-
The Journal of Antimicrobial... Jun 2024To assess the effectiveness of shortened regimens of vancomycin or fidaxomicin in the treatment of Clostridioides difficile infection (CDI). (Observational Study)
Observational Study
OBJECTIVES
To assess the effectiveness of shortened regimens of vancomycin or fidaxomicin in the treatment of Clostridioides difficile infection (CDI).
METHODS
Adult patients with CDI hospitalized from January 2022 to May 2023 were included in this observational study. In patients with CDI treated with vancomycin or fidaxomicin, antibiotic treatment was discontinued after either 5 or 7 days of vancomycin or 5 days of fidaxomicin if there was a clinical response and improvement in laboratory parameters. The control cohort was treated with the standard 10 day regimen of either vancomycin or fidaxomicin. The follow-up was 60 days. Causative C. difficile strains were characterized by ribotyping and toxin gene detection when available.
RESULTS
Twenty-five patients (median age 76 years) received shortened treatment with vancomycin (n = 21), or fidaxomicin (n = 4). Five cases fulfilled the criteria for severe CDI. Twenty-three patients completed follow-up; two died from causes other than CDI, and two developed recurrent CDI (8.0%). Ribotypes (RTs) 001 and 014 were the most prevalent with 20% each. In two C. difficile isolates, binary toxin genes were detected (RTs 078 and 023). In the control group of 22 patients recurrent CDI developed in 5 patients (22.7%). No statistically significant differences were found between the groups.
CONCLUSIONS
Shortened treatment regimens for CDI with vancomycin and fidaxomicin were shown to be effective in our cohort of patients compared with 10 days of treatment. The recurrence rate was lower in the study group. A larger, prospective, double-blind, randomized, multicentre study is needed to support our findings.
Topics: Humans; Clostridium Infections; Aged; Male; Female; Clostridioides difficile; Anti-Bacterial Agents; Vancomycin; Fidaxomicin; Middle Aged; Ribotyping; Aged, 80 and over; Treatment Outcome
PubMed: 38661207
DOI: 10.1093/jac/dkae119 -
PeerJ. Computer Science 2024DNA steganography is a technique for securely transmitting important data using DNA sequences. It involves encrypting and hiding messages within DNA sequences to prevent...
DNA steganography is a technique for securely transmitting important data using DNA sequences. It involves encrypting and hiding messages within DNA sequences to prevent unauthorized access and decoding of sensitive information. Biometric systems, such as fingerprinting and iris scanning, are used for individual recognition. Since biometric information cannot be changed if compromised, it is essential to ensure its security. This research aims to develop a secure technique that combines steganography and cryptography to protect fingerprint images during communication while maintaining confidentiality. The technique converts fingerprint images into binary data, encrypts them, and embeds them into the DNA sequence. It utilizes the Feistel network encryption process, along with a mathematical function and an insertion technique for hiding the data. The proposed method offers a low probability of being cracked, a high number of hiding positions, and efficient execution times. Four randomly chosen keys are used for hiding and decoding, providing a large key space and enhanced key sensitivity. The technique undergoes evaluation using the NIST statistical test suite and is compared with other research papers. It demonstrates resilience against various attacks, including known-plaintext and chosen-plaintext attacks. To enhance security, random ambiguous bits are introduced at random locations in the fingerprint image, increasing noise. However, it is important to note that this technique is limited to hiding small images within DNA sequences and cannot handle video, audio, or large images.
PubMed: 38660173
DOI: 10.7717/peerj-cs.1847 -
BioRxiv : the Preprint Server For... Apr 2024The most well-studied epigenetic marker in humans is the 5-methyl modification of cytosine in DNA, which has great potential as a disease biomarker in liquid biopsies of...
The most well-studied epigenetic marker in humans is the 5-methyl modification of cytosine in DNA, which has great potential as a disease biomarker in liquid biopsies of cell-free DNA. Currently, quantification of DNA methylation relies heavily on bisulfite conversion followed by PCR amplification and NGS or microarray analysis. PCR is subject to potential bias in differential amplification of bisulfite-converted methylated unmethylated sequences. Here, we combine bisulfite conversion with single-molecule kinetic fingerprinting to develop an amplification-free assay for DNA methylation at the branched-chain amino acid transaminase 1 (BCAT1) promoter. Our assay selectively responds to methylated sequences with a limit of detection below 1 fM and a specificity of 99.9999%. Evaluating complex genomic DNA matrices, we reliably distinguish 2-5% DNA methylation at the BCAT1 promoter in whole blood DNA from completely unmethylated whole-genome amplified DNA. Taken together, these results demonstrate the feasibility and sensitivity of our amplification-free, single-molecule quantification approach to improve the early detection of methylated cancer DNA biomarkers.
PubMed: 38645159
DOI: 10.1101/2024.04.06.587997 -
IScience Apr 2024Immune evasion is critical for fungal virulence. However, how the human opportunistic pathogen () accomplishes this is unknown. Here, we present the first genome-wide...
Immune evasion is critical for fungal virulence. However, how the human opportunistic pathogen () accomplishes this is unknown. Here, we present the first genome-wide nucleosome map of the macrophage-internalized consisting of ∼12,000 dynamic and 70,000 total nucleosomes. We demonstrate that CgSnf2 (SWI/SNF chromatin remodeling complex-ATPase subunit)-mediated chromatin reorganization in macrophage-internalized upregulates and downregulates the immunosuppressive seven-gene mannosyltransferase-cluster () and immunostimulatory cell surface adhesin-encoding gene, respectively. Consistently, overexpression and deletion elevated IL-1β (pro-inflammatory cytokine) production and diminished proliferation in macrophages. Further, had higher Epa1 surface expression, and evoked increased IL-1β secretion, and was killed in macrophages. Akt-, p38-, NF-κB- or NLRP3 inflammasome-inhibition partially reversed increased IL-1β secretion in -infected macrophages. Importantly, macrophages responded to multiple pathogens via NF-κB-dependent IL-1β production, underscoring NF-κB signaling's role in fungal diseases. Altogether, our findings directly link the nucleosome positioning-based chromatin remodeling to fungal immunomodulatory molecule expression.
PubMed: 38632999
DOI: 10.1016/j.isci.2024.109607 -
ZooKeys 2024We describe a new species of redbait in the genus collected from fish markets on Panay and Cebu islands in the Visayas region of the Philippines. The species is...
We describe a new species of redbait in the genus collected from fish markets on Panay and Cebu islands in the Visayas region of the Philippines. The species is externally similar to but is diagnosable by two prominent fleshy papillae associated with the cleithrum and fewer pectoral-fin rays (18-19 vs. 19-21) and gill rakers (30-33 vs. 34-41). Additionally, mitochondrial DNA differentiates this taxon from other species of . We generate mitochondrial genomes for two of the three type specimens and several other emmelichthyids to place the new taxon in a phylogenetic context. Analysis of the protein-coding mitochondrial loci calls into question the monophyly of two emmelichthyid genera ( and ) and highlights the need for subsequent analyses targeting the intrarelationships of the Emmelichthyidae.
PubMed: 38602272
DOI: 10.3897/zookeys.1196.111161 -
Forensic Science International. Genetics Jul 2024Massively parallel sequencing (MPS) is increasingly applied in forensic short tandem repeat (STR) analysis. The presence of stutter artefacts and other PCR or sequencing...
Massively parallel sequencing (MPS) is increasingly applied in forensic short tandem repeat (STR) analysis. The presence of stutter artefacts and other PCR or sequencing errors in the MPS-STR data partly limits the detection of low DNA amounts, e.g., in complex mixtures. Unique molecular identifiers (UMIs) have been applied in several scientific fields to reduce noise in sequencing. UMIs consist of a stretch of random nucleotides, a unique barcode for each starting DNA molecule, that is incorporated in the DNA template using either ligation or PCR. The barcode is used to generate consensus reads, thus removing errors. The SiMSen-Seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing) method relies on PCR-based introduction of UMIs and includes a sophisticated hairpin design to reduce unspecific primer binding as well as PCR protocol adjustments to further optimize the reaction. In this study, SiMSen-Seq is applied to develop a proof-of-concept seven STR multiplex for MPS library preparation and an associated bioinformatics pipeline. Additionally, machine learning (ML) models were evaluated to further improve UMI allele calling. Overall, the seven STR multiplex resulted in complete detection and concordant alleles for 47 single-source samples at 1 ng input DNA as well as for low-template samples at 62.5 pg input DNA. For twelve challenging mixtures with minor contributions of 10 pg to 150 pg and ratios of 1-15% relative to the major donor, 99.2% of the expected alleles were detected by applying the UMIs in combination with an ML filter. The main impact of UMIs was a substantially lowered number of artefacts as well as reduced stutter ratios, which were generally below 5% of the parental allele. In conclusion, UMI-based STR sequencing opens new means for improved analysis of challenging crime scene samples including complex mixtures.
Topics: Humans; Microsatellite Repeats; High-Throughput Nucleotide Sequencing; DNA Fingerprinting; Alleles; Multiplex Polymerase Chain Reaction; Polymerase Chain Reaction; Sequence Analysis, DNA; Machine Learning; Genetic Markers
PubMed: 38598919
DOI: 10.1016/j.fsigen.2024.103047 -
Plants (Basel, Switzerland) Mar 2024(syn ) is considered 'true' cinnamon. However, it is reported that less expensive sources of cinnamon from (syn ), , and (toxic coumarin) may be used in the place of...
(syn ) is considered 'true' cinnamon. However, it is reported that less expensive sources of cinnamon from (syn ), , and (toxic coumarin) may be used in the place of . We lack the quality assurance tools that are required to differentiate from other cinnamon species when verifying that the correct species is sourced from ingredient suppliers. The current research on cinnamon species authentication using DNA tools is limited to a few species and the use of high-quality DNA extracted from raw leaf materials. The cinnamon bark traded in the supply chain contains much less DNA and poorer-quality DNA than leaves. Our research advances DNA methods to authenticate cinnamon, as we utilized full-length chloroplast genomes via a genome skimming approach for and to facilitate the design of optimal mini DNA markers. Furthermore, we developed and validated the use of NMR fingerprints for several commercial cinnamon species, including the quantification of 16 molecules. NMR fingerprints provided additional data that were useful for quality assessment in cinnamon extract powders and product consistency. Both the new mini DNA markers and NMR fingerprints were tested on commercial cinnamon products.
PubMed: 38592863
DOI: 10.3390/plants13060841 -
BMC Plant Biology Apr 2024Apple is an important fruit crop that is always in demand due to its commercial and nutraceutical value. Also, the requirement for quality planting material for this...
Apple is an important fruit crop that is always in demand due to its commercial and nutraceutical value. Also, the requirement for quality planting material for this fruit crop for new plantations is increasing continuously. In-vitro propagation is an alternative approach, which may help to produce genetically identical high grade planting material. In this study, for the first time, an efficient and reproducible propagation protocol has been established for apple root stock MM 104 via axillary bud. Culturing axillary buds on Murashige and Skoog apple rootstock (MM 104) resulted in better in-vitro propagation. (MS) basal medium supplemented with 3.0% (w/v) sucrose and 0.8% (w/v) agar. The axillary buds were established in MS basal medium with BA (5.0 µM), NAA (1.0 µM) and further used to establish invitro propagation protocol. Plant Growth Regulators (PGRs), BA (1.0 µM) in combination with NAA (1.0 µM) was found most efficient for shoot multiplication (100%) and produced 9.8 shoots/explants with an average shoot length of (2.4 ± cm). All the shoots produced roots in 0.1 µM IBA with a 5-day dark period. Acclimatization of in-vitro raised plantlets was obtained with vermiculite: perlite: sand: soil (2:2:1:1) resulting in 76% survival under field conditions. The study showed that the use of axillary bud is efficient for multiple-shoot production of apple rootstock (MM 104). This is the first comprehensive report on in-vitro growth of apple root stock MM 104 with an assessment of genetic stability using DNA fingerprinting profiles based on Inter Simple Sequence Repeats (ISSR) and Start Codon Targeted (SCoT). The genetic stability of in-vitro-produced plants, as determined by SCoT and ISSR primers, demonstrated genetic closeness to the mother plant.
Topics: Malus; Codon, Initiator; Plant Growth Regulators; Fruit; Microsatellite Repeats
PubMed: 38570817
DOI: 10.1186/s12870-024-04939-3 -
Plant Biotechnology Journal Mar 2024Carotenoids are indispensable to plants and critical components of the human diet. The carotenoid metabolic pathway is conserved across plant species, but our...
Carotenoids are indispensable to plants and critical components of the human diet. The carotenoid metabolic pathway is conserved across plant species, but our understanding of the genetic basis of carotenoid variation remains limited for the seeds of most cereal crops. To address this issue, we systematically performed linkage and association mapping for eight carotenoid traits using six recombinant inbred line (RIL) populations. Single linkage mapping (SLM) and joint linkage mapping (JLM) identified 77 unique additive QTLs and 104 pairs of epistatic QTLs. Among these QTLs, we identified 22 overlapping hotspots of additive and epistatic loci, highlighting the important contributions of some QTLs to carotenoid levels through additive or epistatic mechanisms. A genome-wide association study based on all RILs detected 244 candidate genes significantly associated with carotenoid traits, 23 of which were annotated as carotenoid pathway genes. Effect comparisons suggested that a small number of loci linked to pathway genes have substantial effects on carotenoid variation in our tested populations, but many loci not associated with pathway genes also make important contributions to carotenoid variation. We identified ZmPTOX as the causal gene for a QTL hotspot (Q10/JLM10/GWAS019); this gene encodes a putative plastid terminal oxidase that produces plastoquinone-9 used by two enzymes in the carotenoid pathway. Natural variants in the promoter and second exon of ZmPTOX were found to alter carotenoid levels. This comprehensive assessment of the genetic mechanisms underlying carotenoid variation establishes a foundation for rewiring carotenoid metabolism and accumulation for efficient carotenoid biofortification.
PubMed: 38548388
DOI: 10.1111/pbi.14346 -
International Journal of Molecular... Mar 2024Body fluid identification plays a crucial role in criminal investigations. Because of their presence in many cases, blood and semen are the most relevant body fluids in...
Body fluid identification plays a crucial role in criminal investigations. Because of their presence in many cases, blood and semen are the most relevant body fluids in forensic sciences. Based on antigen-antibody reactions binding unique proteins for each body fluid, serological assays represent one of the most rapid and highly specific tests for blood and semen. Currently, few studies have assessed the factors affecting body fluid identification by applying these assays. This work aimed to study the effect of different fabrics from clothes and time since deposition on identification through immunochromatographic tests for blood and semen, DNA isolation, and STR profiling from these samples. Body fluids were deposited on black- and white-dyed denim and cotton fabrics, and on leather. Afterward, blood and semen were sampled at 1 day, 30 days, and 90 days after deposition and identified by using the SERATEC HemDirect Hemoglobin Test and the PSA Semiquant and SERATEC BLOOD CS and SEMEN CS tests, respectively. Laboratory and crime scene tests presented similar performances for the detection of blood and semen stains on every tested fabric. No differences were found on band intensities between timepoints for all fabrics. It was possible to recover and identify blood and semen samples up to three months after deposition and to obtain full STR profiles from all the tested fabrics. Both body fluid STR profiles showed differences in their quality between 1 and 90 days after deposition for all fabrics except for black cotton for semen samples. Future research will expand the results, assessing body fluid identification on other substrates and under different environmental conditions.
Topics: Humans; Seeds; Body Fluids; Bodily Secretions; Semen Analysis; DNA; Saliva; DNA Fingerprinting
PubMed: 38542494
DOI: 10.3390/ijms25063522