Origin, evolution, and maintenance of gene-strand bias in bacteria.

Gene-strand bias is a characteristic feature of bacterial genome organization wherein genes are preferentially encoded on the leading strand of replication, promoting co-orientation of replication and transcription. This co-orientation bias has evolved to protect gene essentiality, expression, and genomic stability from the harmful effects of head-on replication-transcription collisions. However, the origin, variation, and maintenance of gene-strand bias remain elusive. Here, we reveal that the frequency of inversions that alter gene orientation exhibits large variation across bacterial populations and negatively correlates with gene-strand bias. The density, distance, and distribution of inverted repeats show a similar negative relationship with gene-strand bias explaining the heterogeneity in inversions. Importantly, these observations are broadly evident across the entire bacterial kingdom uncovering inversions and inverted repeats as primary factors underlying the variation in gene-strand bias and its maintenance. The distinct catalytic subunits of replicative DNA polymerase have co-evolved with gene-strand bias, suggesting a close link between replication and the origin of gene-strand bias. Congruently, inversion frequencies and inverted repeats vary among bacteria with different DNA polymerases. In summary, we propose that the nature of replication determines the fitness cost of replication-transcription collisions, establishing a selection gradient on gene-strand bias by fine-tuning DNA sequence repeats and, thereby, gene inversions.

Single- and two-photon-induced Förster resonance energy transfer in InP-mCherry bioconjugates.

Indium phosphide (InP) quantum dots (QDs) have recently garnered considerable interest in the design of bioprobes due to their non-toxic nature and excellent optical properties. Several attempts for the conjunction of InP QDs with various entities such as organic dyes and dye-labeled proteins have been reported, while that with fluorescent proteins remains largely uncharted. This study reports the development of a Förster resonance energy transfer pair comprising glutathione-capped InP/GaP/ZnS QDs [InP(G)] and the fluorescent protein mCherry. Glutathione on InP(G) undergoes effective bioconjugation with mCherry consisting of a hexahistidine tag, and the nonradiative energy transfer is investigated using steady-state and time-resolved measurements. Selective one-photon excitation of InP(G) in the presence of mCherry shows a decay of the emission of the QDs and a concomitant growth of acceptor emission. Time-resolved investigations prove the nonradiative transfer of energy between InP(G) and mCherry. Furthermore, the scope of two-photon-induced energy transfer between InP(G) and mCherry is investigated by exciting the donor in the optical transparency range. The two-photon absorption is confirmed by the quadratic relationship between the emission intensity and the excitation power. In general, near-infrared excitation provides a path for effective light penetration into the tissues and reduces the photodamage of the sample. The two-photon-induced energy transfer in such assemblies could set the stage for a wide range of biological and optoelectronic applications in the foreseeable future.

To determine the survival, prevalence and associated factors of exclusive breastfeeding practices in South India.

Context: Exclusive breastfeeding (EBF) provides protection to the child from risk of obesity, overweight, type II diabetes and helps in enhancing brain development, learning capabilities and also reduces gastrointestinal infections. Breast problems, societal barriers, insufficient support, poor knowledge, mode of delivery and community beliefs are associated. Aim: To determine the survival and prevalence of exclusive breast-feeding practice and their associated factors. Settings and Design: An ambispective community-based observational study was conducted. Materials and Methods: A sample of 441 mothers was estimated with a prevalence of EBF of 54.9% based on the National Family Health Survey 2015-16. Study Procedure: The selected mothers with an infant less than one year of age and those with infants less than six months were interviewed retrospectively and prospectively and information on the duration of EBF, demography and factors associated were collected. Statistical Analysis Used: The data were analysed using IBM SPSS, version 22. The Chi-square test and binary logistic regression were used to determine the associated factors for EBF. A P value of <0.05 was considered significant. Results: EBF survival rate was good till three months and decreased drastically after five months. EBF practice in the present study was 69.4%. Birth order, maternal age, birth weight, paternal education and religion were significantly associated with EBF. Conclusion: Primary health care providers in the community should also consider the cultural factors and educate the mothers on the practice of EBF to reduce morbidity and mortality and promote better health for a healthy, strong, younger population.

Repeat resection in recurrent glioblastoma (3rGBM) Trial: A randomized care trial.

BACKGROUND: The prognosis for patients with recurrent glioblastoma (GBM) is dismal, and the question of repeat surgery at time of recurrence is common. Re-operation in the management of these patients remains controversial, as there is no randomized evidence of benefit. An all-inclusive pragmatic care trial is needed to evaluate the role of repeat resection. METHODS: 3rGBM is a multicenter, pragmatic, prospective, parallel-group randomized care trial, with 1:1 allocation to repeat resection or standard care with no repeat resection. To test the hypothesis that repeat resection can improve overall survival by at least 3 months (from 6 to 9 months), 250 adult patients with prior resection of pathology-proven glioblastoma for whom the attending surgeon believes repeat resection may improve quality survival will be enrolled. A surrogate measure of quality of life, the number of days outside of hospital/nursing/palliative care facility, will also be compared. Centers are invited to participate without financial compensation and without contracts. Clinicians may apply to local authorities to approve an investigator-led in-house trial, using a common protocol, web-based randomization platform, and simple standardized case report forms. DISCUSSION: The 3rGBM trial is a modern transparent care research framework with no additional risks, tests, or visits other than what patients would encounter in normal care. The burden of proof remains on repeat surgical management of recurrent GBM, because this management has yet to be shown beneficial. The trial is designed to help patients and surgeons manage the uncertainty regarding optimal care. CLINICAL TRIAL REGISTRATION: http://www. CLINICALTRIALS: gov. Unique identifier: NCT04838782.

Nutritive value of guar and copra meal after fermentation with yeast Saccharomyces cerevisiae in the diet of Nile tilapia, Oreochromis niloticus.

Solid-state fermentation increases nutritional bioavailability of plant ingredients by reducing the antinutritional factors and complexity of the nutrients. The present experiment was conducted to replace fish meal (FM) with a mixture (3:1) of yeast fermented guar and copra meal (FGCM) in the diet of Nile tilapia. Five iso-nitrogenous (30% CP) and iso-lipidic (6% CL) diets were formulated replacing FM at 0% (FGCM0), 25% (FGCM 1), 50% (FGCM 2), 75% (FGCM 3), and 100% (FGCM 4) with FGCM mixture. Growth, nutrient utilisation, digestibility, digestive enzyme activity, haematological parameters, and antioxidant capacity were analysed in five treatments after a feeding trial of 75 days. Bioprocessing increased the protein and amino acid content and reduced the antinutritional factors in the guar and copra meal. The weight gain was significantly increased in 25% replaced diet. The feed conversion ratio of tilapia fed with FGCM 1 was similar to that of control and significantly lower (P < 0.05) among the treatments. The group fed with FGCM 1 exhibited significantly higher body protein and lipid content. The activity of digestive enzymes and digestibility of nutrients reduced significantly (P < 0.05) with the replacement of fishmeal beyond 25% with the FGCM mixture. Similarly, the antioxidant enzymes and blood parameters were also negatively affected when more than 25% FM was replaced with FGCM mixture. The cubic regression analysis found that 17.45% FM can be replaced with FGCM mixture for optimum weight gain in tilapia.

Changes in biogenic amines, biochemical and microbial attributes of three spotted crab (Portunus sanguinolentus) during iced and refrigerated storage.

Three spotted crab (Portunus sanguinolentus) is a preferred variety of crab among seafood consumers. Biochemical, microbial and sensory characters along with formation of biogenic amines of whole crabs stored under iced and refrigerated condition was evaluated. Cadaverine, putrescine and spermidine were the major amines formed during spoilage and a strong correlation between cadaverine and psychrotrophs was observed in refrigerated (0.92) and iced storage (0.86) respectively. Histamine was at lower level and not likely to cause any toxicological problems to consumers. Although TVB-N and TMA-N increased significantly (p < 0.01), TVBN was observed as a good indicator of spoilage than TMA-N. Mesophilic and psychrotrophic bacteria crossed 7 log CFU/g on 8th day, rejection day of refrigeration, while it was below spoilage limit in iced storage. A shelf life of 6 and 10 days were observed in storage under refrigeration and icing respectively based on microbiological, biochemical and sensory attributes.

Macromineral and heavy metal profiles of selected deep-sea fish from the Kochi coast of the Arabian Sea, India.

Deep-sea fish from the Arabian Sea in the south western coast of India have been gaining attention as a new edible fish source. Mineral profile of ten selected deep-sea fish from the south west coast of India were assessed for heavy metal and macro mineral content for safety and nutritional quality assessment, respectively. Heavy metal levels were below permissible limits for most of the species studied. But in some species, the levels slightly exceeded the permissible limit of 0.3 mg/kg for Pb, a major heavy metal contaminant in fish, according to the European Union and FSSAI regulations for heavy metals in food. Interestingly, significant content of macro minerals was observed in all the species studied. In conclusion, deep-sea fish were observed to be good source of minerals and were found to be safe for human consumption; except for a couple of species which possess slightly higher Pb content, which may be because of its presence in their habitat.

The roles of replication-transcription conflict in mutagenesis and evolution of genome organization.

Replication-transcription conflicts promote mutagenesis and give rise to evolutionary signatures, with fundamental importance to genome stability ranging from bacteria to metastatic cancer cells. This review focuses on the interplay between replication-transcription conflicts and the evolution of gene directionality. In most bacteria, the majority of genes are encoded on the leading strand of replication such that their transcription is co-directional with the direction of DNA replication fork movement. This gene strand bias arises primarily due to negative selection against deleterious consequences of head-on replication-transcription conflict. However, many genes remain head-on. Can head-on orientation provide some benefit? We combine insights from both mechanistic and evolutionary studies, review published work, and analyze gene expression data to evaluate an emerging model that head-on genes are temporal targets for adaptive mutagenesis during stress. We highlight the alternative explanation that genes in the head-on orientation may simply be the result of genomic inversions and relaxed selection acting on nonessential genes. We seek to clarify how the mechanisms of replication-transcription conflict, in concert with other mutagenic mechanisms, balanced by natural selection, have shaped bacterial genome evolution.

Identification of allergic proteins of Flower tail shrimp (Metapenaeus dobsonii).

Allergy to seafood mainly fish and shellfish has been reported. Tropomyosin is recognized as a major allergen in many crustaceans especially shrimps. A study was carried out to identify the IgE reactive proteins of allergic nature in Flower tail shrimp (Metapenaeus dobsonii), a frequently consumed shrimp in India mainly in dried form. Protein profiling and identification of IgE reactive proteins in raw and cooked extracts of Flower tail shrimp was carried out by SDS-PAGE and immunoblotting using sera of 13 patients having allergic reactions on consumption of shrimp and positive to skin prick test. The IgE binding ability was determined by ELISA and it was found higher in the case of cooked extracts ranging from 0.244 to 0.440 at 490 nm. The SDS-PAGE of raw extract revealed many protein bands between 205 and 6.5 KDa, while in the case of cooked extracts bands of 36, 20, 29 and 70 KDa were prominent. Heat resistant protein of 37 KDa, tropomyosin was showing a clear immune reaction both in the case of raw and cooked extracts was identified as the major allergen by all the patient sera. The minor proteins of raw extract identified by immune reaction are 50, 75 and 100 KDa. The identified allergen can be used for the diagnosis and management of shrimp allergy.

A Prospective Study on the Diagnostic Value of Hyperbilirubinemia as a Predictive Factor for Appendicular Perforation in Acute Appendicitis.

Background Appendicitis is one of the most common surgical emergency in general surgical practices. Early and prompt diagnosis is necessary to avoid life-threatening complications associated with it. The diagnosis is mainly clinically aided by imaging techniques. The physiological obstruction of the bile flow associated with appendicular pathology leads to hyperbilirubinemia, which can be used as a predictive factor of appendicular perforation. Method This prospective study was conducted in the department of general surgery in Madras Medical College and Rajiv Gandhi Government Hospital, Chennai, from January 2012 to November 2012. A total of 378 patients with the features of acute appendicitis or appendicular perforation admitted in the emergency surgical ward were included. Results Out of 378 of the study population, 18% had appendicular perforation and 82% had acute appendicitis. Out of 67 perforations, 60 patients have hyperbilirubinemia (90%) whereas out of 311 patients with appendicitis, only 89 (29%) of them had elevated bilirubin. Hyperbilirubinemia with a cutoff point of 0.9 mg% for appendicitis patients has a sensitivity of 89.6%, specificity of 71.4%, a positive predictive value of 27%, and a negative predictive value of 96.9%. Hyperbilirubinemia with a cutoff point of >1.3 mg% for appendicular perforation has a sensitivity of 80%, specificity of 89%, a positive predictive value of 93%, and a negative predictive value of 96%. Conclusions Hyperbilirubinemia with bilirubin levels more than 1.3 mg% are highly predictive of appendicular perforation and, hence, aid in prompt diagnosis. This can be combined with a clinical diagnosis and imaging for an accurate and precise diagnosis.

A Prospective Study in Comparison of Ambulatory Phlebectomy and Duplex Guided Foam Sclerotherapy in the Management of Varicosities with Isolated Perforator Incompetence.

Perforators are those which connect the superficial and deep venous system either directly to main veins or indirectly through the muscular and soleal venous plexus. The emergence of minimally invasive techniques like ambulatory phlebectomy (AP) and foam sclerotherapy (FS) has led to increasing interest about the appropriate therapy for the treatment of isolated perforator incompetence. There have been no studies which have compared the effectiveness of these in-office procedures in isolated perforator incompetence due to the low prevalence of cases. The primary goal of this study is to compare the clinical parameters (return to normal activity, primary symptom relief), functional parameters (procedure time, change in disease severity, course of venous ulcer), and duplex parameters (recurrence in treated veins, complete occlusion of treated veins) in the management of leg varicosities having isolated primary perforator incompetence by ambulatory phlebectomy and duplex guided foam sclerotherapy. Though the procedure time was shorter with FS than AP, the other parameters of primary symptom relief such as change in disease severity, faster healing of venous ulcer, complete occlusion of treated veins in follow-up duplex examination, and lower recurrence of treated veins are better with AP than FS. In conclusion, the interruption of perforators is effective in decreasing the symptoms of chronic venous insufficiency and for the rapid healing of ulcers. The interruption of the incompetent perforating veins appears to be essential to decrease ambulatory venous hypertension. It is apparent from this study that ambulatory phlebectomy stands distinct with enormous benefits and serves as a superior alternative to foam sclerotherapy in treating patients with isolated perforator incompetence.

DHA and EPA Content and Fatty Acid Profile of 39 Food Fishes from India.

Docosahexaenoic acid (DHA) is the principal constituent of a variety of cells especially the brain neurons and retinal cells and plays important role in fetal brain development, development of motor skills, and visual acuity in infants, lipid metabolism, and cognitive support and along with eicosapentaenoic acid (EPA) it plays important role in preventing atherosclerosis, dementia, rheumatoid arthritis, Alzheimer's disease, and so forth. Being an essential nutrient, it is to be obtained through diet and therefore searching for affordable sources of these ω-3 polyunsaturated fatty acids (PUFA) is important for consumer guidance and dietary counseling. Fish is an important source of PUFA and has unique advantage that there are many food fish species available and consumers have a wide choice owing to availability and affordability. The Indian subcontinent harbors a rich fish biodiversity which markedly varies in their nutrient composition. Here we report the DHA and EPA content and fatty acid profile of 39 important food fishes (including finfishes, shellfishes, and edible molluscs from both marine water and freshwater) from India. The study showed that fishes Tenualosa ilisha, Sardinella longiceps, Nemipterus japonicus, and Anabas testudineus are rich sources of DHA and EPA. Promotion of these species as DHA rich species would enhance their utility in public health nutrition.

The nature of mutations induced by replication­transcription collisions.

The DNA replication and transcription machineries share a common DNA template and thus can collide with each other co-directionally or head-on. Replication­transcription collisions can cause replication fork arrest, premature transcription termination, DNA breaks, and recombination intermediates threatening genome integrity. Collisions may also trigger mutations, which are major contributors to genetic disease and evolution. However, the nature and mechanisms of collision-induced mutagenesis remain poorly understood. Here we reveal the genetic consequences of replication­transcription collisions in actively dividing bacteria to be two classes of mutations: duplications/deletions and base substitutions in promoters. Both signatures are highly deleterious but are distinct from the previously well-characterized base substitutions in the coding sequence. Duplications/deletions are probably caused by replication stalling events that are triggered by collisions; their distribution patterns are consistent with where the fork first encounters a transcription complex upon entering a transcription unit. Promoter substitutions result mostly from head-on collisions and frequently occur at a nucleotide that is conserved in promoters recognized by the major σ factor in bacteria. This substitution is generated via adenine deamination on the template strand in the promoter open complex, as a consequence of head-on replication perturbing transcription initiation. We conclude that replication­transcription collisions induce distinct mutation signatures by antagonizing replication and transcription, not only in coding sequences but also in gene regulatory elements.

Micronutrient Composition of 35 Food Fishes from India and Their Significance in Human Nutrition.

The micronutrients (vitamins and minerals) are required in small amounts but are essential for health, development, and growth. Micronutrient deficiencies, which affect over two billion people around the globe, are the leading cause of many ailments including mental retardation, preventable blindness, and death during childbirth. Fish is an important dietary source of micronutrients and plays important role in human nutrition. In the present investigation, micronutrient composition of 35 food fishes (includes both finfishes and shellfishes) was investigated from varying aquatic habitats. Macrominerals (Na, K, Ca, Mg) and trace elements (Fe, Cu, Zn, Mn, Se) were determined by either atomic absorption spectroscopy (AAS) or inductively coupled plasma mass spectrometry (ICP-MS)/atomic emission spectrometry (ICP-AES). Phosphorus content was determined either spectrophotometrically or by ICP-AES. Fat-soluble vitamins (A, D, E, K) were analyzed by high-performance liquid chromatography (HPLC). The analysis showed that, in general, the marine fishes were rich in sodium and potassium; small indigenous fishes (SIFs) in calcium, iron, and manganese; coldwater fishes in selenium; and the brackishwater fishes in phosphorous. The marine fishes Sardinella longiceps and Epinephelus spp. and the SIFs were rich in all fat-soluble vitamins. All these recommendations were made according to the potential contribution (daily value %) of the species to the recommended daily allowance (RDA). Information on the micronutrients generated would enhance the utility of fish in both community and clinical nutrition.

Crystal structure of (2-methyl-4-phenyl-4H-benzo[4,5]thia-zolo[3,2-a]pyrimidin-3-yl)(phen-yl)methanone.

In the title compound, C24H18N2OS, the pyrimidine ring has a flat envelope conformation with the methine C atom as the flap. The attached phenyl and benzoyl rings are inclined to the mean plane of the pyrimidine ring by 84.87 (8) and 75.33 (9)°, respectively. The benzo-thia-zolo group is planar (r.m.s. deviation = 0.009 Å) and inclined to the mean plane of the pyrimidine ring by 3.27 (6)°. In the crystal, mol-ecules are linked by pairs of C-H⋯N hydrogen bonds, forming inversion dimers.

Crystal structure of ethyl 4-(2,4-di-chloro-phen-yl)-2-methyl-4H-benzo[4,5]thia-zolo[3,2-a]pyrimidine-3-carboxyl-ate.

In the title compound, C20H16Cl2N2O2S, the pyrimidine ring has a screw-boat conformation. The attached di-chloro-phenyl ring is twisted at an angle of 89.29 (13)° with respect to the pyrimidine ring mean plane. The benzo-thia-zole group is approximately planar (r.m.s. deviation = 0.008 Å) and inclined to the pyrimidine ring mean plane by 3.04 (10)°. The carboxyl-ate group assumes an extended conformation with respect to the pyrimidine ring, which can be seen from the O=C-O-C torsion angle of 3.2 (4) °. In the crystal, mol-ecules are linked via C-H⋯O and C-H⋯N hydrogen bonds, forming slabs lying parallel to (100).

Spontaneous regression of Merkel cell carcinoma: A case report and review of the literature.

INTRODUCTION: Merkel cell carcinoma (MCC) is a rare and highly aggressive primary cutaneous neuroendocrine carcinoma, most often occurring in the elderly. Recurrence is frequent and in 40% of cases regional and distant metastases develop. Despite this, there have been reports of spontaneous regression. We report the first case of MCC with primary complete spontaneous regression of the nose in an 86-year-old woman following an incisional biopsy. PRESENTATION OF CASE: An 86-year-old woman presented with a violaceous lump on the left side of the nose measuring 25×25mm. Incisional biopsy of the lesion showed MCC and immunohistochemistry confirmed diagnosis. Following an 8-week period the lesion completely disappeared and histology did not show any residual MCC but immunohistochemistry demonstrated a mixture of T and B cells. DISCUSSION: Complete spontaneous regression (CSR) is rare. The literature documents 22 similar cases of CSR of MCC. From this case report and previous literature the most likely reason for regression is a T-cell mediated immune response. CONCLUSION: To the best of our knowledge, this is the first described case of MCC with primary CSR of the nose. Exact mechanism of regression remains unclear. Further research is needed in identifying pathway of immune response and possible immunotherapy as a cure.

Amino Acid compositions of 27 food fishes and their importance in clinical nutrition.

Proteins and amino acids are important biomolecules which regulate key metabolic pathways and serve as precursors for synthesis of biologically important substances; moreover, amino acids are building blocks of proteins. Fish is an important dietary source of quality animal proteins and amino acids and play important role in human nutrition. In the present investigation, crude protein content and amino acid compositions of important food fishes from different habitats have been studied. Crude protein content was determined by Kjeldahl method and amino acid composition was analyzed by high performance liquid chromatography and information on 27 food fishes was generated. The analysis showed that the cold water species are rich in lysine and aspartic acid, marine fishes in leucine, small indigenous fishes in histidine, and the carps and catfishes in glutamic acid and glycine. The enriched nutrition knowledge base would enhance the utility of fish as a source of quality animal proteins and amino acids and aid in their inclusion in dietary counseling and patient guidance for specific nutritional needs.

Deep brain stimulation effects on memory.

As the population of many countries ages, disorders of cognition and memory-such as Alzheimer's Disease (AD) and dementia associated with Parkinson's Disease-will become a major societal burden. At present, few effective medical therapies against these conditions are available. Deep brain stimulation (DBS) may be a potential therapeutic option, because it can directly target and modulate the activity of structures implicated in circuits subserving memory function. In this article, we review the scientific literature to address some of the mechanisms by which DBS may impact memory and cognition. We then summarize the results of recent clinical experience with DBS in AD and Parkinsonian dementia.