Genome-wide identififi cation and characterization of a plant-specifific Dof transcription factor gene family in olive (Olea europaea) and its comparison with Arabidopsis

Mariyam,Muhammad Shafiq,Muhammad Haseeb,Rana Muhammad Atif,Syed Agha Armaghan Asad Abbas Naqvi,Numan Ali,Muhammad Arshad Javed,Fizza Gillani,Muhammad Saleem Haider 한국원예학회 2021 Horticulture, Environment, and Biotechnology Vol.62 No.6

DNA binding with one fi nger (Dof) proteins are encoded by a ubiquitous plant-specifi c transcription factor gene family thatplays a critical role in various biological processes including fruit ripening and organogenesis. The wild olive ( Olea europaeavar. sylvestris v1.0 ) genome was used to identify Dof gene family members using a set of bioinformatics tools. Gene structure,chromosome locations, phylogeny, protein motifs, miRNA targets and tissue-specifi c expression patterns were analyzed. Here, we identifi ed 51 potential Dof genes unevenly distributed on all chromosomes and a few scaff olds. Dof proteins in oliveclustered into eight subgroups (D1, B2, C3, C2.2, C1, C2.1, B1, and A) based on the established Arabidopsis classifi cation. The prevalence of segmental duplication was observed as compared to tandem duplication, and this was the main factorunderlying the expansion of the Dof gene family in olive. Tissue-specifi c expression profi ling of Oeu Dof genes revealed thatthe majority of Oeu Dof genes were highly expressed in fl owers, stem and meristem tissues. In seed and meristem tissues,cis-regulatory element (CRE) analysis revealed the presence of elements that are specifi cally responsive to light, circadian,auxin, and ABA. In addition, a comparative analysis between Dof genes in olive and Arabidopsis revealed eight groups orsub-families, although the C3 group of Arabidopsis was not represented in olive. This extensive genome evaluation of theDof gene family in olive presents a reference for cloning and functional analysis of the members of this gene family.

A Live<i>Salmonella</i>Gallinarum Vaccine Candidate Secreting an Adjuvant Protein Confers Enhanced Safety and Protection Against Fowl Typhoid

Shafiq, Muhammad Hassan,Kamble, Nitin M.,Kim, Tae Hoon,Choi, Yoonyoung,Lee, John Hwa BioOne (American Association of Avian Pathologists 2015 Avian diseases Vol.59 No.4

<P>Live attenuated vaccines are used for effective protection against fowl typhoid (FT) in domestic poultry. In this study, a lon/cpxR/asd deletion mutant of Salmonella Gallinarum expressing the B subunit of a heat labile toxin (LTB) from Escherichia coli, a known adjuvant, was cloned in a recombinant p15A ori plasmid, JOL1355, and evaluated as a vaccine candidate in chickens. The plasmid was shown to be stable inside the attenuated Salmonella Gallinarum cell after three successive generations. Moreover, from an environmental safety point of view, apart from day 1 the JOL1355 strain was not detected in feces through day 21 postinoculation. For the efficacy of JOL1355, a total of 100 chickens were equally divided into two groups. Group A (control) chickens were intramuscularly inoculated with phosphate-buffered saline at 4 and 8 wk of age. Group B chickens were primed and boosted via the intramuscular route with 200 mL of a bacterial suspension of JOL1355 containing 1 3 10 8 colony forming units. All the chickens in Group A and B were challenged at 3 wk postbooster by oral inoculation with a wild-type Salmonella Gallinarum strain, JOL420. The JOL1355-immunized group showed significant protection and survival against the virulent challenge compared to the nonimmunized group. In addition, Group B exhibited a significantly higher humoral immune response, and the chickens remained healthy without any symptoms of anorexia, diarrhea, or depression. Group B also exhibited a significantly lower mortality rate of 4% compared to the 46% of the control group, which can be attributed to higher immunogenicity and better protection. The Group B chickens had significantly lower lesion scores for affected organs, such as the liver and spleen, compared to those of the control chickens (P < 0.01). These findings suggest that JOL1355 is a promising candidate for a safe and highly immunogenic vaccine against FT.</P>

Biomaterials for Host Cell Recruitment and Stem Cell Fate Modulation for Tissue Regeneration: Focus on Neuropeptide Substance P

Muhammad Shafiq,김수현 한국고분자학회 2016 Macromolecular Research Vol.24 No.11

Substance P (SP) has been recently identified as an injury-inducible messenger responsible for promoting tissue regeneration in a variety of injury models, such as limb ischemia, myocardial infarction, and osteoarthritis. SP mobilizes host stem/progenitor cells, which are then recruited to the injury site. SP also modulates the inflammatory response and polarizes macrophages towards the M2 phenotype, which ultimately lead to accelerated tissue repair. SP has been delivered systemically or immobilized into scaffold materials but is easily cleaved by endogenous proteolytic enzymes; thus, its conjugation with a biomaterial may hold great promise for its use in regenerative medicine and tissue engineering applications. In addition, SP has been shown to induce stem/progenitor cell mobilization by binding to neurokinin-1 receptor. The aim of this review is to critically analyze the recent literature on the use of SP in regenerative medicine and tissue engineering and to explore further avenues. Moreover, we will seek to identify the challenges ahead and how these may be overcome.

Biochemical and Trace Mineral Analysis of Silajit Samples From Pakistan

Muhammad Imtiaz Shafiq,Saeed Ahmad Nagra,Nayab Batool 한국영양학회 2006 Nutritional Sciences Vol.9 No.3

Biochemical and Trace Mineral Analysis of Silajit Samples From Pakistan

Shafiq Muhammad Imtiaz,Nagra Saeed Ahmad,Batool Nayab The Korean Nutrition Society 2006 Nutritional Sciences Vol.9 No.3

Silajit is a blackish brown pitch-like gummy substance. It is an important Unani and Ayurvedic medicine widely used in the treatment of many diseases and as nutritional supplement It is found in certain mountainous regions of Pakistan, Afghanistan, India, Nepal, Australia and Russia. Silajit samples of Pakistani origin were obtained from different sources and analyzed for their physical characteristics and biochemical & elemental composition. X-ray diffraction studies on Silajit showed that it is an amorphous substance and has no crystalline structure. Also, pH studies of Silajit (2 g/L of water) indicated that it was slightly acidic in nature and ranged from 3.45 to 7.23. Conductivity ranged from 157.7 to 330. Amino acid analysis revealed that Silajit contained lysine and alanine in higher amounts than all other amino acids and ranged from 1456 to 2240 and 68 to $1615{\eta}mole/g$, respectively. Mean concentration of arsenic, mercury, cadmium, lead, copper and zinc was 73.15, 104.92, 0.496, 3.89, 4.04 and 17.23 ppm, respectively. Silajit samples were also analyzed for calcium, potassium and sodium.

Optimized and Smart Link Removal Topology Control for Unplanned Wireless Mesh Networks

Muhammad Abid Dar,Muhammad Shafiq,Muddesar Iqbal,Jin-Ghoo Choi 한국산학기술학회 2015 SmartCR Vol.5 No.4

Topology control of a network makes it possible for wireless nodes to reduce extra links while ensuring network connectivity and preserving at least one path for all pairs of the source and destination. The minimum edges should be constructed by allocating a single path to each flow and removing the edge, which do not affect the throughput of the network and ultimately removes all extra links. The resultant network topology then preserves network connectivity while also maintaining the desirable features like reduction in average node degree, quality of service, and throughput. To do so, we developed an algorithm called Link Removal that considers residue Capacity and Delay (LRCD) and removes the redundant links in a network by shifting the data load to suitable links that are responsible for making the path. Simulation results prove the effectiveness of LRCD and show that this not only produces good results, but is also beneficial for establishing a cost effective network.

Covalent Immobilization of MSC-Affinity Peptide on Poly(L-lactide-co- ε-caprolactone) Copolymer to Enhance Stem Cell Adhesion and Retention for Tissue Engineering Applications

Muhammad Shafiq,김수현 한국고분자학회 2016 Macromolecular Research Vol.24 No.11

Electrospun nanofibers mimicking the extracellular microenvironment have tremendous potential for tissue regeneration applications. However, a lack of bioactive functionalities limits the effective utilization of nanofibers fabricated from synthetic biodegradable polymers. The objective of this study was to conjugate mesenchymal stem cell affinity peptide (EPLQLKM, E7) with star-shaped poly(L-lactide-co-ε-caprolactone) (PLCL) copolymer and to evaluate the potential of this modified polymer to enhance stem cell adhesion and proliferation in vitro. MSCadhesive peptide was covalently conjugated with the hydroxyl functionalities of the star-shaped PLCL copolymer and nanofibers were prepared by mixing appropriate proportions of linear PLCL and E7-conjugated star-shaped PLCL copolymers using electrospinning. Nuclear magnetic resonance and amino acid composition analysis revealed that E7 was successfully conjugated to PLCL copolymers. Nanofibers were smooth and homogenous as examined using scanning electron micrography. Nanofibrous meshes containing PLCL-E7 showed significantly higher cell viability and proliferation compared with the control group. In addition, cells spread well on meshes containing PLCL-E7 compared with the control group. The strategy adopted here may be very useful for designing stem cell adhesive polymeric biomaterials to enhance stem cell-based tissue repair. In addition, E7-immobilized PLCL copolymers can be fabricated into different shapes and structures as needed for various tissue engineering applications.

Genetic Diversity for Biometrics Traits in Local Landraces of Wheat (Triticum aestivum L.)

Muhammad Jamil,Saif ullah Ajmal,Shafiq Rehman,Eui Shik Rha 한국국제농업개발학회 2005 韓國國際農業開發學會誌 Vol.17 No.4

<i>In situ</i> cardiac regeneration by using neuropeptide substance P and IGF-1C peptide eluting heart patches

Shafiq, Muhammad,Zhang, Yue,Zhu, Dashuai,Zhao, Zongxian,Kim, Dong-Hwee,Kim, Soo Hyun,Kong, Deling Oxford University Press 2018 Regenerative biomaterials Vol.5 No.5

<P><B>Abstract</B></P><P>Cardiovascular diseases cause huge socio-economic burden worldwide. Although a mammalian myocardium has its own limited healing capability, scaffold materials capable of releasing stem cell recruiting/engrafting factors may facilitate the regeneration of the infarcted myocardium. The aim of this research was to develop cardiac patches capable of simultaneously eluting substance P (SP) and insulin-like growth factor-1C (IGF-1C) peptide. Polycaprolactone/collagen type 1-based patches with or without SP and IGF-1C peptide were fabricated by co-electrospinning, which exhibited nanofibrous morphology. SP and IGF-1C/SP patches recruited significantly higher numbers of bone marrow-mesenchymal stem cells than that of the negative control and patch-only groups <I>in vitro</I>. The developed patches were transplanted in an infarcted myocardium for up to 14 days. Mice underwent left anterior descending artery ligation and received one of the following treatments: (i) sham, (ii) saline, (iii) patch-only, (iv) IGF-1C patch, (v) SP patch and (vi) IGF-1C/SP patch. SP and IGF-1C/SP patch-treated groups exhibited better heart function and attenuated adverse cardiac remodeling than that of the saline, patch-only and individual peptide containing cardiac patches. SP patch and IGF-1C/SP patch-treated groups also showed higher numbers of CD31-positive vessels and isolectin B4-positive capillaries than that of other groups. IGF-1C/SP-treated group also showed thicker left ventricular wall in comparison to the saline and patch-only groups. Moreover, IGF-1C/SP patches recruited significantly higher numbers of CD29-positive cells and showed less numbers of Tunel-positive cells compared with the other groups. These data suggest that SP and IGF-1C peptides may act synergistically for <I>in situ</I> tissue repair. </P>

Fabrication and performance characterization of novel zinc oxide filled cross-linked PVA/PEG 600 blended membranes for CO2/N2 separation

Muhammad Rizwan Dilshad,Atif Islam,Aneela Sabir,Muhammad Shafiq,Muhammad Taqi Zahid Butt,Aamir Ijaz,Tahir Jamil 한국공업화학회 2017 Journal of Industrial and Engineering Chemistry Vol.55 No.-

In this study zinc oxide filled and unfilled polyvinyl alcohol (PVA)/polyethylene glycol (PEG) 600 blended membranes with different degrees of cross-linking (mol%) were prepared using formaldehyde as a crosslinking agent and characterized by FTIR, SEM, TGA, mechanical analysis and permeation testing for CO2 and N2 gases. The effects of synthesis parameters like cross-linking ratio, wt.% PEG content and wt.% zinc oxide content on the membrane characteristics were also investigated. It was found that at 60 mol% degree of cross-linking and 60 wt.% PEG content, the membranes showed maximum CO2/N2 ideal selectivity of 26 and reasonable CO2 permeability of 52.9 Barrers at 25 C and 1.5 bar. It was also found that at 2 wt.% zinc oxide content, membranes showed highest CO2/N2 ideal selectivity of 112.8 and maximum CO2 permeability of 423 Barrers at 25 C and 1.5 bar.