Adsorption and solar light activity of noble metal adatoms (Au and Zn) on Fe(111) surface: a first-principles study.

Noble metals such as gold (Au), zinc (Zn), and iron (Fe) are highly significant in both fundamental and technological contexts owing to their applications in optoelectronics, optical coatings, transparent coatings, photodetectors, light-emitting devices, photovoltaics, nanotechnology, batteries, and thermal barrier coatings. This study presents a comprehensive investigation of the optoelectronic properties of Fe(111) and Au, Zn/Fe(111) materials using density functional theory (DFT) first-principles method with a focus on both materials' spin orientations. The optoelectronic properties were obtained employing the generalized gradient approximation (GGA) and the full-potential linearized augmented plane wave (FP-LAPW) approach, integrating the exchange-correlation function with the Hubbard potential U for improved accuracy. The arrangement of Fe(111) and Au, Zn/Fe(111) materials was found to lack an energy gap, indicating a metallic behavior in both the spin-up state and the spin-down state. The optical properties of Fe(111) and Au, Zn/Fe(111) materials, including their absorption coefficient, reflectivity, energy-loss function, refractive index, extinction coefficient, and optical conductivity, were thoroughly examined for both spin channels in the spectral region from 0.0 eV to 14 eV. The calculations revealed significant spin-dependent effects in the optical properties of the materials. Furthermore, this study explored the properties of the electronic bonding between several species in Fe(111) and Au, Zn/Fe(111) materials by examining the density distribution mapping of charge within the crystal symmetries.

Diffusible signal factor (DSF)-mediated quorum sensing modulates swarming in Xanthomonas albilineans.

Xanthomonas spp. are plant pathogens known for significantly impacting crop yields. Among them, Xanthomonas albilineans (Xal) is notable for colonizing the xylem and causing sugarcane leaf scald disease. This study employed homologous recombination to mutate quorum sensing (QS) regulatory genes (rpf) to investigate their role in Xal pathogenicity. Deletions of rpfF (ΔrpfF), rpfC (ΔrpfC), and rpfG (ΔrpfG) led to reduced swarming, growth, and virulence. However, DSF supplementation restored swarming and growth in the ΔrpfF mutant. Deleting rpfC, rpfG, and rpfF also reduced twitching motility and affected Type IV Pilus (T4P) expression. Transcriptomic analysis revealed that ΔrpfF positively regulates flagellar genes. DSF supplementation in ΔrpfF (ΔrpfF-DSF) modulated the expression of flagellar, chemotaxis, and T4P genes. These findings elucidate the DSF-mediated swarming pathway in Xal and provide valuable insights into its regulatory mechanisms.

Evaluation of blood minerals and oxidative stress changing pattern in prepartum and postpartum Achai and Holstein Friesian dairy cows.

This research focused on evaluating blood mineral levels and malondialdehyde (MDA) as an indicator of oxidative stress before and after giving birth in Achai and Holstein Friesian (HF) dairy cows. Blood samples were obtained from a total of 50 cows representing both breeds on the third, second, and first week prior to calving, as well as on the day of calving (day 0). Subsequently, samples were collected on the 1-3 weeks postpartum to allow a comprehensive evaluation of blood parameters throughout the peripartum period. Results showed a significant (p < .01) decrease in serum zinc (Zn) levels on the day of parturition in both breeds. Additionally, HF cows exhibited higher (p < .01) Zn levels on week 2 before giving birth. Interestingly, blood selenium (Se) concentration increased (p < .01) in HF cows on weeks 2 and 3 after calving. In contrast, Achai cows showed a rise (p < .01) in blood Se on week 3 of parturition. Blood copper (Cu) levels were higher (p < .01) on weeks 2 and 3 after parturition in HF cows and on third week before parturition compared to Achai cows, where serum Cu remained high on week 1 of parturition. The findings indicated that blood magnesium (Mg) was higher (p < .01) on third week before parturition in Achai cows and on weeks 2 and 3 after parturition. Serum calcium (Ca) was higher (p < .01) in both HF and Achai cows on weeks 2 and 3 after parturition, and lower (p < .01) on third week before giving birth in both breeds. The mean blood MDA levels in Achai cows were lower (p < .01) on weeks 1 to 3 postpartum or 3 weeks before giving birth. In HF cows, serum MDA increased (p < .01) just before 2 weeks of parturition and remained elevated until 3 weeks of parturition. Thus, both breeds exhibited a similar pattern of mineral fluctuations; yet, Achai cows demonstrated greater resilience to oxidative stress compared to HF cows during the transition period.

Urea molasses mineral block under various feeding systems improved nutrient digestibility, productive performance and blood biochemical profile of Yaks.

BACKGROUND: The study aimed to investigate the effect of urea molasses mineral blocks (UMMB) on nutrient digestibility, productive performance and blood biochemical profile of indigenous yaks under various feeding systems. A total of sixteen yaks were randomly divided into four groups (n = 4 animal per group) and offered the, following feeding systems: (A) stall feeding, (B), urea molasses mineral block (UMMB) + stall feeding, (C) yard feeding and (D) UMMB + yard feeding. Trial lasted for 40 days. RESULTS: Results showed that nutrients intake (g) and nutrient digestibility (%) of dry matter (DM), organic matter (OM), crude protein (CP), ether extract (EE) and crude fiber (CF) were significantly higher (p < 0.05) in stall and yard feeding groups with UMMB licking. Blood zinc, cobalt, hemoglobin (Hb), red blood cell (RBC), glucose and serum glutamate private transaminase (SGPT) significantly (p < 0.05) increased in stall and yard feeding with UMMB licking. Milk yield, Ca and monounsaturated fatty acid except milk composition improved significantly (p < 0.05) in stall and yard feeding groups with UMMB licking. CONCLUSION: It was concluded that feeding of UMMB improved utilization of low-quality roughages and best results were obtained from stall and yard feedings with UMMB licking as compared to other groups.

Blood metabolic pattern and somatic cells dynamic in Achai and Holstein Friesian cows during transition period.

This study focused on assessing blood metabolites and somatic cell count (SCC) during the transition period in Achai and Holstein Friesian cows. Blood samples were collected from cows of both breeds on days -21, -14, -7 (pre-partum period), on day 0 (parturition day) and then on days 7, 14 and 21 (post-partum period). Additionally, milk samples were obtained on the day of parturition and on days 7, 14 and 21 post-partum for SCC assessment. Among Holstein cows, blood glucose levels showed a significant increase on day -21 before calving, and a decrease on the 14th and 21st days post-partum. Similarly, the blood triglycerides concentration exhibited a significant rise in Holstein cows 21 days before calving, while Achai cows experienced a significant decline in blood triglycerides on the day of parturition and throughout the entire post-partum period. Comparing Holstein and Achai cows, blood cholesterol was significantly higher in Holstein cows on day -21 before calving, whereas Achai cows had significantly lower blood cholesterol levels on the day of parturition. Regarding blood protein, Holstein cows exhibited significantly higher levels on day 14 post-partum, while Achai cows had lower protein levels 7 days before calving. The results further demonstrated that SCC was significantly elevated in Holstein cows on day 21 of parturition and lower on the day of parturition in Achai cows. Overall, the metabolic profile trend and SCC were comparable, yet the studied parameters were more pronounced in Holstein Friesian compared to Achai cows.

Inclusion of the fungus Pleurotus florida in the diet affects performance and feed efficiency traits in calves: a case study on Ravi buffalo.

The objective of the study was to investigate the effects of inclusion of Pleurotus florida treated wheat straw in the total mixed rations (TMRs) on feed intake, growth performance, nutrient digestibility, and nitrogen retention in male buffalo calves. As a pilot study, four TMRs, i.e., TMR1 having 0% P. florida treated wheat straw (FTWS), TMR2 (20% FTWS), TMR3 (40% FTWS), and TMR4 (60% FTWS) with berseem hay as basal diet, were formulated. Sixteen Nili-Ravi male buffalo calves (aged 10-12 months, weighing 73 ± 2.50 kg) were divided into four equal groups and randomly assigned one of four TMRs. A significant increase (P < 0.05) was observed in all nutrients intake, their digestibility, weight gain, and nitrogen retention with TMRs incorporated with FTWS. Highest feed conversion ratio (FCR) of 2.63 was noted with TMR1-0% and the lowest FCR (1.80) with TMR4-60%, on the other hand. In conclusion, the TMR4 (60% FTWS) has the potential to increase the weight gain, nutrient digestibility, nitrogen retention, and feed efficiency in buffalo calves. Therefore, inclusion of 60% Pleurotus florida treated wheat straw is recommended as TMRs with berseem hay based basal diet for feeding buffaloes calves.

Demographic and clinical variables in the dengue epidemic in Punjab, Pakistan.

Objectives: To identify the latest trends in the clinical picture and severity of the disease, which will help better understand and manage dengue. Methodology: It was a cross-sectional, hospital-based study performed in the tertiary care hospitals of Punjab from August 21 to December 2022, in which serologically and polymerase chain reaction (PCR) confirmed patients with dengue infection, were enrolled. Demographic and clinical variables were recorded on a pre-tested Performa, processed and presented in frequency and percentages, and graphs were generated. Mean and standard deviation was used to present continuous variables. Results: Out of a total of 580 patients, 472 were diagnosed with Dengue Fever (DF) and 108 with Dengue Hemorrhagic Fever (DHF). About 79.31% of the patients were male and 20.69% were females. The mean age of patients was 32.5±9 years. Among the clinical features the percentage of high-grade fever, body aches, and vomiting were the highest. The liver function profile showed that serum bilirubin, Serum aspartate transaminase (AST), serum alanine transaminase (ALT,) and alkaline phosphatase (ALP) levels were markedly raised. Conclusion: This study showed that with time the trends in the presentation of dengue are slowly shifting, which will help us better manage the disease burden in the future.

ScGAIL, a sugarcane N-terminal truncated DELLA-like protein, participates in gibberellin signaling in Arabidopsis.

The hormone gibberellin (GA) is crucial for internode elongation in sugarcane. DELLA proteins are critical negative regulators of the GA signaling pathway. ScGAI encodes a DELLA protein that was previously implicated in the regulation of sugarcane culm development. Here, we characterized ScGAI-like (ScGAIL) in sugarcane, which lacked the N-terminal region but was otherwise homologous to ScGAI. ScGAIL differed from ScGAI in its chromosomal location, expression patterns, and cellular localization. Although transgenic Arabidopsis overexpressing ScGAIL were insensitive to GAs, GA synthesis was affected in these plants, suggesting that ScGAIL disrupted the GA signaling pathway. After GA treatment, the expression patterns of GA-associated genes differed between ScGAIL-overexpressing and wild-type Arabidopsis, and the degradation of AtDELLA proteins in transgenic lines was significantly inhibited compared with wild-type lines. A sugarcane GID1 gene (ScGID1) encoding a putative GA receptor was isolated and interacted with ScGAIL in a GA-independent manner. Five ScGAIL-interacting proteins were verified by yeast two-hybrid assays, and only one interacted with ScGAI. Therefore, ScGAIL may inhibit plant growth by modulating the GA signaling pathway.

Novel rrs mutations in second-line injectable drug-resistant clinical isolates of Mycobacterium tuberculosis from the Punjab province of Pakistan.

INTRODUCTION: Phenotypic drug susceptibility testing is the most common approach to assess drug-resistant isolates; however, molecular methods of drug susceptibility testing are fast, accurate hence, offer less time for transmission during the diagnosis period. As data on the molecular methods regarding injectable drug resistance in the Punjab province of Pakistan is limited, therefore in this study, we aimed to analyze the mutations in the rrs gene behind second-line injectable drug resistance. MATERIAL AND METHODS: Mycobacterium tuberculosis isolates were collected from the sputum of 5362 TB suspects. The strains confirmed for resistant to injectable drugs through drug susceptibility testing were further proceeded. The 1537bp rrs gene was amplified with the help of three sets of primers with overlapping regions and DNA sequencing was performed. Obtained sequences were aligned with reference sequence to find mutations. RFLP-PCR method was also optimized for rapid detection of a common (143bp and 205bp) rrs gene mutation. RESULTS: Among 172 rifampicin resistance isolates, 163(95%) were resistant to both rifampicin and isoniazid, and 9 (5%) were resistant to only rifampicin. Among the resistant samples, 12 (6.9%) samples were resistant to all three injectable drugs. Sixty out of 172 (34.9%) samples showed resistance to at least one drug and 10 (5.8%) samples were resistant to two drugs among the 3 s-line drugs. Sequencing analysis showed novel mutations in different samples at positions 443InsC, 19DelT, 29G>A, 48C>T, 50G>C, 265InsT, 423T>G, 476InsA, 446A>G, 563DelA, 695G>A, 805DelA, 900G>A, and 1510A>G, while some already reported mutations at position 1401A>G, 1402A>G, and 1484G>T were also observed. MIC of novel rrs gene mutations in KAN, CAP, and AMK resistant isolates were found between 2.5 mg/L-3.05 mg/L, 2.08 mg/L-3.0 mg/L, and 2.1 mg/L-2.7 mg/L respectively. CONCLUSION: Novel mutations in the rrs gene reported in this study may confer second-line injectable drugs resistance in Mtb. This molecular insight into second-line injectable drug resistance is useful for better management of resistance Mtb in high burden countries.

A Novel Method of Magnetic Nanoparticles Functionalized with Anti-Folate Receptor Antibody and Methotrexate for Antibody Mediated Targeted Drug Delivery.

Therapeutic effects of anticancer medicines can be improved by targeting the specific receptors on cancer cells. Folate receptor (FR) targeting with antibody (Ab) is an effective tool to deliver anticancer drugs to the cancer cell. In this research project, a novel formulation of targeting drug delivery was designed, and its anticancer effects were analyzed. Folic acid-conjugated magnetic nanoparticles (MNPs) were used for the purification of folate receptors through a novel magnetic affinity purification method. Antibodies against the folate receptors and methotrexate (MTX) were developed and characterized with enzyme-linked immunosorbent assay and Western blot. Targeting nanomedicines (MNP-MTX-FR Ab) were synthesized by engineering the MNP with methotrexate and anti-folate receptor antibody (anti-FR Ab). The cytotoxicity of nanomedicines on HeLa cells was analyzed by calculating the % age cell viability. A fluorescent study was performed with HeLa cells and tumor tissue sections to analyze the binding efficacy and intracellular tracking of synthesized nanomedicines. MNP-MTX-FR Ab demonstrated good cytotoxicity along all the nanocomposites, which confirms that the antibody-coated medicine possesses the potential affinity to destroy cancer cells in the targeted drug delivery process. Immunohistochemical approaches and fluorescent study further confirmed their uptake by FRs on the tumor cells' surface in antibody-mediated endocytosis. The current approach is a useful addition to targeted drug delivery for better management of cancer therapy along with immunotherapy in the future.

Exploring context specific anti-smoking warning labels on cigarette packs: A quasi-experiment.

OBJECTIVE: To evaluate the impact of introducing newly-designed warning labels in relation to the available conventional cigarette packs. METHODS: The quasi-experimental study was conducted at four co-educational academic institutions selected using cluster random sampling technique in Gulshan-e-Iqbal town of Karachi from September 2016 to October 2017. The respondents, aged 16-24 years, were exposed with an experimental condition using five graphic cards; each comprising of two separate labels; label 1 being a cigarette pack currently rotated, and label 2 being the newly designed graphic and text warning label. Each participant responded over efficacy measures for each label separately. The difference in the efficacy scores between the two labels was assessed using repeated measure ANOVA with Bonferroni correction in analysis. RESULTS: Of the 388 students, 256(66%) were males and 132(34%) were females. The overall mean age was 18±2.76 years. Also, 188(48.5%) subjects were studying in higher secondary, 179(46.1%) undergraduate and 21(5.4%) postgraduate level. Of them, 104(26.8%) were ever-smokers and 284(73.2%) reported to be never-smokers. A difference was observed in the efficacy of the newly designed label "poverty" compared with current cigarette pack on the measure of not to start smoking(p=0.006). Never-smoking males perceived newly-designed label element 'dead person' as fear-arousing (p=0.045), while never-smoking females considered 'look after family' as efficacious (p=0.024). CONCLUSIONS: There was some evidence of variation in efficacy scores after stratifying on gender and smoking status. A more holistic approach is needed in this regard.

High-Quality Genome Sequence Resource for Fusarium andiyazi Causing Pokkah Boeng Disease of Sugarcane in China.

Sugarcane pokkah boeng disease (PBD) is emerging as a prevalent foliar disease in China. This airborne disease is caused by the Fusarium species complex. To investigate the diversity and evolution of Fusarium spp., we performed whole-genome sequencing of Fusarium andiyazi YN28 using a combination of Oxford Nanopore and Illumina technology. The F. andiyazi YN28 genome was sequenced, assembled, and annotated. A high-quality genome was assembled into 24 contigs with an N50 of 2.80 Mb. The genome assembly generated a total size of 44.1 Mb with a GC content of 47.64%. In total, 15,508 genes were predicted, including 794 genes related to the carbohydrate-active enzymes, 397 noncoding RNA, 155 genes associated with transporter classification, 4,550 genes linked to pathogen-host interactions, and 269 genes involved in effector proteins. Collectively, our results will provide insight into the host-pathogen interactions and will facilitate the breeding of new varieties of sugarcane resistant to PBD.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genome-wide analysis of R2R3-MYB transcription factors family in the autopolyploid Saccharum spontaneum: an exploration of dominance expression and stress response.

BACKGROUND: Sugarcane (Saccharum) is the most critical sugar crop worldwide. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes. RESULTS: A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genomic sequence and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which RT-qPCR validated MYB43, MYB53, MYB65, MYB78, and MYB99. Allelic expression dominance analysis implied the differential expression of alleles might be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C4 photosynthetic regulators by C4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively. CONCLUSIONS: This is the first report on genome-wide analysis of the MYB gene family in sugarcane. SsMYBs probably played an essential role in stem development and the adaptation of various stress conditions. The results will provide detailed insights and rich resources to understand the functional diversity of MYB transcription factors and facilitate the breeding of essential traits in sugarcane.

SARS-CoV-2 nucleocapsid and Nsp3 binding: an in silico study.

Severe acute respiratory syndrome virus 2 (SARS-CoV-2) belongs to the single-stranded positive-sense RNA family. The virus contains a large genome that encodes four structural proteins, small envelope (E), matrix (M), nucleocapsid phosphoprotein (N), spike (S), and 16 nonstructural proteins (nsp1-16) that together, ensure replication of the virus in the host cell. Among these proteins, the interactions of N and Nsp3 are essential that links the viral genome for processing. The N proteins reside at CoV RNA synthesis sites known as the replication-transcription complexes (RTCs). The N-terminal of N has RNA-binding domain (N-NTD), capturing the RNA genome while the C-terminal domain (N-CTD) anchors the viral Nsp3, a component of RTCs. Although the structural information has been recently released, the residues involved in contacts between N-CTD with Nsp3 are still unknown. To find the residues involved in interactions between two proteins, three-dimensional structures of both proteins were retrieved and docked using HADDOCK. Residues at N-CTD were detected in interaction with L499, R500, K501, V502, P503, T504, D505, N506, Y507, I508, T509, K529, K530K532, S533 of Nsp3 and N-NTD to synthesize SARS-CoV-2 RNA. The interaction between Nsp3 and CTD of N protein may be a potential drug target. The current study provides information for better understanding the interaction between N protein and Nsp3 that could be a possible target for future inhibitors.

Epidemiology of molecular probes in Xpert MTB/RIF assay in Khyber Pakhtunkhwa, Pakistan.

Regardless of a plethora of advanced diagnostics, TB and drug resistance remains a principal killer. We proposed gold nanoparticles (AuNPs) attached with probes to enhance the efficiency of GeneXpert MTB/RIF assay instead of conventional dye probes for molecular detection. A total of 15,000 samples were collected from TB suspects and subjected to Xpert MTB/RIF assay, where 6800 (45.3%) were detected as MTB positive, 280 (4.3%) were detected to harbor mutations in the RRDR, while invalid /errors were found in 690 (4.6%) cases. The mutations were detected by probe E, 199 (71.1%), while probes B and D, 30 and 26 (10% and 9%), respectively. In the Xpert MTB/RIF Assay were found mutations picked by probes E and B codons 529-533 (71%) and 512-518 (10%), respectively. The fast-rising works of TB nano-diagnostics, of Xpert probes, may improve by the applications of gold nanoparticle probes.

An in vitro antiviral activity of iodine complexes against SARS-CoV-2.

Since the emergence of COVID-19 pandemic in China in late 2019, scientists are striving hard to explore non-toxic, viable anti-SARS-CoV-2 compounds or medicines. We determined In vitro anti-SARS-CoV-2 activity of oral formulations (syrup and capsule)of an Iodine-complex (Renessans). First, cell cytotoxicity of Renessans on the Vero cells was determined using MTT assay. Afterwards, the antiviral activity of Renessans was determined using viral inhibition assays and TCID50. For this, nontoxic concentrations of the Renessans were used. The results showed that Renessans is nontoxic to the cells up to 50 µg/mL. At 1.5 µg/mL concentration, SARS-CoV-2 production was significantly reduced to 101.43 TCID50 and 101.58 TCID50 for the syrup and capsule, respectively, as compare to virus infected control cells 106.08 TCID50 and we found the dose dependent inhibition of virus replication in the presence of Renessans. Renessans inhibited SARS-CoV-2 with an EC50 value of 0.425 µg/mL and 0.505 µg/mL for syrup and capsule, respectively. Furthermore, there was no virus detected at concentration of 50 µg/mL of Renessans. This study indicates that Renessans, containing iodine, have potential activity against SARS-CoV-2 which needs to be further investigated in human clinical trials.

Structures of SARS-CoV-2 RNA-Binding Proteins and Therapeutic Targets.

BACKGROUND: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) epidemic has resulted in thousands of infections and deaths worldwide. Several therapies are currently undergoing clinical trials for the treatment of SARS-CoV-2 infection. However, the development of new drugs and the repositioning of existing drugs can only be achieved after the identification of potential therapeutic targets within structures, as this strategy provides the most precise solution for developing treatments for sudden epidemic infectious diseases. SUMMARY: In the current investigation, crystal and cryo-electron microscopy structures encoded by the SARS-CoV-2 genome were systematically examined for the identification of potential drug targets. These structures include nonstructural proteins (Nsp-9; Nsp-12; and Nsp-15), nucleocapsid (N) proteins, and the main protease (Mpro). Key Message: The structural information reveals the presence of many potential alternative therapeutic targets, primarily involved in interaction between N protein and Nsp3, forming replication-transcription complexes (RTCs) which might be a potential drug target for effective control of current SARS-CoV-2 pandemic. RTCs consist of 16 nonstructural proteins (Nsp1-16) that play the most essential role in the synthesis of viral RNA. Targeting the physical linkage between the envelope and single-stranded positive RNA, a process facilitated by matrix proteins may provide a good alternative strategy. Our current study provides useful information for the development of new lead compounds against SARS-CoV-2 infections.

Mitochondrial phylogenetic and diversity analysis in Azi-Kheli buffalo.

NOVELTY STATEMENT: The present study was conducted for the first time in Pakistan to investigate Cytochrome C Oxidase Subunit 1 (CO1) gene and full-length Displacement Loop (D-loop) region of mitochondrial DNA in Azi-Kheli buffalo breed native to northern hilly areas of Khyber Pakhtunkhwa Province of Pakistan. The present study was designed to investigate phylogeny and diversity in Azi-Kheli buffalo, through two mitochondrial DNA regions, i.e., Cytochrome C Oxidase Subunit-I (CO1) and Displacement Loop (D-loop) region. Thirty (30) blood samples were taken from Azi-Kheli pure breed animals from original breeding tract, i.e., Khwazakhela, Swat. Polymerase chain reactions using gene-specific primers were carried out for amplifying 709-bp region of CO1 gene and 1159-bp region of D-Loop for identification, phylogeny, and diversity in Azi-Kheli buffalo, respectively. The sequences of CO1 gene revealed four (04) haplotypes, whereas D-loop sequences revealed five (05) haplotypes. Mean interspecific diversity with related species was 2.56%, and mean intraspecific diversity within Azi-Kheli buffalo was 0.25%, estimated via Kimura-2 parameter. Phylogenetic tree (maximum likelihood) revealed clustering of Azi-Kheli haplotypes with river buffalo and is distinct from swamp buffalo and other related species of genus Bubalus. Mean haplotype and nucleotide diversity of D-loop were Hd = 0.9601 ± SD = 0.096 and π = 0.01208 ± SD = 0.00182, respectively. Phylogenetic tree (neighbor-joining) revealed two main clades, i.e., river buffalo and swamp buffalo clade. The haplotypes of Azi-Kheli clustered with haplotypes of different river buffalo breeds at different positions. The current study suggests that Azi-Kheli has common origin with other river buffalo breeds; hence, it is river buffalo which harbors high genetic diversity.

Gene expression profiling of reactive oxygen species (ROS) and antioxidant defense system following Sugarcane mosaic virus (SCMV) infection.

BACKGROUND: Viruses are infectious pathogens, and plant virus epidemics can have devastating consequences to crop yield and quality. Sugarcane mosaic virus (SCMV, belonging to family Potyviridae) is one of the leading pathogens that affect the sugarcane crop every year. To combat the pathogens' attack, plants generate reactive oxygen species (ROS) as the first line of defense whose sophisticated balance is achieved through well-organized antioxidant scavenging pathways. RESULTS: In this study, we investigated the changes occurring at the transcriptomic level of ROS associated and ROS detoxification pathways of SCMV resistant (B-48) and susceptible (Badila) sugarcane genotypes, using Saccharum spontaneum L. genome assembly as a reference genome. Transcriptomic data highlighted the significant upregulation of ROS producing genes such as NADH oxidase, malate dehydrogenase and flavin-binding monooxygenase, in Badila genotype after SCMV pathogenicity. To scavenge the ROS, the Badila genotype illustrated a substantial enhancement of antioxidants i.e. glutathione s-transferase (GST), as compared to its resistant counterpart. GST is supposed to be a key indicator of pathogen attacks on the plant. A remarkably lower GST expression in B-48, as compared to Badila, indicated the development of resistance in this genotype. Additionally, we characterized the critical transcription factors (TFs) involved in endowing resistance to B-48. Among these, WRKY, AP2, NAC, bZIP, and bHLH showed enhanced expression in the B-48 genotype. Our results also confirmed the linkage of transcriptomic data with the enzymatic and qPCR data. The estimation of enzymatic activities for superoxide dismutase, catalase, ascorbate peroxidase, and phenylalanine ammonia-lyase supported the transcriptomic data and evinced higher resistance in B-48 genotype. CONCLUSION: The current study supported the efficiency of the B-48 genotype under SCMV infection. Moreover, comparative transcriptomic data has been presented to highlight the role of significant transcription factors conferring resistance to this genotype. This study provides an in-depth knowledge of the expression profiling of defense mechanisms in sugarcane.

Characterization and synthetic biology of lipase from Bacillus amyloliquefaciens strain.

Lipases with high tolerance to temperature play a significant role in industry from food manufacturing to waste management systems. Thus, there is a need to investigate these enzymes from different geographical areas to look out for a more thermo-stable one. Characterization of lipases through experimental approaches is time consuming process and sometimes the results are ambiguous due to errors. However, integration of computational technologies is quite useful for prediction of optimized conditions. Such technologies can be applied as synthetic biology, which has many major applications in engineered biological approaches for accurate prediction of effects of different physical and chemical parameters on the system. In this study, cloning and expression of a lipase gene from Bacillus amyloliquefaciens, isolated from a novel geographical region of Pakistan, in Escherichia coli DH5α cells followed by sequencing was carried out. To isolate thermostable lipase producing strains, all the samples were kept at 50 °C. Genomic DNA was isolated and signal peptide (1-32 residues) sequence was chopped (ΔSPLipase). The ΔSPLipase was amplified and expressed in Linearized p15TV-L vector. The purified lipase appeared as single band of approximately 26 kDa. Suitable conditions of factors required for maximum lipase activity such as temperature, pH, substrate, organic solvent, detergents and metal ions were predicted through synthetic biology approach and further confirmed in wet lab. The predicted suitable factors for enzyme were almost similar to those determined experimentally. The optimum enzyme activity was recorded at pH 8 and 50 °C temperature. Interestingly, the activity of enzyme was found on a number of solvents, metal ions, detergents, and surfactants. The predicted optimum values and their experimental confirmations highlights the importance of integrated synthetic biology approaches in wet lab experiments. The characterized lipase of B. amyloliquefaciens at molecular level from Pakistani strains displayed good activity on a range of factors that implies this strain to be used for application in industrial level production.