Advancements in Life Sciences (E-Journal, University of the Punjab)
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In Silico Analysis of Differentially Expressed Genes in Colorectal Carcinoma
Get PDFBackground: Colorectal carcinoma (CRC) is a primary cause of morbidity and mortality worldwide. Resistance to therapy contributes to poor patient prognosis. This study aimed to identify key proteins and interaction networks implicated in CRC that may serve as therapeutic targets and help overcome therapy resistance.Methods: We analyzed a microarray dataset comprising 58 CRC cases and 62 controls (total n = 120) to identify differentially expressed genes (DEGs). Protein–protein interaction (PPI) networks were constructed, and Cytoscape analysis was performed to identify the hub proteins. Based on subgraph centrality, betweenness and degree (≥10), hub proteins were selected for further literature search and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis.Results: A total of 95 up-regulated genes and 85 down-regulated genes of CRC patients were selected based on criteria of P 2.0. The PPI analysis revealed STAT3, HNRNPA2B1, RBM8A, RBM25, ATM, HIST1H2BK, SRSF5 and HNRNPDL as hub proteins. Based on criteria set for Cytoscape analysis, STAT3 and HNRNPA2B1 were identified as key hub proteins. KEGG pathway analysis revealed vital role of STAT3 in carcinogenesis.Conclusion: In addition of HNRNPA2B1 activation by STAT3, crosstalk of STAT3 with other oncogenic signaling pathways signifies its role in colorectal carcinogenesis. Our study highlights that STAT3 may be a possible therapeutic target which may help in overcoming the dilemma of resistance to drug treatment in advanced cases.Keywords: STAT3; Drug resistance; Targeted therapy; BioinformaticsEditorial Note: You are viewing latest version of this article having language corrections.
Evaluating the Epidemic Risk Posed by Marek's Disease Virus in Russia
Get PDFBackground: The highly oncogenic avian alpha herpes virus known as Marek's disease virus (MDV) raises concerns about its potential oncogenicity in humans. In this article, authors examine the potential epidemic risks associated with MDV, taking into account the current epidemic and epizootic situation in the Russian Federation, with a particular focus on the modern practices of pig and poultry farming. Given its oncogenic properties, MDV remains a cause for concern in the field of avian herpesviruses.Methods: The study was conducted in 2010-2022 in poultry farms Russian Federation, Republic of Belarus and the Republic of Kazakhstan where authors monitored the rate of vesicular enteritis and MDV. In total, 155 epizootics were examined, including the analysis of 62 epizootics of vesicular enteritis and the population of the studied area exceeded 1 million people.Results: The authors of the study found that vesicular enteritis, distributed over poultry farms in the Russia since 2011, and its safety for the population remains unknown. The increasing incidence of vesicular enteritis was also accompanied by various health issues in contact persons and veterinary personnel, as well as abnormal and concurrent increases in infectious laryngotracheitis and MDV in young birds.Conclusion: Authors come to the conclusion that the consequences of COVID-19 are accompanied by a deficiency of folic acid, which in turn leads to a risk of developing diseases associated with DNA viruses. It is concluded that MDV may contribute to the development of reproductive and breast cancers, highlighting the need for increased awareness and attention to the health risks associated with poultry farming and further research in this area.Keywords: Marek's disease virus; Vesicular enteritis; Herpesvirus infection; COVID-19Editorial Note: This article has post-publication language corrections.
Genetic Characterization of Carbapenem Resistant Acinetobacter baumannii in Tertiary care settings of Lahore, Pakistan
Get PDFBackground: Acinetobacter baumannii is major cause of ventilator associated pneumonia (VAP) as it is an opportunistic nosocomial organism. The current study was to find out the antibiotic resistance pattern of Acinetobacter baumannii, its phenotype and the genetic characterization of Metallo-β-Lactamase (MBL) genes that are responsible for carbapenem resistance.Methods: One hundred and fifty Carbapenem resistant Acinetobacter baumannii (CRAB) specimens were isolated and PCR amplification of organism specific blaOXA-51gene was performed and antibiotic susceptibility was checked. Phenotypic susceptibility analysis was performed by Modified Hodge Test (MHT) and Imipenem-EDTA Double Disc Synergy Test (IMP-EDTA DDST). The carbapenemases and MBL producing genes were amplified by PCR.Results: CRAB showed high resistance against piperacillin/tazobactam (99.3%), cefepime and ceftazidime (99.3% each), amikacin (91.3%), ciprofloxacin (96.7%) and levofloxacin (96.7%). Only one isolate showed resistance to colistin. The isolates positive for both MHT and DDST (n=70) were further characterized to detect metallo-β-lactamase genes. Molecular characterization revealed the presence of blaOXA-51 gene in all tested isolates (100%) followed by bla-VIM 89%, bla-OXA-23 64%, respectively and so on. Few genes coexisted with each other including blaVIM, blaOXA 23, blaOXA 51 and blaNDM-1. None of the isolate was found positive for blaIMP gene.Conclusion: It is concluded that CRAB isolates exhibited a high rate of resistance towards antimicrobials because of the presence of drug-hydrolyzing enzymes such as carbapenemmases and MBLs. This is among the rare study reported recently indicating CRAB isolates co-harboring many resistant genes are very difficult to treat. There is a dire need to develop novel antibiotics against resistant A. baumannii to minimize its prevalence. Moreover, it is recommended that colistin treatment in the clinical settings should be continuously monitored to prevent the development of resistance.Keywords: Acinetobacter baumannii; Carbapenem resistance; Metallo-beta-Lactamases; Resistant genesEditorial Expression of Concern:20 June 2025: Following publication of this paper, the internal audit (consequent to concerns on quality raised by Web of Science) notified Advancements in Life Sciences about an inappropriate category of article type. By this Editorial Expression of Concern, we alert the scientific community of this incidence as do the required corrections.Editorial Note:24 June 2025: You are viewing the latest version of this article having changes in the category section. Expression of concern is hereby revoked
Identification of Plant Flora Affecting Anti-Anxiety and Anti-Depression Disorders Based on Ethnobotanical Knowledge of the Arasbaran Region, Azerbaijan, Iran
Get PDFBackground: Ethnobotany, as a part of every district’s national capital, involves residents' experience and knowledge about plants and their features being the result of a long time of trial and error in nature. The purpose of this study was to obtain and document the culture of the traditional application of Arasbaran medicinal plants from Azerbaijan province in Iran.Methods: In this research, the information and knowledge of the people about the effective medicinal plants on common psychiatric syndromes including anxiety and depression were collected through questionnaires and interviews. Questions contain local names, organ usage, and traditional therapeutic characteristics of plants. Interviews then went on until the repeated answers confirmed the reliability and validity.Results: Labiatae plant family with 4 plants was the most effective herb family for the treatment of common psychiatric diseases. Also, the most plant organs utilized for treating nervous disorders included aerial parts (36%), fruits (22%), flowering branches (each with 21%) and flowers (14%), and seeds (7%). So, identification and documentation of their indigenous knowledge can pave the way for a better application of medicinal plants and their products.Conclusion: In this study, 12 medicinal plant species belonging to 9 families were studied. The largest proportion of plant species was related to the Labiatae family. The most commonly used organs were aerial parts, fruits, and flowering branches, respectively. Native medicinal plants of the Arasbaran region are traditionally used to treat common psychiatric syndromes and can be highly effective in the treatment of disorders such as depression and anxiety. Keywords: Herbal plants; Ethno-botany; Remedy; Psychiatry
RETRACTED ARTICLE: Synteny of Cotton SSR Markers Genomes Paves the Way for Resistance Against Black Root Rot Disease in Cotton
Get PDFBackground: Black root rot disease is documented for substantial reducing cotton yield and fiber quality. The isolation of candidate resistant genes in tetraploid genome AADD cotton species (2n=4x=52) remains challenging in the absence of research of black root rot resistance on progenitor DD genome diploid cotton. In this study, by exploiting Phytozome database, a comparative map of the black root rot-resistance quantitative trait loci in DD genome was constructed.Methods: Simple sequence repeats markers associated with these three quantitative trait loci in the AA genome were used as “anchored-probes” frameworks for establishing relationships between the two cotton genomes AA and DD.Results: Our findings showed that there was conserved orders among mapped simple sequence repeats markers on AA genome and the physical map of these simple sequence repeats markers on DD genome.Conclusion: It was suggested that the syntenic loci on chromosome 2, 7 and 11 on DD genome could harbor the resistance gene against the black root rot disease. This study could serve as a fundamental step in isolating and introducing the resistance gene against black root rot into elite cotton cultivars.Keywords: Comparative mapping; Resistance gene; Phytozome; Simple sequence repeats; Quantitative trait loci Editorial Expression of Concern20 June 2025: Following publication of this paper, the internal audit (consequent to concerns on quality raised by Web of Science) notified Advancements in Life Sciences about suspected plagiarism. By this Editorial Expression of Concern, we alert the scientific community of the errors as we reconcile the records.Editorial Note25 June 2025: While rerunning the Turnitin originality analysis, a similarity index of 80% was found for this article (64% from a single source). Editorial board of Advancements in Life Sciences has started the process of retracting this article due to the above post-publication findings. The process shall be concluded after registering responses from the authors. Meanwhile, full text of the article shall remain unavailable for citations (this notice has been updated following insights derived from relevant COPE cases and the industry standards). Show of cause notice has also been issued to the concerned editorial team member.Retraction Note20 July 2025: The Editor-in-Chief, upon the recommendation of the Inquiry Team, has retracted this article due to plagiarism. An internal audit revealed that several articles, including this one, exhibited a high similarity index without proper disclosure or attribution by the authors. This constitutes a breach of the journal’s editorial policy, and the article is therefore being retracted.The authors have not responded to correspondence regarding this retraction
Isolation of agar-degrading Bacillus sp. AT6 and preliminary application for seaweed saccharification
Get PDFBackground: Agar is a common polysaccharide found in nature. However, agar is strongly resistant to the degradation processing, leading to limitation of its application in various areas. Thus, finding an effective solution for agar saccharification significantly improves the economically effects of agar based substrates.Methods: Soil samples were collected from TienPhong Forestry Ltd. Company, ThuyXuan District, ThuaThien Hue province, Vietnam. Potential agar degrading bacteria were screened on a mineral salt agar medium. The isolate was identified based on 16S rRNA nucleotide sequence, morphological, physiological, and biochemical characteristics. Agarase production was evaluated by modification culture conditions including incubation time, shaking speed, and initial inoculum size. Molecular mass of extracellular agarase was determined by zymogram analysis following SDS-PAGE. The effect of pH, temperature, metal ions, and organic solvents were performed to characterize the enzyme. Application of enzyme was investigated on seaweed saccharification.Results: An agar degrading bacterial strain was isolated from soils and identified as Bacillus sp. AT6. Maximal agarase accumulation was obtained in the culture containing an inoculum size of 10% (v/v), shaking speed of 210 rpm, and 96 hours incubation. The agarase revealed a single band on zymogram analysis with an apparent molecular weight of 180 kDa. The optimal temperature and pH were 40°Cand pH 8.0, respectively. All tested metal ions and organic solvents partially decreased enzyme activity. Treating seaweed with agarase resulted in reducing sugars release present in the reaction, indicating the saccharification of seaweed was successful.Conclusion: Bacillus sp. AT6 is a new report of agarolytic bacteria that produces extracellular agarase enzymes. The present results promise strain AT6 is a great candidate for agar saccharification for industrial application.Keywords: Agar degrading bacterium; Agarase; Hydrolysis, hydrolyzed products; Soil bacteriaEditorial Expression of Concern20 June 2025: Following publication of this paper, the internal audit (consequent to concerns on quality raised by Web of Science) notified Advancements in Life Sciences about problems in use of English language. By this Editorial Expression of Concern, we alert the scientific community as we address the errors.Editorial Note:26 June 2025: You are viewing the latest version of this article having minor corrections related to the use of English language. Expression of concern is hereby revoked
RETRACTED ARTICLE: Genetic Diversity and Screening of Rice Germplasm Lines against Grain Discoloration Disease
Get PDFBackground: The research was conducted to screen out the diverse rice germplasm lines against grain discoloration disease by using 10 SSR primer pairs and on the basis of various morphological characters to evaluate the diversity of the genotypes at Faculty of Agricultural sciences, University of the Punjab, Lahore. Methods: Seed morphological traits were measured and recorded under Randomized Complete Block Design (RCBD) experiment. DNA extraction and PCR analysis was done to measure the genotypic characteristics of rice. Genotypic and phenotypic variability was measured by using ANOVA and correlation. Microsatellite markers, also called simple sequence repeats (SSR) were used for screening and to check the genetic diversity of rice.Results: The PIC values ranged from 0.204 of RM-07 to 0.640 of primer RM-22 along with other genetic characters i.e., number of alleles, percentage of polymorphism chromosomal location etc. The higher PIC (polymorphism information content) value showed the greatest genetic diversity among the genotypes. The polymorphic SSRs produced 3-5 alleles with an average unit of 3.3. The PIC values ranged from 0.204 to 0.640 with an average mean of 0.51. All the genotypes showed significant differences in all the studied traits which gave the significant results and non-significant results at significance level of p<0.05= *; p<0.01=** respectively. A significant association was also observed between seed length with length width ratio, 1000 grain weight (r= 0.1251*; r= 0.1922**) and seed thickness with 1000 grain weight (r=0.1205*). All these traits showed higher variations for different rice lines.Conclusions: From the study it was concluded that some rice found to be highly resistant (Blue Nile, IR 50, Line 9 (4×15) and Line 12 (4×23) against grain discoloration that could be more useful for the production new rice lines with diverse genetic characteristics.Keywords: Oryza sativa; DNA; SSR; Germplasm; Traits; Diversity Retraction Note24 Sept 2025: The Editor-in-Chief has retracted this article due to the below mentioned scientific deficiencies revealed by an internal audit.1. This is the most severe flaw in the paper. The Discussion section contains a paragraph reporting Polymorphism Information Content (PIC) values for the SSR primers that completely contradicts the data presented in Table 4. For example:A. The Discussion claims the PIC range is "RM 109 0.18 to RM 07 0.75". Table 4 shows the actual range is from RM07 (0.204) to RM22 (0.640), with the value for RM109 being 0.550.B. The Discussion claims the lowest PIC values for RM449 and RM84 were "0.04". Table 4 shows the actual values are 0.430 and 0.633, respectively.C. Every single PIC value reported in this paragraph of the discussion is incorrect and inconsistent with the paper's own results table, suggesting the text may have been copied from a different, unrelated study.2. The main text in the "Variance and correlation analysis" section states, "All the genotypes showed significant differences in all the studied traits (Table 2)." This is directly contradicted by Table 2 itself, which clearly marks two of the five traits, Seed Width (SW) and Length/Width ratio (L/W), as "NS" (Non-significant).3. In the "Disease incidence" section, the rice variety IAGS-23 is listed as being in the highest resistance category (score 0-1) and simultaneously in a much lower resistance category (score 2-3). A variety cannot have two different resistance ratings at the same time.The authors have not responded to correspondence regarding this retraction
Effectiveness of the α-tocopherol, ursodeoxycholic acid, and AZHEPOFIT phyto-complex against the statin model of drug-induced hepatitis
Get PDFBackground: Drug-induced hepatitis is a common and serious side effect of many medications. Treatment for this condition is often difficult and limited, and there is a need for effective treatment options. The aim of this study was to investigate the effectiveness of α-tocopherol acetate, ursodeoxycholic acid, and AZHEPOFIT phyto-complex against the background of a statin model of drug-induced hepatitis.Methods: The study was conducted on 70 white mongrel rats, divided into two groups and treated twice daily for 2 weeks. Statistical analysis was carried out by the Mann-Whitney-Wilcoxon method using MS EXCEL and S-PLUS software.Results: Against the background of the statin hepatitis model, the combined use of the phyto-complex and ursodeoxycholic acid showed the best results. The atherogenicity index decreased from 16.03 to 2.29, the De Ritis ratio decreased to 1.49±0.05, and the severity of lipid peroxidation, the content of C-reactive protein (CRP), and medium molecular weight peptides decreased. All of these results indicate the restoration of the functional state of the liver.Conclusion: The use of α-tocopherol acetate, ursodeoxycholic acid, and AZHEPOFIT phyto-complex can be an effective treatment option for drug-induced hepatitis caused by statin medication. The combination of phyto-complex and ursodeoxycholic acid showed the best results in reducing.Keywords: Statin drug-induced hepatitis; α-tocopherol acetate; Ursodeoxycholic acid; AZHEPOFIT phyto-complex; Atherogenicity index; De Ritis ratioEditorial Expression of Concern20 June 2025: Following publication of this paper, the internal audit (consequent to concerns on quality raised by Web of Science) notified Advancements in Life Sciences about problems in use of English language. By this Editorial Expression of Concern, we alert the scientific community as we address the errors.Editorial Note26 June 2025: You are viewing the latest version of this article having minor corrections related to the use of English language. Expression of concern is hereby revoked
RETRACTED ARTICLE: Anti-calponin, anti-PCNA immunohistochemical study of the parenchymatous cells in mice parotid salivary glands exposed to dental radiograph
Get PDFBackground: Radiation therapy with ionizing radiation is associated with an increased risk of salivary gland cancer and xerostomia due to an abnormally high expression of the regulatory protein calponin. PCNA is a cofactor for DNA polymerase-delta and is involved in cell proliferation.Methods: This study evaluated the anti-calponin and anti-PCNA immunohistochemical reactivity in the parotid salivary glands of mice after frequent exposure to dental X-ray.Results: The results showed that exposure to radiation causes marked differences in PCNA reactivity. Radiation therapy has a significant impact on salivary glands, particularly on myoepithelial cells.Conclusion: The exposure to radiation can cause Dental X-ray exposure increases the risk of developing cancer and other health problems due to damage to DNA and inflammatory destruction and further research is needed to mitigate these effects and improve patient outcomes.Keywords: Dental X-ray; Parotid salivary gland; Anti-PCNA; Anti-calponin; Myoepithelial cellsRetraction Note24 Sept 2025: The Editor-in-Chief has retracted this article due to the below mentioned scientific deficiencies revealed by an internal audit.1. The paper presents results for four experimental sub-groups that are never defined or described in the methods section. 2. The manuscript's reporting of its results is problematic.The textual description of the data is filled with statements that are the exact opposite of what the quantitative tables show, indicating a total disconnect between the data and its interpretation.The main conclusion about increased cancer risk is not supported by, and is potentially contradicted by, the study's own data for a cell proliferation marker.3. The data tables report a sample size that is demonstrably false and inconsistent with the total number of animals used in the study.After a thorough review of the evidence, the Editorial Board has provisionally decided to retract this paper from the scientific record. This action is being considered due to the gravity of the issues identified, which we believe pose a risk to the integrity of the citable scientific literature.The authors have not responded to correspondence regarding this retraction
Overdominance in livestock breeding: examples and current status
Get PDFRecent data have revealed that genetic variation could be attributed to overdominance, or heterozygote advantage. However, the genomic survey showed that only a small number of genes with polymorphisms maintained by overdominance, which is consistent with many published papers. Google Web, Google Scholar, NCBI Databases, and OMIC Tools were used to obtain data for this review paper. Different keywords were used to retrieve the required research articles and bioinformatics-based information, such as “overdominance’’ and “overdominance in animals. Research papers used for this review were published over the last 10 to 15 years, and information regarding overdominance in livestock was considered for the current review. It is hoped that in the future, more loci with overdominance will be discovered. In this review, we will illustrate eight examples of overdominance in livestock. We also want to emphasize that given a low number of reported cases of overdominance, it does not reflect the unimportance of heterozygote advantage in adaptive functions.Keywords: Genomic survey; Polymorphisms; Livestock breedingEditorial Expression of Concern20 June 2025: Following publication of this paper, the internal audit (consequent to concerns on quality raised by Web of Science) notified Advancements in Life Sciences about errors in metadata. By this Editorial Expression of Concern, we alert the scientific community of this incidence as we do the required corrections.Editorial Note24 June 2025: You are viewing the latest version of this article having correction in article info (metadata) section. The editorial expression of concern is hereby revoked