Rapid communication: Mapping of the \u3ci\u3eCa\u3csup\u3e2+\u3c/sup\u3e ATPase of fast twitch 1 skeletal muscle sarcoplasmic reticulum (ATP2A1)\u3c/i\u3e gene to porcine chromosome 3

Locus Name. Ca2+ ATPase of fast twitch 1 skeletal muscle sarcoplasmic reticulum. Species. Sus scrofa. Locus Symbol. ATP2A1. Source of Primers. Two sets of PCR primers were designed based on human ATP2A1 sequences (Gen- Bank accession numbers U96773 and U96777) available in the GenBank database. Using pig genomic DNA as a template we used set A primers to amplify approximately 1,100 bp spanning exon 1 to exon 2 and set B primers to amplify 1,200 bp gene segment covering some of exon 8 through part of exon 9. These sequences were deposited in GenBank, accession number AY027797-AY027799

Rapid communication: Mapping of the Ca2+ ATPase of fast twitch 1 skeletal muscle sarcoplasmic reticulum (ATP2A1) gene to porcine chromosome 3

Locus Name. Ca2+ ATPase of fast twitch 1 skeletal muscle sarcoplasmic reticulum. Species. Sus scrofa. Locus Symbol. ATP2A1. Source of Primers. Two sets of PCR primers were designed based on human ATP2A1 sequences (Gen- Bank accession numbers U96773 and U96777) available in the GenBank database. Using pig genomic DNA as a template we used set A primers to amplify approximately 1,100 bp spanning exon 1 to exon 2 and set B primers to amplify 1,200 bp gene segment covering some of exon 8 through part of exon 9. These sequences were deposited in GenBank, accession number AY027797-AY027799

Mapping and Investigation of Two Novel Candidate Genes for Growth and Meat Quality traits in the Pig

Two new candidate genes for growth and meat quality traits were studied. The porcine beta-tropomyosin (TPM2) and the agouti-related protein (AGRP) genes were chosen based on their presumed role in growth and meat quality traits. These genes were genetically mapped and were linked to several markers on porcine chromosomes (SSC) 1 and 6, respectively. Both genes also were physically mapped using a pig/rodent somatic cell hybrid panel. The physical locations of the genes are consistent with linkage results and previous chromosome painting results indicating conserved (similar) regions between human and pig chromosomes. Association studies of the AGRP and TPM2 polymorphisms with growth and meat quality traits in commercial pig populations provided preliminary evidence that an AGRP polymorphism may be associated with variation in several traits of interest for pig breedin

Global, regional, and national levels of maternal mortality, 1990–2015 : a systematic analysis for the Global Burden of Disease Study 2015

Background In transitioning from the Millennium Development Goal to the Sustainable Development Goal era, it is imperative to comprehensively assess progress toward reducing maternal mortality to identify areas of success, remaining challenges, and frame policy discussions. We aimed to quantify maternal mortality throughout the world by underlying cause and age from 1990 to 2015. Methods We estimated maternal mortality at the global, regional, and national levels from 1990 to 2015 for ages 10–54 years by systematically compiling and processing all available data sources from 186 of 195 countries and territories, 11 of which were analysed at the subnational level. We quantifi ed eight underlying causes of maternal death and four timing categories, improving estimation methods since GBD 2013 for adult all-cause mortality, HIVrelated maternal mortality, and late maternal death. Secondary analyses then allowed systematic examination of drivers of trends, including the relation between maternal mortality and coverage of specifi c reproductive health-care services as well as assessment of observed versus expected maternal mortality as a function of Socio-demographic Index (SDI), a summary indicator derived from measures of income per capita, educational attainment, and fertility. Findings Only ten countries achieved MDG 5, but 122 of 195 countries have already met SDG 3.1. Geographical disparities widened between 1990 and 2015 and, in 2015, 24 countries still had a maternal mortality ratio greater than 400. The proportion of all maternal deaths occurring in the bottom two SDI quintiles, where haemorrhage is the dominant cause of maternal death, increased from roughly 68% in 1990 to more than 80% in 2015. The middle SDI quintile improved the most from 1990 to 2015, but also has the most complicated causal profi le. Maternal mortality in the highest SDI quintile is mostly due to other direct maternal disorders, indirect maternal disorders, and abortion, ectopic pregnancy, and/or miscarriage. Historical patterns suggest achievement of SDG 3.1 will require 91% coverage of one antenatal care visit, 78% of four antenatal care visits, 81% of in-facility delivery, and 87% of skilled birth attendance. Interpretation Several challenges to improving reproductive health lie ahead in the SDG era. Countries should establish or renew systems for collection and timely dissemination of health data; expand coverage and improve quality of family planning services, including access to contraception and safe abortion to address high adolescent fertility; invest in improving health system capacity, including coverage of routine reproductive health care and of more advanced obstetric care—including EmOC; adapt health systems and data collection systems to monitor and reverse the increase in indirect, other direct, and late maternal deaths, especially in high SDI locations; and examine their own performance with respect to their SDI level, using that information to formulate strategies to improve performance and ensure optimum reproductive health of their population.GBD 2015 Maternal Mortality Collaborators ...Nicholas J Kassebaum ... Azmeraw T Amare ... Liliana G Ciobanu ... James Hancock ... Ratilal Lalloo ... Yohannes Adama Melaku ... John Nelson Opio ... G A Tessema ... et.al

Protocol for single-cell isolation and genome amplification of environmental microbial eukaryotes for genomic analysis

We describe environmental microbial eukaryotes (EMEs) sample collection, single-cell isolation, lysis, and genome amplification, followed by the rDNA amplification and OTU screening for recovery of high-quality species-specific genomes for de novo assembly. These protocols are part of our pipeline that also includes bioinformatic methods. The pipeline and its application on a wide range of phyla of different sample complexity are described in our complementary paper. In addition, this protocol describes optimized lysis, genome amplification, and OTU screening steps of the pipeline. For complete details on the use and execution of this protocol, please refer to Ciobanu et al. (2021)

Computing with cells: membrane systems - some complexity issues.

Membrane computing is a branch of natural computing which abstracts computing models from the structure and the functioning of the living cell. The main ingredients of membrane systems, called P systems, are (i) the membrane structure, which consists of a hierarchical arrangements of membranes which delimit compartments where (ii) multisets of symbols, called objects, evolve according to (iii) sets of rules which are localised and associated with compartments. By using the rules in a nondeterministic/deterministic maximally parallel manner, transitions between the system configurations can be obtained. A sequence of transitions is a computation of how the system is evolving. Various ways of controlling the transfer of objects from one membrane to another and applying the rules, as well as possibilities to dissolve, divide or create membranes have been studied. Membrane systems have a great potential for implementing massively concurrent systems in an efficient way that would allow us to solve currently intractable problems once future biotechnology gives way to a practical bio-realization. In this paper we survey some interesting and fundamental complexity issues such as universality vs. nonuniversality, determinism vs. nondeterminism, membrane and alphabet size hierarchies, characterizations of context-sensitive languages and other language classes and various notions of parallelism

Stochastic Simulation of Process Calculi for Biology

Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed, many of which are expressive enough to generate unbounded numbers of molecular species and reactions. As a result of this expressiveness, such calculi cannot rely on standard reaction-based simulation methods, which require fixed numbers of species and reactions. Rather than implementing custom stochastic simulation algorithms for each process calculus, we propose to use a generic abstract machine that can be instantiated to a range of process calculi and a range of reaction-based simulation algorithms. The abstract machine functions as a just-in-time compiler, which dynamically updates the set of possible reactions and chooses the next reaction in an iterative cycle. In this short paper we give a brief summary of the generic abstract machine, and show how it can be instantiated with the stochastic simulation algorithm known as Gillespie's Direct Method. We also discuss the wider implications of such an abstract machine, and outline how it can be used to simulate multiple calculi simultaneously within a common framework.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Topological defects in spinor condensates

We investigate the structure of topological defects in the ground states of spinor Bose-Einstein condensates with spin F=1 or F=2. The type and number of defects are determined by calculating the first and second homotopy groups of the order-parameter space. The order-parameter space is identified with a set of degenerate ground state spinors. Because the structure of the ground state depends on whether or not there is an external magnetic field applied to the system, defects are sensitive to the magnetic field. We study both cases and find that the defects in zero and non-zero field are different.Comment: 10 pages, 1 figure. Published versio

A 16.7 kb deletion in \u3ci\u3eSipa1l3\u3c/i\u3e is associated with juvenile cataract in mice

Congenital or juvenile cataract is a disease condition in which opacification of the lenses is present at birth or manifests early in life. It has been attributed to different monogenic factors with a high degree of heterogeneity and is often studied using mouse models. A spontaneous mutation was identified in a mouse line selected for heat loss that influenced lens formation and resulted in juvenile cataracts in mice homozygous for the recessive allele. Genetic dissection of this selection line by combining high-density genotypes and homozygosity mapping uncovered a 906 kb fragment on MMU7 encompassing 21 SNPs split into two groups of con-secutive, homozygous segments specific to the cataract phenotype. Haplotype analysis revealed a 197.5 kb segment unique to cataract-affected mice that in-cluded a single known transcript consisting of the first 14 exons of Sipa1l3. In this region, we discovered a deletion of 1114 bp at the mRNA level, spanning four coding exons, predicted to produce a truncated Sipa1l3 protein lacking a portion of a Rap-GAP domain and two other potentially vital domains. At the genome level, the deletion consisted of 16,733 bp. Genotyping across different samples confirmed that only affected mice were homozygous for the deletion and normal mice were either heterozygous or homozygous for the wild-type allele. Further studies will be required to determine the impact of the truncated Sipa1l3 domains on eye development

Towards the Automated Verification of Weibull Distributions for System Failure Rates

Weibull distributions can be used to accurately model failure behaviours of a wide range of critical systems such as on-orbit satellite subsystems. Markov chains have been used extensively to model reliability and performance of engineering systems or applications. However, the exponentially distributed sojourn time of Continuous-Time Markov Chains (CTMCs) can sometimes be unrealistic for satellite systems that exhibit Weibull failures. In this paper, we develop novel semi-Markov models that characterise failure behaviours, based on Weibull failure modes inferred from realistic data sources. We approximate and encode these new models with CTMCs and use the PRISM probabilistic model checker. The key bene t of this integration is that CTMC-based model checking tools allow us to automatically and e ciently verify reliability properties relevant to industrial critical systems