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Protective role of poncirin against polyethylene microplastics instigated cardiac toxicity via regulating Nrf2/keap1 pathway

Yasmeen Rasheed1, Nazia Ehsan1, Muhammad Faisal Hayat1, Asma Ashraf2, Hammad Ahmad Khan1, Aisha Khatoon3, Muhammad Umar Ijaz1*, Yasir S. Raouf4, Abdelouahid Samadi4*, Samir Chtita5

1Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad 38040, Pakistan

2Department of Zoology, Government College University, Faisalabad 38000, Pakistan

3Department of Pathology, University of Agriculture, Faisalabad 38040, Pakistan

4Department of Chemistry, College of Science, United Arab Emirates University, Ai-Ain P.O. Box 15551, United Arab Emirates

5Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, P.O. Box No. 7955, Casablanca, Morocco

Abstract

Polyethylene microplastics (PEMPs) are one of the most toxic pollutants in our surroundings that induce damage to various organs including heart. Poncirin (PON) is a natural flavonoid that shows diverse pharmacological activities. This study was aimed to assess the alleviative potential of PON against PEMPs provoked cardiac damage in rats. Twenty-four rats were segregated into 4 groups including control, PEMPs (1.5 mg/kg) treated group, PEMPs (1.5 mg/kg) + PON (5mg/kg) exposed group and PON (5mg/kg) alone treated group. It was revealed that PEMPs exposure notably decreased the expression of Nrf2 and its associated antioxidant genes while upregulating the expression of Keap-1. Besides, PEMPs intoxication reduced the activities of superoxide dismutase (SOD), catalase (CAT), heme-oxygenase-1 (HO-1), peroxidase (GPx), glutathione reductase (GSR), and glutathione (GSH) content while increasing reactive oxygen species (ROS) and malondialdehyde (MDA) levels. Additionally, exposure to PEMPs resulted in upregulation of lactate dehydrogenase (LDH), creatine kinase MB (CK-MB), troponin I and phosphokinase (CPK).  Besides, PEMPs administration escalated the levels of TNF- α IL-6, NF-κB, TNF- α, IL-1β, and COX-2 activity. Moreover, the administration of PEMPs escalated the levels of Caspase-3 and Bax, while downregulating the levels of Bcl-2. Additionally, PEMPs exposure disrupted the architecture of cardiac tissues. Nonetheless, PON supplementation remarkably protected the cardiac tissues by regulating the aforementioned damages.

Keywords: Polyethylene microplastics, Poncirin, Cardiac damage, Oxidative stress, Inflammation

Assessing genetic potential and development of crosses for breeding cotton (Gossypium hirsutum L.) against drought

Muhmmad Kashif Shahzad Sarwar1,2, Abdul Ghaffar3, Saghir Ahmad4, Shoaib Ur Rehman1, Ummara Waheed1*

1Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan

2Cotton Research Station, Ayub Agricultural Research Institute, Faisalabad, Pakistan

3Departemnt of Agronomy, MNS University of Agriculture, Multan, Pakistan

4Cotton Research Institute, Multan, Pakistan

Abstract

Cotton diversity has long been studied using physiological and biochemical traits. This diversity has led to the development of various superior cotton cultivars over the year. At present and in face of climate change, development of high yielding and drought tolerant cotton varieties are necessary to fulfill the demand of ever-growing population of the world. In this study, Gossypium hirsutum L. germplasm (200) was evaluated under two irrigation regimes i.e., well-watered (W1) and limited water (W2) conditions. Various morphological and physiological traits were recorded under both irrigation regimes. A considerable reduction was recorded in W2 conditions in all the recorded traits except for glycine betaine, soluble sugars, and proline contents, highlighting the impact of drought on cotton germplasm. Cotton genotypes that maintained higher yield had positive correlation with biochemical traits. Out of 63 best performing genotype (superior parents based on the recorded data), FH-414, FH-415, FH-416, FH-326, FH-492, FH-Anmol, Gomal-105, Marvi, NIAB-878 and VH-327 were selected for hybridization to make crosses following Line x Tester fashion. F1 hybrids (25 crosses) and 10 parents were again planted under W1 and W2 conditions. Out of 25 crosses, FH-326 × Marvi (CS5) and NIAB-878 × FH-414 (CS16) performed better under water deficit conditions. Quantitative real-time PCR was also performed using GhHH3 and GhIDD. CS5 and CS16 had higher expression of drought tolerance causing GhHH3 and GhIDD genes. The newly developed cotton crosses will pave the way for the development of high yielding drought tolerant cotton varieties in face of climate change.

Keywords: Biochemical attributes, Yield and yield components, GhHH3, GhIDD, Drought

Apoptosis induction, cell cycle arrest, and tumor genes expression analysis of tamoxifen and ivermectin loaded chitosan nanoparticles against MCF-7 Cell line

Usama bin Naeem1, Muhammad Adil Rasheed1*, Muhammad Ashraf1, Muhammad Yasir Zahoor2

1Department of Pharmacology and Toxicology, Faculty of Biosciences, University of Veterinary and Animal Sciences Lahore, Pakistan

2Insititue of Biochemistry and Biotechnology, Faculty of Biosciences, University of Veterinary and Animal Sciences Lahore, Pakistan

Abstract

One of the most dominant diseases in the world, particularly among women, is breast cancer. Breast cancer has tumor suppressor genes called CHEK2 and TP53. When there is a mutation in CHEK2 and TP53 genes there are more chances of breast cancer. This study aimed to investigate the already prepared and characterized nanoparticles loaded with Chitosan for Cell death, Mitochondrial Membrane and cell cycle arrest estimated through Flow Cytometry and gene expression analysis of CHEK2 and TP53 genes by real-time PCR. The Livak method was used to evaluate the results. The mean (± S.D) comparison between the control and target genes were used to calculate gene expression. Results showed that Ivermectin and Tamoxifen NPs (B+C) represented 34.8% cell death that is better than other combinations with propidium iodide stain while with Acridine orange stain Tamoxifen+Ivermectin (A+B) combination showed the remarkable and maximum of the all cell cycle arrest with value of 69.7% cell arrest at G0/G1 phase, 7.11% of cell arrest at S Phase and 7.05% of G2/M Phase arrest. It was demonstrated that the expression levels of CHEK2 and TP53 genes were significantly increased (P<0.001) in Ivermectin+Tamoxifen NPs (B+C) compared with control groups. It is concluded that Tamoxifen nanoparticles with Ivermectin showed strong anti-proliferative activity against breast cancer cells. The expression levels of nanoparticles containing Tamoxifen were significantly increased compared to the other treatments and control groups (P<0.001). Gene expression change with change in dose concentrations.

Keywords: Breast cancer, Apoptosis, Cell cycle arrest, Pharmacogenomic, Gene expression

Comparative homology and complete B2L gene-based sequence analysis of ORF virus from sheep and goats in Pakistan

Muhammad Khalid Mansoor*1, Kashif Iqbal1, Ali Hassan2, Muhammad Saqib2, Ali Zohaib1, Sabiqaa Masood3

1Department of Microbiology, Faculty of Veterinary & Animal Science, The Islamia University of Bahawalpur, Pakistan

2Department of Clinical Medicine & Surgery, University of Agriculture, Faisalabad, Pakistan

3Department of Parasitology, Faculty of Veterinary & Animal Science, The Islamia University of Bahawalpur, Pakistan

 

*Corresponding author’s email: khalid.mansoor@iub.edu.pk

Received: 13 September 2023 / Accepted: 5 April 2024 / Published Online: 13 December 2024

 

Abstract

Contagious Ecthyma (CE), also known as scabby mouth disease, is caused by an epitheliotropic parapoxvirus that primarily affects the goat and sheep populations worldwide. This study focused on investigating 12 outbreaks of CE in sheep and goat herds across various regions of Punjab, Pakistan. A total of 35 samples were collected between March 2021 and May 2022, with 34 out of 35 samples testing positive for parapoxvirus through PCR. Subsequently, 24 complete sequences of the major envelope protein B2L gene were successfully obtained. The nucleotide and amino acid sequences of the ORF virus B2L gene were analyzed. The 1206bp amplicons, after Sanger sequencing revealed an open reading frame of 1137bp encoding 378 amino acids. The minimum and maximum nucleotide differences of 0 and 34, respectively, were observed, while the percentage similarity at the nucleotide level and amino acid level ranged from 97.98% to 100% and 97.62% to 100%, respectively, among the ORF strains in this research study. The results of the phylogenetic analysis revealed that all 24 ORF virus isolates from Pakistan belonged to Group-I ORF viruses. The comparative homology of Pakistani ORF virus strains with Indian, Chinese, and Turkish isolates was 99.03%, 98.59%, and 98.15%, respectively. This study contributes to understanding the circulation of Group I ORF viruses in Pakistan and their relationship with strains from neighbouring countries. Furthermore, these findings may offer insights into the genotype of the causative agent responsible for the contagious pustular dermatitis (CPD) outbreak in Punjab, Pakistan.

 

Keywords: B2L gene, Contagious, Contagious pustular dermatitis, ORF

Mechanistic approach to investigate the induction of toxicity by magnesium oxide nanoparticles on testicular, nervous and muscular tissues of albino rats

Gulnaz Afzal1*, Muhammad Irfan Ullah2, Nadeem Ali3, Moeen Afzal1, Riaz Hussain4, Nabil A Alhakamy5, Nisreen Rajeh6, Sarmad Rehan7, Rehana Iqbal8, Muhammad Shahid Iqbal1, Ahrar Khan9*
1Department of Zoology, The Islamia University of Bahawalpur 63100, Pakistan
2Department of Pathobiology, Faculty of Veterinary Sciences, Bahauddin Zakariya University, Multan, Pakistan
3Center of Excellence in Environmental Studies, King Abdulaziz University, Jeddah 21589, Saudi Arabia
4Department of Pathology, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur 63100, Pakistan
5Pharmaceutics Department, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
6Department of Clinical Anatomy, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
7Department of Anatomy, Faculty of Veterinary Sciences, University of Agriculture, Faisalabad, Pakistan
8Institute of Pure and Applied Biology, Zoology Division, Bahauddin Zakariya University, Multan, Pakistan
9Faculty of Veterinary Sciences, University of Agriculture, Faisalabad, Pakistan

Abstract
Nanoparticles are used extensively in various industries, such as agriculture, food packaging, medical diagnostics and electronics. However, their increasing usage raises concerns regarding potential health hazards and environmental risks. This study examined the impact of intra-peritoneal injections of magnesium oxide (MgO) nanoparticles on the brain, testis, and muscles of male albino rats. Mature male rats (n=20) after acclimatization were randomly divided into four groups (G0, G1, G2, G3). The rats in the treated groups (G1-G3) were given MgO NPs @ 25 mg/kg, 50 mg/kg and 75 mg/kg respectively for ten consecutive days. G0 rats served as untreated control group. Results indicated that MgO NPs induced clinical alterations in exposed rats. The exposed organs including brain, and testis gained more weight and their stress parameters [reactive oxygen species (ROS) and thiobarbituric acid reactive substances (TBARS)] increased significantly in a dose dependent manner. Antioxidant enzymes including catalase (CAT), peroxidase (POD), reduced glutathione (GSH) and superoxide dismutase (SOD) reduced significantly in studied organs as compared to control ones. The treated rats have shown atrophy of neurons, microgliosis, cytoplasmic vacuolization, and congestion. Changes in the testis include inflammation, sloughing of cells, damaged spermatogonia, necrosis of spermatids, spermatogonia and arrest of spermatogenesis process. Conclusively, it is suggested that persistent application of nanomaterials at environmentally relevant concentrations may induce adverse toxicological effects in targeted and non-targeted exposed animals.

Keywords: Albino rats, MgO NPs, Oxidative stress, Antioxidant enzymes, Histopathology

Multi-biomarker approach to assess oxidative stress and antioxidants profile in male albino rats exposed to ZnO nanoparticle

Yasir Mahmood1, Nabeel Ijaz2, Aliza Maheen1, Ghulam Mustafa1, Duaa Abdullah Bafail3, Muhammad Rafi Qamar4, Muhammad Aitazaz Ahsan5, Nasir Masood6, Nisreen Rajeh7, Mudassar Mohiuddin8*
1Department of Zoology, The Islamia University, Bahawalpur, Pakistan
2Department of Clinical Sciences, Faculty of Veterinary Sciences, Bahauddin Zakariya University, Multan, Pakistan
3Department of Clinical Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
4Department of Clinical Medicine and Surgery, Faculty of Veterinary & Animal Sciences, The Islamia University, Bahawalpur, Pakistan
5Department of Pathology, Faculty of Veterinary & Animal Sciences, The Islamia University, Bahawalpur, Pakistan
6Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
7Department of Clinical Anatomy, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
8Department of Microbiology, Faculty of Veterinary & Animal Sciences, The Islamia University, Bahawalpur, Pakistan

Abstract
ZnO Nanoparticles (ZnO NPs) have wide applications in many fields of life ranging from health, food, agriculture, veterinary medicine, biotechnology, public health, textile and cosmetics. However, exposure to these NPs poses risks to public health, non-target living organisms and the environment. Hence, this study assessed toxicological impacts of ZnO NPs on hematopoietic tissues (bone marrow) and different visceral organs like lungs, intestine and muscles of male Wistar albino rats. Twenty male (20) Wistar albino rats were placed in four groups such as T0 (control group), T1 (50 mg/kg/day ZnO NPs), T2 (75 mg/kg/day ZnO NPs), and T3 (100 mg/kg ZnO NPs). Treated rats exhibited different signs of toxicity like depression and anxiety at higher doses of ZnO NPs. The bone marrow and other visceral organs/tissues were removed and analyzed to know the status of oxidative stress and antioxidant biomarkers. Results revealed notable increase (P≤0.05) in contents of oxidative stress biomarkers (ROS and TBARS) and significant decrease (P≤0.05) in antioxidant enzymes (POD, SOD, CAT, and GSH) in bone marrow as well as lungs, intestine, and muscles (gums) tissues. Histopathological examination indicated degeneration of muscle fibers, atrophied cells and presence of inflammatory materials in muscles (gums) of treated rats. Histologically, lungs were edematous, hemorrhagic and showed severe interstitial pneumonia while necrosis of epithelium of villi along with degeneration of villi in intestine of rats were observed at higher doses of nanoparticles. In conclusion, it can be suggested that ZnO-NPs may induce oxidative stress in multiple visceral organs of albino rats at higher concentrations highlighting disruption of physiological mechanisms.

Keywords: Nanoparticles, Zinc oxide, Nanoparticle toxicity, Oxidative stress biomarkers

Efficacy of silver oxide nanoparticles against multi-drug resistant Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus in burn wound infections

Hira Ahsan1,2, Maria Ayub1, Mehraj Gul3, Amber Qureshi1, Hani Z. Asfour4, Hafiz Muhammad Bilal5, Muhammad Azeem1, Ammara Wahid1, Nadeem Ali6, Rasheeha Naveed7, Mudasar Shabir8, Nisreen Rajeh9, Ayaz Mammadov10, Abu Baker Siddique1*

1Institute of Microbiology, Government College University, Faisalabad, Pakistan

2Academy of Medical Sciences, College of Henan Medicine, Zhengzhou University, Zhengzhou, Henan, 450052, China

3Quality Control Laboratory, National Institute of Health, Islamabad, Pakistan

4Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah-21589, Saudi Arabia

5Department of Rehabilitation and Allied Health sciences, Riphah International University, Lahore Campus, Lahore, Pakistan

6Center of Excellence in Environmental Studies, King Abdulaziz University, Jeddah-21589, Saudi Arabia

7Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan

8Institute of Advanced Materials and Flexible Electronics (IAMFE), Nanjing University of Information Science and Technology, Nanjing, China

9Department of Clinical Anatomy, Faculty of Medicine, King Abdulaziz University, Jeddah-21589, Saudi Arabia

10Department of Life Sciences, Western Caspian University, Baku, Azerbaijan

Abstract

Multi-drug resistant (MDR) bacterial infections rapidly increase morbidity, mortality, and treatment options. Therefore, the search for, development of, or discovery of antimicrobial drugs capable of combating MDR bacteria is urgently needed. The potential of nanotechnology to advance nanomedicine for human health is being studied. The purpose of the present research is to investigate the antimicrobial activity of silver oxide nanoparticles against carbapenem-resistant Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus. For this purpose, a total of 240 pus and wound samples were collected from the burn patients and further processed for isolation and identification of P. aeruginosa and MRSA according to standard microbiological techniques. Using a species-specific primer for each bacterial strain, polymerase chain reaction was used for molecular detection. Antimicrobial susceptibility was performed according to the Kirby-Bauer Disk Diffusion method. Molecular detection of carbapenemase-producing P. aeruginosa was performed by PCR by using specific primers. The agar well diffusion assay was used to examine the antibacterial properties of silver oxide nanoparticles, and the broth dilution assay was used to estimate the minimum inhibitory concentration and bactericidal concentration respectively. Out of 240 samples, 42 (17%) were identified as P. aeruginosa and 32 were confirmed as S. aureus isolates. From positive isolates of P. aeruginosa, 25 (59%) were recorded MDR P. aeruginosa and from positive isolates of S. aureus, 18 (56.25%) were detected as MRSA. The highly resistant drug against S. aureus was Penicillin G (100%) followed by Gentamicin (84.37%) and Ciprofloxacin (81.25%). The highly resistant drug against P. aeruginosa was Meropenem (100%), Imipenem (100%) followed by piperacillin (71.42%), gentamicin (64.28%), and ciprofloxacin (64.28%). Out of 42 P. aeruginosa isolates, 8(19%) the prevalence of carbapenemase encoding was noted as blaOXA 3(37.5%), blaNDM 2(25%), blaVIM 1(12.5%) blaKPC 1(12.5%) and blaIMP 1(12.5%).  Silver oxide nanoparticles were considered an effective antibacterial agent with 0.0065mg/mL-0.026mg/mL concentrations that highly inhibited the growth of MRSA and 0.39mg/mL-1.56mg/mL concentrations inhibited the growth of P. aeruginosa. The statistical analysis showed that the MIC and MBC for MDR P. aeruginosa were 0.96±0.43 μg/mL and 1.99±0.90 μg/mL, respectively, while for MRSA they were 0.01±0.008 μg/mL and 0.04±0.012 μg/mL, respectively. The MBC values were higher than MIC values for both pathogens. Silver oxide nanoparticles have such effective antibacterial properties that they can be used as an adequate source of antibacterial agents as alternatives to antibiotics.

Keywords: Silver oxide nanoparticles, Methicillin resistant, Gentamicin, Carbapenemase, Antimicrobial activity

Pharmaceuticals and their transformation products in environment and plants

Olga I. Lavrukhina1,2*, Vasiliy G. Amelin1,2, Leonid K. Kish1, Dmitry A. Makarov1, Alexey V. Tretyakov1, Elizaveta S. Kozeicheva1, Andrei S. Khishov1, Saidfatima M. Borunova1,3

1The Russian State Center for Animal Feed and Drug Standardization and Quality, 5, Zvenigorodskoye sh., Moscow, 123022 Russia

2Chemistry Department, Vladimir State University named after A.G. and N.G. Stoletov, 87, ul. Gor’kogo, Vladimir, 600000, Russia

3Department of Disease Diagnostics, Therapy, Obstetrics and Animal Reproduction, Moscow State Academy of Veterinary Medicine and Biotechnology – MVA named after K.I. Skryabin, 23, ul. Akademika Skryabina, Moscow, 109472 Russia

Abstract

Antibacterial drugs, analgesics, anti-infective, contrast media, antiepileptics, anti-inflammatory drugs, beta-blockers, and hormones are transferred to the environment from hospital and agricultural effluents, pharmaceutical industrial waste, human and animal excrements from households and sewers. Residues of pharmaceuticals in water and soil cause damage to the ecosystem. Their transformation products could be equally or more toxic and persistent than parent compounds. Some metabolites save biological activity in the environmental objects, including antibacterial activity. The objective of this review is to describe the environmental occurrence, transformation, eco-toxicity, analytical practices, degradation, and removal strategies used to control and prevent environmental contamination by pharmaceuticals (antibiotics, coccidiostatic agents, nonsteroidal anti-inflammatory drugs, beta-adrenomimetics, anthelmintics, hormones). Their determination in routine analysis through simple on-site devices and approaches is of great interest. Instrumental analysis is making progress in the advancement of qualitative and quantitative methods. Gas and liquid chromatography, capillary electrophoresis, and mass spectrometry are commonly used because of their high specificity, simultaneous multicomponent determination opportunities, and low detection limits. Highly sensitive methods generally with accurate mass spectrometric detection are required. High-performance liquid chromatography coupled with high-resolution mass spectrometry is an effective method. The use of green chemistry principles is preferred for both on-site and instrumental analysis, because fewer toxic reagents and solvents are required. The most promising approach for water treatment and manure detoxification is to merge chemical and biological strategies. Persistent pharmaceuticals will be most effectively eliminated by a combination of different treatment technologies.

Keywords: Pharmaceuticals, Water and soil contamination, Veterinary drugs, Manure Determination, Detoxification

The therapeutic effects of Hexuetongbi formula to combat the oxaliplatin-induced peripheral neuropathy using network pharmacological methods in rat model

Jingyu Feng1,2, Li Yang1, Jiguo Wang1,2, Jing Zhang1,2, Lizhu Lin2,3*

1Department of Oncology, Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen 518133, China

2The First School of Clinical Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou 510405, Guangdong, China

3Department of Oncology, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou 510405, Guangdong, China

Abstract

The objective of this study was to elucidate the mechanism of the Hexuetongbi formula in treating Chemotherapy-induced Peripheral Neuropathy (CIPN) using network pharmacology, pharmacodynamics, and mechanistic approaches in an oxaliplatin-induced peripheral neuropathy rat model. Network pharmacology is crucial for understanding the multi-target effects of the Hexuetongbi formula on CIPN. This approach allows for a comprehensive mapping of the complex interactions between the formula’s constituents and the biological pathways involved in CIPN, revealing potential synergistic effects and enhancing the formula’s pharmacological validation. The Hexue Tongbi formula’s impact was analyzed on rats undergoing peripheral neuropathy, observing changes in the morphology of L4-6 dorsal root ganglion neurons through hematoxylin and eosin (HE) staining. Simultaneously, a network pharmacology approach was employed, utilizing TCMSP and GeneCards databases to identify common targets between CIPN and Hexue Tongbi’s therapeutic entities. These core targets were scrutinized through GO enrichment and KEGG pathway analysis. To validate the findings, mRNA and protein expression levels in the L4-6 dorsal root ganglion were examined using quantitative PCR and Western Blot assays. Significant modifications were observed in the frequency of cold stimulus withdrawal reflexes and the L4-6 dorsal root ganglion neurons, while the mechanical withdrawal reflex threshold displayed a considerable decrease. In rats treated with the Hexuetongbi formula post-oxaliplatin, there was noteworthy mitigation in the cold stimulation paw withdrawal threshold and augmentation in the mechanical stimulation paw withdrawal threshold. Network pharmacology identified 19 active constituents in Hexuetongbi and 35 targets for CIPN, with the PI3K/Akt signaling pathway emerging as a prominent target. There was a significant upregulation in PI3K, Akt1, Akt2, and Bcl-2 compared to controls, suggesting that Hexuetongbi effectively mitigates oxaliplatin-induced peripheral neuropathy through the modulation of the PI3K/Akt and Bcl-2 pathways.

Keywords: Oxaliplatin, Chemotherapy-induced peripheral neuropathy, Traditional Chinese medicine, Dorsal root ganglion, Apoptosis

Syntenic mapping: A powerful tool for comparative genomics in plants

Ikhlaq Ahmad1, Azeem Iqbal Khan2, Safdar Ali3, Rashid Mehmood Rana1*

1Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University, Rawalpindi, Pakistan

2Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan

3Department of Agronomy, University of Agriculture, Faisalabad, Pakistan

Abstract

Comparative genomics has emerged as a great tool in understanding variations/similarities among various species at molecular level. In classical genetics synteny was used to show that two or more loci are present on same chromosome. Now a day’s synteny is being used to answer questions concerning homeology (the remains of completely homologous chromosomes). Chromosome/genome synteny has been observed in closely related species, having several genes with similar map orders. Synteny is helpful in comparing different genomes. It is used in the study of evolution of genomes, observe functional conservation, help in genome annotation and observe genome assembly errors. Synteny among different genomes can be detected by identification of conserved sequence elements among genomes, comparing the conserved proteins with the help of BLASTP or by the combination of both. Numerous tools are available for the detection of synteny among different genomes. Synteny analysis has been used largely to study complex genomes and helped in discoveries at genomic, chromosomal and gene levels. Syntenic mapping in plant breeding holds promising future prospects.

 

Keywords: Comparative genomics, Synteny, Homeology, Chromosome, Genome, Gene