Role of Genetics, Genomics, and Breeding Approaches to Combat Stripe Rust of Wheat

Puccinia striiformis (Pst) is a devastating biotrophic fungal pathogen that causes wheat stripe rust. It usually loves cool and moist places and can cause 100% crop yield losses in a single field when ideal conditions for disease incidence prevails. Billions of dollars are lost due to fungicide application to reduce stripe rust damage worldwide. Pst is a macrocyclic, heteroecious fungus that requires primary (wheat or grasses) as well as secondary host (Berberis or Mahonia spp.) for completion of life cycle. In this review, we have summarized the knowledge about pathogen life cycle, genes responsible for stripe rust resistance, and susceptibility in wheat. In the end, we discussed the importance of conventional and modern breeding tools for the development of Pst-resistant wheat varieties. According to our findings, genetic engineering and genome editing are less explored tools for the development of Pst-resistant wheat varieties; hence, we highlighted the putative use of advanced genome-modifying tools, i.e., base editing and prime editing, for the development of Pst-resistant wheat.

Hemoglobin, Ferritin levels and RBC Indices among children entering school and study of their correlation with one another

OBJECTIVE

To study correlation of various complete blood count variables with one another and to ascertain the values of intercept and slope among those having strong correlation.

METHODS

The cross-sectional study was conducted in Marach 2017 in the Rabwah town of Punjab province in Pakistan, and comprised randomly selected one in four children studying under the Nazrat Taleem School System. Serum sample from each subject was used to analyse complete blood count on an automated analyser, and ferritin levels were checked by enzyme-linked immunosorbent assay. SPSS20 was used for data analysis.

RESULTS

There were 299 children with a median age of 67 months. Mean haemoglobin level was 12.09±0.82gm/dl. There was a very strong positive correlation between haemoglobin and haematocrit; mean corpuscular volume; and red cell distribution width; mean corpuscular volume and mean corpuscular haemoglobin; red cell distribution width and mean corpuscular haemoglobin (p<0.001).Moderate positive correlation was found between haemoglobin and red blood cell count; haematocrit and red blood cell count; mean corpuscular haemoglobin and mean corpuscular haemoglobin concentration (p<0.05). Moderate negative correlation was present between red blood cell count and mean corpuscular volume; red blood cell count and red cell distribution width; red blood cell count and mean corpuscular haemoglobin (p<0.05).

CONCLUSIONS

There were strong to moderate correlation between various complete blood count variables in the studied population. Ferritin level was the only variable which did not have any correlation with any of the other variables.

Identification of Novel Phyto-chemicals from Ocimum basilicum for the Treatment of Parkinson's Disease using In Silico Approach

BACKGROUND

Parkinson's disease is characterized by decreased level of dopaminergic neurotransmitters and this decrease is due to the degradation of dopamine by protein Monoamine Oxidase B (MAO-B). In order to treat Parkinson's disease, MAO-B should be inhibited.

OBJECTIVE

To find out the novel phytochemicals from plant Ocimum basilicum that can inhibit MAO-B by using the in silico methods.

METHODS

The data of chemical constituents from plant Ocimum basilicum was collected and inhibitory activity of these phytochemicals was then predicted by using the Structure-Based (SB) and Ligand-Based Virtual Screening (LBVS) methods. Molecular docking, one of the common Structure-Based Virtual Screening method, has been used during this search. Traditionally, molecular docking is used to predict the orientation and binding affinity of the ligand within the active site of the protein. Molegro Virtual Docker (MVD) software has been used for this purpose. On the other hand, Random Forest Model, one of the LBVS method, has also been used to predict the activity of these chemical constituents of Ocimum basilicum against the MAO-B.

RESULTS

During the docking studies, all the 108 compounds found in Ocimum basilicum were docked within the active site of MAO-B (PDB code: 4A79) out of which, 57 compounds successfully formed the hydrogen bond with tyr 435, a crucial amino acid for the biological activity of the enzyme. Rutin (-182.976 Kcal/mol), Luteolin (-163.171 Kcal/mol), Eriodictyol-7-O-glucoside (- 160.13 Kcal/mol), Rosmarinic acid (-133.484 Kcal/mol) and Isoquercitrin (-131.493 Kcal/mol) are among the top hits with the highest MolDock score along with hydrogen interaction with tyr 435. Using the RF model, ten compounds out of 108 chemical constituent of Ocimum basilicum were predicted to be active, Apigenin (1.0), Eriodictyol (1.0), Orientin (0.876), Kaempferol (0.8536), Luteolin (0.813953) and Rosmarinic-Acid (0.7738095) are predicted to be most active with the highest RF score.

CONCLUSION

The comparison of the two screening methods show that the ten compounds that were predicted to be active by the RF model, are also found in top hits of docking studies with the highest score. The top hits obtained during this study are predicted to be the inhibitor of MAO-B, thus, could be used further for the development of drugs for the treatment of Parkinson's disease (PD).

The level of Cry1Ac endotoxin and its efficacy against H. armigera in Bt cotton at large scale in Pakistan

A biophysical survey was conducted in 15 cotton-growing districts of Pakistan. Four hundred cotton growers were approached and inquired about the production technology of Bt cotton. Further, 25 strip tests using combo strips (Cry1Ac, Cry2Ab, Vip3Aa and Cp4, EPSPS gene) were performed at each farmer’s field. Out of 10,000 total-tested samples, farmers claimed 9682 samples as Bt and 318 samples as non-Bt. After performing a strip test, 1009 and 87 samples were found false negative and false positive, respectively. Only 53 samples were found positive for Cry2Ab, 214 for EPSPS and none for Vip3Aa gene. Quantification of Cry endotoxin and bioassay studies were performed by taking leaves from upper, middle, and lower canopies, and fruiting parts at approximately 80 days after sowing from 89 varieties. Expression was highly variable among different canopies and fruiting parts. Moreover, Cry endotoxin expression and insect mortality varied significantly among varieties from 0.26 µg g⁻¹ to 3.54 µg g⁻¹ with mortality ranging from 28 to 97%, respectively. Highest Cry1Ac expression (3.54 µg g⁻¹) and insect mortality (97%) were observed for variety FH-142 from DG Khan. Cry endotoxin expression varied significantly across various plant parts, i.e., IUB-13 variety from upper canopy documented 0.34 µg g⁻¹ expression with 37% insect mortality in Layyah to 3.42 µg g⁻¹ expression and 96% insect mortality from DG Khan. Lethal dose, LD95 (2.20 µg g⁻¹) of Cry1Ac endotoxin was optimized for effective control of H. armigera. Our results provided evidence of practical resistance in H. armigera and way forward.

NK Cells Negatively Regulate CD8 T Cells to Promote Immune Exhaustion and Chronic Toxoplasma gondii Infection

NK cells regulate CD4+ and CD8+ T cells in acute viral infection, vaccination, and the tumor microenvironment. NK cells also become exhausted in chronic activation settings. The mechanisms causing these ILC responses and their impact on adaptive immunity are unclear. CD8+ T cell exhaustion develops during chronic Toxoplasma gondii (T. gondii) infection resulting in parasite reactivation and death. How chronic T. gondii infection impacts the NK cell compartment is not known. We demonstrate that NK cells do not exhibit hallmarks of exhaustion. Their numbers are stable and they do not express high PD1 or LAG3. NK cell depletion with anti-NK1.1 is therapeutic and rescues chronic T. gondii infected mice from CD8+ T cell exhaustion dependent death, increases survival after lethal secondary challenge and alters cyst burdens in brain. Anti-NK1.1 treatment increased polyfunctional CD8+ T cell responses in spleen and brain and reduced CD8+ T cell apoptosis in spleen. Chronic T. gondii infection promotes the development of a modified NK cell compartment, which does not exhibit normal NK cell characteristics. NK cells are Ly49 and TRAIL negative and are enriched for expression of CD94/NKG2A and KLRG1. These NK cells are found in both spleen and brain. They do not produce IFNγ, are IL-10 negative, do not increase PDL1 expression, but do increase CD107a on their surface. Based on the NK cell receptor phenotype we observed NKp46 and CD94-NKG2A cognate ligands were measured. Activating NKp46 (NCR1-ligand) ligand increased and NKG2A ligand Qa-1b expression was reduced on CD8+ T cells. Blockade of NKp46 rescued the chronically infected mice from death and reduced the number of NKG2A+ cells. Immunization with a single dose non-persistent 100% protective T. gondii vaccination did not induce this cell population in the spleen, suggesting persistent infection is essential for their development. We hypothesize chronic T. gondii infection induces an NKp46 dependent modified NK cell population that reduces functional CD8+ T cells to promote persistent parasite infection in the brain. NK cell targeted therapies could enhance immunity in people with chronic infections, chronic inflammation and cancer.

Molecular docking analyses of CYP450 monooxygenases of Tribolium castaneum (Herbst) reveal synergism of quercetin with paraoxon and tetraethyl pyrophosphate: in vivo and in silico studies

Pest management in stored grain industry is a global issue due to the development of insecticide resistance in stored grain insect pests. Excessive use of insecticides at higher doses poses a serious threat of food contamination and residual toxicity for grain consumers. Since the development of new pesticide incurs heavy costs, identifying an effective synergist can provide a ready and economical tool for controlling resistant pest populations. Therefore, the synergistic property of quercetin with paraoxon and tetraethyl pyrophosphate has been evaluated against the larvae and adults of Tribolium castaneum (Herbst). Comparative molecular docking analyses were carried out to further identify the possible mechanism of synergism. It was observed that quercetin has no insecticidal when applied at the rate of 1.5 and 3.0 mg/g; however, a considerable synergism was observed when applied in combination with paraoxon. The comparative molecular docking analyses of CYP450 monooxygenase (CYP15A1, CYP6BR1, CYP6BK2, CYP6BK3) family were performed with quercetin, paraoxon and tetraethyl pyrophosphate which revealed considerable molecular interactions, predicting the inhibition of CYP450 isoenzyme by all three ligands. The study concludes that quercetin may be an effective synergist for organophosphate pesticides depending upon the dose and type of the compound. In addition, in silico analyses of the structurally diversified organophosphates can effectively differentiate the organophosphates which are synergistic with quercetin.

Ligand based screening of chemical constituents from African medicinal plants for the identification of MAOB inhibitors

Ligand based virtual screening (LBVS) is based on the hypothesis that similar structures have similar biological functions. In this research paper, ligand based virtual screening has been performed in order to predict the inhibitors for monoamine oxidase (MAO-B), an enzyme specifically involved in the metabolism of non-hydroxylated amines such as benzylamine and beta-phenylethylamine (PEA), thus, could be the target to treat various neurodegenerative disorders like Parkinson's disease. For this purpose, Afro Database, a subset of ZINC natural compound database has been screened using Random Forest Modeling (RF). For the training of RF model, 36 reference molecules, the known inhibitors of MAO have been collected from Duke's phyto-chemical and ethno-botanical database. As an outcome of this screening, 31 compounds out of 968 compounds from Afro Database (compounds from African medicinal plants) are predicted to be active as MAO-B inhibitor, Out of the 31 predicted active compounds, Norlichexanthone (ZINC05765089) is predicted to be most active against MAO-B with highest RF score 0.795181, along with the other top hits, could be the putative drug candidates for the prevention/ treatment of Parkinson's disease.

MOLECULAR CHARACTERIZATION OF ASIAN CITRUS PSYLLID (Diaphorina citri) USING MITOCHONDRIAL CYTOCHROME OXIDASE 1 (MTCO1) GENE FROM PUNJAB PAKISTAN

Citrus greening caused by (Candidatus liberibacter spp.) is one of the most destructive bacterial disease of citrus all over the world and it is transmitted by grafting and psyllid (Diaphorina citri) is responsible for its spread. This study was aimed to detect the prevalence of CLas in different varieties of citrus in Pakistan and molecular characterization of mtco1 gene in Diaphorina citri. DNA was extracted from fourteen different citrus cultivars infected with citrus greening from different orchards of Sargodha Punjab, Pakistan. Specific primers were used to amplify (Mtco1 gene) in Diaphorina citri and also Las specific primers were also used to detect HLB pathogen. Amplified fragments of 507bp, 1500bp and 2500bp were observed in CLas and Mtco1 gene of Asian isolates. The resulted fragments were TA cloned and sequenced from both strands. The infectious bacterium was found in 3 samples out of 14 (21.5 %) while from psyllid it was found in 5 samples (37.5%). The weather changes effect the prevalence of CLas in citrus but usually it decrease during autumn and found Las positive vector in spring or summer season up to 42oC. So there is a need to research on management of citrus greening disease in Pakistan as it caused major yield loses

Community-based integrated approach to changing women's family planning behaviour in Pakistan, 2014-2016

Setting: Karachi, Pakistan. Objective: To assess the effectiveness of a community-based integrated approach in changing women's behaviour regarding contraceptive use. Design: The Sukh Initiative is a multipronged approach with door-to-door services using community health workers to provide quality family planning/reproductive health services at both public and private facilities and a 24/7 family planning helpline service that provides youth skill-based education. Methods: Retrospective pre- and post-intervention data using samples of 5140 and 3810 women, respectively. Results: The contraceptive prevalence rate increased by 10.7%, from 42.3% at baseline to 53.0% mid-intervention, with an increase in use of modern contraceptive methods of 9.2%. A significant association was found between door-to-door counselling and the use of contraceptive methods (OR 3.4, 95%CL 2.9-4.1) and access to public and private facilities for modern contraceptives (OR 2.4, 95%CL 2.0-3.0). However, support group meetings and 24/7 helpline use did not show any association with use of contraceptive method. Conclusion: The study helped to increase access to and choice of family planning services through a community-based approach that successfully reduced unmet needs and improved continuity in contraceptive use.

Did diabetes mellitus affect treatment outcome in drug-resistant tuberculosis patients in Pakistan from 2010 to 2014?

Settings: All hospitals managing drug-resistant tuberculosis (DR-TB) according to national guidelines in Pakistan. Objectives: To assess the effect of diabetes mellitus (DM) and factors associated with unfavourable outcomes in DR-TB. Methods: A cross-sectional study based on a retrospective record review of patients enrolled on DR-TB treatment from 2010 to 2014 in Pakistan. DR-TB data reported to Pakistan's National TB Control Programme on a monthly basis were used for the study. Result: Among 5811 patients enrolled on second-line drugs, 8.8% had DM. Overall, 68.9% had favourable outcomes. No association was found between DM and DR-TB treatment outcomes (risk ratio 0.90, 95%CI 0.74-1.05). Unfavourable outcomes were more frequent among DR-TB patients with human immunodeficiency virus (HIV) co-infection (OR 11.58, 95%CI 2.20-60.72), extensively drug-resistant TB patients (OR 5.36, 95%CI 1.00-28.72), patients with exposure to both first-line and second-line anti-tuberculosis drugs (OR 2.45, 95%CI 1.21-4.97) and those with a previous history of treatment in the private sector (OR 1.53, 95%CI 1.16-2.02). Conclusion: Although there were limitations to correctly measuring DM and its management, DM appears not to be a risk factor for unfavourable outcomes in DR-TB patients in our study. DR-TB and HIV co-infection, second-line drug resistance and history of treatment in the private sector were nevertheless more frequently associated with adverse outcomes.

Gastric specimens for diagnosing tuberculosis in adults unable to expectorate in Rawalpindi, Pakistan

Setting: Adult pulmonary tuberculosis (TB) patients unable to expectorate quality sputum represent a diagnostic challenge. A private hospital in Pakistan routinely performs gastric aspiration in adults with difficulties expectorating. Objective: To assess the usefulness of gastric specimens (GS) in diagnosing pulmonary TB (PTB) and drug-resistant TB in adult presumptive TB patients unable to expectorate, and to compare the diagnostic yield and sensitivity of smear, culture and the Xpert^® MTB/RIF assay. Design: This was a comparative cross-sectional study based on retrospective record review. Results: Of 900, 885 and 877 GS tested by smear, Xpert and culture, respectively, interpretable results were obtained for respectively 900 (100%), 859 (97.1%) and 754 (86.0%), with a diagnostic yield of respectively 23.6%, 30.3% and 24.9%. The yield was significantly higher for Xpert in previously treated patients. There were 313 patients with definite TB, defined as positive on Xpert and/or culture. The 82.8% sensitivity of Xpert was significantly higher than that of smear (61.0%) and culture (67.8%). Conclusion: GS obtained by aspiration under routine programme conditions is useful for detecting TB and drug-resistant TB in adult patients unable to expectorate. Xpert, with its rapid testing, high proportion of interpretable results and better sensitivity, can substantially improve the diagnosis of bacteriologically confirmed TB and rifampicin resistance.

Alarming rates of attrition among tuberculosis patients in public-private facilities in Lahore, Pakistan

Setting: All public-private mix (PPM) facilities caring for tuberculosis (TB) patients in Lahore city, Pakistan, under four models: PPM1 (general practitioners), PPM2 (non-governmental organisations), PPM3 (private hospitals) and PPM4 (others). Objective: To assess the pre-treatment loss to follow-up (LTFU), defined as patients documented in the laboratory registers but not in the treatment registers of any PPM facility, among sputum smear-positive TB patients diagnosed during January-March 2015, and unfavourable treatment outcomes among patients registered for treatment and associated factors. Design: This was a retrospective cohort study reviewing existing programme records. Poisson regression was used to identify factors associated with outcomes. Results: Of 2473 patients diagnosed, 1590 (64%) were lost to follow-up before treatment. This was higher among males (68%) and the elderly (79%), and lower among 'high positives' (smear grading 2+ or 3+, 53%) and in the PPM1 model (34%). Of 883 patients started on treatment, 165 (19%) had unfavourable outcomes: 8% LTFU, 5% treatment failure, 3% died and 3% not evaluated. Previously treated patients (34%) and children (44%) had the worst outcomes. Conclusion: Pre-treatment LTFU was alarmingly high and requires urgent attention, including the development and institution of mechanisms for patient tracking using information and mobile phone technology, and making TB notification mandatory in the private sector.

Infection control in hospitals managing drug-resistant tuberculosis in Pakistan: how are we doing?

Setting: Ten hospitals managing drug-resistant tuberculosis (TB) in Pakistan. Objective: To assess the implementation of TB infection control (IC) practices and reasons for non-adherence to guidelines. Design: This was a descriptive study conducted between April and October 2016 with three components: 1) non-participant observation of service delivery areas (SDAs) (n = 82) in hospitals (n = 10) using structured checklists; 2) exit interviews with 100 patients (10 per hospital); and 3) interviews with 100 health-care workers (HCWs, 10/hospital). Results: Of the 82 SDAs, posters were displayed in 34 (41%), mechanical ventilation was implemented in 79% and functional ultraviolet germicidal irradiation (UVGI) was available in only 26%. Patient interviews showed 50-65% adherence to triage and use of personal protective measures. Key reasons for non-adherence were lack of adequate supplies, discomfort using N-95 masks, a lack of knowledge or training, perceived non-cooperation by patients, poor maintenance of mechanical ventilators and UVGI due to unstable electricity supply, a lack of clarity in roles (no-one designated in charge) and staff shortages and subsequent workloads. Adherence to natural ventilation usage was poor for reasons related to climate and privacy. Conclusion: Implementation of TBIC measures in hospitals was suboptimal. Urgent measures need to be put in place, including retraining of HCWs, addressing weaknesses in mask and poster supplies and constant supervision and monitoring.

Pre-treatment loss to follow-up among smear-positive TB patients in tertiary hospitals, Quetta, Pakistan

Setting: Three public sector tertiary care hospitals in Quetta, Balochistan, Pakistan, with anecdotal evidence of gaps between the diagnosis and treatment of patients with tuberculosis (TB). Objectives: To assess the proportion of pre-treatment loss to follow-up (LTFU), defined as no documented evidence of treatment initiation or referral in TB registers, among smear-positive pulmonary TB patients diagnosed in 2015, and the associated sociodemographic factors. Design: A retrospective cohort study involving the review of laboratory and TB registers. Results: Of 1110 smear-positive TB patients diagnosed (58% female, median age 40 years, 5% from outside the province or the country), 235 (21.2%) were lost to follow-up before starting treatment. Pre-treatment LTFU was higher among males; in patients residing far away, in rural areas, outside the province or the country; and in those without a mobile phone number. Conclusion: About one fifth of the smear-positive TB patients were lost to follow-up before starting treatment. Strengthening the referral and feedback mechanisms and using information technology to improve the tracing of patients is urgently required. Further qualitative research is needed to understand the reasons for pre-treatment LTFU from the patient's perspective.

Comparative Analysis of Conventional Natural Killer Cell Responses to Acute Infection with Toxoplasma gondii Strains of Different Virulence

Conventional natural killer (cNK) cells, members of group 1 innate lymphoid cells, are a diverse cell subpopulation based on surface receptor expression, maturation, and functional potential. cNK cells are critical for early immunity to Toxoplasma gondii via IFNγ production. Acute cNK cell responses to infection with different strains of T. gondii have not yet been characterized in detail. Here, we comprehensively performed this analysis with Type I virulent RH, Type II avirulent ME49, and fully attenuated Type I cps1-1 strains. In response to these three parasite strains, murine cNK cells produce IFNγ and become cytotoxic and polyfunctional (IFNγ+CD107a+) at the site of infection. In contrast to virulent RH and avirulent ME49 T. gondii strains, attenuated cps1-1 induced only local cNK cell responses. Infections with RH and ME49 parasites significantly decreased cNK cell frequency and numbers in spleen 5 days post infection compared with cps1-1 parasites. cNK cell subsets expressing activating receptors Ly49H, Ly49D, and NKG2D and inhibitory receptors Ly49I and CD94/NKG2A were similar when compared between the strains and at 5 days post infection. cNK cells were not proliferating (Ki67−) 5 days post infection with any of the strains. cNK cell maturation as measured by CD27, CD11b, and KLRG1 was affected after infection with different parasite strains. RH and ME49 infection significantly reduced mature cNK cell frequency and increased immature cNK cell populations compared with cps1-1 infection. Interestingly, KLRG1 was highly expressed on immature cNK cells after RH infection. After RH and ME49 infections, CD69+ cNK cells in spleen were present at higher frequency than after cps1-1 infection, which may correlate with loss of the mature cNK cell population. Cytokine multiplex analysis indicated cNK cell responses correlated with peritoneal exudate cell, spleen, and serum proinflammatory cytokine levels, including IL-12. qPCR analysis of parasite-specific B1 gene revealed that parasite burdens may affect cNK cell responses. This study demonstrates infection with RH and ME49 parasites impacts cNK cell maturation during acute T. gondii infection. Different cNK cell responses could impact early immunity and susceptibility to these strains.

Ledipasvir and sofosbuvir for treatment of post- renal transplant hepatitis C infection: A case report with review of literature

Liver disease due to hepatitis C infection in renal transplant recipients is difficult to treat and often associated with reduced patient survival. A 43-year-old male, a renal allograft recipient, presented at 6 years follow-up with significant weight loss over 3 months. He was detected to have new onset diabetes mellitus together with hepatitis C virus (HCV) infection (genotype 1). His HCV load remained high despite the change of immuno-suppression from tacrolimus to cyclosporine. A decision to treat with a new anti-viral combination of ledipasvir and sofosbuvir for 12 weeks was taken. Within 3 weeks, his raised serum transaminases levels normalized and viral load became undetectable. At the end of 16 weeks, he continues to do well with normal renal function, has sustained remission from hepatitis C infection and resolution of diabetes.

Success of active tuberculosis case detection among high-risk groups in urban slums in Pakistan

BACKGROUND

In Pakistan, patients with symptoms suggestive of tuberculosis (TB) seek care from a wide array of health care providers, many of whom do not notify cases to the National TB Programme (NTP).

SETTING

We evaluated an active case detection intervention in five randomly selected districts in urban slums of Sindh Province, Pakistan.

OBJECTIVE

To evaluate the increase in case notification of smear-positive TB by active case finding at community-based chest camps by engaging the private providers.

DESIGN

A cross-sectional study of TB case detection associated with a project using integrated intervention and chest camps.

RESULTS

From April 2011 to September 2012, the total number of clients seen in the camps was 165 280. Of all the attendees, 13 481 (12.7%) were examined by sputum smear microscopy. The proportion of smear-positive results was significantly higher among those from engaged private providers than among those referred from camps (OR 1.54, 95%CI 1.42-1.66). During the project, the total number of smear-positive TB notifications increased over the intervention period from 5158 to 8275.

CONCLUSION

Active case detection by engaging private providers and chest camps can significantly increase the number of smear-positive TB case notifications.