Marker assisted breeding for transformability in maize

Corn lines with improved culturability and transformability were produced using Marker Assisted Breeding (MAB) to introgress specific regions from the highly transformable hybrid, Hi-II, into the elite line, FBLL that responds very poorly in culture. FBLL is a female inbred parental stiff-stalk line that has been used to produce a series of some of DEKALB’s historically best selling hybrids. Five unlinked regions important for culturability and transformability were identified by segregation distortion analysis and introgressed into FBLL to produce the highly transformable FBLL-MAB lines. Agrobacterium mediated transformation was used to screen the FBLL-MAB lines and select the most efficient lines for transformation using immature embryo explants. Two highly efficient transformation systems were developed using kanamycin and glyphosate as selective agents. To evaluate agronomics, two testcross hybrids were produced for each of the three lead FBLL-MAB lines. A 25-location, 3-replication yield trial was used to evaluate grain yield, yield stability, and agronomic characteristics of the hybrids. Yields were found to be 2–5% lower and more stable (across a diverse set of environments) among hybrids produced with the FBLL-MAB lines as compared to the same hybrids produced with FBLL.     

Proteomics on the rims: insights into the biology of the nuclear envelope and flagellar pocket of trypanosomes

Trypanosomatids represent the causative agents of major diseases in humans, livestock and plants, with inevitable suffering and economic hardship as a result. They are also evolutionarily highly divergent organisms, and the many unique aspects of trypanosome biology provide opportunities in terms of identification of drug targets, the challenge of exploiting these putative targets and, at the same time, significant scope for exploration of novel and divergent cell biology. We can estimate from genome sequences that the degree of divergence of trypanosomes from animals and fungi is extreme, with perhaps one third to one half of predicted trypanosome proteins having no known function based on homology or recognizable protein domains/architecture. Two highly important aspects of trypanosome biology are the flagellar pocket and the nuclear envelope, where in silico analysis clearly suggests great potential divergence in the proteome. The flagellar pocket is the sole site of endo- and exocytosis in trypanosomes and plays important roles in immune evasion via variant surface glycoprotein (VSG) trafficking and providing a location for sequestration of various invariant receptors. The trypanosome nuclear envelope has been largely unexplored but, by analogy with higher eukaryotes, roles in the regulation of chromatin and most significantly, in controlling VSG gene expression are expected. Here we discuss recent successful proteomics-based approaches towards characterization of the nuclear envelope and the endocytic apparatus, the identification of conserved and novel trypanosomatid-specific features, and the implications of these findings.     

UniDrug-target: a computational tool to identify unique drug targets in pathogenic bacteria

Background

Targeting conserved proteins of bacteria through antibacterial medications has resulted in both the development of resistant strains and changes to human health by destroying beneficial microbes which eventually become breeding grounds for the evolution of resistances. Despite the availability of more than 800 genomes sequences, 430 pathways, 4743 enzymes, 9257 metabolic reactions and protein (three-dimensional) 3D structures in bacteria, no pathogen-specific computational drug target identification tool has been developed.

Methods

A web server, UniDrug-Target, which combines bacterial biological information and computational methods to stringently identify pathogen-specific proteins as drug targets, has been designed. Besides predicting pathogen-specific proteins essentiality, chokepoint property, etc., three new algorithms were developed and implemented by using protein sequences, domains, structures, and metabolic reactions for construction of partial metabolic networks (PMNs), determination of conservation in critical residues, and variation analysis of residues forming similar cavities in proteins sequences. First, PMNs are constructed to determine the extent of disturbances in metabolite production by targeting a protein as drug target. Conservation of pathogen-specific protein''s critical residues involved in cavity formation and biological function determined at domain-level with low-matching sequences. Last, variation analysis of residues forming similar cavities in proteins sequences from pathogenic versus non-pathogenic bacteria and humans is performed.

Results

The server is capable of predicting drug targets for any sequenced pathogenic bacteria having fasta sequences and annotated information. The utility of UniDrug-Target server was demonstrated for Mycobacterium tuberculosis (H37Rv). The UniDrug-Target identified 265 mycobacteria pathogen-specific proteins, including 17 essential proteins which can be potential drug targets.

Conclusions/Significance

UniDrug-Target is expected to accelerate pathogen-specific drug targets identification which will increase their success and durability as drugs developed against them have less chance to develop resistances and adverse impact on environment. The server is freely available at http://117.211.115.67/UDT/main.html. The standalone application (source codes) is available at http://www.bioinformatics.org/ftp/pub/bioinfojuit/UDT.rar.     

Modulation of in vitro activity of zymogenic and mature recombinant human β-secretase by dietary plants

The in vitro activity of human recombinant β-secretase (BACE1) was studied using a fluorogenic substrate based on the cleavage site for the enzyme in the Swedish mutation of amyloid precursor protein. The enzyme was inhibited by a control peptide inhibitor with good repeatability. The enzyme preparation comprised a mixture of pro-enzyme or zymogen and mature enzyme whereby the pro-enzyme sequence forms a 'flap' that can obstruct the binding site. 'Open flap' forms of the zymogen and mature enzyme are active, but the 'closed flap' form of the zymogen is inactive. This mixture of enzyme populations permitted apparent stimulation of enzyme activity under particular conditions, presumably due to facilitating flap-opening of the zymogen. As reported for heparin, enzyme activation was stimulated in the presence of low concentrations of Tween 20 and dimethylsulfoxide before becoming inhibited at higher concentrations. Dietary plant extracts either consistently inhibited (e.g. clove, tea, cinammon) or consistently stimulated (e.g. mushroom, parsley, asparagus) BACE1. Common structural features identified by Fourier transform infrared spectroscopy revealed that BACE1 activity could be explained by differential interactions of either small molecule or polymeric species with mature versus zymogen forms of the enzyme, respectively. Further, enzyme activity could be reversed by mixtures of high and low mass species. These results may have implications for the regulation of β-secretase activity in vivo by either endogenous or possibly dietary factors and for a potential role of BACE1 in stimulation of the production of amyloid beta peptide in sporadic Alzheimer's disease.     

The structure and conformation of a water-insoluble (1-->3)-,(1-->6)-beta-d-glucan from the fruiting bodies of Pleurotus florida

A water-insoluble glucan, PFPSIN, has been isolated from the aqueous extract of an edible mushroom Pleurotus florida. On the basis of total acid hydrolysis, methylation analysis, periodate oxidation, Smith degradation, and (13)C NMR experiments, the repeating unit of the polysaccharide was established as Conformational analysis revealed the triple helical conformation of this glucan.     

Deciphering the “Fuzzy” Interaction of FG Nucleoporins and Transport Factors Using Small-Angle Neutron Scattering

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Cure of tuberculosis using nanotechnology: An overview

Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), a major health issue of the present era. The bacterium inhabits the host macrophage and other immune cells where it modulates the lysosome trafficking protein, hinders the formation of phagolysosome, and blocks the TNF receptor-dependent apoptosis of host macrophage/monocytes. Other limitations such as resistance to and low bioavailability and bio-distribution of conventional drugs aid to their high virulence and human mortality. This review highlights the use of nanotechnology-based approaches for drug formulation and delivery which could open new avenues to limit the pathogenicity of tuberculosis. Moreover phytochemicals, such as alkaloids, phenols, saponins, steroids, tannins, and terpenoids, extracted from terrestrial plants and mangroves seem promising against M. tuberculosis through different molecular mechanisms. Further understanding of the genomics and proteomics of this pathogenic microbe could also help overcome various research gaps in the path of developing a suitable therapy against tuberculosis.     

Prognosis in Acute Cerebrovascular Accidents in Relation to Respiratory Pattern and Blood—gas Tensions

Respiratory pattern and arterial blood gas tensions were assessed in patients with acute cerebrovascular accidents. Hyperventilation, low Pco₂, and high arterial pH were associated with a poor prognosis, whereas patients with normal respiratory pattern and blood gas tensions survived. Periodic and Cheyne-Stokes breathing carried an intermediate prognosis.     

in Vitro Somatic Embryogenesis in Typhonium Trilobatum Schott.

An in vitro protocol was developed for the production of plants via somatic embryogenesis in callus cultures derived from petiole and leaf explants of Typhonium trilobatum. Optimum callus formation was achieved on semisolid Murashige and Skoog's [9] medium supplemented with 0.25 mg L–1 kinetin and 3.0 mgL–1 1-naphthaleneacetic acid (NAA) after 6 weeks of culture. Somatic embryogenesis was achieved upon transferring the callus to a medium containing 1.0 mg Lminus 1 kinetin and 0.25 mg Lminus 1 NAA. In vitro tuberization was also achieved on medium containing 1/2 strength MS basal salts supplemented with 1.0 mg L–1 Kinetin and 0.1 mg L–1 NAA. Embryo maturation and germination was achieved on the MS basal salts supplemented with 0.01 mg L–1 NAA and 2% (w/v) sucrose. Some thousands somatic embryo derived plantlets were hardened in the greenhouse and eventually planted in the open field.