Next-generation sequencing and its potential impact on food microbial genomics

Recent efforts of researchers to elucidate the molecular mechanisms of biological systems have been revolutionized greatly with the use of high throughput and cost-effective techniques such as next generation sequencing (NGS). Application of NGS to microbial genomics is not just limited to predict the prevalence of microorganisms in food samples but also to elucidate the molecular basis of how microorganisms respond to different food-associated conditions, which in turn offers tremendous opportunities to predict and control the growth and survival of desirable or undesirable microorganisms in food. Concurrently, NGS has facilitated the development of new genome-assisted approaches for correlating genotype and phenotype. The aim of this review is to provide a snapshot of the various possibilities that these new technologies are opening up in area of food microbiology, focusing the discussion mainly on lactic acid bacteria and yeasts associated with fermented food. The contribution of NGS to a system level understanding of food microorganisms is also discussed

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene

Here we report an in-silico approach for identification, characterization and validation of deleterious non-synonymous SNPs (nsSNPs) in the interleukin-8 gene using three steps. In first step, sequence homology-based genetic analysis of a set of 50 coding SNPs associated with 41 rsIDs using SIFT (Sorting Intolerant from Tolerant) and PROVEAN (Protein Variation Effect Analyzer) identified 23 nsSNPs to be putatively damaging/deleterious in at least one of the two tools used. Subsequently, structure-homology based PolyPhen-2 (Polymorphism Phenotyping) analysis predicted 9 of 23 nsSNPs (K4T, E31A, E31K, S41Y, I55N, P59L, P59S, L70P and V88D) to be damaging. According to the conditional hypothesis for the study, only nsSNPs that score damaging/deleterious prediction in both sequence and structural homology-based approach will be considered as 'high-confidence' nsSNPs. In step 2, based on conservation of amino acid residues, stability analysis, structural superimposition, RSMD and docking analysis, the possible structural-functional relationship was ascertained for high-confidence nsSNPs. Finally, in a separate analysis (step 3), the IL-8 deregulation has also appeared to be an important prognostic marker for detection of patients with gastric and lung cancer. This study, for the first time, provided in-depth insights on the effects of amino acid substitutions on IL-8 protein structure, function and disease association

Functional outcome of the treatment of AO-ASIF type C distal humerus fracture using Lambda plate

Introduction: Although the use of two plates for the treatment of type-C distal humerus fracture is popular, site of plate placement still is under debate. Use of Lambda plate for the fracture treatment can be easier and settle the dispute. This study aims to evaluate the functional outcome of the surgery using Lambda Plate. This can be a reference for surgeons and helps them make the decision about choice of implant for type C distal humerus fracture treatment among Nepalese people. Methods: This interventional study used Lambda plate for the treatment of type C fracture of distal humerus. Patients were examined at 4, 12, and 24 weeks respectively for the measurement of the outcome. Visual analogous scale was used for assessment of pain, range of motion for functional recovery and Mayo Elbow Performance Score was used for the assessment of functional outcome. Paired-samples t-test and linear regression was used to for data analysis. Results: Functional outcome at the last follow-up was excellent in 24(53.33%) patients, good in 18(40%) patients and fair in 3(6.67%) patients. Range of motion of elbow increased significantly with every follow-up (p-value <0.001). Average angle of flexion at last follow-up was 117.53°±11.74 while loss of extension was 7.53°±4.86. Average number of patients had their fracture union at 19.84±2.38 weeks. There was no association of age, sex and union weeks with functional outcome when measured with MEPS. Conclusion: Fixation of distal humerus fracture by using Lambda plate gave excellent and satisfying outcome in terms of pain, range of motion and objective functional outcome

Synergistic Antibacterial Effects of Metallic Nanoparticle Combinations

© The Author(s) 2019.Metallic nanoparticles have unique antimicrobial properties that make them suitable for use within medical and pharmaceutical devices to prevent the spread of infection in healthcare. The use of nanoparticles in healthcare is on the increase with silver being used in many devices. However, not all metallic nanoparticles can target and kill all disease-causing bacteria. To overcome this, a combination of several different metallic nanoparticles were used in this study to compare effects of multiple metallic nanoparticles when in combination than when used singly, as single elemental nanoparticles (SENPs), against two common hospital acquired pathogens (Staphylococcus aureus and Pseudomonas. aeruginosa). Flow cytometry LIVE/DEAD assay was used to determine rates of cell death within a bacterial population when exposed to the nanoparticles. Results were analysed using linear models to compare effectiveness of three different metallic nanoparticles, tungsten carbide (WC), silver (Ag) and copper (Cu), in combination and separately. Results show that when the nanoparticles are placed in combination (NPCs), antimicrobial effects significantly increase than when compared with SENPs (P < 0.01). This study demonstrates that certain metallic nanoparticles can be used in combination to improve the antimicrobial efficiency in destroying morphologically distinct pathogens within the healthcare and pharmaceutical industry.Peer reviewe

Two glycerol uptake systems contribute to the high osmotolerance of Zygosaccharomyces rouxii

The accumulation of glycerol is essential for yeast viability upon hyperosmotic stress. Here we show that the osmotolerant yeast Zygosaccharomyces rouxii has two genes, ZrSTL1 and ZrSTL2, encoding transporters mediating the active uptake of glycerol in symport with protons, contributing to cell osmotolerance and intracellular pH homeostasis. The growth of mutants lacking one or both transporters is affected depending on the growth medium, carbon source, strain auxotrophies, osmotic conditions and the presence of external glycerol. These transporters are localised in the plasma membrane, they transport glycerol with similar kinetic parameters and besides their expected involvement in the cell survival of hyperosmotic stress, they surprisingly both contribute to an efficient survival of hypoosmotic shock and to the maintenance of intracellular pH homeostasis under non-stressed conditions. Unlike STL1 in Sa. cerevisiae, the two Z. rouxii STL genes are not repressed by glucose, but their expression and activity are downregulated by fructose and upregulated by non-fermentable carbon sources, with ZrSTL1 being more influenced than ZrSTL2. In summary, both transporters are highly important, though Z. rouxii CBS 732(T) cells do not use external glycerol as a source of carbon.The help of Dr. P. Ergang with the real-time PCR experiments is gratefully acknowledged. We thank O. Zimmermannova for critical reading of the paper. This work was supported by the following grants: Grant Agency of the Czech Republic P503/ 10/0307, institutional concept RVO:6798582, Grant Agency of the Charles University 299611/2011/B-Bio/PrF, an Lifelong Learning Programme ERASMUS practical placement grant and by Fundo Europeu de Desenvolvimento Regional – Programa Operacional de Fatores de Competitividade – COMPETE and by national funds from Fundação para a Ciência e Tecnologia through the project PEstC/BIA/UI4050/ 2011.info:eu-repo/semantics/publishedVersio

Application of calcifying bacteria for remediation of stones and cultural heritages

Since ages, architects and artists worldwide have focused on usage of durable stones as marble and limestone for construction of beautiful and magnificent historic monuments as European Cathedrals, Roman, and Greek temples, Taj Mahal etc. But survival of these irreplaceable cultural and historical assets is in question these days due to their degradation and deterioration caused by number of biotic and abiotic factors. These causative agents have affected not only the esthetic appearance of these structures, but also lead to deterioration of their strength and durability. The present review emphasizes about different causative agents leading to deterioration and application of microbially induced calcium carbonate precipitation as a novel and potential technology for dealing with these problems. The study also sheds light on benefits of microbial carbonate binders over the traditional agents and future directions

The establishment of a marine focused biorefinery for bioethanol production using seawater and a novel marine yeast strain

Current technologies for bioethanol production rely on the use of freshwater for preparing the fermentation media and use yeasts of a terrestrial origin. Life cycle assessment has suggested that between 1,388 to 9,812 litres of freshwater are consumed for every litre of bioethanol produced. Hence, bioethanol is considered a product with a high-water footprint. This paper investigated the use of seawater-based media and a novel marine yeast strain ‘Saccharomyces cerevisiae AZ65’ to reduce the water footprint of bioethanol. Results revealed that S. cerevisiae AZ65 had a significantly higher osmotic tolerance when compared with the terrestrial reference strain. Using 15-L bioreactors, S. cerevisiae AZ65 produced 93.50 g/L ethanol with a yield of 83.33% (of the theoretical yield) and a maximum productivity of 2.49 g/L/h when using seawater-YPD media. This approach was successfully applied using an industrial fermentation substrate (sugarcane molasses). S. cerevisiae AZ65 produced 52.23 g/L ethanol using molasses media prepared in seawater with a yield of 73.80% (of the theoretical yield) and a maximum productivity of 1.43 g/L/h. These results demonstrated that seawater can substitute freshwater for bioethanol production without compromising production efficiency. Results also revealed that marine yeast is a potential candidate for use in the bioethanol industry especially when using seawater or high salt based fermentation media

Biallelic and monoallelic variants in PLXNA1 are implicated in a novel neurodevelopmental disorder with variable cerebral and eye anomalies.

PURPOSE: To investigate the effect of PLXNA1 variants on the phenotype of patients with autosomal dominant and recessive inheritance patterns and to functionally characterize the zebrafish homologs plxna1a and plxna1b during development. METHODS: We assembled ten patients from seven families with biallelic or de novo PLXNA1 variants. We describe genotype-phenotype correlations, investigated the variants by structural modeling, and used Morpholino knockdown experiments in zebrafish to characterize the embryonic role of plxna1a and plxna1b. RESULTS: Shared phenotypic features among patients include global developmental delay (9/10), brain anomalies (6/10), and eye anomalies (7/10). Notably, seizures were predominantly reported in patients with monoallelic variants. Structural modeling of missense variants in PLXNA1 suggests distortion in the native protein. Our zebrafish studies enforce an embryonic role of plxna1a and plxna1b in the development of the central nervous system and the eye. CONCLUSION: We propose that different biallelic and monoallelic variants in PLXNA1 result in a novel neurodevelopmental syndrome mainly comprising developmental delay, brain, and eye anomalies. We hypothesize that biallelic variants in the extracellular Plexin-A1 domains lead to impaired dimerization or lack of receptor molecules, whereas monoallelic variants in the intracellular Plexin-A1 domains might impair downstream signaling through a dominant-negative effect

Інноваційна система прискореного навчання плаванню студенток закладів вищої освіти

The article describes the current approach to the accelerated swimming of the students of the foundations of higher education. The technology of organization of the lighting process was optimized, which brought together the brains for the accelerated realization of the potential abilities of female students in professional development and healthy health. A complex of effective benefits, methods and methods of training, which resulted in a significant improvement in the students' knowledge, reduction of those specific skills was assigned. It has been shown that the concept of a differentiated accelerated training of female students can be implemented on the principle of one-hour training quietly, that they are engaged in techniques, which include sports methods of swimming from the stop-and-go method. Seeing at its priority elements of the swimming technique allows, for the minds of the deficit of the hour, the introduced training, to form a system of specific stable ruhovyh nachki, realized in the minds of the water medium. Physical exercises are widely used in the form of a certain system for the prevention of diseases and the promotion of health. The basis of this system is, first of all, aerobic exercises of a cyclic nature. This includes swimming, which best meets the needs and abilities of those involved in different age groups. The initial period of study at the university is a socially and physiologically responsible moment in a student's life. New learning conditions, a high total teaching load, a large volume, novelty and complexity of the material that a student must master, place increased demands on the body.Інноваційна система прискореного навчання плаванню студенток закладів вищої освіти. В статті описано сучасні підходи у прискореному навчанні плаванню студенток закладів вищої освіти. Оптимізовано технологію організації та проведення освітнього процесу, що сприяло створенню умов для прискореної реалізації потенційних можливостей студенток у професійному розвитку та зміцненні здоров'я. Визначено комплекс ефективних засобів, методів та прийомів навчання, використання яких призвело до достовірного збільшення у студенток обсягу знань, умінь та специфічних навичок. Визначено, що концепція диференційованого прискореного навчання студенток може реалізовуватися на принципі одночасного навчання тих, що займаються технікою, чотирьох спортивних способів плавання із застосуванням цілісно-роздільного методу. Виділення у своїй пріоритетних елементів техніки плавання дозволяє за умов дефіциту часу, відведеного навчання, сформувати якісну систему специфічних стійких рухових навичок, реалізованих в умовах водного середовища