Biology subjects

Smith, J.

Publications and source records attributed to Smith, J..

18 recordsLinked to original sources

bioRxiv2018

Spatial relationships between white matter degeneration, amyloid load and cortical volume in amnestic mild cognitive impairment

The spatial-temporal relationships between gray and white matter (WM) degeneration during preclinical and early symptomatic Alzheimers disease are poorly understood. We characterized {beta}-amyloid deposition, cortical volume and WM degeneration in 44 subjects including healthy control (N=23), amnestic mild cognitive impairment (aMCI) (N=19), and early Alzheimers subjects (N=2). Integrated PET-MRI provided simultaneous measurement of 18F-Florbetapir uptake in cortical areas, regional brain volumes from structural MRI, and WM tract integrity metrics from diffusion MRI using biophysical modeling.\n\nAcross the cohort of healthy control and aMCIs, cortical volumes correlated poorly with {beta}-amyloid deposition in the same area (p < 0.05 only in the posterior cingulate and parietal lobe). WM degeneration correlated significantly with both amyloid and volume of connected cortical areas, but more strongly with volume. Diffusion MRI metrics for WM demyelination and/or axonal loss could therefore provide new biomarkers associated with clinical Alzheimers conversion. These WM changes may represent sequential propagation of Alzheimers neurodegeneration between functionally connected regions, and/or evidence of direct WM injury during the Alzheimers pathology cascade.

neuroscience↗

bioRxiv2018

Mining unknown porcine protein isoforms by tissue-based map of proteome enhances the pig genome annotation

A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model. We developed the tissue-based proteome maps using 34 major normal pig tissues. A total of 7,319 unknown protein isoforms were identified and systematically characterized, including 3,703 novel protein isoforms, 669 protein isoforms from 460 genes symbolized beginning with LOC, and 2,947 protein isoforms without clear NCBI annotation in current pig reference genome. These newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing (RNA-seq) of the same pig tissues, further improving the genome annotation of corresponding protein coding genes. Combining the well-annotated genes that having parallel expression pattern and subcellular witness, we predicted the tissue related subcellular components and potential function for these unknown proteins. Finally, we mined 3,656 orthologous genes for 49.95% of unknown protein isoforms across multiple species, referring to 65 KEGG pathways and 25 disease signaling pathways. These findings provided valuable insights and a rich resource for enhancing studies of pig genomics and biology as well as biomedical model application to human medicine.

genomics↗

bioRxiv2018

Expected patterns of local ancestry in a hybrid zone

1The initial drivers of reproductive isolation between species are poorly characterized. In cases where partial reproductive isolation exists, genomic patterns of variation in hybrid zones may provide clues about the barriers to gene flow which arose first during the early stages of speciation. Purifying selection against incompatible substitutions that reduce hybrid fitness has the potential to distort local patterns of ancestry relative to background patterns across the genome. The magnitude and qualitative properties of this pattern are dependent on several factors including migration history and the relative fitnesses for different combinations of incompatible alleles. We present a model which may account for these factors and highlight the potential for its use in verifying the action of natural selection on candidate loci implicated in reducing hybrid fitness.

evolutionary biology↗

bioRxiv2018

Bangers and cash: Baiting efficiency in a heterogeneous population.

O_LIContext: The uptake of baits is a key variable in management actions aimed at the vaccination, training, or control of many vertebrate species. Increasingly, however, it is appreciated that individuals of the target species vary in their likelihood of taking baits. To optimise a baiting program, then, we require knowledge, not only on the rate of bait uptake, and how this changes with bait availability, but also knowledge on the proportion of the target population that will take a bait.\nC_LIO_LIThe invasive cane toad (Rhinella marina) is a major threat to northern quolls (Dasyurus hallucatus), which are poisoned when they attack this novel toxic prey item. Conditioned taste aversion baits (cane toad sausages) can be delivered in the field to train individual northern quolls to avoid toads.\nC_LIO_LIMethods: Here we report on a large-scale field trial across eleven sites across one large property in Western Australia. Camera trapping and statistical modelling was used to estimate the proportion of baitable animals in the population, and the proportion of these that were baited at varying bait availabilities.\nC_LIO_LIResults: Population estimates varied at each site from 3.5 ({+/-}0.76 SD) to 18 ({+/-} 1.58 SD) individual quolls per site, resulting in a range across sites of 0.6-4 baits available per individual. Bait uptake increased with increasing bait availability.\nC_LIO_LIWe also estimate that only 62% of individual quolls are baitable, and that a baiting rate of 3 baits per individual (rather than per area) will result in almost all of these baitable individuals being treated.\nC_LIO_LIWe compared our statistical method with prior data informing the probability of being baitable; and with probability of being baitable set to 1; this resulted in largely differing estimates in relation to an appropriate baiting rate.\nC_LIO_LISynthesis and applications: Data and models such as ours provide wildlife managers with information critical to informed decision making and are fundamental to estimate the cost-efficiency of any baiting campaign.\nC_LI

ecology↗

bioRxiv2018

Genetic risk for schizophrenia and developmental delay is associated with shape and microstructure of midline white matter structures

Genomic copy number variants (CNVs) are amongst the most highly penetrant genetic risk factors for neuropsychiatric disorders. The scarcity of carriers of individual CNVs and their phenotypical heterogeneity limits investigations of the associated neural mechanisms and endophenotypes. We applied a novel design based on CNV penetrance for schizophrenia and developmental delay that allows us to identify structural sequelae that are most relevant to neuropsychiatric disorders. Our focus on brain structural abnormalities was based on the hypothesis that convergent mechanisms contributing to neurodevelopmental disorders would likely manifest in the macro- and microstructure of white matter and cortical and subcortical grey matter. 21 adult participants carrying neuropsychiatric risk CNVs (including those located at 22q11.2, 15q11.2, 1q21.1, 16p11.2, and 17q12) and 15 age- and gender matched controls underwent T1-weighted structural, diffusion and quantitative T1 relaxometry MRI.\n\nThe macro- and microstructural properties of the cingulum bundles were associated with penetrance for both developmental delay and schizophrenia, in particular curvature along the anterior-posterior axis (Sz: pcorr=0.026; DD: pcorr=0.035) and intracellular volume fraction (Sz: pcorr=0.019; DD: pcorr=0.064) Further principal component analysis showed alterations in the interrelationships between the volumes of several mid-line white matter structures (Sz: pcorr=0.055; DD, pcorr=0.027). In particular, the ratio of volumes in the splenium and body of the corpus callosum was significantly associated with both penetrance scores (Sz: p=0.037; DD; p=0.006). Our results are consistent with the notion that a significant alteration in developmental trajectories of mid-line white-matter structures constitutes a common neurodevelopmental aberration contributing to risk for schizophrenia and intellectual disability.

neuroscience↗

bioRxiv2018

Brucella Peptide Cross-Reactive MHC I Presentation Activates SIINFEKL-Specific TCR Expressing T Cells

Brucella spp are intracellular pathogenic bacteria remarkable in their ability to escape immune surveillance and therefore inflict a state of chronic disease within the host. To enable further immune response studies, Brucella were engineered to express the well characterized chicken ovalbumin (OVA). Surprisingly, we found that CD8 T cells bearing T cell receptors (TCR) nominally specific for the OVA peptide SIINFEKL (OT-1) reacted to parental Brucella-infected targets as well as OVA-expressing Brucella variants in cytotoxicity assays. Furthermore, splenocytes from Brucella immunized mice produced IFN-{gamma} and exhibited cytotoxicity in response to SIINFEKL-pulsed target cells. To determine if the SIINFEKL-reactive OT-1 TCR could be cross-reacting to Brucella peptides, we searched the Brucella proteome using an algorithm to generate a list of near-neighbor nonamer peptides that would bind to H2Kb. Selecting five Brucella peptide candidates, along with controls, we verified that several of these peptides mimicked SIINFEKL resulting in T cell activation through the \"SIINFEKL-specific\" TCR. Activation was dependent on peptide concentration as well as sequence. Our results underscore the complexity and ubiquity of cross-reactivity in T cell recognition. This cross-reactivity may enable microbes such as Brucella to escape immune surveillance by presenting peptides similar to the host, and may also lead to the activation of autoreactive T cells.

immunology↗

bioRxiv2018

Congenital glaucoma with anterior segment dysgenesis in individuals with biallelic CPAMD8 variants

PurposeCongenital glaucoma is a significant cause of irreversible blindness. In some instances glaucoma is associated with developmental abnormalities of the ocular anterior segment, which can impair drainage of aqueous humor, leading to an increase in intraocular pressure.\n\nMethodsGenome sequencing was performed on a parent-proband congenital glaucoma trio, with exome sequencing of 79 additional individuals with suspected primary congenital glaucoma.\n\nResultsWe describe a unique ocular anterior segment dysgenesis associated with congenital glaucoma in four individuals from three unrelated families. In each case, disease was associated with compound heterozygous variants in CPAMD8, a gene of unknown function recently associated with ocular anterior segment dysgenesis, myopia, and ectopia lentis. CPAMD8 expression was highest in neural crest-derived tissues of the adult anterior segment, suggesting that CPAMD8 variation may cause malformation of key drainage structures and the development of high intraocular pressure and glaucoma.\n\nConclusionsThis study reveals a unique genetic cause of childhood glaucoma, and expands the phenotypic spectrum of CPAMD8-associated ocular disease.

genetics↗

bioRxiv2018

Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

BackgroundThe domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression atlas for the chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues.\n\nResultsRandomly down-sampling RNA-seq datasets to a common depth and quantifying expression against a reference transcriptome using the mRNA quantitation tool Kallisto ensured that disparate datasets explored comparable transcriptomic space. The network analysis tool Miru was used to extract clusters of co-expressed genes from the resulting expression atlas, many of which were tissue or cell-type restricted, contained transcription factors that have previously been implicated in their regulation, or were otherwise associated with biological processes, such as the cell cycle. The atlas provides a resource for the functional annotation of genes that currently have only a locus ID. We cross-referenced the RNA-seq atlas to a publicly available embryonic Cap Analysis of Gene Expression (CAGE) dataset to infer the developmental time course of organ systems, and to identify a signature of the expansion of tissue macrophage populations during development.\n\nConclusionExpression profiles obtained from public RNA-seq datasets - despite being generated by different laboratories using different methodologies - can be made comparable to each other. This meta-analytic approach to RNA-seq can be extended with new datasets from novel tissues, and is applicable to any species.

genomics↗

bioRxiv2018

Non-parametric and semi-parametric support estimation using SEquential RESampling random walks on biomolecular sequences

Non-parametric and semi-parametric resampling procedures are widely used to perform support estimation in computational biology and bioinformatics. Among the most widely used methods in this class is the standard bootstrap method, which consists of random sampling with replacement. While not requiring assumptions about any particular parametric model for resampling purposes, the bootstrap and related techniques assume that sites are independent and identically distributed (i.i.d.). The i.i.d. assumption can be an over-simplification for many problems in computational biology and bioinformatics. In particular, sequential dependence within biomolecular sequences is often an essential biological feature due to biochemical function, evolutionary processes such as recombination, and other factors.\n\nTo relax the simplifying i.i.d. assumption, we propose a new non-parametric/semi-parametric sequential resampling technique that generalizes \"Heads-or-Tails\" mirrored inputs, a simple but clever technique due to Landan and Graur. The generalized procedure takes the form of random walks along either aligned or unaligned biomolecular sequences. We refer to our new method as the SERES (or \"SEquential RESampling\") method.\n\nTo demonstrate the flexibility of the new technique, we apply SERES to two different applications - one involving aligned inputs and the other involving unaligned inputs. Using simulated and empirical data, we show that SERES-based support estimation yields comparable or typically better performance compared to state-of-the-art methods for both applications.

bioinformatics↗

bioRxiv2018

Liquid-like P granules require ATP hydrolysis to avoid solidification

Corrected version -This version can be cited. RNA granules are dynamic sub-cellular compartments that lack enveloping membranes. RNA granules have been proposed to form by liquid-liquid phase separation, a thermodynamic process that partitions molecules between dilute and condensed liquid phases 1. P granules are archetypal RNA granules in C. elegans that display liquid-like behaviors 2. Here we describe in vivo and ex vivo approaches to analyze the material properties of P granules. We find that the liquid phase of P granules is stabilized by a molecularly-distinct, enveloping shell that is intrinsically non-dynamic. Consistent with a gel phase, the shell is resistant to dilution, high salt, and aliphatic alcohols, and dissolves in SDS. Solidification of RNA granules has been linked to neuronal degeneration 3. Our findings suggest that gel-like polymers are essential components of RNA granules that help stabilize liquid phases in the cellular environment.

molecular biology↗

bioRxiv2017

Mechanisms of KCNQ1 Channel Dysfunction in Long QT Syndrome Involving Voltage Sensor Domain Mutations

Loss-of-function (LOF) mutations in human KCNQ1 are responsible for susceptibility to a life-threatening heart rhythm disorder, the congenital long-QT syndrome (LQTS). Hundreds of KCNQ1 mutations have been identified, but the molecular mechanisms responsible for impaired function are poorly understood. Here, we investigated the impact of 51 KCNQ1 variants located within the voltage sensor domain (VSD), with an emphasis on elucidating effects on cell surface expression, protein folding and structure. For each variant, the efficiency of trafficking to the plasma membrane, the impact of proteasome inhibition, and protein stability were assayed. The results of these experiments, combined with channel functional data, provided the basis for classifying each mutation into one of 6 mechanistic categories. More than half of the KCNQ1 LOF mutations destabilize the structure of the VSD, resulting in mistrafficking and degradation by the proteasome, an observation that underscores the growing appreciation that mutation-induced destabilization of membrane proteins may be a common human disease mechanism. Finally, we observed that 5 of the folding-defective LQTS mutants are located in the VSD S0 helix, where they interact with a number of other LOF mutation sites in other segments of the VSD. These observations reveal a critical role for the S0 helix as a central scaffold to help organize and stabilize the KCNQ1 VSD and, most likely, the corresponding domain of many other ion channels.\n\nOne Sentence SummaryLong QT syndrome-associated mutations in KCNQ1 most often destabilize the protein, leading to mistrafficking and degradation.

biochemistry↗

bioRxiv2017

Transcriptional regulation by NR5A2 couples cell differentiation and inflammation in the pancreas

Tissue-specific differentiation and inflammatory programmes are thought to independently contribute to disease. The orphan nuclear receptor NR5A2 is a key regulator of pancreas differentiation and SNPs in or near the human gene are associated with risk of pancreatic cancer. In mice, Nr5a2 heterozygosity sensitizes the pancreas to damage, impairs regeneration, and cooperates with mutant KRas in tumor progression. Through global transcriptomic analysis, we uncover a basal pre-inflammatory state in the pancreas of Nr5a2 heterozygous mice that is reminiscent of pancreatitis-induced inflammation and is conserved in histologically normal human pancreata with reduced NR5A2 mRNA expression. In Nr5a2+/- mice, Nr5a2 undergoes a dramatic transcriptional switch relocating from tissue-specific to inflammatory loci thereby promoting AP-1-dependent gene transcription. Importantly, deletion of c-Jun in the pancreas of these mice rescues the pre-inflammatory phenotype and the defective regenerative response to damage. These findings provide compelling evidence that the same transcriptional networks supporting homeostasis in normal tissue can be subverted to foster inflammation upon genetic or environmental constraints.

cancer biology↗

bioRxiv2017

Game theoretic consideration of transgenic bacteria in the human gut microbiota as a pro-biotic prophylactic for metabolic syndrome

A game theoretic treatment is introduced to explore the role of nutrition of the gut bacterial microflora as a potential pro-biotic therapy. Rational design of functional foods and nutraceuticals has far reaching public health and therapeutic benefits. Understanding ecological dynamics and how phenotypic manipulations of microbe-microbe interactions of the gut microbiota can provide direct health benefit is currently a fundamental question in bioengineering and more widely in the food, diet and health industries. This work considers a hypothetical adjustment of the microbiome by introducing a transgenic bacterial species that contributes to increased exposure of omega 3 fats in the gut by converting them from the omega 6 fats, dominant in the Western diet. The ratio of the two fats circulating in blood are risk markers, indicators of metabolic syndrome and related conditions. In this work, we consider nutritional exposure to a pro-biotic, a live culture of transgenic bacteria contributing omega 3 fats from omega 6 in the diet. Maintaining a long-term co-existence between native (indigenous) and transgenic bacteria is a challenge. Game theory is the appropriate tool for handling this conflict. The long-term co-existence is guaranteed if the two strains engage in the Snowdrift game. Our game theoretic treatment provides the basis of a model mechanism for prophylactic nutritional therapy for metabolic syndrome by the transgenic bacteria, providing support of indigenous gut microbiota and additional supplementation of a pro-biotic.

bioengineering↗

bioRxiv2017

Not such silly sausages: Northern quolls exhibit aversion to toads after training with toad sausages.

The invasion of toxic cane toads (Rhinella marina) is a major threat to northern quolls (Dasyurus hallucatus) which are poisoned when they attack this novel prey item. Quolls are now endangered as a consequence of the toad invasion. Conditioned taste aversion can be used to train individual quolls to avoid toads, but we currently lack a training technique that can be used at a landscape scale to buffer entire populations from toad impact. Broad scale deployment requires a bait that can be used for training, but there is no guarantee that such a bait will ultimately elicit aversion to toads. Here we test a manufactured bait--a toad sausage--for its ability to elicit aversion to toads in northern quolls. To do this, we exposed one group of quolls to a toad sausage and another to a control sausage and compared the quolls predatory responses when presented with a dead adult toad. Captive quolls that consumed a single toad sausage showed substantially reduced interest in cane toads, interacting with them for less than half the time of their untrained counterparts and showing substantially reduced attack behaviour. We also quantified bait uptake in the field, by both quolls and non-target species. These field trials showed that wild quolls were the most frequent species attracted to the baits, and that approximately 61% of quolls consumed toad-aversion baits when first encountered. Between 40-68% of these animals developed aversion to further bait consumption. Our results suggest that toad-aversion sausages can be used to train wild quolls to avoid cane toads. This opens the possibility for broad-scale quoll training with toad aversion sausages: a technique that may allow wildlife managers to prevent quoll extinctions at a landscape scale.

ecology↗

bioRxiv2017

Extracellular monomeric and aggregated tau efficiently enter human neurons through overlapping but distinct pathways

A current working model is that Alzheimer's disease actively spreads from diseased to healthy neurons, mediated by transfer of extracellular, abnormal, disease-specific forms of the microtubule-associated protein tau. It is currently unclear whether transfer of tau between neurons is a toxic gain-of-function process in dementia, or reflects a constitutive biological process. We report two mechanisms of entry of monomeric tau to neurons: a rapid early dynamin-dependent phase, and a second, slower actin-dependent phase, suggesting that monomeric tau enters neurons via rapid saturable clathrin-mediated endocytosis and also by bulk endocytosis. Aggregated tau entry is independent of actin polymerisation and largely dynamin dependent, consistent with clathrin-mediated endocytosis and distinct from macropinocytosis, the major route for aggregated tau entry reported for non-neuronal cells. Anti-tau antibodies abrogate tau entry into neurons, with tau carrying antibody with it into neurons, indicating that antibody binding is insufficient to prevent neuronal tau entry.

neuroscience↗

bioRxiv2017

Characterising maize viruses associated with maize lethal necrosis symptoms in sub Saharan Africa

Maize lethal necrosis disease (MLN) is an emerging disease in East Africa caused by the introduction of Maize chlorotic mottle virus (MCMV). Recent activity seeking to limit spread of the disease is reliant on effective diagnostics. Traditional diagnostics applied on samples with typical field symptoms of MLN have often given negative results using ELISA or PCR for MCMV and Sugarcane mosaic virus (SCMV). Samples collected in the field with typical MLN symptoms were examined using next generation sequencing (NGS). SCMV was found to be more prevalent than suggested by targeted diagnostics. Additionally, the panel of samples were found to be infected with a range of other viruses, seven of which are described here for the first time. Although not previously identified in the region, Maize yellow mosaic virus (MYMV) was the most prevalent virus after MCMV. The development of targeted diagnostics for emerging viruses is complicated when the extent of field variation is unknown, something that can be negated by using NGS methods. As a result we explored MinION technology which may be more readily deployable in resource poor settings. The results show that this sequencer can diagnose known viruses and future iterations have the potential to identify novel viruses.

microbiology↗

bioRxiv2017

PERTURBATION OF PTEN-PI3K/AKT SIGNALLING IMPAIRED AUTOPHAGY MODULATION IN DYSTROPHIN-DEFICIENT MYOBLASTS

Alteration of single protein regulation has given a massive implication in Muscular Dystrophy pathogenesis. Herein, we investigated the contribution of defected dystrophin that has impaired PI3K/Akt signalling and subsequently reduced autophagy in dystrophin-deficient myoblasts. In this study, dfd13 (dystrophin-deficient) and C2C12 (non-dystrophic) myoblasts were cultured in low mitogen condition for 10 days to induce differentiation. Analyses of protein expression has been done by using immunoblot technique, immunofluorescence and flow cytometry. In our myoblasts differentiation system, the dfd13 myoblasts did not achieved terminal differentiation as fewer myotube formation and fast-myosin heavy chain expression almost not detected. Immunoblot analysis showed that PTEN expression is profoundly increased in dfd13 myoblasts throughout the differentiation day. As a result, the PI3K activity is decreased and has caused serine/threonine kinase Akt inactivation. Both residues; Thr308 and Ser473, on Akt were found not phosphorylated. The mTOR activation by Ser2448 phosphorylation was decreased indicates an impairment for raptor and rictor binding. Unable to form complexes; mTORC1 target protein, p70S6K1 activation was found reduced at the same time explained un-phosphorylated-Akt at Ser473 by rictor-mTORC2. As one of Akt downstream protein, transcription factor FoxO3 regulation was found impaired as it was highly expressed and highly mainly localised in the nucleus in dfd13 towards the end of the differentiation day. This occurrence has caused higher activation of autophagy related genes; Beclin1, Atg5, Atg7, in dfd13 myoblasts. Autophagosome formation was increased as LC3B-I/II showed accumulation upon differentiation. However, ratio of LC3B lipidation and autophagic flux were shown decreased which exhibited dystrophic features. As a conclusion, destabilisation of plasma membrane owing to dystrophin mutation has caused the alteration of plasma membrane protein regulation particularly PTEN-PI3K, thus impaired autophagy modulation that critical for myoblasts development.

cell biology↗

bioRxiv2017

An indicator cell assay for blood-based diagnostics

We have established proof of principle for the Indicator Cell Assay Platform (iCAP), a broadly applicable tool for blood-based diagnostics that uses specifically-selected, standardized cells as biosensors, relying on their innate ability to integrate and respond to diverse signals present in patients blood. To develop an assay, indicator cells are exposed in vitro to serum from case or control subjects and their global differential response patterns are used to train reliable, cost-effective disease classifiers based on a small number of features. In a feasibility study, the iCAP detected pre-symptomatic disease in a murine model of amyotrophic lateral sclerosis (ALS) with 94% accuracy (p-Value=3.81E-6) and correctly identified samples from a murine Huntingtons disease model as non-carriers of ALS. In a preliminary human disease assay, the iCAP detected early stage Alzheimers disease with 72% cross-validated accuracy (p-Value=3.10E-3). For both assays, iCAP features were enriched for disease-related genes, supporting the assays relevance for disease research.

systems biology↗