DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family

SUMMARY: DetectIng Variability in Evolutionary Rates among GEnes (DIVERGE) is a software system to study functional divergence of a protein family by detecting site-specific change in evolutionary rate using a multiple alignment of amino acid sequences for a given phylogenetic tree. The program first conducts a statistical test for site-specific rate shifts along the tree, and predicting candidate amino acid residues responsible for functional divergence based on posterior analysis. These results can then be mapped on the 3D protein structure if available. AVAILABILITY: DIVERGE is available free of charge from http://xgu1.zool.iastate.edu/. Distribution packages for both Linux and Microsoft Windows operating systems are available, including manual and example files.     

A predominantly nuclear protein affecting cytoplasmic localization of beta-actin mRNA in fibroblasts and neurons.

The localization of beta-actin mRNA to the leading lamellae of chicken fibroblasts and neurite growth cones of developing neurons requires a 54-nt localization signal (the zipcode) within the 3' untranslated region. In this study we have identified and isolated five proteins binding to the zipcode. One of these we previously identified as zipcode binding protein (ZBP)1, a 4-KH domain protein. A second is now investigated in detail: a 92-kD protein, ZBP2, that is especially abundant in extracts from embryonic brain. We show that ZBP2 is a homologue of the human hnRNP protein, KSRP, that appears to mediate pre-mRNA splicing. However, ZBP2 has a 47-amino acid (aa) sequence not present in KSRP. Various portions of ZBP2 fused to GFP indicate that the protein most likely shuttles between the nucleus and the cytoplasm, and that the 47-aa insert promotes the nuclear localization. Expression of a truncated ZBP2 inhibits the localization of beta-actin mRNA in both fibroblast and neurons. These data suggest that ZBP2, although predominantly a nuclear protein, has a role in the cytoplasmic localization of beta-actin mRNA.     

Site-specific protein dynamics in communication pathway from sensor to signaling domain of oxygen sensor protein, HemAT-Bs: Time-resolved Ultraviolet Resonance Raman Study

HemAT-Bs is a heme-based signal transducer protein responsible for aerotaxis. Time-resolved ultraviolet resonance Raman (UVRR) studies of wild-type and Y70F mutant of the full-length HemAT-Bs and the truncated sensor domain were performed to determine the site-specific protein dynamics following carbon monoxide (CO) photodissociation. The UVRR spectra indicated two phases of intensity changes for Trp, Tyr, and Phe bands of both full-length and sensor domain proteins. The W16 and W3 Raman bands of Trp, the F8a band of Phe, and the Y8a band of Tyr increased in intensity at hundreds of nanoseconds after CO photodissociation, and this was followed by recovery in ～50 μs. These changes were assigned to Trp-132 (G-helix), Tyr-70 (B-helix), and Phe-69 (B-helix) and/or Phe-137 (G-helix), suggesting that the change in the heme structure drives the displacement of B- and G-helices. The UVRR difference spectra of the sensor domain displayed a positive peak for amide I in hundreds of nanoseconds after photolysis, which was followed by recovery in ～50 μs. This difference band was absent in the spectra of the full-length protein, suggesting that the isolated sensor domain undergoes conformational changes of the protein backbone upon CO photolysis and that the changes are restrained by the signaling domain. The time-resolved difference spectrum at 200 μs exhibited a pattern similar to that of the static (reduced - CO) difference spectrum, although the peak intensities were much weaker. Thus, the rearrangements of the protein moiety toward the equilibrium ligand-free structure occur in a time range of hundreds of microseconds.     

A functional gene array for detection of bacterial virulence elements

Emerging known and unknown pathogens create profound threats to public health. Platforms for rapid detection and characterization of microbial agents are critically needed to prevent and respond to disease outbreaks. Available detection technologies cannot provide broad functional information about known or novel organisms. As a step toward developing such a system, we have produced and tested a series of high-density functional gene arrays to detect elements of virulence and antibiotic resistance mechanisms. Our first generation array targets genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for gene family detection and discrimination. When tested with organisms at varying phylogenetic distances from the four target strains, the array detected orthologs for the majority of targeted gene families present in bacteria belonging to the same taxonomic family. In combination with whole-genome amplification, the array detects femtogram concentrations of purified DNA, either spiked in to an aerosol sample background, or in combinations from one or more of the four target organisms. This is the first report of a high density NimbleGen microarray system targeting microbial antibiotic resistance and virulence mechanisms. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples.     

Serum cholesterol and triglycerides in postpartum beef cows and their relationship to the resumption of ovulation

The variations in lipid metabolism according to the physiological stage and their relationship to the resumption of postpartum ovarian cyclicity were assessed in Limousine beef cows fed a grass diet over 3 yr. Weekly blood samples were collected from 59 cows beginning 10 wk before to 20 wk after calving to evaluate serum cholesterol and triglyceride concentrations and electrophoretic lipoprotein fractions. After parturition, progesterone concentrations were also measured at weekly intervals to determine time of resumption of ovulation. Cows were categorized by resumption of postpartum ovarian cyclicity into 3 groups: early (4 to 6 wk post partum, n = 36); mid (7 to 10 wk post partum, n = 46) and late (after 11 wk post partum, n = 38). Higher serum triglyceride values (P<0.05) were observed during the last 10 wk of pregnancy (0.36+/-0.15 g/L) than during the first 20 wk of suckling (0.29+/-0.09 g/L). Cholesterol values decreased significantly (P<0.05) at the end of pregnancy, were minimal (1.01+/-0.03 g/L) at parturition, and increased again up to 9 wk post calving. Increased cholesterolemia and low serum triglyceride values after calving could be linked to the increased bovine alpha-lipoprotein fraction and decreased beta fraction. Serum triglyceride concentrations were not related to the resumption of postpartum ovarian cyclicity. Higher serum cholesterol values were observed from 2 wk before to 4 wk after calving in cows with early rather than mid and late resumption of ovarian cyclicity. Therefore, modifications in lipid metabolism during the puerperium seem to be related to resumption of cyclicity during the early postpartum period.     

Projecting future grassland productivity to assess the sustainability of potential biofuel feedstock areas in the Greater Platte River Basin

This study projects future (e.g., 2050 and 2099) grassland productivities in the Greater Platte River Basin (GPRB) using ecosystem performance (EP, a surrogate for measuring ecosystem productivity) models and future climate projections. The EP models developed from a previous study were based on the satellite vegetation index, site geophysical and biophysical features, and weather and climate drivers. The future climate data used in this study were derived from the National Center for Atmospheric Research Community Climate System Model 3.0 ‘SRES A1B’ (a ‘middle’ emissions path). The main objective of this study is to assess the future sustainability of the potential biofuel feedstock areas identified in a previous study. Results show that the potential biofuel feedstock areas (the more mesic eastern part of the GPRB) will remain productive (i.e., aboveground grassland biomass productivity >2750 kg ha^?1 year^?1) with a slight increasing trend in the future. The spatially averaged EPs for these areas are 3519, 3432, 3557, 3605, 3752, and 3583 kg ha^?1 year^?1 for current site potential (2000–2008 average), 2020, 2030, 2040, 2050, and 2099, respectively. Therefore, the identified potential biofuel feedstock areas will likely continue to be sustainable for future biofuel development. On the other hand, grasslands identified as having no biofuel potential in the drier western part of the GPRB would be expected to stay unproductive in the future (spatially averaged EPs are 1822, 1691, 1896, 2306, 1994, and 2169 kg ha^?1 year^?1 for site potential, 2020, 2030, 2040, 2050, and 2099). These areas should continue to be unsuitable for biofuel feedstock development in the future. These future grassland productivity estimation maps can help land managers to understand and adapt to the expected changes in future EP in the GPRB and to assess the future sustainability and feasibility of potential biofuel feedstock areas.     

Population suppression of Bemisia tabaci (Hemiptera: Aleyrodidae) using yellow sticky traps and Eretmocerus nr. rajasthanicus (Hymenoptera: Aphelinidae) on tomato plants in greenhouses

We conducted three experiments for management of Bemisia tabaci (Gennadius) biotype ‘B’ on tomatoes under greenhouse conditions: (i) vertically placing yellow sticky cards either parallel or perpendicular to tomato rows at a rate of 1 per 3‐m row; (ii) releasing Eretmocerus sp. nr. rajasthanicus once at 30 adults/m² in the high whitefly density greenhouses (> 10 adults/plant), or twice at 15 adults/m² at a 5‐day interval in the low whitefly density greenhouses (< 10 adults/plant); and (iii) using combinations of yellow sticky cards that were placed vertically parallel to tomato rows and parasitoids released once at 30/m² in high whitefly density greenhouses or twice at 15/m² at a 5‐day interval in low whitefly density greenhouses. Our data show that yellow sticky cards trapped B. tabaci adults and significantly reduced whitefly populations on tomato. The yellow sticky cards that were placed parallel to tomato rows caught significantly more whitefly adults than those placed perpendicular to tomato rows on every sampling date. In the treatment where parasitoids were released once at 30/m² in high whitefly density greenhouses, the number of live whitefly nymphs were reduced from 4.6/leaf to 2.9/leaf in 40 days as compared with those on untreated plants on which live whitefly nymphs increased from 4.4/leaf to 8.9/leaf. In the treatment where parasitoids were released twice at 15/m² in low whitefly density greenhouses, the numbers of live nymphs of B. tabaci on tomato leaves were reduced from 2.1/leaf to 1.7/leaf in 20 days as compared with those on untreated plants on which numbers of live nymphs of B. tabaci increased from 2.2/leaf to 4.5/leaf. In the treatment of yellow sticky cards and parasitoid release once at 30/m² in high whitefly density greenhouses, the numbers of live nymphs of B. tabaci on tomato leaves were reduced from 7.2/leaf to 1.9/leaf, and in the treatment of yellow sticky cards and parasitoid release twice at 15/m² at a 5‐day interval at low whitefly density, the numbers of live nymphs of B. tabaci on tomato leaves were reduced from 2.5/leaf to 0.8/leaf; whereas the numbers of live nymphs of B. tabaci on untreated plants increased from 4.4/leaf to 8.9/leaf. An integrated program for management of B. tabaci on greenhouse vegetables by using yellow sticky cards, parasitoids and biorational insecticides is discussed.     

Eight Functional Polymorphisms in the Estrogen Receptor 1 Gene and Endometrial Cancer Risk: A Meta-Analysis

Background and Objective

Emerging evidence indicates that common functional polymorphisms in the estrogen receptor 1 (ESR1) gene may have an impact on an individual’s susceptibility to endometrial cancer, but individually published results are inconclusive. The aim of this meta-analysis is to derive a more precise estimation of the associations between eight polymorphisms in the ESR1 gene and endometrial cancer risk.

Methods

A literature search of PubMed, Embase, Web of Science and China Biology Medicine (CBM) databases was conducted on publications published before November 1^st, 2012. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. Statistical analyses were performed using the STATA 12.0 software.

Results

Thirteen case-control studies were included with a total of 7,649 endometrial cancer cases and 16,855 healthy controls. When all the eligible studies were pooled into the meta-analysis, the results indicated that PvuII (C>T) polymorphism was associated with an increased risk of endometrial cancer, especially among Caucasian populations. There were also significant associations between rs3020314 (C>T) polymorphism and an increased risk of endometrial cancer. Furthermore, rs2234670 (S/L) polymorphism may decrease the risk of endometrial cancer. However, no statistically significant associations were found in XbaI (A>G), Codon 325 (C>G), Codon 243 (C>T), VNTR (S/L) and rs2046210 (G>A) polymorphisms.

Conclusion

The current meta-analysis suggests that PvuII (C>T) and rs3020314 (C>T) polymorphisms may be risk factors for endometrial cancer, especially among Caucasian populations.     

Clinical Significance of MiR-137 Expression in Patients with Gastric Cancer After Radical Gastrectomy

The dysregulation of miR-137 plays vital roles in the oncogenesis and progression of various types of cancer, but its role in prognosis of gastric cancer patients remains unknown. This study was designed to investigate the expression and prognostic significance of miR-137 in gastric cancer patients after radical gastrectomy. Quantitative real-time PCR (qRT-PCR) was performed to evaluate the expression of miR-137 in human gastric cancer cell lines and tissues in patients with gastric adenocarcinoma. Results were assessed for association with clinical factors and overall survival by using Kaplan-Meier analysis. Prognostic values of miR-137 expression and clinical outcomes were evaluated by Cox regression analysis. The results exhibited that the expression level of miR-137 was decreased in human gastric cancer cell lines and tissues, and down-regulated expression of miR-137 was associated with tumor cell differentiation, N stage, and TNM stage. Decreased miR-137 expression in gastric cancer tissues was positively correlated with poor overall survival of gastric cancer patients. Further multivariate Cox regression analysis suggested that miR-137 expression was an independent prognostic indicator for gastric cancer except for TNM stage. Applying the prognostic value of miR-137 expression to TNM stage III group showed a better risk stratification for overall survival. In conclusion, the results reinforced the critical role for the down-regulated miR-137 expression in gastric cancer and suggested that miR-137 expression could be a prognostic indicator for this disease. In addition, these patients with TNM stage III gastric cancer and low miR-137 expression might need more aggressive postoperative treatment and closer follow-up.     

An apoA-I mimetic peptibody generates HDL-like particles and increases alpha-1 HDL subfraction in mice

The aim of this study is to investigate the capability of an apoA-I mimetic with multiple amphipathic helices to form HDL-like particles in vitro and in vivo. To generate multivalent helices and to track the peptide mimetic, we have constructed a peptibody by fusing two tandem repeats of 4F peptide to the C terminus of a murine IgG Fc fragment. The resultant peptidbody, mFc-2X4F, dose-dependently promoted cholesterol efflux in vitro, and the efflux potency was superior to monomeric 4F peptide. Like apoA-I, mFc-2X4F stabilized ABCA1 in J774A.1 and THP1 cells. The peptibody formed larger HDL particles when incubated with cultured cells compared with those by apoA-I. Interestingly, when administered to mice, mFc-2X4F increased both pre-β and α-1 HDL subfractions. The lipid-bound mFc-2X4F was mostly in the α-1 migrating subfraction. Most importantly, mFc-2X4F and apoA-I were found to coexist in the same HDL particles formed in vivo. These data suggest that the apoA-I mimetic peptibody is capable of mimicking apoA-I to generate HDL particles. The peptibody and apoA-I may work cooperatively to generate larger HDL particles in vivo, either at the cholesterol efflux stage and/or via fusion of HDL particles that were generated by the peptibody and apoA-I individually.