Sarcosin (Krp1) in skeletal muscle differentiation: gene expression profiling and knockdown experiments

SARCOSIN, also named Krp1, has been identified as a protein exclusively expressed in striated muscle tissue. Here we report on the role of SARCOSIN in skeletal muscle development and differentiation. We demonstrate, by means of whole-mount in situ hybridization, that Sarcosin mRNA is expressed in the myotome part of the mature somites in mouse embryos from embryonic day 9.5 onwards. Sarcosin is not expressed in the developing heart at these embryonic stages, and in adult tissues the mRNA expression levels are five times lower in the heart than in skeletal muscle. SARCOSIN protein partially co-localizes with the M-band protein myomesin and between and below laterally fusing myofibrils in adult skeletal muscle tissue. RNA interference mediated knock-down of SARCOSIN in the C2C12 myoblast cell line appeared to be stimulatory in the early phase of differentiation, but inhibitory at a later phase of differentiation.     

Concordance analysis for QTL detection in dairy cattle: a case study of leg morphology

Background

The present availability of sequence data gives new opportunities to narrow down from QTL (quantitative trait locus) regions to causative mutations. Our objective was to decrease the number of candidate causative mutations in a QTL region. For this, a concordance analysis was applied for a leg conformation trait in dairy cattle. Several QTL were detected for which the QTL status (homozygous or heterozygous for the QTL) was inferred for each individual. Subsequently, the inferred QTL status was used in a concordance analysis to reduce the number of candidate mutations.

Methods

Twenty QTL for rear leg set side view were mapped using Bayes C. Marker effects estimated during QTL mapping were used to infer the QTL status for each individual. Subsequently, polymorphisms present in the QTL regions were extracted from the whole-genome sequences of 71 Holstein bulls. Only polymorphisms for which the status was concordant with the QTL status were kept as candidate causative mutations.

Results

QTL status could be inferred for 15 of the 20 QTL. The number of concordant polymorphisms differed between QTL and depended on the number of QTL statuses that could be inferred and the linkage disequilibrium in the QTL region. For some QTL, the concordance analysis was efficient and narrowed down to a limited number of candidate mutations located in one or two genes, while for other QTL a large number of genes contained concordant polymorphisms.

Conclusions

For regions for which the concordance analysis could be performed, we were able to reduce the number of candidate mutations. For part of the QTL, the concordant analyses narrowed QTL regions down to a limited number of genes, of which some are known for their role in limb or skeletal development in humans and mice. Mutations in these genes are good candidates for QTN (quantitative trait nucleotides) influencing rear leg set side view.     

The role of RNA splicing factor PTBP1 in neuronal development

Alternative pre-mRNA splicing, which produces various mRNA isoforms with distinct structures and functions from a single gene, is regulated by specific RNA-binding proteins and is an essential method for regulating gene expression in mammals. Recent studies have shown that abnormal change during neuronal development triggered by splicing mis-regulation is an important feature of various neurological diseases. Polypyrimidine tract binding protein 1 (PTBP1) is a kind of RNA-binding proteins with extensive biological functions. As a well-known splicing regulator, it affects the neuronal development process through its involvement in axon formation, synaptogenesis, and neuronal apoptosis, according to the most recent studies. Here, we summarized the mechanism of alternative splicing, structure and function of PTBP1, and the latest research progress on the role of alternative splicing events regulated by PTBP1 in axon formation, synaptogenesis and neuronal apoptosis, to reveal the mechanism of PTBP1-regulated changes in neuronal development process.     

Rodent eradications as ecosystem experiments: a case study from the Mexican tropics

For effective and efficient pest management it is essential to understand the ecology of the target species and recipient ecosystems. The use of rodent eradication as a restoration tool is well established in temperate regions, but less common in the tropics, presenting an opportunity to undertake scientific learning in tandem with rodent eradications. On a dry tropical archipelago, we used a Before-After-Control-Impact framework to document (1) fluctuations in the abundance and demography of invasive Rattus rattus and Mus musculus on three different islands, (2) the trophic niche of all three invasive rodent populations, and (3) changes in the invertebrate community before and after rodent eradication, also comparing with two rodent free islands. While rat density was high and relatively stable throughout the year, the two mouse populations greatly differed in body size and seasonal dynamics, despite their proximity. The rodents in all three populations were generalist and opportunistic feeders, although stable isotope analyses results indicated major differences among them, driven by food availability and rodent species. Seasonal fluctuations in invertebrate communities depended on rodent invasion status, but recovery in the invertebrate communities one year after rodent removal was limited for all islands. Predictions for other tropical ecosystem biomes require long-term research on more tropical islands. Improving our understanding of island and species-specific contexts of rodent eradications can advance island restoration projects and assist the selection of indicator species for ecosystem recovery.     

Developmental mechanisms of macroevolutionary change in the tetrapod axis: A case study of Sauropterygia

Understanding how developmental processes change on macroevolutionary timescales to generate body plan disparity is fundamental to the study of vertebrate evolution. Adult morphology of the vertebral column directly reflects the mechanisms that generate vertebral counts (somitogenesis) and their regionalisation (homeotic effects) during embryonic development. Sauropterygians were a group of Mesozoic marine reptiles that exhibited an extremely high disparity of presacral vertebral/somite counts. Using phylogenetic comparative methods, we demonstrate that somitogenesis and homeotic effects evolved in a co‐ordinated way among sauropterygians, contrasting with the wider pattern in tetrapods, in which somitogenetic and homeotic shifts are uncorrelated. Changes in sauropterygian body proportions were primarily enabled by homeotic shifts, with a lesser, but important, contribution from differences in postpatterning growth among somites. High body plan plasticity was present in Triassic sauropterygians and was maintained among their Jurassic and Cretaceous descendants. The extreme disparity in the body plan of plesiosaurian sauropterygians did not result from accelerated rates of evolutionary change in neck length, but instead reflect this ancestral versatility of sauropterygian axial development. Our results highlight variation in modes of axial development among tetrapods, and show that heterogeneous statistical models can uncover novel macroevolutionary patterns for animal body plans and the developmental mechanisms that control them.     

Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation

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Selection experiments and the study of phenotypic plasticity1

Abstract Laboratory selection experiments are powerful tools for establishing evolutionary potentials. Such experiments provide two types of information, knowledge about genetic architecture and insight into evolutionary dynamics. They can be roughly classified into two types: (1) artificial selection in which the experimenter selects on a focal trait or trait index, and (2) quasi‐natural selection in which the experimenter establishes a set of environmental conditions and then allows the population to evolve. Both approaches have been used in the study of phenotypic plasticity. Artificial selection experiments have taken various forms including: selection directly on a reaction norm, selection on a trait in multiple environments, and selection on a trait in a single environment. In the latter experiments, evolution of phenotypic plasticity is investigated as a correlated response. Quasi‐natural selection experiments have examined the effects of both spatial and temporal variation. I describe how to carry out such experiments, summarize past efforts, and suggest further avenues of research.     

Antioxidant properties of EPC-K1: a study on mechanisms.

Scavenging effects of L-ascorbic acid 2-[3,4-dihydro-2,5,7,8- tetramethyl-2-(4,8,12-trimethytridecyl)-2H-1-benzopyran- 6-yl-hydrogen phosphate] potassium salt (EPC-K1) on hydroxyl radicals, alkyl radicals and lipid radicals were studied with ESR spin trapping techniques. The inhibition effects of EPC-K1 on lipid peroxidation were assessed by TBA assay. The kinetics of EPC-K1 reacting with hydroxyl radicals and linoleic acid radicals were studied by pulse radiolysis. The active site of EPC-K1 and the structure-antioxidative activity relationships were discussed. The superoxide radicals scavenging capacity of the brain homogenate of EPC-K1-treated rats was measured. The results revealed that in comparison with Trolox and vitamin C, EPC-K1 showed better overall antioxidative capacity in vitro and in vivo. EPC-K1 was a moderate scavenger on hydroxyl radicals and alkyl radicals, a potent scavenger on lipid radicals, and an effective inhibitor on lipid peroxidation. EPC-K1 could react with hydroxyl radicals with a rate constant of 7.1 x 10(8) dm3 mol-1 s-1 and react with linoleic acid radicals with a rate constant of 2.8 x 10(6) dm3 mol-1 s-1. The active site of EPC-K1 was the enolic hydroxyl group. After administration of EPC-K1, the ability of rat brain to scavenge superoxide radicals was significantly increased. The potent scavenging effects of EPC-K1 on both hydrophilic and hydrophobic radicals were relevant with its molecular structure, which consisted of both hydrophilic and hydrophobic groups.     

新月形沙丘稳定性机理——以甘肃河西沙区为例

新月形沙丘是一种重要的沙丘类型,一般存在于绿洲边缘。研究新月形沙丘的稳定性,对于揭示绿洲缘的风沙运动规律有重要学术价值,而到目前新月形沙丘的稳定性还是沙漠生态学领域中一个的尚未解决的科学问题。以河西沙区新月形沙丘为例,通过调查其分布环境、测定沙丘各部位风速和风蚀积沙等,分析了新月形沙丘顶部稳定机理。结果表明:1)甘肃河西沙区的新月形沙丘分布在沙漠边缘的下风向,一般为斑块状分布。分布区域为平坦的沙粘质或沙砾质滩地,丘间地较为开阔且具有明显的主风向。2)主风向(NW)过程是新月形沙丘顶点与沙脊线重合的过程,也是新月形沙丘前移和高度降低的过程;反主风向(SE)过程是新月形沙丘顶点与沙脊线分离的过程,也是新月形沙丘背风坡上部风蚀与沙丘增高的过程。3)新月形沙丘越高大,两翼越长、夹角越小。4)较为开阔的前后滩地是新月形沙丘及新月形沙丘链存在所必须的环境条件,相对单一的主风向是新月形沙丘及新月形沙丘链维持其稳定性的关键因子,反向风及两翼的廊道效应是新月形沙丘增高增大的关键因子,主、反两个方向的风速及其分布频率是控制该区域新月形沙丘及新月形沙丘链高度的限制因子。     

The mechanisms of interference competition: two experiments on foraging waders

Models of population dynamics that include interference competitionhave often been applied to foraging waders and less so to otherforagers, even though these models are, in principle, generallyapplicable. At present, however, it is still unclear whetherinterference competition is of importance for foraging waders.To support this idea experimental evidence and knowledge ofthe mechanisms underlying interference effects are required.We experimentally determined the relationship between foragerdensity and foraging success in two wader species: the red knot(Calidris canutus) and the ruddy turnstone (Arenaria interpres).With each of the two species, we conducted an experiment consistingof 300 one-min trials. In these trials we scored the behaviorand the foraging success of focal individuals at specific combinationsof bird and prey density. Irrespective of prey density, individualsof both species discovered fewer prey items at higher bird densities.Despite this, only in turnstones did intake rates decline withincreasing bird density. Knots compensated for a lower prey-discoveryrate by rejecting fewer prey items at higher bird densities.In knots, bird density had a complex, nonmonotonic effect onthe time spent vigilant and searching. In turnstones the maineffect of increased bird density was a reduction in the prey-encounterrate, that is, the reward per unit search time. Effects on thetime spent vigilant and the time spent searching were less pronouncedthan in knots. Thus, the mechanistic basis of the effects ofbird density was complex for each of the two species and differedbetween them.     

Conceptual-level workflow modeling of scientific experiments using NMR as a case study

Background  

Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration.     

Niche-based mechanisms operating within extreme habitats: a case study of subterranean amphipod communities

It has been suggested that both niche-based and neutral mechanisms are important for biological communities to evolve and persist. For communities in extreme and isolated environments such as caves, theoretical and empirical considerations (low species turnover, high stress, strong convergence owing to strong directional selection) predict neutral mechanisms and functional equivalence of species. We tested this prediction using subterranean amphipod communities from caves and interstitial groundwater. Contrary to expectations, functional morphological diversity within communities in both habitats turned out to be significantly higher than the null model of randomly assembled communities. This suggests that even the most extreme, energy-poor environments still maintain the potential for diversification via differentiation of niches.     

Comparing field and microcosm experiments: a case study on methano- and methylo-trophic bacteria in paddy soil

Methane-oxidising bacteria (MOB) play an important role in the reduction of methane emissions from rice agriculture. In rice fields, they are subjected to many environmental and field management parameters, which may have a significant impact on their community composition. To study this in greater detail, the community structure of methano- and methylo-trophic bacteria was investigated in a rice field in northern Italy during the summer 1999 and compared to a microcosm study described previously. We used PCR-based denaturing gradient gel electrophoresis applying 16S rDNA (9alpha and 10gamma) and mxaF (methanol-dehydrogenase) primer sets. In parallel, population size and activity of MOB were determined. This study provides the first comprehensive investigation of different compartments (bulk soil, rhizosphere, rhizoplane, and homogenate) throughout an entire rice-growing season in the field. Lower cell numbers of MOB were detected in the field compared to the microcosms, possibly due to lower CH4 concentrations in the soil pore water. In both studies, growth of MOB occurred predominantly at the root surface (rhizoplane) and in the root (homogenate), whereas cell numbers in bulk soil showed only minor changes throughout the season. Molecular analysis detected only few changes in alpha-proteobacterial methylotrophs during the season, whereas a higher variability was detected in gamma-proteobacteria. Nevertheless, the sequences of electrophoretic bands showed that the diversity in the field study and in the microcosms was comparable. Activity patterns of MOB and the population structure of methylotrophic bacteria agreed well between both studies, even though the detected quantities differed. Extrapolations of microcosm data to the field scale are thus possible, but should be used carefully when concerning quantitative changes.     

Removal experiments to test mechanisms of plant succession in oldfields

We investigated the effects of total (TR) or partial (PR) removal of the above-ground biomass of the dominant species on early successional trends in two oldfields in central New Jersey, USA. Our objective was to assess the occurrence of facilitation, tolerance, or inhibition as mechanisms of species replacement in the fields studied. In a 2nd-yr oldfield dominated by Ambrosia artemisiifolia, floristic composition and distribution of species cover changed markedly between the 2nd and the 3rd yr, regardless of the removal treatment. In both TR and PR plots and in control plots dominance shifted from an annual (A. artemisiifolia) to a biennial (Erigeron annuus). This indicates that the presence of the annual dominant is not necessary to promote this successional replacement, and therefore facilitation can be ruled out. Most species present in the 3rd-yr community were late summer and fall invaders which were not initially present. In a 7-yr oldfield dominated by Solidago canadensis, a clonal perennial, very little change in the distribution of species cover could be detected between years. Overall physiognomy remained the same, but there was a gradual change in floristic composition. In this field, TR and PR treatments enhanced vegetational change by allowing the increase in cover of suppressed understory species. Both inhibition and tolerance mechanisms may be involved in the pattern of vegetational change in this field. Finally, we stress that the mechanisms of species replacement operating in early secondary succession are dependent on structural and life history characteristics of the species assemblage on a particular site.     

林木共生菌系统及其作用机制——以杨树为例

杨树（Populus）是重要造林树种,也是研究林木基础生物学性状的模式材料。不仅如此,杨树可与多种细菌（内生细菌、内生固氮菌和根际促生菌）和真菌（外生菌根真菌、丛枝菌根真菌和内生真菌）类群建立共生关系,为揭示树木和微生物之间的互惠共生机制提供了理想模型。这些共生菌能积极调控林木生长发育、营养吸收和生理生态过程。目前在杨树-双色蜡蘑（Laccaria bicolor）形成的外生菌根发育、提高杨树耐盐、耐重金属的生理与分子机制、叶片内生真菌群落结构与病害发生、菌根辅助细菌和菌丝内共生细菌-真菌-杨树形成的三重跨界共生等方面取得多项突破。近年来,一批模式草本植物微生物组（microbiome）计划相继实施,对共生菌群落结构和功能的认识有了革命性的进步。以美洲黑杨、毛果杨和胶杨为代表的林木微生物组研究也已启动,表明宿主基因型和环境因子可显著影响共生菌群落结构与物种组成;在根际（rhizosphere）和内生（endosphere）环境存在结构和功能迥异的菌群。另一方面,以根系为诱饵,通过宿主表型来推测菌群功能的反向钓鱼策略将推动林木根际微生物工程研究,为揭示杨树-微生物群落的相互关系、菌群进化搭建了研究模型。总之,深入认识多元微生物对林木表型和生理代谢的表观遗传学调控机制将为今后创制新型菌剂并用于高效育苗和抗性育种提供新的思路,具有重要的科学意义和应用价值。     

Morpholino gene knockdown in adult Fundulus heteroclitus: role of SGK1 in seawater acclimation

The Atlantic killifish (Fundulus heteroclitus) is an environmental sentinel organism used extensively for studies on environmental toxicants and salt (NaCl) homeostasis. Previous research in our laboratory has shown that rapid acclimation of killifish to seawater is mediated by trafficking of CFTR chloride channels from intracellular vesicles to the plasma membrane in the opercular membrane within the first hour in seawater, which enhances chloride secretion into seawater, thereby contributing to salt homeostasis. Acute transition to seawater is also marked by an increase in both mRNA and protein levels of serum glucocorticoid kinase 1 (SGK1) within 15 minutes of transfer. Although the rise in SGK1 in gill and its functional analog, the opercular membrane, after seawater transfer precedes the increase in membrane CFTR, a direct role of SGK1 in elevating membrane CFTR has not been established in vivo. To test the hypothesis that SGK1 mediates the increase in plasma membrane CFTR we designed two functionally different vivo-morpholinos to knock down SGK1 in gill, and developed and validated a vivo-morpholino knock down technique for adult killifish. Injection (intraperitoneal, IP) of the splice blocking SGK1 vivo-morpholino reduced SGK1 mRNA in the gill after transition from fresh to seawater by 66%. The IP injection of the translational blocking and splice blocking vivo-morpholinos reduced gill SGK1 protein abundance in fish transferred from fresh to seawater by 64% and 53%, respectively. Moreover, knock down of SGK1 completely eliminated the seawater induced rise in plasma membrane CFTR, demonstrating that the increase in SGK1 protein is required for the trafficking of CFTR from intracellular vesicles in mitochondrion rich cells to the plasma membrane in the gill during acclimation to seawater. This is the first report of the use of vivo-morpholinos in adult killifish and demonstrates that vivo-morpholinos are a valuable genetic tool for this environmentally relevant model organism.     

Design of antiandrogens and their mechanisms of action: a case study (anandron)

The design of a new drug is conditioned by knowledge of the biochemical mechanisms involved in the etiology of the disease to be treated. With regard to endocrine pathologies, such knowledge can be obtained in the clinic from systematic assays of urinary and plasma hormones, enzyme activities and target tissue receptor concentrations. The present paper describes the results of our assays of plasma 3 alpha-androstanediol glucuronide, 5 alpha-reductase and androgen receptor in prostate cancer patients. The activity of the nonsteroid antiandrogen anandron is discussed in relation to these parameters: anandron may inhibit slightly adrenal androgen biosynthesis but, in particular, counters the action of these adrenal androgens on the prostate. It does not inhibit rat prostate 5 alpha-reductase activity but interacts with androgen receptor to exert an antiandrogen action.