Transcriptomic analysis reveals zinc-mediated virulence and pathogenicity in multidrug-resistant Acinetobacter baumannii.

Acinetobacter baumannii is a gram-negative bacterium well known for its multidrug resistance and connection to nosocomial infections under ESKAPE pathogens. This opportunistic pathogen is ubiquitously associated with nosocomial infections, posing significant threats within healthcare environments. Its critical clinical symptoms, namely, meningitis, urinary tract infections, bloodstream infections, ventilator-associated pneumonia, and pneumonia, catalyze the imperative demand for innovative therapeutic interventions. The proposed research focuses on delineating the role of Zinc, a crucial metallo-binding protein and micronutrient integral to bacterial metabolism and virulence, to enhance understanding of the pathogenicity of A. baumannii. RNA sequencing and subsequent DESeq2 analytical methods were used to identify differential gene expressions influenced by zinc exposure. Exploiting the STRING database for functional enrichment analysis has demonstrated the complex molecular mechanisms underlying the enhancement of pathogenicity prompted by Zinc. Moreover, hub genes like gltB, ribD, AIL77834.1, sdhB, nuoI, acsA_1, acoC, accA, accD were predicted using the cytohubba tool in Cytoscape. This investigation underscores the pivotal role of Zinc in the virulence of A. baumannii elucidates the underlying molecular pathways responsible for its pathogenicity. The research further accentuates the need for innovative therapeutic strategies to combat A. baumannii infections, particularly those induced by multidrug-resistant strains.

Rapid sleep education: If you could tell people one thing about sleep, what should it be?

Informal learning settings such as museums provide unique opportunities for educating a local community about sleep. However, in such settings, information must be capable of immediately inciting interest. We developed a series of sleep "icebreakers" (brief, informal facts) to determine whether they elicited interest in sleep and encouraged behavioural change. There were 859 participants across three cross-sectional samples: (a) members of the local museum; (b) Mechanical Turk workers who responded to a "sleep" study advertisement; and (c) Mechanical Turk workers who responded to a "various topics" study advertisement that did not mention sleep. All three samples demonstrated high interest in sleep topics, though delayed recall of the icebreakers was strongest in participants who expected to learn about the sleep topics. Icebreaker interest ratings were independent of age, gender and race/ethnicity, suggesting that sleep is a topic of universal interest. Importantly, regardless of demographics and sample, the more the icebreakers interested the participants, the more likely participants were to indicate willingness to donate to a sleep exhibit, change their sleep behaviours, and post to social media. Thus, sleep icebreakers can rapidly elicit people's interest, and future outreach efforts should couple icebreakers with opportunities for subsequent personalized learning.

A microRNA binding site polymorphism in the 3' UTR region of VEGF-A gene modifies colorectal cancer risk based on ethnicity: a meta-analysis.

BACKGROUND: Vascular endothelial growth factor A (VEGF-A) plays an integral role in angiogenesis by contributing to growth, development, and metastasis of solid tumors. Recently, a single-nucleotide polymorphism +936C/T located in the VEGF-A 3' untranslated region (UTR) facilitated the susceptibility of colorectal cancer. The association between VEGF-A gene polymorphism +936C/T and colorectal cancer risk has been widely studied in the last decade, but presently, the results furnished remain enigmatic. Hence, the study aimed to investigate the association between VEGF-A +936C/T miRNA binding site polymorphism and the risk of developing colorectal cancer. METHODS: This meta-analysis included 13 published case-control studies covering 3465 cases (colorectal cancer) and 3476 healthy controls. Publication bias was examined by means of Begg's funnel plots and Egger's regression tests. The quality of the studies included was evaluated using Newcastle-Ottawa scale. Subgroup analyses were performed in accordance to the various ethnicities of the study subjects and the study quality. RESULTS: From the data obtained, it is implied that VEGF-A +936C/T polymorphism did not correlate with elevated colorectal cancer risk in all genetic models. But the results acquired from the subgroup analysis in over dominant model (CT vs. CC + TT: OR = 1.5047, 95% CI = 1.19-1.90) suggest that VEGF-A +936C/T polymorphism leads to the raise in the risk of developing CRC among the East Asian population. No association was observed in Caucasian and South Asian population. CONCLUSIONS: Our results indicate that VEGF-A +936C/T polymorphism is not a risk factor for developing CRC in Caucasian and South Asian population. However, the East Asian population was related to an increased risk of developing colorectal cancer due to the presence of the minor allele.

Comparison of potential inhibitors and targeting fat mass and obesity-associated protein causing diabesity through docking and molecular dynamics strategies.

Genome-wide association studies (GWAS) have identified an association between polymorphisms in the FTO gene and obesity. The FTO: rs9939609, an intronic variant, is considered a risk allele for developing diabesity in homozygous and heterozygous forms. This study aimed to investigate the molecular structure of the available inhibitors specific to the FTO mutations along with the rs9939609 variant. We identified the best-suited inhibitor molecules for each mutant type containing the rs9939609 risk allele. Missense mutations unique to obesity and containing the risk allele of rs9939609 were retrieved from dbSNP for this study. Further stability testing for the mutations were carried out using DynaMut and iStable tools. Three mutations (G187A, M223V, and I492V) were highly destabilizing the FTO structure. These three mutants and native FTO were docked with each of the nine-inhibitor molecules collected from literature studies with the help of PyRx and AutoDock. Further structural behavior of the mutants and native FTO were identified with molecular dynamics simulations and MM-PBSA analyses, along with the 19complex inhibitor compound. We found the compound 19complex exhibited better binding interactions and is the top candidate inhibitor for the M223V and I492V mutants. This study provided insights into the structural changes caused due to mutations in FTO, and the binding mechanism of the inhibitor molecules. It could aid in developing antiobesity drugs for treating patients with mutations and risk alleles predisposing to obesity.

Dielectric response of nitrogen in soil amended with chicken litter biochar and urea under Oryza sativa L. cultivation.

Unbalanced utilization of nitrogen (N) rice not economically viable neither is this practice environmental friendly. Co-application of biochar and urea could reduce the unbalanced use of this N fertilizer in rice cultivation. Thus, a field study was carried out to: (i) determine the effects of chicken litter biochar and urea fertilization on N concentration in soil solution of a cultivated rice (MR219) using dielectric measurement at a low frequency and (ii) correlate soil dielectric conductivity with rice grain yield at maturity. Dielectric response of the soil samples at 20, 40, 55, and 75 days after transplanting were determined using an inductance-capacitance-resistance meter HIOKI 3522-50 LCR HiTESTER. Selected soil chemical properties and yield were determined using standard procedures. The dielectric conductivity and permittivity of the soil samples measured before transplanting the rice seedlings were higher than those for the soil samples after transplanting. This was due to the inherent nitrogen of the chicken litter biochar and the low nitrogen uptake at the transplanting stage. The soil N response increased with increasing measurement frequency and N concentration. The permittivity of the soil samples was inversely proportional to frequency but directly proportional to N concentration in the soil solution. The estimated contents of N in the soil using the dielectric conductivity approach at 1000 Hz decreased with increasing days of fertilization and the results were similar to those of soil NH4+ determined using chemical analysis. The conductivity measured within 1000 Hz and 100,000 Hz correlated positively with the rice grain yield suggesting that nitrogen concentration of the soil can be used to estimate grain yield of the cultivated rice plants.

Bladder neoplasms and NF-κB: an unfathomed association.

Introduction: Bladder cancer is the second most common genitourinary tract cancer and is often recurrent and/or chemoresistant after tumor resection. Cigarette smoking, exposure to aromatic amines, and chronic infection/inflammation are bladder cancer risk factors. NF-κB is a transcription factor that plays a critical role in normal physiology and bladder cancer. Bladder cancer patients have constitutively active NF-κB triggered by pro-inflammatory cytokines, chemokines, and hypoxia, augmenting carcinogenesis and progression.Areas covered: NF-κB orchestrates protein interactions (PTEN, survivin, VEGF), regulation (CYLD, USP13) and gene expression (Trp 53) resulting in bladder cancer progression, recurrence and resistance to therapy. This review focuses on NF-κB in bladder inflammation, cancer and resistance to therapy.Expert opinion: NF-κB and bladder cancer necessitate further research to develop better diagnostic and treatment regimens that address progression, recurrence and resistance to therapy. NF-κB is a master regulator that can act with or on minimally one cancer hallmark gene or protein, leading to bladder cancer progression (Tp53, PTEN, VEGF, HMGB1, CYLD, USP13), recurrence (PCNA, BcL-2, JUN) and resistance to therapy (P-gp, twist, SETD6). Thus, an understanding of bladder cancer in relation to NF-κB will offer improved strategies and efficacious targeted therapies resulting in minimal progression, recurrence and resistance to therapy.

Investigating the role of microRNA-27a gene polymorphisms and its interactive effect with risk factors in gastrointestinal cancers.

Gastrointestinal (GI) cancers are known to have a high incidence worldwide and require an early diagnosis to successfully treat them, providing higher survival rates and better quality of life for the patients. MicroRNA-27a is a well-known oncogene that plays a significant role in various GI cancers. It is known to upregulate the expression of numerous oncogenes leading to cancer progression. The miR-27a harbors two polymorphisms rs895819 and rs11671784 which alter the disease susceptibility by interfering with the maturation and expression of miR-27a. In the current study, we aimed to investigate the role played by these polymorphisms in cancers of the GI tract. We conducted a case-control study with 210 GI cancer cases and 210 cancer-free controls to analyze the effect of these polymorphisms. The rs895819 polymorphism was genotyped using PCR-RFLP, and rs11671784 was genotyped on a MassARRAY platform. The association analysis failed to bring out any significant association of the polymorphisms with GI cancer risk. However, genotype-phenotype interaction analysis revealed that the rs895819 was found to increase the risk GI cancers along with the presence of risk factors such as socioeconomic status, diabetes mellitus, hypertension, alcohol consumption, and tobacco chewing.

Comprehensive in silico screening and molecular dynamics studies of missense mutations in Sjogren-Larsson syndrome associated with the ALDH3A2 gene.

Sjögren-Larsson syndrome (SLS) is an autoimmune disorder inherited in an autosomal recessive pattern. To date, 80 missense mutations have been identified in association with the Aldehyde Dehydrogenase 3 Family Member A2 (ALDH3A2) gene causing SLS. Disruption of the function of ALDH3A2 leads to excessive accumulation of fat in the cells, which interferes with the normal function of protective membranes or materials that are necessary for the body to function normally. We retrieved 54 missense mutations in the ALDH3A2 from the OMIM, UniProt, dbSNP, and HGMD databases that are known to cause SLS. These mutations were examined with various in silico stability tools, which predicted that the mutations p.S308N and p.R423H that are located at the protein-protein interaction domains are the most destabilizing. Furthermore, to determine the atomistic-level differences within the protein-protein interactions owing to mutations, we performed macromolecular simulation (MMS) using GROMACS to validate the motion patterns and dynamic behavior of the biological system. We found that both mutations (p.S380N and p.R423H) had significant effects on the protein-protein interaction and disrupted the dimeric interactions. The computational pipeline provided in this study helps to elucidate the potential structural and functional differences between the ALDH3A2 native and mutant homodimeric proteins, and will pave the way for drug discovery against specific targets in the SLS patients.

Differential expression of NF-κB heterodimer RelA/p50 in human urothelial carcinoma.

BACKGROUND: Urothelial carcinoma (UC) is the fifth most common malignancy that accounts for 5% of all cancers. Diagnostic markers that predict UC progressions are inadequate. NF-κB contributes towards disease progression upon constitutive activation in many solid tumors. The nuclear localization of NF-κB indicates increased transcriptional activity while cytoplasmic localization indicates the inactive protein repository that can be utilized readily by a malignant cell. This study delineates the nuclear and cytoplasmic differential expression of NF-κB heterodimers in UC progression. METHODS: The involvement of the NF-κB proteins in UC was analyzed in silico using cytoscape. The expression of NF-κB heterodimers was analyzed by immunohistochemistry. RESULTS: PINA4MS app in cytoscape revealed over expression of RelA and suppression of NF-κB1 (p50 precursor) in UC whereas the expression of NF-κB target proteins remained unhindered. Immunohistochemical localization showed nuclear RelA/p50 in low grade UC whereas in high grade only RelA expression was observed. Conversely, cytoplasmic expression of RelA/p50 remained extensive across high and low grade UC tissues (p < 0.005). RelA nuclear and cytoplasmic expression (p < 0.005) was directly proportional to the disease progression. In our study, some of the high-grade UC tissues with squamous differentiation and muscle invasion had extensive nuclear p50 localization. The phenomenon of RelA/p50 expression seen increased in low-grade UC than high grade UC might be due to their interaction with other members of NF-κB family of proteins. Thus, NF-κB RelA/p50 differential expression may play a unique role in UC pathogenesis and can serve as a biomarker for diagnosis.

The influence of commenting validity, placement, and style on perceptions of computer code trustworthiness: A heuristic-systematic processing approach.

Computer programs are a ubiquitous part of modern society, yet little is known about the psychological processes that underlie reviewing code. We applied the heuristic-systematic model (HSM) to investigate the influence of computer code comments on perceptions of code trustworthiness. The study explored the influence of validity, placement, and style of comments in code on trustworthiness perceptions and time spent on code. Results indicated valid comments led to higher trust assessments and more time spent on the code. Properly placed comments led to lower trust assessments and had a marginal effect on time spent on code; however, the effect was no longer significant after controlling for effects of the source code. Low style comments led to marginally higher trustworthiness assessments, but high style comments led to longer time spent on the code. Several interactions were also found. Our findings suggest the relationship between code comments and perceptions of code trustworthiness is not as straightforward as previously thought. Additionally, the current paper extends the HSM to the programming literature.

A Computational Approach to Identify the Biophysical and Structural Aspects of Methylenetetrahydrofolate Reductase (MTHFR) Mutations (A222V, E429A, and R594Q) Leading to Schizophrenia.

The association between depression and methylenetetrahydrofolate reductase (MTHFR) has been continually demonstrated in clinical studies, yet there are sparse resources available to build a relationship between the mutations associated with MTHFR and depression. The common mutations found to be associated with schizophrenia and MTHFR are A222V, E429A, and R594Q. Although abundant research on structural and functional effects caused by A222V mutation is available, very less amount of studies have been done on the other two mutants (E429A and R594Q). Hence in this study, a comparative analysis was carried out between the most common A222V mutation, a prevalent E429A mutation, and a less prevalent and less deleterious R594Q mutation. To predict structural rearrangements upon mutation, we proposed a computational pipeline using in silico prediction tools, molecular docking, and molecular dynamics simulation analysis. Since the association of flavin adenine dinucleotide (FAD) is important for the functioning of the protein, binding analysis between protein and the coenzyme was performed. This would enable us to understand the interference level of each mutation over FAD-binding activity. Consequently, we found that two mutations (A222V and E429A) showed lesser binding activity and structural deviations when compared to the native molecule and mutant R594Q. Comparatively, higher structural changes were observed with A222V mutant complex in comparison to other mutant complexes. Computational studies like this could render better insights into the structural changes in the protein and their relationship with the disease condition.

Coapplication of Chicken Litter Biochar and Urea Only to Improve Nutrients Use Efficiency and Yield of Oryza sativa L. Cultivation on a Tropical Acid Soil.

The excessive use of nitrogen (N) fertilizers in sustaining high rice yields due to N dynamics in tropical acid soils not only is economically unsustainable but also causes environmental pollution. The objective of this study was to coapply biochar and urea to improve soil chemical properties and productivity of rice. Biochar (5 t ha(-1)) and different rates of urea (100%, 75%, 50%, 25%, and 0% of recommended N application) were evaluated in both pot and field trials. Selected soil chemical properties, rice plants growth variables, nutrient use efficiency, and yield were determined using standard procedures. Coapplication of biochar with 100% and 75% urea recommendation rates significantly increased nutrients availability (especially P and K) and their use efficiency in both pot and field trials. These treatments also significantly increased rice growth variables and grain yield. Coapplication of biochar and urea application at 75% of the recommended rate can be used to improve soil chemical properties and productivity and reduce urea use by 25%.

EGCG mediated downregulation of NF-AT and macrophage infiltration in experimental hepatic steatosis.

SCOPE: Increased fat consumption in industrialized countries has resulted in hepatic steatosis that upregulates atherogenic aspirant genes, leading to atherosclerosis and mortality. Although extensive studies have been carried out to elucidate the atheroprotective efficacy of epigallocatechin-3-gallate (EGCG), the effect of EGCG on hepatic steatosis has not been studied comprehensively. Hence, the current study was designed to find out the effect of EGCG on hepatic events that prelude atherosclerosis with special reference to macrophage infiltration. METHODS AND RESULTS: Male albino rats of Wistar strain were used in this study. Basic biochemical assays along with the protein expression of CAMs, NF-κB, TNF-α and NF-AT were assayed in the current study. EGCG supplementation significantly reverted the alterations in both biochemical and histological parameters and is shown to reduce the TNF-α mediated NF-AT expression and thereby its downstream targets like ICAM-1 and E-selectin expression to a greater extent than NF-κB mediated downstream targets like VCAM-1 and P-selectin in hypercholesterolemic rat liver. CONCLUSION: Our results suggest that EGCG influences the early events of atherosclerosis that occur; thereby modulating the NF-AT pathway and thereby mitigating the hypercholesterolemic stress.

Bilateral limb phase relationship and its potential to alter muscle activity phasing during locomotion.

It is well established that the sensorimotor state of one limb can influence another limb and therefore bilateral somatosensory inputs make an important contribution to interlimb coordination patterns. However, the relative contribution of interlimb pathways for modifying muscle activation patterns in terms of phasing is less clear. Here we studied adaptation of muscle activity phasing to the relative angular positions of limbs using a split-crank ergometer, where the cranks could be decoupled to allow different spatial angular position relationships. Twenty neurologically healthy individuals performed the specified pedaling tasks at different relative angular positions while surface electromyographic (EMG) signals were recorded bilaterally from eight lower extremity muscles. During each experiment, the relative angular crank positions were altered by increasing or decreasing their difference by randomly ordered increments of 30 degrees over the complete cycle [0 degrees (in phase pedaling); 30, 60, 90, 120, 150, and 180 degrees (standard pedaling); and 210, 240, 270, 300, and 330 degrees out of phase pedaling]. We found that manipulating the relative angular positions of limbs in a pedaling task caused muscle activity phasing changes that were either delayed or advanced, dependent on the relative spatial position of the two cranks and this relationship is well-explained by a sine curve. Further, we observed that the magnitude of phasing changes in biarticular muscles (like rectus femoris) was significantly greater than those of uniarticular muscles (like vastus medialis). These results are important because they provide new evidence that muscle phasing can be systematically influenced by interlimb pathways.

Cognitive mechanisms of visuomotor transformation in movement imitation: examining predictions based on models of apraxia and motor control.

When we observe a movement and then reproduce it, how is this visual input transformed into motor output? Studies on stroke patients with apraxia suggest that there may be two distinct routes used for gesture imitation; an indirect route that recruits stored movement memories (motor programs) and a direct route that bypasses them. The present study examined 30 healthy adults ages 18-80 (mean age=44.0 years, SD=19.5) to learn how motor programs are recruited or bypassed in movement imitation depending upon task conditions (whether familiar letters or novel shapes are imitated) and perceptual factors (whether shapes or letters are perceived). Subjects were asked to imitate the movements of a model who formed shapes and letters on a sheer mesh screen, and to report whether they perceived the task as a shape or a letter. Movements were recorded using a Vicon motion analysis system, and subsequently analyzed to determine the degree of difference between the demonstrated and produced movements. As predicted, letter perception on the letter tasks resulted in increased temporal error when the demonstrated stroke order conflicted with subjects' habitual pattern of letter formation. No such interference effects were observed when the letter tasks were perceived as shapes. These findings are discussed in the context of current theories on imitation, and implications for rehabilitation and motor re-learning are presented.

Anthraquinones from the roots of Prismatomeris malayana.

A novel anthraquinone, 1,3-dihydroxy-5,6-dimethoxy-2-methoxymethyl-9,10-anthraquinone (9) and a new natural product, 2-hydroxymethyl-1-methoxy-9,10-anthraquinone (8) were isolated from the roots of Prismatomeris malayana together with seven known anthraquinones, tectoquinone (1), 1-hydroxy-2-methyl-9,10-anthraquinone (2), rubiadin (3), rubiadin-1-methyl ether (4), 1,3-dihydroxy-5,6-dimethoxy-2-methyl-9,10-anthraquinone (5), nordamnacanthal (6), and damnacanthal (7). Their structures were determined on the basis of spectroscopic data. Some of the anthraquinones were tested for anticancer, antifungal, and antimalarial activities.

Isoflavones and rotenoids from the leaves of Millettia brandisiana.

A new isoflavone, 4'-gamma,gamma-dimethylallyloxy-5,7,2',5'-tetramethoxyisoflavone, brandisianin A (1), was isolated from the leaves of Millettia brandisiana, along with one synthetically known isoflavone, 7,4'-di-O-prenylgenistein (2) and twelve known compounds. The structures were elucidated on the basis of extensive spectroscopic analysis. Two isolated compounds were tested for anti-inflammatory activity; 12a-hydroxy-alpha-toxicarol (11) showed significant anti-inflammatory activity.

Cognitive models of apraxia and motor control: linking theories and methods across two complementary research domains.

Apraxia is a complex movement disorder that frequently occurs following left hemisphere stroke. Studies on patients with apraxia constitute an especially interesting body of literature for motor control researchers who seek to understand the cognitive mechanisms involved in the voluntary control of movement. Reciprocally, among apraxia researchers, great interest exists concerning the ways in which methods and theory from the field of motor control can be brought to bear in the clinical and empirical evaluation of this disorder. Here we will review representative evidence on the etiology, frequency, and assessment of apraxia, and suggest how research methods and theories from the field of motor control can be applied to, and also benefit from, a deeper understanding of apraxia. Parallels are proposed between the major cognitive models of apraxia and motor control to facilitate translation of terminology and concepts, and to enrich the emerging dialogue between these two complementary research domains.

Chemical constituents of the roots of Piper sarmentosum.

Sixteen compounds were isolated from the fresh roots of Piper sarmentosum. Seven of these have been previously isolated from the fruits and leaves of this plant: the aromatic alkene (1), 1-allyl-2-methoxy-4,5-methylenedioxybenzene (4), beta-sitosterol, pyrrole amide (6), sarmentine (10), sarmentosine (13) and pellitorine (14). (+)-Sesamin (2), horsfieldin (3), two pyrrolidine amides 11 and 12, guineensine (15) and brachystamide B (16) are new for P. sarmentosum. Sarmentamide A, B, and C (7-9) are new natural products. Compounds 1--4 and 6--16 were tested for antiplasmodial, antimycobacterial and antifungal activities.

Chromones from the branches of Harrisonia perforata.

Four new chromones, perforamone A, B, C, and D have been isolated together with six known compounds, peucenin-7-methyl ether, O-methylalloptaeroxylin, perforatic acid, eugenin, saikochromone A and greveichromenol, from the branches of Harrisonia perforata (Simaroubaceae). The structures were identified by spectroscopic data. The compounds were tested for antimycobacterial and antiplasmodial activities.