Depending on the degree of noise in gene expression dynamics, there are two distinct strategies for increasing the phenotypic variances: via stochasticity in gene expression or via genetic variances. The former strategy, which can work over a faster time scale, leads to a decline in fitness, whereas the latter reduces the robustness of the fitted state. Our results provide insights into how phenotypic variances are preserved and how hosts can escape being attacked by parasites whose genes mutate to adapt to changes in parasites. These two host strategies, which depend on internal and external conditions, can be verified experimentally, for example, via the transcriptome analysis of microorganisms.

category: evolutionary biology


title: A computational study on the role of parameters for identification of thyroid nodules by infrared images (and its comparison with real data)

abstract:
According to experts and medical literature, a healthy thyroid gland, or a thyroid containing benign nodules, tend to be less inflamed and less active than one with malignant nodules. It seems to be a consensus that malignant nodules have more blood veins and it may be related to the maintenance of high and constant temperatures. Investigation of these characteristics, detectable by infrared sensors, and answering if they constitute patterns of malignancy are the aims of this work. Experiments considering biological heat transfer analysis by Finite Element numerical simulations are used to show the influence of nodule and patient characteristics on the identification of malignancy of thyroid nodule by thermography. The used and approved protocol for infrared examination are analyzed and simulated during all its phase that is on transient and steady state behavior, in order to verify how and when their influence can be really recognized in patients. Simulation results and the analysis of infrared exams show that the tissues between the skin and the thyroid, as well as the nodule size, have influence in superficial temperatures. Other thermal parameters of thyroid nodules are also investigated and show little influence on surface temperatures. These characteristics must be considered in nodular infrared analysis and diagnosis by thermography. The infrared examinations of patients that meet the hypotheses related to the vascularization of the nodule confirm the numerical results. All details of the physical parameters used in the simulations, characteristics of the nodules, and their complete thermal examinations are public and available, turning possible that the presented simulation could be compared with other types of heat transfer solutions. This study is a concrete contribution to the answer of under what conditions thermography can be useful in the identification of thyroid nodules.

Author summaryThyroid nodules are very common health problems. These nodules may have different characteristics, and some of them could influence the temperature of the region. Many works in the medical literature report that the healthy thyroid and even benign nodules tend to be less inflamed and active than malignant nodules and therefore should exhibit some variation in patterns of behavior related to the temperature variation between them. The focus of this work is to analyze some parameters of the nodules and details of the patients that can influence the identification and diagnosis of thyroid nodules by infrared images. To reach the objective, simulations of bioheat transfer in the neck (using a simple neck geometry and Finite Elements Analysis in COMSOL Multiphysics Software) and real infrared examinations (performed with a FLIR Infrared Camera model SC620 and a proposed protocol) were analyzed. Our results show the thermal insulation effect of the neck fat tissue, and that the effect of nodule sizes can be decremented by a thicker layer of fat. The analysis of the nodule parameters as blood perfusion rate and metabolic heat, which could be related with the nodule vascularization (an important condition related with malignancy), suggest that the thermal effects of thyroid nodules on the neck surface are not sufficient to differentiate benign from malign, and for this other features or methods must be considered.


title: The extinction and survival of sharks across the end-Cretaceous mass extinction

abstract: Sharks (Selachimorpha) are iconic marine predators that have survived multiple mass extinctions over geologic time. Their fossil record is represented by an abundance of teeth, which traditionally formed the basis for reconstructing large-scale diversity changes among different selachimorph clades. By contrast, corresponding patterns in shark ecology, as measured through morphological disparity, have received comparatively limited analytical attention. Here, we use a geometric morphometric approach to comprehensively examine the dental morphology of multiple shark lineages traversing the catastrophic end-Cretaceous mass extinction -- this event terminated the Mesozoic Era 66 million years ago. Our results show that selachimorphs maintained virtually static levels of dental disparity in most of their constituent clades during the Cretaceous/Paleogene transition. Nevertheless, selective extinctions did impact on apex predator lineages characterized by triangular blade-like teeth, and in particular, lamniforms including the dominant Cretaceous anacoracids. Other groups, such as, triakid carcharhiniforms, squalids, and hexanchids, were seemingly unaffected. Finally, while some lamniform lineages experienced morphological depletion, others underwent a post-extinction disparity increase, especially odontaspidids, which are typified by narrow-cusped teeth adapted for feeding on fishes. This disparity shift coincides with the early Paleogene radiation of teleosts, a possible prey source, as well as the geographic relocation of shark disparity  hotspots, perhaps indicating a regionally disjunct pattern of extinction recovery. Ultimately, our study reveals a complex morphological response to the end-Cretaceous mass extinction event, the dynamics of which we are only just beginning to understand.

category: paleontology


title: Pharmacokinetics of long-term low-dose oral rapamycin in four healthy middle-aged companion dogs

abstract:
ObjectiveTo determine the blood concentration and pharmacokinetic parameters of rapamycin in companion dogs following long-term, low-dose oral administration of rapamycin.

AnimalsFour healthy, middle-aged, medium-to-large breed privately owned dogs participated.

ProceduresAll dogs had been receiving oral rapamycin at a dose of 0.025 mg/kg on Monday, Wednesday, and Friday mornings for at least one month. An initial blood sample was collected prior to morning rapamycin administration, and samples were collected at 1, 2, 6, and 24 hours after rapamycin was given. Blood samples were transferred to blood spot collection cards, air-dried and stored at -80{degrees}C. Rapamycin concentrations were determined via HPLC/MS. All blood collections occurred on Wednesdays, so that the previous dose of rapamycin had taken place 48 hours prior to blood collection.

ResultsFor all dogs, rapamycin Tmax was 2 hours. Median Cmax was 1.47 ng/ml (0.912 - 2.13), and the median AUC0-last was 15.7 ng*hr/mL (1.30 - 36.3). Due to sample size and timing, the only estimates related to elimination rate reported are for mean residence time with a median of 4.70 hrs (0.90 - 7.30).

Conclusions and Clinical RelevanceA 0.025 mg/kg oral dose of rapamycin, administered three times a week, resulted in concentrations of rapamycin in the blood capable of being measured in ng/ml.

category: pharmacology and toxicology


title: Stress and corticotropin releasing factor (CRF) promote necrotizing enterocolitis in a formula-fed neonatal rat model

abstract: The etiology of necrotizing enterocolitis (NEC) is not known. Alterations in gut microbiome, mucosal barrier function, immune cell activation, and blood flow are characterized events in its development, with stress as a contributing factor. The hormone corticotropin-releasing factor (CRF) is a key mediator of stress responses and influences these aforementioned processes. CRF signaling is modulated by NECs main risk factors of prematurity and formula feeding. Using an established neonatal rat model of NEC, we tested hypotheses that: (i) increased CRF levels--as seen during stress--promote NEC in formula-fed newborn rats, and (ii) antagonism of CRF action ameliorates NEC. Newborn pups were formula-fed to initiate gut inflammation and randomized to: no stress, no stress with subcutaneous CRF administration, stress (acute hypoxia followed by cold exposure--NEC model), or stress after pretreatment with the CRF peptide antagonist Astressin. Dam-fed unstressed and stressed littermates served as controls. NEC incidence and severity in the terminal ileum were determined using a histologic scoring system. Changes in CRF, CRF receptor (CRFRs), and toll-like receptor 4 (TLR4) expression levels were determined by immunofluorescence and immunoblotting, respectively. Stress exposure in FF neonates resulted in 40.0% NEC incidence, whereas exogenous CRF administration resulted in 51.7% NEC incidence compared to 8.7% in FF non-stressed neonates (p<0.001). Astressin prevented development of NEC in FF-stressed neonates (7.7% vs. 40.0%; p=0.003). CRF and CRFR immunoreactivity increased in the ileum of neonates with NEC compared to dam-fed controls or FF unstressed pups. Immunoblotting confirmed increased TLR4 protein levels in FF stressed (NEC model) animals vs. controls, and Astressin treatment restored TLR4 to control levels. Peripheral CRF may serve as specific pharmacologic target for the prevention and treatment of NEC.

category: physiology


title: Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies

abstract: Candida albicans, an opportunistic fungal pathogen, is a significant cause of human infections, particularly in immunocompromised individuals. Phenotypic plasticity between two morphological phenotypes, yeast and hyphae, is a key mechanism by which C. albicans can thrive in many microenvironments and cause disease in the host. Understanding the decision points and key driver genes controlling this important transition, and how these genes respond to different environmental signals is critical to understanding how C. albicans causes infections in the host. Here we build and analyze a Boolean dynamical model of the C. albicans yeast to hyphal transition, integrating multiple environmental factors and regulatory mechanisms. We validate the model by a systematic comparison to prior experiments, which led to agreement in 18 out of 22 cases. The discrepancies motivate alternative hypotheses that are testable by follow-up experiments. Analysis of this model revealed two time-constrained windows of opportunity that must be met for the complete transition from the yeast to hyphal phenotype, as well as control strategies that can robustly prevent this transition. We experimentally validate two of these control predictions in C. albicans strains lacking the transcription factor UME6 and the histone deacetylase HDA1, respectively. This model will serve as a strong base from which to develop a systems biology understanding of C. albicans morphogenesis.

category: systems biology


title: Regeneration of spinal motor axons: Negative regulation by Celsr2 implicating Cdc42/Rac1 and JNK/c-Jun signaling

abstract: During development, cadherins Celsr2 and Celsr3 control axon navigation. Unlike Celsr3, Celsr2 remains expressed in the adult, suggesting unexplored roles in maintenance and repair. Here we show that Celsr2 knockdown promotes motor axon regeneration in mouse and human spinal cord explants and cultured motor neurons. Celsr2 downregulation is accompanied by increased levels of GTP-bound Rac1 and Cdc42, and of JNK and c-Jun proteins. Using a branchial plexus injury model, we show that forelimb functional recovery is improved in Celsr2 mutant versus control mice. Compared to controls, in mutant mice, reinnervated biceps muscles are less atrophic, contain more newly formed neuromuscular junctions, and generate larger electromyographic potentials, while motor neuron survival and axon regeneration are improved. GTP-bound Rac1 and Cdc42, JNK and c-Jun are upregulated in injured mutant versus control spinal cord. In conclusion, Celsr2 negatively regulates motor axon regeneration via Cdc42/Rac1/JNK/c-Jun signaling and is a target for neural repair.


title: Transcriptome Analysis of Chloride Intracellular Channel Knockdown in Drosophila Identifies Oxidation-Reduction Function as Possible Mechanism of Altered Sensitivity to Ethanol Sedation

abstract: Chloride intracellular channels (CLICs) are a unique family of evolutionarily conserved metamorphic proteins, switching between stable conformations based on redox conditions. CLICs have been implicated in a wide variety biological processes including ion channel activity, apoptosis, membrane trafficking, and enzymatic oxidoreductase activity. Understanding the molecular mechanisms by which CLICs engage in these activities is an area of active research. Here, the sole Drosophila melanogaster ortholog, Clic, was targeted for RNAi knockdown to identify genes and biological processes associated with Clic expression. Clic knockdown had a substantial impact on global transcription, altering expression of over 9% of transcribed Drosophila genes. Overrepresentation analysis of differentially expressed genes identified enrichment of 23 Gene Ontology terms including Cytoplasmic Translation, Oxidation-Reduction Process, Heme Binding, Membrane, Cell Junction, and Nucleolus. The top term, Cytoplasmic Translation, was enriched almost exclusively with downregulated genes. Drosophila Clic and vertebrate ortholog Clic4 have previously been tied to ethanol sensitivity and ethanol-regulated expression. Clic knockdown-responsive genes from the present study were found to overlap significantly with gene sets from 4 independently published studies related to ethanol exposure and sensitivity in Drosophila. Bioinformatic analysis of genes shared between these studies revealed an enrichment of genes related to amino acid metabolism, protein processing, oxidation-reduction processes, and lipid particles among others. To determine whether the modulation of ethanol sensitivity by Clic may be related to co-regulated oxidation-reduction processes, we evaluated the effect of hyperoxia on ethanol sedation in Clic knockdown flies. Consistent with previous findings, Clic knockdown reduced acute ethanol sedation sensitivity in flies housed under nomoxia. However, this effect was reversed by exposure to hyperoxia, suggesting a common set of molecular-genetic mechanism may modulate each of these processes. This study suggests that Drosophila Clic has a major influence on regulation of oxidative stress signaling and that this function overlaps with the molecular mechanisms of acute ethanol sensitivity in the fly.


title: Differential requirement of NPHP1 for compartmentalized protein localization during photoreceptor outer segment development and maintenance

abstract: Nephrocystin (NPHP1) is a ciliary transition zone protein and its ablation causes nephronophthisis (NPHP) with partially penetrant retinal dystrophy. However, the precise requirements of NPHP1 in photoreceptors are not well understood. Here, we characterize retinal degeneration in a mouse model of NPHP1 and show that NPHP1 is required to prevent infiltration of inner segment plasma membrane proteins into the outer segment during the photoreceptor maturation. We demonstrate that Nphp1 gene-trap mutant mice, which were previously described as null, are in fact hypomorphs due to the production of a small quantity of functional mRNAs derived from nonsense-associated altered splicing and skipping of two exons including the one harboring the gene-trap. In homozygous mutant animals, inner segment plasma membrane proteins such as syntaxin-3 (STX3), synaptosomal-associated protein 25 (SNAP25), and interphotoreceptor matrix proteoglycan 2 (IMPG2) accumulate in the outer segment when outer segments are actively elongating. This phenotype, however, is spontaneously ameliorated after the outer segment elongation is completed. Retinal degeneration also occurs temporarily during the photoreceptor maturation but stops afterward. We further show that Nphp1 genetically interacts with Cep290, another NPHP gene, and that a reduction of Cep290 gene dose results in retinal degeneration that continues until adulthood in Nphp1 mutant mice. These findings demonstrate that NPHP1 is required for the confinement of inner segment plasma membrane proteins during the outer segment development, but its requirement diminishes as photoreceptors mature. Our study also suggests that additional mutations in other NPHP genes may influence the penetrance of retinopathy in human NPHP1 patients.


title: Rab11a mediates cell-cell spread and reassortment of influenza A virus genomes via tunneling nanotubes.

abstract:
Influenza A virus (IAV) genomes comprise eight negative strand RNAs packaged into virions in the form of viral ribonucleoproteins (vRNPs). Rab11a plays a crucial role in the transport of vRNPs from the nucleus to the plasma membrane via microtubules, allowing assembly and virus production. Here, we identify a novel function for Rab11a in the inter-cellular transport of IAV vRNPs using tunneling nanotubes (TNTs) as molecular highways. TNTs are F-Actin rich tubules that link the cytoplasm of nearby cells. In IAV-infected cells, Rab11a was visualized together with vRNPs in these actin-rich intercellular connections. To better examine viral spread via TNTs, we devised an infection system in which conventional, virion-mediated, spread was not possible. Namely, we generated HA-deficient reporter viruses which are unable to produce progeny virions but whose genomes can be replicated and trafficked. In this system, vRNP transfer to neighboring cells was observed and this transfer was found to be dependent on both actin and Rab11a. Generation of infectious virus via TNT transfer was confirmed using donor cells infected with HA-deficient virus and recipient cells stably expressing HA protein. Mixing donor cells infected with genetically distinct IAVs furthermore revealed the potential for Rab11a and TNTs to serve as a conduit for genome mixing and reassortment in IAV infections. These data therefore reveal a novel role for Rab11a in the IAV life cycle, which could have significant implications for within-host spread, genome reassortment and immune evasion.

Author SummaryInfluenza A viruses infect epithelial cells of the upper and lower respiratory tract in humans. Infection is propagated by the generation of viral particles from infected cells, which disseminate within the tissue. Disseminating particles can encounter obstacles in the extracellular environment, including mucus, ciliary movement, antibody neutralization and uptake by phagocytic immune cells. An alternative mode of spread, which avoids these hazards, involves direct transport of viral components between cells. This cell-cell spread of infection is not a well understood process. In this study we demonstrate that the host factor Rab11a mediates the transport of viral genomes in the cell-cell spread of infection. Rab11a is already known to play a pro-viral role in the transport of viral genomes to the plasma membrane for assembly into virus particles. Here, we see that this same transport mechanism is co-opted for direct cell-cell spread through cellular connections called tunneling nanotubes. We show that complexes of Rab11a and viral components can be trafficked across tunneling nanotubes, transmitting infection without the formation of virus particles. Importantly, this route of spread often seeds viral genomes from multiple donor cells into recipient cells, which in turn increases viral genetic diversity.


title: Ribosomal DNA revealed an extensive role of allopolyploidy in the radiation of Ulex L.

abstract:
We studied the phylogeny of Ulex L., a genus of spiny legumes, which its center of diversity in the Iberian Peninsula, using ribosomal DNA markers (rDNA), namely ETS, 5.8S and ITS (45S), and 5S intergenic spacer regions. One of the main findings was the presence of very different haplotypes in 5S-IGS genes and, to a less extent, in ETS and ITS, in seven polyploid taxa. We interpreted these results as an indication of hybrid origins and proposed allopolyploidy for U. argenteus ssp. subsericeus, U. australis ssp. australis, U. australis ssp. welwitschianus, U. densus, U. europaeus ssp. europaeus, U. europaeus ssp. latebracteatus, and U. jussiaei. These results reinforce an early hypothesis which stated that the radiation of Ulex occurred mainly by polyplodization.

Phylograms showed two main clades, one grouping the hydrophilic U. gallii, U. breoganii and U. minor, and the other grouping the southern, xerophytic, taxa. The putative allopolyploids showed haplotypes, which grouped in both clades, indicating that allopolyploidy, occurred through hybridization from these hydrophilic and xerophytic lineages.

The phylogenetic position of U. micranthus is not certain and it is discussed. The 5S-IGS showed to retain more polymorphisms than ETS gene or ITS markers. This result is compatible with the hypothesis that 5S rDNA region is less vulnerable to inter-loci concerted evolution than 45S, providing a more suitable marker for reconstructing histories of allopolyploid species. We discuss the taxonomic consequences of these results.


title: Hearing loss is associated with delayed neural responses to continuous speech

abstract:
We investigated the impact of hearing loss on the neural processing of speech. Using a forward modeling approach, we compared the neural responses to continuous speech of 14 adults with sensorineural hearing loss with those of age-matched normal-hearing peers.

Compared to their normal-hearing peers, hearing-impaired listeners had increased neural tracking and delayed neural responses to continuous speech in quiet. The latency also increased with the degree of hearing loss. As speech understanding decreased, neural tracking decreased in both populations; however, a significantly different trend was observed for the latency of the neural responses. For normal-hearing listeners, the latency increased with increasing background noise level. However, for hearing-impaired listeners, this increase was not observed.

Our results support the idea that the neural response latency indicates the efficiency of neural speech processing. Hearing-impaired listeners process speech in silence less efficiently than normal-hearing listeners. Our results suggest that this reduction in neural speech processing efficiency is a gradual effect which occurs as hearing deteriorates. Moreover, the efficiency of neural speech processing in hearing-impaired listeners is already at its lowest level when listening to speech in quiet, while normal-hearing listeners show a further decrease in efficiency when the noise level increases.

From our results, it is apparent that sound amplification does not solve hearing loss. Even when listing to speech in silence at a comfortable loudness, hearing-impaired listeners process speech less efficiently.


title: Nodal GABA facilitates axon spike transmission in the spinal cord.

abstract: Movement and posture depend on sensory feedback that is regulated by specialized GABAergic neurons (GAD2+) that form axo-axonic contacts onto myelinated proprioceptive sensory axons and are thought to be inhibitory. However, we report here that activating GAD2+ neurons, directly with optogenetics or indirectly by cutaneous stimulation, facilitates sensory feedback to motoneurons in awake rodents and humans. GABAA receptors and GAD2+ innervation at or near nodes of Ranvier of sensory axons cause this facilitation, preventing spike propagation failure at the many axon branch points, which is otherwise common without GABA. In contrast, GABAA receptors are generally lacking from axon terminals (unlike GABAB) and do not presynaptically inhibit transmitter release onto motoneurons. GABAergic innervation near nodes and branch points allows individual branches to function autonomously, with GAD2+ neurons regulating which branches conduct, adding a computational layer to the neuronal networks generating movement and likely generalizing to other CNS axons.


title: GABA facilitates spike propagation at branch points of sensory axons in the spinal cord


title: GABA facilitates spike propagation through branch points of sensory axons in the spinal cord


title: Optimum growth temperature declines with body size within fish species

abstract: According to the temperature-size rule, warming of aquatic ecosystems is generally predicted to increase individual growth rates but reduce asymptotic body sizes of ectotherms. However, we lack a comprehensive understanding of how growth and key processes affecting it, such as consumption and metabolism, depend on both temperature and body mass within species. This limits our ability to inform growth models, link experimental data to observed growth patterns, and advance mechanistic food web models. To examine the combined effects of body size and temperature on individual growth, as well as the link between maximum consumption, metabolism and body growth, we conducted a systematic review and compiled experimental data on fishes from 52 studies that combined body mass and temperature treatments. By fitting hierarchical models accounting for variation between species, we estimated how maximum consumption and metabolic rate scale jointly with temperature and body mass within species. We found that whole-organism maximum consumption increases more slowly with body mass than metabolism, and is unimodal over the full temperature range, which leads to the prediction that optimum growth temperatures decline with body size. Using an independent dataset, we confirmed this negative relationship between optimum growth temperature and body size. Small individuals of a given population may therefore exhibit increased growth with initial warming, whereas larger conspecifics could be the first to experience negative impacts of warming on growth. These findings help advance mechanistic models of individual growth and food web dynamics and improve our understanding of how climate warming affects the growth and size structure of aquatic ectotherms.

category: ecology


title: Regulation by Progestins, Corticosteroids and RU486 of Activation of Elephant Shark and Human Progesterone Receptors: An Evolutionary Perspective

abstract: We investigated progestin and corticosteroid activation of the progesterone receptor (PR) from elephant shark, a cartilaginous fish belonging to the oldest group of jawed vertebrates. Comparison with human PR provides insights into the evolution of steroid activation of human PR. At 1 nM steroid, elephant shark PR is activated by progesterone, 17-hydroxy-progesterone, 20{beta}-hydroxy-progesterone, 11-deoxycorticosterone (21-hydroxyprogesterone) and 11-deoxycortisol. Human PR, in comparison, is activated at 1 nM steroid, only by progesterone and 11-deoxycorticosterone, indicating increased progestin and corticosteroid specificity during the evolution of human PR. RU486, an important clinical antagonist of human PR, did not inhibit progesterone activation of elephant shark PR. Cys-528 in elephant shark PR corresponds to Gly-722 in human PR, which is essential for RU486 inhibition of human PR. Confirming the importance of Cys-528 in elephant shark PR, RU486 inhibited progesterone activation of the Cys528Gly mutant PR. Compared to wild-type human PR, there was an increase in activation of human Gly722Cys PR by11-deoxycortisol and a decrease in activation by corticosterone, which may have been important in selection for the mutation corresponding to human glycine-722 PR that first evolved in platypus PR, a basal mammal.


title: Comparative whole-genome analysis of a Thar desert strain Streptomyces sp. JB150 provides deep insights into the encoded parvome and adaptations to desert edaphic system

abstract: We sequenced the genome of Streptomyces sp. JB150, isolated from a unique site of the Thar desert in India. Genome mining of the JB150 genome revealed the presence of many interesting secondary metabolic biosynthetic gene clusters (BGCs). The encoded parvome of JB150 includes non-ribosomal peptides, polyketides including {beta}-lactone, butyrolactone, ectoine, lantipeptides, lasso peptides, melanin, resorcinol, siderophores, terpenoids, thiopeptides, and other types of hybrid compounds. Among them, ~30% BGCs displayed a high degree of novelty. The genome of JB150 was enriched for a large assortment of specialized genes coding for the production of many interesting biomolecules comprising compatible solutes, multiple stress-response regulators, transport proteins, protein secretion systems, signaling molecules, chaperones and storage reserves, etc. The presence of diverse members of CAZymes enzyme families, high numbers of riboflavin, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), trehalose and aromatic compounds synthesis genes, putative orthologues to several of the classical fatty acid synthesis components, prototrophy for many essential amino acids exhibit metabolic versatility of JB150 to inhabit in the extreme desert environment. Besides, the genome of JB150 was observed to specifically encode thiazole-oxazole-modified thiazolemicrocin (TOMM) and ectoine. The comparison of the complete genomes of Streptomyces sp. JB150 and seven other actinomycete strains belonging to different desert ecosystems unveiled the presence of many previously undetected, distinctive, biological, and genomic signatures. We propose that these genetic traits endowed by these strains are essential for their adaptation in the highly underprivileged, extreme ecosystem of the Thar desert to cope with multiple abiotic stressors, oligotrophic nutrient conditions and to produce a huge repertoire of diverse secondary metabolites.

category: genomics


title: Cooperative and aggressive behaviours vary between ranks in anemonefish social hierarchies

abstract: Many animal groups consist of individuals organised in dominance hierarchies, based on age, size or fighting ability. Lower ranked individuals often do not reproduce themselves but perform cooperative behaviours to help the reproductive output of dominant individuals or the group as a whole. Theoretical models suggest that individuals of higher rank should show increased amounts of aggressive behaviours, such as aggressions towards other group members, but should decrease the amount of cooperative behaviours, such as brood care or territory maintenance. Most empirical tests of these models focus on insect or mammalian systems where kin selection plays a large role, rather than animals that live in groups of unrelated individuals. Here we use two anemonefish species to test hypotheses of variation in cooperation and aggression with respect to social rank and species, for social systems where group members are unrelated. We assessed the behaviours of each rank in 20 groups of Amphiprion percula and 12 groups of A. perideraion in Kimbe Bay, Papua New Guinea. We also performed a removal experiment to test if cooperative and aggressive behaviours are likely adaptive, i.e., if they change as an individual ascends in rank. Our results show differences between the two species, with A. percula showing more cooperative behaviours and A. perideraion showing more aggressive behaviours, despite them being closely related and sharing a very similar ecology. With respect to both cooperation and aggression we found consistent differences between ranks in both species, with higher ranks performing more aggressive as well as more cooperative behaviours. When we experimentally provided lower ranked individuals (rank 4) an opportunity to ascend in the hierarchy, they showed more aggression and more cooperation in line with our observations for rank 3 individuals. Thus, we show that rank specific behavioural patterns are likely adaptive in anemonefishes and that some model predictions do not hold in systems where kin selection benefits are absent. Rather, future fitness benefits through territory inheritance and group augmentation likely motivate cooperative and aggressive behaviours by subordinates in groups of unrelated vertebrates.

category: animal behavior and cognition


title: Welfare at group and individual level: optical flow patterns of broiler chicken flocks are correlated with the behaviour of individual birds

abstract:
Group level measures of welfare such as the optical flow patterns made by broiler chicken flocks have been criticized on the grounds that they give only average measures and overlook the welfare of individual animals. However, we here show that by using the skew and kurtosis in addition to the mean, optical flow patterns can be used to deliver information not just about the flock average but also about the proportion of individuals in different movement categories. We correlated flock optical flow patterns with the behaviour of a sample of 16 birds per flock in two runway tests and a water (latency-to-lie) test. In the runway tests, there was a positive correlation between the time taken to complete the runway and the skew and kurtosis of optical flow on day 28 of flock life (slow individuals came from flocks with a high skew and kurtosis). In the water test, there was a positive correlation between the length of time the birds remained standing and the mean and variance of flock optical flow (the most mobile individuals came from flocks with the highest mean). Patterns at flock level thus contain valuable information about the welfare of the individuals that compose the flock.

Simple SummaryTechnology on farms potentially brings benefits of improved animal health, welfare and productivity as well as reduction in disease, waste and environmental impact. However, it also raises public concern about the welfare of individual animals, particularly when applied to large groups such as broiler (meat) chickens. We here address this issue by showing that camera technology can both provide life-long continuous monitoring of the welfare of whole flocks and also give crucial information about the individuals making up the flock. The cameras detect variation between individuals and are also sensitive to birds moving abnormally. By testing birds individually, we show that slow-moving birds tended to come from flocks that moved slowly overall and showed large variation between individuals whereas fast-moving birds were more likely to come from more active flocks that moved more uniformly. Properly used, camera technology can thus monitor the welfare of flocks continuously throughout their lives while reflecting the behaviour of individual birds.


title: Quickomics: exploring omics data in an intuitive, interactive and informative manner

abstract:
SummaryWe developed Quickomics, a feature-rich R Shiny-powered tool to enable biologists to fully explore complex omics statistical analysis results and perform advanced analysis in an easy-to-use interactive interface. It covers a broad range of secondary and tertiary analytical tasks after primary analysis of omics data is completed. Each functional module is equipped with customizable options and generates both interactive and publication-ready plots to uncover biological insights from data. The modular design makes the tool extensible with ease.

AvailabilityResearchers can experience the functionalities with their own data or demo RNA-Seq and proteomics datasets by using the app hosted at http://quickomics.bxgenomics.com and following the tutorial, https://bit.ly/3rXIyhL. The source code under GPLv3 license is provided at https://github.com/interactivereport/Quickomics for local installation.

Supplementary informationSupplementary materials are available at https://bit.ly/37HP17g.


title: Single Cell Biological Microlasers Powered by Deep Learning

abstract: Cellular lasers are cutting-edge technologies for biomedical applications. Due to the enhanced interactions between light and cells in microcavities, cellular properties and subtle changes of cells can be significantly reflected by the laser emission characteristics. In particular, transverse laser modes from single-cell lasers which utilize Fabry-Perot cavities are highly correlated to the spatial biophysical properties of cells. However, the high chaotic and complex variation of laser modes limits their practical applications for cell detections. Deep learning technique has demonstrated its powerful capability in solving complex imaging problems, which is expected to be applied for cell detections based on laser mode imaging. In this study, deep learning technique was applied to analyze laser modes generated from single-cell lasers, in which a correlation between laser modes and physical properties of cells was built. As a proof-of-concept, we demonstrated the predictions of cell sizes using deep learning based on laser mode imaging. In the first part, bioinspired cell models were fabricated to systematically study how cell sizes affect the characteristics of laser modes. By training a convolutional neuron network (CNN) model with laser mode images, predictions of cell model diameters with a sub-wavelength accuracy were achieved. In the second part, deep learning was employed to study laser modes generated from biological cells. By training a CNN model with laser mode images acquired from astrocyte cells, predictions of cell sizes with a sub-wavelength accuracy were also achieved. The results show the great potential of laser mode imaging integrated with deep learning for cell analysis and biophysical studies.

category: biophysics


title: Osa-miR820 regulatory node primes rice plants to tolerate salt stress in an agronomically advantageous manner

abstract: Plant microRNAs (miRs) play an important role in regulating gene expression under normal and stressful environments. Here we report the functional implications on the role of Osa-miR820, which can be grouped as a young, rice-specific miR. It is a member of the class II transposon-derived small RNA family and is processed as 21-nt and 24-nt length variants, respectively. Size of the miR820 family varies from 1 to 16 across the Oryza AA genomes. The 21-nt Osa-miR820 negatively regulates a de novo methylase, OsDRM2 (domains rearranged methyl transferase) that prevents methylation of the CACTA transposon loci in the rice genome. In an earlier report we have detailed the expression profiles of Osa-miR820 and its target in abiotic stress responses using rice varieties exhibiting varying response to salt stress. In this study, artificial miR based approach was employed to specifically overexpress 21-nt Osa-miR820 in rice plants (OX-820). These plants exhibited enhanced vigour, ~25-30% increase in the number of spikelets per panicle and increased grain filling, under normal and salt stress conditions. The OX-820 lines showed a better water use efficiency and higher proline accumulation under salt stress. These plants can serve as a useful source for dissecting the molecular machinery governed by Osa-miR820:DRM2 node to prime tolerance to salt stress in an agronomically advantageous manner.

category: plant biology


title: Unraveling the origin of Glucose mediated disparate proliferation dynamics of Cancer stem cells

abstract: Cancer stem cells (CSCs) often switch on their self-renewal programming aggressively to cause a relapse of cancer. Intriguingly, glucose differentially triggers the proliferation propensities in CSCs in an origin-dependent manner by controlling the expression of the key transcription factor like Nanog. However, the factors that critically govern this glucose-stimulated proliferation dynamics of CSCs remains elusive. Herein, by proposing a mathematical model of glucose-mediated Nanog regulation in CSCs, we showed that the differential proliferation behavior of CSCs can be explained by considering the experimentally observed varied expression levels of key positive (STAT3) and negative (p53) regulators of Nanog. Our model reconciles various experimental observations and predicts ways to fine-tune the proliferation dynamics of specific CSCs in a context-dependent manner. In future, these modeling insights will be useful in developing improved therapeutic strategies to get rid of harmful CSCs.


title: Hyperoxia Inhibits the Growth of Mouse Forebrain Oligodendrocyte Progenitors

abstract: NG2 chondroitin sulfate proteoglycan positive oligodendrocyte progenitor cells (OPCs) reside throughout the brain. They divide asymmetrically and differentiate into myelinating oligodendrocytes throughout adulthood. OPCs have been successfully isolated from rodents using several techniques including magnetic beads, immunopanning and exploiting differential centripetal adhesion. Whereas rat OPCs are relatively simple to propagate in vitro, it has been difficult to expand mouse OPCs. Therefore, we evaluated the effects of oxygen levels, growth factors and extracellular matrix components to produce a simple and reproducible method to prepare large numbers of nearly homogenous cultures of primary mouse OPCs from postnatal day 0-2 mouse telencephala. Using the McCarthy and de Vellis mechanical separation method OPCs were separated from mixed culture of glial cells. When the OPCs were plated onto fibronectin coated tissue culture plates in a biochemically defined medium that contained fibroblast growth factor-2 (FGF-2) and platelet derived growth factor AA (PDGFAA), and they were maintained in a standard tissue culture incubator, they proliferated very slowly. By contrast, mouse OPCs doubled approximately every 7 days when maintained in a 2% oxygen, nitrogen buffered environment. After 3 passages, greater than 99% of these OPCs were NG2+/PDGFR+. In medium containing only FGF-2, mouse OPCs progressed to late stage OPCs whereupon A2B5 expression decreased and O4 expression increased. When these cells were differentiated between passages 1 and 3, the majority of the OPCs differentiated into MBP+ mature oligodendrocytes However, cells that were repeatedly passaged beyond 4 passages progressed to a late O4+ OPC (even with mitogens present) and when differentiated by mitogen removal a minority of the OPCs differentiated into MBP+ cells. These studies reveal significant differences between mouse and rat OPCs and an inhibitory role for oxygen in mouse OPC proliferation.


title: Neuropsychological assessment and virtual reality training of social prediction in patients with cerebellar malformation

abstract: It has been proposed that impairments of the predictive function exerted by the cerebellum may account for social cognition deficits. Here, we integrated cerebellar functions in a predictive coding framework to elucidate how cerebellar alterations could affect the predictive processing of others behavior. Experiment 1 demonstrated that cerebellar patients were impaired in relying on contextual information during action prediction, and this impairment was significantly associated with social cognition abilities. Experiment 2 indicated that patients with cerebellar malformation showed a domain-general deficit in using contextual information to predict both social and physical events. Experiment 3 provided first evidence that a social-prediction training in virtual reality could boost the ability to use context-based predictions to understand others intentions. These findings shed new light on the predictive role of the cerebellum and its contribution to social cognition, paving the way for new approaches to the rehabilitation of the Cerebellar Cognitive Affective Syndrome.


title: Analysis of HIV Reservoirs in Cellular Conjugates from Peripheral Blood

abstract: Defining distinctive attributes of HIV-infected cells will inform development of HIV cure-directed therapies. Prior ex vivo studies of blood and tissue have suggested that some HIV-infected CD4 T cells are found in conjugates with other cell types. Here, we analyzed levels and sequences of HIV nucleic acids in sorted cellular conjugates from PBMC. Compared to single CD4 T cells, conjugates containing CD4 T cells showed no enrichment for HIV DNA or RNA. However, in several HIV controllers, HIV DNA sequences from sorted conjugates were enriched for sequences closely related to plasma viruses. In ART-treated people, although subgenomic HIV DNA sequences in sorted conjugates and single cells were genetically intermingled, intact proviruses were more frequent in whole blood cells than in magnetically-purified CD4 T cells. We conclude that some HIV-infected cells have attributes that predict preferential loss during sample processing, and that may also reflect vulnerability to therapeutic targeting in vivo.


title: Systemic inflammation recruits fast-acting anti-inflammatory innate myeloid progenitors from BM into lymphatics

abstract: Innate immune cellular effectors are actively consumed during systemic inflammation but the systemic traffic and the mechanisms that support their replenishment remain unknown. Here we demonstrate that acute systemic inflammation induces the emergent activation of a previously unrecognized system of rapid migration of granulocyte-macrophage progenitors and committed macrophage-dendritic progenitors, but not other progenitors or stem cells, from bone marrow (BM) to lymphatic capillaries. The progenitor traffic to the systemic lymphatic circulation is mediated by Ccl19/Ccr7 and is NF{kappa}B independent, Traf6/I{kappa}B-kinase/SNAP23 activation which is responsible for the secretion of pre-stored Ccl19 by a subpopulation of CD205+/CD172a+ conventional dendritic cells type 2 (cDC2) and upregulation of BM myeloid progenitor Ccr7 signaling. The consequence of this progenitor traffic is anti-inflammatory with promotion of early survival and initiation of replenishment of lymph node cDC.


title: Sex-specific differences in the function and differentiation of ABCsmark TLR7-driven immunopathogenesis

abstract: Sex differences characterize immune responses to viruses and autoimmune diseases like SLE. ABCs are an emerging population of CD11c+ T-bet+ B cells critical for antiviral responses and autoimmune disorders. DEF6 and SWAP70, are two homologous molecules whose combined absence in double-knock-out mice (DKOs) leads to a lupus syndrome in females marked by an accumulation of ABCs. Here we demonstrate that DKO ABCs exhibit sex-specific differences in their expansion, upregulation of an ISG signature, and further differentiation. BCR sequencing and fate mapping experiments reveal that DKO ABCs undergo oligoclonal expansion and differentiate into both CD11c+ and CD11c- effector populations with pathogenic and proinflammatory potential. Tlr7 duplication in DKO males overrides the sex-bias and further augments the dissemination and pathogenicity of ABCs resulting in severe pulmonary inflammation and early mortality. Thus, sexual dimorphism shapes the expansion, function, and differentiation of ABCs contributing to the sex-bias that accompanies TLR7-driven immunopathogenesis.


title: N-glycan core synthesis by Alg24 strengthens the hypothesis of an archaeal origin of eukaryal N-glycosylation

abstract:
Protein N-glycosylation is the most common posttranslational modifications found in all three domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in eukaryotes. Here, we report the identification of a thermostable archaeal beta-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed the function as an inverting {beta}-D-GlcNAc-(1[->]4)--D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its functional importance for Agl24. Furthermore, bioinformatics and structural modeling revealed strong similarities between Agl24 and both the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which catalyze the identical or a similar process, respectively. Our data, complemented by phylogenetic analysis of Alg13 and Alg14, revealed similar sequences in Asgardarchaeota, further supporting the hypothesis that the Alg13/14 homologs in eukaryotes have been acquired during eukaryogenesis.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/427365v2_ufig1.gif" ALT="Figure 1">
View larger version (23K):
org.highwire.dtl.DTLVardef@13d1ffdorg.highwire.dtl.DTLVardef@1ff48d0org.highwire.dtl.DTLVardef@1056e75org.highwire.dtl.DTLVardef@196ff58_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIFirst identification and characterization of a thermostable {beta}-D-GlcNAc-(1[->]4)--D-GlcNAc-diphosphodolichol glycosyltransferase (GT family 28) in Archaea.
C_LIO_LIA highly conserved histidine, within a GGH motif in Agl24, Alg14, and MurG, is essential for function of Agl24.
C_LIO_LIAgl24-like homologs are broadly distributed among Archaea.
C_LIO_LIThe eukaryotic Alg13 and Alg14 are closely related to the Asgard homologs, suggesting their acquisition during eukaryogenesis.
C_LI


title: N-glycan chitobiose core biosynthesis by Agl24 strengthens the hypothesis of an archaeal origin of the eukaryal N-glycosylation


title: Patterns of Mustelid gammaherpesvirus 1 (MusGHV-1) genital reactivation linked to stressors in adult European badgers (Meles meles)

abstract:
Herpesvirus infections are common and mostly asymptomatic in vertebrates, but can result in impaired reproduction. It is therefore important to understand infection patterns and associated risk factors, particularly the effects of different stressors. Here we use Mustelid gammaherpesvirus 1 (MusGHV-1) infection in European badgers (Meles meles) as a host-pathogen wildlife model to study the effects of a variety of demographic, social, physiological and environmental stressors on viral reactivation in the genital tract. We collected 251 genital swabs from 151 free-ranging individuals across 3 trapping seasons (spring, summer and autumn). We screened for MusGHV-1 using PCR and explored possible links between genital MusGHV-1 reactivation and stressors, and their interactions, using logistic regression. In adults, reactivation was more likely in males, especially those in poorer body condition during summer. In females, reactivation was more likely when living in social groups comprising a higher percentage of cubs, but counter to our predictions, recent lactation appeared not influential. In relation to age, reactivation was more common in individuals over 8 years old than among prime age adults, and among juveniles (<2 years old), especially females and individuals in better body condition, likely due to early puberty. Environmentally, reactivation was more prevalent in summer when food abundance is typically low. Our results evidence age effects on MusGHV-1 reactivation; in juveniles MusGHV-1 shedding in the genital tract is likely related to primary infection, while in adults, genital MusGHV-1 reactivation from latency was associated with aging, social and/ or environmental stress.

ImportanceThe immuno-suppressive effects of elevated stress levels facilitate disease development, and can ultimately cause host extinction at the population level, especially where diseases are transmitted sexually. The impacts of stress on host-pathogen dynamics through disease, however, are still poorly understood outside the laboratory or captive environments. Our study provides rare evidence from a free-ranging wild mammal population that the infection dynamics of a common and sexually transmittable gammaherpesvirus are linked to demographic, social, physiological and environmental stress. We propose that the effects of stressors on STIs and viral reactivation are an important factor to be taken into account in conservation efforts when working with vulnerable wildlife populations.


title: Myocardial BDNF regulates cardiac bioenergetics through the transcription factor Yin Yang 1

abstract: Circulating Brain-derived Neurotrophic Factor (BDNF) is markedly decreased in heart failure patients. Both BDNF and its receptor, Tropomyosin Related Kinase Receptor (TrkB), are expressed in cardiomyocytes, however the role of myocardial BDNF signaling in cardiac pathophysiology is poorly understood. We found that cardiac-specific TrkB knockout (cTrkB KO) mice displayed a blunted adaptive cardiac response to exercise, with attenuated upregulation of transcription factor networks controlling mitochondrial biogenesis/metabolism, including Peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1). The cTrkB KO mice developed an exacerbated heart failure progression with transaortic constriction. The downregulation of PGC-1 in cTrkB KO mice exposed to exercise or TAC resulted in decreased cardiac energetics. We further unraveled that BDNF induces PGC-1 upregulation and bioenergetics through a novel signaling pathway, the pleiotropic transcription factor Yin Yang 1 (YY1). Taken together, our findings suggest that myocardial BDNF plays a critical role in regulating cellular energetics in the cardiac stress response.


title: Endothelial junctional membrane protrusions serve as hotspots for neutrophil transmigration

abstract: Upon inflammation, leukocytes rapidly transmigrate across the endothelium to enter the inflamed tissue. Evidence accumulates that leukocytes use preferred exit sites, though it is not yet clear how these hotspots in the endothelium are defined and how they are recognized by the leukocyte. Using lattice light sheet microscopy, we discovered that leukocytes prefer endothelial membrane protrusions at cell junctions for transmigration. Phenotypically, these junctional membrane protrusions are present in an asymmetric manner, meaning that one endothelial cell shows the protrusion and the adjacent one does not. Consequently, leukocytes cross the junction by migrating underneath the protruding endothelial cell. These protrusions depend on Rac1 activity and by using a photo-activatable Rac1 probe, we could artificially generate local exit-sites for leukocytes. Overall, we have discovered a new mechanism that uses local induced junctional membrane protrusions to facilitate/steer the leukocyte escape/exit from inflamed vessel walls.

category: cell biology


title: Molecular mechanism for kinesin-1 direct membrane recognition

abstract: The cargo-binding capabilities of cytoskeletal motor proteins have expanded during evolution through both gene duplication and alternative splicing. For the light chains of the kinesin-1 family of microtubule motors, this has resulted in an array of carboxy-terminal domain sequences of unknown molecular function. Here, combining phylogenetic analyses with biophysical, biochemical and cell biology approaches we identify a highly conserved membrane-induced curvature-sensitive amphipathic helix within this region of a newly defined subset of long kinesin light chain paralogues and splice isoforms. This helix mediates the direct binding of kinesin-1 to lipid membranes. Membrane binding requires specific anionic phospholipids and is important for kinesin-1 dependent lysosome positioning, a canonical activity that until now has been attributed exclusively the recognition of organelle-associated cargo adaptor proteins. This leads us to propose a new protein-lipid coincidence detection framework for kinesin-1 mediated organelle transport.


title: T cell self-reactivity during thymic development dictates the timing of positive selection

abstract:
Functional tuning of T cells based on their degree of self-reactivity is established during positive selection in the thymus, although how positive selection differs for thymocytes with relatively low versus high self-reactivity is unclear. In addition, preselection thymocytes are highly sensitive to low-affinity ligands, but the mechanism underlying their enhanced TCR sensitivity is not fully understood. Here we show that murine thymocytes with low self-reactivity experience briefer TCR signals and complete positive selection more slowly than those with high self-reactivity. Additionally, we provide evidence that cells with low self-reactivity retain a preselection gene expression signature as they mature, including genes previously implicated in modulating TCR sensitivity and a novel group of ion channel genes. Our results imply that thymocytes with low self-reactivity down-regulate TCR sensitivity more slowly during positive selection, and suggest that modulation of membrane ion channel function may play a role in regulating TCR tuning throughout development.

Impact StatementDeveloping T cells whose TCRs have relatively low reactivity experience very brief TCR signaling events, delayed positive selection, and do not fully down regulate their TCR sensitivity as they mature.

category: developmental biology


title: Spatio-temporal analysis identifies hotspots of marine mammal strandings along the Indian coastline: implications for developing a National Marine Mammal Stranding Response and Management policy

abstract: Marine mammal strandings provide vital information on their life histories, population health and status of marine ecosystems. Opportunistic reporting of strandings serve as a potent low-cost tool for conservation monitoring of these highly mobile species. We present the results of spatio-temporal analyses of marine mammal stranding events to identify hotpots along Indian coastline. We collated data over a long-time frame (~270 years) available from various open access databases, reports and publications. Given the inadequacy in data collection over these years, we grouped data into four major groups viz. baleen whales, toothed whales, small cetaceans and dugongs. Further, we described the trends in data for marine mammal sightings, incidental mortalities, induced mortalities and stranding events using the last group for spatio-temporal analysis. Annual strandings along the Indian coast has increased considerably in the recent years (11.25 {+/-} 9.10 strandings/ year), peaking in the last two years (2015-17, mean = 27.66{+/-}12.03 strandings /year). We found that number of strandings spiked in June- September along the west coast and December- January along the east coast. We identified several sections of coastline which have consistently received comparatively higher number of stranded animals (0.38 - 1.82 strandings/km) throughout the study period. Use of novel geospatial tool  Emerging Hotspot Analysis revealed new and consecutive hotspots along the north-west coast, and sporadic hotspots along the south-east coast. Despite the challenges of working with an opportunistic database, this study highlights critical areas to be prioritized for monitoring marine mammal strandings in the country. We recommend establishing regional marine mammal stranding response centres at the identified hotspots coordinated by a National Stranding Monitoring Centre with adequate funding support. Regular conduct of stranding response programs for field veterinarians, frontline personnel focused around identified stranding hotspots would help develop a comprehensive picture of marine mammal populations in Indian waters.


title: Neural mechanisms underlying regulation of empathy and altruism by beliefs of others' pain

abstract: Perceived cues signaling others pain induce empathy that in turn motivates altruistic behavior toward those who appear suffering. This perception-emotion-behavior reactivity is the core of human altruism but does not always occur in real life situations. Here, by integrating behavioral and multimodal neuroimaging measures, we investigate neural mechanisms underlying the functional role of beliefs of others pain in modulating empathy and altruism. We show evidence that decreasing (or enhancing) beliefs of others pain reduces (or increases) subjective estimation of others painful emotional states and monetary donations to those who show pain expressions. Moreover, decreasing beliefs of others pain attenuates neural responses to perceived cues signaling others pain within 200 ms after stimulus onset and modulate neural responses to others pain in the frontal cortices and temporoparietal junction. Our findings highlight beliefs of others pain as a fundamental cognitive basis of human empathy and altruism and unravel the intermediate neural architecture.


title: How the Easter Egg Weevils Got Their Spots: Phylogenomics reveals Müllerian Mimicry in Pachyrhynchus (Coleoptera, Curculionidae).

abstract: The evolutionary origins of mimicry in the Easter Egg weevil, Pachyrhynchus, have fascinated researchers since first noted more than a century ago by Alfred Russel Wallace. Mullerian mimicry, or mimicry in which two or more distasteful species look similar, is widespread throughout the animal kingdom. Given the varied but discrete color patterns in Pachyrhynchus, this genus presents one of the best opportunities to study the evolution of both perfect and imperfect mimicry. We analyzed more than 10,000 UCE loci using a novel partitioning strategy to resolve the relationships of closely related species in the genus. Our results indicate that many of the mimetic color patterns observed in sympatric species are due to convergent evolution. We suggest that this convergence is driven by frequency-dependent selection.


title: Translation Inhibitory Elements from Hox a3 and a11 mRNAs use uORFs for translation inhibition

abstract: During embryogenesis, Hox mRNA translation is tightly regulated by a sophisticated molecular mechanism that combines two RNA regulons located in their 5UTR. First, an Internal Ribosome Entry Site (IRES) enables cap-independent translation. The second regulon is a Translation Inhibitory Element or TIE, which ensures concomitant cap-dependent translation inhibition. In this study, we deciphered the molecular mechanisms of Hox a3 and a11 TIE elements. Both TIEs possess an upstream Open Reading Frame (uORF) that is critical to inhibit cap-dependent translation. However, the molecular mechanisms used are different. In TIE a3, we identify a uORF which inhibits cap-dependent translation and we show the requirement of the non-canonical initiation factor eIF2D for this process. The mode of action of TIE a11 is different, it also contains a uORF but it is a minimal uORF formed by an uAUG followed immediately by a stop codon, namely a  start-stop. The a11  start-stop sequence is located upstream of a highly stable stem loop structure which stalls the 80S ribosome and thereby inhibits cap-dependent translation of Hox a11 main ORF.

category: biochemistry


title: Lipid fingerprints are similar between SLC6 transporters in the neuronal membrane

abstract:
We use molecular dynamics simulations to characterise the local lipid annulus, or "fingerprint", of three SLC6 transporters (dDAT, hSERT, and GlyT2) embedded into a complex neuronal membrane. New membrane analysis tools were created to improve leaflet detection and leaflet-dependent properties. Overall, lipid fingerprints are comprised of similar lipids when grouped by headgroup or tail saturation. The enrichment and depletion of specific lipids, including sites of cholesterol contacts, varies between transporters. The subtle differences in lipid fingerprints results in varying membrane biophysical properties near the transporter. Through comparisons to previous literature, we highlight that the lipid-fingerprint in complex membranes is highly dependent on membrane composition. Furthermore, through embedding these transporters in a simplified model membrane, we show that the simplified membrane is not able to capture the biophysical properties of the complex membrane. Our results further characterise how the presence and identity of membrane proteins affects the complex interplay of lipid-protein interactions, including the local lipid environment and membrane biophysical properties.

HIGHLIGHTSO_LILipid fingerprints are comprised of similar lipid classes
C_LIO_LISites of specific lipid contacts, including CHOL, varies between transporters
C_LIO_LIChanges in lipid annulus result in variable local membrane biophysical properties
C_LIO_LIMembrane composition, including that of complex membranes, affects lipid annulus
C_LI

GRAPHICAL ABSTRACT

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title: KSR1-and ERK-dependent Translational Regulation of the Epithelial-to-Mesenchymal Transition

abstract: The epithelial-to-mesenchymal transition (EMT) is considered a transcriptional process that induces a switch in cells from a polarized state to a migratory phenotype. Here we show that KSR1 and ERK promote EMT through the preferential translation of Epithelial-Stromal Interaction 1 (EPSTI1), which is required to induce the switch from E-to N-cadherin and coordinate migratory and invasive behavior. EPSTI1 is overexpressed in human colorectal cancer (CRC) cells. Disruption of KSR1 or EPSTI1 significantly impairs cell migration and invasion in vitro, and reverses EMT, in part, by decreasing the expression of N-cadherin and the transcriptional repressors of E-cadherin expression, ZEB1 and Slug. In CRC cells lacking KSR1, ectopic EPSTI1 expression restored the E-to N-cadherin switch, migration, invasion, and anchorage-independent growth. KSR1-dependent induction of EMT via selective translation of mRNAs reveals its underappreciated role in remodeling the translational landscape of CRC cells to promote their migratory and invasive behavior.

category: cancer biology


title: Tandem-Cleavage Linkers Improve the In Vivo Stability and Tolerability of Antibody-Drug Conjugates

abstract: Although peptide motifs represent the majority of cleavable linkers used in clinical-stage antibody-drug conjugates (ADCs), the sequences are often sensitive to cleavage by extracellular enzymes, such as elastase, leading to systemic release of the cytotoxic payload. This action reduces the therapeutic index by causing off-target toxicities that can be dose-limiting. For example, a common side-effect of ADCs made using peptide-cleavable linkers is myelosuppression, including neutropenia. Only a few reports describe methods for optimizing peptide linkers to maintain efficient and potent tumor payload delivery while enhancing circulating stability. Herein, we address these critical limitations through the development of a tandem-cleavage linker strategy, where two sequential enzymatic cleavage events mediate payload release. We prepared dipeptides that are protected from degradation in the circulation by a sterically-encumbering glucuronide moiety. Upon ADC internalization and lysosomal degradation, the monosaccharide is removed and the exposed dipeptide is degraded, liberating the attached payload inside the target cell. We used CD79b-targeted monomethyl auristatin E (MMAE) conjugates as our model system, and compared the stability, efficacy, and tolerability of ADCs made with tandem-cleavage linkers to ADCs made using standard technology with the vedotin linker. The results--where rat studies showed dramatically improved tolerability in the hematopoietic compartment--highlight the role that linker stability plays in efficacy and tolerability, and offer a means of improving an ADCs therapeutic index for improved patient outcomes.


title: CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks

abstract:
MotivationLigand-receptor (LR) network analysis allows the characterization of cellular crosstalk based on single cell RNA-seq data. However, current methods typically provide a list of inferred LR interactions and do not allow the researcher to focus on specific cell types, ligands or receptors. In addition, most of these methods cannot quantify changes in crosstalk between two biological phenotypes.

ResultsCrossTalkeR is a framework for network analysis and visualisation of LR interactions. CrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological phenotypes, i.e. disease vs. homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of CrossTalkeR for characterisation of changes in cellular crosstalk in disease.

Availability and ImplementationCrosstalkeR is an R package available at https://github.com/CostaLab/CrossTalkeR.


title: Pre-stimulus alpha activities predict the confidence in subjective judgment by modulating post-stimulus theta oscillation

abstract: Even when making arbitrary decisions, people tend to feel varying levels of confidence, which is associated with the pre-stimulus neural oscillation of the brain. We investigated varying confidence in a pure subjective judgment task, and how this confidence was predicted by pre-stimulus alpha oscillations. Participants made pure subjective judgments where their prior experience seems to be helpful but actually useless, and their fluctuating confidence was related to the choice boundary process rather than the evidence accumulation process, suggesting participants underwent varying confidence resulting from the internal signals. With EEG and MEG analyses, we not only revealed the linkage between confidence and pre-stimulus alpha activities, but also successfully located this linkage onto decision-making relevant brain areas, i.e. MCC/PCC and SMA. Moreover, we unveiled a specific pathway underlying such linkage, that is, the influence of pre-stimulus alpha activities on decision confidence was fulfilled through modulating post-stimulus theta activities of SMA.

category: neuroscience


title: The VTA-BLA-NAc circuit for sex reward inhibited by VTA GABAergic neurons under stress in male mice

abstract: Anhedonia, inability to experience pleasure from rewarding or enjoyable activities, is the prominent symptom of depression that involves dysfunction of the reward processing system. Both genetic predisposition and life events are thought to increase the risk for depression, in particular life stress. The cellular mechanism underlying stress modulating the reward processing neural circuits and subsequently disrupting reward-related behaviors remains elusive. We identify the VTA-BLA-NAc pathway as being activated by sex reward. Blockade of this circuit induces depressive-like behaviors, while reactivation of VTA neurons associated with sexual rewarding experience acutely ameliorates the impairment of reward-seeking behaviors induced by chronic restraint stress. Our histological and electrophysiological results show that the VTA neuron subpopulation responding to restraint stress inhibits the responsiveness of the VTA dopaminergic neurons to sexual reward. Together, these results reveal the cellular mechanism by which stress influences the brain reward processing system and provide a potential target for depression treatment.


title: Whole-genome sequence analysis of mutations in rice plants regenerated from zygotes, mature embryos, and immature embryos

abstract: Somaclonal variation was studied by whole-genome sequencing in rice plants (Oryza sativa L.,  Nipponbare) regenerated from the zygotes, mature embryos, and immature embryos of a single mother plant. The mother plant and its seed-propagated progeny were also sequenced. A total of 338 variants of the mother plant sequence were detected in the progeny, and mean values ranged from 9.0 of the seed-propagated plants to 37.4 of regenerants from mature embryos. The ratio of single nucleotide variants among the variants was 74.3%, and the natural mutation rate calculated using the variants in the seed-propagated plants was 1.2 x 10-8. The percentage and the mutation rate were consistent with the values reported previously. Plants regenerated from mature embryos had significantly more variants than different progeny types. Therefore, using zygotes and immature embryos can reduce somaclonal variation during the genetic manipulation of rice.


title: Purification and partial characterization of a high hemagglutinating chitin-binding lectin from Aponogeton natans tubers

abstract:
A novel chitin-binding lectin was isolated from the tubers of a plant Aponogeton natans from the monocot family Aponogetonaceae, designated as ANTL (Aponogeton natans tuber lectin). The lectin agglutinated both untreated and trypsin-treated rabbit erythrocytes, as well as human blood cells of groups A, B and O with different specificities. Lectin activity is inhibited by the oligomers of N-acetylglucosamine. ANTL is a dimeric glycoprotein with molecular weight of [~]66 KDa and has two identical sub-units of 33 KDa. The carbohydrate percent is 8.2% of the total lectin. The lectin was thermo stable up to 50{degrees}C with broad pH optima (pH 4-10). ANTL is found to be potent mitogen for normal murine and human lymphocytes at the concentration as low as 1 {micro}g/ml. Cytotoxic studies of the lectin on human U 266 cell lines has revealed that there is 50% decrease in the proliferation. The confirmation of both the hemagglutination and mitogenic proliferation activity suggests that ANTL is a Chitin-binding lectin with diverse functions. The pharmacological relevance of ANTL as a potent mitogen with some cytotoxic effect in certain cell lines are reported for the first time.

HighlightsO_LIA novel chitin-binding lectin was purified from the tuber extracts of Aponogeton natans (ANTL) in a single step on chitin column by affinity chromatography.
C_LIO_LIANTL is a dimeric glycoprotein with a molecular weight of [~]66 KDa with high hemagglutination activity towards rabbit erythrocytes.
C_LIO_LIThe cytotoxic effect of ATNL on human cell lines U266 has shown 50 % inhibition of their proliferation.
C_LIO_LIANTL displayed potent mitogenic response towards murine and human peripheral blood mononuclear cells.
C_LI


title: Local jasmonic acid cues drive systemic acquired resistance signal generation

abstract: The phytohormones salicylic acid (SA) and jasmonic acid (JA) promote two, mutually antagonistic immune pathways respectively protecting plants from biotrophic pathogens and necrotrophic pathogens or insects. This trade-off largely precludes the exploitation of SA and JA immune components for crop protection, raising the interest in immune signalling components that disrupt SA-JA antagonism. A local pathogen infection primes SA-dependent immunity in systemic tissues. This so-called systemic acquired resistance (SAR) ensures a long-lasting, broad-spectrum disease resistance that is not subject to SA-JA antagonism. Here, we show that two sequence-related LEGUME LECTIN-LIKE PROTEINs (LLPs) promote SAR through spatially separated functions with JA promoting local SAR signal generation through LLP3. In concert with LLP1, which is important for systemic recognition and propagation of SAR signals, LLP3 promotes both SA-dependent SAR and JA-mediated immunity. Thus, exploitation of LLP-associated signalling cues might allow application of plant innate immune signals to promote (crop) plant health.


title: Conserved and non-conserved triggers of 24-nt reproductive phasiRNAs in eudicots

abstract: Plant small RNAs (sRNAs) play important roles in plant growth and development by modulating expression of genes and transposons. In many flowering plant species, male reproductive organs, the anthers, produce abundant phased small interfering RNAs (phasiRNAs). Two classes of reproductive phasiRNAs are generally known, mostly from monocots: pre-meiotic 21-nt phasiRNAs triggered by miR2118, and meiotic 24-nt phasiRNAs triggered by miR2275. Here, we describe conserved and non-conserved triggers of 24-nt phasiRNAs in several eudicots. We found that the abundant 24-nt phasiRNAs in the basal eudicot columbine are produced by the canonical trigger, miR2275, as well as by other non-conserved triggers, miR482/2118 and aco_cand81. These triggering miRNAs are localized in microspore mother cells (MMC) and tapetal cells of meiotic and post-meiotic stage anthers. Furthermore, we identified a new trigger (miR11308) of 24-nt phasiRNAs and an expanded number of 24-PHAS loci in wild strawberry. We validated the presence of miR2275-derived 24-nt phasiRNAs pathway in rose. Finally, we evaluated all the eudicots that have been validated for the presence of 24-nt phasiRNAs as models to study biogenesis and function of 24-nt phasiRNAs and conclude that columbine would be an excellent model because of its extensive number of 24-PHAS loci and its diversity of trigger miRNAs.


title: Different autotrophic enrichments yield efficient inocula for biocathodic applications

abstract: The uptake of extracellular electrons from cathodes by microbes is a recently discovered phenomenon. However, current knowledge on the diversity of microbes accepting extracellular electrons and populating biocathodes is scarce. Research is required to explore the distribution of extracellular electron uptake metabolism in the tree of life across microbial guilds. Here we characterize the electron uptake ability of microbial guilds enriched on H2, S2O32-, or CH4 and NH4+ from the same inoculum taken from a groundwater treatment sand-filter. We hypothesized that functional microbes having dense outer membrane cytochromes in their native pathway, such as pathways of NH4+, CH4, S2O32- and H2, can perform extracellular electron uptake. We aimed of addressing the following questions: (1) Are there any known microbial member of anticipated function performing extracellular electron transfer? (2) How does electron uptake efficiency vary between the different functional guilds? (3) How is the dissipated electron energy distributed across metabolisms? We developed and applied a novel pipeline to identify taxa utilizing direct electron energy and utilizing secondary microbial products. We report the putative direct electron uptake metabolism of types belonging to Methylomonas, UBA6140, and Nitrosomonas. Furthermore, members of Streptococcaceae, Rhizobiaceae, Streptococcus, Brevundimonas, Chryseobacterium, and Pseudomonas are detected as electroactive taxa. Our results reveal novel insights into the diversity, electrochemical activity, and metabolism of taxa performing direct electron uptake.


title: PPi plays a role in sugar starvation tolerance

abstract: H+-PPase acidifies the endo-membrane compartments utilizing the energy of PPi hydrolysis. This acidification creates an electrochemical proton gradient that powers the secondary active transport and allows for vacuolar accumulation of several materials against their concentration gradients. The hydrolysis of the cytosolic PPi is necessary for the forwardness of the PPi-generating reactions. However, information is lacking on the role of PPi in adaptation to sugar starvation and low energy status in plants. Here, several mutants lacking the functional H+-PPases were used to illuminate this role. Three alleles of fugu5 mutants defective in type I H+-PPase exhibited better tolerance to sugar starvation than wild-type plants, when grown on [1/2] and full-strength MS media under photosynthesis-constraining low light intensity. The PPi level in fugu5 mutants was significantly higher than its level in wild type and type II H+-PPase-defective mutants. SnRK1 (Sucrose-non-fermenting1-Related kinase-1) plays a central role in the coordination of the plant transcriptome to the energy signals. SnRK1 senses the energy depletion in plant cells, and controls the expression of genes and phosphorylation of proteins in a way that promotes catabolism, and inhibits anabolism. Sugar starvation significantly induced the SnRK1 phosphorylation activity in wild type and type II H+-PPase lacking mutants. Whereas the activity remained unchanged in sugar-starved fugu5 mutants. This is possibly achieved through activation of PPi-dependent enzymes. Results suggest that the high PPi level in fugu5 mutants might contribute to more efficiently use of low level of ATP under sugar starvation and low light conditions.