BACKGROUND: This paper brings new information about the genome and phenotypic characteristics of Pantoea agglomerans strain DBM 3797, isolated from fresh Czech hop (Humulus lupulus) in the Saaz hop-growing region. Although P. agglomerans strains are frequently isolated from different materials, there are not usually thoroughly characterized even if they have versatile metabolism and those isolated from plants may have a considerable potential for application in agriculture as a support culture for plant growth. METHODS: P. agglomerans DBM 3797 was cultured under aerobic and anaerobic conditions, its metabolites were analyzed by HPLC and it was tested for plant growth promotion abilities, such as phosphate solubilization, siderophore and indol-3-acetic acid productions. In addition, genomic DNA was extracted, sequenced and de novo assembly was performed. Further, genome annotation, pan-genome analysis and selected genome analyses, such as CRISPR arrays detection, antibiotic resistance and secondary metabolite genes identification were carried out. RESULTS AND DISCUSSION: The typical appearance characteristics of the strain include the formation of symplasmata in submerged liquid culture and the formation of pale yellow colonies on agar. The genetic information of the strain (in total 4.8 Mb) is divided between a chromosome and two plasmids. The strain lacks any CRISPR-Cas system but is equipped with four restriction-modification systems. The phenotypic analysis focused on growth under both aerobic and anaerobic conditions, as well as traits associated with plant growth promotion. At both levels (genomic and phenotypic), the production of siderophores, indoleacetic acid-derived growth promoters, gluconic acid, and enzyme activities related to the degradation of complex organic compounds were found. Extracellular gluconic acid production under aerobic conditions (up to 8 g/l) is probably the result of glucose oxidation by the membrane-bound pyrroloquinoline quinone-dependent enzyme glucose dehydrogenase. The strain has a number of properties potentially beneficial to the hop plant and its closest relatives include the strains also isolated from the aerial parts of plants, yet its safety profile needs to be addressed in follow-up research.
- Publikační typ
- časopisecké články MeSH
INTRODUCTION: COVID-19 has been associated with high morbidity and mortality in allogeneic hematopoietic stem cell transplant (allo-HCT) recipients. METHODS: This study reports on 986 patients reported to the EBMT registry during the first 29 months of the pandemic. RESULTS: The median age was 50.3 years (min - max; 1.0 - 80.7). The median time from most recent HCT to diagnosis of COVID-19 was 20 months (min - max; 0.0 - 383.9). The median time was 19.3 (0.0 - 287.6) months during 2020, 21.2 (0.1 - 324.5) months during 2021, and 19.7 (0.1 - 383.9) months during 2022 (p = NS). 145/986 (14.7%) patients died; 124 (12.6%) due to COVID-19 and 21 of other causes. Only 2/204 (1%) fully vaccinated patients died from COVID-19. There was a successive improvement in overall survival over time. In multivariate analysis, increasing age (p<.0001), worse performance status (p<.0001), contracting COVID-19 within the first 30 days (p<.0001) or 30 - 100 days after HCT (p=.003), ongoing immunosuppression (p=.004), pre-existing lung disease (p=.003), and recipient CMV seropositivity (p=.004) had negative impact on overall survival while patients contracting COVID-19 in 2020 (p<.0001) or 2021 (p=.027) had worse overall survival than patients with COVID-19 diagnosed in 2022. DISCUSSION: Although the outcome of COVID-19 has improved, patients having risk factors were still at risk for severe COVID-19 including death.
- MeSH
- COVID-19 * komplikace MeSH
- cytomegalovirové infekce * komplikace MeSH
- homologní transplantace MeSH
- infekční nemoci * komplikace MeSH
- kostní dřeň MeSH
- lidé středního věku MeSH
- lidé MeSH
- registrace MeSH
- transplantace hematopoetických kmenových buněk * škodlivé účinky MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Bacterial genotyping is a crucial process in outbreak investigation and epidemiological studies. Several typing methods such as pulsed-field gel electrophoresis, multilocus sequence typing (MLST) and whole genome sequencing are currently used in routine clinical practice. However, these methods are costly, time-consuming and have high computational demands. An alternative to these methods is mini-MLST, a quick, cost-effective and robust method based on high-resolution melting analysis. Nevertheless, no standardized approach to identify markers suitable for mini-MLST exists. Here, we present a pipeline for variable fragment detection in unmapped reads based on a modified hybrid assembly approach using data from one sequencing platform. RESULTS: In routine assembly against the reference sequence, high variable reads are not aligned and remain unmapped. If de novo assembly of them is performed, variable genomic regions can be located in created scaffolds. Based on the variability rates calculation, it is possible to find a highly variable region with the same discriminatory power as seven housekeeping gene fragments used in MLST. In the work presented here, we show the capability of identifying one variable fragment in de novo assembled scaffolds of 21 Escherichia coli genomes and three variable regions in scaffolds of 31 Klebsiella pneumoniae genomes. For each identified fragment, the melting temperatures are calculated based on the nearest neighbor method to verify the mini-MLST's discriminatory power. CONCLUSIONS: A pipeline for a modified hybrid assembly approach consisting of reference-based mapping and de novo assembly of unmapped reads is presented. This approach can be employed for the identification of highly variable genomic fragments in unmapped reads. The identified variable regions can then be used in efficient laboratory methods for bacterial typing such as mini-MLST with high discriminatory power, fully replacing expensive methods such as MLST. The results can and will be delivered in a shorter time, which allows immediate and fast infection monitoring in clinical practice.
The migratory properties of leukemic cells are commonly associated with their pathological potential and can significantly affect the disease progression. While the research in immunopathology mostly employed powerful indirect methods such as flow cytometry, these cells were rarely observed directly using live imaging microscopy. This is especially true for the malignant cells of the B-cell lineage, such as those originating from chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL). In this study, we employed open-source image analysis tools to automatically and quantitatively describe the amoeboid migration of four B-cell leukemic and lymphoma cell lines and primary CLL cells. To avoid the effect of the shear stress of the medium on these usually non-adherent cells, we have confined the cells using a modified under-agarose assay. Surprisingly, the behavior of tested cell lines differed substantially in terms of basal motility or response to chemokines and VCAM1 stimulation. Since casein kinase 1 (CK1) was reported as a regulator of B-cell migration and a promoter of CLL, we looked at the effects of CK1 inhibition in more detail. Migration analysis revealed that CK1 inhibition induced rapid negative effects on the migratory polarity of these cells, which was quantitatively and morphologically distinct from the effect of ROCK inhibition. We have set up an assay that visualizes endocytic vesicles in the uropod and facilitates morphological analysis. This assay hints that the effect of CK1 inhibition might be connected to defects in polarized intracellular transport. In summary, 1) we introduce and validate a pipeline for the imaging and quantitative assessment of the amoeboid migration of CLL/MCL cells, 2) we provide evidence that the assay is sensitive enough to mechanistically study migration defects identified by the transwell assay, and 3) we describe the polarity defects induced by inhibition or deletion of CK1ε.
- Publikační typ
- časopisecké články MeSH
BACKGROUND AND OBJECTIVE: Short- and long-term mortality following ischemic stroke (IS) and their predictors have not been defined in the Czech population, and studies on long-term mortality are largely missing for the populations of Central Europe. METHODS: Using the National Register of Hospitalized Patients and the Czech National Mortality Registry, we analyzed data on 1-month, 1-year, and 3-year all-cause mortality for patients admitted with IS to any of the 4 hospitals with a certified stroke unit in Brno, Czech Republic, in 2011. We reviewed discharge summaries and recorded potential factors impacting mortality after the index stroke event. Using univariate and multivariable analyses, we identified predictors of mortality at all 3 time points. RESULTS: In our multivariable model, statin use (odds ratio [OR] 0.095, p < 0.0001), age at stroke (OR 1.03, p = 0.0445), and admission National Institutes of Health Stroke Scale (NIHSS) score (OR 1.16, p < 0.0001) predicted 1-month mortality, while statin use (OR 0.43, p = 0.0004), history of cardiac failure (OR 2.17, p = 0.0137), age at stroke (OR 1.07, p < 0.0001), and admission NIHSS score (OR 1.14, p < 0.0001) predicted 1-year mortality. Statin use (OR 0.54, p = 0.0051), history of cardiac failure (OR 2.13, p = 0.0206), age at stroke (OR 1.07, p < 0.0001), and admission NIHSS score (OR 1.11, p < 0.0001) also predicted 3-year mortality. CONCLUSIONS: Our study is the first to report data on short- and long-term mortality rates and their predictors in patients hospitalized with IS in the Czech population. Our results indicate that mortality rates and predictors of mortality are consistent with those reported in studies from other populations throughout the world.
- MeSH
- cévní mozková příhoda * diagnóza epidemiologie terapie MeSH
- ischemická cévní mozková příhoda * MeSH
- ischemie mozku * komplikace diagnóza terapie MeSH
- lidé MeSH
- retrospektivní studie MeSH
- rizikové faktory MeSH
- srdeční selhání * komplikace MeSH
- statiny * MeSH
- stupeň závažnosti nemoci MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
Recently, nanopore sequencing has come to the fore as library preparation is rapid and simple, sequencing can be done almost anywhere, and longer reads are obtained than with next-generation sequencing. The main bottleneck still lies in data postprocessing which consists of basecalling, genome assembly, and localizing significant sequences, which is time consuming and computationally demanding, thus prolonging delivery of crucial results for clinical practice. Here, we present a neural network-based method capable of detecting and classifying specific genomic regions already in raw nanopore signals-squiggles. Therefore, the basecalling process can be omitted entirely as the raw signals of significant genes, or intergenic regions can be directly analyzed, or if the nucleotide sequences are required, the identified squiggles can be basecalled, preferably to others. The proposed neural network could be included directly in the sequencing run, allowing real-time squiggle processing.
- Publikační typ
- časopisecké články MeSH
INTRODUCTION: During the COVID-19 pandemic, studies reported less number of hospitalizations for acute stroke and reduction in the use of recanalization treatments. This study analyzes nationwide data on stroke admissions and management in the Czech Republic during the first wave of the COVID-19 pandemic. METHODS: We compared the early COVID-19 pandemic (March-May 2020) with the pre-pandemic period (January-February 2020 and March-May 2019): (a) the National Register of Reimbursed Health Services provided volume of all admissions for subarachnoid hemorrhage (SAH), intracerebral hemorrhage (ICH), and ischemic stroke (IS), and volume of recanalization treatments (intravenous thrombolysis [IVT] and mechanical thrombectomy [MT]); (b) Registry of Stroke Care Quality provided door-to-needle time (DNT), onset-to-door time (ODT), and stroke severity at admission (National Institutes of Health Stroke Scale, NIHSS) for IS. RESULTS: During the pandemic (March-May 2020), the peak number of COVID-19 patients treated in Czech hospitals was 39 per million. In March-May 2020 versus March-May 2019, hospital admissions decreased as follows: stroke overall by 14% (p < 0.001), IS by 14% (p < 0.001), SAH by 15% (p = 0.07), and ICH by 7% (p = 0.17). The mean age was 74 years versus 74 years (p = 0.33), and 52% versus 51% were men (p = 0.34). The volumes of IVT and MT decreased by 14% (p = 0.001) and 19% (p = 0.01), respectively. The proportions of all IS patients receiving IVT or MT remained unchanged, with, respectively, 17% versus 17% receiving IVT (p = 0.86) and 5% versus 5% receiving MT (p = 0.48). DNT and ODT were 24 versus 25 min (p = 0.58) and 168 versus 156 min (p = 0.23), respectively. NIHSS at admission did not differ (6 vs. 6; p = 0.54). CONCLUSION: Even with a low burden of COVID-19 during the first wave and no change in organization and logistics of stroke services, stroke admissions and volume of recanalization treatments decreased. Public health communication campaigns should encourage people to seek emergency medical care for stroke symptoms during the COVID-19 pandemic.
- MeSH
- cévní mozková příhoda * terapie MeSH
- COVID-19 * epidemiologie terapie MeSH
- lidé MeSH
- pandemie * MeSH
- senioři MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Introduction: We analyzed the incidence, risk factors of central nervous system (CNS) relapse, and outcome of CNS involvement in patients with peripheral T-cell lymphomas (PTCL) from the Czech Lymphoma Study Group Registry NiHiL (Clinical Trial gov. NCT03199066). Materials and Methods: Out of 1,040 patients with PTCL, we identified 29 patients (2.79%) with CNS involvement: 2 patients with primary CNS T cell lymphoma, 11 patients with CNS and systemic disease at diagnosis, and 16 patients (1.54%) at CNS relapse. The most common histology with CNS disease was PTCL, not otherwise specified. Progression-free survival (PFS) was defined as the time interval from diagnosis to progression or death. PFS-2 was defined as the interval from the date of a new relapse until the next relapse. Results: Patients with testicular involvement received intrathecal prophylaxis with methotrexate. High-dose methotrexate-based treatment was administered in 44.8% of patients with CNS disease. Median follow-up was 71.3 months. The difference between the median PFS of 1,027 patients without initial CNS disease (32.6 months) and 11 patients with initial CNS and systemic disease (4.8 months) was significant (p = 0.04). The difference between the median PFS2 in CNS relapses (10.1 months) and 493 relapses outside of CNS (9.1 months) was not significant (p = 0.6). Risk factors for CNS relapses included the following: involvement of more than one extranodal site (p = 0.008), soft tissue involvement (p = 0.003), testicular involvement (p = 0.046), and the presence of B symptoms (p = 0.035). The difference between the median OS of 1,027 patients without initial CNS disease (46.0 months) and 11 patients with initial CNS and systemic disease (18.2 months) was significant (p = 0.02). The median OS2 in CNS relapses was 11.8 months and that in relapses outside of CNS was 21.3 months. CNS involvement was not associated with a significantly worse OS compared to relapsed/refractory patients without CNS involvement (p = 0.1). Conclusions: The incidence of CNS disease at the time of diagnosis and at relapse in PTCL is low and usually associated with other systemic involvement. The prognosis of PTCL with initial CNS involvement is significantly worse when compared to patients without CNS disease at diagnosis. The outcome of CNS relapse is comparable with relapsed PTCL outside of CNS. The optimal treatment is not defined yet.
- Publikační typ
- časopisecké články MeSH
The direct toxicity of cancer treatment threatens patients and survivors with an increased risk of cardiovascular disease or adverse functional changes with subsequent progression of cardiovascular complications. An accumulation of cardiovascular risk factors combined with an unhealthy lifestyle has recently become more common in cancer patients and survivors. It has been recommended to integrate a comprehensive cardiac rehabilitation model called cardio-oncology rehabilitation to mitigate cardiovascular risk. Nevertheless, cardiac rehabilitation interventions limit barriers in low utilization, further exacerbated by the restrictions associated with the COVID-19 pandemic. Therefore, it is essential to integrate alternative interventions such as telehealth, which can overcome several barriers. This literature review was designed as a framework for developing and evaluating telehealth interventions and mobile applications for comprehensive cardio-oncology rehabilitation. We identify knowledge gaps and propose strategies to facilitate the development and integration of cardio-oncology rehabilitation telehealth as an alternative approach to the standard of care for cancer patients and survivors. Despite the limited evidence, the pilot results from included studies support the feasibility and acceptability of telehealth and mobile technologies in cardio-oncology rehabilitation. This new area suggests that telehealth interventions are feasible and induce physiological and psychological benefits for cancer patients and survivors. There is an assumption that telehealth interventions and exercise may be an effective future alternative approach in supportive cancer care.
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- MeSH
- B-buněčný lymfom komplikace mortalita terapie MeSH
- COVID-19 komplikace MeSH
- imunoterapie adoptivní MeSH
- leukemie B-buněčná komplikace mortalita terapie MeSH
- lidé MeSH
- prognóza MeSH
- výsledek terapie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- multicentrická studie MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
