Alteration of Tropomyosin-binding Properties of Tropomodulin-1 Affects Its Capping Ability and Localization in Skeletal Myocytes

Tropomodulin (Tmod) is an actin-capping protein that binds to the two tropomyosins (TM) at the pointed end of the actin filament to prevent further actin polymerization and depolymerization. Therefore, understanding the role of Tmod is very important when studying actin filament dependent processes such as muscle contraction and intracellular transport. The capping ability of Tmod is highly influenced by TM and is 1000-fold greater in the presence of TM. There are four Tmod isoforms (Tmod1–4), three of which, Tmod1, Tmod3, and Tmod4, are expressed in skeletal muscles. The affinity of Tmod1 to skeletal striated TM (stTM) is higher than that of Tmod3 and Tmod4 to stTM. In this study, we tested mutations in the TM-binding sites of Tmod1, using circular dichroism (CD) and prediction analysis (PONDR). The mutations R11K, D12N, and Q144K were chosen because they decreased the affinity of Tmod1 to stTM, making it similar to that of affinity of Tmod3 and Tmod4 to stTM. Significant reduction of inhibition of actin pointed-end polymerization in the presence of stTM was shown for Tmod1 (R11K/D12N/Q144K) as compared with WT Tmod1. When GFP-Tmod1 and mutants were expressed in primary chicken skeletal myocytes, decreased assembly of Tmod1 mutants was revealed. This indicates a direct correlation between TM-binding and the actin-capping abilities of Tmod. Our data confirmed the hypothesis that assembly of Tmod at the pointed-end of the actin filament depends on its TM-binding affinity.     

Fused in Sarcoma (FUS) Protein Lacking Nuclear Localization Signal (NLS) and Major RNA Binding Motifs Triggers Proteinopathy and Severe Motor Phenotype in Transgenic Mice

Dysfunction of two structurally and functionally related proteins, FUS and TAR DNA-binding protein of 43 kDa (TDP-43), implicated in crucial steps of cellular RNA metabolism can cause amyotrophic lateral sclerosis (ALS) and certain other neurodegenerative diseases. The proteins are intrinsically aggregate-prone and form non-amyloid inclusions in the affected nervous tissues, but the role of these proteinaceous aggregates in disease onset and progression is still uncertain. To address this question, we designed a variant of FUS, FUS 1–359, which is predominantly cytoplasmic, highly aggregate-prone, and lacks a region responsible for RNA recognition and binding. Expression of FUS 1–359 in neurons of transgenic mice, at a level lower than that of endogenous FUS, triggers FUSopathy associated with severe damage of motor neurons and their axons, neuroinflammatory reaction, and eventual loss of selective motor neuron populations. These pathological changes cause abrupt development of a severe motor phenotype at the age of 2.5–4.5 months and death of affected animals within several days of onset. The pattern of pathology in transgenic FUS 1–359 mice recapitulates several key features of human ALS with the dynamics of the disease progression compressed in line with shorter mouse lifespan. Our data indicate that neuronal FUS aggregation is sufficient to cause ALS-like phenotype in transgenic mice.     

Modulating the Intrinsic Disorder in the Cytoplasmic Domain Alters the Biological Activity of the N-Methyl-d-aspartate-sensitive Glutamate Receptor

The NMDA-sensitive glutamate receptor is a ligand-gated ion channel that mediates excitatory synaptic transmission in the nervous system. Extracellular zinc allosterically regulates the NMDA receptor by binding to the extracellular N-terminal domain, which inhibits channel gating. Phosphorylation of the intrinsically disordered intracellular C-terminal domain alleviates inhibition by extracellular zinc. The mechanism for this functional effect is largely unknown. Proline is a hallmark of intrinsic disorder, so we used proline mutagenesis to modulate disorder in the cytoplasmic domain. Proline depletion selectively uncoupled zinc inhibition with little effect on receptor biogenesis, surface trafficking, or ligand-activated gating. Proline depletion also reduced the affinity for a PDZ domain involved in synaptic trafficking and affected small molecule binding. To understand the origin of these phenomena, we used single molecule fluorescence and ensemble biophysical methods to characterize the structural effects of proline mutagenesis. Proline depletion did not eliminate intrinsic disorder, but the underlying conformational dynamics were changed. Thus, we altered the form of intrinsic disorder, which appears sufficient to affect the biological activity. These findings suggest that conformational dynamics within the intrinsically disordered cytoplasmic domain are important for the allosteric regulation of NMDA receptor gating.     

Identification of bifidobacteria isolated from Asian elephant (Elephas maximus)

Bifidobacteria are considered as one of the key genera in intestinal tracts of animals, and their species composition vary depending on the host. The aim of this study was to identify faecal bifidobacteria from Asian elephants (Elephas maximus), housed in Zoological gardens (Ostrava, Czech Republic). Using culturing, bifidobacteria were found in counts 7.60?±?0.56 log CFU/g. Twenty-six pure strains were isolated from faeces of Asian elephant. The isolates were clustered into two groups according to fingerprinting profiles and fermentation characteristic. Bacteria were identified by a combination of MALDI-TOF MS, PCR methods and sequencing as B. boum (12 isolates) and B. adolescentis (14 isolates). Elephant strains showed different fingerprinting profiles than type and collection strains. Since these two species are frequently isolated from gastrointestinal tract of herbivores, they seem to be typical of animals fed plant diets.     

Cationic antioxidants as a powerful tool against mitochondrial oxidative stress

This review describes evidence that mitochondrial reactive oxygen species (mROS) are of great importance under many physiological and pathological conditions. The most demonstrative indications favoring this conclusion originate from recent discoveries of the in vivo effects of mitochondria-targeted antioxidants (MitoQ and SkQs). The latter compounds look promising in treating several incurable pathologies as well as aging.     

The Variance of Identity-by-Descent Sharing in the Wright–Fisher Model

Widespread sharing of long, identical-by-descent (IBD) genetic segments is a hallmark of populations that have experienced recent genetic drift. Detection of these IBD segments has recently become feasible, enabling a wide range of applications from phasing and imputation to demographic inference. Here, we study the distribution of IBD sharing in the Wright–Fisher model. Specifically, using coalescent theory, we calculate the variance of the total sharing between random pairs of individuals. We then investigate the cohort-averaged sharing: the average total sharing between one individual and the rest of the cohort. We find that for large cohorts, the cohort-averaged sharing is distributed approximately normally. Surprisingly, the variance of this distribution does not vanish even for large cohorts, implying the existence of “hypersharing” individuals. The presence of such individuals has consequences for the design of sequencing studies, since, if they are selected for whole-genome sequencing, a larger fraction of the cohort can be subsequently imputed. We calculate the expected gain in power of imputation by IBD and subsequently in power to detect an association, when individuals are either randomly selected or specifically chosen to be the hypersharing individuals. Using our framework, we also compute the variance of an estimator of the population size that is based on the mean IBD sharing and the variance in the sharing between inbred siblings. Finally, we study IBD sharing in an admixture pulse model and show that in the Ashkenazi Jewish population the admixture fraction is correlated with the cohort-averaged sharing.IN isolated populations, even purported unrelated individuals often share genetic material that is identical-by-descent (IBD). Traditionally, the term IBD sharing referred to coancestry at a single site (or autozygosity, in the case of a diploid individual) and was widely investigated as a measure of the degree of inbreeding in a population (Hartl and Clark 2006). Recent years have brought dramatic increases in the quantity and density of available genetic data and, together with new computational tools, these data have enabled the detection of IBD sharing of entire genomic segments (see, e.g., Purcell et al. 2007; Kong et al. 2008; Albrechtsen et al. 2009; Gusev et al. 2009; Browning and Browning 2011; Carr et al. 2011; Brown et al. 2012). The availability of IBD detection tools that are efficient enough to detect shared segments in large cohorts has resulted in numerous applications, from demographic inference (Davison et al. 2009; Palamara et al. 2012) and characterization of populations (Gusev et al. 2012a) to selection detection (Albrechtsen et al. 2010), relatedness detection and pedigree reconstruction (Huff et al. 2011; Kirkpatrick et al. 2011; Stevens et al. 2011; Henn et al. 2012), prioritization of individuals for sequencing (Gusev et al. 2012b), inference of HLA type (Setty et al. 2011), detection of haplotypes associated with a disease or a trait (Akula et al. 2011; Gusev et al. 2011; Browning and Thompson 2012), imputation (Uricchio et al. 2012), and phasing (Palin et al. 2011).Recently, some of us used coalescent theory to calculate several theoretical quantities of IBD sharing under a number of demographic histories. Then, shared segments were detected in real populations, and their demographic histories were inferred (Palamara et al. 2012). Here, we expand upon Palamara et al. (2012) to investigate additional aspects of the stochastic variation in IBD sharing. Specifically, we provide a precise calculation for the variance of the total sharing in the Wright–Fisher model, either between a random pair of individuals or between one individual and all others in the cohort.Understanding the variation in IBD sharing is an important theoretical characterization of the Wright–Fisher model, and additionally, it has several practical applications. For example, it can be used to calculate the variance of an estimator of the population size that is based on the sharing between random pairs. In a different domain, the variance in IBD sharing is needed to accurately assess strategies for sequencing study design, specifically, in prioritization of individuals to be sequenced. This is because imputation strategies use IBD sharing between sequenced individuals and genotyped, not-sequenced individuals to increase the number of effective sequences analyzed in the association study (Palin et al. 2011; Gusev et al. 2012b; Uricchio et al. 2012).In the remainder of this article, we first review the derivation of the mean fraction of the genome shared between two individuals (Palamara et al. 2012). We then calculate the variance of this quantity, using coalescent theory with recombination. We provide a number of approximations, one of which results in a surprisingly simple expression, which is then generalized to a variable population size and to the sharing of segments in a length range. We also numerically investigate the pairwise sharing distribution and provide an approximate fit. We then turn to the average total sharing between each individual and the entire cohort. We show that this quantity, which we term the cohort-averaged sharing, is approximately normally distributed, but is much wider than naively expected, implying the existence of hypersharing individuals. We consider several applications: the number of individuals needed to be sequenced to achieve a certain imputation power and the implications to disease mapping, inference of the population size based on the total sharing, and the variance of the sharing between siblings. We finally calculate the mean and the variance of the sharing in an admixture pulse model and show numerically that admixture results in a broader than expected cohort-averaged sharing. Therefore, large variance of the cohort-averaged sharing can indicate admixture. In the Ashkenazi Jewish population, we show that the cohort-averaged sharing is strongly anticorrelated with the fraction of European ancestry.