Large-scale de novo transcriptome analysis reveals specific gene expression and novel simple sequence repeats markers in salinized roots of the euhalophyte <Emphasis Type="Italic">Salicornia europaea</Emphasis>

Glycophytic plants suffer from severe stress and injury when roots are exposed to high salinity in the rhizosphere. In contrast, the euhalophyte Salicornia europaea grows well at 200 mM NaCl and can withstand up to 1000 mM NaCl in the root zone. Analysis of gene expression profiles and the underlying molecular mechanisms responsible for this tolerance have been largely overlooked. Using the Illumina sequencing platform and the short-reads assembly programme Trinity, we generated a total of 40 and 39 million clean reads and further 140,086 and 122,728 unigenes from the 200 mM NaCl and 0 mM NaCl treated tissues of S. europaea roots, respectively. All unigenes in this study were functionally annotated within context of the COG, GO and KEGG pathways. Unigene functional annotation analysis allowed us to identify hundreds of ion transporters related to homeostasis and osmotic adaptation as well as a variety of proteins related to cation, amino acid, lipid and sugar transport. We found significant enrichment in response to stress including the functional categories of “antioxidant activity”, “catalytic activity” and “response to stimuli”. These findings represent for a useful resource for the scientific community working on salt tolerance mechanisms. Conversely, a total of 8639 EST-SSRs from 131,594 unigenes were identified and 4539 non-redundant SSRs primers pairs were developed. These data provide a good foundation for future studies on molecular adaptation mechanisms of euhalophytes roots under saline environments and will likely facilitate the identification of critical salt tolerance traits to be transferred in economically important crops.     

<Emphasis Type="Italic">Braf</Emphasis>, <Emphasis Type="Italic">Kras</Emphasis> and <Emphasis Type="Italic">Helicobacter pylori</Emphasis> epigenetic changes-associated chronic gastritis in Egyptian patients with and without gastric cancer

We aimed to study MLH1 and MGMT methylation status in Helicobacter pylori-associated chronic gastritis in Egyptian patients with and without gastric cancer. 39 patients were included in our study. They were divided into 2 groups; patients without (group I) and with gastric adenocarcinoma (group II). Patients were subjected to clinical examination, abdominal ultrasound and upper endoscopy for gastric biopsy. Biopsies were subjected to urease test, histological examination, and DNA purification. H. pylori, Braf, Kras, MLH1 and MGMT methylation were assessed by quantitative PCR. DNA sequencing was performed to assess Braf and Kras genes mutation. qPCR of H. pylori was significantly higher in patients with adenocarcinoma (group II) than those without adenocarcinoma (group I); with a p < 0.001 as well as in patients with age above 50 years with a p value = 0.008. By applying logistic regression analysis it was reported that the H. pylori qPCR is a significant predictor to the adenocarcinoma with OR = 1.025 (95 % CI: 1. 002–1.048), with sensitivity of 90 % and specificity of 100 %. Adenocarcinoma patients had a significantly higher mean age and levels of H. Pylori, Braf, K-ras, methylated MGMT and methylated MLH1 than those of gastritis patients. DNA sequence analysis of Braf (codon 12) and Kras (codon 600) had genes mutation in gastric adenocarcinoma versus chronic gastritis. Conclusion: H. pylori may cause epigenetic changes predisposing the patients to cancer stomach. Estimation of H. pylori by qPCR can be a good predictor to adenocarcinoma. Braf and Kras genes mutation were reveled in gastritis and adenocarcinoma patients.     

Discovering lethal alleles across the turkey genome using a transmission ratio distortion approach

Deviation from Mendelian inheritance expectations (transmission ratio distortion, TRD) has been observed in several species, including the mouse and humans. In this study, TRD was characterized in the turkey genome using both allelic (specific- and unspecific-parent TRD) and genotypic (additive- and dominance-TRD) parameterizations within a Bayesian framework. In this study, we evaluated TRD for 23 243 genotyped Turkeys across 56 393 autosomal SNPs. The analyses included 500 sires, 2013 dams and 11 047 offspring (trios). Three different haplotype sliding windows of 4, 10 and 20 SNPs were used across the autosomal chromosomes. Based on the genotypic parameterizations, 14 haplotypes showed additive and dominance TRD effects highlighting regions with a recessive TRD pattern. In contrast, the allelic model uncovered 12 haplotype alleles with the allelic TRD pattern which showed an underrepresentation of heterozygous offspring in addition to the absence of homozygous animals. For regions with the allelic pattern, only one particular region showed a parent-specific TRD where the penetrance was high via the dam, but low via the sire. The gene set analysis uncovered several gene ontology functional terms, Reactome pathways and several Medical Subject Headings that showed significant enrichment of genes associated with TRD. Many of these gene ontology functional terms (e.g. mitotic spindle assembly checkpoint, DRM complex and Aneuploidy), Reactome pathways (e.g. Mismatch repair) and Medical Subject Headings (e.g. Adenosine monophosphate) are known to be related to fertility, embryo development and lethality. The results of this study revealed potential novel candidate lethal haplotypes, functional terms and pathways that may enhance breeding programs in Turkeys through reducing mortality and improving reproduction rate.     

Effect of social media use on learning,social interactions,and sleep duration among university students

BackgroundSocial networking sites are widely used by university students. This study investigated the purposes for which social networking sites are used and their effects on learning, social interaction, and sleep duration.Material and methodsA cross-sectional study was conducted among 300, 17–29-year-old female students at Prince Sattam bin Abdul Aziz University. A questionnaire was used to collect data. Chi-squared (Fisher’s exact test) test was used to analyze the data.ResultsThe results showed that 97% of the students used social media applications. Only 1% of them used social media for academic purposes. Whereas 35% of them used these platforms to chat with others, 43% of them browsed these sites to pass time. Moreover, 57% of them were addicted to social media. Additionally, 52% of them reported that social media use had affected their learning activities, 66% of them felt more drawn toward social media than toward academic activities, and 74% of them spent their free time on social media platforms. The most popular applications (i.e., based on usage) were Snapchat (45%), Instagram (22%), Twitter (18%), and WhatsApp (7%). Further, 46% and 39% of them reported going to bed between 11 pm and 12 am and between 1 am and 2 am, respectively. Finally, 68% of them attributed their delayed bedtime to social media use, and 59% of them reported that social media had affected their social interactions.ConclusionsA majority of the participants reported prolonged use of social networking sites for nonacademic purposes. These habitual behaviors can distract students from their academic work, adversely affect their academic performance, social interactions, and sleep duration, and lead to a sedentary lifestyle and physical inactivity, which in turn can render them vulnerable to non-communicable diseases and mental health problems.     

Quinazolinone-based rhodanine-3-acetic acids as potent aldose reductase inhibitors: Synthesis,functional evaluation and molecular modeling study

A series of quinazolinone-based rhodanine-3-acetic acids was synthesized and tested for in vitro aldose reductase inhibitory activity. All the target compounds displayed nanomolar activity against the target enzyme. Compounds 3a, 3b, and 3e exhibited almost 3-fold higher activity as compared to the only marketed reference drug epalrestat. Structure-activity relationship studies indicated that bulky substituents at the 3-phenyl ring of the quinazolinone moiety are generally not tolerated in the active site of the enzyme. Insertion of a methoxy group on the central benzylidene ring was found to have a variable effect on ALR-2 activity depending on the nature of peripheral quinazolinone ring substituents. Removal of the acetic acid moiety led to inactive or weakly active target compounds. Docking and molecular dynamic simulations of the most active rhodanine-3-acetic acid derivatives were also carried out, to provide the basis for further structure-guided design of novel inhibitors.     

Resistance irrelevant CYP417A2v2 was found degrading insecticide in Laodelphax striatellus

Cytochrome P450 monooxygenases (CYP s) usually overexpressed in resistant strain were found involved in oxidative detoxification of insecticides. In this study, an investigation was conducted to confirm if resistance irrelevant CYP s which were not overexpressed in resistant strain before, were capable of degrading insecticides. Three resistance irrelevant CYP s viz. CYP 417A2v2, CYP 425A1v2, and CYP 4DJ 1 from CYP 4 family of Laodelphax striatellus were randomly selected for experiments. CYP 417A2v2 and CYP 425A1v2 were found expressed successfully in Sf9 cell line while CYP 4DJ 1 was not expressed successfully and out of two expressed CYP s, only CYP 417A2v2 showed its efficient catalytic activity. For catalytic activity, three traditional model probe substrates and five insecticides were assayed. For the probe substrates screened, p‐nitroanisole and ethoxycoumarin were preferentially metabolized by CYP 417A2v2 (specific activity 3.76 ± 1.22 and 1.63 ± 0.37 nmol min^?1 mg protein^?1, respectively) and they may be potential diagnostic probes for this enzyme. Among insecticides, only imidacloprid was efficiently degraded by CYP 417A2v2. Incubation of imidacloprid with CYP 417A2v2 of L. striatellus and subsequent HPLC , LC ‐MS , and MS /MS analysis revealed the formation of imidacloprid metabolites, that is, 4′ or 5′hydroxy‐imidacloprid by hydroxylation. This result implies the exemption of CYP s character that it is not always, all the CYP s degrading insecticides being selected and overexpressed in resistant strains and the degrading CYP s without mutations to upregulate could be candidates during insecticide resistance evolution. This characterization of individual insect CYP s in insecticide degradation can provide insight for better understand of insecticide resistance development.     

2-Deoxyglucose combined with wild-type p53 overexpression enhances cytotoxicity in human prostate cancer cells via oxidative stress

Overexpression of the tumor suppressor gene, wild-type p53 (wtp53), using adenoviral vectors (Adp53) has been suggested to kill cancer cells by hydroperoxide-mediated oxidative stress [1,2] and nutrient distress induced by the glucose analog, 2-deoxyglucose (2DG), has been suggested to enhance tumor cell killing by agents that induce oxidative stress via disrupting hydroperoxide metabolism [3,4]. In the current study clonogenic cell killing of PC-3 and DU-145 human prostate cancer cells (lacking functional p53) mediated by 4 h exposure to 50 plaque forming units (pfus)/cell of Adp53 (that caused the enforced overexpression of wtp53) was significantly enhanced by treatment with 2DG. Accumulation of glutathione disulfide was found to be significantly greater in both cell lines treated with 2DG+Adp53 and both cell lines treated with 2DG+Adp53 showed a approximately 2-fold increases in dihydroethidine (DHE) and 5-(and-6)-carboxy-2',7'-dichlorodihydrofluorescein diacetate (CDCFH(2)) oxidation, indicative of increased steady-state levels of O(2)(.-) and hydroperoxides, respectively. Finally, overexpression of catalase or glutathione peroxidase using adenoviral vectors partially, but significantly, protected DU-145 cells from the toxicity induced by 2DG+Adp53 treatment. These results show that treatment of human prostate cancer cells with the combination of 2DG (a nutrient stress) and overexpression of the tumor suppressor gene, wtp53, enhances clonogenic cell killing by a mechanism that involves oxidative stress as well as allowing for the speculation that inhibitors of glucose and hydroperoxide metabolism can be used in combination with Adp53 gene therapy to enhance therapeutic responses.     

A Late Permian flora with Dicroidium from the Dead Sea region, Jordan

Three new species of Dicroidium, D. irnensis, D. jordanensis and D. robustum, are described from the Um Irna Formation (Upper Permian) of the Dead Sea region, Jordan. The plant remains are preserved as compressions with excellent cuticles. These are the earliest unequivocal records of Dicroidium, a genus that is typical for the Triassic of Gondwana. It is also the northernmost occurrence of this genus that apparently originated in the Permian in the palaeotropics. Middle and Late Permian floras from the Arabian Peninsula and adjacent regions show a remarkable mixture of elements from different floral provinces, i.e. Euramerica, Cathaysia and Gondwana. The climatic amelioration in the Early Triassic apparently enabled Dicroidium to migrate southward and eventually colonise the entire Gondwana region. Dicroidium is one of the very few megaplant genera not affected by the end-Permian biotic crisis, the largest Phanerozoic extinction event.     

Ribosome biogenesis is temperature‐dependent and delayed in Escherichia coli lacking the chaperones DnaK or DnaJ†

In Escherichia coli strains carrying null mutations in either the dnaK or dnaJ genes, the late stages of 30S and 50S ribosomal subunit biogenesis are slowed down in a temperature‐dependent manner. At high temperature (44°C), 32S and 45S particles (precursors to 50S subunits) and 21S particles (precursors to 30S subunits) accumulate. The latter are shown by 3′5′ rapid amplification of cDNA ends analysis to contain unprocessed or partially processed 16S ribosomal RNA at the 5′ end, but the 3′ end was never processed. This implies that maturation of 16S ribosomal RNA starts at the 5′‐terminus, and that the 3′‐terminus is only trimmed at a later step. At normal temperatures (30°C?37°C), ribosome assembly in both mutants is not arrested but is significantly delayed, as shown by pulse‐chase analysis. Assembly defects are partially compensated by an overexpression of other heat‐shock proteins, which occurs in the absence of their negative regulator DnaK, or by a plasmid‐driven overexpression of GroES/GroEL, suggesting the involvement of a network of chaperones in ribosome biogenesis.