Genome-wide identification and expression analyses of WRKY transcription factor family members from chickpea (Cicer arietinum L.) reveal their role in abiotic stress-responses

Muhammad Waqas,Muhammad Tehseen Azhar,Iqrar Ahmad Rana,Farrukh Azeem,Muhammad Amjad Ali,Muhammad Amjad Nawaz,정규화,Rana Muhammad Atif 한국유전학회 2019 Genes & Genomics Vol.41 No.4

Background WRKY proteins play a vital role in the regulation of several imperative plant metabolic processes and pathways, especially under biotic and abiotic stresses. Although WRKY genes have been characterized in various major crop plants, their identification and characterization in pulse legumes is still in its infancy. Chickpea (Cicer arietinum L.) is the most important pulse legume grown in arid and semi-arid tropics. Objective In silico identification and characterization of WRKY transcription factor-encoding genes in chickpea genome. Methods For this purpose, a systematic genome-wide analysis was carried out to identify the non-redundant WRKY transcription factors in the chickpea genome. Results We have computationally identified 70 WRKY-encoding non-redundant genes which were randomly distributed on all the chickpea chromosomes except chromosome 8. The evolutionary phylogenetic analysis classified the WRKY proteins into three major groups (I, II and III) and seven sub-groups (IN, IC, IIa, IIb, IIc, IId and IIe). The gene structure analysis revealed the presence of 2–7 introns among the family members. Along with the presence of absolutely conserved signatory WRKY domain, 19 different domains were also found to be conserved in a group-specific manner. Insights of gene duplication analysis revealed the predominant role of segmental duplications for the expansion of WRKY genes in chickpea. Purifying selection seems to be operated during the evolution and expansion of paralogous WRKY genes. The transcriptome data-based in silico expression analysis revealed the differential expression of CarWRKY genes in root and shoot tissues under salt, drought, and cold stress conditions. Moreover, some of these genes showed identical expression pattern under these stresses, revealing the possibility of involvement of these genes in conserved abiotic stress–response pathways. Conclusion This genome-wide computational analysis will serve as a base to accelerate the functional characterization of WRKY TFs especially under biotic and abiotic stresses.

Influence of Endophytic Mutualistic Association on Plant Growth Regulators and Antioxidant Status of Cucumber in Abiotic Stress

Muhammad Waqas,Abdul Latif Khan,Muhammad Kamran,Muhammad Hamayun,Muhammad Arif,Yoon-Ha Kim,Sang-Mo Kang,Duk-Hwan Kim,In-Jung Lee 한국원예학회 2012 한국원예학회 학술발표요지 Vol.2012 No.5

A Review on Triple-A Supply Chain Performance

Muhammad Ishtiaq Ishaq,Nazia Hussain,Waseem Khaliq,Muhammad Waqas 한국유통과학회 2012 Asian Journal of Business Environment (AJBE) Vol.2 No.2

Purpose - Today’s world is rapidly changing due to swift changes in organization’s infrastructures and supply chain is becoming an important factor which affects the organization’s global competitiveness. Research design / data / methodology - Researchers indicated that environment uncertainty is considered an external driving force to establish a unique supply chain. Market competition, reducing the gap of performance and quality between the products are compelling the practitioners and researcher to change the paradigm of managing the business processes effectively and efficiently. Results - In old times, supply chain of any organization was measured on the basis of inventory turns, defect rats, lead times, stock buffering and service level. But, Lee H.L. in 2004, published an article in Harvard Business Review who proposed three A (Adaptable, Agile and Aligned) termed as “Triple-A” of successful supply chain. Conclusions - He claimed that organizations can compete through the creation of Triple-A supply chain. Hence, the basic aim of this review paper is to develop basic insights regarding what is Triple-A of supply chain, its importance and functioning in today’s competitive world.

Evaluating the importance of different computed tomography scan-based factors in predicting the outcome of extracorporeal shock wave lithotripsy for renal stones

Muhammad Waqas,Imad-ud-din Saqib,Muhammad Imran Jamil,Mohammad Ayaz Khan,Saeed Akhter 대한비뇨의학회 2018 Investigative and Clinical Urology Vol.59 No.1

Purpose: To evaluate the impact of various computed tomography scan-based parameters of renal stones on the outcome of extracorporeal shock wave lithotripsy (ESWL). Materials and Methods: We conducted a retrospective study of patients who underwent ESWL for renal stones (sized 5–20 mm) from January 2013 to December 2016. We evaluated body mass index, location of the stone, skin-to-stone distance (SSD), stone attenuation value (SAV), stone diameter, Hounsfield density, stone area, and stone volume. Statistical analysis was done and significance was confirmed by multivariate logistic regression analysis. Results: Of the 203 patients 122 (60.1%) had successful clearance of the stone. The presence of a double J stenting, a lower pole location, a higher SAV, higher Hounsfield density, larger stone area, larger stone diameter, and higher stone volume were negative predictors of ESWL outcome. When these parameters were analyzed with multivariate logistic regression analysis, stone location, SSD, and SAV were the only significant independent predictors of the outcome of ESWL. Conclusions: Stone location, SSD, and SAV are reliable and strong predictors of ESWL outcome for the treatment of renal stones.

Supplemental potassium mediates antioxidant metabolism, physiological processes, and osmoregulation to confer salt stress tolerance in cabbage (Brassica oleracea L.)

Waqas Ahmad,Chaudhary Muhammad Ayyub,Muhammad Asif Shehzad,Khurram Ziaf,Muhammad Ijaz,Ahmad Sher,Tahira Abbas,Jamil Shafi 한국원예학회 2019 Horticulture, Environment, and Biotechnology Vol.60 No.6

Soil salinity is one of the severe threats of climate change that inflicts heavy losses to vegetable production. Potassium (K) has been considered essential approach against abiotic stresses in food crops, however, understanding of K regulated mechanisms for inducing tolerance to NaCl stress in cabbage (Brassica oleracea L.) plants is, still elusive. Here, we report the supplemental K effects on antioxidant defense system and physiological processes that may influence the cabbage production under saline conditions. Initially, cabbage varieties (‘Stone Head’, ‘Golden Acre’, ‘9j-940’, ‘Beauty Ball’, ‘Green Ball’, ‘Green Rise’, ‘Marco F-1’) were tested under NaCl stress (50, 100, 150, and 200 mM) for their higher growth, vigor index and mineral contents. The identified cabbage var. salt-tolerant, cv. Beauty Ball (BB) and salt-sensitive cv. Green Ball (GB) were further exposed to foliar K (5 and 10 mM solutions of KNO3) under the same NaCl regimes. NaCl stress markedly inhibited photosynthetic efficiency, water status and chlorophyll pigments, thereby, resulted in reduced dry biomass of both varieties. Nevertheless, exogenous K spray at 10 mM caused positive gain in leaf water relations, chlorophyll contents in both cabbage varieties. The ameliorative impacts of K were more pronounced in salt-tolerant cv. BB as compared to salt-sensitive cv. GB in terms of higher accumulation of total soluble proteins, total free amino acids, proline contents, upregulated antioxidant activities and enhanced gas exchange characteristics. Hence, improvement in growth and K+/Na+ ratio of cabbage plants by foliar K application (10 mM) were related to up-regulation of physiological and biochemical mechanisms under saline conditions.

A Comparison of Productivity by Variety, Plantlet Size and Planting Period to Improve Aeroponic Seed Potato System in Pakistan

Waqas Ahmed Dogar,Aish Muhammad,Gyoung-Rae Cho,Muhammad Hanif,Kazim Ali,Asad Farooq,Asma Akbar,Sajjad Ahmed,Hoyong Shin 한국국제농업개발학회 2023 韓國國際農業開發學會誌 Vol.35 No.2

An aeroponic seed potato production technology project has been established in Pakistan through the Technical Cooperation Project (TCP) between RDA-KOPIA and PARC. For sustainable potato production, producing high-quality and disease-free potato seeds is critical in Pakistan. The majority of the farmers recycle their own seeds or obtain them through informal ways. Consequently, tuber-borne illnesses proliferate, seeds deteriorate, and yield diminishes. To mitigate such problems, the country moved to sustainable seed potato production by adopting rapid seed multiplication strategies like the combination of tissue culturing with aeroponic seed production technology which is being evaluated as an alternative to traditional pre-basic seed production methods. A series of experiments were carried out to evaluate the shoot development and mini tuber production attributes between two cultivars, different plantlet size and planting period between October 27, 2021, and January 27, 2022, at the NARC aeroponic facility. A CRD design with three replications was used. The study aimed to compare the productivity by variety, plantlet size and planting period to improve aeroponic seed production technology in Pakistan. The results indicated that Lady Rosetta outperformed Asterix in terms of shoot growth and small tuber output. Early planting at an optimal temperature of 27 degrees Celsius in the daytime showed a substantial difference when compared to late planting in November and tuberization was commenced 50-55 days after transplantation. Furthermore, in an aeroponic seed potato production system, normal plantlets (8-10 cm) at the time of transplantation, performed better than medium and small plantlets. In a nutshell, it was determined that normal size plantlets (8-10 cm) of Lady Rosetta cultivar, planted at optimum time to plant showed best results in the aeroponic system at NARC, Islamabad, Pakistan.

Virulence of entomopathogenic fungi Beauveria bassiana and Metarhizium anisopliae against red palm weevil, Rhynchophorus ferrugineus (Olivier)

Muhammad YASIN,Waqas Wakil,Muhammad Usman GHAZANFAR,Mirza Abdul QAYYUM,Muhammad TAHIR,Geoffrey O. BEDFORD 한국곤충학회 2019 Entomological Research Vol.49 No.1

Nineteen different isolates of the entomopathogenic fungi Beauveria bassiana sensu lato (s.l.) and Metarhizium anisopliae s.l. (Ascomycota: Hypocreales), recovered from different soil samples (field crops, fruit orchards, vegetable fields and forests) and insect cadavers were tested against Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae) at two different spore concentrations (1 × 107 and 1 × 108 conidia mL−1). Three isolates of B. bassiana and two of M. anisopliae gave >88 % larval and >75 % adult mortality of R. ferrugineus on their highest dose rate respectively. More sporulating cadavers (mycosis) resulted from a high dose rate compared to low dose on both life stages of R. ferrugineus. The current study confirmed the lethal action of B. bassiana and M. anisopliae isolates with mortality levels usually directly proportional to the conidial concentration. This study further confirmed that the isolates recovered from R. ferrugineus dead cadavers gave more mortality compared to the other sources. In the virulence assay two isolates of B. bassiana caused the highest percentage of both larval and adult mortality at all exposure intervals which suggest that they may be the most promising for use in sustainable management programs aimed at microbial control in date palm orchards.

Phytohormone-producing fungal endophytes and hardwood-derived biochar interact to ameliorate heavy metal stress in soybeans

Waqas, Muhammad,Khan, Abdul Latif,Kang, Sang-Mo,Kim, Yoon-Ha,Lee, In-Jung Springer-Verlag 2014 BIOLOGY AND FERTILITY OF SOILS - Vol.50 No.7

Lumbar Morphometry: A Study of Lumbar Vertebrae from a Pakistani Population Using Computed Tomography Scans

Muhammad M Alam,Muhammad Waqas,Hussain Shallwani,Gohar Javed 대한척추외과학회 2014 Asian Spine Journal Vol.8 No.4

Study Design: A cross-sectional study. Purpose: To describe the characteristics of lumbar vertebrae of Pakistani patients reporting at a tertiary care hospital and compare with studies from other populations. Overview of Literature: Several studies have been conducted to determine morphometry of lumbar vertebrae. Most of the studies involve Caucasian populations, still data on other populations still sparse. This is the first study describing lumbar morphometry of a Pakistani population. Methods: An observational study was conducted based on a review of thin-cut (3 mm) computed topographic images of lumbar vertebrae. Two-hundred and twenty vertebrae from forty-nine patients were studied, and various dimensions were analyzed. Results: Generally, the size of the vertebrae, vertebral canals and recesses were found to be greater in male patients. The difference was statistically significant for transverse and anteroposterior diameters of the vertebral bodies and sagittal diameter of pedicles on the left side (p <0.05). Comparison of populations revealed statistically significant differences in pedicle dimensions between Pakistani population and others. Conclusions: This study provides anatomical knowledge of the lumbar region in a sample population of Pakistan. There were significant differences in various dimensions of lumbar vertebrae between female and male patients. This would prove to be critical for performing a safe operation.

Computed Tomography-Guided Biopsy for Potts Disease: An Institutional Experience from an Endemic Developing Country

Muhammad Waqas,Mohsin Qadeer,Faizuddin Faiz,Mohammad Ali Alvi,Muhammad Ehsan Bari 대한척추외과학회 2015 Asian Spine Journal Vol.9 No.3

Study Design: A retrospective chart review. Purpose: In endemic resource poor countries like Pakistan, most patients are diagnosed and treated for Potts disease on clinical and radiological grounds without a routine biopsy. The purpose of this study was to evaluate the use and effect of computed tomography (CT)-guided biopsy in the management of Potts disease since the technique is becoming increasingly available. Overview of Literature: CT-guided biopsy of spinal lesions is routinely performed. Literature on the utility of the technique in endemic resource poor countries is little. Methods: This study was conducted at the Neurosurgery section of Aga Khan University Hospital Karachi. All the patients with suspected Potts disease who underwent CT-guided biopsy during the 7 year period from 2007 to 2013 were included in this study. Details of the procedure, histopathology and microbiology were recorded. Results: One hundred and seventy-eight patients were treated for suspected Potts disease during the study period. CT-guided biopsies of the spinal lesions were performed in 91 patients (51.12%). Of the 91 procedures, 22 (24.2%) were inconclusive because of inadequate sample (10), normal tissue (6) or reactive tissue (6). Sixty-nine biopsies were positive (75.8%). Granulomatous inflammation was seen in 58 patients (84.05%), positive acid-fast bacillus (AFB) smear in 4 (5.7%) and positive AFB culture in 12 patients (17.3%). All 91 cases in which CT-guided biopsy was performed responded positively to antituberculosis therapy (ATT). Conclusions: 75.8% of the specimens yielded positive diagnoses. Granulomatous inflammation on histopathology was the commonest diagnostic feature. In this series, the rates of positive AFB smear and culture were low compared to previous literature.