title: Shear-Mediated Platelet Activation is Accompanied by Unique Alterations of Platelet Lipid Profile

abstract: Platelet activation by mechanical means such as shear stress, is a vital driver of thrombotic risk in implantable blood-contacting devices used in treatment of heart failure. Lipids are essential in platelets activation and have been studied following biochemical activation. However, little is known regarding lipid alterations occurring with mechanical - shear mediated platelet activation. Here, we determined if shear-activation of platelets induced lipidome changes that differ from those associated with biochemically-mediated platelet activation. We performed high-resolution lipidomic analysis on purified platelets from four healthy human donors. For each donor, we compared the lipidome of platelets that were non-activated or activated by shear, ADP, or thrombin treatment. We found that shear activation altered cell-associated lipids and led to the release of lipids into the extracellular environment. Shear-activated platelets released 21 phospholipids and sphingomyelins at levels statistically higher than platelets activated by biochemical stimulation. Many of the released phospholipids contained an arachidonic acid tail or were phosphatidylserine lipids, which have procoagulant properties. We conclude that shear-mediated activation of platelets alters the basal platelet lipidome. Further, these alterations differ and are unique in comparison to the lipidome of biochemically activated platelets. Our findings suggest that lipids released by shear-activated platelets may contribute to altered thrombosis in patients with implanted cardiovascular therapeutic devices.


title: Skin-resident immune cells actively coordinate their distribution with epidermal cells during homeostasis

abstract: Our organs consist of multiple cell types that ensure proper architecture and function. How different cell types coexist and interact to maintain their homeostasis in vivo remain elusive. The skin epidermis comprises mostly epithelial cells, but also harbors Langerhans cells (LCs) and Dendritic Epidermal T cells (DETCs). In response to injury or infection, LCs and DETCs become activated and play critical immunological roles. During homeostasis, they coexist with epithelial cells in the basal layer of the epidermis. Whether, and how, distributions of LCs and DETCs are regulated during homeostasis is unclear. Here, we addressed this question by tracking LCs, DETCs and epithelial basal cells over time within the skin of live adult mice. We show that LCs and DETCs maintain their overall position despite continuous turnover of neighboring basal epithelial stem cells. Moreover, LCs and DETCs rapidly and maximally explore basal epithelial cell junctions through their dendritic extensions. Altering the epithelial cell density triggers corresponding changes in the immune cell density, but not vice versa, suggesting that epithelial cells determine immune tissue composition in the epidermis. Moreover, LCs and DETCs are organized in a tiling pattern that is actively maintained. When LCs or DETCs are ectopically removed, neighboring epidermal LCs or DETCs, respectively, move into the emptied spaces and re-establish the tiling pattern. Finally, LCs require the GTPase Rac1 to maintain their positional stability, density and tiling pattern. Overall, we discovered that epidermal cells regulate the density of immune cells during homeostasis, and that immune cells actively maintain a non-random spatial distribution, reminiscent of neuronal self-avoidance. We propose that these cellular mechanisms provide the epidermis with an optimal response to environmental insults.

category: cell biology


title: An "individualist" model of an active genome in a developing embryo

abstract: The early Drosophila embryo provides unique experimental advantages for addressing fundamental questions of gene regulation at multiple levels of organization, from individual gene loci to the whole genome. Using Drosophila embryos undergoing the first wave of genome activation, we detected discrete "speckles" of RNA Polymerase II (Pol II), and showed that they overlap with transcribing loci. We characterized the spatial distribution of Pol II speckles and quantified how this distribution changes in the absence of the primary driver of Drosophila genome activation, the pioneer factor Zelda. Although the number and size of Pol II speckles were reduced, indicating that Zelda promotes Pol II speckle formation, we observed a uniform distribution of distances between active genes in the nuclei of both wildtype and zelda mutant embryos. This suggests that the topologically associated domains identified by Hi-C studies do little to spatially constrain groups of transcribed genes at this time. We provide evidence that linear genomic distance between transcribed genes is the primary determinant of measured physical distance between the active loci. Furthermore, we show active genes can have distinct Pol II pools even if the active loci are in close proximity. In contrast to the emerging model whereby active genes are clustered to facilitate co-regulation and sharing of transcriptional resources, our data support an "individualist" model of gene control at early genome activation in Drosophila. This model is in contrast to a "collectivist" model where active genes are spatially clustered and share transcriptional resources, motivating rigorous tests of both models in other experimental systems.

category: developmental biology


title: Does land use matter? Carbon consequences of alternative land use futures in New England

abstract: Globally, forests play an important role in climate change mitigation. However, land-use impacts the ability of forests to sequester and store carbon. Here we quantify the impacts of five divergent future land-use scenarios on aboveground forest carbon stocks and fluxes throughout New England. These scenarios, four co-designed with stakeholders from throughout the region and the fifth a continuation of recent trends in land use, were simulated by coupling a land cover change model with a mechanistic forest growth model to produce estimates of aboveground carbon over 50 years. Future carbon removed through harvesting and development was tracked using a standard carbon accounting methodology, modified to fit our modeling framework. Of the simulated changes in land use, changes in harvesting had the most profound and immediate impacts on carbon stocks and fluxes. In one of the future land-use scenarios including a rapid expansion of harvesting for biomass energy, this changed New Englands forests from a net carbon sink to a net carbon source in 2060. Also in these simulations, relatively small reductions in harvest intensities (e.g., 10% reduction), coupled with an increased percent of wood going into longer-term storage, led to substantial reductions in net carbon emissions (909 MMtCO2eq) as compared to a continuation of recent trends in land use. However, these projected gains in carbon storage and reduction in emissions from less intense harvesting regimes can only be realized if it is paired with a reduction in the consumption of the timber products, and their replacements, that otherwise would result in additional emissions from leakage and substitution.

category: ecology


title: Explosive diversification following continental colonizations by canids

abstract: Colonization of a new environment may trigger an explosive radiation process, defined as an accelerated accumulation of species in a short period of time. However, how often colonization events trigger explosive radiations is still an open question. We studied the worldwide dispersal of the subfamily Caninae, to investigate whether the invasion of new continents resulted in explosive radiations. We used a combination of phylogenetic analyses and ancestral area reconstructions to estimate ancestral ranges of 56 extant and extinct species of Caninae, as well as variation in speciation and extinction rates through time and across clades. Our findings indicate that canids experienced an explosive radiation event when lineages were able to cross the Bering Strait and the Isthmus of Panama to reach Eurasia and South America, respectively, around 11 million years ago. This large number of species arising in a short period of time suggests that canids experienced ecological opportunity events within the new areas, implying that the differences in the ecological settings between continents may be responsible for the variation in clade dynamics. We argue that interaction with other carnivores probably also affected the diversification dynamics of canids.

category: evolutionary biology


title: Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy

abstract: Selective autophagy of damaged mitochondria, intracellular pathogens, protein aggregates, endoplasmic reticulum, and other large cargoes is essential for health. The presence of cargo initiates phagophore biogenesis, which entails the conjugation of ATG8/LC3 family proteins to membrane phosphatidylethanolamine. Current models suggest that the presence of clustered ubiquitin chains on a cargo triggers a cascade of interactions from autophagic cargo receptors through the autophagy core complexes ULK1 and class III PI 3-kinase complex I (PI3KC3-C1), WIPI2, and the ATG7, ATG3, and ATG12-ATG5-ATG16L1 machinery of LC3 lipidation. This model was tested using giant unilamellar vesicles (GUVs), GST-Ub4 as a model cargo, the cargo receptors NDP52, TAX1BP1, and OPTN, and the autophagy core complexes. All three cargo receptors potently stimulated LC3 lipidation on GUVs. NDP52- and TAX1BP1-induced LC3 lipidation required the ULK1 complex together with all other components, however, ULK1 kinase activity was dispensable. In contrast, OPTN bypassed the ULK1 requirement completely. These data show that the cargo-dependent stimulation of LC3 lipidation is a common property of multiple autophagic cargo receptors, yet the details of core complex engagement vary considerably and unexpectedly between the different receptors.

category: biochemistry


title: In Vivo Sublayer Analysis Of Human Retinal Inner Plexiform Layer Obtained By Visible-Light Optical Coherence Tomography

abstract:
PurposeGrowing evidence suggests, in glaucoma, the dendritic degeneration of subpopulation of the retinal ganglion cells (RGCs) may precede RGCs soma death. Since different RGCs synapse in different IPL sublayers, visualization of the lamellar structure of the IPL could enable both clinical and fundamental advances in glaucoma understanding and management. In this pilot study, we investigated whether visible-light optical coherence tomography (vis-OCT) could detect the difference in the inner plexiform layer (IPL) sublayers thicknesses between small cohorts of healthy and glaucomatous subjects.

MethodWe investigated vis-OCT retinal images from nine healthy and five glaucomatous subjects. Four of the healthy subjects were scanned three times each in two separate visits, and five healthy and five glaucoma subjects were scanned three times during a single visit. Raster speckle-reduction scans (3 by 3 by 1.2 mm^3: horizontal; vertical; axial directions with 8192x8x1024 samplings, respectively) of the superior macular were acquired. IPL sublayers were then manually segmented using averaged A-line profiles.

ResultsThe mean ages of glaucoma and healthy subjects are 59.6 +/- 13.4 and 45.4 +/- 14.4 years (p =0.02, Wilcoxon rank-sum test), respectively. The visual field mean deviation (MD) are -26.4 to -7.7 dB in glaucoma patient and -1.6 to 1.1 dB in healthy subjects (p =0.002). The mean circumpapillary retinal nerve fiber layer (RNFL) thicknesses are 59.6 +/- 9.1 m in glaucoma and 99.2 +/- 16.2 m in healthy subjects (p=0.004). Median coefficients of variation (CVs) of intra-session repeatability for the entire IPL and three sublayers are 3.1%, 5.6%, 6.9%, and 5.6% in healthy subjects and 1.8%, 6.0%, 7.7%, and 6.2% in glaucoma patients, respectively. The mean entire IPL thicknesses are 36.2 +/- 1.5 m in glaucomatous and 40.1 +/- 1.7 micrometer in healthy eyes (p=0.003, Mixed-effects model). We found that the middle sublayer thickness was responsible for the majority of the difference (14.2 +/- 1.8 m in glaucomatous and 17.5 +/- 1.4 in healthy eyes, p<0.01).

ConclusionsIPL sublayer analysis revealed that the middle sublayer could be responsible for the majority of IPL thinning in glaucoma. Vis-OCT quantified IPL sublayers with good repeatability in both glaucoma and healthy subjects. Visualization of the IPL sublayers may enable the investigation of lamella-specific changes in the IPL in glaucoma and may help elucidate the response of different types of RGCs to the disease.

category: bioengineering


title: Pin Electrode Reactor: A novel cold atmospheric plasma device and its potential in glioblastoma treatment

abstract: Glioblastoma multiforme (GBM) is the most common and biologically aggressive brain tumour. The current standard therapy for GBM consists in surgical resection, followed by radiotherapy and chemotherapy. Yet, the treatment is limited due to the area for the surgical resection and for the inability of some drugs to cross the brain blood barrier, leading to a general prognostic of no more than a year. Cold atmospheric plasma (CAP) is a new approach in the treatment of this challenging disease. CAP interaction with cells is dependent on physical and chemical factors, with different plasma discharges, cell type, and culture conditions leading to different CAP activity. Considering the plasma self-adaptation that different plasma discharge modes can undergo, which leads to different interaction plasma/cells, the characterization of a new device is essential. In this study we analysed the effect of a novel large pin-to-plate non-thermal atmospheric plasma on U-251 MG cells under different conditions. The analysis of reactive oxygen and nitrogen species (RONS) on plasma, media and cells were also assessed. We were able to demonstrate that the pin-to-plate device is cytotoxic to GBM cells in a dose, time and ROS dependent manner. The measurements of RONS on plasma/media also give us an insight on the chemical effect of this novelty device, and the possibility to better understand the use of this device as a promising GBM therapy.

category: cancer biology


title: Proton-gated coincidence detection is a common feature of GPCR signaling

abstract: The evolutionary expansion of G protein-coupled receptors (GPCRs) has produced a rich diversity of transmembrane sensors for many physical and chemical signals. In humans alone, over 800 GPCRs detect stimuli such as light, hormones, and metabolites to guide cellular decision making primarily using intracellular G protein signaling networks. This diversity is further enriched by GPCRs that function as molecular logic gates capable of discerning multiple inputs to transduce cues encoded in complex, context-dependent signals. Here, we show that many GPCRs are switch-like Boolean-gated coincidence detectors that link proton (H+) binding to GPCR signaling. Using a panel of 28 receptors, covering 280 individual GPCR-G coupling combinations, we show that H+ gating both positively and negatively modulates and controls GPCR signaling. Notably, these observations extend to all modes of GPCR pharmacology including ligand efficacy, potency, and cooperativity. Additionally, we show that GPCR antagonism and constitutive activity are regulated by H+ gating and report the discovery of a new acid sensor, the adenosine A2a receptor (ADORA2A), which can be activated solely by acidic pH. Together, these findings establish a new paradigm for GPCR biology and pharmacology in acidified microenvironments such as endosomes, synapses, tumors, and ischemic vasculature.

category: pharmacology and toxicology


title: Developmental exposure to domoic acid disrupts startle response behavior and circuitry

abstract:
Harmful algal blooms produce potent neurotoxins that accumulate in seafood and are hazardous to human health. Developmental exposure to the harmful algal bloom toxin, domoic acid (DomA), has behavioral consequences well into adulthood, but the cellular and molecular mechanisms are largely unknown. To assess these, we exposed zebrafish embryos to DomA during the previously identified window of susceptibility (2 days post-fertilization) and used the well-known startle response circuit as a tool to identify specific neuronal components that are targeted by exposure to DomA. Exposure to DomA reduced the probability of eliciting a startle after auditory/vibrational or electrical stimuli and led to the dramatic reduction of one type of startle, short latency c-start (SLC) responses. Furthermore, DomA-exposed larvae had altered kinematics of both SLC and long latency c-start (LLC) startle responses, exhibiting shallower bend angles and slower maximal angular velocities. Using vital dye staining, immunolabelling, and live imaging of transgenic lines, we determined that while the sensory inputs were intact, the reticulospinal neurons required for SLC responses were absent in most DomA-exposed larvae. Furthermore, axon tracing revealed that DomA-treated larvae also showed significantly reduced primary motor neuron axon collaterals. Overall, these results show that developmental exposure to DomA leads to startle deficits by targeting specific subsets of neurons. These findings provide mechanistic insights into the neurodevelopmental effects of excess glutamatergic signaling caused by exposure to DomA. It further provides a model for using the startle response circuit to identify neuronal populations targeted by toxin or toxicant exposures.

Summary statementWe used the zebrafish startle response as a tool to identify sensory-motor deficits and the loss of specific neural populations after developmental exposure to the harmful algal bloom toxin domoic acid.

GRAPHICAL ABSTRACT

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title: Super-Resolution Label-free Volumetric Vibrational Imaging

abstract: Innovations in high-resolution optical imaging have allowed visualization of nanoscale biological structures and connections. However, super-resolution fluorescence techniques, including both optics-oriented and sample-expansion based, are limited in quantification and throughput especially in tissues from photobleaching or quenching of the fluorophores, and low-efficiency or non-uniform delivery of the probes. Here, we report a general sample-expansion vibrational imaging strategy, termed VISTA, for scalable label-free high-resolution interrogations of protein-rich biological structures with resolution down to 82 nm. VISTA achieves decent three-dimensional image quality through optimal retention of endogenous proteins, isotropic sample expansion, and deprivation of scattering lipids. Free from probe-labeling associated issues, VISTA offers unbiased and high-throughput tissue investigations. With correlative VISTA and immunofluorescence, we further validated the imaging specificity of VISTA and trained an image-segmentation model for label-free multi-component and volumetric prediction of nucleus, blood vessels, neuronal cells and dendrites in complex mouse brain tissues. VISTA could hence open new avenues for versatile biomedical studies.

category: neuroscience


title: A Bacterial Bile Acid Metabolite Modulates Treg Activity through the Nuclear Hormone Receptor NR4A1

abstract: Bile acids act as signaling molecules that regulate immune homeostasis, including the differentiation of CD4+ T cells into distinct T cell subsets. The bile acid metabolite isoallolithocholic acid (isoalloLCA) enhances the differentiation of anti-inflammatory regulatory T cells (Treg cells) by facilitating the formation of a permissive chromatin structure in the promoter region of the transcription factor forkhead box P3 (Foxp3). Here, we identify gut bacteria that synthesize isoalloLCA from 3-oxolithocholic acid and uncover a gene cluster responsible for the conversion in members of the abundant human gut bacterial phylum Bacteroidetes. We also show that the nuclear hormone receptor NR4A1 is required for the effect of isoalloLCA on Treg cells. Moreover, the levels of isoalloLCA and its biosynthetic genes are significantly reduced in patients with inflammatory bowel diseases, suggesting that isoalloLCA and its bacterial producers may play a critical role in maintaining immune homeostasis in humans.

category: immunology


title: REPEATED INJURY PROMOTES TRACHEOBRONCHIAL TISSUE STEM CELL ATTRITION

abstract: Chronic lung disease has been attributed to stem cell aging and/or exhaustion. To address this issue, we investigated the lifespan of tracheobronchial tissue stem cells (TSC) over time and in response to repeated injury. Chromatin and nucleotide labeling studies in mice indicated that: 1) injury activated a subset of the TSC pool and that this process conserved TSC over time; and 2) activated TSC were predisposed to further proliferation and this activated state lead to terminal differentiation. Analysis of human TSC and clonal isolates indicated that repeated TSC proliferation led to telomere shortening and analysis of TSC from Dyskeratosis Congenita donors indicated that mutations in telomere biology genes accelerated TSC depletion. RNAseq and functional studies indicated that human TSC terminated as a secretory committed cell. These data support a model in which a repeated epithelial injury depletes the TSC pool and initiates the abnormal repair associated with chronic lung disease.


title: Beyond coral-algal regimes: high taxonomic resolution surveys and trait-based analyses reveal multiple benthic regimes

abstract: As coral reef communities change and reorganise in response to anthropogenic and climate disturbances, there is a growing need of detecting and understanding the different emerging species regimes and their contribution to key ecosystem processes. Using a case study on coral reefs at the epicentre of tropical marine biodiversity (North Sulawesi), we explored how application of different biodiversity approaches (i.e. use of major taxonomic categories, high taxonomic resolution categories and trait-based approaches) affects the detection of distinct fish and benthic community assemblages. Our results show that using major categories (family level or above) to study coral reef communities fails to identify distinct regimes. We also show that for detection of different benthic regimes, especially communities dominated by non-coral organisms, monitoring of only scleractinian coral communities is insufficient, and that all types of benthic organisms (e.g. sponges, ascidians, soft corals, algae etc.) need to be considered. We have implemented for the first time, the use of a trait-based approach to study the functional diversity of whole coral reef benthic assemblages, which allowed us to detect five different community regimes, only one of which was dominated by scleractinian corals. We circumvented the challenge that for some benthic groups (e.g. sponges, ascidians or some soft corals) visual identification up to the species level is not possible, by identifying and categorising traits that can be applied to groups of similar organisms instead of specific species. Furthermore, by the parallel study of benthic and fish communities we provide new insights into key processes and functions that might dominate or be compromised in the different community regimes.


title: iRGD-liposomes enhance tumor delivery and therapeutic efficacy of antisense oligonucleotide drugs against primary prostate cancer and bone metastasis

abstract: Nucleotide-based drugs, such as antisense oligonucleotides (ASOs), have unique advantages in treating human diseases as they provide virtually unlimited ability to target any gene. However, their clinical translation faces many challenges, one of which is poor delivery to the target tissue in vivo. This problem is particularly evident in solid tumors. Here, we functionalized liposomes with a tumor-homing and -penetrating peptide, iRGD, as a carrier of an ASO against androgen receptor (AR) for prostate cancer treatment. The iRGD-liposomes exhibited a high loading efficiency of AR-ASO, and an efficient knockdown of AR gene products was achieved in vitro, including AR splice variants. In vivo, iRGD-liposomes significantly increased AR-ASO accumulation in the tumor tissue and decreased AR expression relative to free ASOs in prostate tumors established as subcutaneous xenografts. Similar results were obtained with intra-tibial xenografts modeling metastasis to bones, the predominant site of metastasis for prostate cancer. In treatment studies, iRGD-liposomes markedly improved the AR-ASO efficacy in suppressing the growth of both subcutaneous xenografts and intra-tibial xenografts. The inhibitory effect on tumor growth was also significantly prolonged by the delivery of the AR-ASO in the iRGD-liposomes. Meanwhile, iRGD-liposomes did not increase ASO accumulation or toxicity in healthy organs. Overall, we provide here a delivery system that can significantly increase ASO accumulation and efficacy in solid tumors. These benefits are achieved without significant side effects, providing a way to increase the antitumor efficacy of ASOs.


title: Epstein-Barr Virus Induced Cytidine Metabolism Roles in Transformed B-cell Growth and Survival

abstract: Epstein-Barr virus (EBV) is associated with 200,000 cancers annually, including B-cell lymphomas in immunosuppressed hosts. Hypomorphic mutations of the de novo pyrimidine synthesis pathway enzyme cytidine 5 triphosphate synthase 1 (CTPS1) suppress cell mediated immunity, resulting in fulminant EBV infection and EBV+ central nervous system (CNS) lymphomas. Since CTP is a critical precursor for DNA, RNA and phospholipid synthesis, this observation raises the question of whether the isozyme CTPS2 or cytidine salvage pathways help meet CTP demand in EBV-infected B-cells. Here, we found that EBV upregulated CTPS1 and CTPS2 with distinct kinetics in newly infected B-cells. While CRISPR CTPS1 knockout caused DNA damage and proliferation defects in lymphoblastoid cell lines (LCL), which express the EBV latency III program observed in CNS lymphomas, double CTPS1/2 knockout caused stronger phenotypes. EBNA2, MYC and non-canonical NF-{square}B positively regulated CTPS1 expression. CTPS1 depletion impaired EBV lytic DNA synthesis, suggesting that latent EBV may drive pathogenesis with CTPS1 deficiency. Cytidine rescued CTPS1/2 deficiency phenotypes in EBV-transformed LCL and Burkitt B-cells, highlighting CTPS1/2 as a potential therapeutic target for EBV-driven lymphoproliferative disorders. Collectively, our results suggest that CTPS1 and CTPS2 have partially redundant roles in EBV-transformed B-cells and provide insights into EBV pathogenesis with CTPS1 deficiency.


title: Trans-channel fluorescence learning improves high-content screening for Alzheimer's disease therapeutics

abstract: In microscopy-based drug screens, fluorescent markers carry critical information on how compounds affect different biological processes. However, practical considerations may hinder the use of certain fluorescent markers. Here, we present a deep learning method for overcoming this limitation. We accurately generated predicted fluorescent signals from other related markers and validated this new machine learning (ML) method on two biologically distinct datasets. We used the ML method to improve the selection of biologically active compounds for Alzheimers disease (AD) from high-content high-throughput screening (HCS). The ML method identified novel compounds that effectively blocked tau aggregation, which would have been missed by traditional screening approaches unguided by ML. The method improved triaging efficiency of compound rankings over conventional rankings by raw image channels. We reproduced this ML pipeline on a biologically independent cancer-based dataset, demonstrating its generalizability. The approach is disease-agnostic and applicable across diverse fluorescence microscopy datasets.


title: Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons

abstract: Synaptic transmission, connectivity, and dendritic morphology mature in parallel during brain development and are often disrupted in neurodevelopmental disorders. Yet how these changes influence the neuronal computations necessary for normal brain function are not well understood. To identify cellular mechanisms underlying the maturation of synaptic integration in interneurons, we combined patch-clamp recordings of excitatory inputs in cerebellar stellate cells (SCs), 3D-reconstruction of SC morphology with excitatory synapse location, and biophysical modeling. We found that, during development, synaptic strength was homogeneously reduced along the somato-dendritic axis, but that dendritic integration was always sublinear. However, dendritic branching increased without changes in synapse density, leading to a substantial gain in distal inputs. Thus, changes in synapse distribution, rather than dendrite cable properties, are the dominant mechanism underlying the maturation of neuronal computation. These mechanisms favor the emergence of a spatially compartmentalized two-stage integration model promoting location-dependent integration within dendritic subunits.


title: Decoding the single-cell landscape and intercellular crosstalk in the transplanted liver: a 4-dimension mouse model

abstract: Graft remodeling after transplantation maintains graft functionality and determines graft survival. However, a comprehensive understanding of cellular diversity and interplay during graft remodeling remains to be fully characterized. In this study, we established a well tolerant C57BL/6 to C57BL/6 orthotopic liver transplantation (LT) mice model and observed two stages of graft recovery including an acute phase and a steady phase. We next performed single-cell RNA sequencing (scRNA-seq) and cytometry by time-of-flight (CyTOF) and recorded the cellular hierarchy in the transplanted liver during the two stages. Besides the dynamic change of cell proportion, it was notable that recipient-derived cells took over the transplanted liver in most cell types (e.g., B cells, T cells, dendritic cells, granulocytes and monocytes) except CD206+ MerTK+ macrophages and CD161+ CD49a+ CD49b-natural killer cells. We then focused on macrophages and captured 5 distinct transcriptional signatures to define novel subclusters. Using a ligand-receptor interaction strategy, we identified specific macrophage-hepatocyte interactions during the acute and stable phases, causing metabolic remodeling in the transplanted liver. Our results delineated a 4-dimension cell atlas (type-proportion-source-time) of the transplanted liver, which sheds light on the physiological process of liver graft maintenance and graft-recipient crosstalk.


title: Surveillance of Shiga toxin-producing Escherichia coli associated bloody diarrhea in Argentina

abstract: In Argentina, the hemolytic uremic syndrome associated with Shiga toxin-producing Escherichia coli (STEC-HUS) infection is endemic, and reliable data about prevalence and risk factors are available since 2000. However, information about STEC-associated bloody diarrhea (BD) cases is limited. A prospective study was carried out in seven tertiary-hospitals and 18 Referral Units from different regions, aiming to determine (i) STEC-positive BD cases frequency in 714 children aged 1 to 9 years old; and (ii) rate of progression to HUS. The number and regional distribution of STEC-HUS cases assisted in the same hospitals and period was also assessed. A total of 29 (4.1%) STEC-positive BD cases were confirmed by Shiga Toxin Quik Chek (STQC) and/or mPCR. The highest frequencies were found in the Southern region (Neuquen, 8.7%; Bahia Blanca, 7.9%), in children between 12 and 23 month of age (8.8%), during summertime. Four (13.8%) cases progressed to HUS, three to five days after BD onset. Twenty-seven STEC-HUS children mainly under 5 years old (77.8%) were enrolled, 51.9% were female; 44% were Stx-positive by STQC and all by mPCR. The most common serotypes were O157:H7 and O145:H28 and prevalent genotypes were stx2a-only or associated, both among BD and HUS cases. Considering the endemic behavior of HUS and its impact on public health, it is important to have updated information about the epidemiology of the diarrheal disease for early recognition of infected patients and initiation of supportive treatment. Finally, it also gives the opportunity to respond to outbreak situations effectively and in timely manner.

category: microbiology


title: The repertoire of testicular extracellular vesicles cargoes and their involvement in inter-compartmental communication required for spermatogenesis

abstract: Extracellular vesicles (EVs) secreted by the epididymis and prostate are involved in sperm functions and epigenetic inheritance. However, the EVs in the testis remains unexplored. Here, we have established a testis dissociation protocol that allows the isolation of testicular EVs by minimizing the disruption of fragile sperm cells. We showed that testicular EVs were specifically and efficiently uptaken by somatic cells and germ cells in both interstitial space and seminiferous tubules compartments, including the spermatozoa. We profiled the proteome of testicular EVs and probed the cell types that release them. Moreover, we sequenced the small RNAs cargos of testicular EVs and identified sets of small non-coding RNAs that were overlooked in the testis transcriptome. Selected miRNA candidates in testicular EVs were found in sperm RNA payload and demonstrated specific resistance towards ribonuclease A independent of the vesicle membrane. Small molecule inhibition of EVs secretion increased the apoptosis of germ cells via inter-compartmental communication. Together, our study has provided valuable resources on the cargoes of testicular EVs and revealed the inter-compartmental communication that regulates spermatogenesis and may implicate in paternal inheritance.


title: Sex and origin-specific inbreeding effects on flower attractiveness to specialised pollinators

abstract: We investigate whether inbreeding has particularly fatal consequences for dioecious plants by diminishing their floral attractiveness and the associated pollinator visitation rates disproportionally in females. We also test whether the magnitude of such effects depends on the evolutionary histories of plant populations. We recorded spatial, olfactory, colour and rewarding flower attractiveness traits as well as pollinator visitation rates in experimentally inbred and outbred, male and female Silene latifolia plants from European and North American populations differing in their evolutionary histories. We found that inbreeding specifically impairs spatial and olfactory attractiveness. Our results support that sex-specific selection and gene expression partially magnified these inbreeding costs for females, and that divergent evolutionary histories altered the genetic architecture underlying inbreeding effects across population origins. Moreover, they highlight that inbreeding effects on olfactory attractiveness have a huge potential to disrupt interactions among plants and specialist moth pollinators, which are mediated by elaborate chemical communication.


title: Molecular mechanism of ACAD9 in mitochondrial respiratory complex 1 assembly

abstract: ACAD9 belongs to the acyl-CoA dehydrogenase family, which catalyzes the -{beta} dehydrogenation of fatty acyl-CoA thioesters. Thus, it is involved in fatty acid {beta}-oxidation (FAO). However, it is now known that the primary function of ACAD9 is as an essential chaperone for mitochondrial respiratory complex 1 assembly. ACAD9 interacts with ECSIT and NDUFAF1, forming the mitochondrial complex 1 assembly (MCIA) complex. Although the role of MCIA in the complex 1 assembly pathway is well studied, little is known about the molecular mechanism of the interactions among these three assembly factors. Our current studies reveal that when ECSIT interacts with ACAD9, the flavoenzyme loses the FAD cofactor and consequently loses its FAO activity, demonstrating that the two roles of ACAD9 are not compatible. ACAD9 binds to the carboxy-terminal half (C-ECSIT), and NDUFAF1 binds to the amino-terminal half of ECSIT. Although the binary complex of ACAD9 with ECSIT or with C-ECSIT is unstable and aggregates easily, the ternary complex of ACAD9-ECSIT-NDUFAF1 (i.e., the MCIA complex) is soluble and extremely stable. Molecular modeling and SAXS studies of the MCIA complex identified the possible interaction sites between the three assembly factors and binding sites for other assembly factors, including complex 1 subunits. Furthermore, we have mapped over 40 currently known pathogenic mutation sites onto the homology-modeled ACAD9 structure, giving us the structural basis for their involvement in diseases that result from complex 1 deficiency.


title: Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses in autoimmune disorders

abstract: Cytokines elicit pleiotropic and non-redundant activities despite strong overlap in their usage of receptors, JAKs and STATs molecules. We use IL-6 and IL-27 to ask how two cytokines activating the same signaling pathway have different biological roles. We found that IL-27 induces more sustained STAT1 phosphorylation than IL-6, with the two cytokines inducing comparable levels of STAT3 phosphorylation. Mathematical and statistical modelling of IL-6 and IL-27 signaling identified STAT3 binding to GP130, and STAT1 binding to IL-27R, as the main dynamical processes contributing to sustained pSTAT1 by IL-27. Mutation of Tyr613 on IL-27R decreased IL-27-induced STAT1 phosphorylation by 80% but had limited effect on STAT3 phosphorylation. Strong receptor/STAT coupling by IL-27 initiated a unique gene expression program, which required sustained STAT1 phosphorylation and IRF1 expression and was enriched in classical Interferon Stimulated Genes. Interestingly, the STAT/receptor coupling exhibited by IL-6/IL-27 was altered in patients with Systemic lupus erythematosus (SLE). IL-6/IL-27 induced a more potent STAT1 activation in SLE patients than in healthy controls, which correlated with higher STAT1 expression in these patients. Partial inhibition of JAK activation by sub-saturating doses of Tofacitinib specifically lowered the levels of STAT1 activation by IL-6. Our data show that receptor and STATs concentrations critically contribute to shape cytokine responses and generate functional pleiotropy in health and disease.

category: bioinformatics


title: Structural and mechanistic insight into spectral tuning in flavin-binding fluorescent proteins

abstract: Determining the molecular origin of spectral tuning in photoactive biological systems is instrumental for understanding their function. Spectral-tuning efforts for flavin-binding fluorescent proteins (FbFPs), an emerging class of fluorescent reporters, are limited by their dependency on protein-bound flavins, whose structure and hence electronic properties, cannot be altered by mutation. To address those shortcomings, we here present the photophysical, computational and structural characterization of structurally uncharacterized blue-shifted FbFPs, carrying a previously described lysine substitution within their flavin-binding pocket. X-ray structures reveal displacement of the lysine away from the chromophore and opening up of the structure as cause for the blue shift. Site-saturation mutagenesis and high-throughput screening, yielded a red-shifted variant, in which the lysine side chain of the blue-shifted variant is stabilized in close distance to the flavin by a secondary mutation, mechanistically accounting for the red shift. Thus, a single secondary mutation in a blue-shifted variant is sufficient to generate a red-shifted FbFP. Using spectroscopy, X-ray crystallography and quantum mechanics molecular mechanics calculations, we provide a firm structural and functional understanding of spectral tuning in FbFPs. We also show that the identified blue- and red-shifted variants allow for two-color microscopy based on spectral separation. In summary, the generated blue- and red-shifted variants represent promising new tools that should find application in life sciences.

category: biophysics


title: The role of water mobility in protein misfolding

abstract: The propensity for intrinsically disordered proteins to aggregate is heavily influenced by their surrounding environment. Here, we show that the mobility of the surrounding water molecules directly influences the aggregation rate of -synuclein (aSyn), a protein associated with Parkinsons disease. We observe that the addition of NaCl reduces the mobility of water, while addition of CsI increases the mobility of water. In turn, this reduces and increases the mobility of aSyn, respectively, given the change in strength and lifetime of the intermolecular forces. The reduction of aSyn mobility in the presence of NaCl ions leads to increased aggregation rates, which may be due to aggregation-competent conformations being stable for longer, thereby increasing the likelihood of establishing interactions between two adjacent monomers. In contrast, aSyn is more mobile when CsI is dissolved in the aqueous phase which leads to a reduction of successful monomeric interactions. We thus highlight the importance of the surrounding environment and describe how ion content can influence water mobility and the misfolding rate of amyloidogenic proteins, such as aSyn. By modulating the cellular environment to increase water mobility or finding small molecules to increase protein dynamics, new therapeutic targets may be found.


title: Understanding the holobiont: crosstalk between gut microbiota and mitochondria during endurance

abstract: Endurance exercise has a dramatic impact on the functionality of mitochondria and on the composition of the intestinal microbiome, but the mechanisms regulating the crosstalk between these two components are still largely unknown. Here, we sampled 20 elite horses before and after an endurance race and used blood transcriptome, blood metabolome and fecal microbiome to describe the gut-mitochondria crosstalk. A subset of mitochondria-related differentially expressed genes involved in pathways such as energy metabolism, oxidative stress and inflammation was discovered and then shown to be associated with butyrate-producing bacteria of the Lachnospiraceae family, especially Eubacterium. The mechanisms involved were not fully understood, but through the action of their metabolites likely acted on PPAR{gamma}, the FRX-CREB axis and their downstream targets to delay the onset of hypoglycemia, inflammation and extend running time. Our results also suggested that circulating free fatty acids may act not merely as fuel but drive mitochondrial inflammatory responses triggered by the translocation of gut bacterial polysaccharides following endurance. Targeting the gut-mitochondria axis therefore appears to be a potential strategy to enhance athletic performance.

category: systems biology


title: Expression of a miRNA targeting mutated SOD1 in astrocytes induces motoneuron plasticity and improves neuromuscular function in ALS mice

abstract: In amyotrophic lateral sclerosis (ALS) caused by SOD1 gene mutations, both cell-autonomous and non-cell-autonomous mechanisms lead to the selective degeneration of motoneurons. Here, we evaluate the therapeutic potential of gene therapy targeting mutated SOD1 in mature astrocytes using mice expressing the mutated SOD1G93A protein. An AAV-gfaABC1D vector encoding an artificial microRNA is used to deliver RNA interference against mutated SOD1 selectively in astrocytes. The treatment leads to the progressive rescue of neuromuscular junction occupancy, to the recovery of the compound muscle action potential in the gastrocnemius muscle, and significantly improves neuromuscular function. In the spinal cord, gene therapy targeting astrocytes protects a small pool of fast-fatigable motoneurons until disease end stage. In the gastrocnemius muscle of the treated SOD1G93A mice, the fast-twitch type IIb muscle fibers are preserved from atrophy. Axon collateral sprouting is observed together with muscle fiber type grouping indicative of denervation/re-innervation events. The transcriptome profiling of spinal cord motoneurons shows changes in the expression levels of factors regulating the dynamics of microtubules. Gene therapy delivering RNA interference against mutated SOD1 in astrocytes provides therapeutic effects enhancing motoneuron plasticity and improving neuromuscular function in ALS mice.


title: Fungal Ice2p has remote homology to SERINCs, restriction factors for HIV and other viruses

abstract: Ice2p is an integral endoplasmic reticulum (ER) membrane protein in budding yeast S. cerevisiae named ICE because it is required for Inheritance of Cortical ER. Ice2p has also been reported to be involved in an ER metabolic branch-point that regulates the flux of lipid either to be stored in lipid droplets or to be used as membrane components. Alternately, Ice2p has been proposed to act as a tether that physically bridges the ER at contact sites with both lipid droplets and the plasma membrane via a long loop on the proteins cytoplasmic face that contains multiple predicted amphipathic helices. Here we carried out a bioinformatic analysis to increase understanding of Ice2p. Firstly, regarding topology, we found that diverse members of the fungal Ice2 family have ten transmembrane helices, which places the long loop on the exofacial face of Ice2p, where it cannot form inter-organelle bridges. Secondly, we identified Ice2 as a full-length homologue of SERINC (serine incorporator), a family of proteins with ten transmembrane helices found universally in eukaryotes. Since SERINCs are potent restriction factors for HIV and other viruses, study of Ice2p may reveal functions or mechanisms that shed light on viral restriction by SERINCs.


title: Fungal Ice2p is in the same superfamily as SERINCs, restriction factors for HIV and other viruses


title: Targeting EGFR in glioblastoma with a novel brain-penetrant small molecule EGFR-TKI

abstract: Epidermal growth factor receptor (EGFR) is mutated or amplified in a majority of glioblastoma (GBM), and its mutation and focal amplification correlate with a more aggressive disease course. However, EGFR-directed tyrosine kinase inhibitors (TKIs) tested to date have yielded minimal clinical benefit. Here, we report a novel covalent-binding EGFR-TKI, CM93, as a potential drug to target adult GBMs with aberrant EGFR. CM93 has extraordinary brain exposure, with a brain-to-plasma ratio greater than 20-fold at estimated steady state. While all approved EGFR-TKIs are subject to extensive efflux transporter activity, CM93 does not inhibit the P-glycoprotein (P-gp) and breast cancer resistance protein (BCRP) efflux transporters in Caco-2 cells at expected clinically relevant plasma concentrations. Equally, CM93 demonstrates moderate absorption and permeation in Caco-2 cell monolayers with efflux ratios < 2, suggesting that it is not likely a substrate of an efflux transporter. Collectively, these in vitro data may account for the dramatic increase in brain exposure over plasma as noted above. Pre-clinical efficacy studies showed that CM93 is more effective than other EGFR-TKIs in blocking the proliferation of GBM tumor cells from both patient-derived and cultured human GBM cell lines with EGFR amplification and/or EGFRvIII mutation. In addition, CM93 administered as a single agent was able to attenuate the growth of orthotopic U251-EGFRvIII xenografts and extend the survival of tumor-bearing mice in a dose-dependent manner. Moreover, CM93 inhibited EGFR phosphorylation in GBM tumors derived from a novel genetically-engineered mouse (GEM) model of GBM with EGFRvIII expression both in vitro and in vivo. CM93 also extended the survival of mice bearing orthotopic allografts of GBM. Notably, mice maintained stable body weight during treatments with increasing doses of CM93 up to 75 mg/kg per day. Together, these data suggest that CM93 is a potential EGFR-TKI well suited for the treatment of adult GBM with mutant EGFR.


title: Dependency of LKB1-inactivated lung cancer on aberrant CRTC-CREB activation

abstract: Lung cancer with loss-of-function of the LKB1 tumor suppressor is a common aggressive subgroup with no effective therapies. LKB1-deficiency induces constitutive activation of cAMP/CREB-mediated transcription by a family of three CREB-regulated transcription coactivators (CRTC1-3). However, the significance and mechanism of CRTC activation in promoting the aggressive phenotype of LKB1-null cancer remain poorly characterized. Here we observed overlapping CRTC expression patterns and mild growth phenotypes of individual CRTC-knockouts in lung cancer, suggesting functional redundancy of CRTC1-3. We consequently designed a dominant-negative mutant (dnCRTC) to block all three CRTCs to bind and co-activate CREB. Expression of dnCRTC efficiently inhibited the aberrantly activated cAMP/CREB-mediated oncogenic transcriptional program induced by LKB1-deficiency, and specifically blocked the growth of LKB1-inactivated lung cancer. Collectively, this study provides direct proof for an essential role of the CRTC-CREB activation in promoting the malignant phenotypes of LKB1-null lung cancer and proposes the CRTC-CREB interaction interface as a novel therapeutic target.


title: Multiple Shoot Regeneration from Excised Embryonic Axis Explants of Jute, Corchorus capsularis cv. JRC321

abstract: Interspecific hybrids development by traditional breeding is challenging because of the incompatibility between two cultivated species of genus Corchorus. Under this condition, plant genetic transformation is an alternative tool for the improvement of jute cultivar. In the present study, in vitro multiple shoot regeneration protocol has been developed in jute (Corchorus capsularis cv. JRC 321) from excised embryonic axis as an explant by removing cotyledons, radicle, and tip of epicotyl. The explant is cultured in medium SMM1 supplemented with BAP (1.0 mg/L) for one week and sub-cultured in SMM6 containing IBA (0.5 mg/L) and BAP (0.2 mg/L). Direct adventitious shoot bud formation was observed from cotyledonary nodes and the adjacent region of excised embryonic axis. Interestingly, shoot bud formation was reduced when excised explants with intact epicotyl were cultured in the media combination (SMM1+SMM6) indicating the presence of apical dominance might be the cause of fewer shoot bud formation. While, hypocotyl explants did not produce any shoot in this media combination because nodal meristem was removed. However, the shoot buds developed from the excised embryonic axis were differentiated successfully into multiple shoots and showed further elongation in SMM6 which ultimately rooted in MS-B5 medium (+0.5 mg/L IBA). The plants were transferred successfully in the glasshouse conditions and appeared phenotypically normal.

category: plant biology


title: Long-lasting reduction of intrinsic excitability in O-LM interneurons is mediated by endocannabinoid-dependent up-regulation of Kv7 channels

abstract: KCNQ-Kv7 channels are found at the axon initial segment of pyramidal neurons where they control cell firing and membrane potential. In oriens lacunosum moleculare (O-LM) interneurons, these channels are mainly expressed in the dendrites, suggesting a peculiar function of Kv7 channels in these neurons. The physiology of Kv7 channels is well characterized today but the precise contribution of these channels to neuronal plasticity is still unknown. Here, we show that Kv7 channel activity is up-regulated following induction of presynaptic long-term synaptic depression (LTD) in O-LM interneurons, thus resulting in a synergistic long-term depression of intrinsic neuronal excitability (LTD-IE). Both LTD and LTD-IE involve endocannabinoid (eCB) biosynthesis for their induction. Molecular modeling shows strong interaction of eCBs with Kv7.2/3 channel, suggesting a persistent action of these lipids on Kv7 channel activity. Our data thus unveil a major role for eCB synthesis in triggering both synaptic and intrinsic depression in O-LM interneurons.


title: Variance misperception under skewed empirical noise statistics explains overconfidence in the visual periphery

abstract:
Perceptual confidence typically corresponds to accuracy. However, observers can be overconfident relative to accuracy, termed  subjective inflation. Inflation is stronger in the visual periphery relative to central vision, especially under conditions of peripheral inattention. Previous literature suggests inflation stems from errors in estimating noise, i.e.  variance misperception. However, despite previous Bayesian hypotheses about metacognitive noise estimation, no work has systematically explored how noise estimation may critically depend on empirical noise statistics which may differ across the visual field, with central noise distributed symmetrically but peripheral noise positively skewed. Here we examined central and peripheral vision predictions from five Bayesian-inspired noise-estimation algorithms under varying usage of noise priors, including effects of attention. Models that failed to optimally estimate noise exhibited peripheral inflation, but only models that explicitly used peripheral noise priors -- but used them incorrectly -- showed increasing peripheral inflation under increasing peripheral inattention. Further, only one model successfully captured previous empirical results which showed a selective increase in confidence in incorrect responses under performance reductions due to inattention accompanied by no change in confidence in correct responses; this was the model that implemented Bayesian estimation of peripheral noise, but using an (incorrect) symmetric rather than the correct positively skewed peripheral noise prior. Our findings explain peripheral inflation, especially under inattention, and suggest future experiments that might reveal the noise expectations used by the visual metacognitive system.

SignificancePerceptual confidence can dissociate from accuracy in peripheral visual perception, a phenomenon known as peripheral inflation. No previous model has considered how this phenomenon may arise from metacognitive noise estimation which depends on empirical noise statistics. Here we simulate Bayesian-inspired noise estimation algorithms to show that the systems erroneous beliefs about distributions of noise in the visual periphery can explain the occurrence of peripheral inflation, including how inflation varies with attentional manipulations in surprising ways. Our results explain why peripheral inflation occurs by positing a new Bayesian metacognitive noise estimation mechanism, paving the way for future psychophysical studies.


title: Eye tracking impairments in children with protein-energy malnutrition

abstract: Background: Malnutrition is characterized by impaired nutrient ingestion and absorption, and it is still one of the most substantial causes of morbidity and mortality in children worldwide. To the best of our knowledge, this is the first study investigating eye tracking in children with protein-energy malnutrition (PEM). We sought to investigate how PEM may affect eye movement. Methods: Twenty children without PEM (mean age = 10.8; SD = 1.0 years) and 18 children with PEM (mean age = 10.9; SD = 1.2 years). Here we used three types of tests or stimuli: one formed by a maze and two by seven errors games (boats and elephants). Results: Our results indicated that children with PEM had impaired performance on all of the tests used here. These data suggest that the nutritional impairments during the first year of life, the critical period in visual system development, can have direct impact on eye movement patterns. Conclusions: Our findings must be replicated so that neurophysiological patterns of PEM can be precisely understood. However, this study has repercussions in several areas of knowledge.


title: Bottom-up inputs are required for the establishment of top-down connectivity onto cortical layer 1 neurogliaform cells

abstract: Higher order feedback projections to sensory cortical areas converge on layer 1 (L1), the primary site for integration of top-down information via the apical dendrites of pyramidal neurons and L1 GABAergic interneurons. Here, we investigated the contribution of early thalamic inputs onto L1 interneurons for the establishment of top-down inputs in the primary visual cortex. We find that bottom-up thalamic inputs predominate during early L1 development and preferentially target neurogliaform cells. We find that these projections are critical for the subsequent strengthening of feedback inputs from the anterior cingulate cortex. Enucleation or selective removal of thalamic afferents blocked this phenomenon. Notably, while early activation of anterior cingulate afferents resulted in a premature strengthening of these top-down inputs to neurogliaform cells, this was also dependent on thalamic inputs. Our results demonstrate that the proper establishment of top-down feedback inputs critically depends on bottom-up inputs from the thalamus during early postnatal development.


title: A Novel Approach to Study Gamma-Band Coherence in Ex Vivo Hippocampal Slices from a Mouse Model of Bipolar Disorder.

abstract: Oscillations play crucial roles in many cognitive processes such as memory formation and attention. GABAergic interneurons can synchronize neuronal activity leading to gamma oscillations (30-60 Hz). Abnormalities in oscillatory activity in the hippocampus have been implicated in the pathology of some mental health disorders including schizophrenia and bipolar disorder, however the neurobiological mechanism underlying these abnormal oscillations are not yet fully understood. We set out to develop a reliable approach to study gamma oscillations in ex vivo hippocampal preparations using perforated microelectrode arrays. Perforated microelectrode arrays allow for the simultaneous measurement of electrical activity at multiple sites while allowing solutions to pass through the brain section. We obtained extracellular electrophysiological recordings from acute sections of mouse hippocampus situated on a 60-channel, perforated microelectrode arrays (pMEAs). Bath application of kainate rapidly induced and maintained oscillatory activity in the CA1 and CA3 regions of the hippocampus. Kainate-induced oscillations were quickly abolished by the GABAA receptor antagonist, bicuculline. Furthermore, we employed this approach on a mouse model of bipolar disorder. Sections prepared from mutant mice exhibited an increase in the coherence of gamma power within CA1 despite a reduction in gamma band power.


title: Double stranded RNA drives innate immune responses, sickness behavior and cognitive impairment dependent on dsRNA length, IFNAR1 expression and age

abstract: Double stranded RNA is generated during viral replication. The synthetic analogue poly I:C is frequently used to mimic anti-viral innate immune responses in models of psychiatric and neurodegenerative disorders including schizophrenia, autism, Parkinsons disease and Alzheimers disease. Many studies perform limited analysis of innate immunity despite these responses potentially differing as a function of dsRNA molecular weight and age. Therefore fundamental questions relevant to impacts of systemic viral infection on brain function and integrity remain. Here, we studied innate immune-inducing properties of poly I:C preparations of different lengths and responses in adult and aged mice. High molecular weight (HMW) poly I:C (1-6kb, 12 mg/kg) produced more robust sickness behavior and more robust IL-6, IFN-I and TNF responses than poly I:C of <500 bases (low MW) preparations. This was partly overcome with higher doses of LMW (up to 80 mg/kg), but neither circulating IFN{beta} nor brain transcription of Irf7 were significantly induced by LMW poly I:C, despite brain Ifnb transcription, suggesting that brain IFN-dependent gene expression is predominantly triggered by circulating IFN{beta} binding of IFNAR1. In aged animals, poly I:C induced exaggerated IL-6, IL-1{beta} and IFN-I in the plasma and similar exaggerated brain cytokine responses. This was associated with acute working memory deficits selectively in aged mice. Thus, we demonstrate dsRNA length-, IFNAR1- and age-dependent effects on anti-viral inflammation and cognitive function. The data have implications for CNS symptoms of acute systemic viral infection such as those with SARS-CoV-2 and for models of maternal immune activation.


title: Endogenous Retroviral Elements Generate Pathologic Neutrophils and Elastase Rich Exosomes in Pulmonary Arterial Hypertension

abstract: Neutrophil elastase (NE) is implicated in pulmonary arterial hypertension (PAH) but the role of neutrophils in the pathogenesis of PAH is unclear. Here we show that neutrophils from PAH vs. control subjects produce and release increased NE associated with enhanced extracellular trap formation. PAH neutrophils are highly adherent and show decreased migration consistent with increased vinculin, identified on proteomic analysis and previously linked to an antiviral response. This was substantiated by a transcriptomic interferon signature in PAH neutrophils and an increase in human endogenous retrovirus (HERV-K) envelope protein. NE and interferon genes are induced by HERV-K envelope and vinculin is increased by HERV-K dUTPase that is elevated in PAH plasma. Neutrophil exosomes from PAH plasma contain increased NE and HERV-K envelope and induce pulmonary hypertension in mice, that is mitigated by the NE inhibitor and antiviral agent, elafin. Thus, elevated HERVs explain pathological neutrophils linked to PAH induction and progression.


title: Single cell analyses reveal distinct adaptation of typhoidal and non-typhoidal Salmonella enterica serovars to intracellular lifestyle

abstract: Salmonella enterica is a common foodborne, facultative intracellular enteropathogen. Human-restricted typhoidal S. enterica serovars Typhi (STY) or Paratyphi A (SPA) cause severe typhoid or paratyphoid fever, while S. enterica serovar Typhimurium (STM) has a broad host range and in human hosts usually lead to a self-limiting gastroenteritis. Due to restriction of STY and SPA to primate hosts, experimental systems for studying the pathogenesis of typhoid and paratyphoid fever are limited. Therefore, STM infection of susceptible mice is commonly considered as model system for studying these diseases. The type III secretion system encoded by Salmonella pathogenicity island 2 (SPI2-T3SS) is a key factor for intracellular survival of Salmonella. Inside host cells, the pathogen resides within the Salmonella-containing vacuole (SCV) and induces tubular structures extending from the SCV, termed Salmonella-induced filaments (SIF). This study applies a set of single cell analyses approaches such as dual fluorescent protein reports, effector translocation, or correlative light and electron microscopy to investigate the fate and activities of intracellular STY and SPA. The SPI2-T3SS of STY and SPA is functional in translocation of effector proteins, SCV and SIF formation. However, only a low proportion of intracellular STY and SPA are actively deploying SPI2-T3SS and STY and SPA exhibited a rapid decline of protein biosynthesis upon experimental induction. A role of SPI2-T3SS for proliferation of STY and SPA in epithelial cells was observed, but not for survival or proliferation in phagocytic host cells. Our results indicate that reduced intracellular activities are factors of the stealth strategy of STY and SPA and facilitate systemic spread and persistence of the typhoidal Salmonella.


title: ATAC-seq reveals megabase-scale domains of a bacterial nucleoid

abstract:
Here we adapted ATAC-seq to probe chromosome accessibility of bacterial cells. We found that the chromosome of Caulobacter crescentus is composed of eight differentially compacted regions we name Chromosomal Accessibility Domains (CADs). This domain structure is depended on the cell cycle stage, DNA gyrase activity, and the nucleoid-associated protein (NAP) GapR, but not on the function of SMC. We show the chromosome is punctuated by four highly transposase-inaccessible transcribed regions (HINTs). The HINTs include Caulobacters ribosomal RNA clusters and its largest ribosomal protein gene cluster. Further, we show that HINTs are also formed by rDNA in E. coli and provide evidence that their high levels of transcription do not strictly govern their formation. Overall, this work argues that physical forces, including those created by the activities of DNA gyrase and specific NAPs, significantly contribute to bacterial nucleoid structure at the megabase scale.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/426053v1_ufig1.gif" ALT="Figure 1">
View larger version (56K):
org.highwire.dtl.DTLVardef@2b9812org.highwire.dtl.DTLVardef@cd430org.highwire.dtl.DTLVardef@3ed5cforg.highwire.dtl.DTLVardef@1471dad_HPS_FORMAT_FIGEXP  M_FIG C_FIG SignificanceIn bacteria, chromosomal DNA is highly compacted and organized. Many forces contribute to bacterial DNA compaction, including the transcription, DNA replication, and the activities of topoisomerases and nucleoid-associated proteins. At the megabase scale, the resulting chromosome structure is important for coordinating cell cycle events; for example, in E. coli the improper structuring of a Mb-scale nucleoid domain leads to errors in the fidelity of chromosome segregation. It was previously unknown whether Mb-scale regions of a bacterial chromosome could be differentially compacted, and which factors might contribute to this spatial variation in compaction. Our work provides a novel method for measuring global chromosome compaction in bacteria. By applying this method in the bacterium Caulobacter crescentus, we show that the Caulobacter nucleoids compaction varies between megabase-scale domains. We also show that DNA gyrase and the nucleoid-associated protein GapR are key players in shaping the uneven compaction of the chromosome.


title: Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains

abstract:
CodY is a conserved broad acting transcription factor that regulates the expression of genes related to amino acid metabolism and virulence in methicillin-resistant Staphylococcus aureus (MRSA). CodY target genes have been studied by using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). Here we performed the first in vivo determination of CodY target genes using a novel CodY monoclonal antibody in established ChIP-exo protocols. Our results showed, 1) the same 135 CodY promoter binding sites regulating 165 target genes identified in two closely related virulent S. aureus USA300 TCH1516 and LAC strains; 2) The differential binding intensity for the same target genes under the same conditions was due to sequence differences in the same CodY binding site in the two strains; 3) Based on transcriptomic data, a CodY regulon comprising 72 target genes that are differentially regulated relative to a CodY deletion strain, representing genes that are mainly involved in amino acid transport and metabolism, inorganic ion transport and metabolism, transcription and translation, and virulence; and 4) CodY systematically regulated central metabolic flux to generate branched-chain amino acids (BCAAs) by mapping the CodY regulon onto a genome-scale metabolic model of S. aureus. Our study performed the first system-level analysis of CodY in two closely related USA300 TCH1516 and LAC strains giving new insights into the similarities and differences of CodY regulatory roles between the closely related strains.

ImportanceWith the increasing availability of whole genome sequences for many strains within the same pathogenic species, a comparative analysis of key regulators is needed to understand how the different strains uniquely coordinate metabolism and expression of virulence. To successfully infect the human host, Staphylococcus aureus USA300 relies on the transcription factor CodY to reorganize metabolism and express virulence factors. While CodY is a known key transcription factor, its target genes are not characterized on a genome-wide basis. We performed a comparative analysis to describe the transcriptional regulation of CodY between two dominant USA300 strains. This study motivates the characterization of common pathogenic strains and an evaluation of the possibility of developing specialized treatments for major strains circulating in the population.


title: The Application of Countercurrent Chromatography for the study of Bacteriophages

abstract: 1.Bacteriophages (phages) are viruses that target bacteria, with the ability to lyse and kill host bacterial cells. Due to this, they have been of some interest as a therapeutic since their discovery in the early 1900s, but with the recent increase in antibiotic resistance, phages have seen a resurgence in attention. Current methods of isolation and purification of phages can be long and tedious, with caesium chloride concentration gradients the gold standard for purifying a phage fraction. Isolation of novel phages requires centrifugation and ultrafiltration of mixed samples, such as water sources, effluent or faecal samples etc, to prepare phage filtrates for further testing. We propose countercurrent chromatography as a novel and alternative approach to use when studying phages, as a scalable and high-yield method for obtaining phage fractions. However, the full extent of the usefulness and resolution of separation with this technique has not been researched; it requires optimisation and ample testing before this can be revealed. Here we present an initial study to determine survivability of two phages, T4 and {phi}X174, using only water as a mobile phase in a Spectrum Series 20 HPCCC. Both phages were found to remain active once eluted from the column. Phages do not fully elute from the column and sodium hydroxide is necessary to flush the column between runs to deactivate remaining phages.


title: Unveiling unexpected complexity and multipotentiality of early heart fields

abstract: Complex organs are composed of a multitude of specialized cell types which assemble to form functional biological structures. How these cell types are created and organized remains to be elucidated for many organs including the heart, the first organ to form during embryogenesis. Here, we show the ontogeny of mammalian mesoderm at high-resolution single cell and genetic lineage/clonal analyses, which revealed an unexpected complexity of the contribution and multi-potentiality of mesodermal progenitors to cardiac lineages creating distinct cell types forming specific regions of the heart. Single-cell transcriptomics of Mesp1 lineage-traced cells during embryogenesis and corresponding trajectory analyses uncovered unanticipated developmental relationships between these progenitors and lineages including two mesodermal progenitor sources contributing to the first heart field (FHF), an intraembryonic and a previously uncharacterized extraembryonic-related source, that produce distinct cardiac lineages creating the left ventricle. Lineage-tracing studies revealed that these extraembryonic-related FHF progenitors reside at the extraembryonic-intraembryonic interface in gastrulating embryos and generate cardiac cell types that form the epicardium and the dorsolateral regions of the left ventricle and atrioventricular canal myocardium. Clonal analyses further showed that these progenitors are multi-potent, creating not only cardiomyocytes and epicardial cell types but also extraembryonic mesoderm. Overall, these results reveal unsuspected multiregional origins of the heart fields, and provide new insights into the relationship between intraembryonic cardiac lineages and extraembryonic tissues and the associations between congenital heart disease and placental insufficiency anomalies.


title: Transmission of one predicts another: Apathogenic proxies for transmission dynamics of a fatal virus

abstract: Identifying drivers of transmission prior to an epidemic--especially of an emerging pathogen--is a formidable challenge for proactive disease management efforts. We tested a novel approach in the Florida panther, hypothesizing that apathogenic feline immunodeficiency virus (FIV) transmission could predict transmission dynamics for pathogenic feline leukemia virus (FeLV). We derived a transmission network using FIV whole genome sequences, and used exponential random graph models to determine drivers structuring this network. We used these drivers to predict FeLV transmission pathways among panthers and compared predicted outbreak dynamics against empirical FeLV outbreak data. FIV transmission was primarily driven by panther age class and distances between panther home range centroids. Prospective FIV-based modeling predicted FeLV dynamics at least as well as simpler, often retrospective approaches, with evidence that FIV-based predictions captured the spatial structuring of the observed FeLV outbreak. Our finding that an apathogenic agent can predict transmission of an analogously transmitted pathogen is an innovative approach that warrants testing in other host-pathogen systems to determine generalizability. Use of such apathogenic agents holds promise for improving predictions of pathogen transmission in novel host populations, and could thereby provide new strategies for proactive pathogen management in human and animal systems.


title: Evolution of Crassulacean Acid Metabolism (CAM) as an escape from ecological niche conservatism in Malagasy Bulbophyllum (Orchidaceae)

abstract: Introductory paragraphDespite growing evidence that niche shifts are more common in flowering plants than previously thought, still little is known about the key physiological (e.g. photosynthesis) traits underlying such niche shifts. To address this question, we here combine a comprehensively sampled phylogeny for mostly epiphytic Malagasy Bulbophyllum orchids (c. 210 spp.) with climatic niche and carbon isotope-derived photosynthesis data to infer the groups spatial-temporal history and to test the role of Crassulacean Acid Metabolism (CAM), a highly water-use efficient type of photosynthesis, in facilitating niche shifts and diversification. We find that most extant species still retain niche (Central Highland) and photosynthesis (C3) states as likely present in the single mid-Miocene (c. 12.70 Ma) ancestor colonizing Madagascar. However, we also infer a major transition to CAM, linked to a late Miocene (c. 7.36 Ma) invasion of species from the sub-humid highland niche first into the islands humid eastern coastal, and then into the seasonally dry  Northwest Sambirano rainforests, yet without significant effect on diversification rates. These findings support the rarely recognized hypothesis that CAM in tropical epiphytes may be selectively advantageous even in high rainfall habitats, rather than presenting a mere adaptation to dry environments or epiphytism per se. Overall, our study qualifies CAM as an evolutionary  gateway trait that considerably widened the spatial-ecological amplitude of Madagascars most species-rich orchid genus.


title: Signatures of Mutational Processes in Human DNA Evolution

abstract: The human genome contains over 100 million SNPs, most of which are C/T (G/A) variations. The type and sequence context of these SNPs are not random, suggesting that they are caused by distinct mutational processes. Deciphering the mutational signatures is a crucial step to discovering the molecular processes responsible for DNA variations across human populations, and potentially for causing genetic diseases. Our analyses of the 1000 Genomes Project SNPs and germline de novo mutations suggest that at least four mutational processes are responsible for human genetic variations. One process is European-specific and no longer active. The remaining three processes are currently active in all human populations. Two of the active processes co-occur and leave a single joint mutational signature in human nuclear DNA. The third active process is specific to mitochondrial DNA, and inflicts C-to-T mutations at mostly non-CG sites. We found neither evidence of APOBEC-induced cytosine deamination in the human germline, nor de novo mutation enrichment within certain regions of the human genome.


title: Cancer risk and sexual conflict as constraints to body size evolution

abstract: Selection often favours large bodies, visible as Copes rule over macroevolutionary time -- but size increases are not inevitable. One understudied cost of large bodies is the high number of cell divisions and the associated risk of oncogenic mutations. Our elasticity analysis shows that selection against a proportional increase in size becomes ever more intense with increasing body size if cancer is the sole selective agent. Thus cancer potentially halts body size increases even if no other constraint does so. We then provide multicellular realism with potentially sexually dimorphic body sizes and traits that control cell populations from zygote to maturity and beyond (ontogenetic management). This shows sexual conflict to extend to ontogeny; sexual dimorphism in mortalities and other life history measures may evolve even in the absence of any ecological causes underlying size- or sex-dependent mortality. Coadaptation of ontogenetic management and body size is required for substantial increases in size.


title: Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil

abstract:
The Northeast region of Brazil registered the second highest incidence proportion of chikungunya fever in 2019. In that year an outbreak consisting of patients presented with febrile disease associated with joint pain were reported by the public primary health care service in the city of Natal, Rio Grande do Norte state, in March 2019. At first, the aetiological agent of the disease was undetermined. Since much is still unknown about chikungunya virus (CHIKV) genomic diversity and evolutionary history in this northeasternmost state, we used a combination of portable whole genome sequencing, molecular clock, and epidemiological analyses that revealed the re-introduction of the CHIKV East-Central-South-African (ECSA) lineage into Rio Grande do Norte. We estimated CHIKV ECSA lineage was first introduced into Rio Grande do Norte in early June 2014, while the 2019 outbreak clade diverged around April 2018 during a period of increased chikungunya incidence in the Southeast region, which might have acted as a source of virus dispersion towards the Northeast region. Together, these results confirm the ECSA lineage continues to spread across the country through interregional importation events likely mediated by human mobility.

HIGHLIGHTSCHIKV ECSA lineage introduction into Rio Grande do Norte state, Northeast Brazil, was estimated to early June 2014

At least two CHIKV importation events occurred in Rio Grande do Norte state, Brazil

The 2019 chikungunya outbreak in Rio Grande do Norte was likely caused by a second event of CHIKV introduction imported from Rio de Janeiro state.

category: genomics


title: itsfm, an open-source package to reliably segment and measure sounds by frequency modulation

abstract: Analysing animal vocalisations in detail provides insights into the biomechanics, decision making and sensory processes behind their behaviours. Echolocating bats, and in particular, the CF-FM calls of high-duty cycle bats serve as a convenient model system to illustrate this point. The CF component in the CF-FM call is used for prey detection and the FM component is used in target ranging. According to the behavioural context at hand such as flight with conspecifics or prey capture, bats choose to increase the duration, intensity or spectral range of the components differently. Studying the call component alterations requires an objective methodology that first segments the components and then allows measurements on them. Studies till now have segmented the call components manually, or automatically using what I term the  peak-frequency method. Manual segmentation is error prone, while the  peak-frequency method requires on-axis recordings for good results. Despite multiple papers using a peak-frequency based segmentation, there remain no publicly available software implementations. itsfm is an open-source package that fills this gap with two implemntations that can segment CF-FM calls, one of them being an implementation of the peak-percentage method. itsfm additionally introduces the  pseudo-Wigner-Ville distribution (PWVD) method for call segmentation, thus allowing the segmentation of calls captured under a wider variety of recording conditions. I create a synthetic dataset and assess the performance of the PWVD method and the  peak-frequency method. The PWVD performs consistently well in call component segmentation in comparison to the peak-percentage method. I also discuss the supporting methods in the itsfm package that can help the further automatic segmentation, measurement and analysis of sounds. Though originally developed for the segmentation and measurement of CF-FM bat calls, the methods in itsfm are speciesagnostic, and may be used for vocalisations of any type.

category: animal behavior and cognition


title: Erythroid overproduction of erythroferrone causes iron overload and developmental abnormalities in mice

abstract:
The hormone erythroferrone (ERFE) is produced by erythroid cells in response to hemorrhage, hypoxia or other erythropoietic stimuli, and suppresses the hepatic production of the iron-regulatory hormone hepcidin, thereby mobilizing iron for erythropoiesis. Suppression of hepcidin by ERFE is thought to be mediated by interference with paracrine BMP signaling that regulates hepcidin transcription in hepatocytes. In anemias with ineffective erythropoiesis, ERFE is pathologically overproduced but its contribution to the clinical manifestations of these anemias is not well understood. We generated three lines of transgenic mice with graded erythroid overexpression of ERFE and showed that they developed dose-dependent iron overload, impaired hepatic BMP signaling and relative hepcidin deficiency. These findings add to the evidence that ERFE is a mediator of iron overload in conditions where ERFE is overproduced, including anemias with ineffective erythropoiesis. At the highest levels of ERFE overexpression the mice manifested decreased perinatal survival, impaired growth, small hypofunctional kidneys, decreased gonadal fat depots and neurobehavioral abnormalities, all consistent with impaired organ-specific BMP signaling during development. Neutralizing excessive ERFE in congenital anemias with ineffective erythropoiesis may not only prevent iron overload but may have additional benefits for growth and development.

Key PointsO_LIChronic erythroid overproduction of erythroferrone dose-dependently suppresses hepcidin, causing iron overload even in the absence of anemia
C_LIO_LIHigh level overexpression of erythroferrone can cause delayed growth, impaired kidney function and other developmental abnormalities consistent with altered BMP signaling
C_LI

category: physiology


title: In vivo CGG repeat RNA binding protein capture identifies RAN translation modifiers and suppressors of repeat toxicity.

abstract: Fragile X-associated tremor/ataxia syndrome (FXTAS) is a neurodegenerative disorder caused by a transcribed CGG repeat expansion in the 5 UTR of FMR1. Expanded CGG repeat RNAs both sequester RNA-binding proteins (RBPs) into nuclear foci and undergo repeat-associated non-AUG (RAN) translation into toxic homopolymeric peptides. RBPs that interact with CGG repeats may play a pivotal role in foci formation and/or RAN translation. Here we employed a CGG repeat RNA-tagging system to capture and identify CGG repeat binding RBPs in vivo under different cellular conditions. We found that several SR (serine/arginine-rich domain) proteins interact with CGG repeat RNAs basally and under cellular stress. These same proteins strongly modify toxicity in a Drosophila model of FXTAS, improving eye degeneration and survival. Furthermore, genetic or pharmacological targeting of the serine/arginine protein kinases (SRPKs) suppresses RAN translation in cellular reporters and toxicity in fly models of FXTAS and C9orf72 ALS/FTD. Finally, pharmacological targeting of SRPK1 supressed CGG repeat toxicity and enhanced survival in rodent neurons. Taken together, these findings demonstrate roles for CGG repeat RNA binding proteins in both RAN translation and repeat toxicity and suggest SRPK inhibition may serve as a possible therapeutic strategy in repeat expansion disorders.


title: The neural basis of effort valuation: A meta-analysis of functional magnetic resonance imaging studies

abstract: Choosing how much effort to expend is a critical for everyday decisions. While effort-based decision-making is altered in common psychopathologies and many neuroimaging studies have been conducted to examine how effort is valued, it remains unclear where the brain processes effort-related costs and integrates them with rewards. Using meta-analyses of combined maps and coordinates of functional magnetic resonance imaging (fMRI) studies (total N = 22), we showed that raw effort demands consistently activated the pre-supplementary motor area (pre-SMA). In contrast, the net value of effortful reward consistently activated regions, such as the ventromedial prefrontal cortex (vmPFC) and ventral striatum (VS), that have been previously implicated in value integration in other cost domains. The opposite activation patterns of the pre-SMA and vmPFC imply a double dissociation of these two regions, in which the pre-SMA is involved in pure effort cost representation and the vmPFC in net value integration. These findings advance our understanding of the neural basis of effort-related valuation and reveal potential brain targets to treat motivation-related disorders.


title: Decoupling of global brain activity and cerebrospinal fluid flow in Parkinson's cognitive decline

abstract:
BackgroundDeposition and spreading of misfolded proteins (-synuclein and tau) have been linked to Parkinsons cognitive dysfunction. The glymphatic system may play an important role in the clearance of these toxic proteins via cerebrospinal fluid (CSF) flow through perivascular and interstitial spaces. Recent studies discovered that sleep-dependent global brain activity is coupled to CSF flow that may reflect glymphatic function.

ObjectiveTo determine if the decoupling of brain activity-CSF flow is linked to Parkinsons cognitive dysfunction.

MethodsFunctional and structural MRI data, clinical motor (Unified Parkinson's Disease Rating Scale), and cognitive (Montreal Cognitive Assessment, MoCA) scores were collected from 60 Parkinsons and 58 control subjects. Parkinsons patients were subgrouped into those with (MoCA < 26; N = 29) and without (MoCA [≥] 26; N = 31) mild cognitive impairment (MCI).

The coupling strength between the resting-state global blood-oxygen-level-dependent signal (gBOLD) and associated CSF flow was quantified, compared among groups, and associated with clinical and structural measurements.

ResultsgBOLD-CSF coupling decreased significantly (p < 0.006) in Parkinsons patients showing MCI, compared to those without MCI and controls. Reduced gBOLD-CSF coupling was associated with decreased MoCA scores that was present in Parkinsons patients (p = 0.005) but not in controls (p = 0.65). Weaker gBOLD-CSF coupling in Parkinsons patients also was associated with a thinner right entorhinal cortex (Spearmans correlation = - 0.36; p = 0.012), an early structural change often seen in Alzheimers.

ConclusionsThe decoupling between global brain activity and associated CSF flow is related to Parkinsons cognitive impairment.


title: The Coherent Default Mode Network is not involved in Episodic Recall or Social Cognition

abstract: Resting-state network research is extremely influential, yet the functions of many networks remain unknown. In part, this is due to typical (e.g., univariate) analyses testing the function of individual regions and not the full set of co-activated regions that form a network. Connectivity is dynamic and the function of a region may change based on its current connections. Therefore, determining the function of a network requires assessment at the network-level. Yet popular theories implicating the default mode network (DMN) in episodic memory and social cognition, rest principally upon analyses performed at the level of individual brain regions. Here we use independent component analysis to formally test the role of the DMN in episodic and social processing at the network level. As well as an episodic retrieval task, two independent datasets were employed to assess DMN function across the breadth of social cognition; a person knowledge judgement and a theory of mind task. Each task dataset was separated into networks of co-activated regions. In each, the co-activated DMN, was identified through comparison to an a priori template and its relation to the task model assessed. This co-activated DMN did not show greater activity in episodic or social tasks than high-level baseline conditions. Thus, no evidence was found to support hypotheses that the co-activated DMN is involved in explicit episodic or social processing tasks at a network-level. The networks associated with these processes are described. Implications for prior univariate findings and the functional significance of the co-activated DMN are considered.


title: A Network-level Test of the Role of the Co-activated Default Mode Network in Episodic Recall and Social Cognition


title: The kidney protects against sepsis by enhancing the systemic release of Uromodulin to stimulate macrophage function

abstract:
Sepsis is a significant cause of mortality in hospitalized patients. Concomitant development of acute kidney injury (AKI) increases sepsis mortality through unclear mechanisms. While electrolyte disturbances and toxic metabolite buildup during AKI could be important, it is possible that the kidney produces a protective molecule lost during sepsis with AKI. We previously demonstrated that systemic Tamm-Horsfall Protein (THP, uromodulin), a kidney-derived protein with immunomodulatory properties, falls in AKI. Using a mouse sepsis model without severe kidney injury, we show that the kidney increases circulating THP by enhancing basolateral release of THP from medullary thick ascending limb cells. In sepsis patients, changes in circulating THP are positively associated with critical illness. THP is also found de novo in injured lungs. Genetic ablation of THP in mice leads to increased mortality and bacterial burden during sepsis. Consistent with the increased bacterial burden, the presence of THP in vitro and in vivo leads macrophages and monocytes to upregulate a transcriptional program promoting cell migration, phagocytosis and chemotaxis and treatment of macrophages with purified THP increases phagocytosis. Rescue of septic THP-/- mice with exogenous systemic THP improves survival. Together, these findings suggest that through releasing THP, the kidney modulates the immune response in sepsis by enhancing mononuclear phagocyte function and systemic THP has therapeutic potential in sepsis.

Significance StatementSepsis is a significant contributor to kidney injury as well as morbidity and mortality worldwide. Specific therapies to improve outcomes in sepsis with kidney injury have largely been limited to symptom management and infectious agent control, in part because it is unclear how kidney injury increases sepsis mortality. This paper describes the identification of Tamm-Horsfall protein, previously known to protect in ischemic models of AKI, as protective in preclinical models of sepsis. It demonstrates how the loss of THP leads to decreased mononuclear phagocyte function and diversity, increased pathogen burden and decreased survival. THP also increases in sepsis without severe kidney injury and concentrates in injured organs. Further study of THP in sepsis could lead to novel sepsis therapeutics.


title: The kidney protects against sepsis by producing systemic uromodulin


title: Fitness cost associated with enhanced EPSPS gene copy number and glyphosate resistance in an Amaranthus tuberculatus population

abstract: The evolution of resistance to pesticides in agricultural systems provides an opportunity to study the fitness costs and benefits of novel adaptive traits. Here, we studied a population of Amaranthus tuberculatus (common waterhemp), which has evolved resistance to glyphosate. Following the production of seed families with contrasting levels of glyphosate resistance, we assessed the growth and fitness of seed families in the absence of glyphosate and determined their ability to compete for resources under intra- and interspecific competition. Further investigation revealed a positive correlation between the level of resistance and gene copy number for the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) glyphosate target, thus indicating gene amplification as the mechanism of resistance within the population. Resistant common waterhemp plants were found to have a lower competitive response when compared to the susceptible phenotypes. A substitution rate of 2.76 glyphosate resistant plants was required to have an equal competitive effect as a single susceptible plant. A growth trade-off was associated with the gene amplification mechanism under intra-phenotypic competition where 20 extra gene copies were associated with a 26.5 % reduction in dry biomass. Interestingly, this growth trade-off was mitigated when assessed under interspecific competition from maize.


title: Cortical Mechanisms of Saccadic Suppression

abstract: Saccades are a ubiquitous and crucial component of our visual system, allowing for the efficient deployment of the fovea and its accompanying neural resources. Initiation of a saccade is known to cause saccadic suppression, a temporary reduction in visual sensitivity1, 2 and visual cortical firing rates3-6. While saccadic suppression has been well characterized at the level of perception and single neurons, relatively little is known about the visual cortical networks governing this phenomenon. Here we examine the effects of saccadic suppression on distinct neural subpopulations within visual area V4. We find cortical layer- and cell type-specific differences in the magnitude and timing of peri-saccadic modulation. Neurons in the input layer show changes in firing rate and inter-neuronal correlations prior to saccade onset, indicating that this layer receives information about impending saccades. Putative inhibitory interneurons in the input layer elevate their firing rate during saccades, suggesting they play a role in suppressing the activity of other cortical subpopulations. A computational model of this circuit recapitulates our empirical observations and demonstrates that an input layer-targeting pathway can initiate saccadic suppression by enhancing local inhibitory activity. Collectively, our results provide a mechanistic understanding of how eye movement signaling interacts with cortical circuitry to enforce visual stability.


title: Laminar Mechanisms of Saccadic Suppression in Primate Visual Cortex


title: Co-evolutionary Landscape at the Interface and Non-Interface Regions of Protein-Protein Interaction Complexes

abstract: Proteins involved in interactions throughout the course of evolution tend to co-evolve and compensatory or coordinated changes may occur in interacting proteins to maintain or refine interactions between them. However, certain residue pair alterations may prove to be detrimental for functional interactions. Hence, determining co-evolutionary pairings that could be structurally or functionally relevant for maintaining the conservation of an inter-protein interaction is important. Inter-protein co-evolution analysis in a number of complexes with the help of multiple existing methodologies suggested that co-evolutionary pairings can occur in spatially proximal as well as distant regions of inter-protein interaction complexes. Subsequently, the Co-Var (Correlated Variation) method based on mutual information and Bhattacharyya coefficient was developed, validated and found to perform relatively better than CAPS and EV-complex. Interestingly, while applying the Co-Var measure on a set of protein-protein interaction complexes, co-evolutionary pairings were obtained in spatially proximal and distant regions in inter-protein complexes. Our approach involves determining high degree co-evolutionary pairings which include multiple co-evolutionary connections between particular co-evolved residue positions in one protein and particular residue positions in the binding partner. Detailed analyses of high degree co-evolutionary pairings in protein-protein complexes involved in inter-cellular communication during cancer metastasis were performed. These analyses suggested that most of the residue positions involved in such co-evolutionary pairings mainly occurred within functional domains of constituent proteins and substitution mutations were also common among these co-evolved positions. The physiological relevance of these predictions suggests that Co-Var can predict residues that could be crucial for preserving functional protein-protein interactions. Finally, Co-Var web server that implements this methodology was developed. This web server available at http://www.hpppi.iicb.res.in/ishi/covar/index.html identifies co-evolutionary pairings in intra-protein and inter-protein complexes.