Proteome based mapping and molecular docking revealed DnaA as a potential drug target against Shigella sonnei

Shigella sonnei is one of the major causes of diarrhea and remained a critical microbe responsible for higher morbidity and mortality rates resulting from dysentery every year across the world. Antibiotic therapy of Shigella diseases plays a critical role in decreasing the prevalence as well as the fatality rate of this infection. However, the management of these diseases remains challenging, owing to the overall increase in resistance against many antimicrobials. The situation necessitates the rapid development of effective and feasible S. sonnei treatments. In the present study, the subtractive genomics approach was utilized to find the potential drug targets for S. sonnei strain Ss046. Various tools of bioinformatics were implemented to remove the human-specific homologous and pathogen-specific paralogous sequences from the bacterial proteome. Then, metabolic pathway and subcellular location analysis were performed of essential bacterial proteins to describe their role in various cellular processes. Only one essential protein i-e Chromosomal replication initiator protein DnaA was found in the proteome of the pathogen that could be used as a potent target for designing new drugs. 3D structure prediction of DnaA protein was carried out using Phyre 2. Molecular docking of 5000 phytochemicals was performed against DnaA to identify four top-ranked phytochemicals (Riccionidin A, Dothistromin, Fustin, and Morin) based on scoring functions and interaction with the active site. This study suggests that these phytochemicals could be used as antibacterial drugs to treat S. sonnei infections in the future. To confirm their efficacy and evaluate their drug potency, further in vitro analyses are required.     

Novel molecular classification of colorectal cancer and correlation with survival

IntroductionColorectal cancer (CRC) is one of the most common cancers worldwide. This study was designed to evaluate biological patterns, explore molecular classification and correlate with survival outcome in treatment naïve CRC patients.MethodsOver 11 years consecutive series of 435 CRC patients were operated on as primary surgical therapy. A total of 201 CRC patients were included, whose complete set of clinical information was available, and their good quality tumour blocks were retrieved. Immunohistochemistry was used for tumour analysis, and partitional clustering was performed using R software for cluster analysis.ResultsThe median age was 43 (range 10–85) years; adenocarcinoma was the most commonly seen histological type. The great majority had positive CK20, CEA, E-Cadherin, Ki67, CDX2, and p53 expression. There were four distinct molecular classes found, whereas Ki67, CDX2, and p53 play the main role in partitioning. Younger age negatively impacted survival; overall and disease-specific survival was 26 months only with 50 months’ longest survival.ConclusionColorectal cancer is a biologically heterogeneous disease with at least four distinct molecular patterns, where cell proliferation and gene repair mechanisms appear to play the key role.     

Sub-Micellar Concentration of Sodium Dodecyl Sulphate Prevents Thermal Denaturation Induced Aggregation of Plant Lectin,Jacalin

The irreversible thermal unfolding of jacalin, the lectin purified from jackfruit seeds was accompanied by aggregation, where intermolecular interactions among the subunits are favoured over intramolecular interactions. The extent of aggregation increased as a function of temperature, time and protein concentration. The anionic surfactant, sodium dodecyl sulphate (SDS) significantly suppressed the formation of aggregates as observed by turbidity measurements and Rayleigh scattering assay. Moreover, far UV-CD spectra indicate that the protein β sheet transforms into α helical structure, when denatured in the presence of 3 mM SDS. Further, jacalin when heated in the presence of SDS partially retained the hemagglutination activity when jacalin-SDS mixture was diluted to 1:8 factor since 3 mM SDS was found to lyse the red blood cells. Thus, SDS only altered the aggregation behaviour of jacalin by preventing intermolecular hydrogen bonding among the exposed residues but did not completely stabilize the native conformation.     

Characteristics of Eucheuma cottonii waste from East Malaysia: physical,thermal and chemical composition

The aim of this paper was to examine the characteristics of Eucheuma cottonii waste in order to analyse its potential as renewable material. The morphology of Eucheuma cottonii (raw and wastes) was investigated through scanning electron microscopy (SEM), the thermal behaviour through thermogravimetric analysis (TGA) and the physical properties through FT-IR, XRD, gas pycnometer, particle size analyser, water absorption and moisture content analysis. The chemical compositions were determined by using acid detergent fibre (ADF), neutral detergent fibre (NDF) and acid detergent lignin (ADL) analysis. It was found that Eucheuma cottonii wastes have better thermal stability, higher crude fibre content, lower moisture content and similar density to the raw Eucheuma cottonii, which suggests that these biomass wastes have good potential as renewable filler material.     

Malondialdehyde,an Oxidative Stress Marker in Oral Squamous Cell Carcinoma—A Systematic Review and Meta-Analysis

Objective: To qualitative and quantitatively review published literature assessing the oxidative stress marker malondialdehyde (MDA) in oral squamous cell carcinoma (OSCC). Methodology: Pubmed (MeSH), Science Direct, Scopus, Web of Science, Willey Online Library, Cochrane, and Cross Reference were searched for studies assessing MDA levels in OSCC samples. Results: From the 1008 articles identified, 849 were excluded based on title and abstract screening due to duplication and irrelevance to the topic of interest. Full-text assessment of the remaining 159 articles led to the inclusion of only 46 articles that satisfied the selection criteria. Of these, only 26 studies had data compatible for quantitative analysis. The MDA levels in OSCC groups are significantly increased (p < 0.00001) in plasma, serum, and saliva samples in the majority of the studies evaluated. In contrast, MDA levels in OSCC tissue samples are significantly attenuated (p < 0.00001) compared to healthy controls, supported by fewer studies. Conclusions: The augmented MDA levels in plasma, serum, and saliva samples of the OSCC reflect the heightened oxidative stress level accurately. Further studies are required to understand the attenuated MDA levels in the tissue samples of OSCC. Correlation analysis between MDA levels with established clinicopathological prognostic markers could aid in formulating oxidative stress-based prognostication and treatment planning.     

Mapping and analysis of the LINE and SINE type of repetitive elements in rice

Non-LTR retrotransposons comprise significant portion of the plants genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. The long and short interspersed nucleotide repetitive elements (LINE and SINE) may be responsible for alteration in the expression mechanism of neighboring genes, the complete identification of these elements in the rice genome is essential in order studying their putative functional interactions with the plant genes and its role in genome composition. The main emphasis of this work is to assemble a comprehensive dataset of nonLTR (LINEs and SINEs) and the map of completely inserted LINEs and SINE type of retroelement by both intact ends (3' and 5' ends). The assembled information and work may help for further research in this direction.     

Secondary metabolites from acridocarpus orientalis inhibits 4T1 cells and promotes mesenchymal stem cells (MSCs) proliferation

Molecular Biology Reports - Among medicinal plants, Acridocarpus orientalis (AO) possesses a remarkable anti-cancer potential, possibly because of its anti-oxidant property. In this study, the leaf...     

Hypertension in a young boy: an energy drink effect

Background

The increased heterogeneity in the distribution of social and biological risk factors makes the epidemiology of anaemia a real challenge. A cross-sectional study was conducted at Kassala, Eastern Sudan during the period of January ?? March 2011 to investigate the prevalence and predictors of anaemia among adults (> 15 years old).

Findings

Out of 646, 234 (36.2%) adults had anaemia; 68 (10.5%); 129 (20.0%) and 37 (5.7%) had mild, moderate and severe anaemia, respectively. In logistic regression analyses, age (OR?=?1.0, CI?=?0.9?C1, P?=?0.7), rural vs. urban residency (OR?=?0.9, CI?=?0.7?C1.3, P?=?0.9), female vs. male gender (OR?=?0.8, CI?=?0.6?C1.1, P?=?0.3), educational level????secondary level vs. < secondary level (OR?=?1.0, CI?=?0.6?C1.6, P?=?0.8) and Hudandawa vs. non-Hudandawa ethnicity (OR?=?0.8, CI?=?0.6?C1, P?=?0.1) were not associated with anaemia.

Conclusion

There was a high prevalence of anaemia in this setting, anaemia affected adults regardless to their age, sex and educational level. Therefore, anaemia is needed to be screened for routinely and supplements have to be employed in this setting.     

Molecular identification and characterization of a new type of bovine enterovirus

Bovine enteroviruses belong to the family Picornaviridae. Little is known about their pathogenic potential; however, they cause asymptomatic infections in cattle and are excreted in feces. In the present study, viruses isolated from environmental samples were sequenced. According to phylogenetic analyses and standard picornavirus nomenclature, these isolates constitute a new type of bovine enterovirus serogroup A.     

Conformational Properties of Polyglutamine Sequences in Guanidine Hydrochloride Solutions

Two sets of iso-1-cytochrome c variants have been prepared with N-terminal insertions of pure polyglutamine, i.e., PolyQ variants, or polyglutamine interrupted with lysine every sixth residue, i.e., Gln-rich variants. The polymer properties of these pure polyGln or Gln-rich sequences have been evaluated using equilibrium and kinetic His-heme loop formation methods for loop sizes ranging from 22 to 46 in 1.5, 3.0, and 6.0 M guanidine hydrochloride (GdnHCl). In 6.0 M GdnHCl, the scaling exponent, ν₃, for the pure polyGln sequences, is ∼1.7—significantly less than ν₃ ≈ 2.15 for the Gln-rich sequences. The stability of the His-heme loops becomes progressively greater for the pure polyGln sequences relative to the Gln-rich sequences as GdnHCl concentration decreases from 6.0 to 1.5 M. Thus, the context of the sequence effects the polymer properties of Gln repeats even in denaturing concentrations of GdnHCl. Comparison of data for the Gln-rich variants with previous results for Gly-rich and Ala-rich variants shows that ν₃ ∼ 2.2 for the Gln-rich, Gly-rich, and Ala-rich sequences in 6.0 M GdnHCl, whereas ν₃ remains unchanged at 3.0 M GdnHCl concentration for the Gln-rich and Ala-rich sequences but decreases to ∼1.7 for the Gly-rich sequences. Thus, the polymer properties of Gln-rich and Ala-rich sequences are less sensitive to solvent quality in denaturing solutions of GdnHCl than Gly-rich sequences. Evaluation of Flory’s characteristic ratio, C_n, for the Gln-rich and Ala-rich sequences relative to the Gly-rich sequences shows that Gln-rich sequences are stiffer than Ala-rich sequences at both 3.0 and 6.0 M GdnHCl.