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1.
Helicobacter ; 29(1): e13057, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38415810

RESUMO

BACKGROUND: Helicobacter pylori antibiotic resistance has undergone vast changes in the last two decades. No systematic review has been done on the prevalence of antibiotic resistant H. pylori in India in the last two decades. We evaluated the pattern of resistance rates across various regions of India. MATERIALS AND METHODS: A systematic review of the geographical variations in antibiotic resistance pattern of H. pylori was conducted using PubMed, Google Scholar, Web of Science, Science Direct, etc. for articles published between January 1, 2000 and May 30, 2023. Random effects-model-based Cochran's Q test, I2 statistics, and chi-squared tests were used to measure heterogeneity. RESULTS: The overall resistance was highest against metronidazole (77.65%) followed by amoxicillin (37.78%), levofloxacin (32.8%), clarithromycin (35.64%), furazolidone (12.03%), and tetracycline (11.63%). 14.7% of the H. pylori isolates were multi-drug resistant. Under meta-analysis of each antibiotic, high heterogeneity levels were observed having I2 ranges from 86.53% to 97.70% at p < 0.0001. In sub-group analysis, Metronidazole has a stable rate of resistance as compared to other antibiotics. Other antibiotics have had a downtrend in the last 5 years except for levofloxacin, which has had an uptrend in the resistance rate for the past 5 years. Hence, one should avoid using metronidazole for any kind of first-line treatment. CONCLUSIONS: Metronidazole resistance is high in most regions of India except Assam and Mumbai while clarithromycin is found to be ineffective in South India, Gujarat, and Kashmir. As compared to other antibiotics, resistance to amoxicillin is generally low except in certain regions (Hyderabad, Chennai, and the Gangetic belt of North India). Tetracycline and Furazolidone have the least resistance rates and should be part of anti- H. pylori regimens. The resurgence of high single and multidrug resistance to the commonly used drugs suggests the need for newer antibiotics and regular resistance surveillance studies.


Assuntos
Infecções por Helicobacter , Helicobacter pylori , Humanos , Metronidazol/farmacologia , Metronidazol/uso terapêutico , Claritromicina , Levofloxacino , Furazolidona , Índia/epidemiologia , Infecções por Helicobacter/tratamento farmacológico , Infecções por Helicobacter/epidemiologia , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Amoxicilina , Tetraciclina , Anticorpos , Resistência Microbiana a Medicamentos
2.
Homeopathy ; 2024 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-38821071

RESUMO

BACKGROUND: Even though several initiatives have been undertaken in different locations worldwide to collect clinical data in homeopathy, it is important to further investigate these aspects in the context of health care in India. OBJECTIVE: The study aimed to gather and analyze patients' clinical data and to derive insights into homeopathic treatment using an internet-based software program for data storage, retrieval and repertorization. METHODS: A multi-center observational study was conducted across 14 homeopathy outpatient clinics in India that are affiliated with the Central Council for Research in Homoeopathy (CCRH). Patient symptoms and demographic details were documented anonymously, and prescriptions were guided by repertorial suggestions from the Vithoulkas Compass software. During follow-up visits, treatment outcome was also recorded using an online assessment form. A retrospective analysis of data on patients' demographics, follow-up visits, morbidity (International Classification of Diseases 11th Revision), rubrics used, prescribed medicines and the level of improvement was achieved using Microsoft Excel-generated pivot tables. RESULTS: Throughout the study duration of one year a total of 2,811 patients attended the 14 outpatient clinics, of whom 2,468 were new patients with a total of 2,172 initial homeopathic prescription entries. Across the study, there were 3,491 prescriptions and 1,628 follow-up consultations for 868 follow-up patients, all of which data were thoroughly analyzed. The highest frequency of patients was in the 20-49 age group, and a higher proportion of the patients overall was female. Musculoskeletal, dermatological and respiratory complaints were the most frequently reported. The rubrics "Desire for sweets" and "Desire for spices" emerged as the most commonly used in the repertorizations. Further, Sulphur stood out as the most commonly prescribed medicine overall. With homeopathic treatment, some degree of clinical improvement was reported in 86% of the follow-up cases. CONCLUSION: Homeopathy is prescribed in CCRH outpatient clinics for a wide range of ailments in people across India, with at least some clinical improvement noted in a high proportion of those patients. The large-scale systematic data collection in these clinics has provided clear insights into the use and clinical value of homeopathy in India, with the potential to build a substantive nationwide data inventory over time.

3.
J Am Chem Soc ; 145(10): 5696-5709, 2023 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-36811855

RESUMO

Electron bifurcation is a fundamental energy coupling mechanism widespread in microorganisms that thrive under anoxic conditions. These organisms employ hydrogen to reduce CO2, but the molecular mechanisms have remained enigmatic. The key enzyme responsible for powering these thermodynamically challenging reactions is the electron-bifurcating [FeFe]-hydrogenase HydABC that reduces low-potential ferredoxins (Fd) by oxidizing hydrogen gas (H2). By combining single-particle cryo-electron microscopy (cryoEM) under catalytic turnover conditions with site-directed mutagenesis experiments, functional studies, infrared spectroscopy, and molecular simulations, we show that HydABC from the acetogenic bacteria Acetobacterium woodii and Thermoanaerobacter kivui employ a single flavin mononucleotide (FMN) cofactor to establish electron transfer pathways to the NAD(P)+ and Fd reduction sites by a mechanism that is fundamentally different from classical flavin-based electron bifurcation enzymes. By modulation of the NAD(P)+ binding affinity via reduction of a nearby iron-sulfur cluster, HydABC switches between the exergonic NAD(P)+ reduction and endergonic Fd reduction modes. Our combined findings suggest that the conformational dynamics establish a redox-driven kinetic gate that prevents the backflow of the electrons from the Fd reduction branch toward the FMN site, providing a basis for understanding general mechanistic principles of electron-bifurcating hydrogenases.


Assuntos
Elétrons , Hidrogenase , Hidrogenase/química , NAD/metabolismo , Microscopia Crioeletrônica , Ferredoxinas/química , Oxirredução , Hidrogênio/química , Transporte de Elétrons
4.
Br J Cancer ; 126(10): 1432-1438, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35046521

RESUMO

BACKGROUND: Hepatocellular carcinoma (HCC) occurs in a well-defined high-risk patient population, but better screening tests are needed to improve sensitivity and efficacy. Therefore, we investigated the use of urine circulating tumour DNA (ctDNA) as a screening test. METHODS: Candidate markers in urine were selected from HCC and controls. We then enrolled 609 patients from five medical centres to test the selected urine panel. A two-stage model was developed to combine AFP and urine panel as a screening test. RESULTS: Mutated TP53, and methylated RASSF1a, and GSTP1 were selected as the urine panel markers. Serum AFP outperformed the urine panel among all cases of HCC, but the urine panel identified 49% of HCC cases with low AFP < 20 ng/ml. Using the two-stage model, the combined AFP and urine panel identified 148 of the 186 HCC cases (79.6% sensitivity at 90% specificity), which was 30% more than the cases detected with serum AFP alone. It also increased early-stage HCC detection from 62% to 92% (BCLC stage 0), and 40% to 77% (BCLC stage A). CONCLUSION: Urine ctDNA has promising diagnostic utility in patients in HCC, especially in those with low AFP and can be used as a potential non-invasive HCC screening test.


Assuntos
Carcinoma Hepatocelular , DNA Tumoral Circulante , Neoplasias Hepáticas , Biomarcadores Tumorais/urina , Carcinoma Hepatocelular/diagnóstico , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/patologia , DNA Tumoral Circulante/urina , Humanos , Neoplasias Hepáticas/diagnóstico , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/patologia , alfa-Fetoproteínas/análise
5.
Nat Chem Biol ; 16(4): 387-390, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31873222

RESUMO

Here, we report a rapid CRISPR-Cas9-mediated gene knock-in strategy that uses Cas9 ribonucleoprotein and 5'-modified double-stranded DNA donors with 50-base-pair homology arms and achieved unprecedented 65/40% knock-in rates for 0.7/2.5 kilobase inserts, respectively, in human embryonic kidney 293T cells. The identified 5'-end modification led to up to a fivefold increase in gene knock-in rates at various genomic loci in human cancer and stem cells.


Assuntos
Técnicas de Introdução de Genes/métodos , Região 5'-Flanqueadora/genética , Sistemas CRISPR-Cas/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , DNA/genética , Genoma/genética , Células HEK293 , Humanos , RNA Guia de Cinetoplastídeos/genética , Homologia de Sequência do Ácido Nucleico
6.
Nat Chem Biol ; 16(4): 479, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31942048

RESUMO

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

7.
J Wound Care ; 31(Sup5): S30-S32, 2022 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-35576200

RESUMO

Chordoma is a rare form of cancer that forms from the notochord remnants, and affects the skull and the spine. The standard treatment for a sacrococcygeal chordoma is surgery and radiation. Chordoma has a high rate of recurrence and surgery with radiation treatment can leave patients with surgical site complications, such as wounds, fistulas or sinus tracts. Repeat surgical intervention on an irradiated surgical site increases incidence of complications leading to decreased quality of life, and increased morbidity and mortality. Treatment of wound complications after surgery and high-dose radiation for a chordoma tumour is rarely reported in the literature. Herein, the author describes the case of a chronic sinus tract after surgery and radiation for a sacral chordoma tumour successfully healed by hyperbaric oxygen therapy (HBOT) in conjunction with topical antibiotics.


Assuntos
Cordoma , Fístula , Oxigenoterapia Hiperbárica , Neoplasias da Coluna Vertebral , Cordoma/cirurgia , Humanos , Qualidade de Vida , Neoplasias da Coluna Vertebral/cirurgia
8.
Bratisl Lek Listy ; 123(11): 795-805, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36254637

RESUMO

The human body possesses an endogenous regeneration system based on stem cells, which may be found in practically every tissue type. They are classified as embryonic stem cells (ESCs) or nonembryonic stem cells (NESCs). Despite its enormous promise, the use of ESCs is presently limited because of ethical and scientific issues. Stem cells have the potential to improve healthcare by using and boosting the body's inherent regenerative capabilities. Although the stem cells offer an enormous promise for tissue regeneration and repair, much more about their biology, administration, and safety must be studied before they may be employed therapeutically. Stem cells and their derivatives will have enormous medical promise in the future. Current animal and laboratory investigations are looking into the viability of bringing stem cell therapy into clinical practice for regeneration in muscular dystrophy, intervertebral disc degeneration, cerebral infarctions, and transplantation medicine. This article delves into the many aspects at play, as well as current situation and possible issues with stem cell treatment in patient care and management (Fig. 1, Ref. 86). Keywords: stem cells, tissue engineering, regenerative medicine, stem cell application.


Assuntos
Medicina de Precisão , Pesquisa com Células-Tronco , Animais , Humanos , Degeneração do Disco Intervertebral/terapia , Medicina Regenerativa , Transplante de Células-Tronco , Engenharia Tecidual
9.
Extremophiles ; 26(1): 4, 2021 Dec 17.
Artigo em Inglês | MEDLINE | ID: mdl-34919167

RESUMO

Thermoanaerobacter kivui is a thermophilic acetogen that can grow on carbon monoxide as sole carbon and energy source. To identify the gene(s) involved in CO oxidation, the genome sequence was analyzed. Two genes potentially encoding CO dehydrogenases were identified. One, cooS, potentially encodes a monofunctional CO dehydrogenase, whereas another, acsA, potentially encodes the CODH component of the CODH/ACS complex. Both genes were cloned, a His-tag encoding sequence was added, and the proteins were produced from a plasmid in T. kivui. His-AcsA copurified by affinity chromatography with AcsB, the acetyl-CoA synthase of the CO dehydrogenase/acetyl CoA synthase complex. His-CooS copurified with CooF1, a small iron-sulfur center containing protein likely involved in electron transport. Both protein complexes had CO:ferredoxin oxidoreductase as well as CO:methyl viologen oxidoreductase activity, but the activity of CooSF1 was 15-times and 231-times lower, respectively. To underline the importance of CooS, the gene was deleted in the CO-adapted strain. Interestingly, the ∆cooS deletion mutant did not grow on CO anymore. These experiments clearly demonstrated that CooS is essential for growth of T. kivui on CO. This is in line with the hypothesis that CooS is the CO-oxidizing enzyme in cells growing on CO.


Assuntos
Aldeído Oxirredutases , Monóxido de Carbono , Aldeído Oxirredutases/genética , Complexos Multienzimáticos/genética , Thermoanaerobacter
10.
Extremophiles ; 25(5-6): 513-526, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34647163

RESUMO

Thermoanaerobacter kivui is an acetogenic model organism that reduces CO2 with electrons derived from H2 or CO, or from organic substrates in the Wood-Ljugdahl pathway (WLP). For the calculation of ATP yields, it is necessary to know the electron carriers involved in coupling of the oxidative and reductive parts of metabolism. Analyses of key catabolic oxidoreductases in cell-free extract (CFE) or with purified enzymes revealed the physiological electron carriers involved. The glyceraldehyde-3-phosphate dehydrogenase (GA3P-DH) assayed in CFE was NAD+-specific, NADP+ was used with less than 4% and ferredoxin (Fd) was not used. The methylene-THF dehydrogenase was NADP+-specific, NAD+ or Fd were not used. A Nfn-type transhydrogenase that catalyzes reduced Fd-dependent reduction of NADP+ with NADH as electron donor was also identified in CFE. The electron carriers used by the potential electron-bifurcating hydrogenase (HydABC) could not be unambiguously determined in CFE for technical reasons. Therefore, the enzyme was produced homologously in T. kivui and purified by affinity chromatography. HydABC contained 33.9 ± 4.5 mol Fe/mol of protein and FMN; it reduced NADP+ but not NAD+. The methylene-THF reductase (MetFV) was also produced homologously in T. kivui and purified by affinity chromatography. MetFV contained 7.2 ± 0.4 mol Fe/mol of protein and FMN; the complex did neither use NADPH nor NADH as reductant but only reduced Fd. In sum, these analysis allowed us to propose a scheme for entire electron flow and bioenergetics in T. kivui.


Assuntos
Elétrons , Hidrogenase , Processos Autotróficos , Hidrogenase/metabolismo , NAD/metabolismo , NADP , Oxirredução , Thermoanaerobacter/metabolismo
11.
Anal Biochem ; 610: 113996, 2020 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-33080213

RESUMO

Breast cancer is the most commonly occurring cancer among women which leads to thousands of deaths worldwide. The chances of survival are more if the breast cancer is diagnosed at early stage. At present, mammography, magnetic resonance imaging, ultrasound and tissue biopsies are the main diagnostic techniques available for the detection of breast cancer. However, despite of offering promising results, requirement of expensive setup, skilled supervision, expert analysis, invasive procedure (biopsy) and low capacity of multiplexing are the main limitations of these diagnostic techniques. Due to high cost, these screening tests are out of reach of people belonging to low socioeconomic groups and this poses serious health burden to the society. Recently, biosensor-based diagnostic technology for early detection of various types of cancers and other non-oncological disorders have gained considerable attention because of their several advantageous features over existing diagnostic technologies such as high throughput, noninvasive nature, cost effectiveness, easy interpretable results and capacity for multiplexing. Further, biosensors can be designed for biomarkers which are confined to particular type of cancer. In this review, we have discussed about various genomic, transcriptomic, proteomic and metabolomic biomarkers associated with breast cancer, various biosensors-based diagnostic approaches designed for detection of specific biomarkers associated with breast cancer are also described. Further, this review throws insight on various biomarkers linked with breast cancer which can be effectively exploited to develop new diagnostic technology. The assessment of these biomarkers associated with BC using biosensors in large population are cost-effective, non-invasive and high throughput. They help in risk assessment of disease at very initial stage even in backward areas and also help to lower the disease burden of society and economic cost of treatment for a common man. This review would provide new avenues for the development of biosensor based diagnostic technology for the detection of biomarkers associated with breast cancer.


Assuntos
Biomarcadores Tumorais/metabolismo , Técnicas Biossensoriais/métodos , Neoplasias da Mama/diagnóstico , Proteína BRCA1/genética , Proteína BRCA1/metabolismo , Biomarcadores Tumorais/sangue , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Técnicas Eletroquímicas , Feminino , Humanos , MicroRNAs/metabolismo , Estadiamento de Neoplasias , Receptor ErbB-2/sangue
12.
BMC Gastroenterol ; 18(1): 40, 2018 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-29548283

RESUMO

BACKGROUND: Detection of human hepatitis B virus (HBV) DNA in the urine of patients with chronic hepatitis B infection (CHB) has been reported previously, suggesting urine could provide a potential route of horizontal HBV transmission. However, it is not clear whether the HBV DNA detected in urine is indeed full-length, infectious viral DNA. The aim of this study is to assess the potential infectivity of urine from patients with CHB and to correlate HBV DNA detection in urine with clinical parameters, such as serum viral load and HBeAg status. METHODS: Urine from 60 CHB patients with serum viral loads ranging from undetectable to 108 IU/mL were analyzed for HBV DNA and serum immune markers. HBV DNA was detected from total urine DNA and size-fractionated urine DNA (separated into ≤1 kb and > 1 kb fractions) by PCR analysis of six regions of the HBV genome. RESULTS: Twenty-seven of 59 (45.7%) patients with HBV serum viral load (≥20 IU/mL) contained at least 20 copies per mL of fragmented HBV DNA in urine detected in at least 1 of the 6 PCR assay regions. Only one patient contained HBV DNA detected by all six regions, and was found to have evidence of blood in the urine. Sixteen of 25 urine samples with high viral load (> 105 IU/mL) and 11 of 34 urine samples with low viral load (< 105 IU/mL) contained detectable HBV DNA. Twelve of 27 (44.44%) patients with detectable HBV DNA in urine were HBeAg positive, and only 5 of these HBeAg positive patients were in the group of 33 (15.15%) patients with no detectable HBV DNA in urine. By Fishers' exact test, HBV DNA in urine is significantly associated with high serum viral load (P = 0.0197) and HBeAg (P = 0.0203). CONCLUSIONS: We conclude that urine from CHB patients with healthy kidney function should not contain full-length HBV DNA, and therefore should not be infectious.


Assuntos
DNA Viral/urina , Vírus da Hepatite B/genética , Hepatite B Crônica/virologia , Adulto , Idoso , Feminino , Antígenos E da Hepatite B/sangue , Hepatite B Crônica/transmissão , Hepatite B Crônica/urina , Humanos , Masculino , Pessoa de Meia-Idade , Peso Molecular , Reação em Cadeia da Polimerase , Urina/virologia , Carga Viral
13.
Hum Genet ; 135(9): 1011-28, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27250347

RESUMO

Recent advances in genome-editing techniques have made it possible to modify any desired DNA sequence by employing programmable nucleases. These next-generation genome-modifying tools are the ideal candidates for therapeutic applications, especially for the treatment of genetic disorders like sickle cell disease (SCD). SCD is an inheritable monogenic disorder which is caused by a point mutation in the ß-globin gene. Substantial success has been achieved in the development of supportive therapeutic strategies for SCD, but unfortunately there is still a lack of long-term universal cure. The only existing curative treatment is based on allogeneic stem cell transplantation from healthy donors; however, this treatment is applicable to a limited number of patients only. Hence, a universally applicable therapy is highly desirable. In this review, we will discuss the three programmable nucleases that are commonly used for genome-editing purposes: zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9). We will continue by exemplifying uses of these methods to correct the sickle cell mutation. Additionally, we will present induction of fetal globin expression as an alternative approach to cure sickle cell disease. We will conclude by comparing the three methods and explaining the concerns about their use in therapy.


Assuntos
Anemia Falciforme/tratamento farmacológico , Edição de Genes , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Hemoglobina Fetal/genética , Humanos
15.
Hepatol Res ; 45(11): 1110-23, 2015 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-25382672

RESUMO

AIM: Aberrant methylation of the promoter, P2, and the first exon, E1, regions of the tumor suppressor gene RASSF1A, have been associated with hepatocellular carcinoma (HCC), albeit with poor specificity. This study analyzed the methylation profiles of P1, P2 and E1 regions of the gene to identify the region of which methylation most specifically corresponds to HCC and to evaluate the potential of this methylated region as a biomarker in urine for HCC screening. METHODS: Bisulfite DNA sequencing and quantitative methylation-specific polymerase chain reaction assays were performed to compare methylation of the 56 CpG sites in regions P1, P2 and E1 in DNA isolated from normal, hepatitic, cirrhotic, adjacent non-HCC, and HCC liver tissue and urine samples for the characterization of hypermethylation of the RASSF1A gene as a biomarker for HCC screening. RESULTS: In tissue, comparing HCC (n = 120) with cirrhosis and hepatitis together (n = 70), methylation of P1 had an area under the receiver operating characteristics curve (AUROC) of 0.90, whereas methylation of E1 and P2 had AUROC of 0.84 and 0.72, respectively. At 90% sensitivity, specificity for P1 methylation was 72.9% versus 38.6% for E1 and 27.1% for P2. Methylated P1 DNA was detected in urine in association with cirrhosis and HCC. It had a sensitivity of 81.8% for α-fetoprotein negative HCC. CONCLUSION: Among the three regions analyzed, methylation of P1 is the most specific for HCC and holds great promise as a DNA marker in urine for screening of cirrhosis and HCC.

16.
Indian J Dermatol ; 69(2): 201, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38841219

RESUMO

Background: Tuberculides are characterised by delayed-type of immunologic reactions to Mycobacterium tuberculosis or its products in immuno-competent individuals. We herein describe clinico-epidemiological features and response to treatment in patients with tuberculides from a tertiary care centre from North India. Methods: This was a retrospective analysis of the clinical records of all the cutaneous tuberculosis (TB) patients (year 2000-2019) enrolled in the TB clinic. The patient records fulfilling the diagnostic criteria of tuberculides were considered for analysis. Results: A total of 225 patients attended the tuberculosis clinic; out of this, 34 were diagnosed as tuberculides. Out of these 34 cases, 21 were identified as LS, 2 erythema induratum of Bazin, 1 papulonecrotic tuberculide, and 10 erythema nodosum. History of contact to open cases of TB was present in 15/34 (44.1%) patients. History of BCG vaccination was found in 15/34 (44.1%) patients. The focus of underlying TB could be identified in 20/34 (58.8%) patients. Skin biopsy was performed in all patients. In all patients, the diagnosis was confirmed by clinico-pathological correlation, positive TST, and the underlying focus of TB. All patients received 6 months regimen of anti-tubercular therapy with first-line drugs. Conclusion: In this study, we demonstrated various forms of tuberculides; lichen scrofulosorum was the most common form. We also included erythema nodosum cases also, which responded well to ATT. Observation from our study showed that tuberculides are important cutaneous markers for underlying tuberculosis infection, which helps in early detection of occult tuberculosis and timely management.

17.
PLoS One ; 19(5): e0301000, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38805476

RESUMO

As imaging techniques rapidly evolve to probe nanoscale genome organization at higher resolution, it is critical to consider how the reagents and procedures involved in sample preparation affect chromatin at the relevant length scales. Here, we investigate the effects of fluorescent labeling of DNA sequences within chromatin using the gold standard technique of three-dimensional fluorescence in situ hybridization (3D FISH). The chemical reagents involved in the 3D FISH protocol, specifically formamide, cause significant alterations to the sub-200 nm (sub-Mbp) chromatin structure. Alternatively, two labeling methods that do not rely on formamide denaturation, resolution after single-strand exonuclease resection (RASER)-FISH and clustered regularly interspaced short palindromic repeats (CRISPR)-Sirius, had minimal impact on the three-dimensional organization of chromatin. We present a polymer physics-based analysis of these protocols with guidelines for their interpretation when assessing chromatin structure using currently available techniques.


Assuntos
Cromatina , DNA , Formamidas , Hibridização in Situ Fluorescente , Formamidas/química , Hibridização in Situ Fluorescente/métodos , DNA/química , Cromatina/química , Cromatina/genética , Desnaturação de Ácido Nucleico , Animais
18.
Genome Biol ; 25(1): 77, 2024 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-38519987

RESUMO

BACKGROUND: B-type lamins are critical nuclear envelope proteins that interact with the three-dimensional genomic architecture. However, identifying the direct roles of B-lamins on dynamic genome organization has been challenging as their joint depletion severely impacts cell viability. To overcome this, we engineered mammalian cells to rapidly and completely degrade endogenous B-type lamins using Auxin-inducible degron technology. RESULTS: Using live-cell Dual Partial Wave Spectroscopic (Dual-PWS) microscopy, Stochastic Optical Reconstruction Microscopy (STORM), in situ Hi-C, CRISPR-Sirius, and fluorescence in situ hybridization (FISH), we demonstrate that lamin B1 and lamin B2 are critical structural components of the nuclear periphery that create a repressive compartment for peripheral-associated genes. Lamin B1 and lamin B2 depletion minimally alters higher-order chromatin folding but disrupts cell morphology, significantly increases chromatin mobility, redistributes both constitutive and facultative heterochromatin, and induces differential gene expression both within and near lamin-associated domain (LAD) boundaries. Critically, we demonstrate that chromatin territories expand as upregulated genes within LADs radially shift inwards. Our results indicate that the mechanism of action of B-type lamins comes from their role in constraining chromatin motion and spatial positioning of gene-specific loci, heterochromatin, and chromatin domains. CONCLUSIONS: Our findings suggest that, while B-type lamin degradation does not significantly change genome topology, it has major implications for three-dimensional chromatin conformation at the single-cell level both at the lamina-associated periphery and the non-LAD-associated nuclear interior with concomitant genome-wide transcriptional changes. This raises intriguing questions about the individual and overlapping roles of lamin B1 and lamin B2 in cellular function and disease.


Assuntos
Cromatina , Lamina Tipo B , Animais , Lamina Tipo B/genética , Heterocromatina , Hibridização in Situ Fluorescente , Lamina Tipo A/genética , Lamina Tipo A/metabolismo , Laminas , Expressão Gênica , Mamíferos/genética
19.
Nat Biotechnol ; 42(3): 413-423, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-37156915

RESUMO

Genetic engineering of allogeneic cell therapeutics that fully prevents rejection by a recipient's immune system would abolish the requirement for immunosuppressive drugs or encapsulation and support large-scale manufacturing of off-the-shelf cell products. Previously, we generated mouse and human hypoimmune pluripotent (HIP) stem cells by depleting HLA class I and II molecules and overexpressing CD47 (B2M-/-CIITA-/-CD47+). To determine whether this strategy is successful in non-human primates, we engineered rhesus macaque HIP cells and transplanted them intramuscularly into four allogeneic rhesus macaques. The HIP cells survived unrestricted for 16 weeks in fully immunocompetent allogeneic recipients and differentiated into several lineages, whereas allogeneic wild-type cells were vigorously rejected. We also differentiated human HIP cells into endocrinologically active pancreatic islet cells and showed that they survived in immunocompetent, allogeneic diabetic humanized mice for 4 weeks and ameliorated diabetes. HIP-edited primary rhesus macaque islets survived for 40 weeks in an allogeneic rhesus macaque recipient without immunosuppression, whereas unedited islets were quickly rejected.


Assuntos
Transplante de Células-Tronco Hematopoéticas , Células-Tronco Pluripotentes Induzidas , Transplante das Ilhotas Pancreáticas , Camundongos , Animais , Macaca mulatta , Antígeno CD47 , Rejeição de Enxerto
20.
Cancer ; 119(21): 3830-8, 2013 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-24037801

RESUMO

BACKGROUND: Neurosurgical resection and whole-brain radiation therapy (WBRT) are accepted treatments for single and oligometastatic cancer to the brain. To avoid the decline in neurocognitive function (NCF) linked to WBRT, the authors conducted a prospective, multicenter, phase 2 study to determine whether surgery and carmustine wafers (CW), while deferring WBRT, could preserve NCF and achieve local control (LC). METHODS: NCF and LC were measured in 59 patients who underwent resection and received CW for a single (83%) or dominant (oligometastatic, 2 to 3 lesions) metastasis and received stereotactic radiosurgery (SRS) for tiny nodules not treated with resection plus CW. Preservation of NCF was defined as an improvement or a decline ≤ 1 standard deviation from baseline in 3 domains: memory, executive function, and fine motor skills, evaluated at 2-month intervals. RESULTS: Significant improvements in executive function and memory occurred throughout the 1-year follow-up. Preservation or improvement of NCF occurred in all 3 domains for the majority of patients at each of the 2-month intervals. NCF declined in only 1 patient. The chemowafers were well tolerated, and serious adverse events were reversible. There was local recurrence in 28% of the patients at 1-year follow-up. CONCLUSIONS: Patients with brain metastases had improvements in their cognitive trajectory, especially memory and executive function, after treatment with resection plus CW. The rate of LC (78%) was comparable to historic rates of surgery with WBRT and superior to reports of WBRT alone. For patients who undergo resection for symptomatic or large-volume metastasis or for tissue diagnosis, the addition of CW can be considered as an option.


Assuntos
Neoplasias Encefálicas/tratamento farmacológico , Neoplasias Encefálicas/cirurgia , Carmustina/administração & dosagem , Cognição/efeitos dos fármacos , Recidiva Local de Neoplasia/prevenção & controle , Adulto , Idoso , Idoso de 80 Anos ou mais , Antineoplásicos Alquilantes/administração & dosagem , Neoplasias Encefálicas/secundário , Cognição/fisiologia , Transtornos Cognitivos/epidemiologia , Transtornos Cognitivos/prevenção & controle , Terapia Combinada , Implantes de Medicamento , Feminino , Humanos , Infusões Intralesionais , Masculino , Pessoa de Meia-Idade , Procedimentos Neurocirúrgicos
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