Rare and unknown actinobacteria from unexplored environments have the potential to produce new bioactive molecules. This study aimed to use 16 s rRNA metabarcoding to determine the composition of the actinobacterial community, particularly focusing on rare and undescribed species, in a nature reserve within the Brazilian Cerrado called Sete Cidades National Park. Since this is an inaccessible area without due legal authorization, it is understudied, and, therefore, its diversity and biotechnological potential are not yet fully understood, and it may harbor species with groundbreaking genetic potential. In total, 543 operational taxonomic units (OTUs) across 14 phyla were detected, with Actinobacteria (41.2%), Proteobacteria (26.5%), and Acidobacteria (14.3%) being the most abundant. Within Actinobacteria, 107 OTUs were found, primarily from the families Mycobacteriaceae, Pseudonocardiaceae, and Streptomycetaceae. Mycobacterium and Streptomyces were the predominant genera across all samples. Seventeen rare OTUs with relative abundance < 0.1% were identified, with 82.3% found in only one sample yet 25.5% detected in all units. Notable rare and transient genera included Salinibacterium, Nocardia, Actinomycetospora_01, Saccharopolyspora, Sporichthya, and Nonomuraea. The high diversity and distribution of Actinobacteria OTUs indicate the area's potential for discovering new rare species. Intensified prospection on underexplored environments and characterization of their actinobacterial diversity could lead to the discovery of new species capable of generating innovative natural products.
- MeSH
- Actinobacteria * chemie klasifikace genetika izolace a purifikace MeSH
- biodiverzita MeSH
- metagenom MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- RNA ribozomální 16S analýza MeSH
- taxonomické DNA čárové kódování MeSH
- veřejné parky MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Brazílie MeSH
CssRS is a two-component system that plays a pivotal role in mediating the secretion stress response in Bacillus subtilis. This system upregulates the synthesis of membrane-bound HtrA family proteases that cope with misfolded proteins that accumulate within the cell envelope as a result of overexpression or heat shock. Recent studies have shown the induction of CssRS-regulated genes in response to cell envelope stress. We investigated the induction of the CssRS-regulated htrA promoter in the presence of different cell wall- and membrane-active substances and observed induction of the CssRS-controlled genes by glycopeptides (vancomycin and teicoplanin), polymyxins B and E, certain β-lactams, and detergents. Teicoplanin was shown to elicit remarkably stronger induction than vancomycin and polymyxin B. Teicoplanin and polymyxin B induced the spxO gene expression in a CssRS-dependent fashion, resulting in increased activity of Spx, a master regulator of disulfide stress in Bacillus subtilis. The CssRS signaling pathway and Spx activity were demonstrated to be involved in Bacillus subtilis resistance to teicoplanin and polymyxin B.
- MeSH
- antibakteriální látky * farmakologie MeSH
- Bacillus subtilis * genetika účinky léků metabolismus MeSH
- bakteriální proteiny * genetika metabolismus MeSH
- polymyxin B * farmakologie MeSH
- promotorové oblasti (genetika) MeSH
- regulace genové exprese u bakterií * účinky léků MeSH
- signální transdukce MeSH
- teikoplanin * farmakologie MeSH
- Publikační typ
- časopisecké články MeSH
Halophilic bacteria are extremophiles that thrive in saline environment. Their ability to withstand such harsh conditions makes them an ideal choice for industrial applications such as lignocellulosic biomass degradation. In this study, a halophilic bacterium with the ability to produce extracellular cellulases and hemicellulases, designated as Nesterenkonia sp. CL21, was isolated from mangrove sediment in Tanjung Piai National Park, Malaysia. Thus far, studies on lignocellulolytic enzymes concerning bacterial species under this genus are limited. To gain a comprehensive understanding of its lignocellulose-degrading potential, the whole genome was sequenced using the Illumina NovaSeq 6000 platform. The genome of strain CL21 was assembled into 25 contigs with 3,744,449 bp and a 69.74% GC content and was predicted to contain 3,348 coding genes. Based on taxonomy analysis, strain CL21 shares 73.8 to 82.0% average nucleotide identity with its neighbouring species, below the 95% threshold, indicating its possible status as a distinct species in Nesterenkonia genus. Through in-depth genomic mining, a total of 81 carbohydrate-active enzymes were encoded. Among these, 24 encoded genes were identified to encompass diverse cellulases (GH3), xylanases (GH10, GH11, GH43, GH51, GH127 and CE4), mannanases (GH38 and GH106) and pectinases (PL1, PL9, and PL11). The production of lignocellulolytic enzymes was tested in the presence of several substrates. This study revealed that strain CL21 can produce a diverse array of enzymes which are active at different time points. By combining experimental data with genomic information, the ability of strain CL21 to produce lignocellulolytic enzymes has been elucidated, with potential applications in biorefinery industry.
- MeSH
- bakteriální proteiny genetika metabolismus MeSH
- celulasy genetika metabolismus MeSH
- fylogeneze * MeSH
- genom bakteriální * MeSH
- genomika * MeSH
- geologické sedimenty mikrobiologie MeSH
- glykosidhydrolasy * genetika metabolismus MeSH
- lignin * metabolismus MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenování celého genomu MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
Východiská: Z hľadiska epidemiológie predstavuje kolorektálny karcinóm (KRK) celosvetovo jeden z najčastejšie sa vyskytujúcich nádorov. Pokrok vo výskume sa premietol do zníženia úmrtnosti na toto ochorenie, avšak zníženie veku vzniku KRK vytvára obavy vo väčšine rozvinutých krajín. Identifikácia a validácia účinných prognostických biomarkerov sú kľúčové pre zvýšenie presnosti diagnostiky a individualizáciu liečby. Cieľ: Cieľom práce je analyzovať najnovšie údaje o epidemiológii a rizikových faktoroch KRK. Naratívny prehľad sa zameriava aj na zhrnutie súčasných poznatkov o rôznych prognostických biomarkeroch pri liečbe KRK, vrátane ukazovateľov výkonnostného stavu, nutričných a zápalových markerov. Záver: KRK predstavuje závažný zdravotný problém vo väčšine krajín a nádorové biomarkery, ako aj stav pacienta pred liečbou, sú rozhodujúce pre určenie prognózy ochorenia. Ukazovatele nutričného a výkonnostného stavu zohrávajú zásadnú úlohu pri hodnotení stavu pacienta a ovplyvňujú rozhodnutia o liečbe, s potenciálnym dopadom na jej výsledky. Zápalové markery sa javia ako významný prognostický faktor, korelujúc s imunitnou odpoveďou pacienta na nádor a zápalovými procesmi, ktoré môžu viesť k progresii ochorenia. Napriek ich sľubnej prediktívnej sile sa tieto biomarkery zatiaľ bežne nepoužívajú v klinickej praxi z dôvodu potreby ďalšej vedeckej validácie. Integrácia nových biomarkerov do klinickej praxe by však mohla viesť k personalizovanejším liečebným stratégiam a tým k zlepšeniu prežívania pacientov. Pre komplexnejšie posúdenie validity týchto biomarkerov a ich aplikácie v bežnej klinickej praxi je potrebný ďalší výskum.
Background: In terms of epidemiology, colorectal carcinoma (CRC) represents one of the most prevalent tumors worldwide. Progress in research has translated into reduced mortality of the disease, but the trend of early onset CRC troubles most of the developed countries. Identification and validation of effective prognostic biomarkers are crucial for improving diagnostic accuracy and treatment outcomes. Purpose: The objective of the work is to analyze the latest data on the epidemiology and risk factors of CRC. A narrative review also aims to summarize current knowledge about various prognostic biomarkers in the treatment of CRC, including indicators of performance status, nutritional, and inflammatory markers. Conclusion: CRC pose major health problem in most of the countries and the tumor biomarkers as well as patients pre-treatment condition are crucial to establish prognosis of the disease. Nutritional and performance status indicators play an essential role in assessing the patient’s condition and influence treatment decisions, with a potential impact on treatment outcomes. Inflammatory markers have demonstrated significant prognostic value, correlating with the patient’s immune response to the tumor and inflammatory processes that may promote disease progression. Despite promising predictive capabilities, these biomarkers are not yet routinely used in clinical practice due to the need for further research validation. The integration of new biomarkers into clinical practice could lead to more personalized treatment decisions and improved treatment outcomes. For a more comprehensive assessment of the validity of these biomarkers and their application in regular clinical practice, further research is necessary.
- MeSH
- biologické markery MeSH
- fyziologie výživy MeSH
- genetické testování MeSH
- geny ras genetika MeSH
- kolorektální nádory * epidemiologie MeSH
- lidé MeSH
- mikrosatelitní nestabilita MeSH
- prognóza * MeSH
- protoonkogenní proteiny B-Raf genetika škodlivé účinky MeSH
- rizikové faktory * MeSH
- staging nádorů metody MeSH
- zánět komplikace patofyziologie MeSH
- Check Tag
- lidé MeSH
Differences in survival according to the pTERT mutation subtypes (-124C > T, -146C > T, and tandem -138_139CC > TT) have been observed. The present study aimed to describe the clinical as the histopathological and molecular cutaneous melanoma features according to the presence of the three most prevalent pTERT mutation subtypes (-124C > T, -146C > T, and tandem -138_139CC > TT). A retrospective cross-sectional study including 684 patients was designed, and a Partial Least-Squares Discriminant Analysis (PLS-DA) was performed. After the PSL-DA, it was observed that the tandem -138_139CC > TT subtype differs from the other subtypes. The model demonstrated that the -124C > T and the -138_139 CC > TT subtypes were associated with fast-growing melanomas (OR 0.5, CI 0.29-0.86, p = .012) and with Breslow >2 mm (OR 0.6, CI 0.37-0.97, p = .037), compared to the -146C > T mutation. Finally, the -124C > T appeared to be more associated with the presence of TILs (non-brisk) than the -146C > T (OR 0.6, CI 0.40-1.01, p = .05). These findings confirmed that the -124C > T and the tandem -138_139 CC > TT subtypes are both highly associated with the presence of features of aggressiveness; however, only the -124C > T was highly associated with TILs. This difference could explain the worse survival rate associated with the tandem -138_139CC > TT mutations.
- MeSH
- lidé MeSH
- melanom * genetika patologie mortalita MeSH
- mutace MeSH
- nádory kůže genetika patologie mortalita MeSH
- promotorové oblasti (genetika) * genetika MeSH
- průřezové studie MeSH
- retrospektivní studie MeSH
- telomerasa * genetika MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Chronická lymfocytární leukemie (chronic lymphocytic leukemia, CLL) patří mezi indolentní lymfoproliferativní onemocnění vycházející z B lymfocytů. V západních zemích je CLL nejčastější leukemií v dospělé populaci. Zavedení inhibitorů Brutonovy kinázy (Bruton tyrosine kinase inhibitors, BTKi) znamenalo průlom v léčbě CLL a významně prodloužilo přežití pacientů s touto diagnózou. Ve srovnání a chemoimunoterapií prokazují lepší účinnost i toleranci léčby, zejména u rizikových pacientů s mutací genu TP53 a/nebo delecí 17p. Léčba BTKi dala naději na dlouhodobou kontrolu nemoci pacientům s časným relapsem CLL po chemoimunoterapii a pacientům s chemorefrakterní CLL. Jejich perorální podávání je pro ambulantní léčbu pacientů velkou výhodou. Na druhou stranu, je třeba myslet na specifické nežádoucí účinky této lékové skupiny. Zejména poruchy agregace trombocytů a kardiovaskulární nežádoucí účinky bývají limitací v léčbě a v závažných případech mohou být i život ohrožující. V tomto článku se věnujeme správné indikaci léčby BTKi u CLL, shrnujeme výsledky z klinických studií a doporučení pro management jejich případné toxicity.
Chronic lymphocytic leukemia (CLL) is an indolent B-ceLL lymphoproliferative disorder and the most common leukemia in the adult population in Western countries. Bruton tyrosine kinase inhibitors (BTKi) represent a major breakthrough in the treatment of CLL, significantly prolonging the survival of patients with this disease. Compared to chemoimmunotherapy, BTKi have demonstrated better efficacy and tolerability, particularly in high-risk patients with TP53 mutations or 17p deletions. Bruton tyrosine kinase inhibitors treatment has offered a long-term disease control even in patients with relapsed or refractory CLL after chemoimmunotherapy. The oral administration of these drugs is an additional advantage, allowing for outpatient treatment. However, it is important to be aware of the specific toxicity associated with this drug class. Platelet dysfunction and cardiovascular complications are among the most common issues, and in severe cases, these adverse events can be life-threatening. In this article, we discuss the indications for treatment with Bruton kinase inhibitors, summarize data from clinical trials, and review aspects of treatment-related toxicity.
- MeSH
- chronická lymfatická leukemie * diagnóza farmakoterapie MeSH
- geny p53 genetika účinky léků MeSH
- imunoterapie klasifikace metody MeSH
- klinická studie jako téma MeSH
- lidé MeSH
- nežádoucí účinky léčiv klasifikace MeSH
- proteinkinasa BTK * antagonisté a inhibitory farmakologie terapeutické užití MeSH
- recidiva MeSH
- výsledek terapie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- přehledy MeSH
Abies guatemalensis Rehder, an endangered conifer endemic to Central American highlands, is ecologically vital in upper montane forests. It faces threats from habitat fragmentation, unsustainable logging, and illegal Christmas tree harvesting. While previous genetic studies on mature trees from eighteen populations showed high within-population diversity and limited among-population differentiation, the genetic impact of recent anthropogenic pressures on younger generations has yet to be discovered. Understanding these effects is crucial for developing effective conservation strategies for this vulnerable species. We sampled 170 young trees (< 15 years old) from seven populations across Guatemala. Seven microsatellite markers were used to analyse genetic diversity, population structure, and recent demographic history. Moderate levels of genetic diversity were observed within populations (mean Shannon diversity index = 4.97, mean Simpson's index = 0.51, mean allelic richness = 11.59, mean observed heterozygosity = 0.59). Although genetic structure broadly aligned with mountain corridors, substantial admixture patterns suggest historical connectivity across all populations. Most populations showed evidence of recent bottlenecks (p < 0.05) and inbreeding. The results suggest a potential decline in genetic diversity and increased population structuring (ΦST = 0.274, p < 0.01) over the past decades compared to the previous study on old trees. The observed genetic patterns indicate ongoing impacts of habitat fragmentation and anthropogenic pressures on A. guatemalensis. Conservation efforts should prioritise expanding effective population sizes and facilitating gene flow, particularly for isolated populations. While restoration efforts may be logistically easier within mountain ranges, genetic evidence suggests that increasing overall population connectivity could benefit this species. Management strategies should implement systematic seed collection protocols to maintain genetic diversity in future populations. These findings highlight the urgent need for conservation measures to preserve remaining genetic diversity and promote connectivity among A. guatemalensis populations.
- MeSH
- ekosystém * MeSH
- genetická variace * MeSH
- jedle * genetika MeSH
- mikrosatelitní repetice * genetika MeSH
- ohrožené druhy * MeSH
- populační genetika MeSH
- zachování přírodních zdrojů MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Guatemala MeSH
Allelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), is of critical importance for immune responses to pathogens and vaccines. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread in immunology research making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci. Here, we present a novel algorithm for extrasensitive and specific variable (V) and joining (J) gene allele inference, allowing the reconstruction of individual high-quality gene segment libraries. The approach can be applied for inferring allelic variants from peripheral blood lymphocyte BCR and TCR repertoire sequencing data, including hypermutated isotype-switched BCR sequences, thus allowing high-throughput novel allele discovery from a wide variety of existing data sets. The developed algorithm is a part of the MiXCR software. We demonstrate the accuracy of this approach using AIRR-seq paired with long-read genomic sequencing data, comparing it to a widely used algorithm, TIgGER. We applied the algorithm to a large set of IG heavy chain (IGH) AIRR-seq data from 450 donors of ancestrally diverse population groups, and to the largest reported full-length TCR alpha and beta chain (TRA and TRB) AIRR-seq data set, representing 134 individuals. This allowed us to assess the genetic diversity within the IGH, TRA, and TRB loci in different populations and to establish a database of alleles of V and J genes inferred from AIRR-seq data and their population frequencies with free public access through VDJ.online database.
- MeSH
- alely * MeSH
- algoritmy * MeSH
- genetická variace MeSH
- lidé MeSH
- receptory antigenů B-buněk genetika imunologie MeSH
- receptory antigenů T-buněk genetika imunologie MeSH
- sekvenční analýza DNA metody MeSH
- software * MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: The genetic and epigenetic alterations observed in acute myeloid leukemia (AML) contribute to its heterogeneity, influencing disease progression response to therapy, and patient outcomes. The use of antisense oligonucleotides (ASOs) technology allows for the design of oligonucleotide inhibitors based on gene sequence information alone, enabling precise targeting of key molecular pathways or specific genes implicated in AML. METHODS AND RESULTS: Midostaurin, a FLT3 specific inhibitor and ASOs targeting particular genes, exons, or mutations was conducted using AML models. This ASOs treatment was designed to bind to exon 7 of the MBNL1 (muscleblind-like) gene. Another target was the FLT3 gene, focusing on two aspects: (a) FLT3-ITD (internal tandem duplication), to inhibit the expression of this aberrant gene form, and (b) the FLT3 in general. Treated and untreated cells were analyzed using quantitative PCR (qPCR), dot blot, and Raman spectroscopy. This study contrasts midostaurin with ASOs that inhibit FLT3 protein production or its isoforms via mRNA degradation. A trend of increased FLT3 expression was observed in midostaurin-treated cells, while ASO-treated cells showed decreased expression, though these changes were not statistically significant. CONCLUSIONS: In AML, exon 7 of MBNL1 is involved in several cellular processes and in this study, exon 7 of MBNL1 was targeted for method optimization, with the highest block of the exon 7 gene variant observed 48 h post-transfection. Midostaurin, a multitargeted kinase inhibitor, acts against the receptor tyrosine kinase FLT3, a critical molecule in AML pathogenesis. While midostaurin blocks FLT3 signaling pathways, it paradoxically increases FLT3 expression.
- MeSH
- akutní myeloidní leukemie * genetika farmakoterapie MeSH
- antisense oligonukleotidy * farmakologie genetika MeSH
- exony genetika MeSH
- lidé MeSH
- nádorové buněčné linie MeSH
- proteiny vázající RNA genetika metabolismus MeSH
- regulace genové exprese u leukemie účinky léků MeSH
- staurosporin * analogy a deriváty farmakologie MeSH
- tyrosinkinasa 3 podobná fms * genetika antagonisté a inhibitory metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
