Unveiling the azo-reductase mechanism in Pseudomonas putida for efficient decolorization of textile Reactive dyes: an in-silico study.

The textile industry utilizing affordable azo dyes is a high threat to aquatic life and causes environmental problems due to their toxicity. Biodegradation of azo dyes employing microbes and enzymes has proved to be an efficient method for treating industrial effluent. This study used the novel microbial consortium to decolorize reactive azo dyes (Reactive Red 120; Reactive Black 5 and Reactive Blue 13), and its azo-reductase activity was evaluated. The metagenomic analysis of the consortium identified azo-reductase-producing bacterial species. The molecular docking revealed that PpAzoR from Pseudomonas putida had the highest binding affinities for all the three dyes such as Reactive Black 5 (-9.3 kcal/mol), Reactive Blue 13 (-9.8 kcal/mol) and Reactive Red 120 (-10.7 kcal/mol). The structural rigidity and stability of the docked complex were confirmed through MD simulations evaluated across multiple descriptors from the simulation trajectories. Further, MMPBSA analysis validated the results that binding of the ligands, i.e. dye molecules Reactive Black (RB5), Reactive Blue (RB13) and Reactive Red (RR120) binding with the Azoreductase (PpAzoR) to the screened Azo-dyes was spontaneous. Based on molecular dynamics simulations for 100 ns, RR 120 showed the highest binding affinity (-411.336 ± 46.799 KJ/mol), followed by RB5 (-288.012 ± 33.371 KJ/mol). The dyes (RR120 and RB5) exhibited stable interactions with the target azoreductase (PpAzoR). The present study provides insights that PpAzoR shows the highest decolorization potency, which could be interpreted as a potential dye-degrading protein based on dye-degrading assay findings.Communicated by Ramaswamy H. Sarma.

>90% decolourization observed for all reactive dyes at 72 hAzo reductase-producing bacterial species were identified using metagenomicsPseudomonas putida (PpAzoR) showed maximum binding affinity with all three dyesPositive correlation was established between dye decolourization and in-silico results.

Physico-chemical, sensory, and microbiological quality of raw chicken meat: an exploratory study in the Hisar city of Haryana, India.

A survey was conducted in Hisar, located in Haryana, India, to assess the quality of raw chicken meat. To ensure comprehensive coverage, healthy broiler chickens were obtained from various meat retail outlets in Hisar city, encompassing the majority of such establishments. Additionally, a sample of control chickens was obtained from the Livestock Farm, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences (LUVAS), Hisar, Haryana, India. The raw chicken meat was grouped into two categories, breast cut and thigh cut. The breast muscles, which include pectoralis major and pectoralis minor, and the thigh muscles, which include the abductor muscles, were chosen as the samples for proximate analysis, which included physico-chemical, sensory, and microbiological analyses of raw chicken meat. The analysis of the raw meat in the laboratory revealed inconsistent variations between the control and retail samples in terms of parameters, such as proximate composition, pH, the water-holding capacity (WHC), thiobarbituric acid (TBA), instrumental color analysis, and sensory evaluation. The moisture content of the control breast sample was significantly higher (p < 0.05) than that of the samples from shops 2, 3, and 5. However, it was statistically similar to that of the samples from shops 1, 4, and 6. The total plate and psychrotrophic counts of the control thigh sample were significantly lower than those of the samples from shops 3, 4, 5, and 6. Among the thigh pH values, the samples from shops 1, 2, 5, and 6 had significantly higher pH values than the control sample. The variations in the various parameters were multifactorial and established the superiority of birds slaughtered under laboratory conditions and grown in university farms compared to the raw chicken meat available in retail outlets in Hisar city.

Structural insights of a putative ß-1,4-xylosidase (PsGH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans.

Structural and conformational insights of a putative ß-1,4-xylosidase (PsGH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans were investigated by computational and Circular Dichroism (CD) analyses. PsGH43F was cloned and expressed in E. coli BL21 (DE3) cells and the purified enzyme gave the size ~50 kDa on SDS-PAGE analysis. Multiple Sequence Alignment of PsGH43F sequence followed by superposition of modeled structure with homologous structures displayed the presence of three conserved catalytic amino acid residues, Asp33, Asp149 and Glu212. The secondary structure analysis by CD showed 2.72 % α-helix and 36.06 % ß-strands. The homology modeled structure of PsGH43F displayed a 5-bladed ß-propeller fold for catalytic module at N-terminal and a ß-sandwich structure for CBM6 at the C-terminal. Ramachandran plot displayed 99.5 % of residues in the allowed regions. MD simulation of PsGH43F revealed the compactness and stability of the structure. Molecular docking studies of PsGH43F with xylo-oligosaccharides revealed its maximum binding affinity for xylobiose. MD simulation of PsGH43F-xylobiose complex confirmed the increased structural and conformational stability in presence of substrate. The Hydrodynamic diameter analysis of PsGH43F by DLS was in the range, 0.25-0.28 µm.

Screening of pharmaceuticals in coastal waters of the southern coast of Viti Levu in Fiji, South Pacific.

The global reliance on pharmaceuticals coupled with the lack of effective treatment methods has resulted in pseudo-persistence of pharmaceuticals within the environment. Globally, efforts to quantify and monitor pharmaceuticals within the environment have been well underway, however few studies have been made within small Pacific Islands. This study aims at screening for the occurrence and concentration of pharmaceutical residues within the southern coastal waters of Fiji's main island, Viti Levu. Water samples were collected from a depth of ca. 0.6 m from seven sites and were analyzed for 80 pharmaceuticals via a combination of chromatography and heated electrospray ionization. Seventy-two pharmaceuticals were quantified at least once with average concentrations ranging between 0.04 ng/L (diltiazem) and 19 ng/L (ketoconazole), and with all but two pharmaceuticals (trimethoprim and biperiden) being present in less than 50% of the samples. Findings suggest that even though the release of pharmaceuticals into the marine environment is sporadic and pharmaceuticals are diluted via turbulent mixing, there are measurable concentrations of pharmaceuticals in Fiji and these pollutants are not necessarily restricted to highly populated areas.

Hematemesis, a Rare Presentation for Downhill Esophageal Varices.

Downhill esophageal varices (DEV) are a rare form of esophageal varices associated with superior vena cava obstruction. Obstruction leads to retrograde blood flow through collateral venous channels, including the esophageal venous plexus, to redirect blood flow to the right atrium via the inferior vena cava. This leads to the formation of DEV. It is a rare phenomenon to have gastrointestinal bleeding, especially hematemesis, on a patient's first presentation with this disease process. We describe such a case here involving a patient with DEV secondary to metastatic renal cell carcinoma presenting with hematemesis.

Synergies between local and climate-driven impacts on coral reefs in the Tropical Pacific: A review of issues and adaptation opportunities.

Coral reefs in the tropical Pacific region are exposed to a range of anthropogenic local pressures. Climate change is exacerbating local impacts, causing unprecedented declines in coral reef habitats and bringing negative socio-economic consequences to Pacific communities who depend heavily on coral reefs for food, income and livelihoods. Continued increases in greenhouse gas emissions will drive future climate change, which will accelerate coral reef degradation. Traditional systems of resource governance in Pacific island nations provide a foundation to address local pressures and build reef resilience to climate change. Management and adaptation options should build on the regional diversity of governance systems and traditional knowledge to support community-based initiatives and cross-sectoral cooperation to address local pressures and minimize climate change impacts. Such an inclusive approach will offer enhanced opportunities to develop and implement transformative adaptation solutions, particularly in remote and regional areas where centralized management does not extend.

Interobserver reliability of methods to determine complete resection of adenomas in colonoscopy.

BACKGROUND: Forceps margin biopsy and polypectomy specimen margins have both been used to assess for polypectomy resection adequacy. The interobserver reliability of the two methods has not been well described. METHODS: The interpretability of polypectomy specimens for presence of residual neoplasia at the margin was assessed by two blinded pathologists. Next, the concordance of forceps margin biopsy interpretations between three blinded pathologists was evaluated by calculation of interobserver κ. RESULTS: Rates of polypectomy specimen margin interpretability were low: 24/92 (26 %) for pathologist A, 28/92 (30.4 %) for pathologist B. Concordance of forceps margin biopsy interpretations (n = 129) between pathologists was high. Two internal pathologists showed substantial agreement in margin biopsy interpretations (κ 0.779; 95 %CL 0.543, 0.912). The concordance remained strong after biopsies were reviewed by a third, external pathologist (κ 0.829; 95 %CL 0.658, 0.924). There was complete agreement on 123/129 (95.3 %) between all three pathologists for presence of neoplasia. CONCLUSION: The majority of polypectomy specimen margins were uninterpretable by pathologists for presence of residual neoplasia. Forceps margin biopsy shows strong interobserver reliability in adenomatous lesions.

Computational modeling and small-angle X-ray scattering based structure analysis and identifying ligand cleavage mechanism by processive endocellulase of family 9 glycoside hydrolase (HtGH9) from Hungateiclostridium thermocellum ATCC 27405.

The cellulases of family 9 glycoside hydrolase with subtle difference in amino acid sequence have shown different types of catalytic activities such as endo-, exo- or processive endocellulase. However, the reason behind the different types of catalytic activities still unclear. In this study, the processive endocellulase, HtGH9 of family 9 GH from Hungateiclostridium thermocellum was modeled by homology modeling. The catalytic module (HtGH9t) of HtGH9 modeled structure displayed the (α/α)6 barrel topology and associated family 3 carbohydrate binding module (HtCBM3c) displayed ß-sandwich fold. Ramachandran plot of HtGH9 modeled structure displayed all the amino acid residues in allowed region except Asn225 and Asp317. Secondary structure analysis of modeled HtGH9 showed the presence of 41.3% α-helices and 11.0% ß-strands which was validated through circular dichroism analysis that showed the presence of 42.6% α-helices and 14.5% ß-strands. Molecular Dynamic (MD) simulation of HtGH9 structure for 50 ns showed Root Mean Square Deviation (RMSD), 0.84 nm and radius of gyration (Rg) 3.1 nm. The Small-angle X-ray scattering of HtGH9 confirmed the monodisperse state. The radius of gyration for globular shape (Rg) was 5.50 ± 0.15 nm and for rod shape (Rc) by Guinier plot was 2.0 nm. The loop formed by amino acid residues, 264-276 towards one end of the catalytic site of HtGH9 forms a barrier, that blocks the non-reducing end of the cellulose chain causing the processive cleavage resulting in the release of cellotetraose. The position of the corresponding loop in cellulases of family 9 GH is responsible for different types of cleavage patterns.

Soundscape of green turtle foraging habitats in Fiji, South Pacific.

The soundscape features of the marine environment provide crucial information about ecosystem health for many species, and they are defined by the local biological, geophysical, and anthropogenic components. In this study, we investigated the soundscape at green turtle neritic foraging habitats in Fiji, South Pacific, with the aims of characterizing the contribution of each component and of comparing the levels of acoustic pressure among sites with different abundances of sea turtles. Four sites were selected at two islands, and one hydrophone was deployed at each site. Generalized additive models highlighted that sound pressure levels (SPLs) at low frequencies (125-250 Hz) were especially affected by wind conditions, while at higher frequencies (>250 Hz) SPLs were mostly influenced by fish and crustacean acoustic activity. Higher abundances of green turtles were found at sites with the highest levels of SPLs and the highest number of acoustic emissions by fishes and crustaceans but were not related to maximum seagrass and macroalgae coverage, or the highest number of fish. The selected coastal habitats have negligible anthropogenic noise, thus this study informs physiological and behavioral studies of the acoustic signatures that sea turtles might target and provides a baseline against which potential impact of soundscape changes on sea turtle spatial abundance and distribution can be evaluated.

Microplastics in subsurface coastal waters along the southern coast of Viti Levu in Fiji, South Pacific.

Microplastics (MPs) remain largely understudied in Small Island Developing States. This study is aimed at comparing the abundance and characteristics of MPs in rural and urban marine coastal sites located along the southern coast of Fiji's main inhabited island, Viti Levu. Collection of subsurface waters (at depth of ca. 0.6 m) was performed at seven sites via Niskin bottle. Samples were filtered over a membrane filter to extract MPs and to allow visual analysis and polymer identification by using attenuated total reflectance in Fourier transform infrared spectroscopy. Findings from this study depict widespread presence of MPs in both urban and rural sites, and show no significant differences in the four parameters studied, i.e. abundance of MP pieces (2.0 vs 1.6 MP/L, respectively), form types (dominance of fibers), size (0.5-0.9 and 1.0-1.4 mm totaling 48% of the samples), and color (blue contributing 30%, and red and black contributing 25% each). These findings challenge the common expectation of a higher MPs pollution in urban areas compared to rural areas.

Chronotype, social jet lag, sleep debt and food timing in inflammatory bowel disease.

The preference of the sleep/wake cycle can be grouped into categories or chronotypes. Inflammatory bowel disease (IBD) has been linked to poor sleep quality which correlates with disease severity. Social jet lag (SJL) is the difference between sleep timing on work and free days and is a marker for circadian misalignment which has been linked to increased inflammation. We investigated whether chronotype, SJL, sleep debt (SD), and food timing were associated with an IBD specific complications and a lower quality of life. Overall, 191 subjects (115 IBD subjects and 76 healthy controls (HC)) completed the Pittsburgh Sleep Quality Index (PSQI), Morningness-Eveningness Questionnaire (MEQ), Munich ChronoType Questionnaire (MCTQ), Short Inflammatory Bowel Disease Questionnaire (SIBDQ), and a structured Food Timing Questionnaire. Later chronotype (by MEQ) was associated with a worse SIBDQ (r = -0.209; P < 0.05). SJL was increased in IBD at 1.32 h ± 1.03 vs. 1.05 h ± 0.97 in HC, P < 0.05, when adjusted for age. SJL (>2 h) was present in 40% of severe/complicated Crohn's patients (fistulizing or structuring Crohn's or history of Crohn's related surgery) compared to only 16% of uncomplicated Crohn's patients (P < 0.05). Sleep debt was increased in IBD subjects compared to HC at 21.90 m ± 25.37 vs. 11.49 m ± 13.58, P < 0.05. IBD subjects with inconsistent breakfast or dinner times had lower SIBDQ scores (4.78 ± 1.28 vs. 5.49 ± 1.02, P < 0.05; 4.95 ± 0.31 vs. 5.42 ± 0.32, P < 0.05 respectively). In summary, later chronotype, and markers of circadian misalignment (social jet lag, sleep debt, and inconsistent meal timing) were associated with IBD disease specific complications and/or lower quality of life.

Alternative approaches to polyp extraction in colonoscopy: a proof of principle study.

BACKGROUND AND AIMS: A limitation of determination of the completeness of resection in polypectomy is polyp fragmentation. When a polyp fragments, the pathologist cannot determine resection completeness. Alternative approaches to reduce polyp fragmentation include reducing shearing forces on the polyp or removing polyps through the instrument channel. The primary aim of this study was to assess fragmentation of polyps extracted using different approaches from conventional polyp retrieval. METHODS: Polyps (5-15 mm) resected by cold snare or cautery by 3 colonoscopists were extracted from the colonoscope using 1 of 4 techniques. Method I was the conventional method of pressing the suction valve button and retrieving the polyp through a trap. Method II involved removing the suction valve, covering the open suction valve cylinder with a finger. Method III used a Roth Net polyp retriever placed through the instrument channel. Method IV involved connecting a polyp trap to suction onto the instrument channel port. Fragmentation was defined as multiple pieces of the specimen in formalin, as grossly described by the pathologist. Alternative approaches (methods II, III, and IV) were all compared with the conventional method (method I). RESULTS: The method I fragmentation rate of polyps was 60.3% (123/204). Method II extraction reduced fragmentation to 43.0% (52/121, P = .003), proving that fragmentation occurs with passage through the suction valve channel. Method III had a lower fragmentation rate of 23.1% (6/26, P < .001). Method IV likewise showed a reduced fragmentation rate of 18.5% (5/27, P < .001). CONCLUSIONS: Polyp fragmentation is reduced by removal of the suction valve button. There is also a decrease in fragmentation rates in removing the polyp by connecting the polyp trap to the instrument port. Our study suggests that decreasing polyp fragmentation and improving pathology margin interpretability is possible through methods that extract polyps through the instrument port with currently available devices.

Boat noise prevents soundscape-based habitat selection by coral planulae.

Understanding the relationship between coral reef condition and recruitment potential is vital for the development of effective management strategies that maintain coral cover and biodiversity. Coral larvae (planulae) have been shown to use certain sensory cues to orient towards settlement habitats (e.g. the odour of live crustose coralline algae - CCA). However, the influence of auditory cues on coral recruitment, and any effect of anthropogenic noise on this process, remain largely unknown. Here, we determined the effect of protected reef (MPA), exploited reef (non-MPA) soundscapes, and a source of anthropogenic noise (boat) on the habitat preference for live CCA over dead CCA in the planula of two common Indo-Pacific coral species (Pocillopora damicornis and Acropora cytherea). Soundscapes from protected reefs significantly increased the phonotaxis of planulae of both species towards live CCA, especially when compared to boat noise. Boat noise playback prevented this preferential selection of live CCA as a settlement substrate. These results suggest that sources of anthropogenic noise such as motor boat can disrupt the settlement behaviours of coral planulae. Acoustic cues should be accounted for when developing management strategies aimed at maximizing larval recruitment to coral reefs.

Copper-binding properties of the BIR2 and BIR3 domains of the X-linked inhibitor of apoptosis protein.

The X-linked inhibitor of apoptosis protein (XIAP) is a zinc metalloprotein that has recently been implicated in copper homeostasis. XIAP mediates apoptosis via the inhibition of caspase enzymes through multiple baculovirus IAP repeat (BIR) domains, wherein zinc is coordinated by three cysteine amino acids and one histidine amino acid. XIAP binds copper ions directly at one or more unspecified sites, indicating that the protein may function as a copper sensor. We report the copper-binding properties of an XIAP construct containing the BIR2 and BIR3 domains. Absorption and emission spectroscopic measurements show that XIAP exhibits only a low-to-moderate affinity for Cu(II), but a strong affinity for Cu(I). Cu(I) is observed to bind at multiple sites within the BIR2 and BIR3 domains, including the CXXC motifs of the zinc structural sites and multiple BIR2 surface sites. Mutagenesis-based experiments reveal that surface cysteine residues mediate binding in the BIR2 domain and induce protein oligomerization under elevated copper concentrations. These results constitute the first spectroscopic evidence of copper-XIAP interactions.

Predictors of insulin requirements among hospitalized adults receiving parenteral nutrition.

OBJECTIVE: The objective of this quality improvement project was to determine factors predictive of parenteral nutrition (PN) insulin therapy. METHODS: Patients receiving PN at a tertiary care academic medical center between January 1, 2009, and December 1, 2012, 18 years or older were included. Variables collected included demographics, medical information, and PN-specific data. χ(2) and Student t tests were used to determine differences between patients who did and did not require PN insulin. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to determine associations between characteristics. Stepwise forward logistic regression was used determine the best predictors of PN insulin. RESULTS: A total of 1388 patients were started on PN. After adjusting for potential confounders, strong associations existed between PN insulin requirements and diabetes mellitus (DM) diagnosis (OR, 8.90; 95% CI, 4.98-15.90, P < .001), overweight/obese status (body mass index ≥25.0 kg/m(2)) (OR, 2.12; 95% CI, 1.04-4.30, P = .04), intensive care unit (ICU) admission (OR, 1.79; 95% CI, 1.03-3.11, P = .04), blood glucose (BG) on day of PN start >120 mg/dL (OR, 2.32; 95% CI, 1.32-4.05, P = .003), mean BG >180 mg/dL while receiving PN (OR, 6.10; 95% CI, 2.18-17.04, P = .001), and hemoglobin A1c (A1c) ≥5.7% (OR, 3.18; 95% CI, 1.84-5.50, P < .001). Among variables available at PN initiation, DM diagnosis (P < .001), A1c ≥5.7% (P < .001), BG >120 mg/dL on PN start day (P < .001), and ICU admission (P < .001) predicted the need for PN insulin.

Gymnastics-related injuries to children treated in emergency departments in the United States, 1990-2005.

OBJECTIVE: The objective of this study was to describe the epidemiology of gymnastics-related injuries among children in the United States. METHODS: A retrospective analysis was conducted of data for children 6 through 17 years of age from the National Electronic Injury Surveillance System of the US Consumer Product Safety Commission for 1990 through 2005. Sample weights provided by the National Electronic Injury Surveillance System were used to calculate national estimates of gymnastics-related injuries. Injury rates were calculated for the most frequently occurring types of injury using gymnastics participation data. RESULTS: An estimated 425,900 children 6 through 17 years of age were treated in US hospital emergency departments for gymnastics-related injuries during the 16-year period of 1990-2005. The number of injuries averaged 26,600 annually. The number of injuries sustained per 1000 gymnastics participants per year for the pediatric population was 4.8. The number of injuries sustained per 1000 participants per year was greater for the ages 12 to 17 years (7.4) than for the ages 6 to 11 years (3.6). The place where an injury occurred include school (40.0%), a place of recreation or sports (39.7%), home (14.5%), or on other public property (5.8%). The body parts injured were upper extremity (42.3%), lower extremity (33.8%), head/neck (12.9%), trunk (10.4%), and other (0.6%). Injury diagnoses were strain/sprain (44.5%), fracture/dislocation (30.4%), abrasion/contusion (15.6%), laceration/avulsion (3.7%), concussion/closed head injury (1.7%), and other (4.2%). The majority (97.1%) of patients with gymnastics-related injuries were treated and released from the emergency department. CONCLUSIONS: Gymnastics has one of the highest injury rates of all girls' sports. Establishment of a national database for gymnastics-related injuries, including exposure data for direct calculation of injury rates, would permit better identification and monitoring of risk factors for gymnastics-related injuries and aid in the development, implementation, and evaluation of injury prevention strategies based on epidemiologic evidence.