A note on the Mulder-Landsmeer phenomenon.

Mulder-Landsmeer phenomenon (inability to activiely straighten the interphalangeal joints fully when the metacarpophalangeal joint of a finger is passively held in maximal hyperextension) was confirmed in the normally hypermobile South Indian fingers. A powerful but limited de-extension of the proximal phalanx was noticied, in normagers, during completion of interphalangeal extension when the metacarpophalangeal joint was passively held in maximal hyperextension...     

Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells

Custom-designed zinc finger nucleases (ZFNs), proteins designed to cut at specific DNA sequences, are becoming powerful tools in gene targeting—the process of replacing a gene within a genome by homologous recombination (HR). ZFNs that combine the non-specific cleavage domain (N) of FokI endonuclease with zinc finger proteins (ZFPs) offer a general way to deliver a site-specific double-strand break (DSB) to the genome. The development of ZFN-mediated gene targeting provides molecular biologists with the ability to site-specifically and permanently modify plant and mammalian genomes including the human genome via homology-directed repair of a targeted genomic DSB. The creation of designer ZFNs that cleave DNA at a pre-determined site depends on the reliable creation of ZFPs that can specifically recognize the chosen target site within a genome. The (Cys₂His₂) ZFPs offer the best framework for developing custom ZFN molecules with new sequence-specificities. Here, we explore the different approaches for generating the desired custom ZFNs with high sequence-specificity and affinity. We also discuss the potential of ZFN-mediated gene targeting for ‘directed mutagenesis’ and targeted ‘gene editing’ of the plant and mammalian genome as well as the potential of ZFN-based strategies as a form of gene therapy for human therapeutics in the future.     

能源植物甜高粱种质资源和分子生物学研究进展

世界能源危机和全球生态环境日益恶化迫使人们急需开发可再生能源。生物质能源作为一种清洁的可再生能源已受到世界各国的高度重视。发展生物质能源的瓶颈之一是生物质原料不足。甜高粱的生物学产量和含糖量极高, 同时兼有耐旱、耐涝、耐贫瘠和耐盐碱等诸多优良特性, 被认为是最具开发潜力的能源植物之一。该文从甜高粱的分类学、生物学特点、种质资源评价、功能基因以及基因组信息等方面综述了甜高粱的最新研究进展和存在的问题, 并展望了甜高粱作为能源植物的研发前景。     

Extracellular β-d-xylosidase of Sclerotium rolfsii

Culture conditions are described for the production of extracellular β-d-xylosidase (xylobiase, exo-1,4-β-d-xylosidase, 1,4-β-d-xylan xylohydrolase, EC 3.2.1.37) in shake flasks by Sclerotium rolfsii. At the 1% cellulose level, a maximum activity of 0.82 U ml^?1is obtained in media containing either 1% corn steep liquor or 1% defatted coconut cake. The β-d-xylosidase has a molecular weight of 170 000 and catalyses the hydrolysis of 4-nitrophenyl-β-d-xylopyranoside optimally at pH 4.5 and 50°C. The energy of activation is 44 kJ mol^?1and the pI and K_mare 6.8 and 0.038 mm, respectively.     

Molecular chaperones DnaK and DnaJ share predicted binding sites on most proteins in the E. coli proteome

In Escherichia coli, the molecular chaperones DnaK and DnaJ cooperate to assist the folding of newly synthesized or unfolded polypeptides. DnaK and DnaJ bind to hydrophobic motifs in these proteins and they also bind to each other. Together, this system is thought to be sufficiently versatile to act on the entire proteome, which creates interesting challenges in understanding the interactions between DnaK, DnaJ and their thousands of potential substrates. To address this question, we computationally predicted the number and frequency of DnaK- and DnaJ-binding motifs in the E. coli proteome, guided by free energy-based binding consensus motifs. This analysis revealed that nearly every protein is predicted to contain multiple DnaK- and DnaJ-binding sites, with the DnaJ sites occurring approximately twice as often. Further, we found that an overwhelming majority of the DnaK sites partially or completely overlapped with the DnaJ-binding motifs. It is well known that high concentrations of DnaJ inhibit DnaK-DnaJ-mediated refolding. The observed overlapping binding sites suggest that this phenomenon may be explained by an important balance in the relative stoichiometry of DnaK and DnaJ. To test this idea, we measured the chaperone-assisted folding of two denatured substrates and found that the distribution of predicted DnaK- and DnaJ-binding sites was indeed a good predictor of the optimal stoichiometry required for folding. These studies provide insight into how DnaK and DnaJ might cooperate to maintain global protein homeostasis.     

Loss of miRNA biogenesis induces p19Arf-p53 signaling and senescence in primary cells

Dicer, an enzyme involved in microRNA (miRNA) maturation, is required for proper cell differentiation and embryogenesis in mammals. Recent evidence indicates that Dicer and miRNA may also regulate tumorigenesis. To better characterize the role of miRNA in primary cell growth, we generated Dicer-conditional mice. Ablation of Dicer and loss of mature miRNAs in embryonic fibroblasts up-regulated p19(Arf) and p53 levels, inhibited cell proliferation, and induced a premature senescence phenotype that was also observed in vivo after Dicer ablation in the developing limb and in adult skin. Furthermore, deletion of the Ink4a/Arf or p53 locus could rescue fibroblasts from premature senescence induced by Dicer ablation. Although levels of Ras and Myc oncoproteins appeared unaltered, loss of Dicer resulted in increased DNA damage and p53 activity in these cells. These results reveal that loss of miRNA biogenesis activates a DNA damage checkpoint, up-regulates p19(Arf)-p53 signaling, and induces senescence in primary cells.     

Molecular Markers Reveal Only Two Mud Crab Species of Genus Scylla (Brachyura: Portunidae) in Indian Coastal Waters

The taxonomic ambiguity of the Indian mud crab (genus Scylla de Hann 1833) is still a cause of concern as several papers have been published with misleading identification. This is the first attempt to resolve the taxonomic uncertainty of the mud crab commonly available in Indian coastal waters using molecular genetic markers (ITS-1 and sequencing of COI gene) combined with traditional morphometry. Additionally, we developed a PCR method by which Indian mud crab species can be identified rapidly and effectively. The results clearly indicate that the green morph of the Indian mud crab is Scylla serrata and the brown morph is S. olivacea. The S. serrata commonly mentioned in the literature from India is S. olivacea; the S. tranquebarica noted by many Indian researchers should belong to S. serrata. Caution should be taken when interpreting or implementing the biological, molecular, and aquaculture data in the literature.     

Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens

According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.     

On the conformation of the disulphide group in L-cystine and its derivatives.

The terminal groups in cystine are asymmetric and hence the dissulphide group with right and left chirality may not have equal energy. An attempt is made to resolve this problem through energy calculation using semi-empirical methods involving non-bonded and electrostatic interactions and simple Pauling type torsional potential for the disulphide group. The results are discussed in the light of experimental data.