Single vesicle analysis of endocytic fission on microtubules in vitro

Following endocytosis, internalized molecules are found within intracellular vesicles and tubules that move along the cytoskeleton and undergo fission, as demonstrated here using primary cultured rat hepatocytes. Although the use of depolymerizing drugs has shown that the cytoskeleton is not required to segregate endocytic protein, many studies suggest that the cytoskeleton is involved in the segregation of protein in normal cells. To investigate whether cytoskeletal-based movement results in the segregation of protein, we tracked the contents of vesicles during in vitro microscopy assays. These studies showed that the addition of ATP causes fission of endocytic contents along microtubules, resulting in the segregation of proteins that are targeted for different cellular compartments. The plasma membrane proteins, sodium (Na+) taurocholate cotransporting polypeptide (ntcp) and transferrin receptor, segregated from asialoorosomucoid (ASOR), an endocytic ligand that is targeted for degradation. Epidermal growth factor receptor, which is degraded, and the asialoglycoprotein receptor, which remains partially bound to ASOR, segregated less efficiently from ASOR. Vesicles containing ntcp and transferrin receptor had reduced fission in the absence of ASOR, suggesting that fission is regulated to allow proteins to segregate. A single round of fission resulted in 6.5-fold purification of ntcp from ASOR, and 25% of the resulting vesicles were completely depleted of the endocytic ligand.     

Concurrence of Danish Dementia and Cataract: Insights from the Interactions of Dementia Associated Peptides with Eye Lens α-Crystallin

Familial Danish Dementia (FDD) is an autosomal disease, which is distinguished by gradual loss of vision, deafness, progressive ataxia and dementia. Cataract is the first manifestation of the disease. In this article, we demonstrate a specific correlation between the poisoning of the chaperone activity of the rat eye lens α-crystallins, loss of lens transparency in organ culture by the pathogenic form of the Danish dementia peptide, i.e. the reduced Danish dementia peptide (redADan peptide), by a combination of ex vivo, in vitro, biophysical and biochemical techniques. The interaction of redADan peptide and lens crystallins are very specific when compared with another chaperone, HSP-70, underscoring the specificity of the pathogenic form of Danish dementia peptide, redADan, for the early onset of cataract in this disease.     

Real-time PCR quantification of precursor and mature microRNA

microRNAs (miRNAs) are challenging molecules to amplify by PCR because the miRNA precursor consists of a stable hairpin and the mature miRNA is roughly the size of a standard PCR primer. Despite these difficulties, successful real-time RT-PCR technologies have been developed to amplify and quantify both the precursor and mature microRNA. An overview of real-time PCR technologies developed by us to detect precursor and mature microRNAs is presented here. Protocols describe presentation of the data using relative (comparative C(T)) and absolute (standard curve) quantification. Real-time PCR assays were used to measure the time course of precursor and mature miR-155 expression in monocytes stimulated by lipopolysaccharide. Protocols are provided to configure the assays as low density PCR arrays for high throughput gene expression profiling. By profiling over 200 precursor and mature miRNAs in HL60 cells induced to differentiate with 12-O-tetradecanoylphorbol-13-acetate, it was possible to identify miRNAs who's processing is regulated during differentiation. Real-time PCR has become the gold standard of nucleic acid quantification due to the specificity and sensitivity of the PCR. Technological advancements have allowed for quantification of miRNA that is of comparable quality to more traditional RNAs.     

Quorum sensing in metal tolerance of Acinetobacter junii BB1A is associated with biofilm production

Acinetobacter junii strain BB1A, a novel metal-tolerant bacterium, produced biofilm in the presence of added ions such as Ni(2+), AsO(2)(-), Cd(2+) and Hg(2+) on surfaces such as glass and polystyrene. Generation of a metal-sensitive and adhesion-deficient mutant by transposition of Tn5-mob in the A. junii genome has putatively confirmed the association of metal tolerance with the production of biofilm. The requirement of a critical cell density for biofilm formation and presence of acyl-homoserine lactone-like autoinducer molecules in the cell-free supernatant indicated the phenomenon of quorum sensing. Addition of a natural quorum-sensing inhibitor (garlic extract) or synthetic quorum-sensing inhibitor (4-nitro-pyridine oxide) significantly inhibited cell growth and biofilm formation in the presence of metal/metalloid ions.     

Activated charcoal induced high frequency microspore embryogenesis and efficient doubled haploid production in Brassica juncea

Three Indian Brassica juncea cultivars were studied for embryogenic response of microspores, microspore embryo regeneration, ploidy assessment of microspore-derived plants and their diploidization. Genotype dependence for microspore totipotency was observed and a significant effect of genotype by bud size selection was established. The addition of activated charcoal in NLN medium containing 13% (w/v) sucrose and 10 μM silver nitrate resulted in a fourfold increase in microspore embryogenesis, ranging from 100 to 405 embryos per Petri dish corresponding to 2,700–10,935 embryos per 100 buds. Conversion/germination of embryos produced in presence or absence of activated charcoal was similar but air-drying of microspore embryos was essential. Incubation of microspore embryos at 4 ± 1°C for 10 days in dark resulted in 82.3% conversion. The majority of plants produced from these embryos was haploid. Treating microspore-derived plants at the 3–4 leaf growth stage with 0.34% colchicine for 2–3 h resulted in greatest survival (70%) and chromosome doubling (75%) frequencies. Doubled haploid plants were self-pollinated and grown to maturity under field conditions.     

Appearance of new tetraspanin genes during vertebrate evolution

A detailed phylogenetic analysis of tetraspanins from 10 fully sequenced metazoan genomes and several fungal and protist genomes gives insight into their evolutionary origins and organization. Our analysis suggests that the superfamily can be divided into four large families. These four families-the CD family, CD63 family, uroplakin family, and RDS family-are further classified as consisting of several ortholog groups. The clustering of several ortholog groups together, such as the CD9/Tsp2/CD81 cluster, suggests functional relatedness of those ortholog groups. The fact that our studies are based on whole genome analysis enabled us to estimate not only the phylogenetic relationships among the tetraspanins, but also the first appearance in the tree of life of certain tetraspanin ortholog groups. Taken together, our data suggest that the tetraspanins are derived from a single (or a few) ancestral gene(s) through sequence divergence, rather than convergence, and that the majority of tetraspanins found in the human genome are vertebrate (21 instances), tetrapod (4 instances), or mammalian (6 instances) inventions.     

Biophysical characterization of fibroblast growth factor homologous factor-1b (FHF-1b): sodium dodecyl sulfate promotes two state folding

The current article describes the biophysical characterization and folding studies of fibroblast growth factor homologous factor-1b (FHF-1b) in comparison with acidic fibroblast growth factor (FGF-1). Our data indicates that FHF-1 is significantly more stable than FGF-1. The folding mechanism of these two proteins seems to be different although they share high degree of sequence and structural similarity. FHF-1 unfolds through stable intermediate state while unfolding of FGF-1 is two-state. Interestingly, low concentration of sodium dodecyl sulfate (SDS) drives the folding pathway of FHF-1b to two-state.     

Conservation of freshwater fish resources of India: new approaches, assessment and challenges

The freshwater resources of India are currently experiencing an alarming decline in fish biodiversity due to several factors and as a result, a sizeable portion of fresh water fishes have been categorized as threatened. This emphasizes an immediate need for initiating research and actions for alternative management techniques to protect these aquatic systems. One such option that has potential to protect freshwater ecosystem from numerous threats is the creation of freshwater aquatic sanctuary (FAS) within protected area network. Though similar conservation practices are well established in the terrestrial and marine ecosystem, however, the work on freshwater systems has been very slow and negligible. In the present communication we conceptualized the need and approach for developing FAS within the protected area network based on our observations in the water bodies of the selected wildlife sanctuaries in Northern India as well as success stories of some other countries. In this study we assessed the fish diversity in the selected protected areas of Northern India. The assessment indicated that these sanctuaries harbor 28.26–31.13% of freshwater fishes, which are threatened in other areas. Apart from Indian Major Carps, Tor putitora, Chitala chitala, Pangasius pangasius, Clupisoma gerua, Ailia coila, Aorichthys aor, Wallago attu, Rhinomugil corsula, Ompok pabda, Ombok pabo etc. were the important species encountered in the protected waters. The various issues related to FAS including objectives, approach, potential tools, implementation and management are discussed towards saving endangered fish germplasm resources. Approaches, tools and modus operandi proposed in this communication could be utilized by other developing countries in the region.