Hidden Markov model speed heuristic and iterative HMM search procedure

Background  

Profile hidden Markov models (profile-HMMs) are sensitive tools for remote protein homology detection, but the main scoring algorithms, Viterbi or Forward, require considerable time to search large sequence databases.     

Evaluation of antioxidant activity of <Emphasis Type="Italic">Melothria maderaspatana in vitro</Emphasis>

In this study, an aqueous extract of leaves from Melothria maderaspatana was tested for in vitro antioxidant activity. Free radical scavenging assays, such as hydroxyl radical, hydrogen peroxide, superoxide anion radical and 2,2-diphenyl-1-picryl hydrazyl (DPPH), 2,2’-azinobis-(3-ethyl-enzothiazoline-6-sulfonic acid) (ABTS) radical scavenging, and reducing power assay, were studied. The extract effectively scavenged hydroxyl radical, hydrogen peroxide and superoxide anion radicals. It also scavenged DPPH and ABTS radicals. Furthermore, it was found to have reducing power. All concentrations of leaf extract exhibited free radical scavenging and antioxidant power, and the preventive effects were in a dose-dependent manner. The antioxidant activities of the above were compared to standard antioxidants such as butylated hydroxytoluene (BHT), ascorbic acid, and α-tocopherol. The results obtained in the present study indicate that the M. maderaspatana extract could be considered a potential source of natural antioxidant.     

Two new species of <Emphasis Type="Italic">Ligia</Emphasis> Fabricius, 1798 (Crustacea: Isopoda: Ligiidae) from coasts of the Persian and Aden gulfs

Two new species of Ligia are described, L. persica sp. nov. from the Persian Gulf and L. yemenica sp. nov. from the Gulf of Aden. Ligia persica occurs along the northern coasts of the Persian Gulf and around some Iranian islands such as Qeshm and Kish. A comparison of SEM micrographs shows that the shape and ornamentation of distal parts of the appendix masculina are reliable characters for the identification of morphologically similar Ligia species. They are species-specific and of great importance in the taxonomy of the genus.     

Association of <Emphasis Type="Italic">phospholipase A2 receptor 1</Emphasis> polymorphisms with idiopathic membranous nephropathy in Chinese patients in Taiwan

Background  

Idiopathic membranous nephropathy (IMN) is one of the most common forms of autoimmune nephritic syndrome in adults. The purpose of this study is to evaluate whether polymorphisms of PLA2R1 affect the development of IMN.     

ALDH2 polymorphism for the risk of cervical carcinogenesis

To investigate the clinical significance of ALDH2 genetic polymorphisms in cervical carcinogenesis. ALDH2 polymorphisms together with human papillomavirus (HPV) types were examined in a total of 195 cervical smear in exfoliated cervical cell samples using Real-Time polymerase chain reaction (PCR) System. The frequency for the AG+AA genotype was seven in the normal group (70.0 %), 16 in the LSIL group (57.1 %), and 27 in the HSIL group (90.0 %). A significant difference was found between the LSIL and HSIL groups (P = 0.0064). Patients with HSIL lesions frequently had high-risk HPV infections and concurrently belonged to the AG+AA group. ALDH2 genotype in cervical cell samples may be associated with more severe precancerous lesions of the cervix in a Japanese population.     

Screening for a Potent Antibacterial Peptide to Treat Mupirocin-Resistant MRSA Skin Infections

Mupirocin is the first-line topical antibacterial drug for treating skin infections caused primarily by meticillin-resistant Staphylococcus aureus (MRSA). Its widespread use since its introduction more than 30 years ago has resulted in the global emergence of mupirocin-resistant strains of MRSA. Antimicrobial peptides (AMPs) are a promising class of antibacterial compounds that can potentially be developed to replace mupirocin due to their rapid membrane-targeting bactericidal mode of action and predicted low propensity for resistance development. Herein, we conducted and compared the antibacterial activities of 61 AMPs between 3 and 11 residues in length reported in the literature over the past decade against mupirocin-resistant MRSA. The most potent AMP, 11-residue peptide 50, was selected and tested against a panel of clinical isolates followed by a time-kill and a human dermal keratinocyte cytotoxicity assay. Lastly, peptide 50 was formulated into a topical spray which showed strong in vitro bactericidal effects against mupirocin-resistant MRSA. Our results strongly suggest that peptide 50 has the potential to be further developed into a new class of topical antibacterial agent for treating drug-resistant MRSA skin infections.     

Mapping ephemeral wetlands: manual digitisation and logistic regression modelling in Nelson Mandela Bay Municipality,South Africa

Until recently, little research has been conducted on the distribution and structure of ephemeral systems in semi-arid areas. This information is critical for appropriate wetland management and conservation. The Nelson Mandela Bay Municipality is a semi-arid area along the south-eastern coastline of the Eastern Cape Province of South Africa. The Municipality encapsulates a wide range of geological and geomorphological features as well as vegetation types within an area of some 1950 km², providing an ideal area for such research. The distribution and abundance of wetlands were defined, and a logistic regression (LR) model was used to establish whether this modelling technique is viable in semi-arid areas with highly variable rainfall patterns. Wetlands were delineated manually using geographical information systems, high-resolution aerial photographs and environmental data. More than 1700 wetland polygons were identified, with 80% of the systems being categorised as depressions, seeps and wetland flats. Unchannelled (8%) and channelled (7%) valley bottom wetlands and floodplain wetlands (5%) were also identified. The wetland database was then used to create a wetland occurrence probability model. There were 19 environmental variables used to develop the LR model, with eight variables used in the final model output. The predictive capacity of the model was good, with an area under curve value of 0.68 and an overall accuracy of 66%. This indicates that probabilistic wetland models are useful in highly variable environments with high numbers of small (<1 ha) wetlands. Such predictive models provide a tool to assist in improving the accuracy of land cover datasets in semi-arid areas, and can be used to inform management decisions on flood risk areas and key conservation zones. In addition, abiotic variables that are significant in the model output provide an indication of the factors influencing wetland functioning in the region.     

Eclalbasaponin II Ameliorates the Cognitive Impairment Induced by Cholinergic Blockade in Mice

Eclalbasaponin II derived from Eclipta prostrata L. (Asteraceae) has been reported to have anti-fibrotic, anti-bacterial and autophagic activities, but its effect on cognitive function has not been investigated. We studied the effect of eclalbasaponin II on cholinergic blockade-induced memory impairment in mice using the passive avoidance, Y-maze, and Morris water maze tasks. Eclalbasaponin II (10 or 20 mg/kg, p.o.) significantly ameliorated the cognitive dysfunction induced by scopolamine in the passive avoidance, Y-maze, and the Morris water maze tasks. To identify the mechanism of the memory-ameliorating effect of eclalbasaponin II, acetylcholinesterase (AChE) activity assay, Western blot analysis and electrophysiology were conducted. Eclalbasaponin II inhibited the AChE activity in ex vivo study, and the administration of eclalbasaponin II and its metabolite, echinocystic acid, increased the phosphorylation levels of memory-related signaling molecules, including protein kinase B (Akt) and glycogen synthase kinase-3β (GSK-3β), in the hippocampus. Although eclalbasaponin II did not affect hippocampal long term potentiation (LTP), echinocystic acid significantly enhanced hippocampal LTP formation (30 μM). These results suggest that eclalbasaponin II ameliorates cholinergic blockade-induced cognitive impairment via AChE inhibition, LTP formation and the activation of Akt-GSK-3β signaling, and that eclalbasaponin II may be a useful to treat cognitive impairment derived from cholinergic dysfunction.     

CDK5-Mediated Phosphorylation-Dependent Ubiquitination and Degradation of E3 Ubiquitin Ligases GP78 Accelerates Neuronal Death in Parkinson’s Disease

The molecular mechanisms responsible for the loss of dopaminergic neurons in Parkinson’s disease (PD) remain obscure. Loss of function of E3 ubiquitin ligases is associated with mitochondria dysfunction, dysfunction of protein degradation, and α-synuclein aggregation, which are major contributors to neurodegeneration in PD. Recent research has thus focused on E3 ubiquitin ligase glycoprotein 78 (GP78); however, the role of GP78 in PD pathogenesis remains unclear. Notably, cyclin-dependent kinase 5 (CDK5) controls multiple cellular events in postmitotic neurons, and CDK5 activity has been implicated in the pathogenesis of PD. Thus, we addressed the relationship between CDK5 and GP78 in MPTP-based PD models. We found that GP78 expression is decreased in MPTP-based cellular and animal PD models, and CDK5 directly phosphorylated GP78 at Ser516, which promoted the ubiquitination and degradation of GP78. Importantly, overexpression of GP78 or interference of GP78 Ser516 phosphorylation protected neurons against MPP⁺-induced cell death. Thus, our research reveals that the CDK5-GP78 pathway is involved in the pathogenesis of PD and could be a novel candidate drug target for the treatment of PD.     

Microbial decolorization of spentwash: a review

Spentwash is one of the most complex and cumbersome wastewater with very high BOD, COD and other organic and inorganic toxic constituents. It is dark brown colored and difficult to treat by normal biological process such as activated sludge or anaerobic lagooning. The color is due to the presence of melanoidins, caramels and other polymers. These compounds have anti oxidant properties which render them toxic to microorganisms. Spentwash disposal into the environment is hazardous and has a considerable pollution potential. It affects the aesthetic merit. Its decolorization by physical or chemical methods have been investigated and were found unsuitable. In the recent past, increasing attention has been directed towards utilizing microbial activity for decolorization of spentwash. This review reveals various groups of microorganisms which have potential in spentwash decolorization. The role of enzymes in decolorization and the microbial degradation of individual compounds imparting color to spentwash are also discussed.