Natural variation of submergence tolerance among Arabidopsis thaliana accessions

? The exploitation of natural variation in Arabidopsis thaliana (Arabidopsis) provides a huge potential for the identification of the molecular mechanisms underlying this variation as a result of the availability of a vast array of genetic and genomic resources for this species. Eighty-six Arabidopsis accessions were screened for natural variation in flooding tolerance. This forms the first step towards the identification and characterization of the role of candidate genes contributing to flooding tolerance. ? Arabidopsis accessions at the 10-leaf stage were subjected to complete submergence in the dark. Survival curves were plotted to estimate median lethal times as a measure of tolerance. Flooding-associated survival parameters, such as root and shoot oxygen content, initial carbohydrate content and petiole elongation under water, were also measured. ? There was a significant variation in submergence tolerance among Arabidopsis accessions. However, the order of tolerance did not correlate with root and shoot oxygen content or initial amounts of shoot starch and total soluble sugars. A negative correlation was observed between submergence tolerance and underwater petiole elongation. ? Arabidopsis accessions show considerable variation in the ability to tolerate complete submergence, making it a good species in which to identify and characterize genes and to study mechanisms that contribute to survival under water.     

Modeling metabolic adjustment in <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> upon treatment with isoniazid

Complex biological systems exhibit a property of robustness at all levels of organization. Through different mechanisms, the system tries to sustain stress such as due to starvation or drug exposure. To explore whether reconfiguration of the metabolic networks is used as a means to achieve robustness, we have studied possible metabolic adjustments in Mtb upon exposure to isoniazid (INH), a front-line clinical drug. The redundancy in the genome of M. tuberculosis (Mtb) makes it an attractive system to explore if alternate routes of metabolism exist in the bacterium. While the mechanism of action of INH is well studied, its effect on the overall metabolism is not well characterized. Using flux balance analysis, inhibiting the fluxes flowing through the reactions catalyzed by Rv1484, the target of INH, significantly changes the overall flux profiles. At the pathway level, activation or inactivation of certain pathways distant from the target pathway, are seen. Metabolites such as NADPH are shown to reduce drastically, while fatty acids tend to accumulate. The overall biomass also decreases with increasing inhibition levels. Inhibition studies, pathway level clustering and comparison of the flux profiles with the gene expression data indicate the activation of folate metabolism, ubiquinone metabolism, and metabolism of certain amino acids. This analysis provides insights useful for target identification and designing strategies for combination therapy. Insights gained about the role of individual components of a system and their interactions will also provide a basis for reconstruction of whole systems through synthetic biology approaches.     

Measuring Unsafe Abortion-Related Mortality: A Systematic Review of the Existing Methods

Background

The WHO estimates that 13% of maternal mortality is due to unsafe abortion, but challenges with measurement and data quality persist. To our knowledge, no systematic assessment of the validity of studies reporting estimates of abortion-related mortality exists.

Study Design

To be included in this study, articles had to meet the following criteria: (1) published between September 1^st, 2000-December 1^st, 2011; (2) utilized data from a country where abortion is “considered unsafe”; (3) specified and enumerated causes of maternal death including “abortion”; (4) enumerated ≥100 maternal deaths; (5) a quantitative research study; (6) published in a peer-reviewed journal.

Results

7,438 articles were initially identified. Thirty-six studies were ultimately included. Overall, studies rated “Very Good” found the highest estimates of abortion related mortality (median 16%, range 1–27.4%). Studies rated “Very Poor” found the lowest overall proportion of abortion related deaths (median: 2%, range 1.3–9.4%).

Conclusions

Improvements in the quality of data collection would facilitate better understanding global abortion-related mortality. Until improved data exist, better reporting of study procedures and standardization of the definition of abortion and abortion-related mortality should be encouraged.     

Protease-activated receptor signaling increases epithelial antimicrobial peptide expression

Epithelial tissues provide both a physical barrier and an antimicrobial barrier. Antimicrobial peptides of the human beta-defensin (hBD) family are part of the innate immune responses that play a role in mucosal defense. hBDs are made in epithelia including oral epithelium where the bacterial load is particularly great. hBD-2 and hBD-3 are up-regulated in response to bacterial stimuli. Previous studies show that hBD-2 expression in human gingival epithelial cells (GEC) is stimulated by both nonpathogenic and pathogenic bacteria, including Porphyromonas gingivalis, a Gram-negative pathogen associated with periodontitis. Present evidence suggests that hBD-2 expression in GEC uses several signaling pathways, including an NF-kappaB-mediated pathway but without apparent LPS-TLR4 signaling. Protease-activated receptors (PAR) are G-protein-coupled receptors that mediate cellular responses to extracellular proteinases. P. gingivalis secretes multiple proteases that contribute to its virulence mechanisms. To determine whether PAR signaling is used in hBD-2 induction, GEC were stimulated with wild-type P. gingivalis or mutants lacking one or more proteases. hBD-2 mRNA expression was reduced in GEC stimulated with single protease mutants (11-67% compared with wild type), strongly reduced in double mutants (0.1-16%), and restored to wild-type levels (93%) in mutant with restored protease activity. Stimulation by wild type was partially blocked by inhibitors of phospholipase C, a main signaling pathway for PARs. Expression of hBD-3 was unaffected. Peptide agonist of PAR-2, but not PAR-1 activator, also induced hBD-2 in GEC. Thus, P. gingivalis proteases are directly involved in regulation of hBD-2 in cultured GEC, and this induction partially uses the PAR-2 receptor and signaling pathway.     

Organization of the aerotaxis receptor aer in the membrane of Escherichia coli

The Aer receptor guides Escherichia coli to specific oxygen and energy-generating niches. The input sensor in Aer is a flavin adenine dinucleotide-binding PAS domain, which is separated from a HAMP/signaling output domain by two membrane-spanning segments that flank a short (four-amino-acid) periplasmic loop. In this study, we determined the overall membrane organization of Aer by introducing combinations of residues that allowed us to differentiate intradimeric collisions from interdimeric collisions. Collisions between proximal residues in the membrane anchor were exclusively intra- or interdimeric but, with one exception, not both. Cross-linking profiles were consistent, with a rigid rather than flexible periplasmic loop and a tilted TM2 helix that crossed TM2' at residue V197C, near the center of the lipid bilayer. The periplasmic loop formed a stable neighborhood that (i) included a maximum of three Aer dimers, (ii) did not swap neighbors over time, and (iii) appeared to be constrained by interactions in the cytosolic signaling domain.     

Conformational behavior of polypeptides derived through simultaneous global conservative site-directed mutagenesis of chymotrypsin inhibitor 2

The natural occurrence of conservative residue substitutions in proteins suggests that side-chain packing schemes in protein interiors can accommodate mutational replacements of residues by others of similar nature. To explore the extent to which such substitutions are tolerated, especially when introduced simultaneously and globally over the entire length of a polypeptide chain, we examined the conformational behavior of a model 65 residues-long protein, wild-type chymotrypsin inhibitor 2 (WTCI2), and two globally-mutated (GM) variants named GMCI2-1 and GMCI2-2, each incorporating 55 conservative residue substitutions. GMCI2-1, was soluble over a wide range of pH, and folded into a compact, spherical, monomer marked by (i) complete absence of surface hydrophobicity, (ii) a WTCI2-like betaII-type CD spectrum, (iii) high WTCI2-like thermal stability, and (d) 1D and 2D NMR spectra characteristic of folded protein structure. GMCI2-2 was insoluble over a wide range of pH, and could be solubilized only at pH 4.0, showing non-WTCI2-like far-UV CD spectra characterized by high helical content. These results tentatively indicate that polypeptides incorporating residues of identical nature at equivalent chain locations can show the potential to fold with similar characteristics. However, further detailed investigations would be required to determine whether indeed the structural fold of GMCI2-1 resembles that of WTCI2, and to evaluate the extent to which it does so.     

Growth factors upregulate deposition and remodeling of ECM by endothelial cells cultured for tissue-engineering applications

Appropriate matrix formation, turnover and remodeling in tissue-engineered small diameter vascular conduits are crucial for their long-term function. The interaction between cells and extra-cellular components is indispensable in determining cellular behavior in tissues and on biomaterials. The fibrin that contains fibronectin shows promise in most aspects as a tissue engineering scaffold, whereas, deposition of elastin and collagen by endothelial cells grown in the lumen of the construct is desirable to improve post implant retention, mechanical stability and vaso-responsiveness. So far there is no report on production of extra-cellular matrix (ECM) proteins, elastin and collagen by endothelial cells (EC) in in vitro culture conditions. In this study, we have used a biomimetic approach of providing multiple growth factors (GF) in the fibronectin (FN)-containing fibrin matrix to induce production of elastin and collagen by the endothelial cells for application in vascular tissue engineering. Deposition of elastin and collagens with matrix remodeling is demonstrated through qualitative analysis of the matrices that were recovered after growing cells on the initial fibrin-FN-GF matrix. Expressions of mRNA for both proteins were assessed by real time polymerase chain reaction (RT-PCR) to estimate the effects of multiple growth factor compositions. Marked deposition of elastin and collagen was evidenced by staining the recovered matrix after different culture intervals. Obviously, the biomimetic environment created by adding angiogenic and platelet growth factors in the fibrin-fibronectin-gelatin matrix can induce deposition of collagens and elastin by EC.     

On the macro-micro-morphology of organs of host invasion in hemiparasite Helicanthes elasticus (Desv.) Danser

Loranthaceae family includes hemiparasitic members which are seen invading a wide range of commercial crops. Helicanthes elasticus (Desv.) Danser is very common on mango trees. Though parasitic in nature, this mistletoe is also medicinally important as fetoprotective, against vesicular calculi and kidney infections. This study is an attempt to document macro-microscopical features of parasitic root, fruit and host-mistletoe tissue interaction in the haustorium of H. elasticus growing on mango stems. Collection, preservation, sectioning, staining and photomicrography of the root, fruit and host-mistletoe union were done as per standard methodologies of anatomical studies. Though there is resemblance to the normal roots in morphology as well as anatomy, the microscopic finding of large number of branched stone cells in the roots is interesting. The morpho-anatomical features recorded would help in understanding the infection biology of this mistletoe. The eradication during the earlier stages of its establishment from seed or from the root creeping over the surface of the host can help in controlling this parasite infection on commercially important host plants.