Structural dynamics and functional analysis of Saprolegnia parasitica chitin synthases 5 in a phospholipid bilayer.

Saprolegnia parasitica is an oomycete responsible for a fish disease called saprolegniosis, which poses an economic and environmental burden on aquaculture production. In Saprolegnia, CHS5 of S. parasitica (SpCHS5) contains an N-terminal domain, a catalytic domain of the glycosyltransferase -2 family containing a GT-A fold, and a C-terminal transmembrane domain. No three-dimensional structure of SpCHS5 is reported yet disclosing the structural details of this protein. We have developed a structural model of full-length SpCHS5 and validated it by molecular dynamics simulation technique. From the 1 microsecond simulations, we retrieved the stable RoseTTAFold model SpCHS5 protein to explain characteristics and structural features. Furthermore, from the analysis of the movement of chitin in the protein cavity, we assumed that ARG 482, GLN 527, PHE 529, PHE 530, LEU 540, SER 541, TYR 544, ASN 634, THR 641, TYR 645, THR 641, ASN 772 residues as a main cavity lining site. In SMD analysis, we investigated the opening of the transmembrane cavity required for chitin translocation. The pulling of chitin from the internal cavity to the extracellular region was observed through steered molecular dynamics simulations. A comparison of the initial and final structures of chitin complex showed that there's a transmembrane cavity opening in the simulations. Overall, this present work will help us understand the structural and functional basis of CHS5 and design inhibitors against SpCHS5.Communicated by Ramaswamy H. Sarma.

Effect of Moringa olifera leaves on growth and gut microbiota of Nile tilapia (Oreochromis niloticus) / Efeito das folhas da Moringa olifera no crescimento e na microbiota intestinal da tilápia do Nilo (Oreochromis niloticus)

Abstract The study was conducted to evaluate the effect of Moringa olifera on the growth and gut health of Tilapia (Oreochromis niloticus). The feed having 30% crude protein was prepared as an experimental diet with 4%, 8% and 10% M. olifera leaf supplementation, respectively. The control diet was devoid of M. olifera leaves. The 10 weeks feeding trial was carried out on 60 fish in aquaria. Fish was fed @ 3% of body weight twice a day. Diet with the high level of inclusion of M. olifera leaves significantly increased the growth rate, Survival Rate (SR), Specific Growth Rate (SGR) and Feed Conversion Efficiency (FCE) in all treatment groups compared to the control group. Similarly, Feed Conversion Ratio (FCR) gradually decreased and found highly-significant. To check the gut health of the Tilapia, random samples were selected and dissected. Nutrient agar was used as culture media to check the growth of bacteria. Pour Plate Method was used for viable colonies count by colony counter. Through staining method, the different bacteria such as Escherichia coli, Salmonella, Shigella and Pseudomonas aeruginosa were identify abundantly in the intestine of control diet fish but less number present in treatment diets groups. These results showed that M. olifera leaves up to 10% of dietary protein can be used for Nile tilapia for significant growth and healthy gut microbiota of fish.

Resumo O estudo foi conduzido para avaliar o efeito da Moringa olifera no crescimento e saúde intestinal da tilápia (Oreochromis niloticus). A ração com 30% de proteína bruta foi preparada como dieta experimental com 4%, 8% e 10% de suplementação de folhas de M. olifera, respectivamente. A dieta controle foi desprovida de folhas de M. olifera. O ensaio de alimentação de 10 semanas foi realizado em 60 peixes em aquários. O peixe pesava 3% do peso corporal duas vezes ao dia. A dieta com alto nível de inclusão de folhas de M. olifera aumentou significativamente a taxa de crescimento, taxa de sobrevivência (SR), taxa de crescimento de sobrevivência (SGR) e eficiência de conversão alimentar (FCE) em todos os grupos de tratamento em comparação com o grupo de controle. Da mesma forma, a taxa de conversão de alimentação (FCR) diminuiu gradualmente e foi considerada altamente significativa. Para verificar a saúde intestinal da tilápia, amostras aleatórias foram selecionadas e dissecadas. O ágar nutriente foi usado como meio de cultura para verificar o crescimento das bactérias. O método da placa de Verter foi usado para a contagem de colônias viáveis ​​por contador de colônias. Através do método de coloração, diferentes como Escherichia coli, Salmonella, Shigella e Pseudomonas aeruginosa foram identificados abundantemente no intestino de peixes da dieta controle, mas em menor número nos grupos de dieta de tratamento. Esses resultados mostraram que M. olifera deixa até 10% da proteína dietética e pode ser usado para tilápia do Nilo para um crescimento significativo e microbiota intestinal saudável de peixes.

Effect of Moringa olifera leaves on growth and gut microbiota of Nile tilapia (Oreochromis niloticus)

Abstract The study was conducted to evaluate the effect of Moringa olifera on the growth and gut health of Tilapia (Oreochromis niloticus). The feed having 30% crude protein was prepared as an experimental diet with 4%, 8% and 10% M. olifera leaf supplementation, respectively. The control diet was devoid of M. olifera leaves. The 10 weeks feeding trial was carried out on 60 fish in aquaria. Fish was fed @ 3% of body weight twice a day. Diet with the high level of inclusion of M. olifera leaves significantly increased the growth rate, Survival Rate (SR), Specific Growth Rate (SGR) and Feed Conversion Efficiency (FCE) in all treatment groups compared to the control group. Similarly, Feed Conversion Ratio (FCR) gradually decreased and found highly-significant. To check the gut health of the Tilapia, random samples were selected and dissected. Nutrient agar was used as culture media to check the growth of bacteria. Pour Plate Method was used for viable colonies count by colony counter. Through staining method, the different bacteria such as Escherichia coli, Salmonella, Shigella and Pseudomonas aeruginosa were identify abundantly in the intestine of control diet fish but less number present in treatment diets groups. These results showed that M. olifera leaves up to 10% of dietary protein can be used for Nile tilapia for significant growth and healthy gut microbiota of fish.

Resumo O estudo foi conduzido para avaliar o efeito da Moringa olifera no crescimento e saúde intestinal da tilápia (Oreochromis niloticus). A ração com 30% de proteína bruta foi preparada como dieta experimental com 4%, 8% e 10% de suplementação de folhas de M. olifera, respectivamente. A dieta controle foi desprovida de folhas de M. olifera. O ensaio de alimentação de 10 semanas foi realizado em 60 peixes em aquários. O peixe pesava 3% do peso corporal duas vezes ao dia. A dieta com alto nível de inclusão de folhas de M. olifera aumentou significativamente a taxa de crescimento, taxa de sobrevivência (SR), taxa de crescimento de sobrevivência (SGR) e eficiência de conversão alimentar (FCE) em todos os grupos de tratamento em comparação com o grupo de controle. Da mesma forma, a taxa de conversão de alimentação (FCR) diminuiu gradualmente e foi considerada altamente significativa. Para verificar a saúde intestinal da tilápia, amostras aleatórias foram selecionadas e dissecadas. O ágar nutriente foi usado como meio de cultura para verificar o crescimento das bactérias. O método da placa de Verter foi usado para a contagem de colônias viáveis por contador de colônias. Através do método de coloração, diferentes como Escherichia coli, Salmonella, Shigella e Pseudomonas aeruginosa foram identificados abundantemente no intestino de peixes da dieta controle, mas em menor número nos grupos de dieta de tratamento. Esses resultados mostraram que M. olifera deixa até 10% da proteína dietética e pode ser usado para tilápia do Nilo para um crescimento significativo e microbiota intestinal saudável de peixes.

Lernaeid parasites prevalence in commercial freshwater fish species at various fish farms in Pakistan

Abstract Reports abound on Lernaea parasitizing the brood stock, fingerlings, and marketable-sized culturable freshwater fish species in various parts of the world. We investigated seven small-scale aquaculture farms and how the prevailing Lernaea is impacting them. Randomly seven fish farms were selected to determine the prevalence percentage of lernaeid ectoparasites. Relevant information of the fishponds to estimate the various aspects such as effects of water source and quality, feed, stocking density, treatment used, and weight and length of fish, concerned with Lernaea infestation and prevalence was gathered. The results indicated that Catla catla (F. Hamilton, 1822) showed highest prevalence (41.7%) among the seven fish species, whereas Oreochromis niloticus showed zero. Other five fish species Ctenopharyngodon idella, Cirrhinus cirrhosis, Cyprinus carpio, Labeo rohita and Hypophthalmichthys molitrix showed 13.2%, 8.1%, 7.7%, 7.4%, 0.9% prevalence, respectively. In Royal Fish Farm 84.3% lernaeid infestation was observed, while no parasite was observed in the Vicents Chunnian fish farm. The water source, quality, feed, fertilizers, stocking density, water temperature, and potential treatment options displayed varying tendencies among fish farms and prevalence. Depending on the weight and length, the highest prevalence (56.7%, and 66.7%) was observed in 3501-4000 g and 81-90 cm groups. The infestation rate varied in various fish body parts with the dorsal fin the most vulnerable organ and showed 2.3% overall prevalence (while 18.4% contribution within total 12.6% infestation). Out of 147 infected fish samples, 45 were extensively contaminated by Lernaea spread. In conclusion, our findings confirm that Lernaea could pose a considerable threat to marketable fish, and various treatment options should be educated to the farmers to help mitigate the spread and potential losses. Furthermore, Catla catla is more vulnerable to Lernaea infestation (41.7%), so are the fish species being cultured at higher stocking densities.

Resumo Abundam os relatórios sobre Lernaea parasitando o estoque de cria, alevinos e espécies de peixes de água doce cultiváveis de tamanho comercial em várias partes do mundo. Investigamos sete fazendas de aquicultura de pequena escala e de que maneira a Lernaea predominante está impactando-as. Aleatoriamente, sete fazendas de peixes foram selecionadas para determinar a porcentagem de prevalência de ectoparasitas de Lernaea. Foram recolhidas informações relevantes sobre os viveiros de peixes para estimar os vários aspectos, tais como efeitos da fonte e qualidade da água, alimentação, densidade de povoamento, tratamento utilizado e peso e comprimento dos peixes, relacionados com a infestação e prevalência de Lernaea. Os resultados indicaram que Catla catla (F. Hamilton, 1822) apresentou maior prevalência (41,7%) entre as sete espécies de peixes, enquanto Oreochromis niloticus apresentou zero. Outras cinco espécies de peixes Ctenopharyngodon idella, Cirrhinus cirrhosis, Cyprinus carpio, Labeo rohita e Hypophthalmichthys molitrix apresentaram 13,2%, 8,1%, 7,7%, 7,4%, 0,9% de prevalência, respectivamente. Em Royal Fish Farm, 84,3% de infestação de Lernaea foi observada, enquanto não se observou nenhum parasita na fazenda de peixes Chunnian de Vicent. A fonte de água, qualidade, ração, fertilizantes, densidade de estocagem, temperatura da água e opções de tratamento potenciais exibiram tendências variadas entre as fazendas de peixes e prevalência. Dependendo do peso e comprimento, a maior prevalência (56,7% e 66,7%) foi observada nos grupos de 3501-4000 g e 81-90 cm. A taxa de infestação variou em várias partes do corpo dos peixes, sendo a nadadeira dorsal o órgão mais vulnerável e apresentou 2,3% de prevalência geral (enquanto 18,4% de contribuição dentro do total de 12,6% de infestação). Das 147 amostras de peixes infectados, 45 estavam amplamente contaminadas pela propagação de Lernaea. Em conclusão, nossos resultados confirmam que Lernaea pode representar uma ameaça considerável para peixes comercializáveis, e várias opções de tratamento devem ser educadas para os agricultores para ajudar a mitigar a propagação e as perdas potenciais. Além disso, Catla catla é mais vulnerável à infestação por Lernaea (41,7%), assim como as espécies de peixes sendo cultivadas em densidades de estocagem mais altas.

Unraveling the impact of ORF3a Q57H mutation on SARS-CoV-2: insights from molecular dynamics.

ORF3a is a conserved accessory protein of SARS-CoV-2, linked to viral infection and pathogenesis, with acquired mutations at various locations. Previous studies have shown that the occurrence of the Q57H mutation is higher in comparison to other positions in ORF3a. This mutation is known to induce conformational changes, yet the extent of structural alteration and its role in the viral adaptation process remain unknown. Here we performed molecular dynamics (MD) simulations of wt-ORF3a, Q57H, and Q57A mutants to analyze structural changes caused by mutations compared to the native protein. The MD analysis revealed that Q57H and Q57A mutants show significant structural changes in the dimer conformation than the wt-ORF3a. This dimer conformer narrows down the ion channel cavity, which reduces Na + or K + permeability leading to decrease the antigenic response that can help the virus to escape the host immune system. Non-bonding interaction analysis shows the Q57H mutant has more interacting residues, resulting in more stability within dimer conformation than the wt-ORF3a and Q57A. Moreover, both mutant dimers (Q57H and Q57A) form a novel salt-bridge interaction at the same position between A:Asp142 and B:Lys61, whereas such an interaction is absent in the wt-ORF3a dimer. We have also noticed that the TM3 domain's flexibility in Q57H is increased because of strong inter-domain interactions of TM1 and TM2 within the dimer conformation. These unusual interactions and flexibility of Q57H mutant can have significant impacts on the SARS-CoV-2 adaptations, virulence, transmission, and immune system evasion. Our findings are consistent with the previous experimental data and provided details information on the structural perturbation in ORF3a caused by mutations, which can help better understand the structural change at the molecular level as well as the reason for the high virulence properties of this variant.Communicated by Ramaswamy H. Sarma.

Structure and dynamics of whole-sequence homology model of ORF3a protein of SARS-CoV-2: An insight from microsecond molecular dynamics simulations.

The ORF3a is a large accessory protein in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which plays an important role in virulence and viral replication; especially in inflammasome activation and apoptosis. However,, the existing cryo-EM structure of SARS-CoV-2 ORF3a is incomplete, . making it challenging to understand its structural and functional features. The aim of this study is to investigate the dynamic behaviors of the full-sequence homology model of ORF3a and compare it with the cryo-EM structure using microsecond molecular dynamics simulations. The previous studies indicated that the unresolved residues of the cryo-EM structure are not only involved in the pathogenesis of the SARS-CoV-2 but also exhibit a significant antigenicity. The dynamics scenario of homology model revealed higher RMSD, Rg, and SASA values with stable pattern when compared to the cryo-EM structure. Moreover, the RMSF analysis demonstrated higher fluctuations at specific positions (1-43, 97-110, 172-180, 219-243) in the model structure, whereas the cryo-EM structure displayed lower overall drift (except 1-43) in comparison to the model structure.Secondary structural features indicated that a significant unfolding in the transmembrane domains and ß-strand at positions 166 to 172, affecting the stability and compactness of the cryo-EM structure , whereas the model exhibited noticeable unfolding in transmembrane domains and small-coiled regions in the N-terminal. , The results from molecular docking and steered molecular dynamics investigations showed the model structure had a greater number of non-bonding interactions, leading to enhanced stability when compared to the cryo-EM structure. Consequently, higher forces were necessary for unbinding of the baricitinib and ruxolitinib inhibitors from the model structure.. Our findings can help better understanding of the significance of unresolved residues at the molecular level. Additionally, this information can guide researchers for experimental endeavors aimed at completing the full-sequence structure of the ORF3a.Communicated by Ramaswamy H. Sarma.

Comparison of Recurrent Laryngeal Nerve Injury during Thyroidectomy with and Without Routine Identification of the Nerve Peroperatively.

Thyroidectomy is one of the commonest operative procedures performed in the neck and injury to recurrent laryngeal nerve (RLN) is not uncommon. It results in hoarseness to serious respiratory distress depending on the extent of the injury. The incidence of RLN injury varies widely and is multifactorial depending on the extent of surgical procedures, experience and expertise of the surgeons, nature of the thyroid diseases and a wide range of anatomical variations. Peroperative routine identification of the nerve during thyroidectomy can be a way to prevent injury. Despite recommendation for identification of the RLN peroperatively in thyroid surgery, a debate still exists whether the nerve to be identified peroperatively or not, to avoid its inadvertent injury. The aim of this study was to compare the incidence of RLN injury between two groups where RLN was identified peroperatively in one group and the nerve was not attempted for identification in the other group in thyroid surgery. A comparative cross-sectional study was carried out in the department of surgery and otolaryngology at Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh from June 2018 to November 2019, on patients who underwent elective thyroid surgery. Patients were included in RLN identified group and in RLN not identified group, by individual surgeons' preference to identify or not to identify the RLN peroperatively. Peroperative identification of the nerve was done by direct visualization. All cases were evaluated for vocal cord palsy preoperatively, during extubation and postoperatively. Patient's particulars, other parameters and perioperative data were recorded. A total of 80 cases were included in this study, 40 cases (50.0%) in the peroperative RLN identified group and 40 cases (50.0%) in the RLN not identified group. Unilateral RLN palsy was encountered in 2.5% (2 cases) in the RLN identified group and 6.3% (5 cases) in the nerve not identified group (p value 0.192). Transient unilateral RLN palsy was seen in 7.5% (6 cases) of patients; 2.5% (2 cases) in the RLN identified group and 5.0% (4 cases) in the RLN not identified group. And 1.3% (1 case) of permanent unilateral RLN palsy was encountered in this study, which was in the RLN not identified group; there was no permanent palsy in the RLN identified group. We did not encounter any bilateral RLN palsy. There was no statistically significant difference in the incidence of RLN injury between the peroperatively RLN identified group and no attempt to identify the nerve group despite recommendation for peroperative RLN identification in thyroid surgery to avoid its inadvertent injury. However, from this study, we recommend peroperative RLN identification in thyroid surgery to enhance surgical skill.

Structural and functional effects of the L84S mutant in the SARS-COV-2 ORF8 dimer based on microsecond molecular dynamics study.

The L84S mutation has been observed frequently in the ORF8 protein of SARS-CoV-2, which is an accessory protein involved in various important functions such as virus propagation, pathogenesis, and evading the immune response. However, the specific effects of this mutation on the dimeric structure of ORF8 and its impacts on interactions with host components and immune responses are not well understood. In this study, we performed one microsecond molecular dynamics (MD) simulation and analyzed the dimeric behavior of the L84S and L84A mutants in comparison to the native protein. The MD simulations revealed that both mutations caused changes in the conformation of the ORF8 dimer, influenced protein folding mechanisms, and affected the overall structural stability. In particular, the 73YIDI76 motif has found to be significantly affected by the L84S mutation, leading to structural flexibility in the region connecting the C-terminal ß4 and ß5 strands. This flexibility might be responsible for virus immune modulation.  The free energy landscape (FEL) and principle component analysis (PCA) have also supported our investigation. Overall, the L84S and L84A mutations affect the ORF8 dimeric interfaces by reducing the frequency of protein-protein interacting residues (Arg52, Lys53, Arg98, Ile104, Arg115, Val117, Asp119, Phe120, and Ile121) in the ORF8 dimer.  Our findings provide detail insights for further research in designing structure-based therapeutics against the SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

In silico peptide-based therapeutics against human colorectal cancer by the activation of TLR5 signaling pathways.

OBJECTIVE: Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in both men and women. Toll-like receptor 5 (TLR5), an autoimmune signaling receptor that plays a role in cancer, can be exploited for the suppression of human colon cancer. Salmonella flagellin protein, a novel agonist of TLR5 activating downstream signaling, could be a basis for designing anticancer peptides. METHODS: The three-dimensional crystal structure of TLR5 (PDB ID: 3J0A, Resolution = 26.0 Å) was optimized using the AMBER force field in the YASARA suit. In silico enzymatic digestion tool, PeptideCutter, was used to identify peptides from Salmonella flagellin, an agonist against human TLR5. The 3D structure of the peptides was generated using PEP-FOLD3. These peptides were screened against human TLR5 using shape complementarity principles based on the binding affinity and interactions with the active residue of TLR5 monomer, and the selected peptides were further validated by molecular dynamic (MD) simulation. RESULTS: In this study, we generated 42 peptides from Salmonella flagellin protein by in silico protein digestion. Then, based on a new hidden Markov model sub-optimal conformation sampling approach as well as the size of the fragments, we select 38 effective peptides from these 42 cleavages. These peptides were screened against the monomeric Xray structure of human TLR5 using shape complementarity principles. Based on the binding affinity and interactions with the active residue of TLR5 monomer (residues 294 and 366 of TLR5), nine top-scored peptides were selected for the initial molecular dynamic (MD) simulation. Among these peptides, Clv10, Clv17, and Clv28 showed high stability and less flexibility during MD simulation. A 1 µs MD simulation was performed on TLR5-Clv10, TLR-Clv17, and TLR5-Clv28 complexes to further analyze the stability, conformational changes, and binding mode (Clv10, Clv17, and Clv28). During this MD study, the peptides showed high salt bridges and ionic interactions with residue ASP294 and residue ASP366 throughout the simulation and remained in the concave of the human TLR5 monomer. The RMSD and Rg values showed that the peptide-protein complexes become stable after 200 ns of contraction and extraction. CONCLUSION: These findings can facilitate the rational design of selected peptides as an agonist of TLR5, which have antitumor activity, suppress colorectal cancer tumors, and can be used as promising candidates and novel agonists of TLR5.

Biochemical, physiological, and growth evaluation of different chickpea genotypes under varying salinity regimes.

Biochemical and physiological parameters, growth, and yield of field crops especially salt sensitive crops like chickpea are affected adversely by salinity in arid to semi-arid regions. To investigate the effect of different salinity levels on growth, biochemical and physiological parameters of chickpea genotypes, a pot experiment following CRD, two factor factorial design, was conducted in the glasshouse at the Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan. Ten (10) kg of soil was filled in each pot and salinity levels were maintained @ S0= 0 mM NaCl, S1= 50 mM NaCl, S2= 100 mM NaCl and S3= 150 mM by applying NaCl and 5 genotypes of chickpea (KK-2, Bhakkar-2011, Bittle-98, Punjab-2008, and CM-98) were used. At crop maturity, growth parameters, physiological, biochemical, and ionic parameters were measured using standard analysis procedures. Salinity reduced the growth and yield of all genotypes, but the rate of decrease was different among the genotypes tested. From the results, a decrease in K concentration, K/Na ratio, transpiration rate, stomatal conductance, N, and P was observed in all genotypes with the increase in salinity. An increase in salinity level increased the proline content (35.45%), crude protein (42%), H2O2 (19%), lipid peroxidation (62%), carbohydrates (23.22%), and Na+ concentration (137%). The highest level of salinity, 150 mM NaCl has exhibited the highest salinity stress in all parameters. Genotype KK-2 and Bhakkar-11 showed a lower rate of relative decrease in yield (4.5 and 12%), K+/Na+ ratio (23.34 and 11.47%), and K+ concentration (7.9 and 11%), respectively, and the lowest relative increase in Na+ accumulation (20.3 and 0.48%), @ 50 mM salinity compared to control. Genotype KK-2 and Bhakkar-11 proved better @ 50mM salinity. The findings suggest that the critical level of the salinity must be kept in mind and the salt-tolerant genotypes should be cultivated in salt affected soils.

Epidemiology and clinical features of cutaneous leishmaniasis in Khyber Pakhtunkhwa, Pakistan.

Current cross-sectional study was carried out between September 2019 to January 2020 at the Department of Pathology, Mardan Medical Complex (MMC), Mardan, and District Headquarter Hospital North Waziristan, Khyber Pakhtunkhwa (KP), Pakistan. The objectives of the current study were to determine the prevalence of leishmaniasis and its associated risk factors in selected districts of KP province, Pakistan. Altogether, three hundred and seventy-four (n=374) leishmaniosis patients were included in the current study. Skin specimen from the ulcer border were collected. The slides were stained by Giemsa stain and examined for the presence of amastigote. The prevalence of leishmania infected patients in different region of KP were as follows: North Waziristan region 53.7 (n=201) District Mardan 34.7% (n=130); District Nowshera 6.7% (n=25), District Swabi 1.1% (n=4) and other Districts i.e. Dir, Malakand, Buner and Bajawarr were 3.7% (n=14). The frequency of leishmaniasis were more in male and majority of the infected patients were in the age group of <10 years. Among n=374 patients 95.7% (n= 358) had cutaneous leishmaniasis while 3% (n= 11) had mucocutaneous type of infection and 1.3% (n= 5) patients had both cutaneous and mucocutaneous infection. Upon treatment by Sodium stibogluconate (SSG) 97% (n=362) showed clinical signs of complete or partial recovery of their skin lesions. Conclusively, highest incidence of leishmania infection occurred during short study period and majority of the cases showed positive response to treatment.

Structural characteristics, cation distribution, and elastic properties of Cr3+ substituted stoichiometric and non-stoichiometric cobalt ferrites.

Structural, elastic and cation distribution properties have been investigated on stoichiometric and non-stoichiometric cobalt ferrites. Crystal structure, formation of spinel type ferrite, chemical bonding, cation distribution, and thermal properties of two series of Cr3+ substituted stoichiometric and non-stoichiometric various cobalt ferrites with general formula Co1-x Cr x Fe2O4 (S1), and Co1+x Cr x Fe2-x O4 (S2) were reported. Samples are synthesized by the solid-state reaction technique via planetary ball milling. X-ray diffraction (XRD) analysis confirms the formation of a single phase cubic spinel structure with the space group Fd3̄m. Rietveld refinement results show that Cr occupies both the tetrahedral (A-site) and octahedral sites (B-site). The experimental lattice parameters show increasing trends for both the series with increase of Cr content. The cation-anion vacancies, chemical bonding, and the displacement of oxygen have been evaluated to understand the effect of Cr substitution and how the non-stoichiometry affects the physical and chemical properties of the material. The crystallite size is found to be the decreasing value with an increase of Cr concentration for both series of samples. Specific vibrational modes from the FTIR spectra suggest a gradual change of inversion of the ferrite lattice with the increase of Cr concentration which is also evident from Rietveld refinement data. The elastic properties analysis reveals that the synthesized samples for both series are ductile in nature. The non-stoichiometric structure with excess Co2+ may pave a new way to realize the lowering of Curie temperature of ferrite that is expected to improve the magnetocaloric properties.

Structure and dynamics of membrane protein in SARS-CoV-2.

SARS-CoV-2 membrane (M) protein performs a variety of critical functions in virus infection cycle. However, the expression and purification of membrane protein structure is difficult despite tremendous progress. In this study, the 3 D structure is modeled followed by intensive validation and molecular dynamics simulation. The lack of suitable homologous templates (>30% sequence identities) leads us to construct the membrane protein models using template-free modeling (de novo or ab initio) approach with Robetta and trRosetta servers. Comparing with other model structures, it is evident that trRosetta (TM-score: 0.64; TM region RMSD: 2 Å) can provide the best model than Robetta (TM-score: 0.61; TM region RMSD: 3.3 Å) and I-TASSER (TM-score: 0.45; TM region RMSD: 6.5 Å). 100 ns molecular dynamics simulations are performed on the model structures by incorporating membrane environment. Moreover, secondary structure elements and principal component analysis (PCA) have also been performed on MD simulation data. Finally, trRosetta model is utilized for interpretation and visualization of interacting residues during protein-protein interactions. The common interacting residues including Phe103, Arg107, Met109, Trp110, Arg131, and Glu135 in the C-terminal domain of M protein are identified in membrane-spike and membrane-nucleocapsid protein complexes. The active site residues are also predicted for potential drug and peptide binding. Overall, this study might be helpful to design drugs and peptides against the modeled membrane protein of SARS-CoV-2 to accelerate further investigation. Communicated by Ramaswamy H. Sarma.

Lernaeid parasites prevalence in commercial freshwater fish species at various fish farms in Pakistan.

Reports abound on Lernaea parasitizing the brood stock, fingerlings, and marketable-sized culturable freshwater fish species in various parts of the world. We investigated seven small-scale aquaculture farms and how the prevailing Lernaea is impacting them. Randomly seven fish farms were selected to determine the prevalence percentage of lernaeid ectoparasites. Relevant information of the fishponds to estimate the various aspects such as effects of water source and quality, feed, stocking density, treatment used, and weight and length of fish, concerned with Lernaea infestation and prevalence was gathered. The results indicated that Catla catla (F. Hamilton, 1822) showed highest prevalence (41.7%) among the seven fish species, whereas Oreochromis niloticus showed zero. Other five fish species Ctenopharyngodon idella, Cirrhinus cirrhosis, Cyprinus carpio, Labeo rohita and Hypophthalmichthys molitrix showed 13.2%, 8.1%, 7.7%, 7.4%, 0.9% prevalence, respectively. In Royal Fish Farm 84.3% lernaeid infestation was observed, while no parasite was observed in the Vicent's Chunnian fish farm. The water source, quality, feed, fertilizers, stocking density, water temperature, and potential treatment options displayed varying tendencies among fish farms and prevalence. Depending on the weight and length, the highest prevalence (56.7%, and 66.7%) was observed in 3501-4000 g and 81-90 cm groups. The infestation rate varied in various fish body parts with the dorsal fin the most vulnerable organ and showed 2.3% overall prevalence (while 18.4% contribution within total 12.6% infestation). Out of 147 infected fish samples, 45 were extensively contaminated by Lernaea spread. In conclusion, our findings confirm that Lernaea could pose a considerable threat to marketable fish, and various treatment options should be educated to the farmers to help mitigate the spread and potential losses. Furthermore, Catla catla is more vulnerable to Lernaea infestation (41.7%), so are the fish species being cultured at higher stocking densities.

Reverse Abdominoplasty: A Novel Practical Approach Using Oncoplastic Reconstruction in Managing Major Chest Wall Defects for Patients With Loco-Regional Recurrence Following Breast Cancer Surgery.

Background Loco-regional recurrence of breast cancer in patients with large chest wall defects following mastectomy poses significant oncoplastic challenges. Reverse abdominoplasty is most commonly used to treat patients with excess upper abdominal soft tissue and laxity following massive weight loss. Widely employed as a technique for aesthetic contouring of the upper anterior trunk, as well as in augmentation mammoplasty, its use to date for reconstructive purposes is mainly limited to burns and large site surgical tumour ablation. Method Here we review our experience of using reverse abdominoplasty as a novel approach to filling major anterior chest wall defects in patients with cutaneous manifestations of loco-regional or distant recurrence of breast cancer. Results Seven patients with metastatic breast cancer underwent reverse abdominoplasty for disease recurrence following mastectomy, with good patient-reported outcomes, and minimal surgical complications. Moreover, follow-up data in the patients surveyed also showed minimal to no limitations on their activities of daily living following the procedure. Conclusion Here we demonstrate the successful employment of reverse abdominoplasty - a technique not usually reserved in breast oncoplastic surgery - to treat fungating breast lesions and/or other manifestations of loco-regional recurrence in metastatic breast cancer. This may herald a paradigm shift in the way surgeons approach breast cancer recurrence in patients with pre-existing major chest wall defects.

Effect of Moringa olifera leaves on growth and gut microbiota of Nile tilapia (Oreochromis niloticus).

The study was conducted to evaluate the effect of Moringa olifera on the growth and gut health of Tilapia (Oreochromis niloticus). The feed having 30% crude protein was prepared as an experimental diet with 4%, 8% and 10% M. olifera leaf supplementation, respectively. The control diet was devoid of M. olifera leaves. The 10 weeks feeding trial was carried out on 60 fish in aquaria. Fish was fed @ 3% of body weight twice a day. Diet with the high level of inclusion of M. olifera leaves significantly increased the growth rate, Survival Rate (SR), Specific Growth Rate (SGR) and Feed Conversion Efficiency (FCE) in all treatment groups compared to the control group. Similarly, Feed Conversion Ratio (FCR) gradually decreased and found highly-significant. To check the gut health of the Tilapia, random samples were selected and dissected. Nutrient agar was used as culture media to check the growth of bacteria. Pour Plate Method was used for viable colonies count by colony counter. Through staining method, the different bacteria such as Escherichia coli, Salmonella, Shigella and Pseudomonas aeruginosa were identify abundantly in the intestine of control diet fish but less number present in treatment diets groups. These results showed that M. olifera leaves up to 10% of dietary protein can be used for Nile tilapia for significant growth and healthy gut microbiota of fish.

Surface modification and improvements of wicking properties and dyeability of grey jute-cotton blended fabrics using low-pressure glow discharge air plasma.

Herein, we reported the improvements of wicking properties and dyeability of the jute-cotton blended (40:60) fabrics due to the effect of low-pressure glow discharge (LPGD) air plasma under selected exposure times. The microscopic features, functional groups, wettability, contact angles, wetting area, wicking rates, and reflectance values of the jute-cotton blended fabrics were analyzed using numerous experimental techniques. The scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) techniques were used to investigate the morphological and compositional modifications of plasma-treated jute blended cotton fabrics. The compositional analysis confirmed various functional groups such as -OH, C-O, and COO- on the surface of jute blended cotton fabrics. The average pore radii and diffusion coefficient were calculated by using the modified Lucas-Washburn equation. The plasma-treated fabrics were shown to have an average pore radius of 0.93, 1.46, 2.26, and 4.8 µm under treatment time of 5,10,15, and 20 min. Nearly 50% reduction of contact angle was observed after a plasma treatment time of 20 min. The absorption to scattered ratio, K/S (determined using Kubel-Munk model) of the colored fabrics with 5 min pre-treated plasma was 6.47, although it was raised up to 8.51 after 20 min of pre-treatment. A reactive dye, Bezaktiv Red S-3B, was used for the dyeability test, and our findings showed that the dyeability and the wettability of the fabric were substantially enhanced with the treatment time of LPGD air plasma. Among the samples, only 10 min plasma pre-treated colored fabric exhibited a color difference of less than one compared to the standard one.

Genome Sequences of Two Novel Coronavirus (SARS-CoV-2) Isolates from Dhaka, Bangladesh.

This study reports the genome sequences of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in the nasopharyngeal swab specimens of two coronavirus disease 2019 (COVID-19) patients from Dhaka, Bangladesh.

Effect of pHs on the Structure Evolution of Platinum Nanoclusters and Their Surface Plasmon Resonance Properties.

Multi-structured platinum nanoclusters have been prepared through a one-step aqueous synthetic process by controlling pHs. The included structures are closely packed 3-dimensional (3D) dendrites, loosely packed 3D dendrites, short-order dendritic chains, long-order dendritic chains, flatten nanoclusters and monodisperse nanoparticles. The high resolution transmission electron microscopy images (HRTEM) display that the nanoclusters with a variety of structures are filled with grains of average size ~2.0 nm. The images of the nanoclusters demonstrated that Pt nanoparticles were not fused to each other, but their aggregations were separated by cetyltrimethylammonium bromide (CTAB). The as-prepared Pt nanomaterials were studied by UV-visible absorption spectroscopy to identify their surface plasmon resonance (SPR) activities. The structure dependent SPR signals have been observed from 200 nm-800 nm.

Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2.

SARS-CoV-2 virus outbreak poses a major threat to humans worldwide due to its highly contagious nature. In this study, molecular docking, molecular dynamics, and structure-activity relationship are employed to assess the binding affinity and interaction of 76 prescription drugs against RNA dependent RNA polymerase (RdRp) and Main Protease (Mpro) of SARS-CoV-2. The RNA-dependent RNA polymerase is a vital enzyme of coronavirus replication/transcription complex whereas the main protease acts on the proteolysis of replicase polyproteins. Among 76 prescription antiviral drugs, four drugs (Raltegravir, Simeprevir, Cobicistat, and Daclatasvir) that are previously used for human immunodeficiency virus (HIV), hepatitis C virus (HCV), Ebola, and Marburg virus show higher binding energy and strong interaction with active sites of the receptor proteins. To explore the dynamic nature of the interaction, 100 ns molecular dynamics (MD) simulation is performed on the selected protein-drug complexes and apo-protein. Binding free energy of the selected drugs is performed by MM/PBSA. Besides docking and dynamics, partial least square (PLS) regression method is applied for the quantitative structure activity relationship to generate and predict the binding energy for drugs. PLS regression satisfactorily predicts the binding energy of the effective antiviral drugs compared to binding energy achieved from molecular docking with a precision of 85%. This study highly recommends researchers to screen these potential drugs in vitro and in vivo against SARS-CoV-2 for further validation of utility.