keyword
https://read.qxmd.com/read/38062356/lokatt-a-hybrid-dna-nanopore-basecaller-with-an-explicit-duration-hidden-markov-model-and-a-residual-lstm-network
#1
JOURNAL ARTICLE
Xuechun Xu, Nayanika Bhalla, Patrik Ståhl, Joakim Jaldén
BACKGROUND: Basecalling long DNA sequences is a crucial step in nanopore-based DNA sequencing protocols. In recent years, the CTC-RNN model has become the leading basecalling model, supplanting preceding hidden Markov models (HMMs) that relied on pre-segmenting ion current measurements. However, the CTC-RNN model operates independently of prior biological and physical insights. RESULTS: We present a novel basecaller named Lokatt: explicit duration Markov model and residual-LSTM network...
December 7, 2023: BMC Bioinformatics
https://read.qxmd.com/read/37656070/the-effect-of-crowding-on-the-accuracy-of-3-dimensional-printing
#2
JOURNAL ARTICLE
Tonya Spangler, Rami Ammoun, Caroline K Carrico, Sompop Bencharit, Eser Tüfekçi
INTRODUCTION: Effective aligner hygiene is recognized as an important part of orthodontic treatments and oral hygiene. However, there is no effective cleansing method to clean and disinfect the removable aligners. METHODS: In this study, we incorporated tannic acid (TA) with cetylpyridinium chloride (CPC) to develop the TA-CPC complex. The antibacterial property of 15.8 mg/mL TA-CPC against Escherichia coli and Staphylococcus aureus was evaluated in vitro, which were compared with 5...
September 1, 2023: American Journal of Orthodontics and Dentofacial Orthopedics
https://read.qxmd.com/read/37340457/beem-fast-and-faithful-conversion-of-mmcif-format-structure-files-to-pdb-format
#3
JOURNAL ARTICLE
Chengxin Zhang
BACKGROUND: Although mmCIF is the current official format for deposition of protein and nucleic acid structures to the protein data bank (PDB) database, the legacy PDB format is still the primary supported format for many structural bioinformatics tools. Therefore, reliable software to convert mmCIF structure files to PDB files is needed. Unfortunately, existing conversion programs fail to correctly convert many mmCIF files, especially those with many atoms and/or long chain identifies...
June 20, 2023: BMC Bioinformatics
https://read.qxmd.com/read/37123603/biocatalytic-synthesis-of-homochiral-2-hydroxy-4-butyrolactone-derivatives-by-tandem-aldol-addition-and-carbonyl-reduction
#4
JOURNAL ARTICLE
Carlos J Moreno, Karel Hernández, Samantha Gittings, Michael Bolte, Jesús Joglar, Jordi Bujons, Teodor Parella, Pere Clapés
Chiral 2-hydroxy acids and 2-hydroxy-4-butyrolactone derivatives are structural motifs often found in fine and commodity chemicals. Here, we report a tandem biocatalytic stereodivergent route for the preparation of these compounds using three stereoselective aldolases and two stereocomplementary ketoreductases using simple and achiral starting materials. The strategy comprises (i) aldol addition reaction of 2-oxoacids to aldehydes using two aldolases from E. coli , 3-methyl-2-oxobutanoate hydroxymethyltransferase (KPHMT Ecoli ), 2-keto-3-deoxy-l-rhamnonate aldolase (YfaU Ecoli ), and trans - o -hydroxybenzylidene pyruvate hydratase-aldolase from Pseudomonas putida (HBPA Pputida ) and (ii) subsequent 2-oxogroup reduction of the aldol adduct by ketopantoate reductase from E...
April 21, 2023: ACS Catalysis
https://read.qxmd.com/read/37083406/development-of-a-data-driven-integrative-model-of-a-bacterial-chromosome
#5
JOURNAL ARTICLE
Abdul Wasim, Palash Bera, Jagannath Mondal
The chromosome of archetypal bacteria E. coli is known for a complex topology with a 4.6 × 106 base pairs (bp) long sequence of nucleotides packed within a micrometer-sized cellular confinement. The inherent organization underlying this chromosome eludes general consensus due to the lack of a high-resolution picture of its conformation. Here we present our development of an integrative model of E. coli at a 500 bp resolution (https://github.com/JMLab-tifrh/ecoli_finer), which optimally combines a set of multiresolution genome-wide experimentally measured data within a framework of polymer based architecture...
April 21, 2023: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/37010520/pdc-a-highly-compact-file-format-to-store-protein-3d-coordinates
#6
JOURNAL ARTICLE
Chengxin Zhang, Anna Marie Pyle
Recent improvements in computational and experimental techniques for obtaining protein structures have resulted in an explosion of 3D coordinate data. To cope with the ever-increasing sizes of structure databases, this work proposes the Protein Data Compression (PDC) format, which compresses coordinates and temperature factors of full-atomic and Cα-only protein structures. Without loss of precision, PDC results in 69% to 78% smaller file sizes than Protein Data Bank (PDB) and macromolecular Crystallographic Information File (mmCIF) files with standard GZIP compression...
April 3, 2023: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/36405344/trangru-focusing-on-both-the-local-and-global-information-of-molecules-for-molecular-property-prediction
#7
JOURNAL ARTICLE
Jing Jiang, Ruisheng Zhang, Jun Ma, Yunwu Liu, Enjie Yang, Shikang Du, Zhili Zhao, Yongna Yuan
Molecular property prediction is an essential but challenging task in drug discovery. The recurrent neural network (RNN) and Transformer are the mainstream methods for sequence modeling, and both have been successfully applied independently for molecular property prediction. As the local information and global information of molecules are very important for molecular properties, we aim to integrate the bi-directional gated recurrent unit (BiGRU) into the original Transformer encoder, together with self-attention to better capture local and global molecular information simultaneously...
November 14, 2022: Appl Intell (Dordr)
https://read.qxmd.com/read/36049365/the-oncogene-abl1-regulates-the-inflammatory-response-of-innate-immunity-via-mediating-traf6-ubiquitination
#8
JOURNAL ARTICLE
Feng Xu, Wenjing Yao, Yuanyuan Xue, Qi Sun, Chunxia Cao
The oncogene ABL1 plays an important role in various cancers, while its roles remain unclear in pneumonia. This study aims to investigate the roles of ABL1 in pneumonia and the underlying mechanisms. RNA sequencing was used to determine the expressions of multiple kinases in the PBMCs. A series of overexpression and knockout cell lines were constructed. Besides, an intranasal lung infection mouse model was pre-treated with asciminb. ELISAs and qPCR were used to determine the levels of target genes. In addition, STRING Interaction Network and Immunoblotting assays were used to determine the interaction between target proteins...
September 2022: Immunobiology
https://read.qxmd.com/read/35590263/the-ompa-of-commensal-escherichia-coli-of-crc-patients-affects-apoptosis-of-the-hct116-colon-cancer-cell-line
#9
JOURNAL ARTICLE
Mahsa Mirzarazi, Soroor Bashiri, Ali Hashemi, Mahmoud Vahidi, Bahram Kazemi, Mojgan Bandehpour
BACKGROUND: Colorectal cancer ranks third globally among all types of cancers. Dysbiosis of the gut microbiota of people with CRC is one of the effective agents in the tumorigenesis and metastasis in this type of cancer. The population of Escherichia coli strains, a component of gut microbiota, is increased in the gut of people with CRC compared with healthy people. So, E.coli strains isolated from these patients may have a role in tumorigenesis. Because the most isolated strains belong to the B2 phylogenuetic group, there seems to be a linkage between the bacterium components and malignancy...
May 19, 2022: BMC Microbiology
https://read.qxmd.com/read/34860150/ectyper-in-silico-escherichia-coli-serotype-and-species-prediction-from-raw-and-assembled-whole-genome-sequence-data
#10
JOURNAL ARTICLE
Kyrylo Bessonov, Chad Laing, James Robertson, Irene Yong, Kim Ziebell, Victor P J Gannon, Anil Nichani, Gitanjali Arya, John H E Nash, Sara Christianson
Escherichia coli is a priority foodborne pathogen of public health concern and phenotypic serotyping provides critical information for surveillance and outbreak detection activities. Public health and food safety laboratories are increasingly adopting whole-genome sequencing (WGS) for characterizing pathogens, but it is imperative to maintain serotype designations in order to minimize disruptions to existing public health workflows. Multiple in silico tools have been developed for predicting serotypes from WGS data, including SRST2, SerotypeFinder and EToKi EBEis, but these tools were not designed with the specific requirements of diagnostic laboratories, which include: speciation, input data flexibility (fasta/fastq), quality control information and easily interpretable results...
December 2021: Microbial Genomics
https://read.qxmd.com/read/32802068/impact-of-sequential-passaging-on-protein-expression-of-e-coli-using-proteomics-analysis
#11
JOURNAL ARTICLE
Mohammed S Alhajouj, Ghadah S Alsharif, Ahmed A Mirza
Urinary tract infection (UTI) is one of the most prevalent bacterial infections in the world affecting the bladder and the kidney. Escherichia coli ( E. coli ) is the main causative agent of 80-90% of community-acquired UTIs, about 40% of nosocomial UTIs, and 25% of recurrent UTIs. The field of proteomics has emerged as a great tool to analyze expressed proteins to identify possible biomarkers associated with many pathological states and, to the same extent, those associated with bacterial pathogenesis and their ability to cause recurrent infections...
2020: International Journal of Microbiology
https://read.qxmd.com/read/31863902/the-potential-sensing-molecules-and-signal-cascades-for-protecting-teleost-fishes-against-lipopolysaccharide
#12
JOURNAL ARTICLE
Yunkun Li, Puzhen Xia, Jiayu Wu, Anqi Huang, Guixian Bu, Fengyan Meng, Fanli Kong, Xiaohan Cao, Xingfa Han, Guozhi Yu, Xiaofu Pan, Shiyong Yang, Xianyin Zeng, Xiaogang Du
Lipopolysaccharide (LPS) is a classical pathogen-associated molecular pattern that can trigger strong inflammatory response mainly by TLR4-mediated signaling pathway in mammals, but the molecular mechanism of anti-LPS immunity is unclear in teleost fishes. In this study, we analyzed the gene expression features based on transcriptome analysis in Schizothorax prenanti (S. prenanti), after stimulation with two sources of LPS from Aeromonas hydrophila and Escherichia coli (Ah. LPS and Ecoli. LPS). 921 different expression genes (DEGs) after Ah...
February 2020: Fish & Shellfish Immunology
https://read.qxmd.com/read/31528640/-in-silico-analysis-of-suitable-signal-peptides-for-secretion-of-a-recombinant-alcohol-dehydrogenase-with-a-key-role-in-atorvastatin-enzymatic-synthesis
#13
JOURNAL ARTICLE
Mortaza Taheri-Anganeh, Seyyed Hossein Khatami, Zeinab Jamali, Amir Savardashtaki, Younes Ghasemi, Zohreh Mostafavi-Pour
An elevated cholesterol level might lead to cardiovascular disease (CVD). Statins block the cholesterol synthesis pathway in the liver. Atorvastatin is the most widespread statin worldwide and, its chemical synthesis requires toxic catalysts, resulting in environmental pollution. Hence, enzymatic synthesis of atorvastatin is desirable. This process could be done by Lactobacillus kefir alcohol dehydrogenase (LKADH). Therefore, recombinant enzyme secretion by Escherichia coli using signal peptides (SPs) might result in easy production and purification...
March 2019: Molecular Biology Research Communications
https://read.qxmd.com/read/31119279/in-vitro-and-in-vivo-evaluation-of-thyme-thymus-vulgaris-essential-oil-as-an-alternative-for-antibiotic-in-quail-diet
#14
JOURNAL ARTICLE
Naghmeh Dehghani, Mohsen Afsharmanesh, Mohammad Salarmoini, Hadi Ebrahimnejad
The thyme (Thymus vulgaris) essential oil was assessed as antibiotic growth promoter replacement in quail chick diet and in vitro test. In total, 250 day-old Japanese quail chicks (mixed sex) were allocated into 5 dietary treatments of 5 replications (6 females and 4 males in each cage with the size of 40× 90× 25 cm) under a completely randomized design. The dietary treatments were included the control diet, control diet without any additive, control diet plus 100 ppm flavophospholipol as an antibiotic growth promoter, control diet plus 200 ppm TVE, control diet plus 300 ppm TVE, and control diet plus 400 ppm Thymus vulgaris essential oil (TVE)...
May 22, 2019: Journal of Animal Science
https://read.qxmd.com/read/30498661/a-comprehensive-in-silico-characterization-of-bacterial-signal-peptides-for-the-excretory-production-of-anabaena-variabilis-phenylalanine-ammonia-lyase-in-escherichia-coli
#15
JOURNAL ARTICLE
Hajar Owji, Shiva Hemmati
Anabaena variabilis double mutant (C503S/C565S) phenylalanine ammonia-lyase (PAL) is an appealing enzyme in the enzyme-replacement therapy of phenylketonuria. Yet abundant production of this enzyme has been of concern for industrial production. In this study, we have characterized 1175 bacterial signal peptides (SPs) and identified the most efficient ones for the excretory production of mutant AvPAL. Analysis by SignalP 4.1 revealed that more than 61% of SPs had a D -score greater than 0.7, denoting to be highly efficient...
December 2018: 3 Biotech
https://read.qxmd.com/read/29884932/seasonal-assessment-and-apportionment-of-surface-water-pollution-using-multivariate-statistical-methods-sinos-river-southern-brazil
#16
JOURNAL ARTICLE
Darlan Daniel Alves, Roberta Plangg Riegel, Daniela Müller de Quevedo, Daniela Montanari Migliavacca Osório, Gustavo Marques da Costa, Carlos Augusto do Nascimento, Franko Telöken
Assessment of surface water quality is an issue of currently high importance, especially in polluted rivers which provide water for treatment and distribution as drinking water, as is the case of the Sinos River, southern Brazil. Multivariate statistical techniques allow a better understanding of the seasonal variations in water quality, as well as the source identification and source apportionment of water pollution. In this study, the multivariate statistical techniques of cluster analysis (CA), principal component analysis (PCA), and positive matrix factorization (PMF) were used, along with the Kruskal-Wallis test and Spearman's correlation analysis in order to interpret a water quality data set resulting from a monitoring program conducted over a period of almost two years (May 2013 to April 2015)...
June 8, 2018: Environmental Monitoring and Assessment
https://read.qxmd.com/read/29033918/dna-sequence-based-typing-of-the-cronobacter-genus-using-mlst-crispr-cas-array-and-capsular-profiling
#17
JOURNAL ARTICLE
Pauline Ogrodzki, Stephen J Forsythe
The Cronobacter genus is composed of seven species, within which a number of pathovars have been described. The most notable infections by Cronobacter spp. are of infants through the consumption of contaminated infant formula. The description of the genus has greatly improved in recent years through DNA sequencing techniques, and this has led to a robust means of identification. However some species are highly clonal and this limits the ability to discriminate between unrelated strains by some methods of genotyping...
2017: Frontiers in Microbiology
https://read.qxmd.com/read/29021229/in-vivo-generated-thrombin-and-plasmin-do-not-activate-the-complement-system-in-baboons
#18
JOURNAL ARTICLE
Ravi S Keshari, Robert Silasi, Cristina Lupu, Fletcher B Taylor, Florea Lupu
Sepsis concurrently activates both coagulation and complement systems. Although complement activation by bacteria is well documented, work in mice and in vitro suggests that coagulation proteases can directly cleave complement proteins. We aimed to determine whether generation of coagulation proteases in vivo can activate the complement cascade in 2 highly coagulopathic models. We compared temporal changes in activation biomarkers of coagulation (thrombin-antithrombin [TAT]), fibrinolysis (plasmin-antiplasmin [PAP]), and complement (C3b, C5a, C5b-9) in baboons infused with factor Xa (FXa) and phospholipids (FXa/phosphatidylcholine-phosphatidylserine [PCPS]) vs LD100 Escherichia coli We found that, albeit with different timing, both FXa/PCPS and E coli infusion led to robust thrombin and plasmin generation...
December 14, 2017: Blood
https://read.qxmd.com/read/28874523/-escherichia-coli-responds-to-environmental-changes-using-enolasic-degradosomes-and-stabilized-dicf-srna-to-alter-cellular-morphology
#19
JOURNAL ARTICLE
Oleg N Murashko, Sue Lin-Chao
Escherichia coli RNase E is an essential enzyme that forms multicomponent ribonucleolytic complexes known as "RNA degradosomes." These complexes consist of four major components: RNase E, PNPase, RhlB RNA helicase, and enolase. However, the role of enolase in the RNase E/degradosome is not understood. Here, we report that presence of enolase in the RNase E/degradosome under anaerobic conditions regulates cell morphology, resulting in E coli MG1655 cell filamentation. Under anaerobic conditions, enolase bound to the RNase E/degradosome stabilizes the small RNA (sRNA) DicF, i...
September 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/28479746/cloning-and-over-expression-of-non-coding-rna-rpra-in-e-coli-and-its-resistance-to-kanamycin-without-osmotic-shock
#20
JOURNAL ARTICLE
Azita Sahni, Mohammadreza Hajjari, Jamshid Raheb, Ali Mohammad Foroughmand, Morteza Asgari
Recent reports have indicated that small RNAs have key roles in the response of the E.coli to stress and also in the regulating of virulence factors. It seems that some small non-coding RNAs are involved in multidrug resistance. Previous studies have indicated that rprA can increase the tolerance to Kanamycin in RcsB-deficient Escherichia coli K-12 following osmotic shock. The current study aims to clone and over-express the non-coding RNA rprA in E.coli and investigate its effect on the bacterial resistance to Kanamycin without any osmotic shock...
2017: Bioinformation
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