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1.
Ann Lab Med ; 42(2): 141-149, 2022 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-34635607

RESUMO

Standardization of cell-free DNA (cfDNA) testing processes is necessary to obtain clinically reliable results. The pre-analytical phase of cfDNA testing greatly influences the results because of the low proportion and stability of circulating tumor DNA (ctDNA). In this review, we provide evidence-based clinical practice guidelines for pre-analytical phase procedures of plasma epidermal growth factor receptor gene (EGFR) variant testing. Specific recommendations for pre-analytical procedures were proposed based on evidence from the literature and our experimental data. Standardization of pre-analytical procedures can improve the analytical performance of cfDNA testing.


Assuntos
Ácidos Nucleicos Livres , DNA Tumoral Circulante , Receptores ErbB/genética , Humanos
2.
Ann Lab Med ; 42(2): 274-277, 2022 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-34635619

RESUMO

Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant disease caused by abnormal CAG repeat expansion in the ataxin 1 gene (ATXN1). The presence of CAT interruption(s) is important for diagnosing SCA1 in patients with 39-44 repeat alleles, as only uninterrupted alleles are considered abnormal. Determining the CAT interruption status might also be important for patients with >44 repeats, as the length of the longest uninterrupted CAG repeat stretch has been correlated with age at SCA1 onset. We detected CAT interruption(s) in the archived samples of Korean SCA1 patients using a traditional restriction enzyme method and validated the usefulness of a fluorescence-based tethering PCR procedure. Among the 2,312 alleles analyzed from 1,156 patients, we found 17 expanded alleles with ≥39 repeats, 71% of which harbored 39-44 repeats. Restriction enzyme method of six samples (four with 39-44 repeats and two with >44 repeats) revealed that none of the expanded alleles had CAT interruption(s). Tethering PCR showed the characteristic electropherogram pattern expected without CAT interruption(s). Along with the enzyme restriction method, tethering PCR can be applied to determine the number of allele repeats and provide information on CAT interruption(s) in clinical laboratories.


Assuntos
Ataxina-1 , Ataxias Espinocerebelares , Degenerações Espinocerebelares , Alelos , Ataxina-1/genética , Humanos , Reação em Cadeia da Polimerase , República da Coreia , Ataxias Espinocerebelares/diagnóstico , Ataxias Espinocerebelares/genética , Degenerações Espinocerebelares/genética
3.
Food Chem ; 367: 130635, 2022 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-34352690

RESUMO

In this study, tailored-made citrus pectin-derived compounds were produced through controlled enzymatic and/or chemical modifications of commercial citrus pectin with different degrees of methylesterification (DM) and similar average molecular weight (MW). In the first treatment, degradation of the citrus pectin (CP) materials by endo-polygalacturonase (EPG) yielded pectins with average Mw's (between 2 and 60 kDa). Separation and identification of the oligosaccharide fraction present in these samples, revealed the presence of non-methylesterified galacturonic acid oligomers with degree of polymerization (DP) 1-5. In the second treatment, exploiting the combined effect of EPG and pectin lyase, compounds with MW between 2 and 21 kDa, containing methylesterified and non-methylesterified polygalacturonans (DP 1-6), were generated. Finally, CP was sequentially modified by chemical saponification and the action of EPG. A sample of DM 11% and MW 2.7 kDa, containing POS (DP 1-5), was produced. Diverse pectin-derived compounds were successfully generated for further studies exploring their functionality.


Assuntos
Citrus , Pectinas , Peso Molecular , Oligossacarídeos , Poligalacturonase/genética
4.
Food Chem ; 367: 130617, 2022 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-34352696

RESUMO

The abuse application of glyphosate can result in a potential hazard for environment and human, however its ultrasensitive detection remains challenging. Herein, a Cu2+ modulated DNA-templated silver nanoclusters (DNA-AgNCs) sensor was constructed to sensitively determine glyphosate based on the turn-on fluorescence strategy. The fluorescence quenching of DNA-AgNCs occurred with the existence of Cu2+. Upon the presence of glyphosate, the functional groups on the surface of glyphosate could chelate with Cu2+, following the fluorescence recovery of DNA-AgNCs. Through the stoichiometric methods, we unveil that Cu2+-trigged fluorescence quenching mode is a combination of static and dynamic quenching with the static mode being predominant. In DNA-AgNCs/Cu2+ system, the carboxylate, amine, and phosphonate groups of glyphosate interact with Cu2+ through chelation, in which the carboxylate oxygen, the phosphonate oxygen atoms, and the monoprotonated secondary amine nitrogen atom and Cu2+ form chelate rings. This fluorescence sensor showed a desired linearity of glyphosate analysis under the optimum conditions, ranging from 15 to 100 µg/L with a low detection down to 5 µg/L. Moreover, the proposed sensor was successfully utilized to measure glyphosate in real samples, indicating a promising application in pesticide residues detection.


Assuntos
Nanopartículas Metálicas , Prata , DNA/genética , Glicina/análogos & derivados , Humanos
5.
Food Chem ; 367: 130661, 2022 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-34348197

RESUMO

Cow (CwC) and camel casein (CaC) hydrolysates were generated using Alcalase™ (CwCA and CaCA) and Pronase-E (CwCP and CaCP) each for 3 and 6 h, and investigated for their potential to inhibit key lipid digesting enzymes i.e., pancreatic lipase (PL) and cholesteryl esterase (CE). Results revealed stronger PL and CE inhibition by CaC hydrolysates compared to CwC. Potent hydrolysates (CwCP-3 h and CaCA-6 h) upon simulated gastrointestinal digestion (SGID) showed significant improvement in inhibition of both PL and CE. However, both the SGID hydrolysates showed similar extent of PL and CE inhibition and were further sequenced for peptide identification. Peptides MMML, FDML, HLPGRG from CwC and AAGF, MSNYF, FLWPEYGAL from CaC hydrolysates were predicted to be most active PL inhibitory peptides. Peptide LP found in both CwC and CaC hydrolysates was predicted as active CE inhibitor. Thus, CwC and CaC could be potential source of peptides with promising CE and PL inhibitory properties.


Assuntos
Caseínas , Esterol Esterase , Animais , Camelus , Bovinos , Digestão , Feminino , Hidrólise , Lipase , Peptídeos , Hidrolisados de Proteína , Esterol Esterase/genética
6.
Ann Lab Med ; 42(1): 36-46, 2022 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-34374347

RESUMO

Background: The emergence of carbapenemase-producing Enterobacteriaceae (CPE) represents a major clinical problem. Recently, the occurrence of CPE has increased globally, but epidemiological patterns vary across region. We report the trends in the genotypic distribution and antimicrobial susceptibility of CPE isolated from rectal and clinical samples during a four-year period. Methods: Between January 2016 and December 2019, 1,254 nonduplicated CPE isolates were obtained from four university hospitals in Korea. Carbapenemase genotypes were determined by multiplex real-time PCR. Antimicrobial susceptibility was profiled using the Vitek 2 system (bioMérieux, Hazelwood, MO, USA) or MicroScan Walkaway-96 system (Siemens West Sacramento, CA, USA). The proportions of carbapenemase genotypes and nonsusceptibility were analyzed using Pearson's chi-square test. Results: Among the 1,254 CPE isolates, 486 (38.8%), 371 (29.6%), 357 (28.5%), 8 (0.6%), 8 (0.6%), and 24 (1.9%) were Klebsiella pneumoniae carbapenemase (KPC), oxacillinase (OXA)-48-like, New Delhi metallo-ß-lactamase (NDM), imipenemase (IMP), Verona integron-encoded metallo-ß-lactamase (VIM), and multiple producers, respectively. The predominant species was K. pneumoniae (72.6%), followed by Escherichia coli (6.5%). More than 90% of the isolates harboring KPC, NDM, and OXA-48-like were nonsusceptible to cephalosporins, aztreonam, and carbapenems. Conclusions: The impact of CPE is primarily due to KPC-, NDM-, and OXA-48-like-producing K. pneumoniae isolates. Isolates carrying these carbapenemase are mostly multidrug-resistant. Control strategies based on these genotypic distributions and antimicrobial susceptibilities of CPE isolates are required.


Assuntos
Anti-Infecciosos , Enterobacteriáceas Resistentes a Carbapenêmicos , Infecções por Enterobacteriaceae , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Infecções por Enterobacteriaceae/epidemiologia , Genótipo , Hospitais Universitários , Humanos , Klebsiella pneumoniae , Testes de Sensibilidade Microbiana , República da Coreia , beta-Lactamases/genética
7.
Ann Lab Med ; 42(1): 54-62, 2022 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-34374349

RESUMO

Background: Associations between IgA nephropathy (IgAN) and HLA-DRB1 and -DQB1 alleles have been reported in several ethnic groups. We investigated the association of HLA-DRB1 and -DQB1 alleles with the predisposition for IgAN and disease progression to end-stage kidney disease (ESKD) in Korean patients. Methods: We analyzed HLA-DRB1 and -DQB1 genotypes in 399 IgAN patients between January 2000 and January 2019 using a LIFECODES sequence-specific oligonucleotide (SSO) typing kit (Immucor, Stamford, CT, USA) or a LABType SSO Typing Test (One Lambda, Canoga Park, CA, USA). Alleles with a significant difference in two-digit resolution were further analyzed using in-house sequence-based typing and sequence-specific primer PCR. As controls, 613 healthy hematopoietic stem cell donors were included. Kidney survival was analyzed in 281 IgAN patients with available clinical and laboratory data using Cox regression analysis. Where needed, P-values were adjusted using Bonferroni correction. Results: The allele frequencies of HLA-DRB1*04:05 (corrected P [Pc]<0.001), -DQB1 *04:01 (Pc=0.048), and -DQB1*03:02 (Pc=0.021) were significantly higher in IgAN patients than in controls, whereas those of HLA-DRB1*07:01, -DRB1*15:01, -DQB1*02:02, and -DQB1*06:02 (Pc<0.001 for all) were significantly lower in IgAN patients than in controls. The allele frequency of HLA-DQB1*05:03 (Pc=0.016) was significantly lower in the ESKD group than in the non-ESKD group; however, there was no significant difference for ESKD progression between these groups. Conclusions: We report novel associations of HLA-DRB1*15:01, DQB1*02:02, -DQB1*03:02, and -DQB1*04:01 with IgAN. Further studies of HLA alleles associated with IgAN progression in a larger cohort and in various ethnic groups are needed.


Assuntos
Glomerulonefrite por IGA , Alelos , Predisposição Genética para Doença , Glomerulonefrite por IGA/diagnóstico , Glomerulonefrite por IGA/genética , Cadeias HLA-DRB1/genética , Teste de Histocompatibilidade , Humanos , República da Coreia
8.
Ann Lab Med ; 42(1): 79-88, 2022 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-34374352

RESUMO

Background: Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are genomic imprinting disorders that are mainly caused by a deletion on 15q11-q13, the uniparental disomy of chromosome 15, or an imprinting defect. We evaluated the utility of methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) as a diagnostic tool and for demonstrating the relationship between molecular mechanisms and clinical presentation. Methods: We performed MS-MLPA using DNA samples from 93 subjects (45 PWS, 24 AS, and 24 non-PWS/AS controls) who had previously undergone MS-PCR for the diagnosis of PWS/AS. We compared the results of both assays, and patients' clinical phenotypes were reviewed retrospectively. Results: MS-MLPA showed a 100% concordance rate with MS-PCR. Among the 45 PWS patients, 26 (57.8%) had a deletion of 15q11-q13, and the others (42.2%) had uniparental disomy 15 or an imprinting defect. Among the 24 AS patients, 16 (66.7%) had a deletion of 15q11-q13, 7 AS patients (29.2%) had uniparental disomy 15 or an imprinting defect, and one AS patient (4.2%) showed an imprinting center deletion. Conclusions: MS-MLPA has clinical utility for the diagnosis of PWS/AS, and it is superior to MS-PCR in that it can identify the molecular mechanism underlying the disease.


Assuntos
Síndrome de Angelman , Síndrome de Prader-Willi , Síndrome de Angelman/diagnóstico , Síndrome de Angelman/genética , Cromossomos Humanos Par 15/genética , Metilação de DNA , Humanos , Metilação , Reação em Cadeia da Polimerase Multiplex , Síndrome de Prader-Willi/diagnóstico , Síndrome de Prader-Willi/genética , Estudos Retrospectivos
9.
J Cell Sci ; 135(5)2022 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-34028531

RESUMO

Lipid droplets (LDs) are globular subcellular structures that store neutral lipids. LDs are closely associated with the endoplasmic reticulum (ER) and are limited by a phospholipid monolayer harboring a specific set of proteins. Most of these proteins associate with LDs through either an amphipathic helix or a membrane-embedded hairpin motif. Here, we address the question of whether integral membrane proteins can localize to the surface of LDs. To test this, we fused perilipin 3 (PLIN3), a mammalian LD-targeted protein, to ER-resident proteins. The resulting fusion proteins localized to the periphery of LDs in both yeast and mammalian cells. This peripheral LD localization of the fusion proteins, however, was due to a redistribution of the ER around LDs, as revealed by bimolecular fluorescence complementation between ER- and LD-localized partners. A LD-tethering function of PLIN3-containing membrane proteins was confirmed by fusing PLIN3 to the cytoplasmic domain of an outer mitochondrial membrane protein, OM14. Expression of OM14-PLIN3 induced a close apposition between LDs and mitochondria. These data indicate that the ER-LD junction constitutes a barrier for ER-resident integral membrane proteins.


Assuntos
Gotículas Lipídicas , Proteínas de Membrana , Animais , Retículo Endoplasmático/genética , Proteínas de Membrana/genética , Fosfolipídeos , Saccharomyces cerevisiae
10.
Talanta ; 236: 122813, 2022 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-34635209

RESUMO

Bacillus thuringiensis (Bt) is used as a bioinsecticide since it effectively kills insect larvae. Bt is also genetically similar to Bacillus cereus (Bc), a well recognized foodborne human pathogen; they are both members of the Bacillus cereus group (BC group). Although approved Bt bioinsecticide products have been confirmed to be non-pathogenic to humans, close monitoring of Bt during dissemination is important for cost considerations and to limit impact on biodiversity towards nontarget organisms. As such, developing rapid, sensitive, and specific tools for quantitative detection of Bt spores during and following spray operations is highly desirable. The goals of this study were to investigate commercially available detection reagents for sensitivity and selectivity in detecting Bt spores, and then functionalize a surface of (001) GaAs used in photonic biosensing. To achieve these goals, we (1) screened commercial antibodies for their capacity to bind recombinant proteins from Bt spores, (2) screened antibodies and aptamers for their sensitivity and selectivity against Bt spores, and (3) tested the efficiency of selected antibodies and aptamers in capturing Bt spores on the surface of functionalized GaAs biochips. Seven genes encoding Bt spore proteins were cloned and expressed in Escherichia coli. The binding of each purified spore antigen was tested by commercially available polyclonal and monoclonal antibodies claimed to exclusively target spores. Of the seven targets, Bacillus collagen-like protein A, was the most abundant protein on Bt spores and demonstrated the strongest binding affinity to all test antibodies. The commercial antibodies (Abs) were also tested for specificity to BC Group versus non-BC Group spores. Three of six commercial antibodies showed selectivity to Bt spores, with recombinant Abs providing the most robust lower range of detection (102 to 6 × 103 spores/mL). The sensitivity and selectivity of three published DNA aptamer sequences demonstrated a wide range of detection sensitivity for Bt spores. Two of the three test aptamers also showed reasonable selectivity towards Bt spores while the third demonstrated reactivity to non-BC Group B. megaterium and B. subtilis. Of the reagents tested, a thiolated aptamer and llama recombinant Ab showed highest Bt spore capture efficiency as measured by spore coverage of the GaAs surface. These results confirm that the selected aptamer and llama rAb can be considered strong candidates for the development of GaAs-based biosensing devices.


Assuntos
Bacillus anthracis , Bacillus thuringiensis , Técnicas Biossensoriais , Arsenicais , Bacillus thuringiensis/genética , Gálio , Humanos , Esporos Bacterianos
11.
Talanta ; 236: 122821, 2022 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-34635211

RESUMO

Well-defined structures and compositions of nucleic acids afford oligonucleotide probes with unique chemical properties and biological functions for various biosensing applications. Herein, a unique and special oligonucleotide probe, named multifunction-integrated linear oligonucleotide probe (MI-LOP), was facile designed and reported for label-free and turn-on fluorescent detection of the codon component of genetically modified organisms (GMOs). The MI-LOP contains four different functional regions including recognition of target, serving as polymerization template, and creating polymerization primer-linked G-quadruplex (PP-G-quadruplex). Without the aid of any other oligonucleotides, the introduction of target DNA can make each function of the MI-LOP executed one-by-one, during which the species of target DNA, target analogue, and PP-G-quadruplex can be cyclically utilized and in turn induce a multiplex signal amplification responsible for substantial collection of the G-quadruplex moieties under isothermal conditions. The stable G-quadruplexes can combine with N-methyl mesoporphyrin IX (NMM) and function as efficient fluorescence light-up probes, rapidly leading to a dramatic increase in the fluorescence intensity for the amplified detection of the target codon component. Our results strongly demonstrate that the developed MI-LOP with multiplex amplification effect confers the sensing strategy a high sensitivity and specificity for quantitative and qualitative detection of the target codon. And it has also been successfully applied for analyzing target codon in the complex extractions of soybean. The achievements highlight the significance of using oligonucleotide probes as promising analytical tools to promote the basic biochemical research and help in food and environmental analysis.


Assuntos
Quadruplex G , DNA/genética , Fluorescência , Sondas de Oligonucleotídeos/genética , Plantas Geneticamente Modificadas
12.
Talanta ; 236: 122846, 2022 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-34635236

RESUMO

Simultaneous detection of multiple microRNAs (miRNAs) with high sensitivity can give accurate and reliable information for clinical applications. By uniformly anchoring hairpin probes on the surface of DNA nanolantern, a three-dimensional DNA nanostructure contains abundant and adjustable modification sites, highly integrated DNA nanoprobes were designed and developed as catalytic hairpin assembly (CHA)-based signal amplifiers for enzyme-free signal amplification detection of target miRNAs. The nanolantern-based CHA (NLC) amplifiers, which were facilely prepared via a simple "one-pot" annealing method, showed enhanced biostability, improved cell internalization efficiency, accelerated CHA reaction kinetics, and increased signal amplification capability compared to the single-stranded DNA hairpin probes used in traditional CHA reaction. By co-assembling multiple hairpin probes on a DNA nanolantern surface, as-prepared NLC amplifiers were demonstrated to work well for highly sensitive and specific imaging, expression level fluctuation analysis of two miRNAs in living cells, and miRNAs-guided tumor imaging in living mice. The proposed DNA nanolantern-based nanoamplifier strategy might provide a feasible way to promote the cellular and in vivo applications of nucleic acid probes.


Assuntos
Técnicas Biossensoriais , MicroRNAs , Animais , Catálise , DNA/genética , Camundongos , MicroRNAs/genética , Sondas de Ácido Nucleico
13.
Talanta ; 236: 122902, 2022 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-34635273

RESUMO

Rapid diagnosis of tuberculosis disease (TB) still remained a pressing need for TB control efforts all over the world. However, the existing detection approaches cannot satisfy demand of rapid detection of clinical Mycobacterium tuberculosis (M. tuberculosis) because of the long detection time and high cost. Herein, we proposed a new M. tuberculosis piezoelectric sensor based on AuNPs-mediated enzyme assisted signal amplification. A hairpin-shaped DNA duplex with a protrusion of the 3' end was designed. In the presence of specific 16 S rDNA fragment of M. tuberculosis, the hairpin probe was opened, which triggered the selective cleavage of hairpin probe by Exonuclease III (Exo III), resulting in the release of uncut DNA probe and target DNA. The released target DNA hybridized with another hairpin-shaped DNA duplex, and a new digestion cycle was started, thus generating large amounts of uncut DNA probes. The uncut DNA was pulled to the electrode surface by the hybridization with capture probe modified on the electrode. Subsequently detection probe labeled AuNPs was hybridized with uncut DNA and entered between the two electrodes. The AuNPs linked to hybridized detection probe were grown in the HAuCl4 and Nicotinamide adenine dinucleotide (NADH) solution and offered the conductive connection between the gaps of electrode. The changes were monitored by the piezoelectric sensor. The piezoelectric biosensor could achieve a detection of M. tuberculosis (102-108 CFU mL-1) within 3 h, the detection limit (LOD) was 30 CFU mL-1. The methodology could be transformed into different microbial targets, which is suitable for further development of small portable equipment and multifunctional detection.


Assuntos
Técnicas Biossensoriais , Nanopartículas Metálicas , Mycobacterium tuberculosis , DNA Ribossômico , Ouro , Mycobacterium tuberculosis/genética
14.
Ann Lab Med ; 42(2): 196-202, 2022 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-34635613

RESUMO

Background: Identifying the causal pathogen of encephalitis remains a clinical challenge. A 50-year-old man without a history of neurological disease was referred to our department for the evaluation of an intracranial lesion observed on brain magnetic resonance imaging (MRI) scans, and the pathology results suggested protozoal infection. We identified the species responsible for encephalitis using thymine-adenine (TA) cloning, suitable for routine clinical practice. Methods: We extracted DNA from a paraffin-embedded brain biopsy sample and performed TA cloning using two universal eukaryotic primers targeting the V4-5 and V9 regions of the 18S rRNA gene. The recombinant plasmids were extracted, and the inserted amplicons were identified by Sanger sequencing and a homology search of sequences in the National Center for Biotechnology Information Basic Local Alignment Search Tool. Results: The infection was confirmed to be caused by the free-living amoeba Balamuthia mandrillaris. Two of 41 colonies recombinant with 18S V4-5 primers and 35 of 63 colonies recombinant with the 18S V9 primer contained B. mandrillaris genes; all other colonies contained human genes. Pathogen-specific PCR ruled out Entamoeba histolytica, Naegleria fowleri, Acanthamoeba spp., and Toxoplasma gondii infections. Conclusions: This is the first report of B. mandrillaris-induced encephalitis in Korea based on molecular identification. TA cloning with the 18S rRNA gene is a feasible and affordable diagnostic tool for the detection of infectious agents of unknown etiology.


Assuntos
Balamuthia mandrillaris , Encefalite , Adenina , Balamuthia mandrillaris/genética , Clonagem Molecular , Encefalite/diagnóstico , Eucariotos , Humanos , Masculino , Pessoa de Meia-Idade , Timina
15.
Ann Lab Med ; 42(2): 203-212, 2022 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-34635614

RESUMO

Background: Extraintestinal pathogenic Escherichia coli (ExPEC) causes various infections, including urinary tract infection (UTI), sepsis, and neonatal meningitis. ExPEC strains have virulence factors (VFs) that facilitate infection by allowing bacterial cells to migrate into and multiply within the host. We compared the microbiological characteristics of ExPEC isolates from blood and urine specimens from UTI patients. Methods: We conducted a single-center, prospective study in an 855-bed tertiary-care hospital in Korea. We consecutively recruited 80 hospitalized UTI patients with E. coli isolates, which were isolated from blood and/or urine, and urine alone between March 2019 and May 2020. We evaluated the 80 E. coli isolates for the presence of bacterial genes encoding the sequence types (STs), antimicrobial resistance, and VFs using whole-genome sequencing (WGS). Results: We found no significant differences in STs, antimicrobial resistance patterns, or VFs between isolates from blood and urine specimens. ST131, a pandemic multidrug-resistant clone present in both blood and urine, was the most frequent ST (N=19/80, 24%), and ST131 isolates carried more virulence genes, especially, tsh and espC, than non-ST131 isolates. The virulence scores of the ST131 group and the ST69, ST95, and ST1193 groups differed significantly (P<0.05). Conclusions: We found no STs and VFs associated with bacteremia in WGS data of E. coli isolates from UTI patients. ST131 was the most frequent ST among UTI causing isolates and carried more VF genes than non-ST131 isolates.


Assuntos
Bacteriemia , Infecções por Escherichia coli , Infecções Urinárias , Antibacterianos/farmacologia , Bacteriemia/diagnóstico , Escherichia coli/genética , Infecções por Escherichia coli/diagnóstico , Humanos , Estudos Prospectivos , Infecções Urinárias/diagnóstico , Fatores de Virulência/genética
16.
Ann Lab Med ; 42(2): 213-248, 2022 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-34635615

RESUMO

Background: Sequence-based identification is one of the most effective methods for species-level identification of nontuberculous mycobacteria (NTM). However, it is time-consuming because of the bioinformatics processes involved, including sequence trimming, consensus sequence generation, and public database searches. We developed a simple and fully automated software that enabled species-level identification of NTM from trace files, SnackNTM (https://github.com/Young-gonKim/SnackNTM). Methods: JAVA programing language was used for software development. The SnackNTM diagnostic algorithm utilized 16S rRNA gene sequences, according to the Clinical & Laboratory Standards Institute guidelines, and an rpoB gene region was adjunctively utilized to narrow down the species. The software performance was validated using trace files of 234 clinical cases, comprising 217 consecutive cases and 17 additionally selected cases of unique species. Results: SnackNTM could analyze multiple cases at once, and all the bioinformatics processes required for sequence-based NTM identification were automatically performed with a single mouse click. SnackNTM successfully identified 95.9% (208/217) of consecutive clinical cases, and the results showed 99.0% (206/208) agreement with manual classification results. SnackNTM successfully identified all 17 cases of unique species. In a processing time comparison test, the analysis and reporting of 30 cases, which took 150 minutes manually, took only 40 minutes with SnackNTM. Conclusions: SnackNTM is expected to reduce the workload for NTM identification, especially in clinical laboratories that process large numbers of cases.


Assuntos
Micobactérias não Tuberculosas , Software , Micobactérias não Tuberculosas/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
17.
Ann Lab Med ; 42(2): 268-273, 2022 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-34635618

RESUMO

Salmonella is one of the major causes of food-borne infections. We investigated the serotype distribution and antimicrobial resistance of Salmonella isolates collected in Korea between January 2016 and December 2017. In total, 669 Salmonella isolates were collected from clinical specimens at 19 university hospitals. Serotyping was performed according to the Kauffmann-White scheme, and antimicrobial susceptibility was tested using Sensititre EUVSEC plates or disk diffusion. Among the strains, C (39.8%) and B (36.6%) were the most prevalent serogroups. In total, 51 serotypes were identified, and common serotypes were S. enterica serovar I 4,[5],12:i:- (16.7%), S. Enteritidis (16.1%), S. Bareilly (14.6%), S. Typhimurium (9.9%), and S. Infantis (6.9%). The resistance rates to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole were 32.6%, 12.1%, and 8.4%, respectively. The resistance rates to cefotaxime and ciprofloxacin were 8.1% and 3.0%, respectively, while 5.4% were multidrug-resistant. S. enterica serovar I 4,[5],12:i:- and S. Enteritidis were highly prevalent, and there was an increase in rare serotypes. Multidrug resistance and ciprofloxacin resistance were highly prevalent. Periodic investigations of Salmonella serotypes and antimicrobial resistance are needed.


Assuntos
Antibacterianos , Farmacorresistência Bacteriana , Antibacterianos/farmacologia , Humanos , República da Coreia , Salmonella/genética , Sorogrupo
18.
Food Chem ; 368: 130818, 2022 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-34403998

RESUMO

High value-added utilization of different aquatic by-products is an increasingly urgent issue in aquatic science and industry. In this work, the effects of extraction methods on the molecular characteristics, structural properties, functional properties, and Pickering emulsion stabilization behaviors of silver carp fin gelatins were comprehensively studied. All the results showed molecular characteristics of silver carp fin gelatin was the key parameter to determine their functional properties such as wide gel strength range, excellent water-holding capacity, and excellent Pickering emulsion stabilization ability. The Pickering emulsion stabilization mechanisms of fin gelatins involved an "extraction method - protein molecular characteristics - fat-binding capacity - droplet structure - water phase properties - Pickering emulsion stability" route. This work could be helpful to understand the basic information on how the molecular characteristics determine the functions of gelatins. It would be also useful for the high value-added utilization of aquatic by-products and gelatins.


Assuntos
Carpas , Gelatina , Animais , Carpas/genética , Emulsões , Água
19.
Food Chem ; 368: 130815, 2022 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-34411856

RESUMO

The present investigation aimed at assessing the impact of biological processing techniques on bio-and techno-functional characteristics of foxtail millet (Setaria italica L.). Grains were exposed to soaking, germination, fermentation and combination of aforesaid treatments and significant variation (p < 0.05) in anti-nutritional factors, in vitro starch and protein digestibility, bioactive constituents and associated antioxidant potential was noted. Bioprocessed flours were characterized by altered functional properties due to hydrolytic action of activated enzymes. ATR-FTIR spectra and X-ray diffraction patterns revealed structural variation in macromolecular arrangement, synthesis of bioactive compounds in bioprocessed flours and slight reduction in the crystallinity of starch molecules. Bioprocessed flours exhibited degraded protein matrix; however, only fermentation and combination treatments caused hydrolysis of granular starch. Principal component analysis was employed to validate the differences in processing treatments and observations. The results are suggestive that bioprocessed flours could serve as potential ingredients with improved techno-and bio-functionality in valorized cereal products.


Assuntos
Setaria (Planta) , Farinha , Germinação , Nutrientes , Setaria (Planta)/genética , Amido
20.
Food Chem ; 368: 130816, 2022 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-34416489

RESUMO

Acrylamide (AA), a potential carcinogen, is commonly formed in foods rich in carbohydrates at high heat. It is known that AA-induced mitochondrial dysfunction is responsible for its toxicity. Previously we found AA exposure increased miR-27a-5p expression in livers of SD rats. Here, the regulation mechanism of miR-27a-5p in mitochondrial dysfunction was investigated in rat liver cell lines (IAR20) and SD rats. The results showed that the overexpressed miR-27a-5p contributes to modulating mitochondrial dysfunction and Btf3 is identified as its target gene. The knockdown of Btf3 increases the cleaved PARP1 level and the phosphorylation of ATM and p53, which results in mitochondria-dependent apoptosis. Therefore, the miR-27a-5p-Btf3-ATM-p53 axis might play a vital role in the promotion of AA-induced cell apoptosis through disrupting mitochondrial structure and function. This would provide a potential target for the assessment and intervention of AA toxicity.


Assuntos
MicroRNAs , Acrilamida/toxicidade , Animais , Apoptose , MicroRNAs/genética , Mitocôndrias/genética , Ratos , Ratos Sprague-Dawley
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