Biology subjects

Smith, K.

Publications and source records attributed to Smith, K..

8 recordsLinked to original sources

bioRxiv2018

Mitochondria form cholesterol-rich contact sites with the nucleus during retrograde response

Mitochondria drive cellular adaptation to stress by retro-communicating with the nucleus. This process is known as Mitochondrial Retrograde Response (MRR) and is induced by mitochondrial dysfunctions which perturb cell signalling. MRR results in the nuclear stabilization and activation of pro-survival transcription factors such as the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB). Here we demonstrate that MRR is facilitated by the formation of contact sites between mitochondria and the nucleus which establish microdomains of communication between the two organelles. The 18kD Translocator Protein (TSPO), which de-ubiquitylates and stabilizes the mitochondrial network preventing its mitophagy-mediated segregation, is required for this interaction. The tethering TSPO enacts is mediated by the complex formed with the Protein Kinase A via the A-kinase anchoring protein Acyl-CoA Binding Domain Containing 3 (ACBD3) and allows the redistribution of cholesterol which sustains the pro-survival response by blocking NF-kB de-acetylation. This work proposes a new paradigm in the mitochondrial retro-communication by revealing the existence of contact sites between mitochondrial and the nucleus and a signalling role for cholesterol.

cell biology↗

bioRxiv2018

Baseline human gut microbiota profile in healthy people and standard reporting template

A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with clinical applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individuals microbiome to the growing knowledgebase of \"normal\" microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and abundances the study also generated a list of contigs of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBIs Short Read Archive.

microbiology↗

bioRxiv2018

A role for VPS35 in Brucella intracellular replication revealed by genome-wide siRNA screening

Brucella, the causing agent of brucellosis, is a major zoonotic pathogen with worldwide distribution. Brucella resides and replicates inside infected host cells in membrane-bound compartments called BCVs (Brucella-containing vacuoles). Following uptake, Brucella resides in eBCVs (endosomal BCVs) that gradually mature from early to late endosomal features. Through a poorly understood process that is key to the intracellular lifestyle of Brucella, the eBCV escapes fusion with lysosomes by transitioning to the rBCV (replicative BCV), a replicative niche directly connected to the endoplasmic reticulum (ER). Despite the notion that this complex intracellular lifestyle must depend on a multitude of host factors, a holistic view on which of these components control Brucella cell entry, trafficking and replication is still missing. Here we used a systematic cell-based siRNA knockdown screen in HeLa cells infected with Brucella abortus and identified 425 components of the human infectome for Brucella infection. These include multiple components of pathways involved in central processes such as cell cycle, actin cytoskeleton dynamics or vesicular trafficking. Using assays for pathogen entry, knockdown complementation and co-localization at single-cell resolution, we identified the requirement of the VPS retromer for Brucella to escape the lysosomal degradative pathway and to establish its intracellular replicative niche. We thus validated a component of the VPS retromer as novel host factor critical for Brucella intracellular trafficking. Further, our genome-wide data shed light on the interplay between central host processes and the biogenesis of the Brucella replicative niche.\n\nImportanceWith >300,000 new cases of human brucellosis annually, Brucella is regarded as one of the most important zoonotic bacterial pathogen worldwide. The causing agent of brucellosis resides inside host cells within vacuoles termed Brucella containing vacuoles (BCVs). Although few host components required to escape the degradative lysosomal pathway and to establish the ER-derived replicative BCV (rBCV) have already been identified, the global understanding of this highly coordinated process is still partial and many factors remain unknown. To gain a deeper insight into these fundamental questions we performed a genome-wide RNA interference (RNAi) screen aiming at discovering novel host factors involved in the Brucella intracellular cycle. We identified 425 host proteins that contribute to Brucella cellular entry, intracellular trafficking, and replication. Together, this study sheds light on previously unknown host pathways required for the Brucella infection cycle and highlights the VPS retromer components as critical factors for the establishment of the Brucella intracellular replicative niche.

microbiology↗

bioRxiv2018

Hierarchical Complexity of the Adult Human Structural Connectome

The structural network of the human brain has a rich topology which many have sought to characterise using standard network science measures and concepts. However, this characterisation remains incomplete and the non-obvious features of this topology have largely confounded attempts towards comprehensive constructive modelling. This calls for new perspectives. Hierarchical complexity is an emerging paradigm of complex network topology based on the observation that complex systems are composed of hierarchies within which the roles of hierarchically equivalent nodes display highly variable connectivity patterns. Here we test the hierarchical complexity of the human structural connectomes of a group of seventy-nine healthy adults. Binary connectomes are found to be more hierarchically complex than three benchmark random network models. This provides a new key description of brain structure, revealing a rich diversity of connectivity patterns within hierarchically equivalent nodes. Dividing the connectomes into four tiers based on degree magnitudes indicates that the most complex nodes are neither those with the highest nor lowest degrees but are instead found in the middle tiers. Spatial mapping of the brain regions in each hierarchical tier reveals consistency with the current anatomical, functional and neuropsychological knowledge of the human brain. The most complex tier (Tier 3) involves regions believed to bridge high-order cognitive (Tier 1) and low-order sensorimotor processing (Tier 2). We then show that such diversity of connectivity patterns aligns with the diversity of functional roles played out across the brain, demonstrating that hierarchical complexity can characterise functional diversity strictly from the network topology.

systems biology↗

bioRxiv2018

Hunter-gatherers maintain assortativity in cooperation despite high-levels of residential change and mixing

Widespread cooperation is a defining feature of human societies from hunter-gatherer bands to nation states. But explaining its evolution remains a challenge. While positive assortment - of cooperators with cooperators - is recognized as a basic requirement for the evolution of cooperation, the mechanisms governing assortment are debated. Moreover, the social structure of modern hunter-gatherers, characterized by high mobility, residential mixing and low genetic relatedness, undermine assortment and add to the puzzle of how cooperation evolved. Here, we analyze four years of data (2010, 2013, 2014, 2016) tracking residence and levels of cooperation elicited from a public goods game (PG), in Hadza hunter-gatherers of Tanzania. Data were collected from 56 camps, comprising 383 unique individuals, 137 of whom we have data for two or more years. Despite significant residential mixing, we observe a robust pattern of assortment necessary for cooperation to evolve: In every year, Hadza camps exhibit high between-camp and low within-camp variation in cooperation. We further consider the role of homophily in generating this assortment. We find little evidence that cooperative behavior within individuals is stable over time or that similarity in cooperation between dyads predicts their future cohabitation. Both sets of findings are inconsistent with homophilic models that assume stable cooperative and selfish types. Consistent with social norms, culture and reciprocity theories, the data suggest that the strongest predictor of an individuals level of cooperation in any given year is the mean cooperation of their campmates in that year. These findings underscore the adaptive nature of human cooperation - particularly its responsiveness to social contexts - as a feature important in generating the assortment necessary for cooperation to evolve.

animal behavior and cognition↗

bioRxiv2017

A suite of transgenic driver and reporter mouse lines with enhanced brain cell type targeting and functionality

Modern genetic approaches are powerful in providing access to diverse types of neurons within the mammalian brain and greatly facilitating the study of their function. We here report a large set of driver and reporter transgenic mouse lines, including 23 new driver lines targeting a variety of cortical and subcortical cell populations and 26 new reporter lines expressing an array of molecular tools. In particular, we describe the TIGRE2.0 transgenic platform and introduce Cre-dependent reporter lines that enable optical physiology, optogenetics, and sparse labeling of genetically-defined cell populations. TIGRE2.0 reporters broke the barrier in transgene expression level of single-copy targeted-insertion transgenesis in a wide range of neuronal types, along with additional advantage of a simplified breeding strategy compared to our first-generation TIGRE lines. These novel transgenic lines greatly expand the repertoire of high-precision genetic tools available to effectively identify, monitor, and manipulate distinct cell types in the mouse brain.

neuroscience↗

bioRxiv2017

Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest

West Nile Virus (WNV) has been detected annually in Maricopa County, Arizona, since 2003. With this in mind, we sought to determine if contemporary strains are established within the county or are annually imported. As part of this effort, we developed a new protocol for tiled amplicon sequencing of WNV to efficiently attain greater than 99% coverage of 14 WNV genomes collected directly from positive mosquito pools distributed throughout Maricopa County between 2014 and 2017. Bayesian phylogenetic analyses revealed that the contemporary genomes fall within two major lineages, NA/WN02 and SW/WN03. We found that all of the Arizona strains possessed a mutation known to be under positive selection (NS5-K314R), which has arisen independently four times. The SW/WN03 strains exhibited transient behavior, with at least 10 separate introductions into Arizona when considering both historical and contemporary strains. However, NA/WN02 strains are geographically differentiated and appear to be established in Arizona, with likely origins in New York. The clade of New York and Arizona strains looks to be the most ancestral extant lineage of WNV still circulating in the United States. The establishment of WNV strains in Maricopa County provides the first evidence of local overwintering by a WNV strain over the course of several years in Arizona.

evolutionary biology↗

bioRxiv2017

Human replication licensing factor Cdt1 directly links mitotic kinetochores to spindle microtubules

Robust kinetochore-microtubule (kMT) attachment is critical for accurate chromosome segregation. G2/M-specific depletion of human Cdt1 that localizes to kinetochores in an Ndc80 complex-dependent manner, leads to abnormal kMT attachments and mitotic arrest. This indicates an independent mitotic role for Cdt1 in addition to its prototypic function in DNA replication origin licensing. Here, we show that Cdt1 directly binds to microtubules (MTs). Endogenous or transiently expressed Cdt1 localizes to both mitotic spindle MTs and kinetochores. Deletion mapping of Cdt1 revealed that the regions comprising the middle and C-terminal winged-helix domains but lacking the N-terminal unstructured region was required for efficient MT-binding. Mitotic kinase Aurora B interacts with and phosphorylates Cdt1. Aurora B-phosphomimetic Cdt1 exhibited attenuated MT-binding and its cellular expression induced defective kMT attachments with a concomitant delay in mitotic progression. Thus we provide mechanistic insight into how Cdt1 affects overall kMT stability in an Aurora B kinase phosphorylation-dependent manner; which is envisioned to augment the MT-binding of the Ndc80 complex.\n\neTOC summary* Cdt1 binds to microtubules\n\n* The middle and the C-terminal winged-helix domains of Cdt1 are involved in MT-binding\n\n* Aurora B Kinase phosphorylates Cdt1 and influences its MT-binding\n\n* Aurora B-mediated Cdt1 phosphorylation is necessary for kMT stability and mitotic progression

cell biology↗