Role of Arbuscular Mycorrhizal Fungi in Regulating Growth, Enhancing Productivity, and Potentially Influencing Ecosystems under Abiotic and Biotic Stresses.

Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with the roots of nearly all land-dwelling plants, increasing growth and productivity, especially during abiotic stress. AMF improves plant development by improving nutrient acquisition, such as phosphorus, water, and mineral uptake. AMF improves plant tolerance and resilience to abiotic stressors such as drought, salt, and heavy metal toxicity. These benefits come from the arbuscular mycorrhizal interface, which lets fungal and plant partners exchange nutrients, signalling molecules, and protective chemical compounds. Plants' antioxidant defence systems, osmotic adjustment, and hormone regulation are also affected by AMF infestation. These responses promote plant performance, photosynthetic efficiency, and biomass production in abiotic stress conditions. As a result of its positive effects on soil structure, nutrient cycling, and carbon sequestration, AMF contributes to the maintenance of resilient ecosystems. The effects of AMFs on plant growth and ecological stability are species- and environment-specific. AMF's growth-regulating, productivity-enhancing role in abiotic stress alleviation under abiotic stress is reviewed. More research is needed to understand the molecular mechanisms that drive AMF-plant interactions and their responses to abiotic stresses. AMF triggers plants' morphological, physiological, and molecular responses to abiotic stress. Water and nutrient acquisition, plant development, and abiotic stress tolerance are improved by arbuscular mycorrhizal symbiosis. In plants, AMF colonization modulates antioxidant defense mechanisms, osmotic adjustment, and hormonal regulation. These responses promote plant performance, photosynthetic efficiency, and biomass production in abiotic stress circumstances. AMF-mediated effects are also enhanced by essential oils (EOs), superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), hydrogen peroxide (H2O2), malondialdehyde (MDA), and phosphorus (P). Understanding how AMF increases plant adaptation and reduces abiotic stress will help sustain agriculture, ecosystem management, and climate change mitigation. Arbuscular mycorrhizal fungi (AMF) have gained prominence in agriculture due to their multifaceted roles in promoting plant health and productivity. This review delves into how AMF influences plant growth and nutrient absorption, especially under challenging environmental conditions. We further explore the extent to which AMF bolsters plant resilience and growth during stress.

A 10 year service evaluation of the survival of 439 patients with early oestrogen receptor positive breast cancer who underwent initial OncotypeDX ® testing to guide adjuvant chemotherapy decisions.

OBJECTIVE: To explore the long-term outcome of patients who underwent Oncotype DX® testing. The relationship between the RS, adjuvant treatments received, and clinical outcomes across the entire range of RS results are reported. METHODS: 10-year Kaplan-Meier estimates for distant recurrence/BC-specific survival (BCSS) in this cohort. The analysis included 439 patients. The follow-up time ranged from 14 to 142 months. All analyses were performed using the SPSS v20. RESULTS: More than half of patients had low RS (<18) (55.6%) and 15.3% had RS ≥ 31. Chemotherapy use was consistent with the RS with 4.4%, 7.1%, 28.0%, 71.4% and 91.0% receiving adjuvant chemotherapy in patients with RS < 11, 11-17, 18-25, 26-30, and ≥31, respectively. The overall chemotherapy rate was 27.6%. Distant metastasis free survival (DMFS) differed significantly (P < 0.001) between the RS groups with 10 year DMFS rates of 99% (SE +/- 0.01) in the RS<11, 97% (SE +/- 0.03) in the RS 11-17, 97% (SE +/- 0.02) in the RS 18-25, 85% (SE +/- 0.1) in the RS 26-30 and 74% (SE +/- 0.08) in the RS ≥ 31 group. Ten year breast cancer specific survival also differed significantly (P < 0.001) between the RS groups; this risk was 100% (no deaths from breast cancer reported in the first 10 years) in RS < 11, 95% (SE +/- 0.03) in RS 11-17, 94% (SE +/- 0.04) in RS 18-25, 93% (SE +/- 0.07) in RS 26-30, and 79% (SE +/- 0.07) in the RS ≥ 31 group. CONCLUSIONS: Use of Oncotype DX RS does guide the treatment decisions and correlates with the BCSS and disease-free survival for ER positive, Her2 negative, early-stage, node negative breast cancer patients.

Geriatric assessment tool application in treatment recommendations for older women with breast cancer.

INTRODUCTION: Treatment of early breast cancer in older women is usually not guideline concordant owing to lack of routine evaluation of their potential frailty. We assessed the feasibility and impact of a self-administered geriatric assessment on the decision-making process in women aged 65 and above treated in a UK District General Hospital. METHODS: One hundred and one patients, aged 65 and above, with early stage, non-metastatic breast cancer were prospectively recruited between Dec-2018 and March-2021. Patients with metastatic breast cancer, a previous history of cancer and dementia were excluded. All patients had a geriatric assessment with a self-administered questionnaire (mycarg.org). All cases were discussed in the multidisciplinary meeting (MDT) and a pre geriatric assessment recommendations was made, based on the tumour grade, size, node status and receptor status. The findings of the assessment were later discussed in a second meeting and a further recommendation was made based on the geriatric assessment. Any change in the proposed treatment was recorded. Potential factors (age, Body Mass Index, co-morbidities, medications, instrumental activities of daily living, and basic activities of daily living, social support and psychological status) associated with a change in the treatment recommendation were compared using Pearson's Chi square tests for categorized data, and Mann Whitney U test for continuous data. A multivariate logistic regression was performed to test the association between geriatric assessment domains and change in treatment decision. The multivariate model was built using variables which were associated in the bivariate analysis with a p-value< 0.20. RESULTS: Patients aged less than 70 years were more likely to be diagnosed through screening programme as compared to older women (64.4% vs. 35.6%, p = 0.001). Self-administered geriatric assessment identified patients who were requiring assistance in their daily routine activities, and hence, were assessed to have higher morbidity status. A third of patients required assistance in their routine activities, with 18/101 patients requiring significant help during self-care. 90% patients were independent for Activity of Daily Living (ADL) at baseline and 34.76% for Instrumental Activity of Daily Living (IADL). Among the 101 patients evaluated, proposed change in the initial cancer treatment plan was made in 21.8% of patients after the second MDT. Omission of chemotherapy was recommended in 4 patients, omission of radiotherapy in 15 patients and omission of both chemo and radiotherapy in 2 patients. One patient was advised to omit Zolidronic acid, as she was noted to have renal impairment. No patient in this cohort had suggestion for omission of surgery or endocrine therapy. In the bivariate analysis, need for assistance for activities of daily living (ADLs), low physical performance (KPS), polypharmacy (3 or more medications), lack of social support as assessed using the Social Support: Medical Outcomes Study (MOS) Social Support Survey and high BMI (30 or more) all showed significance but on multivariate analysis only polypharmacy was significantly associated with change in the initial cancer treatment plan. CONCLUSIONS: The results of this study of breast cancer patients aged 65 and above suggest that a self-administered geriatric assessment may influence treatment recommendations in a subset of patients. Recommendations that were influenced by the geriatric assessment mainly included those related to the significant morbidity that may have impacted the use of chemotherapy and/or radiotherapy.

Automated Breast Volume Assessment Derived From Digital Breast Tomosynthesis Images Compared to Mastectomy Specimen Weight and Its Applications in Cosmetic Optimisation.

BACKGROUND: Estimating the size and volume of the breast preoperatively is an important step in surgical planning for many breast procedures such as immediate implant-based breast reconstructions and reduction mammoplasties. Breast volume estimation helps in appropriate implant selection preoperatively. OBJECTIVES: The aim of this study was to objectively evaluate the estimation of breast weight by automatic volumetric breast assessment in digital breast tomosynthesis (DBT) using Quantra™ 2.2 Breast Density Assessment Software (Hologic Inc., Marlborough, Massachusetts, United States). METHODS: Breast specimen weight after mastectomy and volume estimated by Quantra software were recorded. RESULTS: Volume assessment obtained from Quantra software showed a high correlation with actual mastectomy specimen weight, with Pearson's correlation coefficients of 0.952. CONCLUSIONS: The automated DBT-derived breast volume using the Quantra software is a simple and practical method to assess breast size and weight preoperatively.

Using cryo-EM to understand antimycobacterial resistance in the catalase-peroxidase (KatG) from Mycobacterium tuberculosis.

Resolution advances in cryoelectron microscopy (cryo-EM) now offer the possibility to visualize structural effects of naturally occurring resistance mutations in proteins and also of understanding the binding mechanisms of small drug molecules. In Mycobacterium tuberculosis the multifunctional heme enzyme KatG is indispensable for activation of isoniazid (INH), a first-line pro-drug for treatment of tuberculosis. We present a cryo-EM methodology for structural and functional characterization of KatG and INH resistance variants. The cryo-EM structure of the 161 kDa KatG dimer in the presence of INH is reported to 2.7 Å resolution allowing the observation of potential INH binding sites. In addition, cryo-EM structures of two INH resistance variants, identified from clinical isolates, W107R and T275P, are reported. In combination with electronic absorbance spectroscopy our cryo-EM approach reveals how these resistance variants cause disorder in the heme environment preventing heme uptake and retention, providing insight into INH resistance.

HARP: a database of structural impacts of systematic missense mutations in drug targets of Mycobacterium leprae.

Computational Saturation Mutagenesis is an in-silico approach that employs systematic mutagenesis of each amino acid residue in the protein to all other amino acid types, and predicts changes in thermodynamic stability and affinity to the other subunits/protein counterparts, ligands and nucleic acid molecules. The data thus generated are useful in understanding the functional consequences of mutations in antimicrobial resistance phenotypes. In this study, we applied computational saturation mutagenesis to three important drug-targets in Mycobacterium leprae (M. leprae) for the drugs dapsone, rifampin and ofloxacin namely Dihydropteroate Synthase (DHPS), RNA Polymerase (RNAP) and DNA Gyrase (GYR), respectively. M. leprae causes leprosy and is an obligate intracellular bacillus with limited protein structural information associating mutations with phenotypic resistance outcomes in leprosy. Experimentally solved structures of DHPS, RNAP and GYR of M. leprae are not available in the Protein Data Bank, therefore, we modelled the structures of these proteins using template-based comparative modelling and introduced systematic mutations in each model generating 80,902 mutations and mutant structures for all the three proteins. Impacts of mutations on stability and protein-subunit, protein-ligand and protein-nucleic acid affinities were computed using various in-house developed and other published protein stability and affinity prediction software. A consensus impact was estimated for each mutation using qualitative scoring metrics for physicochemical properties and by a categorical grouping of stability and affinity predictions. We developed a web database named HARP (a database of Hansen's Disease Antimicrobial Resistance Profiles), which is accessible at the URL - https://harp-leprosy.org and provides the details to each of these predictions.

Genomics, Computational Biology and Drug Discovery for Mycobacterial Infections: Fighting the Emergence of Resistance.

Tuberculosis (TB) and leprosy are mycobacterial infections caused by Mycobacterium tuberculosis and Mycobacterium leprae respectively. These diseases continue to be endemic in developing countries where the cost of new medicines presents major challenges. The situation is further exacerbated by the emergence of resistance to many front-line antibiotics. A priority now is to design new antimycobacterials that are not only effective in combatting the diseases but are also less likely to give rise to resistance. In both these respects understanding the structure of drug targets in M. tuberculosis and M. leprae is crucial. In this review we describe structure-guided approaches to understanding the impacts of mutations that give rise to antimycobacterial resistance and the use of this information in the design of new medicines.

Preoperative Ultrasound-guided Core Biopsy of Axillary Nodes for Staging of Clinically Negative Axilla in Breast Cancer Patients - A Pilot Study.

Objective The aim of the current study is to determine the feasibility and accuracy of ultrasound-guided core biopsy for staging the axilla in clinically node-negative patients with invasive breast cancer. Introduction Historically, in breast cancer patients, axillary lymph node dissection was performed to stage axilla. Because of the high morbidity of axillary lymph node dissection, sentinel lymph node biopsy (SLNB) became the standard of care in patients with clinically node-negative breast cancer. However, SLNB is expensive, time consuming, can cause morbidity and can be complicated by seroma formation, sensory nerve injury, lymphedema, etc. Many centers rely on the availability of frozen section on sentinel lymph nodes to avoid a second procedure with the accuracy of procedure ranging from 73 to 96%, however, the availability of frozen section is limited in our part of the world. Pre-operative identification of axillary node positivity in patients with clinically negative nodes by ultrasound imaging of the axilla would allow one-stage axillary clearance and can decrease the need for SLNB from 21% to 70%. The aim of the present study is to determine the accuracy and feasibility of ultrasound-guided core biopsy to stage the axilla in clinically node-negative breast cancer patients, comparing with final histopathology as gold standard. Material & methods This was a non-randomized, prospective interventional study, done at Radiology Department of Aga Khan University Hospital. All patients diagnosed with breast cancer (histologically proven) with clinically negative axilla and ipsilateral positive axillary ultrasound were included. These patients underwent axillary lymph node core biopsy. If the result was negative they were subjected to SLNB. Histopathology result was taken as gold standard. Results The sensitivity of ultrasound-guided core biopsy was 88%, specificity 100%, positive predictive values (PPV) 100%, negative predictive values (NPV) 89.28%, diagnostic accuracy 94%. Conclusion In conclusion, the present study demonstrated high accuracy of ultrasound-guided axillary lymph node core biopsy in breast cancer patients with clinically node-negative axilla. Positive core biopsy results can thus obviate the need for sentinel lymph node biopsy and allow breast surgeons to directly proceed to axillary lymph node dissection.

Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India.

Drug-resistant tuberculosis (TB), one of the leading causes of death worldwide, arises mainly from spontaneous mutations in the genome of Mycobacterium tuberculosis. There is an urgent need to understand the mechanisms by which the mutations confer resistance in order to identify new drug targets and to design new drugs. Previous studies have reported numerous mutations that confer resistance to anti-TB drugs, but there has been little systematic analysis to understand their genetic background and the potential impacts on the drug target stability and/or interactions. Here, we report the analysis of whole-genome sequence data for 98 clinical M. tuberculosis isolates from a city in southern India. The collection was screened for phenotypic resistance and sequenced to mine the genetic mutations conferring resistance to isoniazid and rifampicin. The most frequent mutation among isoniazid and rifampicin isolates was S315T in katG and S450L in rpoB respectively. The impacts of mutations on protein stability, protein-protein interactions and protein-ligand interactions were analysed using both statistical and machine-learning approaches. Drug-resistant mutations were predicted not only to target active sites in an orthosteric manner, but also to act through allosteric mechanisms arising from distant sites, sometimes at the protein-protein interface.

Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery.

Of the more than 190 distinct species of Mycobacterium genus, many are economically and clinically important pathogens of humans or animals. Among those mycobacteria that infect humans, three species namely Mycobacterium tuberculosis (causative agent of tuberculosis), Mycobacterium leprae (causative agent of leprosy) and Mycobacterium abscessus (causative agent of chronic pulmonary infections) pose concern to global public health. Although antibiotics have been successfully developed to combat each of these, the emergence of drug-resistant strains is an increasing challenge for treatment and drug discovery. Here we describe the impact of the rapid expansion of genome sequencing and genome/pathway annotations that have greatly improved the progress of structure-guided drug discovery. We focus on the applications of comparative genomics, metabolomics, evolutionary bioinformatics and structural proteomics to identify potential drug targets. The opportunities and challenges for the design of drugs for M. tuberculosis, M. leprae and M. abscessus to combat resistance are discussed.

Dermatological manifestations of dengue fever.

BACKGROUND: Each year dengue related infections are rising in tropical countries. There is not enough data available on dermatological manifestations of dengue fever. This study was conducted to investigate prevalence and type of dermatological manifestations of dengue fever (DF). Dengue Haemorrhagic Fever (DHF), and Dengue Shock Syndrome (DSS). METHODS: A Prospective study was contacted in Department of Medicine, Shaikh Zayed Hospital, Lahore, from 3rd Oct to 20th Nov 2010. Specific serological tests for DF were done in all 60 patients admitted with suspected diagnosis of DF, DHF or DSS. Forty-eight confirmed cases were evaluated for age, gender, mucocutaneous features and outcome of the disease. RESULTS: Forty-eight out of 60 patients had positive serology for dengue fever. Male to female ratio was 1.09:1. Their ages ranged 5-68 years with a mean of 31.5 +/- 15.2. DF, DHF and DSS were found in 71%, 19% and 10% respectively. Common dermatological presentations were oral mucous membrane congestion (66.67%), generalised morbiliform rash (64.58%) and eye congestion (64.58%). Purpuric spots along with mucous membrane congestion, generalised morbiliform rash and eyes congestion was observed in 20.83%, 12.5% and 6.25% patients respectively. All except one patient improved clinically. One patient died of respiratory distress and haemorrhage on second day of admission. CONCLUSION: Dermatological features are significantly noticeable in dengue fever patients. These may help us in early diagnosis and better management of patients.

Clinical characteristics of patients with dengue fever: report of 48 patients in 2010.

BACKGROUND: Dengue fever is a mosquito born viral disease. It occurs in tropical and sub-tropical areas of the world. Symptoms appear 3-14 days after the infective bite. Mortality can occur in dengue hemorrhagic fever and dengue shock syndrome unless prompt and adequate management is provided. OBJECTIVE: To determine the clinical and epidemiological characteristics along with outcome of patients with dengue fever (DF) dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). DESIGN: Prospective, follow-up study. PLACE AND DURATION OF STUDY: Department of Medicine, Shaikh Zayed Federal Postgraduate Medical Institute, Lahore from 3rd Oct 2010 to 20th Nov 2010. PATIENTS AND METHODS: Specific serological tests for dengue fever were done in all 60 patients admitted with suspected diagnosis of DF, DHF and DSS. Forty-eight confirmed cases were evaluated for age, gender, clinical features and outcome of the disease. RESULTS: Forty-eight out of 60 patients had positive serology for dengue fever. Male to female ratio was 1.09:1. Their ages ranged from 5 years to 68 years with the mean of 31.5 +/- 15.2 years. DF, DHF and DSS were found in 71%, 19% and 10% cases respectively. Common presentations were fever (100%), skin rash (83.33%), myalgia (69.75%), restlessness (66.67%) and rigors and chills (66.67%). All, except one patient improved clinically. One patient died on second day of admission. CONCLUSION: Dengue fever, a viral infection is re-emerging as a serious public health problem. Fever, rash, myalgia with rigors and chills were common presenting features.

Fixed drug eruption and intradermal provocation tests.

OBJECTIVE: To determine the role of Intradermal Provocation (IDP) tests in Fixed Drug Eruption (FDE). STUDY DESIGN: Quasi-experimental study. PLACE AND DURATION OF STUDY: Dermatology Unit, Shaikh Zayed Hospital, Lahore, from August 2004 to July 2006. METHODOLOGY: The tests were performed in 96 patients in two stages. At stage I, suspected drugs were given intradermally. Changes at injection site in FDE lesions or any systemic effects were observed. In patients showing no response to IDP, Oral Provocation (OP) was performed (stage II) and its effects in FDE lesions or any systemic effect were observed. The positive response of FDE lesions after IDP and OP were compared with local changes at injection site. Control intradermal tests were repeated in normal persons with drugs and in FDE patients with distilled water on normal skin. RESULTS: At stage I, 46 positive cases had local signs of erythematous indurated nodule with or without hemorrhagic centre, urticarial weal with hemorrhagic centre and erythematous indurated nodule with central vesicle. At stage II, 41 patients had similar local signs. The changes at injection site to those of FDE lesions were compared. Z-test for proportions showed no significant difference between groups (p-value > 0.05). Control tests were negative. CONCLUSION: The drug producing erythematous indurated nodule with or without hemorrhagic centre, vesicle or urticarial weal with hemorrhagic centre at injection site was the most likely drug causing fixed eruption.

Metastatic duodenal GIST: role of surgery combined with imatinib mesylate.

BACKGROUND: The best possible treatment of metastatic high grade large duodenal GIST is controversial. Surgery (with or without segmental organ resection) remains the principal treatment for primary and recurrent GIST. However, patients with advanced duodenal GIST have a high risk of early tumour recurrence and short life expectancy. METHOD: We present a case of a young man treated with a combined modality of surgery and imatinib for an advanced duodenal GIST. RESULTS: He remains asymptomatic and disease free 42 months following this combined approach. CONCLUSION: Treatment with imatinib has dramatically improved the outlook for patients with advanced, unresectable and/or metastatic disease.

Prevalence of hepatitis B surface antigen carrier state in patients with lichen planus--report of 200 cases from Lahore, Pakistan.

BACKGROUND: To determine the prevalence of hepatitis B surface antigen carrier state in patients with lichen planus. METHODS: A quasi experimental cross sectional study was done at Department of Dermatology, Shaikh Zayed Federal Postgraduate Medical Institute, Lahore, Pakistan, from April 2003 to March 2005. Two hundred clinically diagnosed cases of LP and equal number of patients with other dermatoses not reportedly associated with hepatitis B virus (HBV) infection (control group) were collected from Skin Out Patient Department. They were screened for hepatitis B surface antigen (HBsAg) by Enzyme Linked Immunosorbent Assay (ELISA). Statistical analysis was done by using SPSS package version 11. RESULTS: Out of 200 patients of each group, three patients with LP and seven patients from control group were positive for HBsAg. The test of significance for proportions revealed that there was no significant difference (p > 0.1) between two groups. CONCLUSION: No association between HBsAg carrier state and LP was found in our study.

Fixed drug eruption: topical provocation and subsequent phenomena.

OBJECTIVE: To determine the usefulness of topical provocation in detecting the incriminated drug causing fixed eruption. DESIGN: Quasi-experimental study. PLACE AND DURATION OF STUDY: Department of Dermatology, Shaikh Zayed FPGMI, Lahore, from November 2002 to December 2005. PATIENTS AND METHODS: Three hundred and five, clinically diagnosed cases of Fixed Drug Eruption (FDE) of either gender and of any age were subjected to topical provocation with different drugs by using concentration of 1% (n=203), 2% (n=210) and 5% (n=235) in white soft paraffin. Drug ointment of one strength was applied one at a time on normal skin of flexor surface of right or left forearm. The effects of tests on involved and uninvolved skin were observed for 48 hours. The changes in lesions like erythema, hyperpigmentation, itching, burning or appearance of new lesion were considered a positive response. In case of no change, the patients (n=5) were subjected to oral provocation test, by giving half to full therapeutic dose of the suspected drug depending upon the severity of the initial attack. A patient who exhibited see-sawing phenomenon with 5% metamizole TPT was given oral challenge with same drug. Control topical tests were repeated in equal number of normal persons with various drug ointments and in patients of FDE with white soft paraffin on normal and affected skin. RESULTS: One hundred and thirty-seven patients were males and one hundred and sixty-eight patients were females. Maximum number of patients belonged to third decade. With 1% drug preparations 12 out of 316, with 2% drug preparations 28 out of 422 and with 5% drug preparations, 312 out of 523 TPTs were positive. The comparison revealed a highly significant association (Chi-square 448.1 and p < 0.000) among various strengths of preparations and positive response. Sulphamethoxazole was found to be the most commonly incriminated cause of FDE applied in 5% concentration yielded sensitivity rate of 91% compared to 4% with lower concentrations. Positive patch test was also observed with oxytetracycline. Five patients who were given oral provocation with different drugs were found to be positive to tinidazole, dapsone, propylphenazone, belladonna and phenobarbitone. Interesting phenomena like earlier reactivation of lesion situated distal to site of application of preparation, marching, see-sawing (with oral metamizole) and lightening observed, are not yet reported in literature. CONCLUSION: Topical provocation test with 5% drug concentration applied on normal skin of patient with FDE is a possible first line investigation in finding the incriminated drug.