Advancements in Life Sciences (E-Journal, University of the Punjab)
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Molecular detection and probiotic treatment for bacteria that cause diarrhea
Get PDFBackground: Misdiagnosis of the pathogen leads to serious consequences. Diarrhea is a worldwide health problem that kills 1.3 million people each year. Diarrhea can be induced by a variety of causes. However, infectious agents like bacteria are among the leading causes. Several resistant bacterial strains are emerging that tend to spread globally; hence, resistance of bacteria to antibiotics is a global health threat. The study aimed to ascertain the Saccharomyces boulardii filtrate impact on lowering the virulence of the bacterial species that cause diarrhea and the extent of genetic affinity between those organisms.Methods: 350 stool samples were investigated for all age groups who suffer from diarrhea, using biochemical and molecular methods.Results: Biochemical diagnoses were 0.28% for Salmonella and 0.57% for Enterobacter aerogenes, while molecular diagnosis did not record any percentage for the mentioned bacteria, therefore molecular test was a better way to properly diagnose bacterial species, the causes of diarrhea are bacteria, viruses, parasites, medications, and toxins. The molecular identification of isolates by PCR technique and sequencing of 16S rRNA gene indicated that 12 isolates belonged to the species Enterobacter cloacae, Cronobacter sakazakii, and Aeromonas hydrophila. The study revealed that there is a difference in the rates of resistance of isolates to some antibiotics before and after exposing them to probiotics. Where the percentage of antibiotic resistance was recorded before exposure to probiotics were piperacillin (91.6%), cefotaxime/clavulanic acid (41.6%), and tetracycline (25%), while the percentage of antibiotic resistance after exposure to probiotics were (58.3%) piperacillin, (0%) cefotaxime/clavulanic acid, and (0%) tetracycline. Where the resistance of bacteria to antibiotics decreases after exposing them to probiotics.Conclusion: The molecular diagnostic method is a more accurate approach for bacterial species identification in this study. The Saccharomyces boulardii filtrate had an effective role in reducing or suppressing bacterial resistance against piperacillin, cefotaxime/clavulanic acid, and tetracycline, while it did not affect the bacterial resistance towards amoxicillin clavulanic acid.Keywords: Molecular detection; Phylogenetic tree; Antibiotics; ProbioticsEditorial Note: This article has been updated with language corrections
Molecular Profiling of Pakistani Selected Advance Lines of Rice for Amylose Content
Get PDFBackground: Pakistani rice is well-known for its quality. Its consumption increases with the increase in population. The gel consistency (GC) amylose content (AC) and gelatinization temperature (GT) are the most important rice characters, which are associated directly to eating and cooking attributes. But for its good taste and eating quality depends on its endosperm starch quality and quantity. Amylose, a chief determinant of rice attribute, is principally synthesized and controlled by a major gene (Waxy gene) encoding an enzyme called granule bound starch synthase (GBBS).Methods: Current investigation was carried out to characterize advance lines of rice by both conventional and molecular approaches. In present study Waxy gene was identified in advance lines of rice.Results: Show that out of 17 advanced lines, 9 lines were waxy or low amylose, and 1 line was non waxy or high amylose rice because of the presence of 425 bp fragment and 225 bp fragment of Wx gene respectively. For morphological data 14 morphological quantitative traits were studied.Conclusion: Advance lines of rice analyzed during the present investigation showed better grain quality. A number of advance lines contain extra-long and medium slender grains which have intermediate to high gelatinization temperatures. Thus these advance lines are appropriate for the improvement of saline rice. Except one advance line 19 that showed Hard gel consistency and the majority of advance lines fall in the category of soft gel consistency and thus are of excellent quality.Keywords: Rice; Amylose; Gelatinization; Wx genes
Protective role of ITPA rs1127354-CA polymorphism against anemia in HCV patients using sofosbuvir ribavirin therapy: age and gender match case-control study
Get PDFBackground: Hepatitis C virus is affecting around 80 million people. Sofosbuvir ribavirin-based therapy is associated with certain side effects, especially anemia. Inosine triphosphatase (ITPA) genetic polymorphisms cause functional impairment in ITPase enzyme, leading protection against anemia and improving sustained viral response. This study aims to explore the impact of ITPA variants on hemoglobin decline, ribavirin dose reduction, and sustained viral response (SVR) achievement.Methods: This is prospective gender and age matched case-control study of HCV genotype-3a infected individuals taking sofosbuvir-ribavirin treatment. Patient CBC, viral RNA, liver function test, and ribavirin dose reduction were recorded monthly. ITPA polymorphisms (rs1127354) were determined and confirmed by restriction fragment length polymorphism and sanger sequencing. Effects of polymorphism on hemoglobin level, ribavirin dose and treatment outcome were analyzed.Results: ITPA rs1127354-CC genotype patients experience significant reduction in level of Hb leading to ribavirin dose reduction. Low mean Hb levels were observed in these individuals at first and last month of treatment. No statistical difference was observed in adverse effects on basis of ITPA genotype except fever. Age, BMI, and ITPA genotype rs1127354-CC were independently associated (p< 0.05) with a decrease in Hb level ≥ 2g/dl below the baseline and ribavirin dose reduction. All patients with rs1127354 CA genotype achieved SVR.Conclusion: Pretreatment determination of ITPA polymorphism can further optimize HCV treatment with new direct-acting antivirals. ITPA rs1127354-CA has a protective role against ribavirin-associated anemia development and individualized management of ribavirin dose and along with the achievement of better SVR rates.Keywords: ITPA; HCV; Anemia; Ribavirin Editorial Note: You are viewing the latest version of this article having language and data presentation corrections.
RETRACTED ARTICLE: Association Mapping Study of Various Desirable Traits of Rice
Get PDFBackground: This study was performed to evaluate the diversity of various morphological characters and their relationship with yield in rice. The goal of this work was to find quantitative trait loci (QTL) for yield, yield components, and other agronomic variables in 100 different rice germplasm samples, as well as to assess the genetic structure and degree of linkage disequilibrium in the rice germplasm diversity panel. To establish Linkage Disequilibrium (LD) between markers and causative mutations, marker density is essential. Linkage disequilibrium (LD) patterns of various SNP markers on all chromosomes. If markers are sufficiently dense to have good coverage of LD, the LD decay with distance can be compared to the marker density.Methods: Different 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 GWAS.Results: For pair-wise markers, linkage disequilibrium is calculated as R square and plotted versus the distance between the markers. In this study, the overall phenotypic variability among the examined traits was represented by R2 and ranged from 11.47% to 25.44%. The genetic architecture of these traits may be implied by the recently identified genomic regions (loci). An influential replacement for bi-parental gene maps, genome-wide association studies (GWAS) use data from genome-wide markers in large amounts of easily obtained germplasm.Conclusion: The linkage disequilibrium, which is the non-random link between an allele at two or more loci, is used in this mapping method to infer the innate relationships between phenotypic variations and marker polymorphisms. Genome Wide Association Study (GWAS) of genotypes provides the information about for the selection of genotypes and determination of new marker trait association.Keywords: Oryza sativa L; Rice; DNA; Association mapping; Traits 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. The "Methods" and "Results" sections describe an association mapping study using SSR (microsatellite) markers. However, the "Discussion" section describes the results of a completely different analysis using SNP (single nucleotide polymorphism) markers from a "10k SNP array". The number of associated markers and the phenotypic variance values are completely different for the same traits between the "Results" (SSR data) and "Discussion" (SNP data) sections. The document states that "216 polymorphic SSR markers were employed" for the study. However, the discussion later claims a result was obtained "With the use of 204 polymorphic SSR markers".2. The text states there are "thirteen SSR markers" for this trait. It then describes their locations as "two markers were from chromosomes 4, 6 and 8 and the remaining were from chromosomes 1, 2, 3, 5, 9, 11 and 9". Listing chromosome 9 twice appears to be an error, and the count is confusing (3 chromosomes x 2 markers + 7 chromosomes x 1 marker = 13 markers, but chromosome 9 is repeated).3. The distribution of 14 markers is described as "four on chromosome 5, three on each of chromosomes 1, 2, and 10, two on each of chromosomes 1, 2, and 9, and one on chromosome 4". Chromosomes 1 and 2 are listed twice with different marker counts (three and two), making the description contradictory and impossible to parse.4. The abstract states the overall phenotypic variability (R2) ranged from 11.47% to 25.44%. However, the results section lists multiple marker-trait associations with phenotypic variance values outside this range, such as 28.57% for plant height, 29.78% for spikelets per panicle, 26.85% for primary branches, 26.97% for secondary branches, 28.68% for seed thickness, and 29.88% for 1000-seed weight.5. The methods state, "Markers were considered significant if the adjusted P value was greater than 0.05". This is scientifically incorrect. A significance threshold is conventionally set as a p-value less than a certain value (e.g., P<0.05).6. The "Discussion" section is based on a Genome-Wide Association Study (GWAS) using a "10k SNP array" and "GAPIT in the R software". These materials and methods are never mentioned in the "Methods" section, which only describes SSR marker analysis using TASSEL and STRUCTURE software.7. The method for multiple testing correction is described as "50000 mutations per mutation", which is nonsensical. This is likely a typographical error for "50,000 permutations".8. The PCR program is described as consisting of "6 cycles". The subsequent description details multiple steps, including an initial denaturation, a final extension, and "36 repeated cycles" of amplification. This is a single multi-step program, not "6 cycles".The authors have not responded to correspondence regarding this retraction
RETRACTED ARTICLE: Molecular Analysis of Cold Responsive (COR) Genes in Selected Sugarcane and Saccharum spontaneum L.
Get PDFBackground: Sugarcane (Saccharum derived) is an important commercially harvested crop in all parts of the world including tropical and subtropical areas. Saccharum hybrid is the tall perennial true grasses with sweet stalk rich in sucrose and it is the main source of sugar.Methods: Initially, 23 genes differentially expressed during cold stress in other Andropogoneae tribe members were retrieved from NCBI GenBank and were investigated in the genome of selected sugarcane and Saccharum spontaneum L. Samples. Their presence in our samples was analyzed and confirmed through PCR and Agarose Gel Electrophoresis (AGE).Results: Most of these (COR) genes (21/23) were confirmed in cold tolerant cultivars namely, SPSG-394, CP-851491 and Saccharum spontaneum L. while the least number of genes was observed in cold sensitive cultivar namely, CP-77400. Moreover 10 cold responsive genes, namely CBF1, CBF2, CBF3, COR 6.6, COR 78, COR 47, WCOR 80, WCOR14, C17 and 85KDA were sent for sequencing. Nucleotide sequences analysis of selected genes revealed the homology to stress responsive protein. Furthermore, during a conserved domain search, three conserved domains had been detected, namely gypsy transposon, zinc binding for reverse transcriptase and pepsin like aspartate proteases.Conclusion: The analysis of cold responsive genes in sugarcane could help breeders to select cold tolerant sugarcane cultivars through PCR amplification.Keywords: NCBI; Sugarcane; COR genes; Conserved domainEditorial 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 34% was found for this article (21% 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 do not agree to this retraction
Moxifloxacin ameliorates clinical disease activity and histopathological changes of acetic acid-induced colitis model in rat possibly through its effect on proinflammatory mediators and oxidative stress
Get PDFBackground: Moxifloxacin (MFX), a fluoroquinolone antibiotic, was found in previous study to exert an anti-inflammatory effect including reduction of proinflammatory cytokine expression, the aim of this research was to investigate the potential anti-inflammatory effect of MFX on acetic acid (AA)-induced colitis model in rats.Methods: Forty male Wistar rats were divided into four groups (n = 10/group): negative (healthy) control, AA-colitis, sulfasalazine (SLS) group, and MFX group. Colitis induction was done by intra-rectal injection of 2 mL AA (4% v/v). Two hours after AA induction (day 1), SLS (100 mg/kg/day) and MFX (8 mg/kg/day) were administered orally once daily for seven consecutive days. Animals were euthanized 24 hours after the last dose.Results: The administration of MFX substantially decreased the disease activity index (DAI), and histopathological alterations triggered by AA. Moreover, AA induced a significant rise in the production of the proinflammatory cytokine IL-1β, the adhesion molecules ICAM-1, and the oxidative stress (OS) biomarker myeloperoxidase (MPO) in colon homogenate. The MFX administration significantly reduced the production of proinflammatory cytokine IL-1β, adhesion molecules ICAM-1, and the OS biomarker myeloperoxidase (MPO) in colon homogenate, which were elevated by AA. The influences of MFX seemed comparable to those of SLS, with no significant difference between them.Conclusion: Consequently, MFX may possess a beneficial property in the treatment of ulcerative colitis (UC).Keywords: Ulcerative; Colitis; Moxifloxacin; Sulfasalazine; ICAM-1; IL-1β; MPOEditorial Note: This article has been updated with language and data corrections
Assessment of Antimicrobial and Antioxidant Activity of methanolic extract from Arnebia decumbens aerial parts growing wild in Aja Mountain
Get PDFBackground: Many plants are a rich source of secondary metabolites with potential antimicrobial and antioxidant properties. Amongst the customary plant herbs used as a phytomedicine in Hail province, which has been selected for the current study, Kehail plant, Arnebia decumbens (A. decumbens). Therefore, this study sought to assess the antimicrobial and antioxidant activities against high-risk bacteria and yeasts.Methods: The cup-plate agar diffusion method and Microdilution assays were adopted with minor modifications to assess the antibacterial activity. The Qualitative and quantitative tests were employed to assess the antioxidant activities of Kehail by determining its phytochemicals, 2, 2-diphenyl-1-picrylhydrazyl (DPPH), ABTS(2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), and β-carotene in vitro assays.Results: The results indicated that methanolic Kehail extract (KME) exhibited antibacterial activity against pathogenic bacteria, including Staphylococcus epidermidis (M13), Enterobacter cloacae, Pseudomonas aeruginosa, Escherichia coli ATCC 10536 and Klebsiella pneumoniae, while the mean inhibition zone was 10.66 ± 0.57 mm, 10.77 ± 0.57735 mm, 10.33 ± 0.57 mm, and 9.55 ± 0.57 mm, respectively. Furthermore, the antimicrobial activity increased in a concentration-dependent manner. Indeed, E. cloacae were the plant extract most inhibited bacteria. The plant extract has strong antifungal activity against Candida albicans ATCC 10231 and C. tropicalis ATCC 9362, whereas the mean inhibition zone was 12.77 ± 0.57 and 13.11 ± 1.52 mm, respectively. The extract of A. decumbens plant was also proven to be efficient as a source of antioxidant compounds such as saponins, terpenes, polyphenols, and flavonoids.Conclusion: The acquired outcomes uncover promising antioxidant activities of the tested Kehail methanolic extract. The study encourages the separation of active components and the development of new medications from the Kehail plant.Keywords: Arnebia decumbens; Methanolic extract; Disk diffusion assay; Microdilution assay; Antioxidant activitiesEditorial 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 Note26 June 2025: Similar usage sequence of commonly used scientific terms, names of species and chemicals have been found as major sources of total verbatim similarity (23%). Therefore, it may not be considered as plagiarism. High incidence of plagiarism reported earlier was false as it took content published after publication of this article into account when calculating similarity index during re-analysis. Hence, the Editorial Expression of Concern is revoked
Effects of Salinity Stress on Growth and Physio-biochemical Parameters of Three Pea (Pisum sativum L.) Cultivars of Different Maturity Duration
Get PDFBackground: Salinity is one of the leading abiotic stresses that negatively affects the growth of many important food crops and significantly reduces the productivity and yield value.Methods: The present study was conducted to study the effects of NaCl stress on three pea (Pisum sativum) cultivars (Climax, Lina Pak and Pea-267) of different maturity level (Late, early, and mid-season flowering) under In vitro conditions. Two weeks old In vitro grown shoots of three pea cultivars were subjected to stress condition in MS medium supplemented with five levels of NaCl (0, 20, 40, 80 and 100mM NaCl) for one month and different morphological and physio-biochemical traits including length of shoot, number of leaves, shoot biomass, chlorophyll, proline and total phenolic content, total proteins and non-enzymatic antioxidant (DPPH) activities were studied.Results: The results were analyzed using different statistical approaches (ANOVA, MNOVA, PCA, correlation and regression) to identify the tolerance level of each genotype. Shoot length and shoot fresh weight were increased at 20 and 40mM in Climax, while proline content progressively increased with an increase in stress concentration in all the genotypes. Total protein content increased in cvs. Climax and Pea-267 and decreased in Lina Pak above 20mM and DPPH was increased in Climax and Pea-267 at 20 and 40mM, while in Lina Pak it showed an increase at only 20mM NaCl concentration. According to the results of MNOVA and regression analysis, significant changes occurred in biomass, proline content and DPPH values. A strong positive correlation of shoot dry weight was found with total phenolic and proline content. Maximum value of stress tolerance index was recorded for Climax.Conclusion: Biplot analysis clustered cvs. Climax and Pea-267 cultivars into tolerant group and Lina Pak in sensitive group based on the mean performance of studied parameters to NaCl stress and control treatments
Frequency of Helicobacter Pylori Infections and Its Associated Risk Factors in Patients Attending Tertiary Care Hospital of Bhakkar, Pakistan
Get PDFBackground: Helicobacter Pylori is a gram-negative bacteria that is the main cause of chronic gastritis and plays a significant role in peptic ulcers, gastric carcinoma, and gastric lymphoma. The prevalence of H. pylori cases is 75-90% worldwide. The objective of the study was to determine the frequency of H. pylori and its associated risk factors in the Bhakkar district.Methods: A total of 102 participants with problems in the gastrointestinal tract were taken from June 2021 to May 2022. Stool antigen was performed to confirm H. pylori infection. A complete blood count (CBC) was also performed on the blood sample. Results: The current study showed that a total of 102 samples were collected in this study. It was concluded that out of 102 participants, 63 (61.8%) were H. pylori positive and 39 (38.2%) were H. pylori-negative participants. Females were more infected with H. pylori 38 (60.3%) as compared to males 25 (39.7). The frequency of factors such as smoking (52% vs 51%), weekly consumption of junk food (52.4% vs 43.6%), fizzy drinks (33.3% vs 23.1%) and drinking of unfiltered water (54% vs 53%) was more in H. pylori-infected group compared with the uninfected group but difference was not statistically significant with odds ratio less than 1.Conclusion: The current study concluded that female genders, ethnicities, and history of stomach infection are risk factors for H. pylori. Exposure to Smoking, unfiltered drinking water, fizzy drinks, and Junk food is more in the affected group than in the unaffected group.Keywords: Helicobacter pylori; Stool antigen test; Risk factors; CBC 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 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 Note24 June 2025: You are viewing the latest version of this article having changes in the category section. Expression of concern is hereby revoked
The Association of Nine Novel Variants in the ZEB2 Gene with Serum Levels of TNF-α, TGF-β and IFN-γ
Get PDFBackground: ZEB1 and ZEB2, are expressed by a variety of immune cells of both myeloid and lymphoid lineages, they act to regulate important transcriptional networks necessary for cell differentiation, maintenance, and function. The study was carried out in the Department of Clinical Laboratories / College of Applied Medical Sciences / University of Kerbala during the period from January 2021 to September 2021. The study aimed to shed light on the association between the variation of the ZEB2 gene and serum levels of some cytokines (TNF-α, TGF-β, INF-γ) involved in immune cell differentiation in the Iraqi population.Methods: A total of 80 healthy volunteers, randomly chosen, were enrolled in this study, with an age ranged 20-50 years at the time of the investigation. The variation of the ZEB2 gene was investigated by the Sanger sequencing method. The serum levels of TNF-α, TGF-β and INF-γ were measured by ELISA.Results: The results identified presence of nine novel non-registered variants in 27 samples, 5 out of 9 variants were detected in exon1 region, while the other 4 were detected in the 5`UTR region. These variants might be of interest to the ZEB2 gene studies due to their presence in the coding and regulatory regions that regulate the gene expression.Conclusion: The two variants, 144520053 G/A and 144520162 T/A, among the nine novel variants might be the most important variants because both showed significant effects on some study parameters.Keywords: Novel variants; ZEB2; TNF-alpha; TGF- beta; IFN-gamma