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.

Channel Clustering and QoS Level Identification Scheme for Multi-Channel Cognitive Radio Networks

Ali, Amjad,Yaqoob, Ibrar,Ahmed, Ejaz,Imran, Muhammad,Kwak, Kyung Sup,Ahmad, Adnan,Hussain, Syed Asad,Ali, Zulfiqar IEEE 2018 IEEE communications magazine Vol.56 No.4

<P>The increasing popularity of wireless services and devices necessitates high bandwidth requirements; however, spectrum resources are not only limited but also heavily underutilized. Multiple license channels that support the same levels of QoS are desirable to resolve the problems posed by the scarcity and inefficient use of spectrum resources in multi-channel cognitive radio networks (MCRNs). One reason is that multimedia services and applications have distinct, stringent QoS requirements. However, due to a lack of coordination between primary and secondary users, identifying the QoS levels supported over available licensed channels has proven to be problematic and has yet to be attempted. This article presents a novel Bayesian non-parametric channel clustering scheme, which identifies the QoS levels supported over available license channels. The proposed scheme employs the infinite Gaussian mixture model and collapsed Gibbs sampler to identify the QoS levels from the feature space of the bit rate, packet delivery ratio, and packet delay variation of licensed channels. Moreover, the real measurements of wireless data traces and comparisons with baseline clustering schemes are used to evaluate the performance of the proposed scheme.</P>

Genome and transcriptome-wide analyses of cellulose synthase gene superfamily in soybean

Nawaz, Muhammad Amjad,Rehman, Hafiz Mamoon,Baloch, Faheem Shehzad,Ijaz, Babar,Ali, Muhammad Amjad,Khan, Iqrar Ahmad,Lee, Jeong Dong,Chung, Gyuhwa,Yang, Seung Hwan G. Fischer 2017 Journal of plant physiology Vol. No.

<P><B>Abstract</B></P> <P>The plant cellulose synthase gene superfamily belongs to the category of type-2 glycosyltransferases, and is involved in cellulose and hemicellulose biosynthesis. These enzymes are vital for maintaining cell-wall structural integrity throughout plant life. Here, we identified 78 putative cellulose synthases (CS) in the soybean genome. Phylogenetic analysis against 40 reference <I>Arabidopsis</I> CS genes clustered soybean CSs into seven major groups (CESA, CSL A, B, C, D, E and G), located on 19 chromosomes (except chromosome 18). Soybean CS expansion occurred in 66 duplication events. Additionally, we identified 95 simple sequence repeat makers related to 44 CSs. We next performed digital expression analysis using publically available datasets to understand potential CS functions in soybean. We found that CSs were highly expressed during soybean seed development, a pattern confirmed with an Affymatrix soybean IVT array and validated with RNA-seq profiles. Within CS groups, CESAs had higher relative expression than CSLs. Soybean CS models were designed based on maximum average RPKM values. Gene co-expression networks were developed to explore which CSs could work together in soybean. Finally, RT-PCR analysis confirmed the expression of 15 selected CSs during all four seed developmental stages.</P>

Microsatellite Analysis of Rosa damascena from Pakistan and Iran

Amjad Farooq,Mahnaz Kiani,Muhammad Aslam Khan,Atif Riaz,Asif Ali Khan,Natalie Anderson,David H. Byrne 한국원예학회 2013 Horticulture, Environment, and Biotechnology Vol.54 No.2

For the perfume industry, Rosa damascena is the most important species used in the production of rose attar which is made by distilling volatile oils from the petals of flowers. It is also used widely in the manufacture of rose water, as a flavoring agent. Other species like Rosa gallica L., Rosa centifolia L., Rosa × borboniana Desp. and the rose cultivar Gruss an Teplitz also exhibit the fragrance that is sought by perfumeries in the world. The main rose oil producers in the world are Turkey and Bulgaria, and they are obtaining the rose oil almost exclusively from the single clone of R. damascena. In the recent studies a wide genetic diversity for R. damascena has been revealed in Iran, but there was a need to explore and evaluate the R. damascena in the neighboring areas of Iran. Thus the new research project was planned with the objective to evaluate the genetic diversity amongst R. damascena landraces grown in Pakistan and the subsequent comparison with tested germplasm grown in Iran. Further, the study is based on the collection of Damask and selected garden roses from Pakistan, Iran and USA, determining the characterization through microsatellite markers. The SSR markers confirmed the high level of diversity of the Rosa damascena germplasm within Iran and showed that the Pakistani genotypes were similar to those from the Iranian provinces of Isfahan, Kerman and Fars. The garden rose cultivars were distantly related.

Some folded issues related to over-shielded and unplanned rooms for medical linear accelerators - A case study

Muhammad, Wazir,Ullah, Asad,Hussain, Amjad,Ali, Nawab,Alam, Khan,Khan, Gulzar,Matiullah,,Maeng, Seongjin,Lee, Sang Hoon 한국물리학회 2015 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol. No.

A New Quadratic Boost Converter with Voltage Multiplier Cell : an Analysis and Assessment

Muhammad Zeeshan Malik,Amjad Ali,Qunwei Xu,Guozhu Chen 보안공학연구지원센터 2016 International Journal of Smart Home Vol.10 No.8

A new topology of high gain DC-DC quadratic boost converter with voltage multiplier cell (VMC) is introduced in this paper. The proposed VMC technique is derived from the traditional quadratic boost converter, which has an advantage with high voltage gain and stress across the semiconductor devices are lower than the output voltage. To validate efficacy of the proposed method simulation has been performed in Mat lab Simulink software to compare the voltage gain of proposed method with others five modified boost converters. The input voltage of proposed converter and other topologies are same 10VDC but the output voltage of proposed converter is much higher than others converters which are discussed in this paper.

Some Folded Issues Related to Over-shielded and Unplanned Rooms for Medical Linear Accelerators - A Case Study

Wazir Muhammad,Asad Ullah,Amjad Hussain,Nawab Ali,Khan Alam,Gulzar Khan,Matiullah,뱅수진,이상훈 한국물리학회 2015 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.67 No.3

A medical linear accelerator (LINAC) room must be properly shielded to limit the outside radiation exposure to an acceptable safe level defined by individual state and international regulations. However, along with this prime objective, some additional issues are also important. The current case-study was designed to unfold the issues related to over-shielded and unplanned treatment rooms for LINACs. In this connection, an apparently unplanned and over-shielded treatment room of 610 × 610 cm2 in size was compared with a properly designed treatment room of 762 × 762 cm2 in size (i.e., by following the procedures and recommendations of the IAEA Safety Reports Series No. 47 and NCRP 151). Evaluation of the unplanned room indicated that it was over-shielded and that its size was not suitable for total body irradiation (TBI), although the license for such a treatment facility had been acquired for the installed machine. An overall 14.96% reduction in the total shielding volume (i.e., concrete) for an optimally planned room as compared to a non-planned room was estimated. Furthermore, the inner room’s dimensions were increased by 25%, in order to accommodate TBI patients. These results show that planning and design of the treatment rooms are imperative to avoid extra financial burden to the hospitals and to provide enough space for easy and safe handling of the patients. A spacious room is ideal for storing treatment accessories and facilitates TBI treatment.

Effect of w/b ratio and binder content on the properties of self-compacting high performance concrete (SCHPC)

조병완,Muhammad Ali Sikandar,Zafar Baloch,Amjad Naseer,Naveed Jan,Qaiser Jamal 한양대학교 세라믹연구소 2018 Journal of Ceramic Processing Research Vol.19 No.2

Silica fume is most commonly used mineral admixture both in high performance concrete (HPC) and self-compacting concrete(SCC). While the incorporation of silica fume in concrete has been extensively investigated in HPC and SCC, furtherresearches are needed to optimize the dosage of silica fume and cement content in self-compacting high performance concrete(SCHPC). This paper presents the results of tests carried out to study the effect of w/b ratio and binder content (cement andsilica fume content) on properties of SCHPC. Eighteen batches of concrete with binder content ranging from 500-600 kg/m3were produced at two w/b ratios (0.23 and 0.25); with silica fume amount varying from 0 to 20 percent by weight of cement. Super Plasticizer (SP) dosage, porosity, water absorption, compressive strength, modulus of elasticity, splitting tensile strength,autogenous shrinkage (AS) and hydration characteristics were evaluated for all SCHPC mixes. The results indicate thatoptimum w/b ratio and binder content (cement and silica fume content) is required to get better performance from SCHPC,as high cement content and silica fume dosage tend to deteriorate the overall performance owing to reduced mechanicalperformances, high degree of hydration and greater autogenous shrinkage in SCHPC mixes incorporating silica fume.

Laparoscopy offers better clinical outcomes and long-term survival in patients with right colon cancer: experience from national cancer center

Shah, Muhammad Fahd,Naeem, Awais,Haq, Ihtisham ul,Riaz, Shehryar,Shakeel, Osama,Panteleimonitis, Sofoklis,Khattak, Shahid,Syed, Aamir Ali,Parvaiz, Amjad 대한대장항문학회 2022 Annals of Coloproctolgy Vol.38 No.3

Purpose: Laparoscopic approach to colonic tumor requires skill set and resources to be established as routine standard of care in most centers around the world. It presents particular challenge in country like Pakistan due to economic constrain and lack of teaching and training opportunities available for surgeons to be trained to deliver such service. The aim of this study is to look into changing practice of our institution from conventional approach of open to laparoscopic surgery for right colon cancer. Methods: Consecutive patients between January 2010 to December 2018 who presented to Shaukat Khanum Memorial Cancer Hospital and Research Centre with diagnosis of right colon (cecum, ascending and transverse colon) adenocarcinoma and underwent surgical resections were included in this study. Results: A total of 230 patients with adenocarcinoma of the right colon underwent curative resections during the study period. Of these, 141 patients (61.3%) underwent laparoscopic surgery while open resection was performed in 89 patients (38.7%). Five-year disease-free survival (DFS) of patients with American Joint Committee on Cancer (AJCC) stage III (80.9% vs. 54.8%, P=0.021) was significantly better if these patients underwent laparoscopic surgery while a trend toward better DFS (96.7% vs. 84.1%, P=0.111) was also observed in AJCC stage II patients, although this difference was not significant. Conclusion: This study demonstrates the adoption of a laparoscopic approach for right colon cancer over 10 years. With a standardized approach and using the principle of oncological surgery, we incorporated this in our minimally invasive surgery practice at our institution.

Energy efficient watchman based flooding algorithm for IoT-enabled underwater wireless sensor and actor networks

Draz, Umar,Ali, Tariq,Zafar, Nazir Ahmad,Alwadie, Abdullah Saeed,Irfan, Muhammad,Yasin, Sana,Ali, Amjad,Khattak, Muazzam A. Khan Electronics and Telecommunications Research Instit 2021 ETRI Journal Vol.43 No.3

In the task of data routing in Internet of Things enabled volatile underwater environments, providing better transmission and maximizing network communication performance are always challenging. Many network issues such as void holes and network isolation occur because of long routing distances between nodes. Void holes usually occur around the sink because nodes die early due to the high energy consumed to forward packets sent and received from other nodes. These void holes are a major challenge for I-UWSANs and cause high end-to-end delay, data packet loss, and energy consumption. They also affect the data delivery ratio. Hence, this paper presents an energy efficient watchman based flooding algorithm to address void holes. First, the proposed technique is formally verified by the Z-Eves toolbox to ensure its validity and correctness. Second, simulation is used to evaluate the energy consumption, packet loss, packet delivery ratio, and throughput of the network. The results are compared with well-known algorithms like energy-aware scalable reliable and void-hole mitigation routing and angle based flooding. The extensive results show that the proposed algorithm performs better than the benchmark techniques.