Nucleotide sequence of initiator tRNA from Mycobacterium smegmatis.

The nucleotide sequence of initiator tRNA from Mycobacterium smegmatis was determined to be pCGCGGGGUGGAGCAGCUCGGDAGCUCGCUGGGCUCAUAACCCAGAGm7GUCG CAGGU psi CGm1AAUCCUGUCCCCGCUACCAOH . The nucleotide sequence of Mycobacterium initiator tRNA was found to be the same as that of Streptomyces initiator tRNA, except that G46 and A57 were replaced by m7G46 and G57 , respectively. The striking feature of Mycobacterium initiator tRNA is the absence of ribothymidine at residue 54, and the presence of 1-methyladenosine at residue 58 which makes the sequence of this tRNA similar to that of eukaryotic initiator tRNA.     

Differential patterns of peroxynitrite mediated apoptosis in proximal tubular epithelial cells following ATP depletion recovery

Ischemia-reperfusion injury (IRI) is characterized by ATP depletion in the ischemic phase, followed by a rapid increase in reactive oxygen species, including peroxynitrite in the reperfusion phase. In this study, we examined the role of peroxynitrite on cytotoxicity and apoptosis in an in vitro model of ATP depletion-recovery. Porcine proximal tubular epithelial (LLC-PK₁) cells were ATP depleted for either 2 h (2/2) or 4 h (4/2) followed by recovery in serum free medium for 2 h. A subset of cells was treated with 100 μM of the peroxynitrite scavenger, iron (III) tetrakis (N-methyl-4′pyridyl) porphyrin pentachloride (FeTMPyP) 30 min prior to and during treatment/recovery. Treatment with FeTMPyP reduced cytotoxicity and superoxide levels at both the 2/2 and 4/2 time points, however FeTMPyP decreased nitric oxide only at the 2/2 time point. FeTMPyP also partially blocked caspase-3 and caspase-8 activation at both 2/2 and 4/2 time points. At the 4/2 time point, FeTMPyP also partially inhibited the ATP depletion mediated increase in tumor necrosis factor alpha (TNF-α) and decreased Bax and FasL gene expression. These data show that peroxynitrite induces apoptosis by activation of multiple pathways depending on length and severity of insult following ATP depletion-recovery.     

Novel phosphate solubilizing bacteria ‘Pantoea cypripedii PS1’ along with Enterobacter aerogenes PS16 and Rhizobium ciceri enhance the growth of chickpea (Cicer arietinum L.)

Phosphate solubilizing bacteria (PSB) are known to convert the insoluble forms of phosphate to soluble one and make them available for plant uptake. The present study aimed to isolate PSB from the rhizosphere of chickpea (Cicer arietinum L. cv. GPF2) and examine their effect on the growth and seed number. The isolated PSB were analyzed for phosphate solubilization, indole acetic acid and siderophore production. PSB were characterized for phenotypic and biochemical properties, BIOLOG and whole-cell fatty acid methyl ester profile and found to be closely related to Pantoea cypripedii and Enterobacter aerogenes based on 16s rRNA gene sequencing. A high increase in growth of C. arietinum was observed when innoculated with PSB in tricalcium phosphate amended soils. A higher uptake in total P (53 %) of plants was observed when inoculated with mixture of P. cypripedii and E. aerogenes along with Rhizobium ciceri as compared to respective control plants which significantly increased the seed number (98.3 %) and seed weight (46.1 %). This study demonstrated the ability of novel PSB P. cypripedii along with E. aerogenes and R. ciceri to promote chickpea growth.     

A hybrid model of intercellular tension and cell–matrix mechanical interactions in a multicellular geometry

Biomechanics and Modeling in Mechanobiology - Epithelial cells form continuous sheets of cells that exist in tensional homeostasis. Homeostasis is maintained through cell-to-cell junctions that...     

Sea level,topography and island diversity: phylogeography of the Puerto Rican Red‐eyed Coquí, Eleutherodactylus antillensis

Quaternary climatic oscillations caused changes in sea level that altered the size, number and degree of isolation of islands, particularly in land‐bridge archipelagoes. Elucidating the demographic effects of these oscillations increases our understanding of the role of climate change in shaping evolutionary processes in archipelagoes. The Puerto Rican Bank (PRB) (Puerto Rico and the Eastern Islands, which comprise Vieques, Culebra, the Virgin Islands and associated islets) in the eastern Caribbean Sea periodically coalesced during glaciations and fragmented during interglacial periods of the quaternary. To explore population‐level consequences of sea level changes, we studied the phylogeography of the frog Eleutherodactylus antillensis across the archipelago. We tested hypotheses encompassing vicariance and dispersal narratives by sequencing mtDNA (c. 552 bp) of 285 individuals from 58 localities, and four nuDNA introns (totalling c. 1633 bp) from 173 of these individuals. We found low support for a hypothesis of divergence of the Eastern Islands populations prior to the start of the penultimate interglacial c. 250 kya, and higher support for a hypothesis of colonization of the Eastern Islands from sources in eastern Puerto Rico during the penultimate and last glacial period, when a land bridge united the PRB. The Río Grande de Loíza Basin in eastern Puerto Rico delineates a phylogeographic break. Haplotypes shared between the PRB and St. Croix (an island c. 105 km south‐east of this archipelago) likely represent human‐mediated introductions. Our findings illustrate how varying degrees of connectivity and isolation influence the evolution of tropical island organisms.     

G protein betagamma11 complex translocation is induced by Gi, Gq and Gs coupling receptors and is regulated by the alpha subunit type

G protein activation by Gi/Go coupling M2 muscarinic receptors, Gq coupling M3 receptors and Gs coupling beta2 adrenergic receptors causes rapid reversible translocation of the G protein gamma11 subunit from the plasma membrane to the Golgi complex. Co-translocation of the beta1 subunit suggests that gamma11 translocates as a betagamma complex. Pertussis toxin ADP ribosylation of the alphai subunit type or substitution of the C terminal domain of alphao with the corresponding region of alphas inhibits gamma11 translocation demonstrating that alpha subunit interaction with a receptor and its activation are requirements for the translocation. The rate of gamma11 translocation is sensitive to the rate of activation of the G protein alpha subunit. alpha subunit types that show high receptor activated rates of guanine nucleotide exchange in vitro support high rates of gamma11 translocation compared to alpha subunit types that have a relatively lower rate of guanine nucleotide exchange. The results suggest that the receptor induced translocation of gamma11 is controlled by the rate of cycling of the G protein through active and inactive forms. They also demonstrate that imaging of gamma11 translocation can be used as a non-invasive tool to measure the relative activities of wild type or mutant receptor and alpha subunit types in a live cell.     

Discovery of novel inhibitors of the ZipA/FtsZ complex by NMR fragment screening coupled with structure-based design

ZipA is a membrane anchored protein in Escherichia coli that interacts with FtsZ, a homolog of eukaryotic tubulins, forming a septal ring structure that mediates bacterial cell division. Thus, the ZipA/FtsZ protein-protein interaction is a potential target for an antibacterial agent. We report here an NMR-based fragment screening approach which identified several hits that bind to the C-terminal region of ZipA. The screen was performed by 1H-15N HSQC experiments on a library of 825 fragments that are small, lead-like, and highly soluble. Seven hits were identified, and the binding mode of the best one was revealed in the X-ray crystal structure. Similar to the ZipA/FtsZ contacts, the driving force in the binding of the small molecule ligands to ZipA is achieved through hydrophobic interactions. Analogs of this hit were also evaluated by NMR and X-ray crystal structures of these analogs with ZipA were obtained, providing structural information to help guide the medicinal chemistry efforts.     

Bioinformatic requirements for protein database searching using predicted epitopes from disease-associated antibodies

We describe a new approach to identify proteins involved in disease pathogenesis. The technology, Epitope-Mediated Antigen Prediction (E-MAP), leverages the specificity of patients' immune responses to disease-relevant targets and requires no prior knowledge about the protein. E-MAP links pathologic antibodies of unknown specificity, isolated from patient sera, to their cognate antigens in the protein database. The E-MAP process first involves reconstruction of a predicted epitope using a peptide combinatorial library. We then search the protein database for closely matching amino acid sequences. Previously published attempts to identify unknown antibody targets in this manner have largely been unsuccessful for two reasons: 1) short predicted epitopes yield too many irrelevant matches from a database search and 2) the epitopes may not accurately represent the native antigen with sufficient fidelity. Using an in silico model, we demonstrate the critical threshold requirements for epitope length and epitope fidelity. We find that epitopes generally need to have at least seven amino acids, with an overall accuracy of >70% to the native protein, in order to correctly identify the protein in a nonredundant protein database search. We then confirmed these findings experimentally, using the predicted epitopes for four monoclonal antibodies. Since many predicted epitopes often fail to achieve the seven amino acid threshold, we demonstrate the efficacy of paired epitope searches. This is the first systematic analysis of the computational framework to make this approach viable, coupled with experimental validation.