M. Branković, E. Stefanova, Gorana Mandić, A. Marjanovic, V. Dobričić, A. Maver, Gaber Bergant, Z. Stevic, M. Janković, I. Novaković, B. Peterlin, V. Kostic
As life span rises, dementia has become a growing public health issue. According to current estimates, almost 50 million people worldwide have dementia, and the number is expected to grow. Next generation sequencing (NGS) methods have helped significantly with identifying causative gene variants related to various cognitive disorders. Our study aimed to analyze the genetic basis of cognitive disorders using NGS clinical exome panel. The study included a total number of 15 unrelated cases diagnosed with cognitive disorders, all negative after standard targeted genetic testing was performed (available at Neurology Clinic, UCCS, Belgrade, Serbia). Preference was given to familial cases with early presentation or complex phenotype. Sequencing of a clinical exome (CE) panel for 4813 genes with known associated clinical phenotypes was performed using TruSight One sequencing panel on an Illumina MiSeq NGS platform according to the manufacturer?s instructions (Illumina, San Diego, CA, USA). Variants were analyzed with Illumina Variant Studio v3 software provided by Illumina as well as a previously developed pipeline. Variants analysis and interpretation were based on phenotype gene target approach, literature and databases search, allele frequency, and pathogenicity prediction by in silico software. All causative variants were confirmed by Sanger sequencing. Whenever possible, additional family members were studied for segregation analysis. CE panel analysis revealed a likely genetic cause in four patients. We have detected two missense heterozygous pathogenic variants in the PSEN1 gene in one patient each and homozygous nonsense pathogenic variant in the OPTN gene in two more patients. Detected pathogenic variants are in line with the clinical phenotype of our patients. In the rest of the 11 cases, genetic diagnosis remains unclear. The results of our study emphasize the significance of CE panel analysis in establishing a diagnosis for patients with dementia. Furthermore, give us insight into the complexity of the genetic background of this group of disorders.
随着寿命的延长，痴呆症已成为一个日益严重的公共卫生问题。根据目前的估计，全世界有近5000万人患有痴呆症，预计这一数字还会增长。下一代测序(NGS)方法在识别与各种认知障碍相关的致病基因变异方面发挥了重要作用。本研究旨在利用NGS临床外显子组分析认知障碍的遗传基础。该研究共包括15例诊断为认知障碍的不相关病例，在进行标准靶向基因检测后均为阴性(可在塞尔维亚贝尔格莱德UCCS神经病学诊所获得)。优先考虑具有早期表现或复杂表型的家族性病例。根据制造商的要求，使用TruSight One测序板在Illumina MiSeq NGS平台上对4813个已知相关临床表型基因的临床外显子组(CE)面板进行测序。(Illumina, San Diego, CA, USA)。变体分析使用Illumina提供的Illumina Variant Studio v3软件以及先前开发的管道。变异分析和解释基于表型基因靶标法、文献和数据库检索、等位基因频率和计算机软件的致病性预测。所有致病变异均经Sanger测序证实。只要有可能，就研究其他家庭成员进行分离分析。CE小组分析显示，4名患者可能存在遗传原因。我们在一名患者的PSEN1基因中检测到两种错义杂合致病变异，在另外两名患者的OPTN基因中检测到纯合无义致病变异。检测到的致病变异符合我们患者的临床表型。在其余11例中，基因诊断仍不清楚。我们的研究结果强调CE面板分析在建立痴呆患者诊断中的意义。此外，让我们深入了解这组疾病的遗传背景的复杂性。
{"title":"Analysis of “clinical exome” panel in Serbian patients with cognitive disorders","authors":"M. Branković, E. Stefanova, Gorana Mandić, A. Marjanovic, V. Dobričić, A. Maver, Gaber Bergant, Z. Stevic, M. Janković, I. Novaković, B. Peterlin, V. Kostic","doi":"10.2298/gensr2203351b","DOIUrl":"https://doi.org/10.2298/gensr2203351b","url":null,"abstract":"As life span rises, dementia has become a growing public health issue. According to current estimates, almost 50 million people worldwide have dementia, and the number is expected to grow. Next generation sequencing (NGS) methods have helped significantly with identifying causative gene variants related to various cognitive disorders. Our study aimed to analyze the genetic basis of cognitive disorders using NGS clinical exome panel. The study included a total number of 15 unrelated cases diagnosed with cognitive disorders, all negative after standard targeted genetic testing was performed (available at Neurology Clinic, UCCS, Belgrade, Serbia). Preference was given to familial cases with early presentation or complex phenotype. Sequencing of a clinical exome (CE) panel for 4813 genes with known associated clinical phenotypes was performed using TruSight One sequencing panel on an Illumina MiSeq NGS platform according to the manufacturer?s instructions (Illumina, San Diego, CA, USA). Variants were analyzed with Illumina Variant Studio v3 software provided by Illumina as well as a previously developed pipeline. Variants analysis and interpretation were based on phenotype gene target approach, literature and databases search, allele frequency, and pathogenicity prediction by in silico software. All causative variants were confirmed by Sanger sequencing. Whenever possible, additional family members were studied for segregation analysis. CE panel analysis revealed a likely genetic cause in four patients. We have detected two missense heterozygous pathogenic variants in the PSEN1 gene in one patient each and homozygous nonsense pathogenic variant in the OPTN gene in two more patients. Detected pathogenic variants are in line with the clinical phenotype of our patients. In the rest of the 11 cases, genetic diagnosis remains unclear. The results of our study emphasize the significance of CE panel analysis in establishing a diagnosis for patients with dementia. Furthermore, give us insight into the complexity of the genetic background of this group of disorders.","PeriodicalId":50423,"journal":{"name":"Genetika-Belgrade","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68296523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ramazan Sabırlı, Aylin Köseler, E. Mete, İbrahim Türkçüer
Inflammatory processes play an important role in the pathogenesis of heart failure. The accumulation of unfolded proteins in the endoplasmic reticulum lumen and the unfolded protein response signal path is activated. The IL-1? gene is located in the Chromosome 2.q14 region. -31 and -511 single nucleotide polymorphisms (SNPs) were detected in the IL-1?promoter region. These two SNPs affect IL-1expression. This study aims to investigate the presence of IL-1?(-511 C / T) and IL-1? (-31 T / C) gene polymorphisms and the relationship between ER stress markers and inflammatory markers. Patients who applied to the department of emergency medicine with the findings of acute decompensated heart failure. Polymorphic sites of theIL-1? gene were determined by DNA sequencing. In all study, individuals with IL-1?(-31 T / C) T allele have higher serum PERK, GRP-78, CHOP and CRP levels median values than individuals with IL-1?(-31 T/C) C allele (p = 0.0001, p = 0.002, p = 0.002 and p =0.011, respectively). Serum ERK and GRP-78 values in HF group were higher in individuals with IL-1?(-31 T / C) T allele compared to individuals with C allele (p = 0.0001 and p = 0.006). There was a statistically significant difference in serum CHOP levels in the control group with the IL-1? (-511 C / T) T allele and the individuals with the C allele in the HF group (p = 0.002). In conclusion, we consider that the inflammatory response caused by IL-1? (-31 T / C) gene polymorphism increased and the ER stress response increased, inflammatory pathway and ER stress of having IL-1?(-31 T / C) T / T genotype or T allele.
炎症过程在心力衰竭的发病机制中起重要作用。未折叠蛋白在内质网腔内的积累和未折叠蛋白反应信号通路被激活。il - 1 ?基因位于2号染色体上。q14地区。-31和-511单核苷酸多态性(snp)在IL-1?启动子区域。这两个snp影响il -1的表达。本研究旨在探讨IL-1?(- 511c / T)和IL-1?(-31 T / C)基因多态性及内质网应激标志物与炎症标志物的关系。向急诊科申请急性失代偿性心力衰竭的患者。il -1的多态性位点基因序列测定。在所有的研究中，IL-1?(-31 T / C) T等位基因的血清PERK、GRP-78、CHOP和CRP水平中位数高于IL-1?(-31 T/C) C等位基因(p = 0.0001, p = 0.002, p = 0.002, p =0.011)。HF组血清ERK和GRP-78值在IL-1?(-31 T / C) T等位基因与C等位基因个体相比(p = 0.0001和p = 0.006)。对照组血清CHOP水平与IL-1?(-511 C / T) T等位基因与HF组携带C等位基因个体的差异(p = 0.002)。综上所述，我们认为IL-1?(-31 T / C)基因多态性增加，内质网应激反应增加，IL-1?(-31 T / C) T / T基因型或T等位基因。
{"title":"Association of il-1β(-511 c / t) and il-1β (-31 t / c) gene polymorphism with endoplasmic reticulum stress marker levels in acute decompensated heart failure with low ejection fraction","authors":"Ramazan Sabırlı, Aylin Köseler, E. Mete, İbrahim Türkçüer","doi":"10.2298/gensr2201329s","DOIUrl":"https://doi.org/10.2298/gensr2201329s","url":null,"abstract":"Inflammatory processes play an important role in the pathogenesis of heart failure. The accumulation of unfolded proteins in the endoplasmic reticulum lumen and the unfolded protein response signal path is activated. The IL-1? gene is located in the Chromosome 2.q14 region. -31 and -511 single nucleotide polymorphisms (SNPs) were detected in the IL-1?promoter region. These two SNPs affect IL-1expression. This study aims to investigate the presence of IL-1?(-511 C / T) and IL-1? (-31 T / C) gene polymorphisms and the relationship between ER stress markers and inflammatory markers. Patients who applied to the department of emergency medicine with the findings of acute decompensated heart failure. Polymorphic sites of theIL-1? gene were determined by DNA sequencing. In all study, individuals with IL-1?(-31 T / C) T allele have higher serum PERK, GRP-78, CHOP and CRP levels median values than individuals with IL-1?(-31 T/C) C allele (p = 0.0001, p = 0.002, p = 0.002 and p =0.011, respectively). Serum ERK and GRP-78 values in HF group were higher in individuals with IL-1?(-31 T / C) T allele compared to individuals with C allele (p = 0.0001 and p = 0.006). There was a statistically significant difference in serum CHOP levels in the control group with the IL-1? (-511 C / T) T allele and the individuals with the C allele in the HF group (p = 0.002). In conclusion, we consider that the inflammatory response caused by IL-1? (-31 T / C) gene polymorphism increased and the ER stress response increased, inflammatory pathway and ER stress of having IL-1?(-31 T / C) T / T genotype or T allele.","PeriodicalId":50423,"journal":{"name":"Genetika-Belgrade","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68292543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Khan, A. Nadeem, M. Javed, W. Shehzad, Asad Ali
Staphylococcus aureus (S. aureus) is a Gram-positive coccus with golden-colored colonies 0.5-1.5 ?m in diameter. It is an opportunistic pathogen and colonizes as healthy flora. When the host defense system is breached it provides a source for the introduction of (Methicillin-resistant S. aureus) MRSA. The incorporation of the mecA gene shift S. aureus into MRSA, mecA is a primary gene for the confirmation of MRSA, so, it is used as a useful marker to determine Methicillin resistance in S. aureus. In this study, we investigated the molecular characterization of mecA, Panton-Valentine Leukocidin (PVL), and 16S rRNA genes in MRSA to determine diversity, phylogenetic analysis, and multidrug resistance (MDR) of MRSA isolated from chronic bovine wounds. A total of 8 antibiotics were used for MDR profiling and the results obtained are as follows: 100% of MRSA isolates were resistant to Augmentin and Cefipime, 81.8% to Vancomycin and Tetracyclin, 36.4% to Streptomycin and Ciprofloxacin, Azithromycin 54.5 and 0% to Chloramphenicol which warrants that it?s the best antibiotic according to this study. Multiplex PCRs were performed for the confirmation of targeted genes and diversity analysis. The diversity of MRSA in the bovine population was 22% (11/50) on the microbiological scale that considered high as compared to reported data. When the PCR of MRSA isolates was performed, there was a unique phenomenon observed i.e., no mecA gene was present in 2 isolates 18.18% (2/11) which connotes the importance of molecular methods/PCR for the identification of microbes. The prevalence of the PVL gene was 18.18%, comparatively high as compared to previous studies conducted on bovine chronic wounds. When the Sanger sequencing of 16S rRNA of MRSA isolates was performed there was a change of one nucleotide identified (C>T) at position 1031. After performing phylogenetic analysis with S. aureus of different countries distinct and separate dendrogram was obtained which differentiates the Pakistani S. aureus isolates from other countries.
{"title":"Molecular characterization of methicillin-resistant Staphylococcus aureus (MRSA)isolated from bovine wounds","authors":"M. Khan, A. Nadeem, M. Javed, W. Shehzad, Asad Ali","doi":"10.2298/gensr2201411k","DOIUrl":"https://doi.org/10.2298/gensr2201411k","url":null,"abstract":"Staphylococcus aureus (S. aureus) is a Gram-positive coccus with golden-colored colonies 0.5-1.5 ?m in diameter. It is an opportunistic pathogen and colonizes as healthy flora. When the host defense system is breached it provides a source for the introduction of (Methicillin-resistant S. aureus) MRSA. The incorporation of the mecA gene shift S. aureus into MRSA, mecA is a primary gene for the confirmation of MRSA, so, it is used as a useful marker to determine Methicillin resistance in S. aureus. In this study, we investigated the molecular characterization of mecA, Panton-Valentine Leukocidin (PVL), and 16S rRNA genes in MRSA to determine diversity, phylogenetic analysis, and multidrug resistance (MDR) of MRSA isolated from chronic bovine wounds. A total of 8 antibiotics were used for MDR profiling and the results obtained are as follows: 100% of MRSA isolates were resistant to Augmentin and Cefipime, 81.8% to Vancomycin and Tetracyclin, 36.4% to Streptomycin and Ciprofloxacin, Azithromycin 54.5 and 0% to Chloramphenicol which warrants that it?s the best antibiotic according to this study. Multiplex PCRs were performed for the confirmation of targeted genes and diversity analysis. The diversity of MRSA in the bovine population was 22% (11/50) on the microbiological scale that considered high as compared to reported data. When the PCR of MRSA isolates was performed, there was a unique phenomenon observed i.e., no mecA gene was present in 2 isolates 18.18% (2/11) which connotes the importance of molecular methods/PCR for the identification of microbes. The prevalence of the PVL gene was 18.18%, comparatively high as compared to previous studies conducted on bovine chronic wounds. When the Sanger sequencing of 16S rRNA of MRSA isolates was performed there was a change of one nucleotide identified (C>T) at position 1031. After performing phylogenetic analysis with S. aureus of different countries distinct and separate dendrogram was obtained which differentiates the Pakistani S. aureus isolates from other countries.","PeriodicalId":50423,"journal":{"name":"Genetika-Belgrade","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68292782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The genus Alcea that is a member of Malvaceae family, is a Mediterranean perennial herb with major diversity centers in the Middle East and Western Mediterranean Basin. Alcea is a unique genus with several endemic taxa, and many of these endemic taxa from the Irano-Turanian phytogeographical area are particularly interesting. The genus contains 34 species in Iran, 15 of which are endemic. As a result of the importance of Alcea species, molecular data were collected for this genus in this research. For this study, 83 plants were used, which were randomly obtained from 5 species found in 6 provinces. Genomic DNA Amplification with 5 primers resulted in 75 bands, 66 of which were polymorphic (88.12%). The high average MI and PIC values indicated that SCoT primers have a high capacity for detecting polymorphic loci among the species of Alcea. The range of genetic similarities between 5 collected species was estimated to be between 0.77 and 0.89. The SCoT markers analysis revealed that the species Alcea angulata and Alcea popovii had the least similarity, while Alcea loftusii and Alcea sulphurea had the most similarity. The current study?s objectives are as follows: 1) is it possible to identify Alcea species through SCoT markers, 2) what genetic structure do these species have in Iran, and 3) what is the species inter-relationship? The current research found that SCoT markers can be used to identify the species.
{"title":"Species identification and genetic diversity of Alcea (Malvaceae) using SCoT molecular markers: Medicinal plant","authors":"Yanxia Sun, Hanxiu Jiang, Fang Zeng, X. Pan, Xiaoxia Wu, Yue Qi, Xiaoyong Wu","doi":"10.2298/gensr2201369s","DOIUrl":"https://doi.org/10.2298/gensr2201369s","url":null,"abstract":"The genus Alcea that is a member of Malvaceae family, is a Mediterranean perennial herb with major diversity centers in the Middle East and Western Mediterranean Basin. Alcea is a unique genus with several endemic taxa, and many of these endemic taxa from the Irano-Turanian phytogeographical area are particularly interesting. The genus contains 34 species in Iran, 15 of which are endemic. As a result of the importance of Alcea species, molecular data were collected for this genus in this research. For this study, 83 plants were used, which were randomly obtained from 5 species found in 6 provinces. Genomic DNA Amplification with 5 primers resulted in 75 bands, 66 of which were polymorphic (88.12%). The high average MI and PIC values indicated that SCoT primers have a high capacity for detecting polymorphic loci among the species of Alcea. The range of genetic similarities between 5 collected species was estimated to be between 0.77 and 0.89. The SCoT markers analysis revealed that the species Alcea angulata and Alcea popovii had the least similarity, while Alcea loftusii and Alcea sulphurea had the most similarity. The current study?s objectives are as follows: 1) is it possible to identify Alcea species through SCoT markers, 2) what genetic structure do these species have in Iran, and 3) what is the species inter-relationship? The current research found that SCoT markers can be used to identify the species.","PeriodicalId":50423,"journal":{"name":"Genetika-Belgrade","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68293083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Spine gourd (Momordica dioica Roxb.) is a highly nutritious vegetable crop with dioecious reproductive nature. Forty-eight spine gourd genotypes including 32 female and 16 male genotypes were assessed for molecular divergence to establish phenotypic relationships using ISSR markers. Twenty-two out of a total of 25 ISSR primers studied yielded a total of 88 bands of which 80 bands were polymorphic, with three of them being unique in their profile. Each primer thus produced a mean of 4.0 bands per marker, with 3.64 mean polymorphic bands per marker. Fifteen primers showed 100 percent polymorphism. In the dendrogram, genotypes were distinguished from each other with a similarity range of 0.465 to 0.959. A wider range of molecular diversity detected by ISSR markers reflected the presence of a high level of genetic variation forming different 5 broad groups of clusters. The clustering pattern based on molecular variation during this investigation revealed five clusters; of which cluster three had twenty-eight (all 16 malealong with 12 female genotypes) genotypes; while cluster 4 and 5 were mono-genotypic.
{"title":"Assessment of molecular diversity and establishing phenotypic relationships in female and male genotypes of spine gourd (Momordica dioica Roxb.)","authors":"S. Dodake, V. Chimote, P. Kulwal","doi":"10.2298/gensr2202589d","DOIUrl":"https://doi.org/10.2298/gensr2202589d","url":null,"abstract":"Spine gourd (Momordica dioica Roxb.) is a highly nutritious vegetable crop with dioecious reproductive nature. Forty-eight spine gourd genotypes including 32 female and 16 male genotypes were assessed for molecular divergence to establish phenotypic relationships using ISSR markers. Twenty-two out of a total of 25 ISSR primers studied yielded a total of 88 bands of which 80 bands were polymorphic, with three of them being unique in their profile. Each primer thus produced a mean of 4.0 bands per marker, with 3.64 mean polymorphic bands per marker. Fifteen primers showed 100 percent polymorphism. In the dendrogram, genotypes were distinguished from each other with a similarity range of 0.465 to 0.959. A wider range of molecular diversity detected by ISSR markers reflected the presence of a high level of genetic variation forming different 5 broad groups of clusters. The clustering pattern based on molecular variation during this investigation revealed five clusters; of which cluster three had twenty-eight (all 16 malealong with 12 female genotypes) genotypes; while cluster 4 and 5 were mono-genotypic.","PeriodicalId":50423,"journal":{"name":"Genetika-Belgrade","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68293411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Masoumeh Norouzi, A. Maleki, E. Aboualigalehdari, S. Ghafourian
The over use of antibiotics to treat infections in humans and animals made a phenomenon of the antibiotic-resistant bacteria. While studies focused to find on new antibiotics but, identification of novel antibacterial targets in bacteria is very important. By Toxin antitoxin systems this hypothesis could be done, whereas by the activation of a toxin or inactivation of an antitoxin, the raised toxin kills the bacterium. These systems are attractive target for antimicrobial therapy. However, the most important step for potency of TA system, as an antibacterial target, is to identify a TA system that is prevalent in all resistant clinical isolates. So, the prevalence of different TA systems among clinical isolates of Acinetobacter baumannii in Emam khomeini hospital, Ilam, Iran was evaluated to determine which TA system is prevalent in all antibiotic resistant A. baumannii. So, one hundred A. baumannii clinical isolates were identified during one-year period in Emam khomeini hospital, Ilam, Iran. A. baumannii clinical isolates were isolated from hospitalized patients in ICU and burn patients. All isolates were resistant to at least one antibiotic. Then, the isolates were subjected to evaluation to find mazEF and higBA TA genes by PCR. The results showed the frequency of mazEF and highBA TA genes in all isolates was 72% and 39%, respectively. mazEF or higBA TA systems are not presented in all isolates. So, the potency of these two TA systems are in challenged. Also, all isolates were not positive for one TA gene. So, more research in different geographical area should be done with functionality of TA genes.
{"title":"Type II toxin- antitoxin systems in clinical isolates of antibiotic resistant Acinetobacter baumannii","authors":"Masoumeh Norouzi, A. Maleki, E. Aboualigalehdari, S. Ghafourian","doi":"10.2298/gensr2202625n","DOIUrl":"https://doi.org/10.2298/gensr2202625n","url":null,"abstract":"The over use of antibiotics to treat infections in humans and animals made a phenomenon of the antibiotic-resistant bacteria. While studies focused to find on new antibiotics but, identification of novel antibacterial targets in bacteria is very important. By Toxin antitoxin systems this hypothesis could be done, whereas by the activation of a toxin or inactivation of an antitoxin, the raised toxin kills the bacterium. These systems are attractive target for antimicrobial therapy. However, the most important step for potency of TA system, as an antibacterial target, is to identify a TA system that is prevalent in all resistant clinical isolates. So, the prevalence of different TA systems among clinical isolates of Acinetobacter baumannii in Emam khomeini hospital, Ilam, Iran was evaluated to determine which TA system is prevalent in all antibiotic resistant A. baumannii. So, one hundred A. baumannii clinical isolates were identified during one-year period in Emam khomeini hospital, Ilam, Iran. A. baumannii clinical isolates were isolated from hospitalized patients in ICU and burn patients. All isolates were resistant to at least one antibiotic. Then, the isolates were subjected to evaluation to find mazEF and higBA TA genes by PCR. The results showed the frequency of mazEF and highBA TA genes in all isolates was 72% and 39%, respectively. mazEF or higBA TA systems are not presented in all isolates. So, the potency of these two TA systems are in challenged. Also, all isolates were not positive for one TA gene. So, more research in different geographical area should be done with functionality of TA genes.","PeriodicalId":50423,"journal":{"name":"Genetika-Belgrade","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68293937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sedigheh Rahimi, M. Sheidai, A. Mehrabian, F. Koohdar
The genus Epilobium has about 200 species in which taxonomic subdivisions are difficult but possible. Species E. minutiflorum due to its fluffy white inflorescence and small miniature flowers and beaked seeds, it is one of the most prominent species of the genus Epilobium in the region. We have no data on the population genetic structure of this species in the Iran. Therefore a population genetic and morphological investigation was performed through light on genetic and morphological variability in this taxa. We used SCoT molecular markers for population genetic investigation. Genetic diversity analyses revealed a moderate genetic variability between E. minutiflorum populations, while PCoA showed some degree of genetic admixture among populations. AMOVA produced significant genetic difference among populations. Morphometric analysis showed that high degree of overlap among the studied populations. However, the results showed that SCoT marker has a good discrimination power and can differentiate the studied populations. This marker can be used to evaluate genetic diversity and identify genotypes of E. minutiflorum populations.
{"title":"Population genetic study in Epilobium minutiflorum (Onagraceae) in Iran","authors":"Sedigheh Rahimi, M. Sheidai, A. Mehrabian, F. Koohdar","doi":"10.2298/gensr2202677r","DOIUrl":"https://doi.org/10.2298/gensr2202677r","url":null,"abstract":"The genus Epilobium has about 200 species in which taxonomic subdivisions are difficult but possible. Species E. minutiflorum due to its fluffy white inflorescence and small miniature flowers and beaked seeds, it is one of the most prominent species of the genus Epilobium in the region. We have no data on the population genetic structure of this species in the Iran. Therefore a population genetic and morphological investigation was performed through light on genetic and morphological variability in this taxa. We used SCoT molecular markers for population genetic investigation. Genetic diversity analyses revealed a moderate genetic variability between E. minutiflorum populations, while PCoA showed some degree of genetic admixture among populations. AMOVA produced significant genetic difference among populations. Morphometric analysis showed that high degree of overlap among the studied populations. However, the results showed that SCoT marker has a good discrimination power and can differentiate the studied populations. This marker can be used to evaluate genetic diversity and identify genotypes of E. minutiflorum populations.","PeriodicalId":50423,"journal":{"name":"Genetika-Belgrade","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68294113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marija Jovanović, J. Milovanović, M. Nonić, M. Šijačić‐Nikolić
In this study, we used leaf geometric morphometrics to quantify the differences among Quercus cerris L. and Quercus frainetto Ten. and their populations in the Sumadija region in Serbia. We sampled 2200 leaves from eight populations and on each leaf recorded 13 landmarks. To analyze how leaf morphology varies across species and populations, we used Procrustes ANOVA, a two-block partial least-squares analysis, a principal component analysis and a canonical variate analysis. The results showed a clear discrimination between species, followed by different levels of leaf shape variability in Q. cerris and Q. frainetto. The leaves of Q. cerris displayed higher levels of variability and higher differences among populations compared to Q. frainetto. The patterns of population grouping in the two species greatly differed, indicating that in these species different factors contribute to intraspecific variability. This study provides preliminary results of the leaf morphometric variability of oak species in the Sumadija region in Serbia. Future studies should include genetic and environmental analyses to understand the origins of phenotypic differences between species and populations, and to fully recognize which factors mostly determine relationships between taxa.
{"title":"Inter- and intraspecific variability of Quercus cerris L. and Quercus frainneto Ten. in the Sumadija region (Serbia) based on leaf geometric morphometrics","authors":"Marija Jovanović, J. Milovanović, M. Nonić, M. Šijačić‐Nikolić","doi":"10.2298/gensr2202787j","DOIUrl":"https://doi.org/10.2298/gensr2202787j","url":null,"abstract":"In this study, we used leaf geometric morphometrics to quantify the differences among Quercus cerris L. and Quercus frainetto Ten. and their populations in the Sumadija region in Serbia. We sampled 2200 leaves from eight populations and on each leaf recorded 13 landmarks. To analyze how leaf morphology varies across species and populations, we used Procrustes ANOVA, a two-block partial least-squares analysis, a principal component analysis and a canonical variate analysis. The results showed a clear discrimination between species, followed by different levels of leaf shape variability in Q. cerris and Q. frainetto. The leaves of Q. cerris displayed higher levels of variability and higher differences among populations compared to Q. frainetto. The patterns of population grouping in the two species greatly differed, indicating that in these species different factors contribute to intraspecific variability. This study provides preliminary results of the leaf morphometric variability of oak species in the Sumadija region in Serbia. Future studies should include genetic and environmental analyses to understand the origins of phenotypic differences between species and populations, and to fully recognize which factors mostly determine relationships between taxa.","PeriodicalId":50423,"journal":{"name":"Genetika-Belgrade","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68294205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Igor Milunović, V. Popović, N. Rakaščan, J. Ikanović, V. Trkulja, V. Radojević, G. Drazic
Rye is a dual-purpose crop, for nutrition but also for bioenergy. The selection of rye is aimed at its improvement as a plant for human and animal consumption, but also it is interesting for bioenergy production as it combines high biomass production with low environmental impact. There is a growing demand for sustainable sources of biomass worldwide. Directions for achieving rye selection for energy purposes include selection to increase biomass yield and corresponding physiological properties. During three years (2019-2021), four rye genotypes were examined. The aim of this study was to examine the influence of genotype (G), year (Y) and their interaction (G?Y) on rye productivity parameters: plant height (PH), spike length (SL), 1000-grain weight (TGW), hectoliter mass (HM), green biomass yield (GBY), biogas yield (BGY) as well as the possibility of using rye as an alternative fuel. Rye is an excellent raw material for the production of healthy food, but also for the production of biofuels. The study discussed the potential use of four high yielding genotypes for biofuel production. Genotype G1 (25.29 t ha-1) had a statistically significantly higher average green biomass yield compared to genotypes G2, G3 and G4 (22.98 t ha-1, 23.56 t ha-1 and 23.76 t ha-1). Significant G?Y interactions demonstrate differences between rye genotypes in response to environmental conditions. Plant height was directly proportional to biomass yield. As one of the targets in breeding programs, to develop taller cultivars as biofuel feedstock. Screening and selection of appropriate rye varieties for each region is critical for optimum results.
黑麦是一种双重用途作物，既能提供营养，又能提供生物能源。选择黑麦的目的是为了改善其作为人类和动物消费的植物，但它也很有趣，因为它结合了高生物量生产和低环境影响。世界范围内对可持续生物质资源的需求不断增长。实现黑麦能量选择的方向包括提高生物量产量和相应生理特性的选择。在3年(2019-2021)期间，检测了4种黑麦基因型。本研究旨在探讨基因型(G)、年份(Y)及其互作(G?Y)对黑麦产量参数(株高(PH)、穗长(SL)、千粒重(TGW)、百升质量(HM)、绿色生物质产量(GBY)、沼气产量(BGY)的影响，以及利用黑麦作为替代燃料的可能性。黑麦是生产健康食品的优良原料，也是生产生物燃料的优良原料。该研究讨论了四种高产基因型在生物燃料生产中的潜在用途。基因型G1 (25.29 t ha-1)的平均绿色生物量产量显著高于基因型G2、G3和G4 (22.98 t ha-1、23.56 t ha-1和23.76 t ha-1)。重要的G ?Y相互作用表明黑麦基因型对环境条件的响应存在差异。株高与生物量产量成正比。培育作为生物燃料原料的高大品种是育种计划的目标之一。筛选和选择适合每个地区的黑麦品种是获得最佳结果的关键。
{"title":"Genotype × year interaction on rye productivity parameters cultivated on sandy chernozem soil","authors":"Igor Milunović, V. Popović, N. Rakaščan, J. Ikanović, V. Trkulja, V. Radojević, G. Drazic","doi":"10.2298/gensr2202887m","DOIUrl":"https://doi.org/10.2298/gensr2202887m","url":null,"abstract":"Rye is a dual-purpose crop, for nutrition but also for bioenergy. The selection of rye is aimed at its improvement as a plant for human and animal consumption, but also it is interesting for bioenergy production as it combines high biomass production with low environmental impact. There is a growing demand for sustainable sources of biomass worldwide. Directions for achieving rye selection for energy purposes include selection to increase biomass yield and corresponding physiological properties. During three years (2019-2021), four rye genotypes were examined. The aim of this study was to examine the influence of genotype (G), year (Y) and their interaction (G?Y) on rye productivity parameters: plant height (PH), spike length (SL), 1000-grain weight (TGW), hectoliter mass (HM), green biomass yield (GBY), biogas yield (BGY) as well as the possibility of using rye as an alternative fuel. Rye is an excellent raw material for the production of healthy food, but also for the production of biofuels. The study discussed the potential use of four high yielding genotypes for biofuel production. Genotype G1 (25.29 t ha-1) had a statistically significantly higher average green biomass yield compared to genotypes G2, G3 and G4 (22.98 t ha-1, 23.56 t ha-1 and 23.76 t ha-1). Significant G?Y interactions demonstrate differences between rye genotypes in response to environmental conditions. Plant height was directly proportional to biomass yield. As one of the targets in breeding programs, to develop taller cultivars as biofuel feedstock. Screening and selection of appropriate rye varieties for each region is critical for optimum results.","PeriodicalId":50423,"journal":{"name":"Genetika-Belgrade","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68294242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bojana Petrović, J. Joksimović, D. Šljivančanin, Luka Joksimovic, Aleksandra Drinic, J. Stamenković
Second trimester ultrasound examination for risk assessment of chromosomal abnormalities remains an important component of prenatal evaluation. We have conducted a retrospective study to evaluate the efficiency of ultrasonographic screening for the markers of chromosomal aberrations and to classify ultrasonographic markers according to the aberration they were found with. Over a 10 year period we performed 620 karyotype analyses of fetal blood taken by cordocentesis after detection of fetal anomalies in a second trimester scan in unselected population and 216 samples of peripheral blood of neonates having phenotypic features suspected for chromosomopathies. Ultrasound examination and cytogenetic data were obtained from the laboratory database. Chromosomal abnormalities were found in 36 (5,8%) fetuses with anomalies. Most frequently chromosomal aberrations were detected in fetuses with multiple anomalies (13,3%), heart anomalies (11,5%), short femurs (12,5%) and polyhydramnios (7,7%). The success rate of sonographic examination in detection of Down syndrome was 85%, and in detection of sex chromosome trisomies 80%. Trisomy 18, trisomy 13 and polyploidy were found prenatally in 100% each. Nearly 42% of trisomy 21 fetuses had heart anomaly, 35,3% polyhydramnios and 17,7% short femurs. Trisomy 18 fetuses had polyhydramnios in 87,5%, CNS anomalies in 62,5% and symmetrical IUGR in 50% of cases. All of the fetuses with monosomy X had short femurs. Ultrasonographic evaluation is the most sensitive screening method for the identification of fetuses having a high risk rate for chromosomal abnormalities in a low risk population.
{"title":"Ultrasound markers of chromosome aberrations on routine second trimester screening","authors":"Bojana Petrović, J. Joksimović, D. Šljivančanin, Luka Joksimovic, Aleksandra Drinic, J. Stamenković","doi":"10.2298/gensr2202921p","DOIUrl":"https://doi.org/10.2298/gensr2202921p","url":null,"abstract":"Second trimester ultrasound examination for risk assessment of chromosomal abnormalities remains an important component of prenatal evaluation. We have conducted a retrospective study to evaluate the efficiency of ultrasonographic screening for the markers of chromosomal aberrations and to classify ultrasonographic markers according to the aberration they were found with. Over a 10 year period we performed 620 karyotype analyses of fetal blood taken by cordocentesis after detection of fetal anomalies in a second trimester scan in unselected population and 216 samples of peripheral blood of neonates having phenotypic features suspected for chromosomopathies. Ultrasound examination and cytogenetic data were obtained from the laboratory database. Chromosomal abnormalities were found in 36 (5,8%) fetuses with anomalies. Most frequently chromosomal aberrations were detected in fetuses with multiple anomalies (13,3%), heart anomalies (11,5%), short femurs (12,5%) and polyhydramnios (7,7%). The success rate of sonographic examination in detection of Down syndrome was 85%, and in detection of sex chromosome trisomies 80%. Trisomy 18, trisomy 13 and polyploidy were found prenatally in 100% each. Nearly 42% of trisomy 21 fetuses had heart anomaly, 35,3% polyhydramnios and 17,7% short femurs. Trisomy 18 fetuses had polyhydramnios in 87,5%, CNS anomalies in 62,5% and symmetrical IUGR in 50% of cases. All of the fetuses with monosomy X had short femurs. Ultrasonographic evaluation is the most sensitive screening method for the identification of fetuses having a high risk rate for chromosomal abnormalities in a low risk population.","PeriodicalId":50423,"journal":{"name":"Genetika-Belgrade","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68294513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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