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Article: Prediction and analysis of multi epitope based vaccine against Newcastle disease virus based on haemagglutinin neuraminidase protein.

Raza, Adnan / Asif Rasheed, Muhammad / Raza, Sohail / Tariq Navid, Muhammad / Afzal, Amna / Jamil, Farrukh

2022 Volume 29, Issue 4, Page(s) 3006–3014

Abstract: Newcastle disease virus (NDV), an avian orthoavulavirus, is a causative agent of Newcastle disease named (NDV), and can cause even the epidemics when disease is not treated. Previously several vaccines based on attenuated and inactivated viruses have ... ...

Abstract	Newcastle disease virus (NDV), an avian orthoavulavirus, is a causative agent of Newcastle disease named (NDV), and can cause even the epidemics when disease is not treated. Previously several vaccines based on attenuated and inactivated viruses have been reported which are rendered useless with the passage of time due to versatile changes in viral genome. Therefore, we aimed to develop an effective multi-epitope vaccine against the haemagglutinin neuraminidase (HN) protein of 26 NDV strains from Pakistan through a modern immunoinformatic approaches. As a result, a vaccine chimaera was constructed by combining T-cell and B-cell epitopes with the appropriate linkers and adjuvant. The designed vaccine was highly immunogenic, non-allergen and antigenic; therefore, the potential 3D-structureof multi epitope vaccine was constructed, refined and validated. A molecular docking study of a multiepitope vaccine candidate with the chicken Toll-like receptor-4 indicated successful binding. An
Language	English
Publishing date	2022-01-20
Publishing country	Saudi Arabia
Document type	Journal Article
ZDB-ID	2515206-3
ISSN	2213-7106 ; 1319-562X
ISSN (online)	2213-7106
ISSN	1319-562X
DOI	10.1016/j.sjbs.2022.01.036
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Article ; Online: Identification and genome-wide analysis provide insights into the genetic diversity and biotechnological potentials of novel cold-adapted Acinetobacter strain.

Kayani, Hajra / Rasheed, Muhammad Asif / Alonazi, Wadi B / Jamil, Farrukh / Hussain, Annam / Yan, ChangHui / Ahmed, Raza / Ibrahim, Muhammad

Extremophiles : life under extreme conditions

2023 Volume 27, Issue 2, Page(s) 14

Abstract: Extreme cold environments, such as polar regions or high-altitude mountains, are known for their challenging conditions including low temperatures, high salinity, and limited nutrient availability. Microbes that thrive in these environments have evolved ... ...

Abstract	Extreme cold environments, such as polar regions or high-altitude mountains, are known for their challenging conditions including low temperatures, high salinity, and limited nutrient availability. Microbes that thrive in these environments have evolved specialized strategies to survive and function under such harsh conditions. The study aims to identify, sequence the genome, perform genome assembly, and conduct a comparative genome-wide analysis of Acinetobacter sp. strain P1, which was isolated from the Batura glacier regions of Pakistan. A basic local alignment search tool of NCBI using 16 s RNA gene sequence confirmed the strain Acinetobacter following phylogenetic analysis revealed that strain P1 clustered with Acinetobacter sp. strain AcBz01. The high-throughput Genome sequencing was done by the NovaSeq 6000 sequencing system following de novo genome assembly reported 23 contigs, a genome size of 3,732,502 bp containing approximately 3489 genes and 63 RNAs (60 tRNA, 3 rRNA). The comparative genome analysis revealed that Acinetobacter sp. strain P1 exhibited the highest homology with the Acinetobacter baumannii ATCC 17978 genome and encompassed 1668 indispensable genes, 1280 conserved genes 1821 specific genes suggesting high genomic plasticity and evolutionary diversity. The genes with functional assignments include exopolysaccharide phosphotransferase enzyme, cold-shock proteins, T6SS, membrane modifications, antibiotic resistance, and set of genes related to a wide range of metabolic characteristics such as exopolysaccharides were also present. Moreover, the structural prediction analysis of EPS proteins reveals that structural flexibility allows for conformational modifications during catalysis, which boosts or increases the catalytic effectiveness at lower temperatures. Overall, the identification of Acinetobacter, a cold-adapted bacterium, offers promising applications in bioremediation, enzyme production, food preservation, pharmaceutical development, and astrobiology. Further research and exploration of these microorganisms can unlock their full biotechnological potential and contribute to various industries and scientific endeavors.
MeSH term(s)	Acinetobacter/genetics ; Phylogeny ; Catalysis ; Genomics ; Genetic Variation ; Genome, Bacterial
Language	English
Publishing date	2023-06-24
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1481278-2
ISSN	1433-4909 ; 1431-0651
ISSN (online)	1433-4909
ISSN	1431-0651
DOI	10.1007/s00792-023-01301-7
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Article ; Online: Utilizing sludge-based activated carbon for targeted leachate mitigation in wastewater treatment.

Mushtaq, Sarah / Jamil, Farrukh / Hussain, Murid / Inayat, Abrar / Majeed, Khaliq / Akhter, Parveen / Khurram, Muhammad Shahzad / Shanableh, Abdallah / Kim, Young Mo / Park, Young-Kwon

Environmental research

2024 Volume 249, Page(s) 118326

Abstract: Activated carbon (AC) based adsorbents derived from waste sludge were utilized to remediate mixed contaminants in wastewater as an integrated waste-to-resource approach promoting a paradigm shift in management of refuse sludge and wastewater. This review ...

Abstract	Activated carbon (AC) based adsorbents derived from waste sludge were utilized to remediate mixed contaminants in wastewater as an integrated waste-to-resource approach promoting a paradigm shift in management of refuse sludge and wastewater. This review specifically focuses on the remediation of constituents of landfill leachate by sludge-based activated carbon (SBAC). The adsorption effectiveness of SBAC for the exclusion of leachate characters including heavy metals, phenols, dyes, phosphates, and phosphorus were explored with regard to modifiers such as pH, temperature, properties of the adsorbent including functional groups, initial doses of absorbent and adsorbate, and duration of exposure to note the impact of each parameter on the efficiency of adsorption of the sludge adsorbent. Through the works of various researchers, it was noted that the properties of the adsorbent, pH and temperature impact the working of SBACs. The pH of the adsorbent by influencing the functional groups. Temperature was expected to have a paramount effect on the adsorption efficiency of the SBACs. The importance of the regeneration and recycling of the adsorbents as well as their leachability is highlighted. Sludge based activated carbon is recommended as a timely, resource-efficient, and sustainable approach for the remediation of wastewater.
Language	English
Publishing date	2024-02-06
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	205699-9
ISSN	1096-0953 ; 0013-9351
ISSN (online)	1096-0953
ISSN	0013-9351
DOI	10.1016/j.envres.2024.118326
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Article: Analysis of the conformational changes caused by the mutations in mitofusin2 gene by Insilico approach.

Rasheed, Muhammad Asif / Kanwal, Sumaira / Jamil, Farrukh / Ibrahim, Muhammad / Perveen, Shazia

JPMA. The Journal of the Pakistan Medical Association

2021 Volume 70, Issue 12(B), Page(s) 2342–2345

Abstract: Objective: To find the effect of pathogenic Mitofusin 2 mutations, responsible for Charcot-Marie-Tooth hereditary neuropathy type 2A, on protein structure.: Methods: The study was conducted at department of biosciences COMSATS University Islamabad, ... ...

Abstract	Objective: To find the effect of pathogenic Mitofusin 2 mutations, responsible for Charcot-Marie-Tooth hereditary neuropathy type 2A, on protein structure. Methods: The study was conducted at department of biosciences COMSATS University Islamabad, Sahiwal campus from September 2016 to July 2017, and comprised patients with Charcot Marie-Tooth hereditary neuropathy type 2A who were divided into early-onset severe group A and late-onset mild group B. Bioinformatics and molecular analysis was done to find the changes in the protein structure caused by the mutation. Three mutations were selected in two domains of the gene. These were: p. Arg94Trp, p. His165Arg and p. Thr362Met. Results: Of the 10 patients, 5(50%) were in each of the two groups. Change in the structure was predicted in the mutated protein at position p. Arg94Trp, and, due to the mutation, an extra alpha helix was formed in the mutated protein. Conclusions: Change in the structure of protein can be in a critical position that is involved in the mitochondrial fusion process. However, further studies are required to validate and explain the findings.
MeSH term(s)	Charcot-Marie-Tooth Disease/genetics ; GTP Phosphohydrolases/genetics ; Humans ; Mitochondrial Proteins/genetics ; Mutation ; Phenotype
Chemical Substances	Mitochondrial Proteins ; GTP Phosphohydrolases (EC 3.6.1.-)
Language	English
Publishing date	2021-01-21
Publishing country	Pakistan
Document type	Journal Article
ZDB-ID	603873-6
ISSN	0030-9982
ISSN	0030-9982
DOI	10.47391/JPMA.063
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Article ; Online: An In silico study of derivative of Newcastle disease virus epitopes based vaccine against Hemagglutunin neuraminidase protein.

Jamil, Farrukh / Aslam, Laiba / Laraib / Ali, Hira / Shoukat, Kainaat / Rasheed, Muhammad Asif / Raza, Sohail / Ibrahim, Muhammad

Journal of animal science

2022

Abstract: The causative agent of Newcastle disease (ND) is Newcastle disease virus. It belongs to avian species of Orthoavulavirus, Avulavirinae subfamily and if left untreated it may cause epidemic in poultry. Many vaccines have been made against Newcastle ... ...

Abstract	The causative agent of Newcastle disease (ND) is Newcastle disease virus. It belongs to avian species of Orthoavulavirus, Avulavirinae subfamily and if left untreated it may cause epidemic in poultry. Many vaccines have been made against Newcastle disease based on inactivated and attenuated viruses but become useless due to the genetic changes in the virus. We have recently reported epitope based vaccine by using immunoinformatics approaches. The vaccine was previously constructed against Hemagglutunin neuraminidase protein of Newcastle disease virus. Here we extended our work to develop several chimera of the proposed vaccine to design a new multi-epitope vaccine by shuffling the cytotoxic T lymphocytes (CTL) segments of the vaccine. Total 5040 constructs have been analyzed by shuffling 7 CTL epitopes. Highest antigenic multi-epitope construct was selected for the further study. Our new multi-epitope vaccine (MEV) construct contains 259 amino acids and is immunogenic, more antigenic and non-allergen. The refinement of the structure of MEV construct was performed. Molecular docking analyses showed its maximum binding with avian Toll-like 4 receptor. Subsequently, immune simulations showed its predicted ability to induce the host primary and secondary responses. Study suggests that our new multi-epitope vaccine chimera is more effective and stable protein against Newcastle disease virus strains in Pakistan. However, further studies are required to validate the vaccine through In vitro and In vivo studies.
Language	English
Publishing date	2022-11-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	390959-1
ISSN	1525-3163 ; 0021-8812
ISSN (online)	1525-3163
ISSN	0021-8812
DOI	10.1093/jas/skac375
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Article ; Online: A review on activated carbon modifications for the treatment of wastewater containing anionic dyes.

Azam, Kshaf / Shezad, Nasir / Shafiq, Iqrash / Akhter, Parveen / Akhtar, Farid / Jamil, Farrukh / Shafique, Sumeer / Park, Young-Kwon / Hussain, Murid

Chemosphere

2022 Volume 306, Page(s) 135566

Abstract: Polluted water resources, particularly those polluted with industrial effluents' dyes, are carcinogenic and hence pose a severe threat to sustainable and longstanding worldwide development. Meanwhile, adsorption is a promising process for polluted/ ... ...

Abstract	Polluted water resources, particularly those polluted with industrial effluents' dyes, are carcinogenic and hence pose a severe threat to sustainable and longstanding worldwide development. Meanwhile, adsorption is a promising process for polluted/wastewater treatment. In particular, activated carbon (AC) is popular among various wastewater treatment adsorbents, especially in the organic contaminants' remediation in wastewater. Hence, the AC's synthesis from degradable and non-degradable resources, the carbon activation involved in the AC synthesis, and the AC's modification to cutting-edge and effective materials have been modern-research targets in recent years. Likewise, the main research focuses worldwide have been the salient AC characteristics, such as its surface chemistry, porosity, and enhanced surface area. Notably, various modified-AC synthesis methods have been employed to enhance the AC's potential for improved contaminants-removal. Hence, we critically analyze the different modified ACs (with enhanced (surface) functional groups and textural properties) of their capacity to remove different-natured anionic dyes in wastewater. We also discuss the corresponding AC modification techniques, the factors affecting the AC properties, and the modifying agents' influence on the AC's morphological/adsorptive properties. Finally, the AC research of future interest has been proposed by identifying the current AC research gaps, especially related to the AC's application in wastewater treatment.
MeSH term(s)	Adsorption ; Charcoal/chemistry ; Coloring Agents ; Waste Water/chemistry ; Water Pollutants, Chemical/analysis
Chemical Substances	Coloring Agents ; Waste Water ; Water Pollutants, Chemical ; Charcoal (16291-96-6)
Language	English
Publishing date	2022-07-01
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	120089-6
ISSN	1879-1298 ; 0045-6535 ; 0366-7111
ISSN (online)	1879-1298
ISSN	0045-6535 ; 0366-7111
DOI	10.1016/j.chemosphere.2022.135566
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Article: Waste quail beaks as renewable source for synthesizing novel catalysts for biodiesel production

Khan, Haris Mahmood / Iqbal, Tanveer / Ali, Chaudhry Haider / Yasin, Saima / Jamil, Farrukh

Renewable energy. 2020 July, v. 154

2020

Abstract: In the current study, waste biomass (quail beaks) has been considered for synthesizing highly active hydroxyapatite (HAp) catalyst and used for biodiesel production. The produced HAp is characterized by several analytical techniques such as ... ...

Abstract	In the current study, waste biomass (quail beaks) has been considered for synthesizing highly active hydroxyapatite (HAp) catalyst and used for biodiesel production. The produced HAp is characterized by several analytical techniques such as Thermogravimetric analysis/differential scanning calorimetry (TGA/DSC), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), Scanning electron microscopy (SEM), Energy dispersive X-ray spectroscopy (EDX), Hammett indicator-benzene benzoic acid titration method and BET surface area. TGA/DSC analysis confirmed the complete removal of organic matter from the raw quail beaks. The XRD results revealed that the crystallinity of HAp phase was enhanced by thermal calcination with crystallite size of 37.33 nm at 900 °C. FTIR results showed the peaks of phosphate (PO4−3) and hydroxyl groups (OH−1) belonging to HAp molecules. EDX analysis revealed the presence of calcium (Ca) and phosphorus (P) compositions were 28.5 and 11.4 wt %, respectively. Total basicity and BET surface area of the synthesized catalyst were found to be 12.9 mmol/g and 4.54 m2/g, respectively. Furthermore, the treated HAp at temperature of 900 °C was used for biodiesel production from canola oil, rapeseed oil and waste cooking oil. Thus, HAp was opted to be highly active for biodiesel production with promising reusability.
Keywords	Fourier transform infrared spectroscopy ; X-ray diffraction ; benzoic acid ; biodiesel ; biomass ; calcium ; canola oil ; catalysts ; cooking fats and oils ; crystal structure ; crystallites ; differential scanning calorimetry ; energy-dispersive X-ray analysis ; fuel production ; hydroxyapatite ; kitchen waste ; organic matter ; phosphorus ; quails ; scanning electron microscopy ; surface area ; temperature ; thermogravimetry ; titration
Language	English
Dates of publication	2020-07
Size	p. 1035-1043.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2001449-1
ISSN	0960-1481
ISSN	0960-1481
DOI	10.1016/j.renene.2020.03.079
Database	NAL-Catalogue (AGRICOLA)

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Article: Human and ecological risk assessment of heavy metals in different particle sizes of road dust in Muscat, Oman

Al-Shidi, Hilal K. / Sulaiman, Hameed / Al-Reasi, Hassan A. / Jamil, Farrukh / Aslam, Muhammad

Environmental science and pollution research. 2021 July, v. 28, no. 26

2021

Abstract: Heavy metal contamination of Hg, As, Cu, Cr, Zn, and Pb was investigated in three different fractions 45, 125, and 200 μm of road dust in Muscat, Oman. Dust samples were collected from three different traffic roads, viz. high, medium, and low based on ... ...

Abstract	Heavy metal contamination of Hg, As, Cu, Cr, Zn, and Pb was investigated in three different fractions 45, 125, and 200 μm of road dust in Muscat, Oman. Dust samples were collected from three different traffic roads, viz. high, medium, and low based on traffic volume and then sieved individually before they analyzed using inductively coupled plasma optical emission spectrometry (ICP-OES). Cu has the highest level among the analyzed metals while the lowest amount was for Hg. Most of the metals in all traffic sites have higher concentration in finer fraction and the concentrations of Cu, Pb, and Zn in HT road dust decreased significantly from finer fraction (45 μm) to bigger fraction size (200 μm). The risks of analyzed heavy metals to the urban ecosystem and human health were calculated by the potential ecological risk index and human exposure model, respectively. Risk index levels of studied metals in the three fractions and roads vary from strong to very strong potential. Hg found to have the greatest contribution in risk index in the three different fractions and roads. The values of risk levels for individual metal contamination in the dust street samples from different roads and fractions were ranked in the following order: Hg > Cu > Pb > Cr > Zn. Ingestion is the main pathway of exposure to road dust particles for both children and adults, followed by dermal contact absorption. The HI for children and adults exposed to 45- and 125-μm particles were higher than exposed to 200-μm particles, which indicated that finer particles tend to have higher non-carcinogenic risk. The non-carcinogenic risks of the studied heavy metals to children and adults are within safe threshold value; however, health risks of Cr, Pb, and Cu were relatively high for children.
Keywords	absorption ; atomic absorption spectrometry ; dust ; environmental assessment ; exposure models ; heavy metals ; human health ; humans ; pollution ; research ; risk ; traffic ; urban areas ; Oman
Language	English
Dates of publication	2021-07
Size	p. 33980-33993.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-020-09319-6
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Article: Comprehensive kinetic study of Imperata Cylindrica pyrolysis via Asym2sig deconvolution and combined kinetics

Hidayat, Syarif / Bakar, Muhammad S. Abu / Ahmed, Ashfaq / Iryani, Dewi Agustina / Hussain, Murid / Jamil, Farrukh / Park, Young-Kwon

Journal of analytical and applied pyrolysis. 2021 June, v. 156

2021

Abstract: This study examined the non-isothermal kinetics of the slow pyrolysis of Imperata Cylindrica (IC). Pyrolysis conditions were developed under the pure N₂ flow and non-isothermal conditions at the heating rates of 2.5, 5, 10, and 17.5 K/min and over the ... ...

Abstract	This study examined the non-isothermal kinetics of the slow pyrolysis of Imperata Cylindrica (IC). Pyrolysis conditions were developed under the pure N₂ flow and non-isothermal conditions at the heating rates of 2.5, 5, 10, and 17.5 K/min and over the temperature range of 303–1173 K. The IC pyrolysis profiles could be identified into three parallel reactions, each of which corresponded to pseudo-hemicelluloses (P-Hem), pseudo-cellulose (P-Cell), and pseudo-lignin (P-Lig) decomposition. A systematic kinetic study of the pyrolysis of IC via thermogravimetric analysis (TGA) deconvolution using Asymmetric Double Sigmoidal (Asym2sig), Friedman differential iso-conversional and combined kinetics of biomass pseudo-components was carried out. The kinetics parameters of pseudo components fitted well with the pyrolysis experimental data for all the heating rates. Differential master-plots showed that the reaction mechanisms for pseudo hemicellulose (P-Hem) and pseudo cellulose (P-Cell) were diffusional and order based, and high order based (3rd order) for the pseudo lignin (P-Lig). Mechanism of P-Hem, P-Cell and P-Lig could be further reconstructed to Sestak and Berggren model of fα=α-0.98751-α1.325-ln⁡(1-α)0.0209,fα=α0.33131-α1.4731-ln⁡(1-α)0.0215 and fα=α-2.95511-α2.7642-ln⁡(1-α)0.0074, respectively. The combined kinetic reported the activation energies of pseudo-components were as 194.709 kJ/mol, 179.968 kJ/mol and 219.226 kJ/mol for P-Hem, P-Cell and P-Lig, respectively.
Keywords	Imperata cylindrica ; biomass ; cellulose ; hemicellulose ; lignin ; models ; pyrolysis ; temperature ; thermogravimetry
Language	English
Dates of publication	2021-06
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ISSN	0165-2370
DOI	10.1016/j.jaap.2021.105133
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Article: Upgradation of waste cooking oil to biodiesel in the presence of green catalyst derived from date seeds

Inayat, Abrar / Jamil, Farrukh / Raza, Mohsin / Khurram, Shahzad / Ghenai, Chaouki / Al-Muhatseb, Ala’a H.

Biofuels. 2021 Nov. 26, v. 12, no. 10

2021

Abstract: The present work reports a valorization of waste cooking oil (WCO) conversion to biodiesel in the presence of carbon catalyst derived from waste date seeds. The leftover carbon material is treated to remove impurities and modified further by impregnating ...

Abstract	The present work reports a valorization of waste cooking oil (WCO) conversion to biodiesel in the presence of carbon catalyst derived from waste date seeds. The leftover carbon material is treated to remove impurities and modified further by impregnating KOH, and is then used for biodiesel production. The optimization of the complete biodiesel production process was carried out considering the operating parameters reaction temperature (°C), retention time (min), catalyst composition/amount and methanol:WCO ratio. Three types of catalysts were prepared to predict the best composition of green catalysts derived from waste date seeds. Within the limit of set constraints, the maximum biodiesel yield obtained from WCO by a transesterification process was 93%. This high product conversion was achieved at an operating reaction temperature of 65 °C, using synthesized green catalyst type II with 3 wt% KOH on carbon, with a retention time of 90 min and a methanol:WCO ratio of 10:1. The synthesized biodiesel was characterized to evaluate and report its quality in line with international American Society for Testing and Materials (ASTM) and European Norms (EN) standards. The results show that the demonstrated work successfully produced biodiesel with high yield and within set safe standard quality limits.
Keywords	biodiesel ; carbon ; catalysts ; temperature ; transesterification
Language	English
Dates of publication	2021-1126
Size	p. 1245-1250.
Publishing place	Taylor & Francis
Document type	Article
ISSN	1759-7277
DOI	10.1080/17597269.2019.1608036
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