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1.
Artigo em Inglês | MEDLINE | ID: mdl-39406957

RESUMO

OPINION STATEMENT: Mutations in isocitrate dehydrogenase-1 (IDH1) are recurrent in several malignancies and prevalent in acute myeloid leukemia (AML). Olutasidenib and ivosidenib are inhibitors that target mutant IDH1 (mIDH1) and are FDA approved for the treatment of patients with mIDH1 AML. Olutasidenib and ivosidenib were identified through unique molecular screens and thus are structurally very different molecules. A difference in clinical outcomes has been observed with olutasidenib, which has a longer duration of response than ivosidenib, despite similar rates of response being achieved with the two drugs, such as complete remission (CR) or CR with partial hematologic recovery (CR/CRh). In the absence of a head-to-head trial, this review examines both the extent of differences in clinical outcomes with the two drugs and provides the first comparison of the unique molecular and mechanistic features of each drug, such as molecular structure and binding kinetics, that may contribute to the observed clinical difference in outcomes. Olutasidenib is structurally smaller with a lower molecular weight than ivosidenib (FW 355 vs FW 583) and thus occupies less space in the binding pocket of IDH1 dimers, making it resistant to displacement by IDH1 second-site mutations. In biochemical studies, olutasidenib selectively inhibits mutant but not wild-type IDH1, whereas ivosidenib appears to potently block both mutant and wild-type IDH1. Although they have the same target, olutasidenib and ivosidenib have unique molecular features, which may translate to selectivity differences in their inhibitory activity against IDH1.

2.
Nucleic Acids Res ; 52(D1): D586-D589, 2024 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-37904617

RESUMO

Many microorganisms produce natural products that are frequently used in the development of medicines and crop protection agents. Genome mining has evolved into a prominent method to access this potential. antiSMASH is the most popular tool for this task. Here we present version 4 of the antiSMASH database, providing biosynthetic gene clusters detected by antiSMASH 7.1 in publicly available, dereplicated, high-quality microbial genomes via an interactive graphical user interface. In version 4, the database contains 231 534 high quality BGC regions from 592 archaeal, 35 726 bacterial and 236 fungal genomes and is available at https://antismash-db.secondarymetabolites.org/.


Assuntos
Produtos Biológicos , Vias Biossintéticas , Bases de Dados Genéticas , Genoma Microbiano , Vias Biossintéticas/genética , Família Multigênica , Software
3.
J Med Chem ; 66(24): 17086-17104, 2023 12 28.
Artigo em Inglês | MEDLINE | ID: mdl-38079537

RESUMO

A set of focused analogues have been generated around a lead indirect adenosine monophosphate-activated kinase (AMPK) activator to improve the rat clearance of the molecule. Analogues were focused on inhibiting amide hydrolysis by the strategic placement of substituents that increased the steric environment about the secondary amide bond between 4-aminopiperidine and pyridine-5-carboxylic acid. It was found that placing substituents at position 3 of the piperidine ring and position 4 of the pyridine could all improve clearance without significantly impacting on-target potency. Notably, trans-3-fluoropiperidine 32 reduced rat clearance from above liver blood flow to 19 mL/min/kg and improved the hERG profile by attenuating the basicity of the piperidine moiety. Oral dosing of 32 activated AMPK in mouse liver and after 2 weeks of dosing improved glucose handling in a db/db mouse model of Type II diabetes as well as lowering fasted glucose and insulin levels.


Assuntos
Diabetes Mellitus Tipo 2 , Camundongos , Ratos , Animais , Proteínas Quinases Ativadas por AMP , Diamida , Glucose , Piridinas/farmacologia , Piperidinas , Amidas
4.
ACS Med Chem Lett ; 14(12): 1700-1706, 2023 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-38116420

RESUMO

Dimethyl fumarate 1 is approved for the treatment of multiple sclerosis but is also associated with off-target activation of the niacin receptor. By using a tetrazolone or triazolone bioisostere approach to the fumarate and vinyl sulfone series of Nrf2 activators, we have optimized the electrophilicity of the double bond to tune the on-target Nrf2 activation with PK properties to achieve efficacy in animal models of multiple sclerosis. The study linked highly potent, highly electrophilic molecules to low plasma stability and, subsequently, limited efficacy. By contrast, a sulfonylvinyltriazolone 17 retains on-target potency but shows much weaker electrophilic potential. As a consequence, in vivo high exposures of 17 are obtained, resulting in efficacy in the EAE model similar to that observed for DMF. 17 (R079) is Ames negative, is not cytotoxic to cells, and shows little inhibition of either the niacin receptor or a panel of off-target receptors.

5.
Clin Nutr ESPEN ; 56: 152-157, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-37344066

RESUMO

BACKGROUND: Parenteral nutrition (PN) deficient in mitochondrial substrates and thiamine may lead to acidosis. This, combined with fatigue seen in patients with intestinal failure (IF), may suggest suboptimal oxidative metabolism. We therefore studied oxygen utilisation in otherwise apparently well-nourished individuals with intestinal failure receiving long term PN. METHODS: This was a retrospective analysis conducted in a tertiary IF institution, from 2010 to 2019, comparing treadmill/bicycle cardiopulmonary exercise test (CPET) derived variables including peak oxygen consumption (VO2 peak), anaerobic threshold (AT) and ventilatory efficiency (minute ventilation (VE)/CO2 output (VCO2) of patients with IF (cases) to those without (controls), matched in a 1:2 ratio for age ( ± 3 years), gender, use of beta-blockers and physiology parameters of p-POSSUM score ( ± 5). All subjects were free of sepsis and metastatic malignancy. Mann-Whitney or Student's t-test for continuous and Fisher's exact or chi-squared test for categorical variables were used as appropriate. Data shown represent mean or median values. RESULTS: Participants (31 cases, 62 controls) were comparable in age (65.4 vs. 65.3, p = 0.98); p-POSSUM parameters (18.0 vs. 17.0, p = 0.45); gender (p = 1.00); smoking status (p = 0.52); use of beta-blockers (p = 1.00) and ≤10 mg/day of oral steroids (p = 0.34). Participants had been on PN for 11.0 (6.0-24.0) months and were adequately nourished (requirements 27.6 kcal/kg/day, replacement 23.5 kcal/kg/day). No differences were found between VO2 peak (15.2 vs. 14.6 ml/kg/min, p = 0.96), AT (10.4 vs. 11.0 ml/kg/min, p = 0.44) and VE/VCO2 (33.0 vs. 33.0, p = 0.96) of the examined groups. CONCLUSION: Patients with intestinal failure receiving PN who are apparently well-nourished also appear to have normal oxygen utilisation, suggesting alternative causes for fatigue. More studies will be required to determine whether CPET could reliably be used to assess perioperative risk in this group of patients.


Assuntos
Insuficiência Intestinal , Oxigênio , Humanos , Estudos Retrospectivos , Estudos de Casos e Controles , Teste de Esforço
6.
Nucleic Acids Res ; 51(W1): W46-W50, 2023 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-37140036

RESUMO

Microorganisms produce small bioactive compounds as part of their secondary or specialised metabolism. Often, such metabolites have antimicrobial, anticancer, antifungal, antiviral or other bio-activities and thus play an important role for applications in medicine and agriculture. In the past decade, genome mining has become a widely-used method to explore, access, and analyse the available biodiversity of these compounds. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org/) has supported researchers in their microbial genome mining tasks, both as a free to use web server and as a standalone tool under an OSI-approved open source licence. It is currently the most widely used tool for detecting and characterising biosynthetic gene clusters (BGCs) in archaea, bacteria, and fungi. Here, we present the updated version 7 of antiSMASH. antiSMASH 7 increases the number of supported cluster types from 71 to 81, as well as containing improvements in the areas of chemical structure prediction, enzymatic assembly-line visualisation and gene cluster regulation.


Assuntos
Computadores , Software , Bactérias/genética , Bactérias/metabolismo , Archaea/genética , Genoma Microbiano , Família Multigênica , Metabolismo Secundário/genética
7.
Pharmacoecon Open ; 7(3): 455-467, 2023 May.
Artigo em Inglês | MEDLINE | ID: mdl-36811822

RESUMO

BACKGROUND: For many patients with resected epidermal growth factor receptor mutation-positive (EGFRm) non-small cell lung cancer (NSCLC), current standard of care (SoC) is adjuvant chemotherapy; however, disease recurrence remains high. Based on positive results from ADAURA (NCT02511106), adjuvant osimertinib was approved for treatment of resected stage IB‒IIIA EGFRm NSCLC. OBJECTIVE: The aim was to assess the cost-effectiveness of adjuvant osimertinib in patients with resected EGFRm NSCLC. METHODS: A five-health-state, state-transition model with time dependency was developed to estimate lifetime (38 years) costs and survival of resected EGFRm patients treated with adjuvant osimertinib or placebo (active surveillance), with/without prior adjuvant chemotherapy, using a Canadian Public Healthcare perspective. Transitions between health states were modeled using ADAURA and FLAURA (NCT02296125) data, Canadian life tables, and real-world data (CancerLinQ Discovery®). The model used a 'cure' assumption: patients remaining disease free for 5 years after treatment completion for resectable disease were deemed 'cured.' Health state utility values and healthcare resource usage estimates were derived from Canadian real-world evidence. RESULTS: In the reference case, adjuvant osimertinib treatment led to a mean 3.20 additional quality-adjusted life-years (QALYs; (11.77 vs 8.57) per patient, versus active surveillance. The modeled median percentage of patients alive at 10 years was 62.5% versus 39.3%, respectively. Osimertinib was associated with mean added costs of Canadian dollars (C$)114,513 per patient and a cost/QALY (incremental cost-effectiveness ratio) of C$35,811 versus active surveillance. Model robustness was demonstrated by scenario analyses. CONCLUSIONS: In this cost-effectiveness assessment, adjuvant osimertinib was cost-effective compared with active surveillance for patients with completely resected stage IB‒IIIA EGFRm NSCLC after SoC.

8.
Rehabil Process Outcome ; 11: 11795727221137213, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36419648

RESUMO

The workforce of the medical specialty of Rehabilitation Medicine (RM) in the UK is 10 times less than the European average for the specialty of Physical and Rehabilitation Medicine (PRM). This can be explained partly by the difference in the scope of practice within the specialty between the UK and other European countries and USA. This opinion paper aims to compare the rehabilitation needs in chronic medical conditions and compare the scope of practice between countries within Europe and other regions of the world. The potential advantages of a broader remit specialty to improve rehabilitation care for patients by involving rehabilitation physicians in various medical conditions is explored. Recommendations have been put forward in the Rehabilitation Medicine Expansion Proposal (RMEP), which is likely to make the medical specialty of RM/ PRM more satisfying for the doctors working in the specialty and a more attractive career choice for those entering training in the specialty. There is a need for an international universal framework for the scope of the specialty to have a greater impact on improving the lives of those with chronic medical conditions.

9.
Bioorg Med Chem ; 71: 116951, 2022 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-35973281

RESUMO

Using an in-cell AMPK activation assay, we have developed structure-activity relationships around a hit pyridine dicarboxamide 5 that resulted in 40 (R419). A particular focus was to retain the on-target potency while also improving microsomal stability and reducing off-target activities, including hERG inhibition. We were able to show that removing a tertiary amino group from the piperazine unit of hit compound 5 improved microsomal stability while hERG inhibition was improved by modifying the substitution of the central core pyridine ring. The SAR resulted in 40, which continues to maintain on-target potency. Compound 40 was able to activate AMPK in vivo after oral administration and showed efficacy in animal models investigating activation of AMPK as a therapy for glucose control (both db/db and DIO mouse models).


Assuntos
Proteínas Quinases Ativadas por AMP , Hipoglicemiantes , Proteínas Quinases Ativadas por AMP/metabolismo , Animais , Ativação Enzimática , Hipoglicemiantes/farmacologia , Camundongos , Piridinas , Relação Estrutura-Atividade
10.
Nucleic Acids Res ; 49(W1): W29-W35, 2021 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-33978755

RESUMO

Many microorganisms produce natural products that form the basis of antimicrobials, antivirals, and other drugs. Genome mining is routinely used to complement screening-based workflows to discover novel natural products. Since 2011, the "antibiotics and secondary metabolite analysis shell-antiSMASH" (https://antismash.secondarymetabolites.org/) has supported researchers in their microbial genome mining tasks, both as a free-to-use web server and as a standalone tool under an OSI-approved open-source license. It is currently the most widely used tool for detecting and characterising biosynthetic gene clusters (BGCs) in bacteria and fungi. Here, we present the updated version 6 of antiSMASH. antiSMASH 6 increases the number of supported cluster types from 58 to 71, displays the modular structure of multi-modular BGCs, adds a new BGC comparison algorithm, allows for the integration of results from other prediction tools, and more effectively detects tailoring enzymes in RiPP clusters.


Assuntos
Produtos Biológicos/metabolismo , Genoma Microbiano , Software , Bactérias/genética , Vias Biossintéticas/genética , Fungos/genética , Metabolismo Secundário/genética
11.
World J Surg Oncol ; 19(1): 68, 2021 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-33750413

RESUMO

BACKGROUND: We present our 9-year consecutive case series of skull base chordomas and chondrosarcomas from a UK tertiary referral centre, discussing treatments offered and outcomes. This was carried out to improve understanding around current treatment and to better inform the management of future patients. METHODS: Consecutive case series over a 9-year period (2007-2016). Retrospective data analysis from the electronic skull base multidisciplinary team database and the digital patient records at a UK tertiary referral centre RESULTS: Twenty-four patients were identified (11 chordomas, 13 chondrosarcomas, mean age 52). Nineteen had proton beam therapy (PBT) postoperatively; two had intensity-modulated radiotherapy; two had no further treatment. One patient was lost to follow-up. All chordomas were resected via a transnasal endoscopic approach. Of the 19 patients undergoing resection with PBT, 13 were disease free at latest follow-up, and six patients had local recurrence, of which two died (mean follow up 7.4 years). Of the three patients treated with surgery then IMRT/TomoTherapy, one died 4 years post-treatment, and the other two are alive after 4 and 5 years of follow-up respectively. Of the two patients treated with surgery alone, one was lost to follow-up, and the other is alive after more than 8 years. Chondrosarcoma 5-year survival was 91.6%, and chordoma 4-year survival was 75%. CONCLUSION: Skull base chordomas and chondrosarcomas can be challenging to resect, and most cases require adjuvant therapy to achieve control. Where complete resection is not possible, it is critical to undertake sufficient resection to permit high-dose radiation.


Assuntos
Condrossarcoma , Cordoma , Condrossarcoma/cirurgia , Cordoma/cirurgia , Seguimentos , Humanos , Pessoa de Meia-Idade , Recidiva Local de Neoplasia/terapia , Prognóstico , Estudos Retrospectivos , Base do Crânio , Resultado do Tratamento
12.
Front Endocrinol (Lausanne) ; 12: 697445, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34975743

RESUMO

Aim: We evaluated the efficacy of a novel brain permeable "metformin-like" AMP-activated protein kinase activator, R481, in regulating glucose homeostasis. Materials and Methods: We used glucose sensing hypothalamic GT1-7 neuronal cells and pancreatic αTC1.9 α-cells to examine the effect of R481 on AMPK pathway activation and cellular metabolism. Glucose tolerance tests and hyperinsulinemic-euglycemic and hypoglycemic clamps were used in Sprague-Dawley rats to assess insulin sensitivity and hypoglycemia counterregulation, respectively. Results: In vitro, we demonstrate that R481 increased AMPK phosphorylation in GT1-7 and αTC1.9 cells. In Sprague-Dawley rats, R481 increased peak glucose levels during a glucose tolerance test, without altering insulin levels or glucose clearance. The effect of R481 to raise peak glucose levels was attenuated by allosteric brain permeable AMPK inhibitor SBI-0206965. This effect was also completely abolished by blockade of the autonomic nervous system using hexamethonium. During hypoglycemic clamp studies, R481 treated animals had a significantly lower glucose infusion rate compared to vehicle treated controls. Peak plasma glucagon levels were significantly higher in R481 treated rats with no change to plasma adrenaline levels. In vitro, R481 did not alter glucagon release from αTC1.9 cells, but increased glycolysis. Non brain permeable AMPK activator R419 enhanced AMPK activity in vitro in neuronal cells but did not alter glucose excursion in vivo. Conclusions: These data demonstrate that peripheral administration of the brain permeable "metformin-like" AMPK activator R481 increases blood glucose by activation of the autonomic nervous system and amplifies the glucagon response to hypoglycemia in rats. Taken together, our data suggest that R481 amplifies the counterregulatory response to hypoglycemia by a central rather than a direct effect on the pancreatic α-cell. These data provide proof-of-concept that central AMPK could be a target for future drug development for prevention of hypoglycemia in diabetes.


Assuntos
Proteínas Quinases Ativadas por AMP/metabolismo , Sistema Nervoso Autônomo/efeitos dos fármacos , Glicemia/efeitos dos fármacos , Hipoglicemia/metabolismo , Proteínas Quinases Ativadas por AMP/antagonistas & inibidores , Proteínas Quinases Ativadas por AMP/efeitos dos fármacos , Animais , Sistema Nervoso Autônomo/fisiologia , Benzamidas/farmacologia , Glicemia/metabolismo , Encéfalo/efeitos dos fármacos , Encéfalo/metabolismo , Células Cultivadas , Hipoglicemia/patologia , Hipoglicemia/fisiopatologia , Hipotálamo/efeitos dos fármacos , Hipotálamo/metabolismo , Masculino , Permeabilidade/efeitos dos fármacos , Piperidinas/farmacologia , Pirimidinas/farmacologia , Ratos , Ratos Sprague-Dawley
13.
Nucleic Acids Res ; 49(D1): D490-D497, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33010170

RESUMO

Computational analysis of biosynthetic gene clusters (BGCs) has revolutionized natural product discovery by enabling the rapid investigation of secondary metabolic potential within microbial genome sequences. Grouping homologous BGCs into Gene Cluster Families (GCFs) facilitates mapping their architectural and taxonomic diversity and provides insights into the novelty of putative BGCs, through dereplication with BGCs of known function. While multiple databases exist for exploring BGCs from publicly available data, no public resources exist that focus on GCF relationships. Here, we present BiG-FAM, a database of 29,955 GCFs capturing the global diversity of 1,225,071 BGCs predicted from 209,206 publicly available microbial genomes and metagenome-assembled genomes (MAGs). The database offers rich functionalities, such as multi-criterion GCF searches, direct links to BGC databases such as antiSMASH-DB, and rapid GCF annotation of user-supplied BGCs from antiSMASH results. BiG-FAM can be accessed online at https://bigfam.bioinformatics.nl.


Assuntos
Vias Biossintéticas/genética , Bases de Dados Genéticas , Família Multigênica , Clostridium/genética , Ferramenta de Busca , Streptomyces/genética
14.
FASEB J ; 35(1): e21218, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33337559

RESUMO

Growth differentiating factor-15 (GDF15) is an emerging target for the treatment of obesity and metabolic disease partly due to its ability to suppress food intake. GDF15 expression and secretion are thought to be regulated by a cellular integrated stress response, which involves endoplasmic reticulum (ER) stress. AMPK is another cellular stress sensor, but the relationship between AMPK, ER stress, and GDF15 has not been assessed in vivo. Wildtype (WT), AMPK ß1 deficient (AMPKß1-/- ), and CHOP-/- mice were treated with three distinct AMPK activators; AICAR, which is converted to ZMP mimicking the effects of AMP on the AMPKγ isoform, R419, which indirectly activates AMPK through inhibition of mitochondrial respiration, or A769662, a direct AMPK activator which binds the AMPKß1 isoform ADaM site causing allosteric activation. Following treatments, liver Gdf15, markers of ER-stress, AMPK activity, adenine nucleotides, circulating GDF15, and food intake were assessed. AICAR and R419 caused ER and energetic stress, increased GDF15 expression and secretion, and suppressed food intake. Direct activation of AMPK ß1 containing complexes by A769662 increased hepatic Gdf15 expression, circulating GDF15, and suppressed food intake, independent of ER stress. The effects of AICAR, R419, and A769662 on GDF15 were attenuated in AMPKß1-/- mice. AICAR and A769662 increased GDF15 to a similar extent in WT and CHOP-/- mice. Herein, we provide evidence that AMPK plays a role in mediating the induction of GDF15 under conditions of energetic stress in mouse liver in vivo.


Assuntos
Proteínas Quinases Ativadas por AMP/metabolismo , Estresse do Retículo Endoplasmático , Fator 15 de Diferenciação de Crescimento/metabolismo , Fígado/metabolismo , Proteínas Quinases Ativadas por AMP/genética , Animais , Fator 15 de Diferenciação de Crescimento/genética , Camundongos , Camundongos Knockout , Fator de Transcrição CHOP/genética , Fator de Transcrição CHOP/metabolismo
15.
Nucleic Acids Res ; 49(D1): D639-D643, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33152079

RESUMO

Microorganisms produce natural products that are frequently used in the development of antibacterial, antiviral, and anticancer drugs, pesticides, herbicides, or fungicides. In recent years, genome mining has evolved into a prominent method to access this potential. antiSMASH is one of the most popular tools for this task. Here, we present version 3 of the antiSMASH database, providing a means to access and query precomputed antiSMASH-5.2-detected biosynthetic gene clusters from representative, publicly available, high-quality microbial genomes via an interactive graphical user interface. In version 3, the database contains 147 517 high quality BGC regions from 388 archaeal, 25 236 bacterial and 177 fungal genomes and is available at https://antismash-db.secondarymetabolites.org/.


Assuntos
Mineração de Dados , Bases de Dados como Assunto , Enzimas/classificação , Vias Biossintéticas/genética , Família Multigênica , Ferramenta de Busca
16.
J Thorac Dis ; 12(Suppl 2): S153-S162, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-33214920

RESUMO

BACKGROUND: Post-polio syndrome is characterised by symptoms of fatigue, pain and new-onset neuromuscular weakness, and emerges decades after the initial poliovirus infection. We sought to evaluate the only post-polio syndrome specific self-management programme in the United Kingdom. METHODS: This was a retrospective study of patients who had completed a residential self-management programme led by a multi-disciplinary clinical team. Following a confirmed diagnosis of post-polio syndrome by rehabilitation and neurology specialists, patients were offered to participate in the programme. Although group-based, patients also received individually tailored support on physical exercise and fatigue management. Physical effects, physical function, psychosocial well-being measures were assessed at baseline and 6 months follow-up. Knowledge was tested at baseline and immediately following the programme. Statistical comparisons were made using paired t-test and Wilcoxon signed rank test according to the data distribution. RESULTS: Over a period of 17 years, 214 participants (median age 61.3 years old, 63% female) attended 31 programmes. At 6 months the following post-polio syndrome specific symptoms improved significantly: fatigue, as measured by the Multidimensional Assessment of Fatigue scale [37.6 (7.1) vs. 34.2 (9.3), P=0.005]; and pain [15.0 (6.1) vs. 13.1 (6.7), P=0.001], atrophy [10.0 (8.0-12.0) vs. 9.0 (7.0-11.0), P=0.002] and bulbar symptoms [3.0 (1.0-5.0) vs. 2.0 (0-4.0), P=0.003] as measured by the Index of Post-polio Sequelae scale. Knowledge related to post-polio syndrome also significantly increased [14.0 (11.0-16.0) vs. 17.0 (16.0-19.0), P=0.001]. Participants were able to walk at a faster speed over 10 meters [0.77 (0.59-1.00) vs. 0.83 (0.67-1.10) m/s, P=0.003] and walked longer distances during the 2-minute walk test [76.9 (31.7) vs. 82.0 (38.4) m, P=0.029]. Depression and anxiety scores did not change over time [PHQ-9, 2.0 (0.3-10.8) vs. 2.0 (0.3-6.8), P=0.450; GAD-7, 2.0 (0-7.0) vs. 1.0 (0-3.0), P=0.460] nor was there change in self-reported quality of life {60 [50-70] vs. 60 [55-70], P=0.200}. CONCLUSIONS: This study suggests that a post-polio syndrome self-management programme led to improvement in symptoms, knowledge and walking speed, but not quality of life. Anxiety and depression scores remained low.

17.
Synth Syst Biotechnol ; 5(2): 99-102, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32596519

RESUMO

CRISPR/Cas9 systems are an established tool in genome engineering. As double strand breaks caused by the standard Cas9-based knock-out techniques can be problematic in some organisms, new systems were developed that can efficiently create knock-outs without causing double strand breaks to elegantly sidestep these issues. The recently published CRISPR-BEST base editor system for actinobacteria is built around a C to T or A to G base exchange. These base editing systems however require additional constraints to be considered for designing the sgRNAs. Here, we present an updated version of the interactive CRISPy-web single guide RNA design tool https://crispy.secondarymetabolites.org/that was built to support "classical" CRISPR and now also CRISPR-BEST workflows.

18.
Nucleic Acids Res ; 48(D1): D454-D458, 2020 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-31612915

RESUMO

Fueled by the explosion of (meta)genomic data, genome mining of specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played a central role through the analysis of Biosynthetic Gene Clusters (BGCs). Thousands of candidate BGCs from microbial genomes have been identified and stored in public databases. Interpreting the function and novelty of these predicted BGCs requires comparison with a well-documented set of BGCs of known function. The MIBiG (Minimum Information about a Biosynthetic Gene Cluster) Data Standard and Repository was established in 2015 to enable curation and storage of known BGCs. Here, we present MIBiG 2.0, which encompasses major updates to the schema, the data, and the online repository itself. Over the past five years, 851 new BGCs have been added. Additionally, we performed extensive manual data curation of all entries to improve the annotation quality of our repository. We also redesigned the data schema to ensure the compliance of future annotations. Finally, we improved the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases. The repository is accessible online at https://mibig.secondarymetabolites.org/.


Assuntos
Bases de Dados Genéticas , Genoma Bacteriano , Genômica/métodos , Família Multigênica , Software , Vias Biossintéticas/genética , Anotação de Sequência Molecular
19.
Nucleic Acids Res ; 47(W1): W81-W87, 2019 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-31032519

RESUMO

Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org) has assisted researchers in this, both as a web server and a standalone tool. It has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (BGCs) in bacterial and fungal genome sequences. Here, we present an entirely redesigned and extended version 5 of antiSMASH. antiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, ß-lactones, fungal RiPPs, RaS-RiPPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines. For type II polyketide synthase-encoding gene clusters, antiSMASH 5 now offers more detailed predictions. The HTML output visualization has been redesigned to improve the navigation and visual representation of annotations. We have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. A new output file in the standard JavaScript object notation (JSON) format is aimed at downstream tools that process antiSMASH results programmatically.


Assuntos
Genoma Bacteriano/genética , Genoma Fúngico/genética , Genômica , Software , Bactérias/genética , Vias Biossintéticas/genética , Biologia Computacional , Mineração de Dados , Fungos/genética , Internet
20.
J Ind Microbiol Biotechnol ; 46(3-4): 469-475, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30610412

RESUMO

The software antiSMASH examines microbial genome data to identify and analyze biosynthetic gene clusters for a wide range of natural products. So far, type II polyketide synthase (PKS) gene clusters could only be identified, but no detailed predictions for type II PKS gene clusters could be provided. In this study, an antiSMASH module for analyzing type II PKS gene clusters has been developed. The module detects genes/proteins in the type II PKS gene cluster involved with polyketide biosynthesis and is able to make predictions about the aromatic polyketide product. Predictions include the putative starter unit, the number of malonyl elongations during polyketide biosynthesis, the putative class and the molecular weight of the product. Furthermore, putative cyclization patterns are predicted. The accuracy of the predictions generated with the new PKSII antiSMASH module was evaluated using a leave-one-out cross validation. The prediction module is available in antiSMASH version 5 at https://antismash.secondarymetabolites.org .


Assuntos
Família Multigênica , Policetídeo Sintases/genética , Software , Bactérias/genética , Bactérias/metabolismo , Vias Biossintéticas/genética , Fungos/genética , Fungos/metabolismo , Genoma Bacteriano , Genoma Fúngico , Policetídeo Sintases/metabolismo , Policetídeos/química
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