Search results for: Shagufta Tazin Shathy

Authors: Shagufta Tazin Shathy, Mohammad Imam Hasan Reza

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Fragmentation due to urbanization and agricultural expansion has become the main reason for destruction of forest area and loss of biodiversity particularly in the developing world. At present, the world is experiencing the largest wave of urban growth in human history, and it is estimated that this influx will be mainly taking place in developing world. Therefore, study on urban fragmentation is vital for a sustainable urban development. Landscape fragmentation is one of the most important conservation issues in the last few decades. Habitat fragmentation due to landscape alteration has caused habitat isolation, destruction in ecosystem pattern and processes. Thus, this research analyses the spatial and temporal extent of urban fragmentation using landscape indices in the Kuala Lumpur (KL) – the capital and most populous city in Malaysia. The objective of this study is to examine the urban fragmentation index in KL city. Fragmentation metrics used in the study are: a) Urban landscape ratio (the ratio of urban landscape area and build up area), b) Infill (development that occurred within urbanized open space), and c) Extension (development of exterior open space). After analyzing all three metrics, these are calculated for the combined urban fragmentation index (UFI). In this combined index, all three metrics are given an equal weight. Land cover/ land use maps of the year 1996 and 2005 have been developed from the Landsat TM 30 m resolution satellite image. The year 1996 is taken as a reference year to analyze the changes. The UFI calculated for the year of 1996 and2005 found that the KL city has undergone rapid landscape changes destructing forest ecosystem adversely. Increasing UFI for the year of 1996 compared to 2005 indicates that the developmental activities have been occupying open spaces and fragmenting natural lands and forest. This index can be implemented in other unplanned and rapidly urbanizing Asian cities for example Dhaka and Delhi to calculate the urban fragmentation rate. The findings from the study will help the stakeholders and urban planners for a sustainable urban management planning in this region.

Keywords: GIS, index, sustainable urban management, urbanization

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Authors: Shagufta Tabassum, V. P. Pawar

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The study of static dielectric properties in a binary mixture of 1,2 dichloroethane (DE) and n,n dimethylformamide (DMF) polar liquids has been carried out in the frequency range of 10 MHz to 30 GHz for 11 different concentration using time domain reflectometry technique at 10ºC temperature. The dielectric relaxation study of solute-solvent mixture at microwave frequencies gives information regarding the creation of monomers and multimers as well as interaction between the molecules of the binary mixture. The least squares fit method is used to determine the values of dielectric parameters such as static dielectric constant (ε₀), dielectric constant at high frequency (ε_∞) and relaxation time (τ).

Keywords: shagufta shaikhexcess parameters, relaxation time, static dielectric constant, time domain reflectometry

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Authors: Shagufta Tabassum

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The study of dielectric properties in a binary mixture of liquids is very useful to understand the liquid structure, molecular interaction, dynamics, and kinematics of the mixture. Time-domain reflectometry (TDR) is a powerful tool for studying the cooperation and molecular dynamics of the H-bonded system. In this paper, we discuss the basic calibration and normalization procedure for time-domain reflectometry measurements. Our approach is to explain the different types of error occur during TDR measurements and how these errors can be eliminated or minimized.

Keywords: time domain reflectometry measurement techinque, cable and connector loss, oscilloscope loss, and normalization technique

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Authors: Shagufta Tabassum, V. P. Pawar, jr., G. N. Shinde

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The study of dielectric relaxation properties of polar liquids in the binary mixture has been carried out at 10, 15, 20 and 25 ºC temperatures for 11 different concentrations using time domain reflectometry technique. The dielectric properties of a solute-solvent mixture of polar liquids in the frequency range of 10 MHz to 30 GHz gives the information regarding formation of monomers and multimers and also an interaction between the molecules of the liquid mixture under study. The dielectric parameters have been obtained by the least squares fit method using the Debye equation characterized by a single relaxation time without relaxation time distribution.

Keywords: excess properties, relaxation time, static dielectric constant, and time domain reflectometry technique

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Authors: Neelma Munir, Zirwa Sarwar, Rubab Naseem, Maria Hasnain, Shagufta Naz

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Wastewater discharge from different sources causes contamination of water bodies and eutrophication. Stegiocolonium and Spirogyra are commonly found algal species in the water bodies of Pakistan. These algal species were tested for their bioremediation potential using different wastewaters. Different parameters, i.e., BOD, COD, pH, nitrates, phosphates and microflora, were analyzed to observe the phycoremediation efficiency of the tested algal strains. When these different wastewaters were treated with these algae, reduction of BOD and COD was observed helped in the reduction of pollutants from the environment. From the results of the present study, it was evident that Ulothrix sp. and Oedogonium sp. showed a high biomass production in different wastewaters as compared to Stigeoclonium sp. and Spirogyra sp. Whereas the oil content of Stigeoclonium sp. was greater than Spirogyra sp. Oil extracted from algal strains was then utilized for converting it to biodiesel, indicating that these algal species can be cultured in wastewater to produce biodiesel.

Keywords: algae, wastewater, biofuel, bioremediation

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Authors: Shagufta Jahangir, Raisa Jahangir

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According to researches the 3rd world youth crave to go to developed countries just merely to get sustainable economic situation. To accomplish their wish they use each and every thing like cross boarder marriages is one of them. The basic and main point of cross boarder marriages is financial sustainability neither cross boarder culture nor cross boarder religion or others. The consequences of this research are that 60% to 70% men of 3rd world do cross boarder marriages just for only economic firmness. Due to this thoughts these men flipside to their native areas with only economic firmness rather social attitudes, moral attitudes behaviors, norms, myths and religion.40% to 50 % men do cross boarder marriages to get firmness even they have families in their native areas.2nd family formation is the easy way to get their desired, according to their eyes. After satisfying their needs they back unaccompanied to their native areas even they leave their offspring. They give precedence to their inhabitant families. This study has been design to find out that economic perspective is the basic phenomena of cross boarder marriages in the 3rd world countries men.

Keywords: cross boarder marriages, moral attitudes, native areas, flipside, norms

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Authors: Abida Kausar, Shagufta Parveen

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The priming of seeds was carried out by two amino acids (phenylalanine and glycine) to improve the drought tolerance potential of two wheat varieties. As wheat is a staple food of more than half of the population of the world, including Pakistan. However, its productivity is mainly adversely affected by abiotic stresses. The current research plan was to investigate the effect of hydropriming and priming by amino acids on wheat varieties under drought stress (50% field capacity). Therefore morphological, biochemical, physiological, and yield attributes were recorded. It was revealed that drought stress significantly decreased the biochemical, morpho-physiological, and growth attributes of the wheat crop. However, the priming treatments have shown a positive correlation with all the studied attributes. It was concluded that priming might involve plant signaling to produce the drought tolerance metabolites under stress conditions which, as a consequence, enhanced the drought tolerance potential of crops.

Keywords: plant biomass, biochemical parameters, chlorophyll contents, yield

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Authors: Ghulam Mustafa Peerzada, Shagufta Rashid, Nadeem Bashir

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These the influence of initial reagent concentrations on the Belousov-Zhabotinsky (BZ) system with Mn2+/Mn3+ as redox catalyst, inorganic bromate as oxidant and pyrogallol as organic substrate was studied. The reactions were monitored by potentiometery in oxidation reduction potential (ORP) mode. The aforesaid reagents were mixed with varying concentrations to evolve the optimal concentrations at which the reaction system exhibited better oscillations. The various oscillatory parameters such as induction period (tin), time period (tp), frequency (v), amplitude (A) and number of oscillations (n) were derived and the dependence of concentration of the reacting species on these oscillatory parameters was interpreted on the basis of the Field-Koros-Noyes mechanism. Ferroin based BZ system with pyrogallol as organic substrate was optimized under CSTR condition at temperature of 30±0.1oC Effect of molecules like monomer and polymer as additives to the system was checked and their interaction with the system was also studied. It has been observed that the monomer affects the time period, while the polymer has its effect on the amplitude of oscillations because of monomer’s interaction with the bromine and polymer’s with that of the Ferroin.

Keywords: Belousov Zhabotinsky reaction, oscillatory parameters, polymer, pyrogallol

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Authors: J. K. Kapoor, Shagufta Jabin, H. S. Bhatia

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Polyamine flocculants were synthesized by poly-condensation of diphenylamine and epichlorohydrin using 1, 2-diaminoethane as modifying agent. The polyelectrolytes were prepared by taking epichlohydrin-diphenylamine in a molar ratio of 1:1, 1.5:1, 2:1, and 2.5:1. The flocculation performance of these polyelectrolytes was evaluated with rice industry waste water. The polyelectrolytes have been used in conjunction with alum for coagulation- flocculation process. Prior to the coagulation- flocculation process, air flotation technique was used with the aim to remove oil and grease content from waste water. Significant improvement was observed in the removal of oil and grease content after the air flotation technique. It has been able to remove 91.7% oil and grease from rice industry waste water. After coagulation-flocculation method, it has been observed that polyelectrolyte with epichlohydrin-diphenylamine molar ratio of 1.5:1 showed best results for the removal of pollutants from rice industry waste water. The highest efficiency of turbidity and TSS removal with polyelectrolyte has been found to be 97.5% and 98.2%, respectively. Results of these evaluations also reveal 86.8% removal of COD and 87.5% removal of BOD from rice industry waste water. Thus, we demonstrate optimization of coagulation–flocculation technique which is appropriate for waste water treatment.

Keywords: coagulation, flocculation, air flotation technique, polyelectrolyte, turbidity

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Authors: Shagufta Jahangir, Raisa Jahangir, Nadeemullah

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In many societies sports is considered inappropriate for women. It traditionally associated with mascunity. The proposed study aims at undertaking a critical situation analysis of sports women in Pakistan from a gender perspective by examining various aspects of sports women by gender including wrong social values, unstable economical position, wrong religious perspective and the role of media towards women in sports, while sports can provide a channel for informing women about their social and legal rights as well as their health issues, productive health and others. A major concern of the study is to identify the basic causes which depriving Pakistani women from sports. The Human Rights Commission of Pakistan and the Joint Action Committee for People’s Rights organized a symbolic mini marathon on 21 May 2005 in Pakistan to challenge arbitrary curbs on women’s public participation in sport and to highlight rising violence against women. Historically, sport has engaged the perception of gender-hierarchy in order to reproduce the ideology of male superiority, a notion which is often translated into ‘usual superiority’ within the superior communal order. However, it is argued here that we are presently in a state of communal instability with esteem to women's participation in sport.

Keywords: mascunity, gender, productive health, inappropriate, rights

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Authors: Shagufta Jahangir, Nadeemullah, Yaqoob, Raisa Jahangir

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The Persian language word ‘Purdah’ and in Arabic ‘Hajab’ is used for veil. Veil has been used by women for being escaped from men. In one way or the other veil has been continuously used in ancient as well as modern civilizations by women. Developed nations have blamed the use of veil an obstacle in the process of development. Therefore, modern nations have struggled to get rid of the use of veil. They argue that it is a sign of slavery for women and it is an obstacle in the path of development. The modern secular Muslims considered veil as the biggest obstacle for social and economic development. It makes a woman helpless, as being zanjir in her feet. It has become an obstacle in the process of development for women. It is also considered as a tool for segregation among men and women. The so called Muslims of the modern era are trying to introduce changes in religion by imitation the modern nations of the world. In particular ways for Muslim woman use of veil in Islam is must. It is a right provided her by religion. It provides her strength. In the Holy Quran word ‘Hajab’ is used 5 times. Islam is against domination and forceful practice of veil, as a part of teaching of Islam it is being adopted by women as a protection. This article aims at: (1) historical background of veil (2) Its existence in civilizations, (3) Meaning and interpretation of veil in Islamic context, (4) Economic impact of it on women (5) Discussion on its practice in Islamic (eastern) and other (European) circles and conclusions followed by concerted bibliography.

Keywords: veil, economic development, civilizations, obstacle, secular Muslims, segregation

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Authors: Somaiya Mateen, Shagufta Moin, Abdul Qayyum, Atif Zafar

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Cytokines and reactive species play an important role in the pathophysiology of rheumatoid arthritis (RA). This study was done to determine the levels of reactive oxygen and nitrogen species (ROS and RNS), inflammatory cytokines and the markers of protein, DNA and lipid oxidation in the blood of RA patients, with the aim to study the antioxidant and anti-inflammatory role of moderate intensity exercises in the management of RA. RA patients were subdivided into two groups- first group (n=30) received treatment with conventional RA drugs while the second group (n=30) received moderate exercise therapy along with the conventional drugs for a period of 12 weeks. The levels of ROS, RNS, inflammatory cytokines and markers of biomolecule oxidation were monitored before and after 12 weeks of treatment. RA patients showed a marked increase in the levels of ROS, RNS, inflammatory cytokines, lipid, protein and DNA oxidation as compared to the healthy controls. These parameters were ameliorated after treatment with drugs alone and exercise combined with drugs, with the amelioration being more significant in patients given drugs along with the moderate intensity exercise treatment. In conclusion, the role of ROS, RNS and inflammatory cytokines in the pathogenesis of RA has been confirmed by this study. These may also serve as potential biomarker for assessing the disease severity. Finally, the addition of moderate intensity exercises in the management of RA may be of great value.

Keywords: rheumatoid arthritis, reactive oxygen species, inflammatory cytokines, moderate intensity exercises

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Authors: Munir Ashraf, Shagufta Riaz

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Personal protective equipment (PPE) and bioactive textiles are highly important for the health care of front line hospital workers, patients, and the general population to be safe from highly infectious diseases. This was even more critical in the wake of COVID-19 outbreak. Most of the medical textiles are inactive against various viruses and bacteria, hence there is a need to wash them frequently to avoid the spread of microorganisms. According to survey conducted by the world health organization, more than 500 million people get infected from hospitals, and more than 13 million died due to these hospitals’ acquired deadly diseases. The market available PPE are though effective against the penetration of pathogens and to kill bacteria but, they are not breathable and active against different viruses. Therefore, there was a great need to develop textiles that are not only effective against bacteria, fungi, and viruses but also are comfortable to the medical personnel and patients. In the present study, waterproof breathable, and biologically active textiles were developed using antiviral and antibacterial nanomaterials. These nanomaterials like TiO₂, ZnO, Cu, and Ag were immobilized at the surface of cotton fabric by using different silane coupling agents and electroless deposition that they retained their functionality even after 30 industrial laundering cycles. Afterwards, the treated fabrics were coated with a waterproof breathable film to prevent the permeation of liquid droplets, any particle or microorganisms greater than 80 nm. The developed cotton fabric was highly active against bacteria and viruses. The good durability of nanomaterials at the cotton surface after several industrial washing cycles makes this fabric an ideal candidate for bioactive textiles used in the medical field.

Keywords: antibacterial, antiviral, cotton, durable

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Authors: Shagufta Gulraiz, Abu Saeed Hashmi, Muhammad Mohsin Javed

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Lysine required for poultry feed is imported in Pakistan to fulfil the desired dietary needs. Present study was designed to produce maximum lysine by utilizing cheap sources to save the foreign exchange. To achieve the goal of lysine production through fermentation, large scale production of lysine was carried out in 7.5 L stirred glass vessel fermenter with wild and mutant Brevibacterium flavum (B. flavum) using all pre-optimized conditions. The identification of produced lysine was carried out by TLC and amino acid analyzer. Toxicity evaluation of produced lysine was performed before feeding to broiler chicks. During biological trial concentrated fermented broth having 8% lysine was used in poultry rations as a source of Lysine for test birds. Fermenter scale studies showed that the maximum lysine (20.8 g/L) was produced at 250 rpm, 1.5 vvm aeration, 6.0% inoculum under controlled pH conditions after 56 h of fermentation with wild culture but mutant (BFENU2) gave maximum yield of lysine 36.3 g/L under optimized condition after 48 h. Amino acid profiling showed 1.826% Lysine in fermented broth by wild B. flavum and 2.644% by mutant strain (BFENU2). Toxicity evaluation report showed that the produced lysine is safe for consumption by broilers. Biological evaluation results showed that produced lysine was equally good as commercial lysine in terms of weight gain, feed intake and feed conversion ratio. A cheap and practical bioprocess of Lysine production was concluded, that can be exploited commercially in Pakistan to save foreign exchange.

Keywords: lysine, fermentation, broiler chicks, biological evaluation

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Authors: Somaiya Mateen, Shagufta Moin, Mohammad Owais, Abdul Khan, Atif Zafar

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In rheumatoid arthritis (RA), impaired oxidative metabolism and imbalance between pro-and anti-inflammatory cytokines are responsible for causing inflammation and the degradation of cartilage and bone. The present study was done to evaluate the level and hence the role of reactive oxygen species (ROS) and inflammatory cytokines in the pathogenesis of RA. The present study was performed in the blood of 80 RA patients and 55 age and sex-matched healthy controls. The level of ROS (in 5% hematocrit) and the plasma level of pro-inflammatory cytokines [TNF-α, interleukin-6 (IL-6), IL-22] and anti-inflammatory cytokines (IL-4 and IL-5) were monitored in healthy subjects and RA patients. For evaluating the role of rheumatoid factor (RF) in the pathogenesis of RA, patients were sub-divided on the basis of presence or absence of RF. Reactive species and inflammatory cytokines were correlated with disease activity measure-Disease Activity Score for 28 joints (DAS28). The level of ROS, TNF-α, IL-6 and IL-22 were found to be significantly higher in RA patients as compared to the healthy controls, with the increase being more significant in patients positive for rheumatoid factor and those having high disease severity. On the other hand, a significant decrease in the level of IL-4 and IL-10 were observed in RA patients compared with healthy controls, with the decrease being more prominent in severe cases of RA. Higher ROS (indicative of impaired anti-oxidant defence system) and pro-inflammatory cytokines level in RA patients may lead to the damage of biomolecules which in turn contributes to tissue damage and hence to the development of more severe RA. The imbalance between pro-and anti-inflammatory cytokines may lead to the development of multi-system immune complications. ROS and inflammatory cytokines may also serve as a potential biomarker for assessing the disease severity.

Keywords: rheumatoid arthritis, reactive oxygen species, pro-inflammatory cytokines, anti-inflammatory cytokines

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Authors: Mohsin Shahab, Shagufta Rehmat, Faisal F. Khan

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Background: The global COVID-19 pandemic has generated health problems worldwide. Health care workers are the front-line warriors against the pandemic. The aim of this study was to find out the prevalence of COVID-19 (7th May 2021 to 3rd August 2021) amongst Health Care Workers (HCWs) and to assess the complications associated with it and its effects on their quality of life. Material and Method: The study was conducted in healthcare facilities which serve as pandemic hospitals in district Swat. A total of 140 healthcare workers, who were employed in the COVID-19 health care facilities, including the department of Pulmonology, Intensive Care Unit (ICU), and COVID-19 wards. Participants were tested for COVIID-19 using RT PCR test. A Case Report Form (CRF) for conditions during and post COVID-19 was filled to assess the complications and quality of life of health care workers. Results: A total of 140 Health Care Workers were studied, out of which 40% were doctors, 22% nursing staff, 17% paramedic staff, 9% cleaning staff, lab technologist 6%, 2% operation theater staff, administration staff, and pharmacist. The respondents were also investigated for pre-existing illness prior to SARS-CoV-2 infection, hypertension was the most prevalent, followed by chronic heart diseases and neurological disorders. Fever was the most common symptom, recorded 76.42% in the participants, while 55.71% of participants had dry cough, 55% had a sore throat, following by chest pain 43.56%. Reinfection rate was 10%, with chest pain being recorded in 85.71%. Post disease complication analysis showed that 47.14% of the participants were diagnosed with a new diagnosis after the COVID-19 recovery. Pulmonological diseases were recorded the most as a new diagnosis in, followed by gastrointestinal and psychological problems. Conclusions: The results of the study illustrates how COVID-19 has affected the overall health and quality of life of HCWs in District Swat of Khyber Pakhtunkhwa, Pakistan.

Keywords: SARS-CoV-2, COVID-19, HCW's, symptoms, questionnaire, post COVID-19

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Authors: Shagufta Riaz, Ayesha Younus, Munir Ashraf, Tanveer Hussain

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Aesthetic and performance are two most important considerations along with quality, durability, comfort and cost that affect the garment credibility. Fabric drape is perhaps the most important clothing characteristics that distinguishes fabric from the sheet, paper, steel or other film materials. It enables the fabric to mold itself under its own weight into desired and required shape when only part of it is directly sustained. The fabric has the ability to be crumpled charmingly in bent folds of single or double curvature due to its drapeability to produce a smooth flowing i.e. ‘the sinusoidal-type folds of a curtain or skirt’. Drape and seam strength are two parameters that are considered for aesthetic and performance of fabric for both apparel and home textiles. Until recently, no such study have been conducted in which effect of weave designs on drape and seam strength of fabric and garment is inspected. Therefore, the aim of this study was to measure seam strength and drape of fabric and garment objectively by changing weave designs and quality of the fabric. Also, the comparison of 2-D drape and 3-D drape was done to find whether a fabric behaves in same manner or differently when sewn and worn on the body. Four different cotton weave designs were developed and pr-treatment was done. 2-D Drape of the fabric was measured by drapemeter attached with digital camera and a supporting disc to hang the specimen on it. Drape coefficient value (DC %) has negative relation with drape. It is the ratio of draped sample’s projected shadow area to the area of undraped (flat) sample expressed as percentage. Similarly, 3-D drape was measured by hanging the A-line skirts for developed weave designs. BS 3356 standard test method was followed for bending length examination. It is related to the angle that the fabric makes with its horizontal axis. Seam strength was determined by following ASTM test standard. For sewn fabric, stitch density of seam was found by magnifying glass according to standard ASTM test method. In this research study, from the experimentation and evaluation it was investigated that drape and seam strength were significantly affected by change of weave design and quality of fabric (PPI & yarn count). Drapeability increased as the number of interlacement or contact point deceased between warp and weft yarns. As the weight of fabric, bending length, and density of fabric had indirect relationship with drapeability. We had concluded that 2-D drape was higher than 3-D drape even though the garment was made of the same fabric construction. Seam breakage strength decreased with decrease in picks density and yarn count.

Keywords: drape coefficient, fabric, seam strength, weave

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Authors: Shagufta Jabeen, Faez Jesse Firdaus Abdullah, Zunita Zakaria, Nurulfiza Mat Isa, Yung Chie Tan, Wai Yan Yee, Abdul Rahman Omar

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Pasteurella multocida is associated with acute, as well as, chronic infections in avian and bovine such as pasteurellosis and hemorrhagic septicemia (HS) in cattle and buffaloes. Iron is one of the most important nutrients for pathogenic bacteria including Pasteurella and acts as a cofactor or prosthetic group in several essential enzymes and is needed for amino acid, pyrimidine, and DNA biosynthesis. In our recent study, we showed that 2% of Pasteurella multocida serotype A strain PMTB2.1 encode for iron regulating genes (Accession number CP007205.1). Genome sequencing of other Pasteurella multocida serotypes namely PM70 and HB01 also indicated up to 2.5% of the respective genome encode for iron regulating genes, suggesting that Pasteurella multocida genome comprises of multiple systems for iron uptake. Since P. multocida PMTB2.1 has more than 40 CDs out of 2097 CDs (approximately 2%), encode for iron-regulated. The gene expression profiling of four iron-regulating genes namely fbpb, yfea, fece and fur were characterized under iron-restricted environment. The P. multocida strain PMTB2.1 was grown in broth with and without iron chelating agent and samples were collected at different time points. Relative mRNA expression profile of these genes was determined using Taqman probe based real-time PCR assay. The data analysis, normalization with two house-keeping genes and the quantification of fold changes were carried out using Bio-Rad CFX manager software version 3.1. Results of this study reflect that iron reduced environment has significant effect on expression profile of iron regulating genes (p < 0.05) when compared to control (normal broth) and all evaluated genes act differently with response to iron reduction in media. The highest relative fold change of fece gene was observed at early stage of treatment indicating that PMTB2.1 may utilize its periplasmic protein at early stage to acquire iron. Furthermore, down-regulation expression of fece with the elevated expression of other genes at later time points suggests that PMTB2.1 control their iron requirements in response to iron availability by down-regulating the expression of iron proteins. Moreover, significantly high relative fold change (p ≤ 0.05) of fbpb gene is probably associated with the ability of P. multocida to directly use host iron complex such as hem, hemoglobin. In addition, the significant increase (p ≤ 0.05) in fbpb and yfea expressions also reflects the utilization of multiple iron systems in P. multocida strain PMTB2.1. The findings of this study are very much important as relative scarcity of free iron within hosts creates a major barrier to microbial growth inside host and utilization of outer-membrane proteins system in iron acquisition probably occurred at early stage of infection with P. multocida. In conclusion, the presence and utilization of multiple iron system in P. multocida strain PMTB2.1 revealed the importance of iron in the survival of P. multocida.

Keywords: iron-related genes, real-time PCR, gene expression profiling, fold changes

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Authors: Shagufta Jabeen, Faez J. Firdaus Abdullah, Zunita Zakaria, Nurulfiza M. Isa, Yung C. Tan, Wai Y. Yee, Abdul R. Omar

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Pasteurella multocida (PM) is an important veterinary opportunistic pathogen particularly associated with septicemic pasteurellosis, pneumonic pasteurellosis and hemorrhagic septicemia in cattle and buffaloes. P. multocida serotype A has been reported to cause fatal pneumonia and septicemia. Pasteurella multocida subspecies multocida of serotype A Malaysian isolate PMTB2.1 was first isolated from buffaloes died of septicemia. In this study, the genome of P. multocida strain PMTB2.1 was sequenced using third-generation sequencing technology, PacBio RS2 system and analyzed bioinformatically via de novo analysis followed by in-depth analysis based on comparative genomics. Bioinformatics analysis based on de novo assembly of PacBio raw reads generated 3 contigs followed by gap filling of aligned contigs with PCR sequencing, generated a single contiguous circular chromosome with a genomic size of 2,315,138 bp and a GC content of approximately 40.32% (Accession number CP007205). The PMTB2.1 genome comprised of 2,176 protein-coding sequences, 6 rRNA operons and 56 tRNA and 4 ncRNAs sequences. The comparative genome sequence analysis of PMTB2.1 with nine complete genomes which include Actinobacillus pleuropneumoniae, Haemophilus parasuis, Escherichia coli and five P. multocida complete genome sequences including, PM70, PM36950, PMHN06, PM3480, PMHB01 and PMTB2.1 was carried out based on OrthoMCL analysis and Venn diagram. The analysis showed that 282 CDs (13%) are unique to PMTB2.1and 1,125 CDs with orthologs in all. This reflects overall close relationship of these bacteria and supports the classification in the Gamma subdivision of the Proteobacteria. In addition, genomic distance analysis among all nine genomes indicated that PMTB2.1 is closely related with other five Pasteurella species with genomic distance less than 0.13. Synteny analysis shows subtle differences in genetic structures among different P.multocida indicating the dynamics of frequent gene transfer events among different P. multocida strains. However, PM3480 and PM70 exhibited exceptionally large structural variation since they were swine and chicken isolates. Furthermore, genomic structure of PMTB2.1 is more resembling that of PM36950 with a genomic size difference of approximately 34,380 kb (smaller than PM36950) and strain-specific Integrative and Conjugative Elements (ICE) which was found only in PM36950 is absent in PMTB2.1. Meanwhile, two intact prophages sequences of approximately 62 kb were found to be present only in PMTB2.1. One of phage is similar to transposable phage SfMu. The phylogenomic tree was constructed and rooted with E. coli, A. pleuropneumoniae and H. parasuis based on OrthoMCL analysis. The genomes of P. multocida strain PMTB2.1 were clustered with bovine isolates of P. multocida strain PM36950 and PMHB01 and were separated from avian isolate PM70 and swine isolates PM3480 and PMHN06 and are distant from Actinobacillus and Haemophilus. Previous studies based on Single Nucleotide Polymorphism (SNPs) and Multilocus Sequence Typing (MLST) unable to show a clear phylogenetic relatedness between Pasteurella multocida and the different host. In conclusion, this study has provided insight on the genomic structure of PMTB2.1 in terms of potential genes that can function as virulence factors for future study in elucidating the mechanisms behind the ability of the bacteria in causing diseases in susceptible animals.

Keywords: comparative genomics, DNA sequencing, phage, phylogenomics

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