Pub Date : 2024-11-01Epub Date: 2024-10-21DOI: 10.1007/s13205-024-04127-y
Prithvi Singh, Gulnaz Tabassum, Mohammad Masood, Saleha Anwar, Mansoor Ali Syed, Kapil Dev, Md Imtaiyaz Hassan, Mohammad Mahfuzul Haque, Ravins Dohare, Indrakant Kumar Singh
As one of the most prevalent malignancies, lung cancer displays considerable biological variability in both molecular and clinical characteristics. Lung cancer is broadly categorized into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) with the latter being most prevalent. The primary histological subtypes of NSCLC are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). In the present work, we primarily extracted mRNA count data from a publicly accessible database followed by differentially expressed genes (DEGs) and differentially expressed mitophagy-related genes (DEMRGs) identification in case of both LUAD and LUSC cohorts. Next, we identified important DEMRGs via clustering approach followed by enrichment, survival, and mutational analyses. Lastly, the finalized prognostic biomarker was validated using wet-lab experimentations. Primarily, we obtained 986 and 1714 DEGs across LUAD and LUSC cohorts. Only 7 DEMRGs from both cohorts had significant membership values as indicated by the clustering analysis. Most significant pathway, Gene Ontology (GO)-biological process (BP), GO-molecular function (MF), GO-cellular compartment (CC) terms were macroautophagy, GTP metabolic process, magnesium ion binding, mitochondrial outer membrane. Among all, only TDRKH reported significant overall survival (OS) and 14% amplification across LUAD patients. Lastly, we validated TDRKH via immunohistochemistry (IHC) and semi-quantitative polymerase chain reaction (PCR). In conclusion, our findings advocate for the exploration of TDRKH and their genetic alterations in precision oncology therapeutic approaches for LUAD, emphasizing the potential for target-driven therapy and early diagnostics.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04127-y.
{"title":"Investigating the role of prognostic mitophagy-related genes in non-small cell cancer pathogenesis via multiomics and network-based approach.","authors":"Prithvi Singh, Gulnaz Tabassum, Mohammad Masood, Saleha Anwar, Mansoor Ali Syed, Kapil Dev, Md Imtaiyaz Hassan, Mohammad Mahfuzul Haque, Ravins Dohare, Indrakant Kumar Singh","doi":"10.1007/s13205-024-04127-y","DOIUrl":"10.1007/s13205-024-04127-y","url":null,"abstract":"<p><p>As one of the most prevalent malignancies, lung cancer displays considerable biological variability in both molecular and clinical characteristics. Lung cancer is broadly categorized into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) with the latter being most prevalent. The primary histological subtypes of NSCLC are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). In the present work, we primarily extracted mRNA count data from a publicly accessible database followed by differentially expressed genes (DEGs) and differentially expressed mitophagy-related genes (DEMRGs) identification in case of both LUAD and LUSC cohorts. Next, we identified important DEMRGs via clustering approach followed by enrichment, survival, and mutational analyses. Lastly, the finalized prognostic biomarker was validated using wet-lab experimentations. Primarily, we obtained 986 and 1714 DEGs across LUAD and LUSC cohorts. Only 7 DEMRGs from both cohorts had significant membership values as indicated by the clustering analysis. Most significant pathway, Gene Ontology (GO)-biological process (BP), GO-molecular function (MF), GO-cellular compartment (CC) terms were macroautophagy, GTP metabolic process, magnesium ion binding, mitochondrial outer membrane. Among all, only <i>TDRKH</i> reported significant overall survival (OS) and 14% amplification across LUAD patients. Lastly, we validated <i>TDRKH</i> via immunohistochemistry (IHC) and semi-quantitative polymerase chain reaction (PCR). In conclusion, our findings advocate for the exploration of <i>TDRKH</i> and their genetic alterations in precision oncology therapeutic approaches for LUAD, emphasizing the potential for target-driven therapy and early diagnostics<i>.</i></p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04127-y.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11493942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492768","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}
Pub Date : 2024-11-01Epub Date: 2024-10-29DOI: 10.1007/s13205-024-04119-y
Banisha Phukela, Hanna Leonard, Yuval Sapir
R2R3-MYBs are an important group of transcription factors that regulate crucial developmental processes across the plant kingdom; yet no comprehensive analysis of the R2R3-MYBs in the early-diverging eudicot clade of Ranunculaceae has been conducted so far. In the present study, Aquilegia coerulea is chosen to understand the extent of conservation and divergence of R2R3-MYBs as a representative of the family by analysing the genomic distribution, organization, gene structure, physiochemical properties, protein architecture, evolution and possible mode of expansion. Genome-wide analysis showed the presence of 82 putative homologues classified into 21 subgroups, based on phylogenetic analysis of full-length protein sequences. The domain has remained largely conserved across all homologues with few differences from the characterized Arabidopsis thaliana R2R3-MYBs. The topology of the phylogenetic tree remains the same when full-length protein sequences are used, indicating that the evolution of R2R3-MYBs is driven by the domain region only. This is supported by the presence of similar structures of exon-intron and conserved motifs within the same subgroup. Furthermore, comparisons of the AqcoeR2R3-MYB members with monocots and core-eudicots revealed the evolutionary expansion of a few functional clades, such as A. thaliana R2R3-MYB subgroup 6 (SG6), the upstream regulatory factors of floral pigment biosynthesis and floral color. The reconstructed evolutionary history of SG6-like genes across angiosperms highlights the occurrence of independent duplication events in the genus Aquilegia. AqcoeR2R3-MYB genes are present in all seven chromosomes of A. coerulea, most of which result from local and segmental duplications. Selection analysis of these duplicated gene pairs indicates purifying selection except one, and the physiochemical analyses of R2R3-MYBs reveal differences among the MYBs signifying their functional diversification. This study paves the way for further investigation of paralogous copies and their probable role in the evolution of different floral traits in A. coerulea. It lays the foundation for functional genomic studies of R2R3-MYBs in the basal eudicots and facilitates comparative studies among angiosperms. The work also provides a framework for deciphering novel genetic regulatory pathways that govern the diversity of floral morphology.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04119-y.
{"title":"In silico analysis of R2R3-MYB transcription factors in the basal eudicot model, <i>Aquilegia coerulea</i>.","authors":"Banisha Phukela, Hanna Leonard, Yuval Sapir","doi":"10.1007/s13205-024-04119-y","DOIUrl":"10.1007/s13205-024-04119-y","url":null,"abstract":"<p><p>R2R3-MYBs are an important group of transcription factors that regulate crucial developmental processes across the plant kingdom; yet no comprehensive analysis of the R2R3-MYBs in the early-diverging eudicot clade of Ranunculaceae has been conducted so far. In the present study, <i>Aquilegia coerulea</i> is chosen to understand the extent of conservation and divergence of R2R3-MYBs as a representative of the family by analysing the genomic distribution, organization, gene structure, physiochemical properties, protein architecture, evolution and possible mode of expansion. Genome-wide analysis showed the presence of 82 putative homologues classified into 21 subgroups, based on phylogenetic analysis of full-length protein sequences. The domain has remained largely conserved across all homologues with few differences from the characterized <i>Arabidopsis thaliana</i> R2R3-MYBs. The topology of the phylogenetic tree remains the same when full-length protein sequences are used, indicating that the evolution of R2R3-MYBs is driven by the domain region only. This is supported by the presence of similar structures of exon-intron and conserved motifs within the same subgroup. Furthermore, comparisons of the AqcoeR2R3-MYB members with monocots and core-eudicots revealed the evolutionary expansion of a few functional clades, such as <i>A. thaliana</i> R2R3-MYB subgroup 6 (SG6), the upstream regulatory factors of floral pigment biosynthesis and floral color. The reconstructed evolutionary history of SG6-like genes across angiosperms highlights the occurrence of independent duplication events in the genus <i>Aquilegia</i>. AqcoeR2R3-MYB genes are present in all seven chromosomes of <i>A. coerulea</i>, most of which result from local and segmental duplications. Selection analysis of these duplicated gene pairs indicates purifying selection except one, and the physiochemical analyses of R2R3-MYBs reveal differences among the MYBs signifying their functional diversification. This study paves the way for further investigation of paralogous copies and their probable role in the evolution of different floral traits in <i>A. coerulea</i>. It lays the foundation for functional genomic studies of R2R3-MYBs in the basal eudicots and facilitates comparative studies among angiosperms. The work also provides a framework for deciphering novel genetic regulatory pathways that govern the diversity of floral morphology.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04119-y.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542975","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}
Pub Date : 2024-11-01Epub Date: 2024-10-29DOI: 10.1007/s13205-024-04122-3
Nootjalee Supromin, Siraporn Potivichayanon
The purpose of this study was to investigate the optimum conditions, including aerobic and anoxic conditions, for operating a long-term bioreactor system to decrease the toxicity of industrial electroplating wastewater effluents containing metal cyanide using Agrobacterium tumefaciens SUTS 1 and Pseudomonas monteilii SUTS 2. The initial results revealed that bacteria performed better under aerobic conditions than under anoxic conditions. An aerobic bioreactor system was subsequently set up in a long-term study lasting 30 days under optimum operating conditions. Both mixed-culture bacteria and indigenous bacteria promoted the high-efficiency treatment of cyanide and metals in the first 7 days of the study. When the system had high removal rates, cyanide removal was greater than that of zinc, copper, nickel, and chromium (CN- > Zn > Cu > Ni > Cr), with removal efficiencies of 96.67%, 93.93%, 74.17%, 63.43%, and 44.65%, respectively, with residual concentrations of 0.15 ± 0.01, 0.24 ± 0.005, 0.03 ± 0.002, 18.41 ± 0.06 and 14.26 ± 0.15 mg/L, respectively. The cell concentration in the bioreactor increased to approximately 107 CFU/mL over 30 days from initial cell concentrations of 6.15 × 105 CFU/mL and 1.05 × 103 CFU/mL for the mixed culture and indigenous inoculation, respectively. These results implied that the bacteria were resistant to heavy metal toxicity. The addition of an appropriate carbon source with sufficient aeration to a bioreactor resulted in increased cyanide degradation.
{"title":"Bioremediation of metal cyanide complexes from electroplating wastewater for long-term application using <i>Agrobacterium tumefaciens</i> SUTS 1 and <i>Pseudomonas monteilii</i> SUTS 2.","authors":"Nootjalee Supromin, Siraporn Potivichayanon","doi":"10.1007/s13205-024-04122-3","DOIUrl":"10.1007/s13205-024-04122-3","url":null,"abstract":"<p><p>The purpose of this study was to investigate the optimum conditions, including aerobic and anoxic conditions, for operating a long-term bioreactor system to decrease the toxicity of industrial electroplating wastewater effluents containing metal cyanide using <i>Agrobacterium tumefaciens</i> SUTS 1 and <i>Pseudomonas monteilii</i> SUTS 2. The initial results revealed that bacteria performed better under aerobic conditions than under anoxic conditions. An aerobic bioreactor system was subsequently set up in a long-term study lasting 30 days under optimum operating conditions. Both mixed-culture bacteria and indigenous bacteria promoted the high-efficiency treatment of cyanide and metals in the first 7 days of the study. When the system had high removal rates, cyanide removal was greater than that of zinc, copper, nickel, and chromium (CN<sup>-</sup> > Zn > Cu > Ni > Cr), with removal efficiencies of 96.67%, 93.93%, 74.17%, 63.43%, and 44.65%, respectively, with residual concentrations of 0.15 ± 0.01, 0.24 ± 0.005, 0.03 ± 0.002, 18.41 ± 0.06 and 14.26 ± 0.15 mg/L, respectively. The cell concentration in the bioreactor increased to approximately 10<sup>7</sup> CFU/mL over 30 days from initial cell concentrations of 6.15 × 10<sup>5</sup> CFU/mL and 1.05 × 10<sup>3</sup> CFU/mL for the mixed culture and indigenous inoculation, respectively. These results implied that the bacteria were resistant to heavy metal toxicity. The addition of an appropriate carbon source with sufficient aeration to a bioreactor resulted in increased cyanide degradation.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556881","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}
Pub Date : 2024-11-01Epub Date: 2024-10-06DOI: 10.1007/s13205-024-04108-1
Peng Zhang, Wei Ding, Heng Zheng
In this study, high-throughput sequencing (HTS) technology was used to investigate the composition and diversity of endophytic bacteria and their effects on succinic acid biosynthesis in P. ternata tubers from three different geographical locations (MS, SL, and ZT). A total of 1777 amplicon sequence variants (ASVs) were annotated, and the diversity and composition of endophytic bacteria in P. ternata tubers were significantly different among different regions. The ZT samples presented the highest α diversity, and the Shannon diversity, richness, and Pielou evenness index were all ZT > MS > SL. Co-occurrence network analysis revealed that endophytic bacterial groups such as Stenotrophomonas, Pseudomonas, Mycobacterium, and Chryseomicrobium were key groups in the endophytic bacterial interaction network, indicating that they play a role in maintaining community stability. In addition, some endophytic bacteria were associated with the biosynthesis of succinic acid, a key bioactive compound in P. ternata. The succinate content was positively correlated with the genera Brevundimonas, Ensifer, Nocardioides, and Paenibacillus, while it was negatively correlated with the genera Lentimicrobium, Anaerovorax, and Pajaroellobacter. These findings highlight the key role of endophytic bacteria in regulating the efficacy of P. ternata. These findings provide key information for further elucidating the mechanism by which endophytic bacteria affect the synthesis of bioactive compounds.
本研究采用高通量测序(HTS)技术研究了三个不同地理位置(MS、SL和ZT)的P. ternata块茎中内生细菌的组成和多样性及其对琥珀酸生物合成的影响。共注释了 1777 个扩增子序列变异(ASVs),不同地区 P. ternata 块茎中内生细菌的多样性和组成存在显著差异。ZT 样品的 α 多样性最高,香农多样性、丰富度和 Pielou 均匀度指数均为 ZT > MS > SL。共生网络分析显示,内生细菌群(如 Stenotrophomonas、Pseudomonas、Mycobacterium 和 Chryseomicrobium)是内生细菌相互作用网络中的关键群,表明它们在维持群落稳定性方面发挥作用。此外,一些内生细菌与琥珀酸的生物合成有关,琥珀酸是 P. ternata 的一种关键生物活性化合物。琥珀酸含量与 Brevundimonas 属、Ensifer 属、Nocardioides 属和 Paenibacillus 属呈正相关,而与 Lentimicrobium 属、Anaerovorax 属和 Pajaroellobacter 属呈负相关。这些发现凸显了内生细菌在调节 P. ternata 的功效方面所起的关键作用。这些发现为进一步阐明内生细菌影响生物活性化合物合成的机制提供了关键信息。
{"title":"Composition and diversity of endophytic bacterial communities in the tubers of <i>Pinellia ternata</i> from different regions and their effects on succinate biosynthesis based on high-throughput sequencing.","authors":"Peng Zhang, Wei Ding, Heng Zheng","doi":"10.1007/s13205-024-04108-1","DOIUrl":"10.1007/s13205-024-04108-1","url":null,"abstract":"<p><p>In this study, high-throughput sequencing (HTS) technology was used to investigate the composition and diversity of endophytic bacteria and their effects on succinic acid biosynthesis in <i>P. ternata</i> tubers from three different geographical locations (MS, SL, and ZT). A total of 1777 amplicon sequence variants (ASVs) were annotated, and the diversity and composition of endophytic bacteria in <i>P. ternata</i> tubers were significantly different among different regions. The ZT samples presented the highest α diversity, and the Shannon diversity, richness, and Pielou evenness index were all ZT > MS > SL. Co-occurrence network analysis revealed that endophytic bacterial groups such as <i>Stenotrophomonas</i>, <i>Pseudomonas</i>, <i>Mycobacterium</i>, and <i>Chryseomicrobium</i> were key groups in the endophytic bacterial interaction network, indicating that they play a role in maintaining community stability. In addition, some endophytic bacteria were associated with the biosynthesis of succinic acid, a key bioactive compound in <i>P. ternata</i>. The succinate content was positively correlated with the genera <i>Brevundimonas</i>, <i>Ensifer</i>, <i>Nocardioides</i>, and <i>Paenibacillus</i>, while it was negatively correlated with the genera <i>Lentimicrobium</i>, <i>Anaerovorax</i>, and <i>Pajaroellobacter</i>. These findings highlight the key role of endophytic bacteria in regulating the efficacy of <i>P. ternata</i>. These findings provide key information for further elucidating the mechanism by which endophytic bacteria affect the synthesis of bioactive compounds.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11456575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387131","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}
Pub Date : 2024-11-01Epub Date: 2024-10-19DOI: 10.1007/s13205-024-04099-z
Thaynara Lorenzoni Entringer, José Maria Rodrigues da Luz, Tomás Gomes Reis Veloso, Lucas Louzada Pereira, Karen Mirella Souza Menezes, Dério Brioschi Júnior, Maria Catarina Megumi Kasuya, Marliane de Cássia Soares da Silva
Understanding the effects of microorganisms on coffee fermentation is crucial to ensure sensory quality and food security. The analysis of the dynamics of the microbial community during fermentation can contribute to a better understanding of the beneficial and harmful effects of microorganisms and help select starter cultures to improve coffee quality. Furthermore, the anaerobic environment produced by carbonic maceration of the coffee fruits inhibits aerobic respiratory processes and stimulates fermentative metabolism, modulating the microbial community during coffee fermentation. This study evaluated the effects of carbonic maceration in the fungal community dynamics during the fermentation of Coffea arabica fruits at 18, 28, and 38 °C for 24, 48, 72, 96, and 120 h. Fungal diversity was accompanied by high-throughput sequencing (NGS) of the Internal Transcribed Spacer (ITS) region. During the coffee fermentation, the fungal community changed over time, with the most significant changes occurring at 18 and 28 °C after 72 h. However, at 38 °C, there were greater variations in fungal composition and fungal diversity was highest after 120 h. The yeast Pichia cephalocereana was predominant in the fermentations. These results indicated that temperature and fermentation conditions influence the fungal community during coffee fermentation. Lower temperatures might favor a more stable microbial environment, while higher temperatures lead to more intense changes. Thus, our data from NGS can help in the identification, isolation, and metabolic characterization of fungi for the fermentation of coffee fruits.
了解微生物对咖啡发酵的影响对于确保感官质量和食品安全至关重要。分析发酵过程中微生物群落的动态有助于更好地了解微生物的有益和有害影响,并帮助选择启动培养物以提高咖啡质量。此外,咖啡果实碳酸浸渍产生的厌氧环境会抑制有氧呼吸过程,刺激发酵代谢,从而调节咖啡发酵过程中的微生物群落。本研究评估了碳酸浸渍对阿拉比卡咖啡果实在 18、28 和 38 °C 温度下发酵 24、48、72、96 和 120 小时期间真菌群落动态的影响。在咖啡发酵过程中,真菌群落随着时间的推移而变化,在 18 和 28 °C 温度下,72 小时后的变化最为显著;但在 38 °C 温度下,真菌组成的变化更大,120 小时后真菌多样性最高。这些结果表明,温度和发酵条件会影响咖啡发酵过程中的真菌群落。较低的温度可能有利于更稳定的微生物环境,而较高的温度则会导致更剧烈的变化。因此,我们从 NGS 中获得的数据有助于咖啡果实发酵过程中真菌的鉴定、分离和代谢特征描述。
{"title":"Genetic diversity of the fungal community that contributes to the sensory quality of coffee beverage after carbonic maceration and fermentation.","authors":"Thaynara Lorenzoni Entringer, José Maria Rodrigues da Luz, Tomás Gomes Reis Veloso, Lucas Louzada Pereira, Karen Mirella Souza Menezes, Dério Brioschi Júnior, Maria Catarina Megumi Kasuya, Marliane de Cássia Soares da Silva","doi":"10.1007/s13205-024-04099-z","DOIUrl":"10.1007/s13205-024-04099-z","url":null,"abstract":"<p><p>Understanding the effects of microorganisms on coffee fermentation is crucial to ensure sensory quality and food security. The analysis of the dynamics of the microbial community during fermentation can contribute to a better understanding of the beneficial and harmful effects of microorganisms and help select starter cultures to improve coffee quality. Furthermore, the anaerobic environment produced by carbonic maceration of the coffee fruits inhibits aerobic respiratory processes and stimulates fermentative metabolism, modulating the microbial community during coffee fermentation. This study evaluated the effects of carbonic maceration in the fungal community dynamics during the fermentation of <i>Coffea arabica</i> fruits at 18, 28, and 38 °C for 24, 48, 72, 96, and 120 h. Fungal diversity was accompanied by high-throughput sequencing (NGS) of the Internal Transcribed Spacer (ITS) region. During the coffee fermentation, the fungal community changed over time, with the most significant changes occurring at 18 and 28 °C after 72 h. However, at 38 °C, there were greater variations in fungal composition and fungal diversity was highest after 120 h. The yeast <i>Pichia cephalocereana</i> was predominant in the fermentations. These results indicated that temperature and fermentation conditions influence the fungal community during coffee fermentation. Lower temperatures might favor a more stable microbial environment, while higher temperatures lead to more intense changes. Thus, our data from NGS can help in the identification, isolation, and metabolic characterization of fungi for the fermentation of coffee fruits.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11490598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455454","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}
Pub Date : 2024-11-01Epub Date: 2024-10-23DOI: 10.1007/s13205-024-04121-4
NandhaGopal SoundharaPandiyan, Carlton Ranjith Wilson Alphonse, Subramoniam Thanumalaya, Samuel Gnana Prakash Vincent, Rajaretinam Rajesh Kannan
The Caridina pseudogracilirostris is commonly found in the brackish waters of the southwestern coastal regions of India. This study provides a comprehensive genomic investigation of the shrimp species C. pseudogracilirostris, offering insights into its genetic makeup, evolutionary dynamics, and functional annotations. The genomic DNA was isolated from tissue samples, sequenced using next-generation sequencing (NGS), and stored in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (Accession No: PRJNA847710). De novo sequencing indicated a genome size of 1.31 Gbp with a low heterozygosity of about 0.81%. Repeat masking and annotation revealed that repeated elements constitute 24.60% of the genome, with simple sequence repeats (SSRs) accounting for 7.26%. Gene prediction identified 14,101 genes, with functional annotations indicating involvement in critical biological processes such as development, cellular function, immunological responses, and reproduction. Furthermore, phylogenetic analysis revealed genomic links among Malacostraca species, indicating gene duplication as a strategy for genetic diversity and adaptation. C. pseudogracilirostris has 1,856 duplicated genes, reflecting a distinct genomic architecture and evolutionary strategy within the Malacostraca branch. These findings enhance our understanding of the genetic characteristics and evolutionary relationships of C. pseudogracilirostris, providing significant insights into the overall evolutionary dynamics of the Malacostraca group.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04121-4.
{"title":"Genome sequencing of <i>Caridina pseudogracilirostris</i> and its comparative analysis with malacostracan crustaceans.","authors":"NandhaGopal SoundharaPandiyan, Carlton Ranjith Wilson Alphonse, Subramoniam Thanumalaya, Samuel Gnana Prakash Vincent, Rajaretinam Rajesh Kannan","doi":"10.1007/s13205-024-04121-4","DOIUrl":"10.1007/s13205-024-04121-4","url":null,"abstract":"<p><p>The <i>Caridina pseudogracilirostris</i> is commonly found in the brackish waters of the southwestern coastal regions of India. This study provides a comprehensive genomic investigation of the shrimp species <i>C. pseudogracilirostris</i>, offering insights into its genetic makeup, evolutionary dynamics, and functional annotations. The genomic DNA was isolated from tissue samples, sequenced using next-generation sequencing (NGS), and stored in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (Accession No: PRJNA847710). De novo sequencing indicated a genome size of 1.31 Gbp with a low heterozygosity of about 0.81%. Repeat masking and annotation revealed that repeated elements constitute 24.60% of the genome, with simple sequence repeats (SSRs) accounting for 7.26%. Gene prediction identified 14,101 genes, with functional annotations indicating involvement in critical biological processes such as development, cellular function, immunological responses, and reproduction. Furthermore, phylogenetic analysis revealed genomic links among Malacostraca species, indicating gene duplication as a strategy for genetic diversity and adaptation. <i>C. pseudogracilirostris</i> has 1,856 duplicated genes, reflecting a distinct genomic architecture and evolutionary strategy within the Malacostraca branch. These findings enhance our understanding of the genetic characteristics and evolutionary relationships of <i>C. pseudogracilirostris</i>, providing significant insights into the overall evolutionary dynamics of the Malacostraca group.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04121-4.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11499489/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492767","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}
Pub Date : 2024-11-01Epub Date: 2024-10-24DOI: 10.1007/s13205-024-04126-z
Vinod Kumar Yata
The microbiota-gut-brain axis involves complex bidirectional communication through neural, immune, and endocrine pathways. Microbial metabolites, such as short-chain fatty acids, influence gut motility and brain function by interacting with gut receptors and modulating hormone release. Additionally, microbial components such as lipopolysaccharides and cytokines can cross the gut epithelium and the blood-brain barrier, impacting immune responses and cognitive function. Ex vivo models, which preserve gut tissue and neural segments, offer insight into localized gut-brain communication by allowing for detailed study of nerve excitability in response to microbial signals, but they are limited in systemic complexity. Miniaturized in vitro models, including organ-on-chip platforms, enable precise control of the cellular environment and simulate complex microbiota-host interactions. These systems allow for the study of microbial metabolites, immune responses, and neuronal activity, providing valuable insights into gut-brain communication. Despite challenges such as replicating long-term biological processes and integrating immune and hormonal systems, advancements in bioengineered platforms are enhancing the physiological relevance of these models, offering new opportunities for understanding the mechanisms of the microbiota-gut-brain axis. This review aims to describe the ex vivo and miniaturized in vitro models which are used to mimic the in vivo conditions and facilitate more precise studies of gut brain communication.
{"title":"Ex vivo and miniaturized in vitro <i>models</i> to study microbiota-gut-brain axis.","authors":"Vinod Kumar Yata","doi":"10.1007/s13205-024-04126-z","DOIUrl":"10.1007/s13205-024-04126-z","url":null,"abstract":"<p><p>The microbiota-gut-brain axis involves complex bidirectional communication through neural, immune, and endocrine pathways. Microbial metabolites, such as short-chain fatty acids, influence gut motility and brain function by interacting with gut receptors and modulating hormone release. Additionally, microbial components such as lipopolysaccharides and cytokines can cross the gut epithelium and the blood-brain barrier, impacting immune responses and cognitive function. Ex vivo models, which preserve gut tissue and neural segments, offer insight into localized gut-brain communication by allowing for detailed study of nerve excitability in response to microbial signals, but they are limited in systemic complexity. Miniaturized in vitro models, including organ-on-chip platforms, enable precise control of the cellular environment and simulate complex microbiota-host interactions. These systems allow for the study of microbial metabolites, immune responses, and neuronal activity, providing valuable insights into gut-brain communication. Despite challenges such as replicating long-term biological processes and integrating immune and hormonal systems, advancements in bioengineered platforms are enhancing the physiological relevance of these models, offering new opportunities for understanding the mechanisms of the microbiota-gut-brain axis. This review aims to describe the ex vivo and miniaturized in vitro models which are used to mimic the in vivo conditions and facilitate more precise studies of gut brain communication.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11502650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142516252","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}
Fusion transcripts (FTs) are well known cancer biomarkers, relatively understudied in plants. Here, we developed PFusionDB (www.nipgr.ac.in/PFusionDB), a novel plant-specific fusion-transcript database. It is a comprehensive repository of 80,170, 39,108, 83,330, and 11,500 unique fusions detected in 1280, 637, 697, and 181 RNA-Seq samples of Arabidopsis thaliana, Oryza sativa japonica, Oryza sativa indica, and Cicer arietinum respectively. Here, a total of 76,599 (Arabidopsis thaliana), 35,480 (Oryza sativa japonica), 72,099 (Oryza sativa indica), and 9524 (Cicer arietinum) fusion transcripts are non-recurrent i.e., only found in one sample. Identification of FTs was performed by using a total of five tools viz. EricScript-Plants, STAR-Fusion, TrinityFusion, SQUID, and MapSplice. At PFusionDB, available fundamental details of fusion events includes the information of parental genes, junction sequence, expression levels of fusion transcripts, breakpoint coordinates, strand information, tissue type, treatment information, fusion type, PFusionDB ID, and Sequence Read Archive (SRA) ID. Further, two search modules: 'Simple Search' and 'Advanced Search', along with a 'Browse' option to data download, are present for the ease of users. Three distinct modules viz. 'BLASTN', 'SW Align', and 'Mapping' are also available for efficient query sequence mapping and alignment to FTs. PFusionDB serves as a crucial resource for delving into the intricate world of fusion transcript in plants, providing researchers with a foundation for further exploration and analysis. Database URL: www.nipgr.ac.in/PFusionDB.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04132-1.
{"title":"PFusionDB: a comprehensive database of plant-specific fusion transcripts.","authors":"Ajay Arya, Simran Arora, Fiza Hamid, Shailesh Kumar","doi":"10.1007/s13205-024-04132-1","DOIUrl":"10.1007/s13205-024-04132-1","url":null,"abstract":"<p><p>Fusion transcripts (FTs) are well known cancer biomarkers, relatively understudied in plants. Here, we developed PFusionDB (www.nipgr.ac.in/PFusionDB), a novel plant-specific fusion-transcript database. It is a comprehensive repository of 80,170, 39,108, 83,330, and 11,500 unique fusions detected in 1280, 637, 697, and 181 RNA-Seq samples of <i>Arabidopsis thaliana</i>, <i>Oryza sativa japonica</i>, <i>Oryza sativa indica</i>, and <i>Cicer arietinum</i> respectively. Here, a total of 76,599 (<i>Arabidopsis thaliana</i>), 35,480 (<i>Oryza sativa japonica</i>), 72,099 (<i>Oryza sativa indica</i>), and 9524 (<i>Cicer arietinum</i>) fusion transcripts are non-recurrent i.e., only found in one sample. Identification of FTs was performed by using a total of five tools viz. EricScript-Plants, STAR-Fusion, TrinityFusion, SQUID, and MapSplice. At PFusionDB, available fundamental details of fusion events includes the information of parental genes, junction sequence, expression levels of fusion transcripts, breakpoint coordinates, strand information, tissue type, treatment information, fusion type, PFusionDB ID, and Sequence Read Archive (SRA) ID. Further, two search modules: 'Simple Search' and 'Advanced Search', along with a 'Browse' option to data download, are present for the ease of users. Three distinct modules viz. 'BLASTN', 'SW Align', and 'Mapping' are also available for efficient query sequence mapping and alignment to FTs. PFusionDB serves as a crucial resource for delving into the intricate world of fusion transcript in plants, providing researchers with a foundation for further exploration and analysis. Database URL: www.nipgr.ac.in/PFusionDB.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04132-1.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11519250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542976","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}
Pub Date : 2024-11-01Epub Date: 2024-11-03DOI: 10.1007/s13205-024-04139-8
Yimin Wang, Yong Wang, Zhuangli Bi, Yuhan Liu, Chunchun Meng, Jie Zhu, Guangqing Liu, Chuanfeng Li
Co-infection with novel goose parvovirus (NGPV) and novel duck reovirus (NDRV) is common, significantly impeding duck growth and resulting in considerable economic losses within the duck farming industry. To facilitate rapid and accurate diagnosis and differentiation of these two viruses, this study developed a SYBR Green I-based duplex real-time quantitative polymerase chain reaction (qPCR) assay. This assay enabled the simultaneous detection of NGPV and NDRV by exploiting their distinct melting temperatures (Tm): 78.5 ± 0.50 °C for NGPV and 84.5 ± 0.50 °C for NDRV. No amplification was observed for other prevalent non-target duck viruses. The intra- and inter-assay coefficients of variation were less than 1.75%. The assay showed good performance with the same detection limit of 102 copies/μL for both NGPV and NDRV. The results of the clinical testing indicated that 45.3% (34/75) of the samples tested positive for NGPV, while 38.7% (29/75) were positive for NDRV. Notably, 13.3% (10/75) exhibited co-infection. These results revealed that the sensitivity of the developed method exceed that of conventional polymerase chain reaction (PCR). The developed method for the identifying of NGPV and NDRV shows good specificity, sensitivity, and repeatability, rendering it an effective tool for the simultaneous detection of co-infection with NGPV and NDRV.
{"title":"Simultaneous detection of novel goose parvovirus and novel duck reovirus by SYBR Green I-based duplex real-time quantitative polymerase chain reaction.","authors":"Yimin Wang, Yong Wang, Zhuangli Bi, Yuhan Liu, Chunchun Meng, Jie Zhu, Guangqing Liu, Chuanfeng Li","doi":"10.1007/s13205-024-04139-8","DOIUrl":"10.1007/s13205-024-04139-8","url":null,"abstract":"<p><p>Co-infection with novel goose parvovirus (NGPV) and novel duck reovirus (NDRV) is common, significantly impeding duck growth and resulting in considerable economic losses within the duck farming industry. To facilitate rapid and accurate diagnosis and differentiation of these two viruses, this study developed a SYBR Green I-based duplex real-time quantitative polymerase chain reaction (qPCR) assay. This assay enabled the simultaneous detection of NGPV and NDRV by exploiting their distinct melting temperatures (Tm): 78.5 ± 0.50 °C for NGPV and 84.5 ± 0.50 °C for NDRV. No amplification was observed for other prevalent non-target duck viruses. The intra- and inter-assay coefficients of variation were less than 1.75%. The assay showed good performance with the same detection limit of 10<sup>2</sup> copies/μL for both NGPV and NDRV. The results of the clinical testing indicated that 45.3% (34/75) of the samples tested positive for NGPV, while 38.7% (29/75) were positive for NDRV. Notably, 13.3% (10/75) exhibited co-infection. These results revealed that the sensitivity of the developed method exceed that of conventional polymerase chain reaction (PCR). The developed method for the identifying of NGPV and NDRV shows good specificity, sensitivity, and repeatability, rendering it an effective tool for the simultaneous detection of co-infection with NGPV and NDRV.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581853","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}
Divergent banana streak viruses (BSV) were characterized from banana plants exhibiting diverse symptoms in the Northeast region (NER) of India. Using rolling circle amplification (RCA), the complete genome sequences of seven episomal banana streak MY virus (BSMYV) isolates, including two novel variants, and two new banana streak IM virus (BSIMV) isolates were characterized. The novel BSMYV genetic variants were associated with conspicuous necrosis on newly emerged leaves, peduncle distortion, pseudostem internal necrosis, in addition to common streak symptoms. For complete genome nucleotide sequences, BSMYV-IN4 and IN5 shared 77-79% identity with other BSMYVs, while BSMYV-IN7 and IN8 exhibited identities of 77-97%. This study reports for the first time, the complete genomes of two banana streak IM virus (BSIMV-IN1 and -IN2) infecting triploid banana hybrids exhibiting leaf distortion, stunted rosette-like growth, and necrosis, sharing 87% sequence identity with reference BSIMV genome (GenBank accession no. HQ593112). Phylogenetic inference based on complete genomes revealed the distinct and congruent placement of BSMYV-IN4 and IN5 within the BSMYV cluster. Pairwise sequence comparisons of the conserved RT/RNase H nucleotide (nt) sequences revealed that the BSMYV-IN7 and IN4 isolates showed 85% and 97% identity to BSMYV (AY805074), respectively, which shared highest nt identity with BSMYV-IN6, IN9, and IN10, at 100%. The RT/RNase H nt sequences of BSIMV-IN1 and IN2 had 98% identity with the BSIMV (HQ593112), but were characterized as novel variants of BSIMV based on complete genomes. An analysis of relative synonymous codon usage (RSCU) pattern in the ORFIII polyprotein of BSMYV and BSIMV isolates revealed AGA and AGG (arginine) as the most frequently overrepresented codons (>1.5), evolutionary conserved in the genome of both species. A total of 14 recombination events were detected among the 36 BSV genomes, with recombination breakpoints mainly located in the ORFI, III, and IGR genomic regions. A novel phylogenetic cluster, comprised of BSMYV-IN4 and IN5 within the clade I was probably derived from heterologous recombination between parents resembling banana streak VN virus (BSVNV; AY750155) and banana streak GF virus (BSGFV; KJ013507) isolates. The present study conclusively reports the infection of genetically and symptomatically distinct variants of BSMYV and BSIMV infecting banana hybrids in NER India.
{"title":"Novel genetic variants of banana streak MY virus and banana streak IM virus naturally infecting banana in Northeast India.","authors":"Richa Rai, Yumlembam Rupert Anand, Sapam Monteshori, Damini Diksha, Saurabh Kumar Dubey, Virendra Kumar Baranwal, Susheel Kumar Sharma","doi":"10.1007/s13205-024-04113-4","DOIUrl":"10.1007/s13205-024-04113-4","url":null,"abstract":"<p><p>Divergent banana streak viruses (BSV) were characterized from banana plants exhibiting diverse symptoms in the Northeast region (NER) of India. Using rolling circle amplification (RCA), the complete genome sequences of seven episomal banana streak MY virus (BSMYV) isolates, including two novel variants, and two new banana streak IM virus (BSIMV) isolates were characterized. The novel BSMYV genetic variants were associated with conspicuous necrosis on newly emerged leaves, peduncle distortion, pseudostem internal necrosis, in addition to common streak symptoms. For complete genome nucleotide sequences, BSMYV-IN4 and IN5 shared 77-79% identity with other BSMYVs, while BSMYV-IN7 and IN8 exhibited identities of 77-97%. This study reports for the first time, the complete genomes of two banana streak IM virus (BSIMV-IN1 and -IN2) infecting triploid banana hybrids exhibiting leaf distortion, stunted rosette-like growth, and necrosis, sharing 87% sequence identity with reference BSIMV genome (GenBank accession no. HQ593112). Phylogenetic inference based on complete genomes revealed the distinct and congruent placement of BSMYV-IN4 and IN5 within the BSMYV cluster. Pairwise sequence comparisons of the conserved RT/RNase H nucleotide (nt) sequences revealed that the BSMYV-IN7 and IN4 isolates showed 85% and 97% identity to BSMYV (AY805074), respectively, which shared highest nt identity with BSMYV-IN6, IN9, and IN10, at 100%. The RT/RNase H nt sequences of BSIMV-IN1 and IN2 had 98% identity with the BSIMV (HQ593112), but were characterized as novel variants of BSIMV based on complete genomes. An analysis of relative synonymous codon usage (RSCU) pattern in the ORFIII polyprotein of BSMYV and BSIMV isolates revealed AGA and AGG (arginine) as the most frequently overrepresented codons (>1.5), evolutionary conserved in the genome of both species. A total of 14 recombination events were detected among the 36 BSV genomes, with recombination breakpoints mainly located in the ORFI, III, and IGR genomic regions. A novel phylogenetic cluster, comprised of BSMYV-IN4 and IN5 within the clade I was probably derived from heterologous recombination between parents resembling banana streak VN virus (BSVNV; AY750155) and banana streak GF virus (BSGFV; KJ013507) isolates. The present study conclusively reports the infection of genetically and symptomatically distinct variants of BSMYV and BSIMV infecting banana hybrids in NER India.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11499479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492697","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}