Pub Date : 2022-03-30DOI: 10.1101/2022.03.29.486262
Umit Akkose, Ogun Adebali
Sequence content is heterogeneous throughout genomes. Therefore, Genome-wide NGS reads biased towards specific nucleotide profiles are affected by the genome-wide heterogeneous nucleotide distribution. Boquila generates sequences that mimic the nucleotide profile of true reads, which can be used to correct the nucleotide-based bias of genome-wide distribution of NGS reads. Boquila can be configured to generate reads from only specified regions of the reference genome. It also allows the use of input DNA sequencing to correct the bias due to the copy number variations in the genome. Boquila uses standard file formats for input and output data, and it can be easily integrated into any workflow for high-throughput sequencing applications.
{"title":"Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis","authors":"Umit Akkose, Ogun Adebali","doi":"10.1101/2022.03.29.486262","DOIUrl":"https://doi.org/10.1101/2022.03.29.486262","url":null,"abstract":"Sequence content is heterogeneous throughout genomes. Therefore, Genome-wide NGS reads biased towards specific nucleotide profiles are affected by the genome-wide heterogeneous nucleotide distribution. Boquila generates sequences that mimic the nucleotide profile of true reads, which can be used to correct the nucleotide-based bias of genome-wide distribution of NGS reads. Boquila can be configured to generate reads from only specified regions of the reference genome. It also allows the use of input DNA sequencing to correct the bias due to the copy number variations in the genome. Boquila uses standard file formats for input and output data, and it can be easily integrated into any workflow for high-throughput sequencing applications.","PeriodicalId":23358,"journal":{"name":"Turkish Journal of Biology","volume":"47 1","pages":"158 - 163"},"PeriodicalIF":2.2,"publicationDate":"2022-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45607419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The term of cancer is used to describe diseases in which abnormal cells that grow out of control and invade other tissues. There are multiple types of cancer and many types of cancer have various subtypes with different clinical and biological implications. These differences show that diverse methods should be followed for the treatment of different subtypes of cancer. Discovering cancer subtypes is an important problem in bioinformatics, as it can help improve personalized medicine. Knowing the subtype of cancer is useful for determine the treatment steps and prognosis. Computational bioinformatics methods help performing cancer analysis to design targeted treatments by exposing the common molecular pathology of different cancer subtypes. Thus far, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data, and result in ill-conditioned solution. To resort this shortcoming, in this thesis, we propose an alternative unsupervised computational method to stratify cancer into subtypes using applied numerical algebra techniques. More specifically, we applied this label propagation-based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder and breast tumors. We then evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches. tiplerinin
{"title":"Developing a label propagation approach for cancer subtype identification problem","authors":"Pınar Güner, B. Güngör, Mustafa Coşkun","doi":"10.55730/1300-0152.2582","DOIUrl":"https://doi.org/10.55730/1300-0152.2582","url":null,"abstract":"The term of cancer is used to describe diseases in which abnormal cells that grow out of control and invade other tissues. There are multiple types of cancer and many types of cancer have various subtypes with different clinical and biological implications. These differences show that diverse methods should be followed for the treatment of different subtypes of cancer. Discovering cancer subtypes is an important problem in bioinformatics, as it can help improve personalized medicine. Knowing the subtype of cancer is useful for determine the treatment steps and prognosis. Computational bioinformatics methods help performing cancer analysis to design targeted treatments by exposing the common molecular pathology of different cancer subtypes. Thus far, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data, and result in ill-conditioned solution. To resort this shortcoming, in this thesis, we propose an alternative unsupervised computational method to stratify cancer into subtypes using applied numerical algebra techniques. More specifically, we applied this label propagation-based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder and breast tumors. We then evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches. tiplerinin","PeriodicalId":23358,"journal":{"name":"Turkish Journal of Biology","volume":"1 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45915196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Diclofenac sodium (DS), a potent inhibitor of cyclooxygenase, reduces the release of arachidonic acid and formation of prostaglandins. Being a nonsteroid drug that shows antiinflammatory action, the possible side effects of fetal DS administration gain importance in public and medical applications. Herein, the effects of DS administration (1 mg/kg) during gestational days 5–20 were investigated on the performance of Wistar rat pups in a variety of behavioral tasks. Four-week-old pups were subjected to sensory motor tests, a plus maze, an open field, the Morris water maze, and a radial arm maze. Fetal DS disrupted some sensory motor performances, such as visual placing and climbing in both females and males. In the open field, DS females had a higher level of anxiety and male DS pups habituated to the environment slowly compared to controls. The DS pups showed slower rates of learning, whereas no substantial between-group differences were found in the performance of spatial memory compared to both controls. Furthermore, working memory was negatively affected by fetal DS. In conclusion, it was indicated that DS administration during pregnancy had slight behavioral impacts with a delay in learning and a defect in the short-term memory in juvenile rats.
{"title":"Prenatal exposure of diclofenac sodium alters the behavioral development of young Wistar rats","authors":"B. Elibol, Begüm ARITAN OĞUR, H. Doğru","doi":"10.3906/biy-1904-33","DOIUrl":"https://doi.org/10.3906/biy-1904-33","url":null,"abstract":"Diclofenac sodium (DS), a potent inhibitor of cyclooxygenase, reduces the release of arachidonic acid and formation of prostaglandins. Being a nonsteroid drug that shows antiinflammatory action, the possible side effects of fetal DS administration gain importance in public and medical applications. Herein, the effects of DS administration (1 mg/kg) during gestational days 5–20 were investigated on the performance of Wistar rat pups in a variety of behavioral tasks. Four-week-old pups were subjected to sensory motor tests, a plus maze, an open field, the Morris water maze, and a radial arm maze. Fetal DS disrupted some sensory motor performances, such as visual placing and climbing in both females and males. In the open field, DS females had a higher level of anxiety and male DS pups habituated to the environment slowly compared to controls. The DS pups showed slower rates of learning, whereas no substantial between-group differences were found in the performance of spatial memory compared to both controls. Furthermore, working memory was negatively affected by fetal DS. In conclusion, it was indicated that DS administration during pregnancy had slight behavioral impacts with a delay in learning and a defect in the short-term memory in juvenile rats.","PeriodicalId":23358,"journal":{"name":"Turkish Journal of Biology","volume":"43 1","pages":"305 - 313"},"PeriodicalIF":2.2,"publicationDate":"2019-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3906/biy-1904-33","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45952632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Head and neck cancer (HNC) is the sixth most common cancer worldwide and therefore presents a global public health problem. There are no standard algorithms for the diagnosis and follow-up of the disease, and no effective current treatment approaches exist. Therefore, the discovery of new biomolecules and the design of new strategies to aid in early diagnosis is necessary, along with establishing prognostic factors of HNC. In several cancer studies, the upregulation of SET Domain, Bifurcated 1 (SETDB1) has been reported to be tumor-inducing and to indicate a cancer-invasive prognosis, leading to the modulation of genes associated with different signaling pathways; however, the literature is sparse regarding the relationship between SETDB1 and HNC. In our study, three HNC primary cell lines and their corresponding metastatic cell lines were used. The quantitative reverse transcriptase-polymerase chain reaction and western blotting data indicated that the SETDB1 mRNA and protein expression levels were higher in all metastatic cell lines compared to their primary cell lines (P < 0.05 for all). To investigate the role of SETDB1 in HNC biology, in vitro functional analyses were carried out using small interference RNA (siRNA) technology, cell viability, scratch wound-healing, and the caspase-3 activity assay of gene expression of SETDB1 to compare primary and metastatic cell lines of HNC. Metastatic cells were more susceptible to this suppression, which decreased the vitality of cells and their ability of wound-healing and induced level of caspase-3 activity (P < 0.05 for all). This functional study has shown that SETDB1 plays an important role in head and neck carcinogenesis. Therefore, SETDB1 may be an attractive therapeutic target molecule and also a potential diagnostic and prognostic biomarker in HNC.
{"title":"Knockdown of SET Domain, Bifurcated 1 suppresses head and neck cancer cell viability and wound-healing ability in vitro","authors":"S. Özdaş","doi":"10.3906/biy-1903-71","DOIUrl":"https://doi.org/10.3906/biy-1903-71","url":null,"abstract":"Head and neck cancer (HNC) is the sixth most common cancer worldwide and therefore presents a global public health problem. There are no standard algorithms for the diagnosis and follow-up of the disease, and no effective current treatment approaches exist. Therefore, the discovery of new biomolecules and the design of new strategies to aid in early diagnosis is necessary, along with establishing prognostic factors of HNC. In several cancer studies, the upregulation of SET Domain, Bifurcated 1 (SETDB1) has been reported to be tumor-inducing and to indicate a cancer-invasive prognosis, leading to the modulation of genes associated with different signaling pathways; however, the literature is sparse regarding the relationship between SETDB1 and HNC. In our study, three HNC primary cell lines and their corresponding metastatic cell lines were used. The quantitative reverse transcriptase-polymerase chain reaction and western blotting data indicated that the SETDB1 mRNA and protein expression levels were higher in all metastatic cell lines compared to their primary cell lines (P < 0.05 for all). To investigate the role of SETDB1 in HNC biology, in vitro functional analyses were carried out using small interference RNA (siRNA) technology, cell viability, scratch wound-healing, and the caspase-3 activity assay of gene expression of SETDB1 to compare primary and metastatic cell lines of HNC. Metastatic cells were more susceptible to this suppression, which decreased the vitality of cells and their ability of wound-healing and induced level of caspase-3 activity (P < 0.05 for all). This functional study has shown that SETDB1 plays an important role in head and neck carcinogenesis. Therefore, SETDB1 may be an attractive therapeutic target molecule and also a potential diagnostic and prognostic biomarker in HNC.","PeriodicalId":23358,"journal":{"name":"Turkish Journal of Biology","volume":"43 1","pages":"281 - 292"},"PeriodicalIF":2.2,"publicationDate":"2019-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3906/biy-1903-71","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44221259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
E2F6 is a member of the E2F family of transcription factors involved in regulation of a wide variety of genes through both activation and repression. E2F6 has been reported as overexpressed in breast cancers but whether or not this is important for tumor development is unclear. We first checked E2F6 expression in tumor cDNAs and the protein level in a range of breast cancer cell lines. RNA interference-mediated depletion was then used to assess the importance of E2F6 expression in cell lines with regard to cell cycle profile using fluorescence-activated cell sorting and a cell survival assay using (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). The overexpression of E2F6 was confirmed in breast tumor cDNA samples and breast cancer cell lines. Depletion of E2F6 in the breast cancer cells reduced cell viability in MCF-7, T-47D, and MDA-MB-231 cells. There was little effect in the nontumor breast cell line MCF-10A. The deleterious effect on cancer cells was greater during replication stress, leading to an increase in the proportion of breast cancer cells with sub-G1 DNA content. These results suggest that E2F6 might be essential for the survival of breast cancer cells experiencing replication stress, and therefore it could be a target for combined therapy.
{"title":"E2F6 is essential for cell viability in breast cancer cells during replication stress","authors":"I. J. Lafta","doi":"10.3906/biy-1905-6","DOIUrl":"https://doi.org/10.3906/biy-1905-6","url":null,"abstract":"E2F6 is a member of the E2F family of transcription factors involved in regulation of a wide variety of genes through both activation and repression. E2F6 has been reported as overexpressed in breast cancers but whether or not this is important for tumor development is unclear. We first checked E2F6 expression in tumor cDNAs and the protein level in a range of breast cancer cell lines. RNA interference-mediated depletion was then used to assess the importance of E2F6 expression in cell lines with regard to cell cycle profile using fluorescence-activated cell sorting and a cell survival assay using (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). The overexpression of E2F6 was confirmed in breast tumor cDNA samples and breast cancer cell lines. Depletion of E2F6 in the breast cancer cells reduced cell viability in MCF-7, T-47D, and MDA-MB-231 cells. There was little effect in the nontumor breast cell line MCF-10A. The deleterious effect on cancer cells was greater during replication stress, leading to an increase in the proportion of breast cancer cells with sub-G1 DNA content. These results suggest that E2F6 might be essential for the survival of breast cancer cells experiencing replication stress, and therefore it could be a target for combined therapy.","PeriodicalId":23358,"journal":{"name":"Turkish Journal of Biology","volume":"43 1","pages":"293 - 304"},"PeriodicalIF":2.2,"publicationDate":"2019-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3906/biy-1905-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49448948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Azhar, A. Farooq, S. Haque, S. Bano, Lubna Zaheer, S. Faizi
Tagetes patula is used to treat cancer patients in alternative healthcare systems. However, its cytotoxic and genotoxic effects have not been reported. Therefore, themethanol extract of T. patula flower, the ethyl acetate fraction, and the pure compound patuletin were evaluatedusing the Allium test.The methanol extract and fraction contained ~3% and ~36% patuletin, respectively, with ~98% purity. The methanol extract caused inhibition of Allium root growth displaying an IC50 value of ~500 µg/mL, while the fraction and patuletin were more potent by ~2 and ~5 times, respectively. The Allium root tips demonstrated a decline in prophase, metaphase, anaphase, and telophase stages with concomitant decrease in percent mitotic index in the methanol extract (~5.64), fraction, and patuletin (~4) as compared to the control (~7.61). However, in only methanol extract-treated root tips, an increase in metaphase stage was noted. In addition, the methanol extract predominantly induced c-type, misaligned, and multipolar chromosomal abnormalities while the fraction and patuletin displayed fragments and sticky chromosomes. The fraction and patuletin also produced micronuclei (~2%). In conclusion, T. patula flower methanol extract and ethyl acetate fraction are cytotoxicand genotoxic, which most likely could be due to the patuletin. Further preclinical and clinical studies are required to justify its clinical use.
{"title":"Cytotoxic and genotoxic action of Tagetes patula flower methanol extract and patuletin using the Allium test","authors":"M. Azhar, A. Farooq, S. Haque, S. Bano, Lubna Zaheer, S. Faizi","doi":"10.3906/biy-1906-7","DOIUrl":"https://doi.org/10.3906/biy-1906-7","url":null,"abstract":"Tagetes patula is used to treat cancer patients in alternative healthcare systems. However, its cytotoxic and genotoxic effects have not been reported. Therefore, themethanol extract of T. patula flower, the ethyl acetate fraction, and the pure compound patuletin were evaluatedusing the Allium test.The methanol extract and fraction contained ~3% and ~36% patuletin, respectively, with ~98% purity. The methanol extract caused inhibition of Allium root growth displaying an IC50 value of ~500 µg/mL, while the fraction and patuletin were more potent by ~2 and ~5 times, respectively. The Allium root tips demonstrated a decline in prophase, metaphase, anaphase, and telophase stages with concomitant decrease in percent mitotic index in the methanol extract (~5.64), fraction, and patuletin (~4) as compared to the control (~7.61). However, in only methanol extract-treated root tips, an increase in metaphase stage was noted. In addition, the methanol extract predominantly induced c-type, misaligned, and multipolar chromosomal abnormalities while the fraction and patuletin displayed fragments and sticky chromosomes. The fraction and patuletin also produced micronuclei (~2%). In conclusion, T. patula flower methanol extract and ethyl acetate fraction are cytotoxicand genotoxic, which most likely could be due to the patuletin. Further preclinical and clinical studies are required to justify its clinical use.","PeriodicalId":23358,"journal":{"name":"Turkish Journal of Biology","volume":"43 1","pages":"326 - 339"},"PeriodicalIF":2.2,"publicationDate":"2019-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44782292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This study reports a new Helicoverpa armigera nucleopolyhedrovirus (NPV) isolated from Heliothis peltigera (Denis & Schiffermuller), collected in the vicinity of Adana, Turkey. Infection was confirmed by tissue polymerase chain reaction and sequence analysis. Results showed that dead H. peltigera larvae contain Helicoverpa armigera nucleopolyhedrovirus. Thus, the isolate was named as HearNPV-TR. Microscopy studies indicated that occlusion bodies were 0.73 to 1.66 μm in diameter. The nucleocapsids are approximately 184 × 41 nm in size. The genome of HearNPV-TR was digested with KpnI and XhoI enzymes and calculated as 130.5 kb. Phylogenetic analysis showed that HearNPV-TR has close relation with the H. armigera SNPV-1073 China isolate. The Kimura analysis confirmed that the isolate is a variant of H. armigera NPV. Bioassays were performed using six different concentrations (1 × 103 to 1 × 108 occlusion bodies (OBs)/mL) on 2nd instar larvae of H. peltigera, H. armigera, Heliothis viriplaca, Heliothis nubigera. LC50 values were calculated to be 9.5 × 103, 1.9 × 104, 8.6 × 104 and 9.2 × 104 OBs/mL within 14 days, respectively. Results showed that it is a promising biocontrol agent against Heliothinae species.
{"title":"<b>A new Helicoverpa armigera Nucleopolyhedrovirus isolate from</b> Heliothis peltigera <b>(Denis & Schiffermuller) (Lepidoptera: Noctuidae) in Turkey</b>.","authors":"Gözde Büşra Eroğlu, Remziye Nalçacioğlu, Zihni Demirbağ","doi":"10.3906/biy-1902-64","DOIUrl":"10.3906/biy-1902-64","url":null,"abstract":"<p><p>This study reports a new Helicoverpa armigera nucleopolyhedrovirus (NPV) isolated from Heliothis peltigera (Denis & Schiffermuller), collected in the vicinity of Adana, Turkey. Infection was confirmed by tissue polymerase chain reaction and sequence analysis. Results showed that dead H. peltigera larvae contain Helicoverpa armigera nucleopolyhedrovirus. Thus, the isolate was named as HearNPV-TR. Microscopy studies indicated that occlusion bodies were 0.73 to 1.66 μm in diameter. The nucleocapsids are approximately 184 × 41 nm in size. The genome of HearNPV-TR was digested with KpnI and XhoI enzymes and calculated as 130.5 kb. Phylogenetic analysis showed that HearNPV-TR has close relation with the H. armigera SNPV-1073 China isolate. The Kimura analysis confirmed that the isolate is a variant of H. armigera NPV. Bioassays were performed using six different concentrations (1 × 10<sup>3</sup> to 1 × 10<sup>8</sup> occlusion bodies (OBs)/mL) on 2nd instar larvae of H. peltigera, H. armigera, Heliothis viriplaca, Heliothis nubigera. LC<sub>50</sub> values were calculated to be 9.5 × 10<sup>3</sup>, 1.9 × 10<sup>4</sup>, 8.6 × 10<sup>4</sup> and 9.2 × 10<sup>4</sup> OBs/mL within 14 days, respectively. Results showed that it is a promising biocontrol agent against Heliothinae species.</p>","PeriodicalId":23358,"journal":{"name":"Turkish Journal of Biology","volume":"43 1","pages":"340-348"},"PeriodicalIF":1.1,"publicationDate":"2019-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6823914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44942014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kandelia candel is one of the mangrove species that are most resistant to environmental stress. As a typical nonsalt-secreting mangrove plant, K. candel is an ideal biological material to analyze the molecular mechanism of salt tolerance in woody plants. In this study, changes in protein abundance and expression profile in K. candel roots under high-salinity stress of 600 mmol L-1 NaCl were analyzed using isobaric tags for relative and absolute quantification (iTRAQ) assay. Moreover, the physiological parameters associated with metabolic pathways in which the differentially abundant proteins (DAPs) are involved were determined. A total of 5577 proteins were identified by iTRAQ analysis of the K. candel root proteins, of which 227 were DAPs with a fold change ratio >1.2 or a fold change ratio <0.83 and a P-value <0.05. A total of 227 DAPs consisting of 110 up-regulated and 117 down-regulated proteins were identified. Our Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the DAPs were primarily involved in biological processes including carbohydrate and energy metabolisms, stress response and defense, cell wall structure, and secondary metabolism. The results of the physiological parameters showed that their profile changes were consistent with those of the proteome analysis. The results of the proteome and physiological parameters showed that K. candel roots could resist high-salinity stress by maintaining a normal Embden-Meyerhof-Parnas and tricarboxylic acid (EMP-TCA) pathway, increasing the activities of various antioxidant enzymes and antioxidant contents, stabilizing the cell wall structure, and accumulating secondary metabolites such as triterpenoids.
{"title":"Proteomic and physiological responses in mangrove Kandelia candel roots under short-term high-salinity stress","authors":"Jianhong Xing, Dezhuo Pan, Lingxia Wang, Fanglin Tan, Wei Chen","doi":"10.3906/biy-1906-22","DOIUrl":"https://doi.org/10.3906/biy-1906-22","url":null,"abstract":"Kandelia candel is one of the mangrove species that are most resistant to environmental stress. As a typical nonsalt-secreting mangrove plant, K. candel is an ideal biological material to analyze the molecular mechanism of salt tolerance in woody plants. In this study, changes in protein abundance and expression profile in K. candel roots under high-salinity stress of 600 mmol L-1 NaCl were analyzed using isobaric tags for relative and absolute quantification (iTRAQ) assay. Moreover, the physiological parameters associated with metabolic pathways in which the differentially abundant proteins (DAPs) are involved were determined. A total of 5577 proteins were identified by iTRAQ analysis of the K. candel root proteins, of which 227 were DAPs with a fold change ratio >1.2 or a fold change ratio <0.83 and a P-value <0.05. A total of 227 DAPs consisting of 110 up-regulated and 117 down-regulated proteins were identified. Our Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the DAPs were primarily involved in biological processes including carbohydrate and energy metabolisms, stress response and defense, cell wall structure, and secondary metabolism. The results of the physiological parameters showed that their profile changes were consistent with those of the proteome analysis. The results of the proteome and physiological parameters showed that K. candel roots could resist high-salinity stress by maintaining a normal Embden-Meyerhof-Parnas and tricarboxylic acid (EMP-TCA) pathway, increasing the activities of various antioxidant enzymes and antioxidant contents, stabilizing the cell wall structure, and accumulating secondary metabolites such as triterpenoids.","PeriodicalId":23358,"journal":{"name":"Turkish Journal of Biology","volume":"43 1","pages":"314 - 325"},"PeriodicalIF":2.2,"publicationDate":"2019-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3906/biy-1906-22","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48020071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Didem Karakas, R. Akar, Zeliha Gökmen, N. Deniz, E. Ulukaya
Breast cancer is the most-diagnosed cancer type among women. The triple-negative subtype is an especially aggressive type of breast cancer. Although chemotherapy is almost the only option for the treatment of triple-negative breast cancer (TNBC), currently used chemotherapeutics are not effective enough, considering the poor survival rate of patients. Therefore, novel compounds need to be developed to improve survival rates. It has been known that quinonic compounds, which are found in nature, have antibacterial, antifungal, and antitumorigenic properties. Naphthoquinones are members of the quinone family and are widely used in research due to their promising properties. In this study, we evaluated the cytotoxic activity of a novel naphthoquinone-derived compound (1,4-naphthoquinone (1,4-NQ)) against two different breast cancer cells: a hormone-responsive cell line (MCF-7) and a triple-negative cell line (MDA-MB-231). As a result, 1,4-NQ decreased cell viability in both tested cell lines in a dose-dependent manner. Increased apoptotic markers (presence of pyknotic nuclei, annexin-V positivity, caspase 3/7 activity, and decreased mitochondrial membrane potential) and DNA damage were especially observed in MDA-MB-231 cells after treatment with the compound. Considering the promising cytotoxic effect of the compound, 1,4-NQ needs further evaluation as a potential candidate for the treatment of TNBC.
{"title":"A novel 1,4-naphthoquinone-derived compound induces apoptotic cell death in breast cancer cells","authors":"Didem Karakas, R. Akar, Zeliha Gökmen, N. Deniz, E. Ulukaya","doi":"10.3906/biy-1901-19","DOIUrl":"https://doi.org/10.3906/biy-1901-19","url":null,"abstract":"Breast cancer is the most-diagnosed cancer type among women. The triple-negative subtype is an especially aggressive type of breast cancer. Although chemotherapy is almost the only option for the treatment of triple-negative breast cancer (TNBC), currently used chemotherapeutics are not effective enough, considering the poor survival rate of patients. Therefore, novel compounds need to be developed to improve survival rates. It has been known that quinonic compounds, which are found in nature, have antibacterial, antifungal, and antitumorigenic properties. Naphthoquinones are members of the quinone family and are widely used in research due to their promising properties. In this study, we evaluated the cytotoxic activity of a novel naphthoquinone-derived compound (1,4-naphthoquinone (1,4-NQ)) against two different breast cancer cells: a hormone-responsive cell line (MCF-7) and a triple-negative cell line (MDA-MB-231). As a result, 1,4-NQ decreased cell viability in both tested cell lines in a dose-dependent manner. Increased apoptotic markers (presence of pyknotic nuclei, annexin-V positivity, caspase 3/7 activity, and decreased mitochondrial membrane potential) and DNA damage were especially observed in MDA-MB-231 cells after treatment with the compound. Considering the promising cytotoxic effect of the compound, 1,4-NQ needs further evaluation as a potential candidate for the treatment of TNBC.","PeriodicalId":23358,"journal":{"name":"Turkish Journal of Biology","volume":"43 1","pages":"256 - 263"},"PeriodicalIF":2.2,"publicationDate":"2019-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3906/biy-1901-19","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45924891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Microsatellite polymorphism has always been a challenge for genome assembly and sequence alignment due to sequencing errors, short read lengths, and high incidence of polymerase slippage in microsatellite regions. Despite the information they carry being very valuable, microsatellite variations have not gained enough attention to be a routine step in genome sequence analysis pipelines. After the completion of the 1000 Genomes Project, which aimed to establish the most detailed genetic variation catalog for humans, the consortium released only two microsatellite prediction sets generated by two tools. Many other large research efforts have failed to shed light on microsatellite variations. We evaluated the performance of three different local assembly methods on three different experimental settings, focusing on genotype-based performance, coverage impact, and preprocessing including flanking regions. All these experiments supported our initial expectations on assembly. We also demonstrate that overlap-layout-consensus (OLC)-basedassembly methods show higher sensitivity to microsatellite variant calling when compared to a de Bruijn graph-based approach. We conclude that assembly with OLC is the better method for genotyping microsatellites. Our pipeline is available at https://github.com/gulfemd/STRAssembly.
{"title":"Characterizing microsatellite polymorphisms using assembly-based and mapping-based tools","authors":"Gülfem Demi̇r, C. Alkan","doi":"10.3906/biy-1903-16","DOIUrl":"https://doi.org/10.3906/biy-1903-16","url":null,"abstract":"Microsatellite polymorphism has always been a challenge for genome assembly and sequence alignment due to sequencing errors, short read lengths, and high incidence of polymerase slippage in microsatellite regions. Despite the information they carry being very valuable, microsatellite variations have not gained enough attention to be a routine step in genome sequence analysis pipelines. After the completion of the 1000 Genomes Project, which aimed to establish the most detailed genetic variation catalog for humans, the consortium released only two microsatellite prediction sets generated by two tools. Many other large research efforts have failed to shed light on microsatellite variations. We evaluated the performance of three different local assembly methods on three different experimental settings, focusing on genotype-based performance, coverage impact, and preprocessing including flanking regions. All these experiments supported our initial expectations on assembly. We also demonstrate that overlap-layout-consensus (OLC)-basedassembly methods show higher sensitivity to microsatellite variant calling when compared to a de Bruijn graph-based approach. We conclude that assembly with OLC is the better method for genotyping microsatellites. Our pipeline is available at https://github.com/gulfemd/STRAssembly.","PeriodicalId":23358,"journal":{"name":"Turkish Journal of Biology","volume":"43 1","pages":"264 - 273"},"PeriodicalIF":2.2,"publicationDate":"2019-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3906/biy-1903-16","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47010862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}