Bacillus tequilensis influences metabolite production in tomato and restores soil microbial diversity during Fusarium oxysporum infection

This study evaluates cellular damage, metabolite profiling, and defence-related gene expression in tomato plants and soil microflora during Fusarium wilt disease after treatment with B. tequilensis PBE-1. Histochemical analysis showed that PBE-1 was the primary line of defence through lignin deposition and reduced cell damage. GC-MS revealed that PBE-1 treatment ameliorated stress caused by F. oxysporum infection. PBE-1 also improved transpiration, photosynthesis, and stomatal conductance in tomato. qRT-PCR suggested that the defence-related genes FLS2, SERK, NOS, WRKYT, NHO, SAUR, and MYC2, which spread infection, were highly upregulated during F. oxysporum infection, but either downregulated or expressed normally in PBE-1 + P treated plants. This indicates that the plant not only perceives the bio-control agent as a non-pathogen entity but its presence in normal metabolism and gene expression within the host plant is maintained. The study further corroborated findings that application of PBE-1 does not cause ecological disturbances in the rhizosphere. Activity of soil microflora across four treatments, measured by Average Well Colour Development (AWCD), showed continuous increases from weeks 1 to 4 post-pathogen infection, with distinct substrate usage patterns like tannic and fumaric acids impacting microbial energy source utilization and diversity. Principal Component Analysis (PCA) and diversity indices like McIntosh, Shannon, and Simpson further illustrated significant microbial community shifts over the study period. In conclusion, our findings demonstrate that B. tequilensis PBE-1 is an ideal bio-agent for field application during Fusarium wilt disease management in tomato.

A computational investigation of potential plant-based bioactive compounds against drug-resistant Staphylococcus aureus of multiple target proteins

Drug-resistant Staphylococcus aureus (DRSA) poses a significant global health threat, like bacteremia, endocarditis, skin, soft tissue, bone, and joint infections. Nowadays, the resistance against conventional drugs has been a prompt and focused medical concern. The present study aimed to explore the inhibitory potential of plant-based bioactive compounds (PBBCs) against effective target proteins using a computational approach. We retrieved and verified 22 target proteins associated with DRSA and conducted a screening process that involved testing 87 PBBCs. Molecular docking was performed between screened PBBCs and reference drugs with selected target proteins via AutoDock. Subsequently, we filtered the target proteins and top PBBCs based on their binding affinity scores. Furthermore, molecular dynamic simulation was carried out through GROMACS for a duration of 100 ns, and the binding free energy was calculated using the gmx_MMPBSA. The result showed consistent hydrogen bonding interactions among the amino acid residues Ser 149, Arg 151, Thr 165, Thr 216, Glu 239, Ser 240, Ile 14, as well as Asn 18, Gln 19, Lys 45, Thr 46, Tyr 109, with their respective target proteins of the penicillin-binding protein and dihydrofolate reductase complex. Additionally, we assessed the pharmacokinetic properties of screened PBBCs via SwissADME and AdmetSAR. The findings suggest that β-amyrin, oleanolic acid, kaempferol, quercetin, and friedelin have the potential to inhibit the selected target proteins. In future research, both in vitro and in vivo, experiments will be needed to establish these PBBCs as potent antimicrobial drugs for DRSA.Communicated by Ramaswamy H. Sarma.

Oxidant and antioxidant status among tobacco users: A cross-sectional study

Background

Smokeless and smoking tobacco use results in increased oxidative stress and lipid peroxidation, which play a major role in the causation of cancer in tobacco habituates. Malondialdehyde (MDA) is a product of lipid peroxidation, and glutathione peroxidase (GPx) and superoxide dismutase (SOD), the main enzymes in the antioxidant defense system, are assessed among tobacco users. This study gave insight into the relationship between tobacco use, oxidative stress, and antioxidant enzyme activity.

Aims and Objectives

This study aimed to estimate the levels of lipid peroxidation product MDA and antioxidant enzymes SOD and GPx among tobacco users and compare them with controls.

Method

A case-control study comprising 30 smokeless tobacco users, 30 smokers, and 30 controls was enrolled for the study. Serum MDA was assayed by the thiobarbituric acid method; serum SOD and GPx were assayed using Ransel antioxidant kits. The results were statistically analyzed using descriptive and inferential statistical analysis.

Results

Serum MDA levels, which indicate oxidative stress, were increased among all tobacco users and significantly increased among smokeless tobacco users as compared to smokers. Serum SOD and GPx levels were decreased among both forms of tobacco users compared with controls. With an increase in duration and frequency of tobacco use, there was a significant increase in serum MDA levels among both smokers and chewers and a decrease in serum SOD and GPx levels.

Conclusion

In the present day, the tobacco epidemic has attained enormous proportions with the tobacco habit starting as early as 13-14 years and leading to serious conditions with high morbidity and mortality. These biochemical parameters such as MDA, SOD, and GPx, which act as marker of oxidant and antioxidant system, can constitute important tools for evidence-based medicine for educating patients and motivating interventions in tobacco cessation therapy.

Identification of a candidate dwarfing gene in Pallas, the first commercial barley cultivar generated through mutational breeding

Many induced mutants are available in barley (Hordeum vulgare L.). One of the largest groups of induced mutants is the Erectoides (ert) mutants, which is characterized by a compact and upright spike and a shortened culm. One isolated mutant, ert-k.32, generated by X-ray treatment and registered in 1958 under the named "Pallas", was the first ever induced barley mutant to be released on the market. Its value was improved culm strength and enhanced lodging resistance. In this study, we aimed to identify the casual gene of the ert-k.32 mutant by whole genome sequencing of allelic ert-k mutants. The suggested Ert-k candidate gene, HORVU.MOREX.r3.6HG0574880, is located in the centromeric region of chromosome 6H. The gene product is an alpha/beta hydrolase with a catalytic triad in the active site composed of Ser-167, His-261 and Asp-232. In comparison to proteins derived from the Arabidopsis genome, ErtK is most similar to a thioesterase with de-S-acylation activity. This suggests that ErtK catalyzes post-translational modifications by removing fatty acids that are covalently attached to cysteine residues of target proteins involved in regulation of plant architecture and important commercial traits such as culm stability and lodging resistance.

Sex matters: predator presence induces sexual dimorphism in a monomorphic prey, from stress genes to morphological defences

Inducible defences allow prey to increase survival chances when predators are present while avoiding unnecessary costs in their absence. Many studies report considerable inter-individual variation in inducible defence expression, yet what underlies this variation is poorly understood. A classic vertebrate example of a predator-induced morphological defence is the increased body depth in crucian carp (Carassius carassius), which reduces the risk of predation from gape-size limited predators. Here, we report that among-individual variation in morphological defence expression can be linked to sex. We documented sexual dimorphism in lakes in which crucian carp coexisted with predators, where females showed shallower relative body depths than males, but not in a predator-free lake. When exposing crucian carp from a population without predators to perceived predation risk in a laboratory environment (presence/absence of pike, Esox lucius), we found that males expressed significantly greater morphological defence than females, causing sexual dimorphism only in the presence of predators. We uncovered a correlative link between the sex-specific inducible phenotypic response and gene expression patterns in major stress-related genes (POMC, MC3R, and MC4R). Together, our results highlight that sex-specific responses may be an important, yet underappreciated, component underlying inter-individual differences in the expression of inducible defences, even in species without pronounced sexual dimorphism.

Correlating multi-functional role of cold shock domain proteins with intrinsically disordered regions

Cold shock proteins (CSPs) are an ancient and conserved family of proteins. They are renowned for their role in response to low-temperature stress in bacteria and nucleic acid binding activities. In prokaryotes, cold and non-cold inducible CSPs are involved in various cellular and metabolic processes such as growth and development, osmotic oxidation, starvation, stress tolerance, and host cell invasion. In prokaryotes, cold shock condition reduces cell transcription and translation efficiency. Eukaryotic cold shock domain (CSD) proteins are evolved form of prokaryotic CSPs where CSD is flanked by N- and C-terminal domains. Eukaryotic CSPs are multi-functional proteins. CSPs also act as nucleic acid chaperons by preventing the formation of secondary structures in mRNA at low temperatures. In human, CSD proteins play a crucial role in the progression of breast cancer, colon cancer, lung cancer, and Alzheimer's disease. A well-defined three-dimensional structure of intrinsically disordered regions of CSPs family members is still undetermined. In this article, intrinsic disorder regions of CSPs have been explored systematically to understand the pleiotropic role of the cold shock family of proteins.

Restricted X chromosome introgression and support for Haldane's rule in hybridizing damselflies

Contemporary hybrid zones act as natural laboratories for the investigation of species boundaries and may shed light on the little understood roles of sex chromosomes in species divergence. Sex chromosomes are considered to function as a hotspot of genetic divergence between species; indicated by less genomic introgression compared to autosomes during hybridization. Moreover, they are thought to contribute to Haldane's rule, which states that hybrids of the heterogametic sex are more likely to be inviable or sterile. To test these hypotheses, we used contemporary hybrid zones of Ischnura elegans, a damselfly species that has been expanding its range into the northern and western regions of Spain, leading to chronic hybridization with its sister species Ischnura graellsii. We analysed genome-wide SNPs in the Spanish I. elegans and I. graellsii hybrid zone and found (i) that the X chromosome shows less genomic introgression compared to autosomes, and (ii) that males are underrepresented among admixed individuals, as predicted by Haldane's rule. This is the first study in Odonata that suggests a role of the X chromosome in reproductive isolation. Moreover, our data add to the few studies on species with X0 sex determination system and contradict the hypothesis that the absence of a Y chromosome causes exceptions to Haldane's rule.

Wolbachia-driven selective sweep in a range expanding insect species

Background

Evolutionary processes can cause strong spatial genetic signatures, such as local loss of genetic diversity, or conflicting histories from mitochondrial versus nuclear markers. Investigating these genetic patterns is important, as they may reveal obscured processes and players. The maternally inherited bacterium Wolbachia is among the most widespread symbionts in insects. Wolbachia typically spreads within host species by conferring direct fitness benefits, and/or by manipulating its host reproduction to favour infected over uninfected females. Under sufficient selective advantage, the mitochondrial haplotype associated with the favoured maternally-inherited symbiotic strains will spread (i.e. hitchhike), resulting in low mitochondrial genetic variation across the host species range.

Method

The common bluetail damselfly (Ischnura elegans: van der Linden, 1820) has recently emerged as a model organism for genetics and genomic signatures of range expansion during climate change. Although there is accumulating data on the consequences of such expansion on the genetics of I. elegans, no study has screened for Wolbachia in the damselfly genus Ischnura. Here, we present the biogeographic variation in Wolbachia prevalence and penetrance across Europe and Japan (including samples from 17 populations), and from close relatives in the Mediterranean area (i.e. I. genei: Rambur, 1842; and I. saharensis: Aguesse, 1958).

Results

Our data reveal (a) multiple Wolbachia-strains, (b) potential transfer of the symbiont through hybridization, (c) higher infection rates at higher latitudes, and (d) reduced mitochondrial diversity in the north-west populations, indicative of hitchhiking associated with the selective sweep of the most common strain. We found low mitochondrial haplotype diversity in the Wolbachia-infected north-western European populations (Sweden, Scotland, the Netherlands, Belgium, France and Italy) of I. elegans, and, conversely, higher mitochondrial diversity in populations with low penetrance of Wolbachia (Ukraine, Greece, Montenegro and Cyprus). The timing of the selective sweep associated with infected lineages was estimated between 20,000 and 44,000 years before present, which is consistent with the end of the last glacial period about 20,000 years.

Conclusions

Our findings provide an example of how endosymbiont infections can shape spatial variation in their host evolutionary genetics during postglacial expansion. These results also challenge population genetic studies that do not consider the prevalence of symbionts in many insects, which we show can impact geographic patterns of mitochondrial genetic diversity.

A meta analysis for evaluation of marginal bone level changes at dental implants

Aim

The aim of this study was to assess the marginal bone level changes at dental implants after 1 year in function.

Methods

Detailed searches from PubMed databases were made. A MEDLINE search (PubMed) published in the English language from 1980 to December 2018 was included in this study.

Results

The electronic database research (MEDLINE) produced 166 corresponding articles. One hundred and twenty studies were excluded on the basis of abstract while the 46 researches were used chosen for full-text examination after the title and abstract testing, and 41 studies were excluded that did not meet the requirements of our inclusion and exclusion criteria. A total of 5 studies for a quantitative analysis were taken into account.

Conclusion

Within the limits of the study, the mean marginal bone loss (MBL) was found to be 0.56 mm. A statistically significant difference in the MBL was found between the various studies.

Seasonal dynamics and impact factors of atmospheric CO2 concentration over subtropical forest canopies: observation from eddy covariance tower and OCO-2 satellite in Northwest Himalaya, India

Carbon dioxide (CO₂) is the key atmospheric gas that controls the earth's greenhouse effect, and forests play a major role in abating the atmospheric CO₂ by storing carbon as biomass. Therefore, it is vital to understand the role of different forests in regulating the spatiotemporal dynamics of atmospheric CO₂ concentration. In this study, we have used eddy covariance (EC) tower-based atmospheric CO₂ concentration measurements and satellite-retrieved column average CO₂ concentration of 2018 to understand the diurnal and seasonal dynamics of atmospheric CO₂ concentration over the sub-tropical forest in the foothills of northwest Himalaya, Uttarakhand, India. EC study revealed that the CO₂ concentration over the forest canopy peaks during mid-night to early morning and drop to a minimum during the afternoon. On a monthly scale, peak atmospheric CO₂ concentration was observed during July in both the sites, which was a result of more release of CO₂ by the forest ecosystem through ecosystem respiration and microbial decomposition. Enhanced photosynthetic activities during the late monsoon and post-monsoon resulted in the decrease of atmospheric CO₂ concentration over the forest ecosystem. Among the meteorological variables, rainfall was found to have the highest control over the seasonal variability of the atmospheric CO₂ concentration. Orbiting Carbon Observatory-2 (OCO-2) satellite-retrieved column average CO₂ (XCO₂) was also examined to comprehend its reliability on an ecosystem scale. The OCO-2 retrieved XCO₂ value was higher than the EC carbon flux tower-measured atmospheric CO₂ concentration, which might be due to differences in the vertical resolution of the CO₂ column and scale difference. However, the monthly atmospheric XCO₂ retrieved from OCO-2 strongly adheres with the ground-measured monthly pattern. Our study highlights that forests with varying functional traits within the same climatic conditions show variability in the regulation of atmospheric CO₂ concentration.

Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study

BACKGROUND

This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery.

METHODS

This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery.

RESULTS

A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498).

CONCLUSION

There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.

Peptidoglycan-treated tumor antigen-pulsed dendritic cells impart complete resistance against tumor rechallenge

Solid tumors elicit suppressive T cell responses which impair antigen-presenting cell (APC) functions. Such immune suppression results in uncontrolled tumor growth and mortality. Addressing APC dysfunction, dendritic cell (DC)-mediated anti-tumor vaccination was extensively investigated in both mice and humans. These studies never achieved full resistance to tumor relapse. Herein, we describe a repetitive RM-1 murine tumor rechallenge model for recurrence in humans. Using this newly developed model, we show that priming with tumor antigen-pulsed, Toll-like receptor (TLR)2 ligand-activated DCs elicits a host-protective anti-tumor immune response in C57BL/6 mice. Upon stimulation with the TLR2 ligand peptidoglycan (PGN), the tumor antigen-pulsed DCs induce complete resistance to repetitive tumor challenges. Intra-tumoral injection of PGN reduces tumor growth. The tumor resistance is accompanied by increased expression of interleukin (IL)-27, T-box transcription factor TBX21 (T-bet), IL-12, tumor necrosis factor (TNF)-α and interferon (IFN)-γ, along with heightened cytotoxic T lymphocyte (CTL) functions. Mice primed four times with PGN-stimulated tumor antigen-pulsed DCs remain entirely resistant to repeat challenges with RM-1 tumor cells, suggesting complete prevention of relapse and recurrence of tumor. Adoptive transfer of T cells from these mice, which were fully protected from RM-1 rechallenge, confers anti-tumor immunity to syngeneic naive recipient mice upon RM-1 challenge. These observations indicate that PGN-activated DCs induce robust host-protective anti-tumor T cells that completely resist tumor growth and recurrence.

Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes

Sex chromosomes have evolved from the same autosomes multiple times across vertebrates, suggesting that selection for recombination suppression has acted repeatedly and independently on certain genetic backgrounds. Here, we perform comparative genomics of a bird clade (larks and their sister lineage; Alaudidae and Panuridae) where multiple autosome-sex chromosome fusions appear to have formed expanded sex chromosomes. We detected the largest known avian sex chromosome (195.3 Mbp) and show that it originates from fusions between parts of four avian chromosomes: Z, 3, 4A and 5. Within these four chromosomes, we found evidence of five evolutionary strata where recombination had been suppressed at different time points, and show that stratum age explained the divergence rate of Z-W gametologs. Next, we analysed chromosome content and found that chromosome 3 was significantly enriched for genes with predicted sex-related functions. Finally, we demonstrate extensive homology to sex chromosomes in other vertebrate lineages: chromosomes Z, 3, 4A and 5 have independently evolved into sex chromosomes in fish (Z), turtles (Z, 5), lizards (Z, 4A), mammals (Z, 4A) and frogs (Z, 3, 4A, 5). Our results provide insights into and support for repeated evolution of sex chromosomes in vertebrates.

Clinical evaluation of photodynamic therapy for the treatment of refractory oral Lichen planus - A case series

Oral lichen planus (OLP) is a chronic inflammatory, immune mediated mucocutaneous disorder of uncertain etiology. Psychologic stress has been found to be a main contributing factor in onset and progression of lesions. Most erosive OLP patients are refractory to available therapies, even corticosteroids, and report remarkable side effects. As photodynamic therapy (PDT) has proved it to be an effective and safe alternative treatment of abnormal or neoplastic cells we employed PDT for this diagnosis. Due to limited literature on application of this method for treatment of refractory erosive OLP, we present a series of 10 cases of bilateral erosive LP treated by 5 -Aminolevulinic acid mediated PDT. Outcome of our clinical cases showed remarkable improvement in lesions with reduction in Reticulation, Erythema, Ulceration (REU) score (from 5 to 3) and burning sensation as recorded by Visual Analogue Scale (Pretreatment VAS ranged from 5 to 8, posttreatment VAS was 0-1). PDT could be used as a complementary treatment method for symptomatic resistant OLP lesions, although our findings necessitate further research to validate the efficacy of this method for control of resistant oral lichen planus.

Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat

Non-recombining sex chromosomes (Y and W) accumulate deleterious mutations and degenerate. This poses a problem for the heterogametic sex (XY males; ZW females) because a single functional gene copy often implies less gene expression and a potential imbalance of crucial expression networks. Mammals counteract this by dosage compensation, resulting in equal sex chromosome expression in males and females, whereas birds show incomplete dosage compensation with significantly lower expression in females (ZW). Here, we study the evolution of Z and W sequence divergence and sex-specific gene expression in the common whitethroat (Sylvia communis), a species within the Sylvioidea clade where a neo-sex chromosome has been formed by a fusion between an autosome and the ancestral sex chromosome. In line with data from other birds, females had lower expression than males at the majority of sex-linked genes. Results from the neo-sex chromosome region showed that W gametologs have diverged functionally to a higher extent than their Z counterparts, and that the female-to-male expression ratio correlated negatively with the degree of functional divergence of these gametologs. We find it most likely that sex-linked genes are being suppressed in females as a response to W chromosome degradation, rather than that these genes experience relaxed selection, and thus diverge more, by having low female expression. Overall, our data of this unique avian neo-sex chromosome system suggest that incomplete dosage compensation evolves, at least partly, through gradual accumulation of deleterious mutations at the W chromosome and declining female gene expression.

Pronator teres accessorius: A new variant in flexor antebrachial musculature

Muscles of flexor compartment of forearm have a common origin from medial epicondyle of humerus. Additional bellies of flexor muscles are commonly reported but presence of supernumerary muscles is an infrequent phenomenon. The present study describes an unusual muscle mass in flexor compartment of forearm simulating pronator teres. During routine dissection the upper limb of a 50 years old male cadaver, a supernumerary muscle was found on left side of the upper limb in the flexor compartment. The origin of the muscle was 2cm wide and aponeurotic in nature and attached to an oblique line extending from the inferior surface of the medial epicondyle and the medial surface of the trochlea. It was inserted on an oblique line 2.5cm wide on the radius in area between supinator superiorly and flexor digitorum profundus inferiorly. Existence of accessory muscles, which connect flexor muscles, could be explained embryologically by incomplete cleavage of flexor mass during development. The flexor muscles of the forearm develop from the flexor mass which subsequently divides into two layers: superficial and deep. The deep layer gives rise to flexor digitorum superficialis, flexor digitorum profundus and flexor pollicis longus. These supernumerary muscles are extremely rare entities and probably represent deranged embryological development or the process of atavism in which the anomalous part persist for a longer time in the tree of evolution.

BIOBETTERS: THE BETTER BIOLOGICS AND THEIR REGULATORY OVERVIEW

The continuous innovation of the biopharmaceutical industry has led to development of a new category of biopharmaceuticals i.e. Biobetters or Biosuperiors. Biobetters may have better efficacy, a longer half-life, lower dosing frequency, a reduced risk of immunogenicity, reduced toxicity and side effects along with lower early-stage research risk and development costs. Biobetters rather than biosimilars may capture significant share of market and are the next wave for companies to ride on. Although it sounds intuitive, biobetters will have to face various ordeals like identification of the apparent unmet need, quantification of the potential market opportunity, expensive investment in clinical trials, challenging regulatory approval, pressures of price erosion and patent litigations. Thus, development of biobetters truly requires the right balance between providing life-changing medical management for patients and maintaining an innovative pipeline for continued business success. This review will focus on technical and regulatory prospects of biobetters.

Redundant and regulatory roles for Toll-like receptors in Leishmania infection

Toll-like receptors (TLRs) are germline-encoded, non-clonal innate immune receptors, which are often the first receptors to recognize the molecular patterns on pathogens. Therefore, the immune response initiated by TLRs has far-reaching consequences on the outcome of an infection. As soon as the cell surface TLRs and other receptors recognize a pathogen, the pathogen is phagocytosed. Inclusion of TLRs in the phagosome results in quicker phagosomal maturation and stronger adaptive immune response, as TLRs influence co-stimulatory molecule expression and determinant selection by major histocompatibility complex (MHC) class II and MHC class I for cross-presentation. The signals delivered by the TCR-peptide-MHC complex and co-stimulatory molecules are indispensable for optimal T cell activation. In addition, the cytokines induced by TLRs can skew the differentiation of activated T cells to different effector T cell subsets. However, the potential of TLRs to influence adaptive immune response into different patterns is severely restricted by multiple factors: gross specificity for the molecular patterns, lack of receptor rearrangements, sharing of limited number of adaptors that assemble signalling complexes and redundancy in ligand recognition. These features of apparent redundancy and regulation in the functioning of TLRs characterize them as important and probable contributory factors in the resistance or susceptibility to an infection.

Nonmetric analysis of caroticoclinoid foramen in foothills of Himalayas: Its clinicoanatomic perspective

OBJECTIVE OF THE STUDY

Study was conducted to evaluate the incidence of caroticoclinoid foramen in north Indian population. Authors have also endeavoured to discuss its clinical and embryological implications.

MATERIALS AND METHODS

Study was conducted on 108 dry human skulls in department of anatomy SGRR medical college, Dehradun. Incidence of caroticoclinoid foramen was evaluated in accordance with side.

RESULTS

A percentage of 22.22 skulls presented with the caroticoclinoid foramen with maximum incidence of unilateral and incomplete type. Incidence revealed no bias towards side.

CONCLUSION

Anatomical knowledge about CCF may be helpful to radiologists and neurosurgeons in providing an additional insight into the diagnosis and management of various pathologies around sellar region.

Transcriptome profiling in the damselfly Ischnura elegans identifies genes with sex-biased expression

Background

Sexual dimorphism occurs widely across the animal kingdom and has profound effects on evolutionary trajectories. Here, we investigate sex-specific gene expression in Ischnura elegans (Odonata: dragonflies and damselflies), a species with pronounced sexual differences including a female-limited colour polymorphism with two female-like gynochrome morphs and one male-mimicking, androchrome morph. Whole-organism transcriptome profiling and sex-biased gene expression analysis was conducted on adults of both sexes (pooling all females as well as separating the three morphs) to gain insights into genes and pathways potentially associated with sexual development and sexual conflict.

Results

The de novo transcriptome assembly was of high quality and completeness (54 k transcripts; 99.6% CEGMA score; 55% annotated). We identified transcripts of several relevant pathways, including transcripts involved in sex determination, hormone biosynthesis, pigmentation and innate immune signalling. A total of 1,683 genes were differentially expressed (DE) between males and all females (1,173 were female-biased; 510 male-biased). The DE genes were associated with sex-specific physiological and reproductive processes, olfaction, pigmentation (ommochrome and melanin), hormone (ecdysone) biosynthesis and innate immunity signalling pathways. Comparisons between males and each female morph category showed that the gynochromes differed more from males than the androchrome morph.

Conclusions

This is the first study to characterize sex-biased gene expression in odonates, one of the most ancient extant insect orders. Comparison between I. elegans sexes revealed expression differences in several genes related to sexual differences in behaviour and development as well as morphology. The differential expression of several olfactory genes suggests interesting sexual components in the detection of odours, pheromones and environmental volatiles. Up-regulation of pigmentation pathways in females indicates a prominent role of ommochrome pigments in the formation of the genetically controlled female colour polymorphism. Finally, the female-biased expression of several immunity genes suggests a stronger immune response in females, possibly related to the high levels of male mating harassment and recurrent matings in this species, both of which have been shown to injure females and expose them to sexually transmitted diseases and toxins contained in seminal fluids.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3334-6) contains supplementary material, which is available to authorized users.

Oral pH in gastroesophageal reflux disease

AIMS AND OBJECTIVES

The aim of this study is to compare surface pH in various parts of the oral cavity between patients with gastroesophageal reflux disease (GERD) and healthy controls.

METHODS

Using a flat pH meter sensor, fixed electrode pen type digital pH meter, oral pH levels were assessed at different mucosal sites among 34 GERD patients and 32 healthy controls. Salivary flow rates and buffering capacity were also assessed in them. A thorough oral examination was performed to screen for any oral and dental changes.

RESULT

A significantly lower pH of 6.65 ± 0.13 (mean ± SD) was found in the GERD group compared to control group 7.23 ± 0.12 (p < 0.05). Least pH was found in the floor of the mouth 6.594 ± 0.17 and highest in the lower labial mucosa among the GERD patients. Salivary flow rate and buffering capacity were low in these patients. Significant changes were noticed in the hard and soft tissues of the oral cavity among the GERD group.

CONCLUSION

Oral mucosal pH is altered in GERD patients and may contribute to effects on the oral cavity.

Tumor markers: A diagnostic tool

The purpose of this review is to give a brief background to enable the judicious use of widely performed serum cancer markers. The markers could be product of cancerous cell or as response to cancer. They are usually proteins, which are mainly found in blood or urine. These markers may be employed to predict primary or secondary tumor risk. Sometimes, non-cancerous conditions can also cause elevation of some tumor markers to be higher than normal. Besides, not every cancer patient may have raised level of a tumor marker. For these reasons, knowledge about cancer biomarkers has increased tremendously. Awareness for cancer and related tumor markers providing great opportunities for improving the management of cancer patients by enhancing the efficiency of detection and efficacy of treatment.

NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction

The nucleotide binding site leucine-rich repeats (NBSLRRs) belong to one of the largest known families of disease resistance genes that encode resistance proteins (R-protein) against the pathogens of plants. Various defence mechanisms have explained the regulation of plant immunity, but still, we have limited understanding about plant defence against different pathogens. Identification of R-proteins and proteins having R-protein-like features across the genome, transcriptome and proteome would be highly useful to develop the global understanding of plant defence mechanisms, but it is laborious and time-consuming task. Therefore, we have developed a support vector machine-based high-throughput pipeline called NBSPred to differentiate NBSLRR and NBSLRR-like protein from Non-NBSLRR proteins from genome, transcriptome and protein sequences. The pipeline was tested and validated with input sequences from three dicot and two monocot plants including Arabidopsis thaliana, Boechera stricta, Brachypodium distachyon Solanum lycopersicum and Zea mays.

AVAILABILITY AND IMPLEMENTATION

The NBSPred pipeline is available at http://soilecology.biol.lu.se/nbs/

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

CONTACT

sandeep.kushwaha@biol.lu.se.

Is dosimetry still a necessity in current dental practice?

Today, dentists have a wide range of imaging modalities to choose from, the film based techniques, digital techniques, and the recent introduction of 3D volumetric or cone beam computed tomography (CBCT). The inherent design features of the new generation dental x-ray equipment has significantly improved over the years with no evidence of substandard x-ray units in operation. In dental facilities radiological workload is comparatively low, newer radiation equipments and accessories follow safety guidelines and employ better radiation protection measures for the patient and the operator. Dentists' knowledge and expertise in radiation protection measures is good, enabling them to carry out riskfree radiation procedures in their practice. Therefore, the present study is aimed at assessing the need for dosimeters in current dental scenario. 'Is there currently a significant risk from dental radiography to merit the use of personal dosimetery in dental practice. 'Dental health professionals (Oral radiologists) and radiographic assistants of fourteen dental colleges in Karnataka state participated in this questionnaire study. The questionnaire consisted of the following questions--the make, type, year of manufacture of radiographic machines used in their setup, number of radiographs made per day in the institution, type of receptors used, number of personnel at risk for radiation exposure, radiation protection measures used, regular monitoring by personal dosimeters, equivalent dosage readings for the past 12 months and whether the reading of thermoluminescent dosimeters (TLD) for any personnel had exceeded the recommended exposure value in the last 3 years. Dosimetry records of the radiology staff in the last three years shows doses no more than 1.50 mSv per year. The various institutions' dose (person mSv) was in the range of 3.70 mSv-3.90 mSv. Personal monitoring for Dentists can be omitted in the dental colleges since the estimated dose of oral radiologists contributed less than 0.01 mSv to the total average annual effective dose equivalent. Hence personal monitoring services (TLD Badges) for dentists employed in dental colleges should not be made mandatory.

Rhinocerebral Mucormycosis Among Diabetic Patients: An Emerging Trend

Mucormycosis is an acute necrotic fungal infection with a fulminant course. Earlier considered a rare entity, mucormycosis is being reported with increasing frequency in recent years, possibly due to the increase in immunocompromised population especially diabetic patients. We report three cases of rhinocerebral mucormycosis among poorly controlled diabetic patients. This article emphasizes the need for further awareness of this disease, early diagnosis, and treatment to counter this opportunistic infection.

Quality and Acceptability of Meat Nuggets with Fresh Aloe vera Gel

Aloe vera has been used worldwide for pharmaceutical, food, and cosmetic industries due to its wide biological activities. However, quality improvement of low fat meat products and their acceptability with added Aloe vera gel (AVG) is scanty. The aim of this study was to explore the feasibility of using fresh AVG on physicochemical, textural, sensory and nutritive qualities of goat meat nuggets. The products were prepared with 0%, 2.5%, and 5% fresh AVG replacing goat meat and were analyzed for proximate composition, physicochemical and textural properties, fatty acid profile and sensory parameters. Changes in lipid oxidation and microbial growth of nuggets were also evaluated over 9 days of refrigerated storage. The results showed that AVG significantly (p<0.05) decreased the pH value and protein content of meat emulsion and nuggets. Product yield was affected at 5% level of gel. Addition of AVG in the formulation significantly affected the values of texture profile analysis. The AVG reduced the lipid oxidation and microbial growth in nuggets during storage. Sensory panelists preferred nuggets with 2.5% AVG over nuggets with 5% AVG. Therefore, AVG up to 2.5% level could be used for quality improvement in goat meat nuggets without affecting its sensorial, textural and nutritive values.

De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes

BACKGROUND

There is growing interest in odonates (damselflies and dragonflies) as model organisms in ecology and evolutionary biology but the development of genomic resources has been slow. So far only one draft genome (Ladona fulva) and one transcriptome assembly (Enallagma hageni) have been published. Odonates have some of the most advanced visual systems among insects and several species are colour polymorphic, and genomic and transcriptomic data would allow studying the genomic architecture of these interesting traits and make detailed comparative studies between related species possible. Here, we present a comprehensive de novo transcriptome assembly for the blue-tailed damselfly Ischnura elegans (Odonata: Coenagrionidae) built from short-read RNA-seq data. The transcriptome analysis in this paper provides a first step towards identifying genes and pathways underlying the visual and colour systems in this insect group.

RESULTS

Illumina RNA sequencing performed on tissues from the head, thorax and abdomen generated 428,744,100 paired-ends reads amounting to 110 Gb of sequence data, which was assembled de novo with Trinity. A transcriptome was produced after filtering and quality checking yielding a final set of 60,232 high quality transcripts for analysis. CEGMA software identified 247 out of 248 ultra-conserved core proteins as 'complete' in the transcriptome assembly, yielding a completeness of 99.6%. BLASTX and InterProScan annotated 55% of the assembled transcripts and showed that the three tissue types differed both qualitatively and quantitatively in I. elegans. Differential expression identified 8,625 transcripts to be differentially expressed in head, thorax and abdomen. Targeted analyses of vision and colour functional pathways identified the presence of four different opsin types and three pigmentation pathways. We also identified transcripts involved in temperature sensitivity, thermoregulation and olfaction. All these traits and their associated transcripts are of considerable ecological and evolutionary interest for this and other insect orders.

CONCLUSIONS

Our work presents a comprehensive transcriptome resource for the ancient insect order Odonata and provides insight into their biology and physiology. The transcriptomic resource can provide a foundation for future investigations into this diverse group, including the evolution of colour, vision, olfaction and thermal adaptation.

Role of physicochemical properties in the estimation of skin permeability: in vitro data assessment by Partial Least-Squares Regression

Skin provides passage for the delivery of drugs. The in vitro and in vivo testing of chemicals for estimation of dermal absorption is very time consuming, costly and has many ethical difficulties related to human and animal testing. The solution to the problem is Quantitative structure-permeability relationships. This method relates dermal penetration properties of a range of chemical compounds to their physicochemical parameters. In the present study, an effort has been made to develop models for the accurate prediction of skin permeability using a large, diverse dataset through the combination of various regression methods coupled with the Genetic Algorithm (GA)/Interval Partial Least-Squares Algorithm (iPLS). The descriptors were calculated using e-DRAGON and ADME Pharma Algorithms-Abrahams descriptors. The original dataset was divided into a training set and a testing set using the Kennard-Stone Algorithm. The selection of descriptors was made by the GA and iPLS. The model applicability domain was determined. The results showed that a three-parameter model built through Partial Least-squares Regression was most accurate with r(2) of 0.936.

Model based design of inhibitors for c-jun

Literature shows that various molecular cascades are activated by stress, UV rays and pollutants leading to wrinkle formation of the skin. These cascades start from five types of receptors (EGFR, PDGFR, PAFR, IL1R, TNFRB) and terminate with the production of matrix metalloproteinase's, which degrades collagen leading to wrinkle formation. Signaling pathway leading to wrinkle formation showed that c-jun is involved in these cascades. Therefore, c-jun is the preferential choice for inhibition to reduce the intensity of collagen degradation. Hence, the 3D structure of c-jun was modeled using segment based homology modeling by MODELLER 9v5. Evaluation of the constructed model was done by PROCHECK, WHAT CHECK and through RMSD/RMSF calculations. Ligands for the inhibitory sites were designed using LIGANDSCOUT. The interaction study of ligand and receptor was performed by AUTODOCK. A library of analogues was constructed for three known inhibitory sites. The receptor-analogue study was performed using the software MOLEGRO Virtual Docker. The analogues constructed from the designed novel reference ligands showed good binding with the receptor binding sites. It should be noted that these predicted data should be validated using suitable assays for further consideration.

Y-chromosomal STR haplotypes in two endogamous tribal populations of Karnataka, India

POPULATION

Approximately 5.0 mL of blood sample was collected from a total of 150 men belonging to two tribal populations of coastal Uttar Kannada district of Karnataka, with their informed written consent. Both the populations are endogamous and they belong to the Dravidian linguistic family. Halakki is a tribal group having a population size of c. 3383. They claim that they originally belong to Gujarat and Rajasthan, and migrated through Andhra Pradesh to Karnataka. Kunabhi is also a tribal population, c. 35,214 in number. They were hunters and gatherers but presently they practice agriculture.

Evaluation of low dose ACTH stimulation test in suspected secondary adrenocortical insufficiency

BACKGROUND

Several studies in the last few years have shown that the standard 250 micro g dose used in ACTH stimulation test may be very high and have suggested that a dose of 1 micro g may be sufficient for evaluating hypothalamo-pituitary adrenal (HPA) axis.

AIMS

To evaluate the role of low dose ACTH stimulation test in patients with suspected Secondary Adrenal Insufficiency (SAI).

SUBJECTS AND METHODS

Thirty-one patients of suspected SAI with a documented pituitary lesion and seven normal healthy controls were included in the study. All the subjects underwent ACTH stimulation test with standard high dose (HD= 250 microg) and low dose (LD= 1 microg) ACTH. Insulin Induced Hypoglycaemia (IIH) test was done in 7 out of 9 patients in whom the results of the two tests were discordant. The cut off for normal HD stimulation test was taken as peak cortisol response > 18 microg/dl and for LD test, either a cortisol response of > 18 microg/dl or an increment of more than 7 micro g/dl over the basal value at any time during the test, on the basis of response observed in controls.

RESULTS

22/31 patients (74%) in SAI group showed concordant results with both tests, whereas nine patients had discordant results. These nine patients showed AI with LD ACTH, but HD ACTH test showed a normal response. In 7 of these 9 patients who underwent IIH, AI was confirmed in 6.

CONCLUSION

The LD ACTH stimulation test seems to be better than HD ACTH stimulation test for evaluating HPA axis in patients with suspected SAI. When basal cortisol is normal, LD ACTH stimulation test detects subtle SAI.