Genomic organization and sequence analysis of the vomeronasal receptor V2R genes in mouse genome

Two multigene superfamilies, named V1R and V2R, encoding seven-transmembrane-domain G-protein coupled receptors (GPCRs) have been identified as pheromone receptors in mammals. Three V2R gene families have been described in mouse and rat. Here we screened

Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca)

A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.

Trend and growth analysis of marine fish production in Bangladesh

The study based on time series marine fish production data during the period of 1983-1984 to 2007-2008 in Bangladesh. For this growth analysis six deterministic time series models are considered. The estimated best fitting models are the cubic, quadratic and quadratic model is appropriate for industrial marine fish production, artisanal marine fish production and total marine fish production in Bangladesh respectively. The study attempts to provide forecasts of marine fish production in Bangladesh for the year of 2008-09 to 2012-13. The magnitude of instability in marine fish production was attempted by computing the coefficient of variation (CV) and the percentage deviation from three years moving average values. The study revealed that the total marine fish production was observed to be relatively stable (CV being 31.85%) compared to the artisanal marine fish production (CV being 32.04%) and industrial marine fish (CV being 47.20%). For the three components of marine fish production the growth rates were different over different time points. The variation of the growth rates in industrial marine fish production was -21.6% to 13.12%, in artisanal marine fish production was 2.39% to 5.29% and in total marine fish production was 11.23% to 24.85% during the study period.

Venomics and biological analysis of Scatophagus argus argus (Spotted scat) venom isolated in Persian Gulf, extraction and purification of hemolytic protein

Green scat namely as Scatophagus argus argus is a venomous aquarium fish belonging to Scatophagidae family. It can induce painful wounds in injured hand with partial paralysis to whom that touch the spines. Dorsal and ventral rough spines contain cells that produce venom with toxic activities. According to unpublished data collected from local hospitals in southern coastal region of Iran, S. argus is reported as a venomous fish. Envenomation induces clinical symptoms such as local pain, partial paralysis, erythema and itching. In the present study green scat (spotted scat) was collected from Persian Gulf coastal waters. SDS-PAGE indicated 12 distinct bands in the venom ranged between 10-250 KDa. The crude venom had hemolytic activity on human erythrocytes (1%) with an LC100 (Lytic Concentration) of about 1.7 μg. The crude venom can release 813 μg proteins from 0.5% casein. Phospholipase C activity was recorded at 3.125 μg of total venom. Our findings showed that the edematic activity remained over 48 h after injection. The purification of the venom was done by HPLC and 30 peaks were obtained within 80 min but only one peak in 68 min retention time showed hemolytic activity at 90% acetonitril was isolated. The area percentage of the hemolytic protein showed that this hemolytic protein consist of 32 percent of total proteins and its molecular weight was 72 KDa in SDS_PAGE. The results demonstrated that crude venom extracted from Iranian coastal border has different toxic and enzymatic activities.

Report of the training in database and spatial analysis for Marine Protected Areas staff in Indonesia's BOBLME region, Medan, Indonesia, 30 June-4 July, 2015

Training included: Geographic Information System (GIS)concept and software; Global Positioning System (GPS); Ecological Gap Analysis and Marine Protected Area (MPA) design using Marine Reserve Design using Spatially Explicit Annealing (MARXAN); and cartography.

Lake Nasser fisheries: literature review and situation analysis

This study sought to improve the baseline knowledge of the fisheries of Lake Nasser and to make recommendations for the improved management of the fisheries, including stock assessment. This review draws heavily from the most recent reviews of Lake Nasserr and its fisheries, including van Zwieten et al. (2011), Habib et al. (2014) and Habib (2015). It is supplemented with findings from the field study described in the final technical report, Lake Nasser fisheries: Recommendations for management, including monitoring and stock assessment (Halls 2015).

Molecular and morphological analysis of endangered species Gymnodiptychus integrigymnatus (Teleostei: Cyprinidae)

Gymnodiptychus integrigymnatus is a critically endangered species endemic to the Gaoligongshan Mountains. It was thought to be only distributed in several headwater-streams of the Longchuanjiang River (west slope of the Gaoligongshan Mountains, belonging to the Irrawaddy River drainage). In recent years, dozens of G. integrigymnatus specimens have been collected in some streams on the east slope of the Gaoligongshan Mountains (the Salween drainage). We performed a morphological and genetic analyses (based on cytochrome b and D-loop) of the newly discovered populations of G. integrigymnatus to determine whether the degree of separation of these populations warrants species status. Our analysis from the cytochrome b gene revealed that nine individuals from the Irrawaddy drainage area and seven individuals from the Salween drainage area each have only one unique haplotype. The genetic distance between the two haplotypes is 1.97%. Our phylogenetic analysis revealed that G. integrigymnatus is closely related to highly specialized schizothoracine fishes. Analysis from the mitochondrial control region revealed that G. integrigymnatus has relatively high genetic diversity (pi was 0.00891 and h was 0.8714), and individuals from different river drainages do not share the same haplotypes. The AMOVA results indicated 87.27% genetic variability between the Salween and Irrawaddy populations. Phylogenetic trees show two major geographic groups corresponding to the river systems. We recommend that G. integrigymnatus should be considered as a high priority for protected species status in the Gaoligongshan Mountains National Nature Reserve, and that the area of the Gaoligongshan Mountains National Nature Reserve should be expanded to cover the entire distribution of G. integrigymnatus. Populations of G. integrigymnatus from different river systems should be treated as evolutionarily significant units.

Identification, characteristic and phylogenetic analysis of type II DNA topoisomerase gene in Giardia lamblia

The genes encoding type II DNA topoisomerases were investigated in Giardia lamblia genome, and a type IIA gene, GlTop 2 was identified. It is a single copy gene with a 4476 by long ORF without intron. The deduced amino acid sequence shows strong homology to eukaryotic DNA Top 2. However, some distortions were found, such as six insertions in the ATPase domain and the central domain, a similar to 100 as longer central domain; a similar to 200 as shorter C-terminal domain containing rich charged residues. These features revealed by comparing with Top 2 of the host, human, might be helpful in exploiting drug selectivity for antigiardial therapy. Phylogenetic analysis of eukaryotic enzymes showed that kinetoplastids, plants, fungi, and animals were monophyletic groups, and the animal and fungi lineages shared a more recent common ancestor than either did with the plant lineage; microsporidia grouped with fungi. However, unlike many previous phylogenetic analyses, the "amitochondriate" G. lamblia was not the earliest branch but diverged after mitochondriate kinetoplastids in our trees. Both the finding of typical eukaryotic type IIA topoisomerase and the phylogenetic analysis suggest G. lamblia is not possibly as primitive as was regarded before and might diverge after the acquisition of mitochondria. This is consistent with the recent discovery of mitochondrial remnant organelles in G. lamblia.

Cloning,Expression and Sequence Analysis of A Luciferase Gene from the Chinese Firefly Pyrocoelia pygidialis

从一种来自中国日行性萤火虫(云南窗萤)发光器官mRNA中克隆、测序并表达了有功能的荧光素酶.云南窗萤荧光素酶的cDNA序列有1647个碱基,编码548个氨基酸残基.从推测得到的氨基酸序列的比对分析得出:云南窗萤的荧光素酶与来自Lampyris noctiluca,L.turkestanicus和Nyctophila cf.caucasica三种萤火虫的荧光素酶有97.8%的序列一致性.从推测得出的氨基酸序列进行系统发育分析,其结果表明:云南窗萤和Lampyris+Nyctophila聚在一起,与同属的发光强夜行性的萤火虫不形成的单系.云南窗萤荧光素酶在大肠杆菌中表达的条带大约70kDa,并且在有荧光素存在时发出黄绿色荧光.对荧光素酶的结构模拟和分析表明,云南窗萤荧光素酶基因的氨基端和羧基端结构域之间的裂沟处存在这5个多肽环,这正是从其他荧光素酶推测得到的催化荧光反应时的底物结合位点.云南窗萤和窗萤属的其他3种萤火虫的荧光素酶卡目比,有13个不同氨基酸位点,位于模拟分子结构的表面.对于这些多肽环、不刚氨基酸残基和晶体结构的进一步研究有利于解释日行和夜行性萤火虫荧光素酶的差异.

Nutrient status and thermal stratification in Lake Victoria

Worldwide, human activity in the watershed has been found to induce lake responses at various levels, including at population and ecosystem scale. Recently, Carignan and Steedman (2000) reported on disruptions of biogeochemical cycles in temperate lakes following watershed deforestation and lor wildfire and Carignan et al., (2000 a, b) concluded that water quality and aquatic biota are strongly influenced by disturbances in the watershed. Similarly, Lake Victoria is no exception as people in its catchment have exploited it for the last hundred years or more, but have now begun to understand the extent to which they have thrown the lake into disorder and how their increasing activity in the watershed have driven some environmental changes within and around the lake.

Social and gender analysis report: Barotse Floodplain, Western Province,Zambia

There is increasing awareness that integrating gender into development frameworks is critical for effective implementation of development strategies. In working to alleviate rural poverty, the CGIAR Research Program on Aquatic Agricultural Systems (AAS) recognizes that “business as usual” gender integration approaches will not deliver lasting and widespread improvements in agricultural productivity, poverty reduction and food security. In response, AAS operationalized a gender transformative approach. The approach is informed by conceptual frameworks that explicitly recognize the potent influence of social relations on creating and perpetuating gender inequalities. In this way, AAS aims to address the underlying causes of rural poverty and gender inequality in Zambia’s Barotse Floodplain, where people rely extensively on riverine and wetland ecosystems for food and livelihood security. A central question guiding the research program is “How do social norms and gendered power relations influence agricultural development outcomes?” The findings presented in this report provide insights that help answer this question. The report presents a review of literature relevant to livelihoods, ecosystem services, and gender and social relations in Zambia, with a specific focus on Western Province, where AAS is currently implemented. It also presents a synthesis of findings of a social and gender analysis conducted in 2013 in 10 focal communities situated in and around the Barotse Floodplain.

High Altitude Adaptation and Phylogenetic Analysis of Tibetan Horse Based on the Mitochondrial Genome

研究测定了西藏那曲(4,500 m)、云南中甸(3,300 m)、云南德钦(3,300 m)地区3匹藏马线粒体全基因组序列.3个地区的藏马线粒体基因组全长以及结构均与韩国济州岛的马类似,但比瑞典马线粒体基因组短.藏马基因组在DNA序列上的两两相似性达99.3%.通过对线粒体蛋白编码区的分析发现,NADH6基因的蛋白序列在三匹藏马中均表现快速进化的现象.这表明NADH6基因在藏马高原适应进化过程中扮演着重要角色.此外,利用7匹藏马的D-loop区域序列以及与其亲缘关系较近的马的序列首次构建的藏马的系统发育树显示,那曲藏马与中甸、德钦藏马属于不同的分支,且存在较大的遗传多样性,表明藏马可能为多地区起源.

The topological configuration and conformational analysis of mRNA in translation

The theoretical model construction of mRNA hairpin structure and single-stranded structure as well as the simulation studies on RNA structure determined by the X-ray crystal diffraction and nuclear magnetic resonance revealed that in translation, after mRNA being unfolded into single-stranded structure, its topological configuration was closely correlative with the original hairpin structure. The conformational features of single-stranded mRNA appeared as helical regions alternating with curly regions to different extents, which might exert the influence on the folding of nascent polypeptide by various regulating effects including different translational rates.