Sex alteration in soft-shell clams (Mya arenaria) in an intertidal zone of the Saint Lawrence river (Quebec,Canada)

The purpose of this study was to verify whether any changes in sex ratio might occur in soft-shell clams (Mya arenaria) located in an intertidal harbor zone located at the mouth of the Saguenay Fjord in the Saint Lawrence estuary (Baie Sainte-Catherine (BSC), Québec, Canada) likely to be contaminated by organotin compounds. Bivalves were harvested at the BSC harbor site and from two reference sites. Condition index (weight to length ratio), gonado-somatic index, sex ratio, vitellin-like proteins, organotin concentrations in gonad tissue, maturation stages of the gonads, the number of estradiol-17beta binding sites and the capacity of female gonad extracts to produce estradiol-17beta were determined in collected animals. Results showed that sex ratio in clams was significantly skewed toward males. Moreover, the condition and gonad-somatic indices, vitellin-like proteins in female gonads and the capacity of female gonads to produce estradiol-17beta were significantly reduced at the harbor site with respect to the reference sites. Maturation status of male gonads was clearly delayed at the harbor site. Additionally, gonad tissue contained tributyltin (TBT) at an average level of 109+/-18 ngSn/gdry wt. at the harbor site while organotins were not detected from the reference sites. Finally, female gonads had a higher number of unoccupied estradiol binding sites at the harbor site indicating low levels of this steroid in this tissue. Overall, this paper is first to report that clams collected in the vicinity of a TBT contaminated harbor are subject to masculinizing effects which seems to be consistent with biological effects that organotins are known to exert toward some other marine invertebrates.     

F9 embryonal carcinoma cells engineered for tamoxifen-dependent Cre-mediated site-directed mutagenesis and doxycycline-inducible gene expression

The study of gene functions in complex genetic environments such as mammalian cells would greatly benefit from systems allowing a tight control of gene expression. The tetracycline-inducible gene expression system and the site-specific Cre/loxP recombination system have gained increasing popularity for conditional expression and gene disruption. To facilitate the analysis of gene functions in a cell autonomous system, we have established an F9 murine embryonal carcinoma cell line, constitutively expressing both the doxycycline-controlled transactivator rtTA and the tamoxifen-dependent Cre recombinase Cre-ER(T). The expression of a reporter gene placed under the control of tetracycline operators was induced about 1000-fold by doxycycline, and tamoxifen-induced excision of a loxP-flanked DNA segment occurred in all cells. This genetically engineered cell line, which allows, upon simple ligand addition, sophisticated genetic manipulations, such as sequential inactivation of loxP-flanked genes, and tightly controlled reexpression of their cDNAs, should be a valuable tool for studying mammalian gene functions.     

Mutants provide evidence of the importance of glycosydic chains in the activation of lipase 1 from Candida rugosa

Sequence analysis of Candida rugosa lipase 1 (LIP1) predicts the presence of three N-linked glycosylation sites at asparagine 291, 314, 351. To investigate the relevance of sugar chains in the activation and stabilization of LIP1, we directed site mutagenesis to replace the above mentioned asparagine with glutamine residues. Comparison of the activity of mutants with that of the wild-type (wt) lipase indicates that both 314 and 351 Asn to Gln substitutions influence, although at a different extent, the enzyme activity both in hydrolysis and esterification reactions, but they do not alter the enzyme water activity profiles in organic solvents or temperature stability. Introduction of Gln to replace Asn351 is likely to disrupt a stabilizing interaction between the sugar chain and residues of the inner side of the lid in the enzyme active conformation. The effect of deglycosylation at position 314 is more difficult to explain and might suggest a more general role of the sugar moiety for the structural stability of lipase 1. Conversely, Asn291Gln substitution does not affect the lipolytic or the esterase activity of the mutant that behaves essentially as the wt enzyme. This observation supports the hypothesis that changes in activity of Asn314Gln and Asn351Gln mutants are specifically due to deglycosylation.     

CHO细胞基因组NW-003614092.1内稳定表达位点的发现*

目的:获得中国仓鼠卵巢细胞(Chinese hamster ovary cells,CHO)内稳定表达位点信息,为构建重组蛋白CHO稳定表达株、缩短研发时间线提供信息明确的稳定位点。方法:对慢病毒随机整合Zsgreen1基因的具有潜在稳定表达位点的CHO-K1-1d2细胞株进行连续传代培养,验证表达稳定性;通过染色体步移分析慢病毒载体整合位点,并利用CRISPR/Cas9技术验证位点的可编辑性。结果:CHO-K1-1d2细胞在连续贴壁培养20代、悬浮培养50代过程中,能够100 %发绿色荧光,且荧光强度稳定,能够稳定表达Zsgreen1蛋白;染色体步移分析测序结果表明,CHO-K1-1d2细胞中慢病毒载体整合于CHO细胞基因组NW-003614092.1上第1 159 463与1 159 467碱基间;共转染sgRNA与Cas9质粒后,测序结果表明,该位点可被CRISPR/Cas9技术编辑。结论:CHO细胞基因组NW-003614092.1内存在一个信息明确的、能够被CRISPR/Cas9技术编辑的稳定表达位点。     

CHIH-DFT determination of the molecular structure infrared spectra,UV spectra and chemical reactivity of three antitubercular compounds: Rifampicin,Isoniazid and Pyrazinamide

Three of the most frequent antitubercular agents employed against Mycobacterium tuberculosis are: Rifampicin, Isoniazid and Pyrazinamide. It has been proven that the use of these antitubercular agents together, shortens the treatment period from 12–18 months to 6 months [1]. In this work we use a new Density Functional Theory chemistry model called CHIH-DFT (Chihuahua-Heterocycles-Density Functional Theory) that reflects the mixture of Hartree Fock exchange and DFT exchange, according to a mixing parameter based on empirical rules suited for heterocyclic systems. This new chemistry model was used to calculate the molecular structure of these antitubercular compounds, as well as their infrared, UV spectra, chemical reactivity and electronic properties. The UV and infrared spectra were obtained by experimental techniques. The calculated molecular structure, UV and IR spectra values from CHIH-DFT were compared with experimentally obtained values and theoretical studies. These results are in good agreement with experimental and theoretical studies. We also predicted using the relative electrophilicity and relative nucleophilicity concepts as defined by Roy et al. [2] the chemical active sites for the three antitubercular compounds as well as their electronegativity, ionization potential, electron affinity, hardness, dipole moment, E_HOMO-E_LUMO gap energy, etc.      

Molecular simulations study of novel 1,4‐dihydropyridines derivatives with a high selectivity for Cav3.1 calcium channel

1,4‐Dihydropyridines (DHPs) have been developed to treat hypertension, angina, and nerve system disease. They are thought to mainly target the L‐type calcium channels, but low selectivity prompts them to block Cav1.2 and Cav3.1 channels simultaneously. Recently, some novel DHPs with different hydrophobic groups have been synthesized and among them M12 has a higher selectivity for Cav3.1. However, the structural information about Cav3.1‐DHPs complexes is not available in the experiment. Thus, we combined homology modeling, molecular docking, molecular dynamics simulations, and binding free energy calculations to quantitatively elucidate the inhibition mechanism of DHPs. The calculated results indicate that our model is in excellent agreement with experimental results. On the basis of conformational analysis, we identify the main interactions between DHPs and calcium channels and further elaborate on the different selectivity of ligands from the micro perspective. In conjunction with energy distribution, we propose that the binding sites of Cav3.1‐DHPs is characterized by several interspersed hydrophobic amino acid residues on the IIIS6 and IVS6 segments. We also speculate the favorable function groups on prospective DHPs. Besides, our model provides important information for further mutagenesis experiments.     

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications

Background

Most biological processes are influenced by protein post-translational modifications (PTMs). Identifying novel PTM sites in different organisms, including humans and model organisms, has expedited our understanding of key signal transduction mechanisms. However, with increasing availability of deep, quantitative datasets in diverse species, there is a growing need for tools to facilitate cross-species comparison of PTM data. This is particularly important because functionally important modification sites are more likely to be evolutionarily conserved; yet cross-species comparison of PTMs is difficult since they often lie in structurally disordered protein domains. Current tools that address this can only map known PTMs between species based on known orthologous phosphosites, and do not enable the cross-species mapping of newly identified modification sites. Here, we addressed this by developing a web-based software tool, PhosphOrtholog (www.phosphortholog.com) that accurately maps protein modification sites between different species. This facilitates the comparison of datasets derived from multiple species, and should be a valuable tool for the proteomics community.

Results

Here we describe PhosphOrtholog, a web-based application for mapping known and novel orthologous PTM sites from experimental data obtained from different species. PhosphOrtholog is the only generic and automated tool that enables cross-species comparison of large-scale PTM datasets without relying on existing PTM databases. This is achieved through pairwise sequence alignment of orthologous protein residues. To demonstrate its utility we apply it to two sets of human and rat muscle phosphoproteomes generated following insulin and exercise stimulation, respectively, and one publicly available mouse phosphoproteome following cellular stress revealing high mapping and coverage efficiency. Although coverage statistics are dataset dependent, PhosphOrtholog increased the number of cross-species mapped sites in all our example data sets by more than double when compared to those recovered using existing resources such as PhosphoSitePlus.

Conclusions

PhosphOrtholog is the first tool that enables mapping of thousands of novel and known protein phosphorylation sites across species, accessible through an easy-to-use web interface. Identification of conserved PTMs across species from large-scale experimental data increases our knowledgebase of functional PTM sites. Moreover, PhosphOrtholog is generic being applicable to other PTM datasets such as acetylation, ubiquitination and methylation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1820-x) contains supplementary material, which is available to authorized users.     

Population change in hyper-oceanic liverworts before and after hydroelectric power development: a preliminary study

Introduction. The best sites for oceanic bryophytes are typically in ravines that offer good potential for hydroelectric power (HEP) development. This preliminary study is the first to investigate population change in oceanic bryophytes of conservation concern at a site subject to HEP development.

Methods. Populations of five hyperoceanic liverworts were measured, Aphanolejeunea microscopica, Drepanolejeunea hamatifolia, Harpalejeunea molleri, Jubula hutchinsiae and Radula voluta, at two time periods, before and after HEP installation.

Results. Spanning almost four years, results reveal a dynamic system, with significant change in fine-scale distribution patterns, including many colony extinctions and colonisations. About 23% of colony losses of A. microscopica, D. hamatifolia and H. molleri appeared to result from exclusion by larger bryophytes, involving at least 17 species, in particular Ctenidium molluscum.

Conclusions. Inference with regards to effects of the HEP is not advised from this type of preliminary before and after study, based at a single site without controls. Given rapid recent growth of small HEP development and the enormous future potential, both in Britain and around the world, it is important to build upon this work and undertake comprehensive studies to detect possible impacts on bryophytes of conservation concern.     

唐家河国家级自然保护区林麝排便点偏好

林麝（Moschus berezovskii）是重要的资源动物,也是生态系统中的重要一员,由于过度捕猎和栖息地破碎化等导致其种群急剧下降。恢复林麝种群的根本方法是保护和恢复其栖息地。林麝的排便点分布在其整个活动区内,且有很好的指示作用。本研究通过分析林麝排便点位置,了解林麝栖息地选择偏好。在唐家河国家级自然保护区内不同海拔梯度布置17个1 km × 1 km的样方,每个样方内至少1条样线,样线每隔400 m设置搜索样线,以发现排便点为中心设置1个10 m × 10 m 利用样方,若未发现排便点,在搜索样线中部设置1个10 m × 10 m 对照样方,并记录样方内的生境因子。采用Ivlev的选择性指数、广义线性模型及多重对应法分析林麝对生境因子的偏好。结果发现,林麝最为偏好的植被类型为针阔混交林（E = 0.528）,而规避常绿阔叶林（E =﹣1）、次生落叶阔叶林（E =﹣0.816）和常绿落叶阔叶林（E =﹣0.585）。此外,海拔、灌丛盖度和坡度也显著影响林麝栖息地偏好,其排便点集中分布在海拔2 000 ~ 2 600 m区间,并且偏好有一定灌丛盖度且坡度陡的生境。