A Rad53 kinase-dependent surveillance mechanism that regulates histone protein levels in S. cerevisiae

Rad53 and Mec1 are protein kinases required for DNA replication and recovery from DNA damage in Saccharomyces cerevisiae. Here, we show that rad53, but not mec1 mutants, are extremely sensitive to histone overexpression, as Rad53 is required for degradation of excess histones. Consequently, excess histones accumulate in rad53 mutants, resulting in slow growth, DNA damage sensitivity, and chromosome loss phenotypes that are significantly suppressed by a reduction in histone gene dosage. Rad53 monitors excess histones by associating with them in a dynamic complex that is modulated by its kinase activity. Our results argue that Rad53 contributes to genome stability independently of Mec1 by preventing the damaging effects of excess histones both during normal cell cycle progression and in response to DNA damage.     

Effect of pH-sodium lauryl sulfate combination on solubilization of PG-300995 (an Anti-HIV agent): A technical note

Conclusion  Solubilization of PG-300995 has been achieved using SLS at low pH. However, at a pH where both the solute and surfactant are ionized, desolubilization can occur owing to the formation of an insoluble estolate salt. This salt can be solubilized by higher concentrations of SLS.     

Robust photosystem I activity by Cyanothece sp. (Cyanobacteria) and its role in prolonged bloom persistence in lake St Lucia,South Africa

Worldwide, cyanobacterial blooms are becoming more frequent, exacerbated by eutrophication, anthropogenic effects, and global climate change. Environmental factors play a direct role in photosynthesis of cyanobacteria and subsequent cellular changes, growth, and bloom dynamics. This study investigated the photosynthetic functioning of a persistent bloom-forming (18 months) cyanobacterium, Cyanothece sp., isolated from Lake St Lucia, South Africa. DUAL-PAM fluorometric methods were used to observe physiological responses in Cyanothece sp. photosystems I and II. Results show that photosystem I activity was maintained under all environmental conditions tested, while photosystem II activity was not observed at all. Out of the environmental factors tested (temperature, salinity, and nitrogen presence), only temperature significantly influenced photosystem I activity. In particular, high temperature (40 °C) facilitated faster electron transport rates, while effects of salinity and nitrogen were variable. Cyanothece sp. has shown to sustain bloom status for long periods largely because of the essential role of photosystem I activity during highly dynamic and even extreme (e.g., salinities higher than 200) environmental conditions. This ensures the continual supply of cellular energy (e.g. ATP) to important processes such as nitrogen assimilation, which is essential for protein synthesis, cell growth and, therefore, bloom maintenance.

     

Ethnobotanical assessment of plant resources of Banda Daud Shah,District Karak,Pakistan

Background

The Indigenous knowledge of plants is scientifically and culturally very significant. This paper elucidates the empirical findings of an ethnobotanical survey of Banda Daud Shah, District Karak, Pakistan.

Methods

Data collection was carried out from October 2011 to September 2012. Total twelve survey trips were made, three in each season. About 100 respondents were interviewed; most of them were aged people between 60–70 years. Interviews were conducted using structured questionnaire composed of variety of questions regarding ethnomedicinal uses of plants of the study area. Direct matrix ranking (DMR), informant citations and market survey of multipurpose plants were also carried out.

Results

The local community was using 58 plant species belonging to 52 genera and 34 families for different purposes. A total of 25 plant species were herbs followed by 18 shrubs. Leaf (45%) was the most commonly used plant part followed by the whole plants (23%). In total, 40 plant species were medicinally used to treat variety of diseases, of which highest number of species being used for gastro-intestinal problems (19 spp.), expectorant (3 spp.) and antipyretic (3 spp.). Beside medicinal values, 25 species were used for fuel and 18 for fodder purposes. Informant consensus showed that gastrointestinal and respiratory infections were ranked highest (F_IC?=?0.75) among all ailments. According to DMR output, Dalbergia sisso ranked first due to high multipurpose uses among all species and was found most threatened with higher market value.

Conclusion

The investigated area is rural in nature and the inhabitants are highly dependent on the native plants for their health care needs and other requirements like fuel wood and fodder due to financial constraints and unavailability of resources. Medicinal plants for high ranked diseases may be phtyochemicaly and pharmacologically investigated to prove their efficacy. The local medicinal flora is facing overexploitation, overgrazing and improper way of collection. Proper conservation strategies such as controlled grazing, reforestation and rangeland management among many others may be adopted to promote the sustainable use of medicinal plants.

     

Evaluation of Physical and Functional Protein-Protein Interaction Prediction Methods for Detecting Biological Pathways

Background

Cellular activities are governed by the physical and the functional interactions among several proteins involved in various biological pathways. With the availability of sequenced genomes and high-throughput experimental data one can identify genome-wide protein-protein interactions using various computational techniques. Comparative assessments of these techniques in predicting protein interactions have been frequently reported in the literature but not their ability to elucidate a particular biological pathway.

Methods

Towards the goal of understanding the prediction capabilities of interactions among the specific biological pathway proteins, we report the analyses of 14 biological pathways of Escherichia coli catalogued in KEGG database using five protein-protein functional linkage prediction methods. These methods are phylogenetic profiling, gene neighborhood, co-presence of orthologous genes in the same gene clusters, a mirrortree variant, and expression similarity.

Conclusions

Our results reveal that the prediction of metabolic pathway protein interactions continues to be a challenging task for all methods which possibly reflect flexible/independent evolutionary histories of these proteins. These methods have predicted functional associations of proteins involved in amino acids, nucleotide, glycans and vitamins & co-factors pathways slightly better than the random performance on carbohydrate, lipid and energy metabolism. We also make similar observations for interactions involved among the environmental information processing proteins. On the contrary, genetic information processing or specialized processes such as motility related protein-protein linkages that occur in the subset of organisms are predicted with comparable accuracy. Metabolic pathways are best predicted by using neighborhood of orthologous genes whereas phyletic pattern is good enough to reconstruct central dogma pathway protein interactions. We have also shown that the effective use of a particular prediction method depends on the pathway under investigation. In case one is not focused on specific pathway, gene expression similarity method is the best option.     

CGI-58 facilitates the mobilization of cytoplasmic triglyceride for lipoprotein secretion in hepatoma cells

Comparative Gene Identification-58 (CGI-58) is a member of the alpha/beta-hydrolase family of proteins. Mutations in the human CGI-58 gene are associated with Chanarin-Dorfman syndrome, a rare autosomal recessive genetic disease in which excessive triglyceride (TG) accumulation occurs in multiple tissues. In this study, we investigated the role of CGI-58 in cellular lipid metabolism in several cell models and discovered a role for CGI-58 in promoting the packaging of cytoplasmic TG into secreted lipoprotein particles in hepatoma cells. Using both gain-of-function and loss-of-function approaches, we demonstrate that CGI-58 facilitates the depletion of cellular TG stores without altering cellular cholesterol or phospholipid accumulation. This depletion of cellular TG is attributable solely to augmented hydrolysis, whereas TG synthesis was not affected by CGI-58. Furthermore, CGI-58-mediated TG hydrolysis can be completely inhibited by the known lipase inhibitors diethylumbelliferyl phosphate and diethyl-p-nitrophenyl phosphate, but not by p-chloro-mercuribenzoate. Intriguingly, CGI-58-driven TG hydrolysis was coupled to increases in both fatty acid oxidation and secretion of TG. Collectively, this study reveals a role for CGI-58 in coupling lipolytic degradation of cytoplasmic TG to oxidation and packaging into TG-rich lipoproteins for secretion in hepatoma cells.     

Decreased dopamine D2 receptor function in cerebral cortex and brain stem: their role in hepatic ALDH regulation in ethanol treated rats

Ethanol exerts numerous pharmacological effects through its interaction with various neurotransmitters. The dopaminergic pathway is associated with cognitive, endocrine, and motor functions, and reinforcement of addictive substances or behaviours. Aldehyde dehydrogenase (ALDH) is a vital enzyme involved with alcohol metabolism and detoxification. In the present study, we investigated the role of cerebral cortex and brain stem dopamine D₂ receptors in the functional regulation on ALDH enzyme activity, in ethanol administrated rats. Two groups of rats were selected viz. control and alcoholic. Cerebral cortex, brain stem and the liver dopamine content was decreased significantly (P < 0.05, 0.05, 0.001, respectively) and homovanillic acid/dopamine (HVA/DA) ratio has significantly increased (P < 0.05, 0.001 and 0.001), respectively in ethanol treated rats when compared to control. Scatchard analysis of [³H]YM-09151-2 binding to synaptic membrane preparations of cerebral cortex and brain stem showed a significant decrease (P < 0.001, 0.05, respectively) in B _max in ethanol treated rats compared to control and the K _d also decreased significantly (P < 0.05). The ALDH analysis showed a significant increase (P < 0.05) in V _max in cerebral cortex, plasma and liver of experimental rats when compared with control without having significant change in brain stem but with decreased K _m (P < 0.001). Our results suggest that decreased function of dopamine mediated through DA D₂ receptor in the cerebral cortex and brain stem enhanced the brain, plasma and liver ALDH activity in ethanol treated rats. This ALDH regulation has significance to correct alcoholics from addiction due to allergic reaction observed in aldehyde accumulation.     

Genome editing in cereal crops: an overview

Transgenic Research - Genome-editing technologies offer unprecedented opportunities for crop improvement with superior precision and speed. This review presents an analysis of the current state of...     

Genome Sequencing of Idiopathic Pulmonary Fibrosis in Conjunction with a Medical School Human Anatomy Course

Even in cases where there is no obvious family history of disease, genome sequencing may contribute to clinical diagnosis and management. Clinical application of the genome has not yet become routine, however, in part because physicians are still learning how best to utilize such information. As an educational research exercise performed in conjunction with our medical school human anatomy course, we explored the potential utility of determining the whole genome sequence of a patient who had died following a clinical diagnosis of idiopathic pulmonary fibrosis (IPF). Medical students performed dissection and whole genome sequencing of the cadaver. Gross and microscopic findings were more consistent with the fibrosing variant of nonspecific interstitial pneumonia (NSIP), as opposed to IPF per se. Variants in genes causing Mendelian disorders predisposing to IPF were not detected. However, whole genome sequencing identified several common variants associated with IPF, including a single nucleotide polymorphism (SNP), rs35705950, located in the promoter region of the gene encoding mucin glycoprotein MUC5B. The MUC5B promoter polymorphism was recently found to markedly elevate risk for IPF, though a particular association with NSIP has not been previously reported, nor has its contribution to disease risk previously been evaluated in the genome-wide context of all genetic variants. We did not identify additional predicted functional variants in a region of linkage disequilibrium (LD) adjacent to MUC5B, nor did we discover other likely risk-contributing variants elsewhere in the genome. Whole genome sequencing thus corroborates the association of rs35705950 with MUC5B dysregulation and interstitial lung disease. This novel exercise additionally served a unique mission in bridging clinical and basic science education.