Fourier transform coupled to tryptophan-scanning mutagenesis: lessons from its application to the prediction of secondary structure in the acetylcholine receptor lipid-exposed transmembrane domains

Although Fourier transform (FT) and tryptophan-scanning mutagenesis (TrpScanM) have been extremely useful for predicting secondary structures of membrane proteins, they are deemed to be low-resolution techniques. Herein, we describe the combined use of FT and TrpScanM (FT-TrpScanM) as a more reliable approach for the prediction of secondary structure. Five TrpScanM studies of the acetylcholine receptor lipid-exposed transmembrane domains (LETMDs) were revisited and analyzed by FT-TrpScanM. FT analysis of the raw data from the aforementioned TrpScanM studies supports and validates the conclusions derived from their tryptophan-periodicity profiles. Furthermore, by FT-TrpScanM, we were able to determine the minimum number of consecutive tryptophan substitutions necessary for more robust prediction of alpha-helical secondary structures and evaluate the quality of structure predictions by alpha-helical character curves. Finally, this study encourages future utilization of FT-TrpScanM to more reliably predict secondary structures of the membrane protein LETMDs.     

Melanoma differentiation-associated gene-7/IL-24 gene enhances NF-kappa B activation and suppresses apoptosis induced by TNF

Melanoma differentiation-associated gene-7 (mda-7), also referred to as IL-24, is a novel growth regulatory cytokine that has been shown to regulate the immune system by inducing the expression of inflammatory cytokines, such as TNF, IL-1, and IL-6. Whether the induction of these cytokines by MDA-7 is mediated through activation of NF-kappaB or whether it regulates cytokine signaling is not known. In the present report we investigated the effect of MDA-7 on NF-kappaB activation and on TNF-induced NF-kappaB activation and apoptosis in human embryonic kidney 293 cells. Stable or transient transfection with mda-7 into 293 cells failed to activate NF-kappaB. However, TNF-induced NF-kappaB activation was significantly enhanced in mda-7-transfected cells, as indicated by DNA binding, p65 translocation, and NF-kappaB-dependent reporter gene expression. Mda-7 transfection also potentiated NF-kappaB reporter activation induced by TNF receptor-associated death domain and TNF receptor-associated factor-2. Cytoplasmic MDA-7 with deleted signal sequence was as effective as full-length MDA-7 in potentiating TNF-induced NF-kappaB reporter activity. Secretion of MDA-7 was not required for the potentiation of TNF-induced NF-kappaB activation. TNF-induced expression of the NF-kappaB-regulated gene products cyclin D1 and cyclooxygenase-2, were significantly up-regulated by stable expression of MDA-7. Furthermore, MDA-7 expression abolished TNF-induced apoptosis, and suppression of NF-kappaB by IkappaBalpha kinase inhibitors enhanced apoptosis. Overall, our results indicate that stable or transient MDA-7 expression alone does not substantially activate NF-kappaB, but potentiates TNF-induced NF-kappaB activation and NF-kappaB-regulated gene expression. Potentiation of NF-kappaB survival signaling by MDA-7 inhibits TNF-mediated apoptosis.     

Benthic habitat and fish assemblage structure from shallow to mesophotic depths in a storm-impacted marine protected area

Coral Reefs - Baseline ecological studies of mesophotic coral ecosystems are lacking in the equatorial Indo-West Pacific region where coral reefs are highly threatened by anthropogenic and...     

Growth characteristics of Saccharomyces cerevisiae S288C in changing environmental conditions: auxo-accelerostat study

The effect of individual environmental conditions (pH, pO₂, temperature, salinity, concentration of ethanol, propanol, tryptone and yeast extract) on the specific growth rate as well as ethanol and glycerol production rate of Saccharomyces cerevisiae S288C was mapped during the fermentative growth in aerobic auxo-accelerostat cultures. The obtained steady-state values of the glycerol to ethanol formation ratio (0.1 mol mol⁻¹) corresponding to those predicted from the stoichiometric model of fermentative yeast growth showed that the complete repression of respiration was obtained in auxostat culture and that the model is suitable for calculation of Y _ATP and Q _ATP values for the aerobic fermentative growth. Smooth decrease in the culture pH and dissolved oxygen concentration (pO₂) down to the critical values of 2.3 and 0.8%, respectively, resulted in decrease in growth yield (Y _ATP) and specific growth rate, however the specific ATP production rate (Q _ATP) stayed almost constant. Increase in the concentration of biomass (>0.8 g dwt l⁻¹), propanol (>2 g l⁻¹) or NaCl (>15 g l⁻¹) lead at first to the decrease in the specific growth rate and Q _ATP, while Y _ATP was affected only at higher concentrations. The observed decrease in Q _ATP was caused by indirect rather than direct inhibition of glycolysis. The increase in tryptone concentration resulted in an increase in the specific growth rate from 0.44 to 0.62 h⁻¹ and Y _ATP from 12.5 to 18.5 mol ATP g dwt⁻¹. This study demonstrates that the auxo-accelerostat method, besides being an efficient tool for obtaining the culture characteristics, provides also decent conditions for the experiments elucidating the control mechanisms of cell growth.     

Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesia longinaris Spence Bate, 1888 (Decapoda,Penaeidae) from DNA barcoding: implications for fishery management

Artemesia longinaris is a marine shrimp endemic to the southwestern Atlantic and distributed from Atafona, Rio de Janeiro (Brazil) to Rawson, Chubut (Argentina). In recent years, this species has become an important target of the commercial fishery as a consequence of the decline in the fishery of more traditional and profitable marine shrimps. In addition, phenotypic variations have been documented in populations along its distribution. Therefore, investigations on the genetics of the fishing stocks are necessary for the development of sustainable management strategies and for understanding the possible sources of these variations. The mitochondrial gene Cytochrome Oxidase I (COI) was used to search for evidence of genetic structure among the populations of Artemesia longinaris and to analyze the phylogenetic relationships among them. A total of 60 specimens were collected from seven different localities, covering its geographical range. The final alignment showed 53 haplotypes (48 individuals and 5 shared), with no biogeographical pattern. The low genetic divergence found, with a non-significant FST value, also suggests the absence of population structure for this gene. These findings indicate a continuous gene flow among the populations analyzed, suggesting that the phenotypic variation is a consequence of different environmental conditions among the localities.     

Network theory and metapopulation persistence: incorporating node self‐connections

Network analysis is gaining increasing importance in conservation planning. However, which network metrics are the best predictors of metapopulation persistence is still unresolved. Here, we identify a critical limitation of graph theory‐derived network metrics that have been proposed for this purpose: their omission of node self‐connections. We resolve this by presenting modifications of existing network metrics, and developing entirely new metrics, that account for node self‐connections. Then, we illustrate the performance of these new and modified metrics with an age‐structured metapopulation model for a real‐world marine reserve network case study, and we evaluate the robustness of our findings by systematically varying particular features of that network. Our new and modified metrics predict metapopulation persistence much better than existing metrics do, even when self‐connections are weak. Existing metrics become good predictors of persistence only when self‐connections are entirely absent, an unrealistic scenario in the overwhelming majority of metapopulation applications. Our study provides a set of novel tools that can substantially enhance the extent to which network metrics can be employed to understand, and manage for, metapopulation persistence.     

PI3 kinase blockade by Ad-PTEN inhibits invasion and induces apoptosis in RGP and metastatic melanoma cells

BACKGROUND: Melanoma is an aggressive tumor with a propensity to rapidly metastasize. The PTEN gene encodes a phosphatase with an unusual dual specificity for proteins and lipids. Mutations of PTEN have been found in various human cancers, including glioblastoma, prostate, breast, lung, and melanoma. Here we investigate in vitro the effects of blocking PI3K signaling using adenoviral-delivered PTEN (Ad-PTEN) in cell lines derived from both early- and late-stage melanoma. MATERIALS AND METHODS: Ad-PTEN transduced melanoma cell lines or normal cells were assayed for cell death, apoptosis, gene expression, invasion and migration, and regulation of angiogenesis. RESULTS: The PTEN locus from RGP and metastatic melanoma cell lines was sequenced; no coding region mutations were found. Adenoviral transfer of PTEN into melanoma cells containing wild-type PTEN alleles led to tumor-specific apoptosis and growth inhibition, with coordinate inhibition of AKT phosphorylation. Ad-PTEN suppressed cell migration by metastatic melanoma cells with concomitant increase in the level of cell surface E-cadherin. Immunohistochemical and confocal analyses localized PTEN to the cytoplasm and demonstrated enrichment at the cell membrane. Ad-PTEN inhibited angiogenesis as demonstrated by the tube formation assay using human vascular endothelial cells. CONCLUSIONS: These studies indicate that Ad-PTEN can inhibit tumor cells via multiple mechanisms and has pro-apoptotic, anti-metastatic, and anti-angiogenic properties. Thus, PI3K blockade via Ad-PTEN may be a promising approach for the treatment of early- and late-stage melanoma, even in tumors that do not harbor PTEN mutations.     

Trichuris suis: detection of antibacterial activity in excretory-secretory products from adults.

Antibacterial activity was detected in excretory-secretory products (ESP) of adult Trichuris suis cultured in vitro in serum-free media. Gram-negative bacteria (Campylobacter jejuni, Campylobacter coli, and Escherichia coli) and Gram-positive bacteria (Staphylococcus aureus) were sensitive to ESP. Susceptibility was dependent on the concentration of ESP but not on the inoculum size. Preliminary assessment of the mode of action suggests a bacteriocidal mechanism. This antibacterial activity was heat stable and resistant to digestion with pronase E and trypsin. Based on ultrafiltration experiments, the activity is less than 10,000 MW. This excreted/secreted antibacterial activity from T. suis is likely a component of a humoral defense system for this helminth.