First Evidence of Fowl Adenovirus Induced Inclusion Body Hepatitis in Chicken in Bangladesh.

Background: The livestock sector contributes 1.90% to the GDP in Bangladesh during 2021-22. Poultry is one of the important subsectors struggling with diseases. Fowl adenoviruses (FAdVs) cause numerous diseases resulting in economic losses to the poultry industry worldwide. Several FAdV serotypes cause inclusion body hepatitis in chicken. Although FAdV infection was suspected, there was no confirmatory report from Bangladesh. The study was conducted to investigate the FAdV infection and antibodies in chicken. Methods: A total of 50 samples, each composed of liver and spleen, were collected from different chickens of Gazipur, Dinajpur, and Panchagarh district. Each location belongs to A, B, and C poultry zones of Bangladesh, respectively. Viruses were detected by real-time PCR and conventional PCR. Blood samples (n = 303) were collected at the beginning and after the recovery from infection and tested by indirect ELISA. Sequencing of PCR products was done for serotyping and phylogenetic analysis. Results: Clinical signs were observed including anorexia, drowsiness, ruffled feathers, reduced body weight, lack of uniformity, and high mortality (15-25%). Enlarged friable liver with yellow to tan color mottled with the focal soft area, fluid in pericardial sac, swollen and hemorrhagic kidneys, enlarged congested spleen and pancreas, etc. were found on postmortem examination. FAdVs were detected in 90% of the flocks except commercial layer flock from Dinajpur. Three serotypes, namely, 8b (70%), 11 (10%), and 5 (10%) were detected. Anti-FAdV antibody was detected in 80% flocks at the beginning of infection and in 90% of the flocks after recovery from infection. The antibody titer increases significantly (p < 0.05) after recovery from infection. Phylogenetic analysis revealed that the Bangladeshi FAdVs have close identity with viruses from Asia, Europe, and South and North America. Conclusions: These findings suggested that several introductions of FAdVs were taken place in Bangladesh. To combat the disease, vaccination along with maintenance of biosecurity is essential.

Revisiting pharmacological potentials of Nigella sativa seed: A promising option for COVID-19 prevention and cure.

Nigella sativa seed and its active compounds have been historically recognized as an effective herbal panacea that can establish a balanced inflammatory response by suppressing chronic inflammation and promoting healthy immune response. The essential oil and other preparations of N. sativa seed have substantial therapeutic outcomes against immune disturbance, autophagy dysfunction, oxidative stress, ischemia, inflammation, in several COVID-19 comorbidities such as diabetes, cardiovascular disorders, Kawasaki-like diseases, and many bacterial and viral infections. Compelling evidence in the therapeutic efficiency of N. sativa along with the recent computational findings is strongly suggestive of combating emerged COVID-19 pandemic. Also, being an available candidate in nutraceuticals, N. sativa seed oil could be immensely potential and feasible to prevent and cure COVID-19. This review was aimed at revisiting the pharmacological benefits of N. sativa seed and its active metabolites that may constitute a potential basis for developing a novel preventive and therapeutic strategy against COVID-19. Bioactive compounds of N. sativa seed, especially thymiquinone, α-hederin, and nigellidine, could be alternative and promising herbal drugs to combat COVID-19. Preclinical and clinical trials are required to delineate detailed mechanism of N. sativa's active components and to investigate their efficacy and potency under specific pathophysiological conditions of COVID-19.

iMGEins: detecting novel mobile genetic elements inserted in individual genomes.

BACKGROUND: Recent advances in sequencing technology have allowed us to investigate personal genomes to find structural variations, which have been studied extensively to identify their association with the physiology of diseases such as cancer. In particular, mobile genetic elements (MGEs) are one of the major constituents of the human genomes, and cause genome instability by insertion, mutation, and rearrangement. RESULT: We have developed a new program, iMGEins, to identify such novel MGEs by using sequencing reads of individual genomes, and to explore the breakpoints with the supporting reads and MGEs detected. iMGEins is the first MGE detection program that integrates three algorithmic components: discordant read-pair mapping, split-read mapping, and insertion sequence assembly. Our evaluation results showed its outstanding performance in detecting novel MGEs from simulated genomes, as well as real personal genomes. In detail, the average recall and precision rates of iMGEins are 96.67 and 100%, respectively, which are the highest among the programs compared. In the testing with real human genomes of the NA12878 sample, iMGEins shows the highest accuracy in detecting MGEs within 20 bp proximity of the breakpoints annotated. CONCLUSION: In order to study the dynamics of MGEs in individual genomes, iMGEins was developed to accurately detect breakpoints and report inserted MGEs. Compared with other programs, iMGEins has valuable features of identifying novel MGEs and assembling the MGEs inserted.

Assessment of Polycyclic Aromatic Hydrocarbons in School Playground Soils in Urban Gwangju, South Korea.

Soil samples from school playground of Gwangju City were analyzed for 16 polycyclic aromatic hydrocarbons (PAHs), and the soil contamination status and the potential cancer risk for students and adults were investigated. Soil samples were collected from 57 sites from 5 districts of Gwangju City in the summer of 2013. Regardless of the sampling site, the ∑PAHs concentrations ranged from 13.2 to 145.5 ng/g (mean 51.2 ng/g). Four and five-ring PAHs were predominant in the soil samples while the fraction of two-ring PAHs was the lowest. Seven carcinogenic PAHs contributed ~ 55% of ∑PAHs in school playground soils. The benzo[a]pyrene (46.4%) and dibenz[a,h]anthracene (41.2%) were the major contributors to toxic equivalent quantity. The strong correlation between carcinogenic PAHs suggested that they originated from the same source either vehicular emission or coal combustion, because they are markers of these pollution sources. The mean cancer risk for students (3.61 × 10-7) and adults (8.41 × 10-6) was in the U.S. EPA safety range (< 10-6).

Immobilization and reduction of bioavailability of lead in shooting range soil through hydrothermal treatment.

Immobilization of Pb in contaminated soil by hydrothermal treatment (HT) under subcritical conditions was investigated using a lab-scale apparatus. The Pb immobilization was evaluated thorough investigating the transformation of Pb fractions and by single chemical extraction. The results showed that HT and treatment temperature significantly affected the immobilization through redistribution of Pb fractions. The results of bioavailability and eco-toxicity assessment demonstrated a drastic decrease in the bioavailable fraction from 41.33 to 14.66%, and an increase in the non-bioavailable fraction from 2.90 to 15.76%. Moreover, the leaching potential of Pb was significantly reduced after treatment. Based on the risk assessment code (RAC), the treated soil residues exhibited medium risk (21.7-14.6 of RAC value for treated soil), which represented a decrease from high risk (41.3 for untreated soil). Immobilization was associated with Pb fractionation from weakly bound to stable fractions. A variety of mechanisms including adsorption and precipitation were suspected to be responsible for Pb immobilization. The findings of this study suggest that the HT may facilitate quantitative reduction of the bioavailability and eco-toxicity of Pb-contaminated soil. Considering the effectiveness of HT in remediating contaminated soil with organic pollutants, this approach might enable remediation of soil co-contaminated with organics and heavy metals.

Chemical Speciation and Quantitative Evaluation of Heavy Metal Pollution Hazards in Two Army Shooting Range Backstop Soils.

The chemical speciation and ecological risk assessment of heavy metals in two shooting range backstop soils in Korea were studied. Both soils were highly contaminated with Cd, Cu, Pb, and Sb. The chemical speciation of heavy metals reflected the present status of contamination, which could help in promoting management practices. We-rye soil had a higher proportion of exchangeable and carbonate bound metals and water-extractable Cd and Sb than the Cho-do soil. Bioavailable Pb represented 42 % of the total Pb content in both soils. A significant amount of Sb was found in the two most bioavailable fractions, amounting to ~32 % in the soil samples, in good agreement with the batch leaching test using water. Based on the values of ecological risk indices, both soils showed extremely high potential risk and may represent serious environmental problems.

Subcritical water treatment of explosive and heavy metals co-contaminated soil: Removal of the explosive, and immobilization and risk assessment of heavy metals.

Co-contamination of explosives and heavy metals (HMs) in soil, particularly army shooting range soil, has received increasing environmental concern due to toxicity and risks to ecological systems. In this study, a subcritical water (SCW) extraction process was used to remediate the explosives-plus-HMs-co-contaminated soil. A quantitative evaluation of explosives in the treated soil, compared with untreated soil, was applied to assess explosive removal. The immobilization of HMs was assessed by toxicity characteristic leaching procedure tests, and by investigating the migration of HMs fractions. The environmental risk of HMs in the soil residue was assessed according to the risk assessment code (RAC) and ecological risk indices (Er and RI). The results indicated that SCW treatment could eliminate the explosives, >99%, during the remediation, while the HM was effectively immobilized. The effect of water temperature on reducing the explosives and the risk of HMs in soil was observed. A marked increase in the non-bioavailable concentration of each HM was observed, and the leaching rate of HMs was decreased by 70-97% after SCW treatment at 250 °C, showing the effective immobilization of HMs. According to the RAC or RI, each tested HM showed no or low risk to the environment after treatment.

Organochlorine insecticide residues are found in surface, irrigated water samples from several districts in Bangladesh.

The purpose of this study was to investigate the occurrence and distribution of organochlorines such as aldrin, dieldrin, dichlorodiphenyldichloroethylene (DDE), dichlorodiphenyldichloroethane (DDD), dichlorodiphenyltrichloroethane (DDT), endrin, lindane and heptachlor insecticide residues in irrigated surface water samples collected from 22 districts in Bangladesh. The concentrations of the pesticides were determined using gas chromatography mass spectrophotometry. Water samples from five locations (Feni, Nawabganj, Putia, Burichang and Chatak) were contaminated with DDT; the highest DDT concentration detected was 8.29 µg/L, and its metabolite, DDE, was detected at 4.06 µg/L. Water samples from four other locations (Natore, Sikderpara, Chatak and Rajoir) were contaminated with heptachlor residues, and the highest level detected was 5.24 µg/L, which is the above the maximum contaminant level recommended by the World Health Organisation. A water sample collected from Chatak, Sunamganj, was contaminated with both DDT and heptachlor pesticide residues. None of the water samples were contaminated with aldrin, DDD, dieldrin, endrin or lindane. It is concluded that continuous, long-term monitoring and essential steps to limit the use of the pesticides in Bangladesh are needed.

Potentials of curcumin against polycystic ovary syndrome: Pharmacological insights and therapeutic promises.

Polycystic ovary syndrome (PCOS) is a common hormonal disorder among women (4%-20%) when the ovaries create abnormally high levels of androgens, the male sex hormones that are typically present in women in trace amounts. The primary characteristics of PCOS include oxidative stress, inflammation, hyperglycemia, hyperlipidemia, hyperandrogenism, and insulin resistance. Generally, metformin, spironolactone, eflornithine and oral contraceptives are used to treat PCOS, despite their several side effects. Therefore, finding a potential candidate for treating PCOS is necessary. Curcumin is a major active natural polyphenolic compound derived from turmeric (Curcuma longa). A substantial number of studies have shown that curcumin has anti-inflammatory, anti-oxidative stress, antibacterial, and anti-apoptotic activities. In addition, curcumin reduces hyperglycemia, hyperlipidemia, hyperandrogenism, and insulin resistance in various conditions, including PCOS. The review highlighted the therapeutic aspects of curcumin against the pathophysiology of PCOS. We also offer a hypothesis to improve the development of medicines based on curcumin against PCOS.

RNAi-Based Therapy: Combating Shrimp Viral Diseases.

Shrimp aquaculture has become a vital industry, meeting the growing global demand for seafood. Shrimp viral diseases have posed significant challenges to the aquaculture industry, causing major economic losses worldwide. Conventional treatment methods have proven to be ineffective in controlling these diseases. However, recent advances in RNA interference (RNAi) technology have opened new possibilities for combating shrimp viral diseases. This cutting-edge technology uses cellular machinery to silence specific viral genes, preventing viral replication and spread. Numerous studies have shown the effectiveness of RNAi-based therapies in various model organisms, paving the way for their use in shrimp health. By precisely targeting viral pathogens, RNAi has the potential to provide a sustainable and environmentally friendly solution to combat viral diseases in shrimp aquaculture. This review paper provides an overview of RNAi-based therapy and its potential as a game-changer for shrimp viral diseases. We discuss the principles of RNAi, its application in combating viral infections, and the current progress made in RNAi-based therapy for shrimp viral diseases. We also address the challenges and prospects of this innovative approach.

Occurrence of organophosphorus and carbamate pesticide residues in surface water samples from the Rangpur district of Bangladesh.

We report the presence of organophosphorus and carbamate residues in 24 surface water samples and five ground water samples from Pirgacha Thana, Rangpur district, Bangladesh using high-performance liquid chromatography. A number of samples of surface water from paddy fields were found to contain chlorpyriphos, carbofuran and carbaryl at concentrations ranging from 0-1.189, 0-3.395 and 0-0.163 µg/L, respectively. Surface water from the lakes had chlorpyriphos, carbofuran and carbaryl at concentrations ranging from 0.544-0.895, 0.949-1.671 and 0-0.195 µg/L, respectively. This result indicates that the general public living in the area of Rangpur is at high risk of pesticide exposure from contaminated waters in the environment.

Pesticide residues in tobacco leaves from the Kushtia district in Bangladesh.

In this study, tobacco leaf samples (n = 26) were collected from different areas in Kushtia to determine the presence of residues of cypermethrin, diazinon, heptachlor, methoxychlor dichlorodiphenyltrichloroethane (DDT), dichlorodiphenyldichloroethan (DDD) and dichlorodiphenyldichloroethylene (DDE). The analysis was conducted by a High Performance Liquid Chromatography (HPLC) system that was equipped with a photodiode array detector. Both cypermethrin and diazinon were detected in tobacco samples from six districts, namely, Mirzapur, Shahebnagar, Kodalipara, Pragpur, Farakpur and Taragunia. The highest concentration of cypermethrin was found in Kodalipara (2.00 ppm) while the highest concentration of diazinon was detected in a sample from Pragpur (0.15 ppm). The pesticide DDT was only detected in the sample from Pragpur at 4.00 ppm. This is the first study in Bangladesh that reports pesticide residue concentrations in tobacco leaf samples.

Seroprevalence of Treponema Pallidum antibody among pregnant population of Bangladesh.

AIM: The aim of this study was to investigate the seroprevalence of antibody to Treponema pallidum among pregnant women and its association with age, sexual behavior and socioeconomic status. MATERIALS AND METHODS: In this cross-sectional study, 1266 sera were collected from pregnant women attending Bangabandhu Sheikh Mujib Medical University and Rajshahi, Khulna and Chittagong Medical College Hospitals between February 2007 and April 2008. From each hospital, samples were collected from about a quarter of the total recruited pregnant women. Sera were tested to identify the antibody to T. pallidum using Treponema pallidum hemagglutination at the Virology Department of Bangabandhu Sheikh Mujib Medical University. Logistic regression was used to explore potential risk factors for syphilis. RESULTS: Among 1250 sera tested (16 sera were discarded due to hemolysis), 37 (2.96%) were positive for T. pallidum antibody. Higher seropositivity was associated with couples with no formal education, low socioeconomic status (P = 0.006), marriage at or before 18 years of age (P = 0.002), multiple marriages of the husband (P = 0.031) and sexual activity for more than 10 years (P = 0.007). Among these factors, low education level of women, early age of marriage and multiple marriages of the husband showed individual effects on high seropositivity to T. pallidum. CONCLUSIONS: The high seroprevalence of syphilis among pregnant women attending the antenatal clinics of these hospitals indicates the need for the incorporation of screening for syphilis in routine antenatal screening in Bangladesh. Improvement of education level in the female population, prevention of early marriage and preventing polygamy of husbands may play an important role in prevention of syphilis among women.

Sequencing and annotation of the complete mitochondrial genome of a threatened labeonine fish, Cirrhinus reba.

The mitochondrial genome of a species is an essential resource for its effective conservation and phylogenetic studies. In this article, we present sequencing and characterization of the complete mitochondrial genome of a threatened labeonine fish, Cirrhinus reba collected from Khulna region of Bangladesh. The complete mitochondrial genome was 16,597 bp in size, which formed a circular double-stranded DNA molecule containing a total of 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes) with two non-coding regions, an origin of light strand replication (OL) and a displacement loop (D-loop), similar structure with other fishes of Teleostei. The phylogenetic tree demonstrated its close relationship with labeonine fishes. The complete mitogenome of Cirrhinus reba (GenBank no. MN862482) showed 99.96% identity to another haplotype of Cirrhinus reba (AP013325), followed by 90.18% identity with Labeo bata (AP011198).

Inclusion of molecular descriptors in predictive models improves pesticide soil-air partitioning estimates.

The soil-air exchange of pesticides is one potential fate and exposure pathways, and this process is generally thought to be governed by soil properties and environmental conditions. The experimental determination of soil-air partitioning coefficient (Ksa) is laborious and costly and typically, Ksa's are predicted from a semiempirical or a simple linear regression approach with soil and environmental variables. Here we developed a model that combined linear regression of soil, environmental and molecular parameters with the quantitative structural-property relationship (QSPR) to predict Ksa for pesticides. The values of theoretical descriptors of pesticides were calculated and the best descriptors selected using the Boruta Algorithm. Seventy-six experimental logKsa values for 17 pesticides were used in model development. Multiple linear regression (MLR) with a soil (organic carbon fraction), physicochemical (octanol-air partitioning coefficient), environmental (temperature and humidity) and molecular descriptor (Gmin, a 2D E-state molecular parameter), called as MLR-QSPR combined model exhibited better predictability (adj. r2 = 0.95) of logKsa compared to MLR (adj. r2 = 0.87) or QSPR (adj. r2 = 0.82) itself. MLR-QSPR also showed the best performance in five-fold cross-validation (adj. r2 = 0.94) and test set verification (adj. r2 = 0.96). The developed model was validated and characterized by the applicability domain. Results showed that the proposed MLR-QSPR approach is highly predictive and statistically robust with >95% of predictions within ±0.5 log unit of the measured Ksa. Therefore, this approach can be used in estimating the soil-air partitioning of pesticides to better predict it's fate and transport in environments.

Remediation approach for organic compounds and arsenic co-contaminated soil using the pressurized hot water extraction process.

Successful remediation of soil with co-existing organics contaminants and arsenic (As) is a challenge as the chemical and remediation technologies are different for each group of pollutants. In this study, the treatment effectiveness of the pressurized hot water (PHW) extraction process was investigated for remediation of soil co-contaminated with phenol, crude oil, polycyclic aromatic hydrocarbons (PAHs), and As. An elimination percentage of about 99% was achieved for phenol, and in the range of 63-100% was observed for the PAHs at 260°C for 90 min operation. The performance of PHW extraction in the removal of total petroleum hydrocarbons was found to be 86%. Of the 87 mg/kg of As in untreated soil, 67% of which was eliminated after treatment. The removal of organic contaminants was mainly via desorption, dissolution and degradation in subcritical water, while As was eliminated probably by oxidation and dissolution of arsenic-bearing minerals. According to the experimental results, the PHW extraction process can be suggested as an alternative cleaning technology, instead of using any organic solvents for remediation of such co-contaminated soil.

Enhanced biomethane recovery from fat, oil, and grease through co-digestion with food waste and addition of conductive materials.

In this study, the effect of conductive additives on co-digestion of fat, oil, and grease (FOG) and food waste (FW) was evaluated. Initially, biochemical methane potential (BMP) test was conducted for optimization of mixing ratio of FW and FOG. The optimal methane production (800 L (kg VS)-1) was obtained from co-digestion of 70% FW + 30% FOG (w/w), which was 1.2 times and 12 times of that obtained from mono-digestion of FW and FOG, respectively. This optimal mixing ratio was used for subsequent fed-batch studies with the addition of two conductive additives, granular activated carbon (GAC) and magnetite. The addition of GAC significantly shortened the lag phase (from 7 to 3 d), reduced accumulation of various volatile fatty acids (VFAs), and enhanced methane production rate (50-80% increase) compared to the control and magnetite-amended bioreactor. Fourier transformation infrared (FTIR) analysis suggested that the degradation of lipids, protein and carbohydrates was the highest in GAC amended reactor, followed by magnetite and control reactors. GAC addition also enriched more abundant and diverse bacteria and methanogens than control. Magnetite addition also showed similar trends but to a lesser degree. The substantial enrichment of syntrophic LCFA ß-oxidizing bacteria (e.g. Syntrophomonas) and methanogenic archaea in the GAC-amended bioreactor likely attributed to the superior methanogenesis kinetics in GAC amended bioreactor. Our findings suggest that the addition of GAC could provide a sustainable strategy to enrich kinetically efficient syntrophic microbiome to favor methanogenesis kinetics in co-digestion of FW and FOG.

Medical students' perceptions of their learning environment during clinical years at Chitwan Medical College in Nepal.

BACKGROUND: The educational environment of an institution affects learning and has a significant role in determining students' academic achievement. The objective of the study was to determine the undergraduate medical students' perception about educational environment in clinical years of study utilizing Dundee Ready Education Environment Measure (DREEM) questionnaire. METHODS: A descriptive cross-sectional questionnaire-based study was conducted among fourth and fifth-year medical students toward the end of their 2016 academic year in Chitwan Medical College, Bharatpur, Nepal. The 50-item DREEM questionnaire was used to collect the data. The items were scored based on a 5-point Likert scale. The data were analyzed using SPSS version 20. Scores obtained were expressed as mean±SD. RESULTS: The mean total DREEM score was 122/200. The mean score for Students' Perceptions of Learning, Students' Perceptions of Teachers, Students' Academic Self-Perceptions, Students' Perceptions of Atmosphere, and Students' Social Self-Perceptions were 29.8/48, 25.9/44, 20.3/32, 28.6/48, and 17.27/28, respectively. This shows the environment for learning was satisfactory. There were nine problem areas with a mean score of ≤2. There was no significant difference observed in educational environment subscales scores according to enrollment year, gender, or funding source for education. CONCLUSION: The overall student's perception of the educational environment was satisfactory. Nevertheless, the study revealed some problematic areas in the learning environment which require remedial measures to make the environment more conducive for learning to satisfy the students and achieve a far better outcome.

Heavy metal stabilization in contaminated soil by treatment with calcined cockle shell.

In several previous studies, the efficacy of various liming waste materials on the immobilization of heavy metals has been tested and it was found that soils contaminated with heavy metals can be stabilized using this technique. Since lime (CaO) has been identified as the main phase of calcined cockle shell (CCS), it was hypothesized that CCS could be used as a soil amendment to immobilize heavy metals in soil. However, to date, no studies have been conducted using CCS. In this study, the effectiveness of CCS powder on the immobilization of Cd, Pb, and Zn in mine tailing soil was evaluated. After 28 days of incubation, the treated soil samples were exposed to weathering (four cycles of freezing-thawing and four cycles of wetting-drying) for 8 days before being subjected to a leaching test. The results of this study revealed that the soil pH increased from 7.5 to 12.2 with the addition of 5% CCS. A similar soil pH was obtained when the soil was amended with 5% pure CaO. By leaching with 0.1 M HCl, extracted Cd, Pb, and Zn were reduced by up to 85, 85, and 91%, respectively. Therefore, CCS is suggested as a low-cost lime-based soil amendment for stabilizing heavy metals in abandoned mining sites.

Optimizing T4 DNA polymerase conditions enhances the efficiency of one-step sequence- and ligation-independent cloning.

Previously, we developed a one-step sequence- and ligation-independent cloning (SLIC) method that is simple, fast, and cost-effective. However, although one-step SLIC generally works well, its cloning efficiency is occasionally poor, potentially due to formation of stable secondary structures within the single-stranded DNA (ssDNA) region generated by T4 DNA polymerase during the 2.5 min treatment at room temperature. To overcome this problem, we developed a modified thermo-regulated one-step SLIC approach by testing shorter T4 DNA polymerase treatment durations (5 s-2.5 min) over a wide range of temperatures (25-75°C). The highest cloning efficiency resulted when inserts with homology lengths <20 bases were treated with T4 DNA polymerase for 30 s at 50°C. This briefer T4 polymerase treatment at a higher temperature helps increase cloning efficiency for inserts with strong secondary structures at their ends, increasing the utility of one-step SLIC for the cloning of short fragments.