Construction and characterization of bacterial artificial chromosome library of black-handed spider monkey (Ateles geoffroyi)

The large-insert genomic DNA library is a critical resource for genome-wide genetic dissection of target species. We constructed a high-redundancy bacterial artificial chromosome (BAC) library of a New World monkey species, the black-handed spider monkey

Construction of a BAC library for Chinese amphioxus Branchiostoma belcheri and identification of clones containing Amphi-pax genes

Amphioxus is a crucial organism for the study of vertebrate evolution. Although a genomic BAC library of Branchiostoma floridae has been constructed, we report here another BAC library construction of its distant relative species Branchiostoma belcheri. The amphioxus BAC library established in present study consists of 45,312 clones arrayed in one hundred and eighteen 384-well plates. The average insert fragment size was 120 kb estimated by Pulsed Field Gel Electrophoresis (PFGE) analysis of 318 randomly selected clones. The representation of the library is about 12 equivalent to the genome, allowing a 99.9995% probability of recovering any specific sequence of interest. We further screened the library with 4 single copied Amphi-Pax genes and identified total of 26 positive clones with average of 6.5 clones for each gene. The result indicates this library is well suited for many applications and should also serve as a useful complemental resource for the scientific community.

Construction, characterization and chromosomal mapping of bacterial artificial chromosome (BAC) library of Yunnan snub-nosed monkey (Rhinopithecus bieti)

We constructed a high redundancy bacterial artificial chromosome library of a seriously endangered Old World Monkey, the Yunnan snub-nosed monkey (Rhinopithecus bieti) from China. This library contains a total of 136 320 BAC clones. The average insert size of BAC clones was estimated to be 148 kb. The percentage of small inserts (50-100 kb) is 2.74%, and only 2.67% non-recombinant clones were observed. Assuming a similar genome size with closely related primate species, the Yunnan snub-nosed monkey BAC library has at least six times the genome coverage. By end sequencing of randomly selected BAC clones, we generated 201 sequence tags for the library. A total of 139 end-sequenced BAC clones were mapped onto the chromosomes of Yunnan snub-nosed monkey by fluorescence in-situ hybridization, demonstrating a high degree of synteny conservation between humans and Yunnan snub-nosed monkeys. Blast search against human genome showed a good correlation between the number of hit clones and the size of the chromosomes, an indication of unbiased chromosomal distribution of the BAC library. This library and the mapped BAC clones will serve as a valuable resource in comparative genomics studies and large-scale genome sequencing of nonhuman primates. The DNA sequence data reported in this paper were deposited in GenBank and assigned the accession number CG891489-CG891703.

In vitro construction of a recombinant human embryonic brain-derived neurotrophin-4 gene and pEGFP-N1 vector

BACKGROUND: Neurotrophin-4 (NT-4) can promote neuronal growth, development, differentiation, maturation, and survival. NT-4 can also improve recovery and regeneration of injured neurons, but cannot pass through the blood-brain barrier, which limits its ac

Construction of habitat suitability models (HSMs) for benthic macroinvertebrate and their applications to instream environmental flows: A case study in Xiangxi River of Three Gorges Reservior region, China

Based on a long-term ecological monitoring, the present study chose the most dominant benthic macroinvertebrate (Baetis spp.) as target organisms in Xiangxi River, built the habitat suitability models (HSMs) for water depth, current velocity and substrate, respectively, which is the first aquatic organisms model for habitat suitability in the Chinese Mainland with a long-term consecutive in situ measurement. In order to protect the biointegrity and function of the river ecosystem, the theory system of instream environmental flow should be categorized into three hierarchies, namely minimum required instream flow (hydrological level), minimum instream environmental flow (biospecies level), and optimum instream environmental flow (ecosystem level). These three hierarchies of instream environmental flow models were then constructed with the hydrological and weighted usable area (WUA) method. The results show that the minimum required instream flow of Xiangxi River calculated by the Tennant method (10% of the mean annual flow) was 0.615 m(3) s(-1); the minimum instream environmental flow accounted for 19.22% of the mean annual flow (namely 1.182 m(3) s(-1)), which was the damaged river channel. ow in the dry season; and 42.91% of the mean annual flow (namely 2.639 m(3) s(-1)) should be viewed as the optimum instream environmental flow in order to protect the health of the river ecosystem, maintain the instream biodiversity, and reduce the impact of small hydropower stations nearby the Xiangxi River. We recommend that the hydrological and biological methods can help establish better instream environmental. ow models and design best management practices for use in the small hydropower station project. (C) 2008 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

Changes in benthic algal communities following construction of a run-of-river dam

Ecological responses to dam construction are poorly understood, especially for downstream benthic algal communities. We examined the responses of benthic algal communities in downstream reaches of a tributary of the Xiangxi River, China, to the construction of a small run-of-river dam. From February 2003 to August 2006, benthic algae, chemical factors, and habitat characteristics were monitored upstream and downstream of the dam site. This period spanned 6 mo before dam construction and 37 mo after dam construction. Benthic algal sampling yielded 199 taxa in 59 genera that belonged to Bacillariophyta, Chlorophyta, and Cyanophyta. Some physical factors (flow velocity, water depth, and channel width) and 3 algal metrics (diatom species richness, Margalef diversity, and % erect individuals) were significantly affected by the dam construction, whereas chemical factors (e.g., NH4-N, total N, SiO2) were not. Nonmetric multidimensional scaling (NMS) ordinations showed that overall algal assemblage structure downstream of the dam sites was similar to that of upstream control sites before dam construction and for 1 year after dam construction (p > 0.05). However, sites belonging to upstream and downstream reaches were well separated on NMS axis 1 during the 2(nd) and 3(rd) years after dam construction. Our results suggest that impacts of dam construction on benthic algal communities took 2 to 3 y to emerge. Further development of a complete set of indicators is needed to address the impact of small-dam construction. Our observations underscore the need for additional studies that quantify ecological responses to dam construction over longer time spans.

Construction of cytoplasmic molecular markers distinguishing Danio rerio from Gobiocypris rarus at high identity domains based on MP-PCR strategy and Sybr Green I detection

To distinguish the cytoplasm of Danio rerio from that of Gobiocypris rarus, we cloned G. rarus COXI and constructed cytoplasmic molecular markers at the high identity domains of COXI by mutated primer PCR (MP-PCR for short). Then Sybr Green I was used to detect the single amplicon. As a result, we succeeded in getting the cytoplasmic molecular markers, G.M COXI and Z.M COXI, by MP-PCR strategy. They were used to detect the sperm-derived mtDNA in the sexual hybrid embryos (D. rerio female x G. rarus male) before the sphere stage. In the present study, all results demonstrate that MP-PCR approach and Sybr Green I detection are feasible to construct the molecular markers to identify genes that shared high identity.