惠东幼年绿海龟的洄游规律及觅食地选择

绿海龟(Chelonia mydas)为全球性濒危物种、我国Ⅰ级重点保护野生动物.栖息地保护是野生绿海龟保护的一种极为重要和有效的保护策略,但我国幼年绿海龟的生活习性及其栖息地分布尚不明确,故开展相关洄游行为及栖息地分布研究意义重大.2011至2015年间,将6只来自广东惠东海龟国家级自然保护区人工培育2～14a的幼年...     

Recovery in the survival capacity of ultraviolet-irradiated 3T3 mouse cells at G0 cannot be solely dependent on the excision of pyrimidine dimers

Mouse cells (3T3 line) excised at most 20% of the pyrimidine dimers introduced into their DNA by a dose of short-wavelength ultraviolet radiation that allows a significant fraction of the cells to survive. When irradiation was delivered at the pre-replicative stage, a significant repair of lethal events was observed, as the cells progressed toward S phase. The recovery in survival cannot be accounted for solely by excision of pyrimidine dimers. Therefore, either another lesion produced by ultraviolet radiation is critical in terms of lethality, or the dimer, which may trigger the lethal event, becomes no longer an obstacle for the replication system after a certain period of time.     

Nurse rocks influence forest expansion over native grassland in southern Brazil

Questions: Do small rocky outcrops favor forest plant colonization and establishment in grasslands? If so, what are the potential mechanisms involved in this process? Location: Araucaria forest and Campos grassland mosaic in southern Brazilian highlands (29°29′S, 50°12′W). Methods: We collected data on the density of forest woody species in plots located on rocky outcrops and in open fields subject to different management regimes. We evaluated the influence of outcrops on the density of forest plants ≤60‐cm tall, and the effects of other environmental variables and of site on plant density; we also used information on diaspore traits of the species to discuss the way in which plants disperse to the outcrops. Results: Rocky outcrops harbored a significantly higher density of forest plants than open fields, irrespective of site effect, and rock height was the best predictor for plant density on outcrops. Diaspores of all recorded species possess characteristics associated with dispersal by birds or mammals or by both. Conclusions: Small rocky outcrops markedly influence forest expansion by acting as perches for vertebrate dispersers and as nurse objects and safe sites for plants. Forest expansion starting in small outcrops possibly occurs as follows: perching of dispersers and increase of seed rain on rocks, promotion of better conditions of establishment for forest plants by nurse rocks, protection of plants sensitive to grazing and fire, and nucleation of forest vegetation.     

Improved NADPH supply for xylitol production by engineered Escherichia coli with glycolytic mutations

Escherichia coli engineered to uptake xylose while metabolizing glucose was previously shown to produce high levels of xylitol from a mixture of glucose and xylose when expressing NADPH-dependent xylose reductase from Candida boidinii (CbXR) (Cirino et al., Biotechnol Bioeng. 2006;95:1167-1176). We then described the effects of deletions of key metabolic pathways (e.g., Embden-Meyerhof-Parnas and pentose phosphate pathway) and reactions (e.g., transhydrogenase and NADH dehydrogenase) on resting-cell xylitol yield (Y RPG: moles of xylitol produced per mole of glucose consumed) (Chin et al., Biotechnol Bioeng. 2009;102:209-220). These prior results demonstrated the importance of direct NADPH supply by NADP+-utilizing enzymes in central metabolism for driving heterologous NADPH-dependent reactions. This study describes strain modifications that improve coupling between glucose catabolism (oxidation) and xylose reduction using two fundamentally different strategies. We first examined the effects of deleting the phosphofructokinase (pfk) gene(s) on growth-uncoupled xylitol production and found that deleting both pfkA and sthA (encoding the E. coli-soluble transhydrogenase) improved the xylitol Y RPG from 3.4 ± 0.6 to 5.4 ± 0.4. The second strategy focused on coupling aerobic growth on glucose to xylitol production by deleting pgi (encoding phosphoglucose isomerase) and sthA. Impaired growth due to imbalanced NADPH metabolism (Sauer et al., J Biol Chem. 2004;279:6613-6619) was alleviated upon expressing CbXR, resulting in xylitol production similar to that of the growth-uncoupled precursor strains but with much less acetate secretion and more efficient utilization of glucose. Intracellular nicotinamide cofactor levels were also quantified, and the magnitude of the change in the NADPH/NADP+ ratio measured from cells consuming glucose in the absence vs. presence of xylose showed a strong correlation to the resulting Y RPG.     

Investigation on BRCA1 SNPs and its effects on mastitis in Chinese commercial cattle

The main objective of this study was to investigate whether the bovine breast cancer 1 (BRCA1) gene was associated with mastitis resistance in Chinese commercial cattle. A total of 51 SNPs were screened from public data resources and DNA sequencing. Three SNPs (c.5682G>C,c.26198C>T and c.46126G>T) were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and created restriction site PCR (CRS-PCR) methods and 21 combinations of these SNPs were observed. The single SNP and their genetic effects on somatic cell score (SCS) were evaluated and a significant association with SCS was found in c.46126G>T. The mean SCS of individuals with genotype KK was significantly lower than those of genotypes KL and LL. The results of combined genotypes analysis of three SNPs showed that HHLLNN genotype with the highest SCS was easily for the mastitis susceptibility, whereas GGKKMM genotype with the lowest SCS was favorable for the mastitis resistance. The information provided in the present study will be very useful for improving mastitis resistance in dairy cattle by marker-assisted selection (MAS).     

AutoMatch: target-binding protein design and enzyme design by automatic pinpointing potential active sites in available protein scaffolds

Proteins perform their functions mainly via active sites, whereas other parts of the proteins comprise the scaffolds, which support the active sites. One strategy for protein functional design is transplanting active sites, such as catalytic sites for enzyme or binding hot spots for protein-protein interactions, onto a new scaffold. AutoMatch is a new program designed for efficiently elucidating suitable scaffolds and potential sites on the scaffolds. Backrub motions are used to treat backbone flexibility during the design process. A step-by-step checking strategy and cluster-representation examination strategy were developed to solve the large combinatorial problem for the matching of active-site conformations. In addition, a grid-based binding energy scoring method was used to filter the solutions. An enzyme design benchmark and a protein-protein interaction design benchmark were built to test the algorithm. AutoMatch could identify the hot spots in the nonbinding protein and rank them within the top five results for 8 of 10 target-binding protein design cases. In addition, among the 15 enzymes tested, AutoMatch can identify the catalytic active sites in the apoprotein and rank them within the top five results for 13 cases. AutoMatch was also tested for screening scaffold library in designing binding proteins targeting influenza hemagglutinin, HIV gp120, and epidermal growth factor receptor kinase, respectively. AutoMatch, and the two test sets, ActApo and ActFree, are available for noncommercial applications at http://mdl.ipc.pku.edu.cn/cgi-bin/down.cgi.     

CPhos: A program to calculate and visualize evolutionarily conserved functional phosphorylation sites

Profiling using high‐throughput MS has discovered an overwhelming number of novel protein phosphorylation sites (“phosphosites”). However, the functional relevance of these sites is not always clear. In light of recent studies on the evolutionary mechanism of phosphorylation, we have developed CPhos, a Java program that can assess the conservation of phosphosites among species using an information theory‐based approach. The degree of conservation established using CPhos can be used to assess the functional significance of phosphosites. CPhos has a user friendly graphical user interface and is available both as a web service and as a standalone Java application to assist phosphoproteomic researchers in analyzing and prioritizing lists of phosphosites for further experimental validation. CPhos can be accessed or downloaded at http://helixweb.nih.gov/CPhos/ .     

The stereochemical resolution of the enantiomers of aspartame on an immobilized alpha-chymotrypsin HPLC chiral stationary phase: the effect of mobile-phase composition and enzyme activity

The enantioselective and diastereoselective resolutions of the stereoisomers of N alpha-aspartyl-phenylalanine 1-methyl ester (APME) have been accomplished on an HPLC chiral stationary phase based upon alpha-chymotrypsin (the ACHT-CSP) with observed enantioselectivities (alpha 1) for the DL-/LD-enantiomer of as high as 29.17 and for the DD-/LL-enantiomers of as high as 28.97. In addition, the effect on the chromatographic retention of the APME stereoisomers of the activity of the ACHT and the composition of the mobile phase--structure of the anionic component, molarity, and pH--have been studied. The results of this study suggest that the aspartyl moiety and/or the aspartyl-phenylalanine amide linkage play key roles in the observed enantioselectivity; the APME stereoisomers containing L-phenylalanine, i.e., DL- and LL-APME, bind at a different site in the ACHT molecule (the L-Phe site) than the APME stereoisomers containing D-phenylalanine (the D-Phe site); and the observed enantioselectivity is a measure of the difference in the binding affinities at the two sites rather than the consequence of differential affinities at a single site.     

Abundance and length polymorphism of microsatellite repeats in Beta vulgaris L.

Simple sequence repeats (SSRs) are known to exhibit high degrees of variability even among closely related individuals. Their usage as nuclear genetic markers requires their conversion into sequence-tagged sites (STSs). In this paper we present the development of simple sequences as STSs for Beta vulgaris. This species comprises wild, cultivated, and weedy forms; the latter are thought to originate from accidental hybridisation between the other two. Two partial genomic libraries were screened with simple sequence motifs (AT, CA, CT, ATT, GTG, and CA, CT, respectively). Clones of 22 CA, nine CT, eight ATT, and one GTG sequence were obtained. AT micro satellites were present in compound motifs, not recognised by the probe. Sequence comparisons revealed that 20 CA clones containing short motifs (<16 bp) were variants of a previously described approximately 320-bp satellite DNA (Schmidt et al. 1991), and hence did not correspond to unique loci. Polymorphism of one (ATT)₁₅ and three (CT)_n, with n=15, 17 and 26, was detected by PCR on a sample of 64 plants from the different forms of B. vulgaris. 13 (ATT), 13 (CT), nine (CT) alleles and one (CT) allele were detected. One of the ATT alleles was much larger than the others (>800 bp). Genetic variability was high among wild beets, lower among cultivated beets, and intermediate among weed beets. One allele of each locus was found at high frequencies in cultivated beets and, to a lower extent, in weed beets. The combination of three polymorphic loci allowed the individual identification of 17/17 wild and 15/15 weed beets, and 21/32, mostly homozygous, cultivated beets.     

Isolation and characterization of a cDNA encoding a putative high mobility group (HMG) – box protein from stored mRNA in resting cysts of the ciliate Oxytricha (Sterkiella) nova – Ciliate macronuclear gene encoding a putative HMG-box protein

We have isolated an cDNA after applying a DDRT-PCR analysis on mRNA from mature resting cysts of the ciliate Oxytricha (Sterkiella) nova. From this cDNA fragment the complete macronuclear minichromosome was obtained by using the Mac-End-PCR method. After cloning and sequencing, this cDNA shown certain similarity to HMG-like proteins. The analysis of the inferred amino acid sequence shown that this putative HMG-like protein has one HMG-box interrupted by a intron. The analysis of others characteristics (including a 3D model) confirms that it is a HMGB family protein. It is the first time that a macronuclear gene encoding a putative HMG-box protein is isolated from resting cysts of a stichotrich ciliate. The possible implications of this stored mRNA in the ciliate cryptobiotic stage are discussed.