National Center For Biotechnology Information Research Articles

Metagenomics and proteomics profiling of extracellular polymeric substances from municipal waste sludge and their application for soil and water bioremediation

This study assessed the components of anaerobically digested sludge, activated sludge, and microbial and extracellular polymeric substance (EPS) enzymes to identify the mechanisms underlying nitrogen removal and soil regeneration. 16S rRNA gene amplicon-based sequencing was used to determine the microbial community composition and the related National Center for Biotechnology Information (NCBI) protein database was used to construct a conventional library from the observed community. EPS components were identified using gel-free proteomic (Liquid Chromatography with tandem mass spectrometry-LC/MS/MS) methods. Alginate-like EPS from aerobically activated sludge have strong potential for soil aggregation and water-holding capacity, whereas total EPS from anaerobic sludge have significant potential for ammonia removal under salt stress. Fourier transform infrared spectroscopy (FTIR) revealed that both EPS may contain proteins, carbohydrates, humic compounds, uronic acid, and DNA and determined the presence of O–H, N–H, C–N, CO, and C–H functional groups. These results demonstrate that the overall enzyme activity may be inactivated at 30 g L-1 of salinity. An annotation found in Kyoto Encyclopedia of Genes and Genomes (KEGG)- KEGG Automatic Annotation Server (KAAS) revealed that the top two metabolic activities in the EPS generated from the anaerobic sludge were methane and nitrogen metabolism. Therefore, we focused on the nitrogen metabolism reference map 00910. EPS from the anaerobically digested sludge exhibited nitrate reductase, nitrite reductase, and dehydrogenase activities. Assimilatory nitrate reduction, denitrification, nitrification, and anammox removed ammonia biochemically. The influence of microbial extracellular metabolites on water-holding capacity and soil aggregation was also investigated. The KAAS-KEGG annotation server was used to identify the main enzymes in the activated sludge-derived alginate-like extracellular EPS (ALE-EPS) samples. These include hydrolases, oxidoreductases, lyases, ligases, and transporters, which contribute to soil fertility and stability. This study improves our understanding of the overall microbial community structure and the associated biochemical processes, which are related to distinct functional genes or enzymes involved in nitrogen removal and soil aggregation. In contrast to conventional methods, microbial association with proteomics can be used to investigate ecological relationships, establishments, key player species, and microbial responses to environmental changes. Linking the metagenome to off-gel proteomics and bioinformatics solves the problem of analyzing metabolic pathways in complex environmental samples in a cost-effective manner.

The Impact of Viral Infection on the Chemistries of the Earth's Most Abundant Photosynthesizes: Metabolically Talented Aquatic Cyanobacteria.

Cyanobacteria are the most abundant photosynthesizers on earth, and as such, they play a central role in marine metabolite generation, ocean nutrient cycling, and the control of planetary oxygen generation. Cyanobacteriophage infection exerts control on all of these critical processes of the planet, with the phage-ported homologs of genes linked to photosynthesis, catabolism, and secondary metabolism (marine metabolite generation). Here, we analyze the 153 fully sequenced cyanophages from the National Center for Biotechnology Information (NCBI) database and the 45 auxiliary metabolic genes (AMGs) that they deliver into their hosts. Most of these AMGs are homologs of those found within cyanobacteria and play a key role in cyanobacterial metabolism-encoding proteins involved in photosynthesis, central carbon metabolism, phosphate metabolism, methylation, and cellular regulation. A greater understanding of cyanobacteriophage infection will pave the way to a better understanding of carbon fixation and nutrient cycling, as well as provide new tools for synthetic biology and alternative approaches for the use of cyanobacteria in biotechnology and sustainable manufacturing.

The use of radiomics in magnetic resonance imaging for the pre-treatment characterisation of breast cancers: A scoping review.

Radiomics is an emerging field that aims to extract and analyse a comprehensive set of quantitative features from medical images. This scoping review is focused on MRI-based radiomic features for the molecular profiling of breast tumours and the implications of this work for predicting patient outcomes. A thorough systematic literature search and outcome extraction were performed to identify relevant studies published in MEDLINE/PubMed (National Centre for Biotechnology Information), EMBASE and Scopus from 2015 onwards. The following information was retrieved from each article: study purpose, study design, extracted radiomic features, machine learning technique(s), sample size/characteristics, statistical result(s) and implications on patient outcomes. Based on the study purpose, four key themes were identified in the included 63 studies: tumour subtype classification (n = 35), pathologically complete response (pCR) prediction (n = 15), lymph node metastasis (LNM) detection (n = 7) and recurrence rate prediction (n = 6). In all four themes, reported accuracies widely varied among the studies, for example, area under receiver characteristics curve (AUC) for detecting LNM ranged from 0.72 to 0.91 and the AUC for predicting pCR ranged from 0.71 to 0.99. In all four themes, combining radiomic features with clinical data improved the predictive models. Preliminary results of this study showed radiomics potential to characterise the whole tumour heterogeneity, with clear implications for individual-targeted treatment. However, radiomics is still in the pre-clinical phase, currently with an insufficient number of large multicentre studies and those existing studies are often limited by insufficient methodological transparency and standardised workflow. Consequently, the clinical translation of existing studies is currently limited.

Molecular detection and pyrG sequence analysis of Avibacterium paragallinarum using clinical samples of infraorbital exudates from layer chickens with infectious coryza symptoms in Indonesia.

Infectious coryza (IC) or snot, is caused by Avibacterium paragallinarum and leads to upper respiratory disease in poultry. Various diagnostic methods are available, including isolation and identification through bacterial culture and biochemical tests. However, the isolation and subsequent identification of A. paragallinarum are challenging because the bacteria are fastidious and require specific growth factors. This study aimed to detect A. paragallinarum in clinical samples taken from the exudate of the infraorbital sinus of layer hens showing clinical signs of IC. Samples were collected from 10 layer hens with IC symptoms. Following DNA extraction, HPG-2 polymerase chain reaction (PCR) assays were performed. The PCR amplicons underwent electrophoresis to determine those of the correct target size (511 bp), and these were sequenced. The resultant sequences were analyzed using the National Center for Biotechnology Information (NCBI) basic local alignment search tool. MEGA X was used for bioinformatics analysis. The presence of A. paragallinarum was confirmed by HPG-2 PCR in 4/10 samples. Bioinformatics analysis showed that the amino acid sequence of the samples and the A. paragallinarum reference sequences in the NCBI database were grouped within the same cluster. Furthermore, the nucleotide sequences showed 98.64%-100% of similarity with the reference sequences. The phylogenetic reconstruction of partial pyrG sequences from 55 A. paragallinarum strains/isolates deposited in GenBank confirmed that the four HPG-2 PCR-positive samples fell within the A. paragallinarum cluster, separate from the Pasteurella multocida, Avibacterium spp., and Rodentibacter pneumotropicus clusters. Avibacterium paragallinarum infection was molecularly confirmed in 4/10 (40%) samples by HPG-2 PCR amplicon detection. Clustering of the pyrG partial gene sequences revealed that the positive samples fell within the A. paragallinarum cluster.

First identification of Xanthomonas nasturtii as the cause of black rot of watercress in Hawaii.

Watercress (Nasturtium officinale) has been in continuous production in Hawaii for over a century and is part of the local diet. Black rot of watercress was first identified as caused by Xanthomonas nasturtii in Florida (Vicente et al., 2017), but symptoms of this disease have also been regularly observed in Hawaii production in all islands, mostly during the rainy season from December to April in areas with poor air circulation (McHugh & Constantinides, 2004). Initially, this disease was attributed to X. campestris due to similar symptoms to black rot of brassicas. Samples of watercress with symptoms that could be attributed to a bacterial disease including yellow spots and lesions on leaves and stunting and deformation of plants in more advanced stages, were collected from a farm in Aiea in the island of Oahu, Hawaii, in October 2017. Isolations were performed at the University of Warwick. Fluid from macerated leaves was streaked into plates of King's B (KB) medium and Yeast Dextrose Calcium Carbonate Agar (YDC). After 48-72 hrs incubation at 28°C, the plates showed a range of mixed colonies. Single cream-yellow mucoid colonies were sub-cultured several times and pure isolates including WHRI 8984 were stored at -76°C as previously described (Vicente et al., 2017). Colony morphology was observed in KB plates and, in contrast to the type strain from Florida (WHRI 8853 = NCPPB 4600), isolate WHRI 8984 did not cause browning of the medium. Pathogenicity was tested on four-week old watercress and Savoy cabbage cv. Wirosa F1 plants by inoculations on leaves as previously described (Vicente et al., 2017). WHRI 8984 did not produce symptoms when inoculated on cabbage but produced typical symptoms on watercress. A re-isolation from a leaf showing a V-shaped lesion, produced isolates with the same morphology, including isolate WHRI 10007A, that was also shown to be pathogenic to watercress therefore completing the Koch's postulates. Fatty acid profiling was performed on WHRI 8984 and 10007A and controls grown on trypticase soy broth agar (TSBA) plates at 28°C for 48 hrs as described by Weller et al. (2000). Profiles were compared with the RTSBA6 v6.21 library; as the database does not include X. nasturtii, the results were only interpreted at the genus level, and both isolates were shown to be Xanthomonas sp. For molecular analysis, DNA was extracted and the gyrB partial gene was amplified and sequenced as described by Parkinson et al. (2007). Comparisons with sequences available in the National Centre for Biotechnology Information (NCBI) databases using the Basic Local Alignment Search Tool (BLAST) showed that partial gyrB of WHRI 8984 and 10007A were identical to the type strain from Florida therefore confirming that they belong to X. nasturtii. For whole genome sequencing, genomic libraries for WHRI 8984 were prepared using Illumina's Nextera XT v2 kit and sequenced on a HiSeq Rapid Run flowcell. The sequences were processed as previously described (Vicente et al., 2017) and the whole genome assembly has been deposited in GenBank (accession QUZM00000000.1); the phylogenetic tree shows that WHRI 8984 is close, but not identical to the type strain. This is the first identification of X. nasturtii in watercress crops in Hawaii. Control of this disease generally involves the use of copper bactericides and minimizing moisture on leaves by reducing overhead irrigation and increasing air circulation (McHugh & Constantinides, 2004); seed testing might help to select batches that are disease free and, in longer term, breeding for disease resistance might produce cultivars that can be part of management strategies.

The Genus Ageratina (Asteraceae) in America: An Insight into its Chemistry and Pharmacological Potential.

Ageratina is an American genus of the tribe Eupatorieae (Asteraceae), comprising about 320 species. In Mexico, some species of this genus are highly valued for their medicinal properties, particularly A. pichinchensis, A. petiolaris, and A. grandifolia. Furthermore, herbal preparations of A. pichinchensis are available for treating several mycoses. The present review is aimed to summarize the chemical and pharmacological properties of 37 species of the Ageratina genus up to April, 2022. Data were recorded using online scientific databases, including Scopus, PubMed, Google Scholar, Taylor and Francis Imprints, National Center for Biotechnology Information, Science Direct, JSTOR, and SciFinder. The information was gathered from research articles, relevant books on herbal medicinal plants and the history of medicinal plants from Mexico, theses, reports, and web pages. The specialized metabolites present in the Ageratina genus belong to different chemical classes, including flavonoids, benzyl benzoates, benzofurans, chromenes, and terpenoids. The chromenes, benzofurans, and benzyl benzoates are the metabolites most widespread in the genus. So far, the species more thoroughly investigated is A. adenophora. Ageratina has received little attention from the pharmacological point of view. The studies are limited to 10 species. Biological studies have been conducted on extracts and/or compounds isolated from plants collected mainly from China and Mexico. The results revealed that the extracts and metabolites possess several biological activities, including antiviral, antioxidant, antimicrobial, anti-inflammatory, antinociceptive, antifeedant, larvicidal, acaricidal, antidiabetic, antiprotozoal, and wound-healing properties. In the case of A. pichinchensis, A. petiolaris, and A. grandifolia, the pharmacological studies provided evidence for their use for treating gastrointestinal complaints and diabetes. Furthermore, herbal preparations of A. pichinchensis are now widely used for alleviating onychomycosis. A. adenophora, is the most investigated species, chemically and biologically; however, some hepatotoxicity effect has been recorded. This review recapitulates information on the Ageratina genus, highlighting the phytochemistry and biological activities of the species investigated. It is important to point out that the pharmacological potential of this large genus remains largely unexplored.

ANALISIS KEANEKARAGAMAN GEN MYOSTATIN (MSTN) SECARA IN-SILICO PADA CATTLE DI INDONESIA

Cattle is one of the largest livestock products in Indonesia. The purpose of this study was to determine the diversity of the myostatin (MSTN) gene found in several cattle in Indonesia. This research was a descriptive analysis research based on several literature studies. Gene data was taken from the National Center for Biotechnology Information (NCBI). The gene data taken were from several species such as Bos indicus, Bos indicus×Bos taurus, and Bos taurus. Meanwhile, Bubalus bubalis, Capra hircus, and Cervis sp. were selected as outgroups. DNA sequence data analysis was aligned using MEGA XI software. MSTN gene parameters showed results between the kinship of several cattle in Indonesia. From these results it can be found that there were still several species of cattle in Indonesia that were not yet found in the NCBI database on the MSTN gene. For example, Madura cattle (Bos javanicus), PO Kebumen, PO Aceh, and several livestock products that do not yet have the MSTN gene characterization database. Therefore, to improve the quality of beef in Indonesia, it is necessary to characterize the MSTN gene in several species that are not yet in the database as a benchmark for the quality level of cattle in Indonesia.

Update on Rapid-Eye-Movement Sleep Behavior Disorder (RBD): Focus on Its Strong Association with α-Synucleinopathies

REM sleep behavior disorder (RBD) is a parasomnia in which the customary generalized skeletal muscle atonia of REM sleep, “REM-atonia”, is compromised, allowing for the injurious acting-out of dreams. RBD can be idiopathic/isolated (iRBD) or symptomatic of neurological disorders, and can be triggered by most antidepressants. RBD mainly affects middle-aged and older adults, and is strongly linked with alpha-synucleinopathies, mainly Parkinson’s disease (PD) and dementia with Lewy bodies (DLB). iRBD is now known to be the earliest and strongest predictor of future PD/DLB, which has stimulated a major international clinical and basic science research effort to enroll iRBD patients for upcoming neuroprotective/disease-modifying trials and to identify the most promising interventions to test in these cohorts. This review will provide the latest pertinent information on the rapidly expanding field of RBD. The methods included a PubMed literature search that included PubCrawlers, which utilizes the NCBI (National Center for Biotechnology Information) E-utils tools for publication retrieval, using the keywords “REM sleep behavior disorder” and “RBD”. The results yielded the latest updates on iRBD as prodromal PD/DLB, with the most promising biomarkers for phenoconversion provided, along with a presentation of three clinical research consortiums that are systematically gathering patients in preparation for enrollment in upcoming clinical trials: (i) The International RBD Study Group; (ii) The North American Prodromal Synucleinopathy (NAPS and NAPS2) Consortium; and (iii) The FARPRESTO Italian multicenter RBD research consortium. In addition, updates on the Parasomnia Overlap Disorder (RBD + NREM parasomnia) and on narcolepsy-RBD are provided, along with new epidemiologic data, the latest RBD management guidelines, and updates on animal models of RBD. Emerging areas of critical RBD research are also highlighted. In conclusion, RBD is a notable example of clinical and translational neuroscience research.

Pathogenomic Signature and Aberrant Neurogenic Events in Experimental Cerebral Ischemic Stroke: A Neurotranscriptomic-Based Implication for Dementia.

Cerebral ischemic stroke is caused due to neurovascular damage or thrombosis, leading to neuronal dysfunction, neuroinflammation, neurodegeneration, and regenerative failure responsible for neurological deficits and dementia. The valid therapeutic targets against cerebral stroke remain obscure. Thus, insight into neuropathomechanisms resulting from the aberrant expression of genes appears to be crucial. In this study, we have elucidated how neurogenesis-related genes are altered in experimental stroke brains from the available transcriptome profiles in correlation with transcriptome profiles of human postmortem stroke brain tissues. The transcriptome datasets available on the middle cerebral artery occlusion (MCAo) rat brains were obtained from the Gene Expression Omnibus, National Center for Biotechnology Information. Of the available datasets, 97 samples were subjected to the meta-analysis using the network analyst tool followed by Cytoscape-based enrichment mapping analysis. The key differentially expressed genes (DEGs) were validated and compared with transcriptome profiling of human stroke brains. Results revealed 939 genes are differently expressed in the brains of the MCAo rat model of stroke, in which 30 genes are key markers of neural stem cells, and regulators of neurogenic processes. Its convergence with DEGs from human stroke brains has revealed common targets. This study has established a panel of highly important DEGs to signify the potential therapeutic targets for neuroregenerative strategy against pathogenic events associated with cerebral stroke. The outcome of the findings can be translated to mitigate neuroregeneration failure seen in various neurological and metabolic disease manifestations with neurocognitive impairments.

CRISPR Target-based Single-guide RNA (sgRNA) for Diagnostic Testing of Hepatitis B Virus

Background: Indonesia is the second-highest country with hepatitis B cases in the South East Asian region. Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 12 (Cas12) could be developed as a diagnostic tool to detect hepatitis B infection. This study was aimed to develop a diagnostic method for hepatitis B virus by designing CRISPR target-based single-guide RNA (sgRNA).Materials and method: The preCore/Core-gene sequences of hepatitis B virus were collected from the National Center for Biotechnology Information (NCBI) website. The selected sequence was submitted to Cas Designer and CRISPOR tools to design sgRNA. The resulting sgRNA was cloned in silico into an expression vector using Benchling software.Results: The 23-nucleotide sequence 5'- GTAGTCAGTTATGTCAATGTTAA-3’ had 30% GC content, 68.3 out-of-frame and 76 predicted efficiencies. This sequence had no mismatch based on analysis.Conclusion: This preliminary study will help design a CRISPR-based diagnostic kit for the detection of hepatitis B virus in Indonesia. However, further in vitro and in vivo studies are required to demonstrate its potential and efficiency.Keywords: CRISPR-Cas12b, diagnostic, HBV, sgRNA 

Genome-based classification of the class Halobacteria and description of Haladaptataceae fam. nov. and Halorubellaceae fam. nov.

Currently, there are four mainstream taxonomic opinions on the classification of the class Halobacteria at the family and order levels. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria (ICSP), List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Centre for Biotechnology Information (NCBI) adopted taxonomies have three to four orders and up to eight families, while the Genome Taxonomy Database (GTDB) taxonomy proposes only one order with nine families. To resolve the taxonomic inconsistency, phylogenomic analyses based on concatenated single-copy orthologous proteins and 122 concatenated conserved single-copy marker proteins were conducted to infer the taxonomic status of the current representatives of the class Halobacteria at the family and order levels. The current 76 genera with validly published names of the class Halobacteria were able to be assigned into eight families in one order. On the basis of these results, it is proposed that the current species with validly published names of the class Halobacteria should be remerged into the order Halobacteriales, then assigned to eight families, Haladaptataceae, Haloarculaceae, Halobacteriaceae, Halococcaceae, Haloferacaceae, Natronoarchaeaceae, Natrialbaceae and Halorubellaceae. Thus, Haladaptataceae fam. nov. is described based on Haladaptatus, Halomicrococcus and Halorussus and Halorubellaceae fam. nov. is proposed incorporating Haloarchaeobius and Halorubellus, respectively.

Important roles of Hif1a in maternal or adult BPA exposure induced pancreatic injuries

Bisphenol A (BPA) is a monomer to produce polycarbonate plastics and can be released into the environment through human activities, leading to its accumulation in animals, plants and humans through direct contact or environmental exposure. Epidemiological studies have reported that BPA exposure is associated with metabolic disorders. The pancreas is an important endocrine organ and plays an important role in metabolic disorders. To explore the possible long-term effects of BPA exposure on neonatal health, bioinformatic methods were used to identify differentially expressed genes (DEGs) by comparing the neonatal pancreas after maternal exposure to BPA with the adult pancreas after direct exposure to BPA. Two datasets about BPA exposure and pancreatic abnormality, GSE82175 and GSE126297 in Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) were collected. Control (or BPA-exposed) offspring (maternal exposure) and Control (or BPA-exposed) adults (direct exposure) were defined as Control (or BPA) groups. The results showed that BPA disturbed the normal function of the pancreas in both offspring and adults, with offspring showing higher susceptibility to BPA than adults. Seventeen insulin secretion-related DEGs (Stxbp5l, Fam3d, Mia3, Igf1, Hif1a, Aqp1, Kif5b, Tiam1, Map4k4, Cyp51, Pde1c, Rab3c, Arntl, Clock, Edn3, Kcnb1, and Krt20) in the BPA group were identified, and 15 regulator DEGs (Zfp830, 4931431B13Rik, Egr1, Ddit4l, Cep55, G530011O06Rik, Hspa1b, Hspa1a, Cox6a2, Ibtk, Banf1, Slc35b2, Golt1b, Lrp8, and Pttg1) with opposite expression trends and a regulator gene Cerkl with the similar expression trend in the Control and BPA groups were identified. Hif1α might be an important molecular target for pancreatic cancer caused by BPA exposure, and pregnancy is a critical window of susceptibility to BPA exposure.

What can traditional plant therapy do in the face of Covid-19? Examples from traditional Chinese medicine.

Until June 2022, more than 540.9 million people had been diagnosed with COVID-19, and the pandemic had claimed more than six million lives worldwide. Two years after fighting the virus, we faced a more uncertain position. SARS-CoV-2 is constantly mutating and reappears regularly, particularly with Omicron variants showing high genetic variation and immune escape mechanisms. The efficacy and duration of protection of existing vaccines against new variants of SARS-CoV-2 remains uncertain. The world needs time to develop new variant-specific drugs, including monoclonal topics, vaccines, and other antiviral drugs, to fight the epidemic. The aim of this study was to illustrate the scientific, effective and systematic nature of three classical prescriptions of traditional Chinese medicine (TCM) for the treatment of COVID-19 through comparison of disease symptoms, diagnostic process, and treatment methods and evidence-based and pharmacological studies. We analysed the "Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia" (Version 9) made by China, "WHO-2019-nCoV-therapeutics", "Therapeutic Guidelines" published by Australian Therapeutic Guidelines Limited, "Shanghan Lun (Treatise on Febrile Diseases)", "Jinkui Yaolue (Golden Chamber Synopsis), and "Wenyi Lun (The Epidemic Febrile Disease)". We manually retrieved the dictionary of traditional Chinese medicine (Version II). In addition, we searched the Wiley online library, National Center for Biotechnology Information (NCBI), VIP, WHO website, and China National Knowledge Infrastructure (CNKI) for relevant literature from 2001 to 2022. We searched the original plants, ingredients, pharmacology, functions and indications, usage and dosage, drug efficacy, literature sources, and conduct an evidence-based studies. We quantified the strength of pharmacological action to show the pertinence of disease development. We found that the diagnosis and treatment of pulmonary infection caused by epidemic disease in TCM classics is consistent with the diagnostic process of modern medical therapeutic guidelines. The three classic prescriptions have significant symptomatic therapeutic effects on the respiratory, gastrointestinal, urinary and hematological symptoms of the clinical manifestations of COVID-19. It was found that the herbal functional group of Houpo (Cortex Magnoliae Officinalis), Chaihu (Radix Bupleuri), Cangzhu (Rhizoma Atractylodis), Qianghuo (Notopterygii Rhizoma et Radix), etc showed strong anti-inflammatory activity and had a positive effect on treating and preventing the outbreaks of systemic inflammatory factors. TCM can obtain obvious curative effect in symptomatic treatment, has strong anti-inflammatory effect, and can effectively reduce symptoms and patients' pain.

AMAnD: an automated metagenome anomaly detection methodology utilizing DeepSVDD neural networks.

The composition of metagenomic communities within the human body often reflects localized medical conditions such as upper respiratory diseases and gastrointestinal diseases. Fast and accurate computational tools to flag anomalous metagenomic samples from typical samples are desirable to understand different phenotypes, especially in contexts where repeated, long-duration temporal sampling is done. Here, we present Automated Metagenome Anomaly Detection (AMAnD), which utilizes two types of Deep Support Vector Data Description (DeepSVDD) models; one trained on taxonomic feature space output by the Pan-Genomics for Infectious Agents (PanGIA) taxonomy classifier and one trained on kmer frequency counts. AMAnD's semi-supervised one-class approach makes no assumptions about what an anomaly may look like, allowing the flagging of potentially novel anomaly types. Three diverse datasets are profiled. The first dataset is hosted on the National Center for Biotechnology Information's (NCBI) Sequence Read Archive (SRA) and contains nasopharyngeal swabs from healthy and COVID-19-positive patients. The second dataset is also hosted on SRA and contains gut microbiome samples from normal controls and from patients with slow transit constipation (STC). AMAnD can learn a typical healthy nasopharyngeal or gut microbiome profile and reliably flag the anomalous COVID+ or STC samples in both feature spaces. The final dataset is a synthetic metagenome created by the Critical Assessment of Metagenome Annotation Simulator (CAMISIM). A control dataset of 50 well-characterized organisms was submitted to CAMISIM to generate 100 synthetic control class samples. The experimental conditions included 12 different spiked-in contaminants that are taxonomically similar to organisms present in the laboratory blank sample ranging from one strain tree branch taxonomic distance away to one family tree branch taxonomic distance away. This experiment was repeated in triplicate at three different coverage levels to probe the dependence on sample coverage. AMAnD was again able to flag the contaminant inserts as anomalous. AMAnD's assumption-free flagging of metagenomic anomalies, the real-time model training update potential of the deep learning approach, and the strong performance even with lightweight models of low sample cardinality would make AMAnD well-suited to a wide array of applied metagenomics biosurveillance use-cases, from environmental to clinical utility.

Base Substitution Patterns in Partial of the Cytochrome C Oxidase Unit I (COI) mtDNA Genes in the Red Junglefowl (Gallus sp.) of North Sulawesi and some Gallus sp. accessions.

Partial of the cytochrome C oxidase unit I (COI) mtDNA genes of the red jungle fowl (Gallus sp.) were isolated and sequenced to examine the base substitution pattern compared to several accessions taken from GenBank. Samples were collected from several areas in North Sulawesi in the form of muscle tissue and prepared with 95% alcohol, and stored at temperatures below 500 C. Total DNA was isolated using the innuPREP DNA micro kit with a modified protocol. The target gene amplification used the primers BirdR1 and BirdF1, and the amplicons were sequenced at the Singapore FirstBase laboratory. Target gene sequences have been blasted through the nucleotide blast program provided by the National Center for Biotechnology Information (NCBI)—sequence analysis using MEGA5 and DnaSPv5 software. Target gene sequences were aligned using the Clustal-W program on MEGA5. The amplified target gene sequence length was 490 bp. The blast results showed that the target gene sequence was 98% identical to the COI gene sequence from several Gallus-gallus accessions from GenBank. The results of multiple alignments between the sequences of some of the genes examined showed the presence of polymorphic sites (S). The number of polymorphic sites (S) is 11, while the conserved sequence (C) is 386/397 = 0.977. The number of haplotypes (h) is 5, and the diversity of haplotypes (Hd) is 0.703. The overall genetic distance average was 0.008. The polymorphic sites and base substitution events occurred at sites number 145 (A↔G), 241 (G↔C), 268 (C↔A), 295 (C↔A), 348 (T↔C), 381(A) ↔T), 384 (T↔C), 390 (T↔A), 393 (C↔T), 394 (T↔C) and 395 (C↔T). The substitution pattern at these polymorphic sites consists of substitution transitions and transversions. The ratio of transition substitution and transversion events (Ts/Tv) = 1.4056. The substitution events at these sites are located at the bases in the first and third positions of the codon. Substitution events at these polymorphic sites partially cause the exchange of amino acids. The exchange of amino acids occurs at codons 49, 81, 90, 99 and 130.

The Implications of Obesity on Total Hip Arthroplasties: A Literature Review of the Associated Complications

Introduction: Obesity is a global pandemic and public health crisis associated with a wide range of comorbidities, including osteoarthritis, leading to a significantly younger age at the time of primary total hip arthroplasty (THA) and an increased rate of complications compared to nonobese individuals. As our population continues to get older, combined with an increasing rate of obesity, an increased rate of consultations for total hip arthroplasty is expected. This has led to concerns regarding the implications of obesity on the need for THA itself and the associated complications, especially for arthroplasty surgeons. Unfortunately, few articles provide an all-encompassing review of different complications surrounding obesity within orthopedic surgery, and even fewer around total hip arthroplasty. This literature review aims to provide a comprehensive review of the implications obesity has on total hip arthroplasties, its associated complications, and how we can potentially modify these risks. Methods: Sources and research articles were identified by searching the databases of PubMed, Google Scholar, and the National Center for Biotechnology Information (NCBI) from 2000 to July 2022. Our search used the specific terms located within the abstract/title, including: “total hip arthroplasty” AND “complications,” AND “obesity, OR obese.” Inclusion criteria for research articles were the English language and peer-reviewed articles published from inception to July 2022. Articles not directly examining the effect of obesity on the incidence of complications following primary THA were excluded. Studies with outcomes of interest included the incidence of postoperative complications, primary THA in obese patients, and clinical outcome measures. A total of 265 studies were identified upon initial search. Thirty-one articles were selected for reference in this literature review. Results: Obese patients undergo primary THA at an earlier age and experience an increased duration of surgery, higher rates of infection, dislocation, periprosthetic fractures, and venous thromboembolism compared to nonobese patients. The role of pre-operative bariatric surgery before total hip arthroplasty has failed to show reductions in complication rates. Harris Hip Scores are lower in obese patients pre-operatively and post-operatively, but the degree of improvement following THA is similar compared to nonobese patients. Long-term survival of total hip prostheses is similar when compared to nonobese patients. Conclusion: Current literature strongly suggests increased complication rates in obese patients who undergo THA. This phenomenon is not solely due to biomechanical forces and is multifactorial, including inflammatory and genetic predispositions, which need further study. The decision to perform THA on obese patients should not solely be based on BMI. Other factors, such as management of comorbidities, surgical exposure, and nursing care, should be considered when deciding on surgical candidacy.

REDH: A database of RNA editome in hematopoietic differentiation and malignancy.

The conversion of adenosine (A) to inosine (I) through deamination is the prevailing form of RNA editing, impacting numerous nuclear and cytoplasmic transcripts across various eukaryotic species. Millions of high-confidence RNA editing sites have been identified and integrated into various RNA databases, providing a convenient platform for the rapid identification of key drivers of cancer and potential therapeutic targets. However, the available database for integration of RNA editing in hematopoietic cells and hematopoietic malignancies is still lacking. We downloaded RNA sequencing (RNA-seq) data of 29 leukemia patients and 19 healthy donors from National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database, and RNA-seq data of 12 mouse hematopoietic cell populations obtained from our previous research were also used. We performed sequence alignment, identified RNA editing sites, and obtained characteristic editing sites related to normal hematopoietic development and abnormal editing sites associated with hematologic diseases. We established a new database, "REDH", represents RNA editome in hematopoietic differentiation and malignancy. REDH is a curated database of associations between RNA editome and hematopoiesis. REDH integrates 30,796 editing sites from 12 murine adult hematopoietic cell populations and systematically characterizes more than 400,000 edited events in malignant hematopoietic samples from 48 cohorts (human). Through the Differentiation, Disease, Enrichment, and knowledge modules, each A-to-I editing site is systematically integrated, including its distribution throughout the genome, its clinical information (human sample), and functional editing sites under physiological and pathological conditions. Furthermore, REDH compares the similarities and differences of editing sites between different hematologic malignancies and healthy control. REDH is accessible at http://www.redhdatabase.com/ . This user-friendly database would aid in understanding the mechanisms of RNA editing in hematopoietic differentiation and malignancies. It provides a set of data related to the maintenance of hematopoietic homeostasis and identifying potential therapeutic targets in malignancies.

Technical aspects and outcomes of using homografts in atrioventricular valve surgery: a systematic review

Objective: To summarize and critically appraise the world experience with homografts in mitral and tricuspid valve surgery.Methods: We conducted a systematic review according to the PRISMA criteria. We searched the following terms in available databases, such as PubMed (National Center for Biotechnology Information), Cochrane Library, Web of Science (Clarivate), and Google Scholar: ((mitral homograft) OR (tricuspid homograft) OR (homograft) AND (valve replacement) OR (valve repair)).Results: We recruited 3 specialists to search the information matching our inclusion and exclusion criteria and selected 23 publications covering the period 1988-2021 for analysis. The mean follow-up period was 15 [6-60] months. Survival at the end of the follow-up period was 100% [90.7%-100.0%]; freedom from graft dysfunction was 100%, and freedom from reoperation was 100% [79%-100%].Conclusion: The world experience with homografts in atrioventricular valve surgery is limited to small case series with inconclusive surgical aspects and a heterogeneous follow-up period. The immediate results suggest that homografts could be used as an alternative valve substitute for a wide spectrum of diseases both in primary and revision surgery. Received 19 April 2023. Revised 14 May 2023. Accepted 15 May 2023. Funding: The study did not have sponsorship. Conflict of interest: The authors declare no conflict of interest. Contribution of the authorsConception and study design: M.D. Nuzhdin, R.N. KomarovData collection and analysis: M.D. Nuzhdin, D.A. Matsuganov, I.Yu. Melnikov, A.V. TsaregorodtsevStatistical analysis: D.A. MatsuganovDrafting the article: M.D. NuzhdinCritical revision of the article: R.N. Komarov, M.D. NuzhdinFinal approval of the version to be published: M.D. Nuzhdin, R.N. Komarov, D.A. Matsuganov, I.Yu. Melnikov, A.V. Tsaregorodtsev

COVID-19 progression towards ARDS: a genome wide study reveals host factors underlying critical COVID-19.

Coronavirus disease 2019 (COVID-19) is a viral infection produced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus epidemic, which was declared a global pandemic in March 2020. The World Health Organization has recorded around 43.3 billion cases and 59.4 million casualties to date, posing a severe threat to global health. Severe COVID-19 indicates viral pneumonia caused by the SARS-CoV-2 infections, which can induce fatal consequences, including acute respiratory distress syndrome (ARDS). The purpose of this research is to better understand the COVID-19 and ARDS pathways, as well as to find targeted single nucleotide polymorphism. To accomplish this, we retrieved over 100 patients' samples from the Sequence Read Archive, National Center for Biotechnology Information. These sequences were processed through the Galaxy server next generation sequencing pipeline for variant analysis and then visualized in the Integrative Genomics Viewer, and performed statistical analysis using t-tests and Bonferroni correction, where six major genes were identified as DNAH7, CLUAP1, PPA2, PAPSS1, TLR4, and IFITM3. Furthermore, a complete understanding of the genomes of COVID-19-related ARDS will aid in the early identification and treatment of target proteins. Finally, the discovery of novel therapeutics based on discovered proteins can assist to slow the progression of ARDS and lower fatality rates.

Putrescine Detected in Strains of Staphylococcus aureus.

Most forms of life, including the archaea, bacteria, and eukaryotes synthesize the polyamine putrescine. Although putrescine is widely distributed, several Gram-positive bacteria, including Staphylococcus aureus (S. aureus), appear to be the exceptions. We report here that strains of S. aureus can produce the polyamine putrescine, as well as the derivative N-acetyl-putrescine. Three strains of S. aureus from the American Type Culture Collection (ATCC), one strain listed in the National Center for Biotechnology Information (NCBI) database, whose genomic sequence is well defined, and well as eight strains from S. aureus-induced brain abscesses of individual patients from multiple geographic locations were evaluated. Each strain was grown in complete chemically defined medium (CDM) under stringent conditions, after which the partially purified conditioned medium (CM) was analyzed by mass spectroscopy (MS), and the data were reported as the ratio of experimental results to controls. We confirmed the synthesis of putrescine by S. aureus by using 13C/15N-labeled arginine as a tracer. We found that agmatine, N-acetyl-putrescine, ornithine, citrulline, proline, and NH3 were all labeled with heavy isotope derived from 13C/15N-labeled arginine. None of the strains examined produced spermine or spermidine, but strains from either ATCC or human brain abscesses produced putrescine and/or its derivative N-acetyl-putrescine.