Characteristics and genetic diversity of bioluminescent Shewanella woodyi strains isolated from the Gulf of Izmir, Turkey

The purpose of this study was to isolate bioluminescent strains and to phenotypically and biochemically identify them based on the 16S rRNA gene sequence. 16S rRNA gene sequence analysis of the 11 isolates revealed that they belonged to Shewanella woodyi. Nevertheless, they were determined to exhibit various growth characteristics, enzymatic activities, assimilation of carbon and nitrogen sources, and different characteristics in antibiotic resistance profiles, and also, it was determined that different growth conditions affect the amount of biofilm. Pulsed-field gel electrophoresis (PFGE) analysis of S. woodyi strains performed with SmaI and NotI restriction enzymes revealed that they exhibited restriction fragment pattern homology ranging from 56 to 89 % and from 82 to 94 %, respectively. As a result, PFGE analysis of the genome S. woodyi (as the first record) revealed that although these strains inhabiting the Gulf of Izmir exhibit common characteristics, they also have high levels of genomic polymorphism.     

The population genomic landscape of human genetic structure,admixture history and local adaptation in Peninsular Malaysia

Peninsular Malaysia is a strategic region which might have played an important role in the initial peopling and subsequent human migrations in Asia. However, the genetic diversity and history of human populations—especially indigenous populations—inhabiting this area remain poorly understood. Here, we conducted a genome-wide study using over 900,000 single nucleotide polymorphisms (SNPs) in four major Malaysian ethnic groups (MEGs; Malay, Proto-Malay, Senoi and Negrito), and made comparisons of 17 world-wide populations. Our data revealed that Peninsular Malaysia has greater genetic diversity corresponding to its role as a contact zone of both early and recent human migrations in Asia. However, each single Orang Asli (indigenous) group was less diverse with a smaller effective population size (N _e) than a European or an East Asian population, indicating a substantial isolation of some duration for these groups. All four MEGs were genetically more similar to Asian populations than to other continental groups, and the divergence time between MEGs and East Asian populations (12,000—6,000 years ago) was also much shorter than that between East Asians and Europeans. Thus, Malaysian Orang Asli groups, despite their significantly different features, may share a common origin with the other Asian groups. Nevertheless, we identified traces of recent gene flow from non-Asians to MEGs. Finally, natural selection signatures were detected in a batch of genes associated with immune response, human height, skin pigmentation, hair and facial morphology and blood pressure in MEGs. Notable examples include SYN3 which is associated with human height in all Orang Asli groups, a height-related gene (PNPT1) and two blood pressure-related genes (CDH13 and PAX5) in Negritos. We conclude that a long isolation period, subsequent gene flow and local adaptations have jointly shaped the genetic architectures of MEGs, and this study provides insight into the peopling and human migration history in Southeast Asia.     

The RAS subfamily Evolution – tracing evolution for its utmost exploitation

In the development of multicellularity, signaling proteins has played a very important role. Among them, RAS family is one of the most widely studied protein family. However, evolutionary analysis has been carried out mainly on super family level leaving sub family information in scanty. Thus, a subfamily evolutionary study on RAS evolutionary expansion is imperative as it will aid in better drug designing against dreadful diseases like Cancer and other developmental diseases. The present study was aimed to understand RAS evolution on both holistic as well as reductive level. All human RAS family genes and protein were subjected to BLAST tools to find orthologs and paralogs with different parameters followed by phylogenetic tree generation. Our results clearly showed that H-RAS is the most primitive RAS in higher eukaryotes and then diverged into other RAS family members due to different gene modification events. Furthermore, a site specific selection pressure analysis was carried out using SELECTON server which showed that H-RAS, M-RAS and N-RAS are evolving faster than K-RAS and R-RAS. Thus, the results ascertain a new ground to cancer biologists to exploit negatively selected K-RAS and R-RAS as potent drug targets in cancer therapeutics.     

Chemical Composition and Biological Activities of Tunisian Cupressus arizonica Greene Essential Oils

The chemical composition of the essential oils obtained by hydrodistillation of leaves, stems, and female cones of Cupressus arizonica Greene , grown in Tunisia, was studied by GC‐FID and GC/MS analyses. Altogether, 62 compounds were identified, 62 in the leaf oil, 19 in the cone oil, and 24 in the stem oil. The cone and stem oils were mainly composed by monoterpene hydrocarbons (96.6 and 85.2%, resp.). In the leaf oil, the total sesquiterpene fraction constituted 36.1% and that of the monoterpene hydrocarbons 33.8% of the total oil composition. The three oils were evaluated for their in vitro herbicidal activity by determining their influence on the germination and the shoot and root growth of the four weed species Sinapis arvensis L., Lolium rigidum Gaudin , Trifolium campestre Schreb ., and Phalaris canariensis L. At the highest doses tested (0.8 and 1.0 mg/ml), the leaf essential oil inhibited either totally or almost completely the seed germination and the shoot and root growth of S. arvensis and T. campestre. The oils were also tested for their antifungal activity; however, their effects on the fungal growth were statistically not significant.     

Fragmentation Genetics of Vateria indica: implications for management of forest genetic resources of an endemic dipterocarp

Tropical agro-forest landscapes are potentially valuable reserves of forest genetic resources for forestry and restoration of degraded forests. The Dipterocarpaceae is a dominant Southeast Asian family of tree species of global significance for the tropical timber industry. Very little information exists about how effective human modified landscapes are for conserving genetic diversity in dipterocarp species. This study provides a baseline for understanding how fragmented agro-forest landscapes in India sustain forest genetic resources in an endemic dipterocarp tree. We compare genetic diversity and fine-scale spatial genetic structure (FSGS) in the threatened tree species Vateria indica within an isolated and a continuous forest site in the Western Ghats, South India. We place these results in the context of dipterocarps from both the Seychelles and Borneo. Parentage analysis of 694 progeny using twelve nuclear microsatellite markers is applied to estimate pollen and seed dispersal. Using a nursery trial we evaluate effects of inbreeding on growth performance. Our results show that levels of FSGS, and gene dispersal are comparable between a small isolated and a large continuous site of V. indica. Realized long-distance pollen flow into the isolated patch appears to help maintaining genetic diversity. The nursery experiment suggests that selection favours outbred progeny. Individuals of V. indica in close proximity appear less related to each other than in another highly fragmented and endangered dipterocarp species from the Seychelles, but more related than in three dipterocarp species studied in continuous forest in Borneo. We discuss the wider implications of our findings in the context of conservation and restoration of dipterocarp forest genetic resources in fragmented populations.     

Targeting proapoptotic protein BAD inhibits survival and self-renewal of cancer stem cells

Emerging evidence suggests that the resistance of cancer stem cells (CSC) to many conventional therapies is one of the major limiting factors of cancer therapy efficacy. Identification of mechanisms responsible for survival and self-renewal of CSC will help design new therapeutic strategies that target and eliminate both differentiated cancer cells and CSC. Here we demonstrated the potential role of proapoptotic protein BAD in the biology of CSC in melanoma, prostate and breast cancers. We enriched CD44⁺/CD24⁻ cells (CSC) by tumorosphere formation and purified this population by FACS. Both spheres and CSC exhibited increased potential for proliferation, migration, invasion, sphere formation, anchorage-independent growth, as well as upregulation of several stem cell-associated markers. We showed that the phosphorylation of BAD is essential for the survival of CSC. Conversely, ectopic expression of a phosphorylation-deficient mutant BAD induced apoptosis in CSC. This effect was enhanced by treatment with a BH3-mimetic, ABT-737. Both pharmacological agents that inhibit survival kinases and growth factors that are involved in drug resistance delivered their respective cytotoxic and protective effects by modulating the BAD phosphorylation in CSC. Furthermore, the frequency and self-renewal capacity of CSC was significantly reduced by knocking down the BAD expression. Consistent with our in vitro results, significant phosphorylation of BAD was found in CD44⁺ CSC of 83% breast tumor specimens. In addition, we also identified a positive correlation between BAD expression and disease stage in prostate cancer, suggesting a role of BAD in tumor advancement. Our studies unveil the role of BAD in the survival and self-renewal of CSC and propose BAD not only as an attractive target for cancer therapy but also as a marker of tumor progression.Although tumors initially respond positively to anti-cancer agents, several cancers, despite the best care and significant improvements in treatment, recur and progress to advanced stages of the disease. The mechanisms underlying this recurrence and metastasis are not clearly understood. Over the past decade, substantial evidence supported the cancer stem cell (CSC) hypothesis as a viable explanation for the initiation, progression and recurrence of cancer. According to this hypothesis, each tumor harbors a small subpopulation of specialized cells among cellular heterogeneity, known as CSC. These cells exhibit self-renewal property that drives tumorigenesis and plasticity to differentiate into multiple cell types contributing to tumor cellular heterogeneity. Support for this hypothesis came from the studies by Lapidot et al. who identified tumor-initiating cells in acute myeloid leukemia.^{1, 2} Subsequently, CSCs have been identified in several cancers.^{3, 4, 5, 6, 7, 8, 9, 10}Accumulating evidence suggests that current cancer therapies can only shrink tumors as they target and kill the differentiated cancer (DC) cells, but are unable to target the rare CSC population.^{11, 12} Thus, despite a wealth of information on DC cells, the active survival and self-renewal pathways in CSCs have not been characterized thoroughly. An understanding of the molecular mechanisms involved in the survival, self-renewal and resistance of CSCs to current therapeutic regimens is of immense clinical interest. This information will help in developing novel strategies for more effective treatments for cancer.Most anti-cancer drugs exert their effects through triggering the apoptotic pathways. However, malignant cancer cells can escape apoptosis by altering the expression level of proapoptotic and antiapoptotic BCL-2 family members. Considering the potential role of BCL-2 family members in tumorigenesis and cancer cell survival, their role in CSC biology has been increasingly studied.^{13, 14} BAD (BCL2-antagonist of cell death) is a member of the BH3-only BCL-2 family protein that when dephosphorylated promotes apoptosis by heterodimerizing with the antiapoptotic proteins BCL-XL and BCL-2.¹⁵ The cytotoxic effects of BAD are controlled by mechanisms that regulate its phosphorylation on at least two distinct serine residues, S112 and S136.^{16, 17, 18} Previously, we showed that phosphorylation at either site is sufficient to protect prostate cancer cells from apoptosis.^{19, 20, 21} We also showed that BAD promotes prostate tumor growth in mouse models.²² Clinically, while BAD expression was associated with relapse in tamoxifen-treated breast cancer patients,^{23, 24} phospho-BAD expression was associated with cisplatin resistance and poor overall survival in ovarian cancer.²⁵Our previous findings along with other reports showing the role of BAD in the apoptosis modulation and growth of DC cells^{19, 22, 26} prompted us to explore the potential role of BAD in the biology of CSCs. We started our investigation by assessing the role of BAD in survival and self-renewal of CSCs. As we observed a significant role for BAD in CSC''s biology, we extended our work to assess the BAD phosphorylation in CSCs of breast cancer patient tumors and for a potential correlation between BAD expression and disease progression in prostate cancer.     

Inhibitory Potency of 8-Methoxypsoralen on Cytochrome P450 2A6 (CYP2A6) Allelic Variants CYP2A6*15, CYP2A6*16, CYP2A6*21 and CYP2A6*22: Differential Susceptibility Due to Different Sequence Locations of the Mutations

Human cytochrome P450 2A6 (CYP2A6) is a highly polymorphic isoform of CYP2A subfamily. Our previous kinetic study on four CYP2A6 allelic variants (CYP2A6*15, CYP2A6*16, CYP2A6*21 and CYP2A6*22) have unveiled the functional significance of sequence mutations in these variants on coumarin 7-hydroxylation activity. In the present study, we further explored the ability of a typical CYP2A6 inhibitor, 8-methoxypsoralen (8-MOP), in inhibition of these alleles and we hypothesized that translational mutations in these variants are likely to give impact on 8-MOP inhibitory potency. The CYP2A6 variant and the wild type proteins were subjected to 8-MOP inhibition to yield IC₅₀ values. In general, a similar trend of change in the IC₅₀ and K_m values was noted among the four mutants towards coumarin oxidation. With the exception of CYP2A6*16, differences in IC₅₀ values were highly significant which implied compromised interaction of the mutants with 8-MOP. Molecular models of CYP2A6 were subsequently constructed and ligand-docking experiments were performed to rationalize experimental data. Our docking study has shown that mutations have induced enlargement of the active site volume in all mutants with the exception of CYP2A6*16. Furthermore, loss of hydrogen bond between 8-MOP and active site residue Asn297 was evidenced in all mutants. Our data indicate that the structural changes elicited by the sequence mutations could affect 8-MOP binding to yield differential enzymatic activities in the mutant CYP2A6 proteins.     

MSH1-Induced Non-Genetic Variation Provides a Source of Phenotypic Diversity in Sorghum bicolor

MutS Homolog 1 (MSH1) encodes a plant-specific protein that functions in mitochondria and chloroplasts. We showed previously that disruption or suppression of the MSH1 gene results in a process of developmental reprogramming that is heritable and non-genetic in subsequent generations. In Arabidopsis, this developmental reprogramming process is accompanied by striking changes in gene expression of organellar and stress response genes. This developmentally reprogrammed state, when used in crossing, results in a range of variation for plant growth potential. Here we investigate the implications of MSH1 modulation in a crop species. We found that MSH1-mediated phenotypic variation in Sorghum bicolor is heritable and potentially valuable for crop breeding. We observed phenotypic variation for grain yield, plant height, flowering time, panicle architecture, and above-ground biomass. Focusing on grain yield and plant height, we found some lines that appeared to respond to selection. Based on amenability of this system to implementation in a range of crops, and the scope of phenotypic variation that is derived, our results suggest that MSH1 suppression provides a novel approach for breeding in crops.     

Statin Therapy Is Associated with Improved Survival in Patients with Non-Serous-Papillary Epithelial Ovarian Cancer: A Retrospective Cohort Analysis

Aim

To determine whether statin use is associated with improved epithelial ovarian cancer (OvCa) survival.

Methods

This is a single-institution retrospective cohort review of patients treated for OvCa between 1992 and 2013. Inclusion criteria were International Federation of Gynecology and Obstetrics (FIGO) stage I–IV OvCa. The primary exposures analyzed were hyperlipidemia and statin use. The primary outcomes were progression-free survival (PFS) and disease-specific survival (DSS).

Results

442 patients met inclusion criteria. The cohort was divided into three groups: patients with hyperlipidemia who used statins (n = 68), patients with hyperlipidemia who did not use statins (n = 28), and patients without hyperlipidemia (n = 346). OvCa outcomes were evaluated. When we analyzed the entire cohort, we found no significant differences in PFS or DSS among the groups. The median PFS for hyperlipidemics using statins, hyperlipidemics not using statins, and non-hyperlipidemics was 21.7, 13.6, and 14.7 months, respectively (p = 0.69). Median DSS for hyperlipidemics using statins, hyperlipidemics not using statins, and non-hyperlipidemics was 44.2, 75.7, and 41.5 months, respectively (p = 0.43). These findings did not change after controlling for confounders. However, a secondary analysis revealed that, among patients with non-serous-papillary subtypes of OvCa, statin use was associated with a decrease in hazards of both disease recurrence (adjusted HR = 0.23, p = 0.02) and disease-specific death (adjusted HR = 0.23, p = 0.04). To augment the findings in the retrospective cohort, the histology-specific effects of statins were also evaluated in vitro using proliferation assays. Here, statin treatment of cell lines resulted in a variable level of cytotoxicity.

Conclusion

Statin use among patients with non-serous-papillary OvCa was associated with improvement in both PFS and DSS.     

Stimulatory Effects of Polysaccharide Fraction from Solanum nigrum on RAW 264.7 Murine Macrophage Cells

The polysaccharide fraction from Solanum nigrum Linne has been shown to have antitumor activity by enhancing the CD4⁺/CD8⁺ ratio of the T-lymphocyte subpopulation. In this study, we analyzed a polysaccharide extract of S. nigrum to determine its modulating effects on RAW 264.7 murine macrophage cells since macrophages play a key role in inducing both innate and adaptive immune responses. Crude polysaccharide was extracted from the stem of S. nigrum and subjected to ion-exchange chromatography to partially purify the extract. Five polysaccharide fractions were then subjected to a cytotoxicity assay and a nitric oxide production assay. To further analyze the ability of the fractionated polysaccharide extract to activate macrophages, the phagocytosis activity and cytokine production were also measured. The polysaccharide fractions were not cytotoxic, but all of the fractions induced nitric oxide in RAW 264.7 cells. Of the five fractions tested, SN-ppF3 was the least toxic and also induced the greatest amount of nitric oxide, which was comparable to the inducible nitric oxide synthase expression detected in the cell lysate. This fraction also significantly induced phagocytosis activity and stimulated the production of tumor necrosis factor-α and interleukin-6. Our study showed that fraction SN-ppF3 could classically activate macrophages. Macrophage induction may be the manner in which polysaccharides from S. nigrum are able to prevent tumor growth.