Related Sequences Research Articles

Unravelling Different Water Management Strategies in Three Olive Cultivars: The Role of Osmoprotectants, Proteins, and Wood Properties

Understanding the responses of olive trees to drought stress is crucial for improving cultivation and developing drought-tolerant varieties. Water transport and storage within the plant is a key factor in drought-tolerance strategies. Water management can be based on a variety of factors such as stomatal control, osmoprotectant molecules, proteins and wood properties. The aim of the study was to evaluate the water management strategy under drought stress from an anatomical and biochemical point of view in three young Italian olive cultivars (Giarraffa, Leccino and Maurino) previously distinguished for their physiological and metabolomic responses. For each cultivar, 15 individuals in pots were exposed or not to 28 days of water withholding. Every 7 days, the content of sugars (including mannitol), proline, aquaporins, osmotins, and dehydrins, in leaves and stems, as well as the chemical and anatomical characteristics of the wood of the three cultivars, were analyzed. ‘Giarraffa’ reduced glucose levels and increased mannitol production, while ‘Leccino’ accumulated more proline. Both ‘Leccino’ and ‘Maurino’ increased sucrose and aquaporin levels, possibly due to their ability to remove embolisms. ‘Maurino’ and ‘Leccino’ accumulated more dehydrins and osmotins. While neither genotype nor stress affected wood chemistry, ‘Maurino’ had a higher vessel-to-xylem area ratio and a larger hydraulic diameter, which allows it to maintain a high transpiration rate but may make it more susceptible to cavitation. The results emphasized the need for an integrated approach, highlighting the importance of the relative timing and sequence of each parameter analyzed, allowing, overall, to define a “strategy” rather than a “response” to drought of each cultivar.

Full Genome Characterization of the First Oropouche Virus Isolate Imported in Europe from Cuba.

On 27 May 2024, the Cuban Ministry of Health reported the first outbreak of Oropouche fever on the island. The etiologic agent, Oropouche virus (OROV), is a poorly understood arbovirus that has been known since the 1960s and represents a public health burden in Latin America. We report the whole-genome characterization of the first European OROV isolate from a returning traveler from Cuba with Oropouche fever-like symptoms. The isolate was obtained from the patient's serum; whole-genome sequencing was performed by next-generation sequencing, followed by phylogenetic analysis and genetic variability studies. The analysis showed that the most closely related sequence was from the French Guiana 2020 outbreak. Interestingly, our isolate is a reassortant virus, included in a highly supported monophyletic clade containing recent OROV cases (Brazil 2015-Colombia 2021), separated from the other four previously known genotypes. More deeply, it was found to be included in a distinct branch containing the sequences of the Brazil 2022-2024 outbreak. The reassortment event involved the S and L segments, which have high similarity with sequences belonging to a new cluster (here defined as OROV_SCDC_2024), while the M segment shows high similarity with older sequences. These results likely describe the viral strain responsible for the current outbreak in Cuba, which may also reflect the ongoing outbreak in Latin America. Further studies are needed to understand how OROV evolves towards traits that facilitate its spread and adaptation outside its original basin, and to track its spread and evolution in the European continent.

Microbiome Geographic Population Structure (mGPS) Detects Fine-Scale Geography.

Over the past decade, sequencing data generated by large microbiome projects showed that taxa exhibit patchy geographical distribution, raising questions about the geospatial dynamics that shape natural microbiomes and the spread of antimicrobial resistance (AMR) genes. Answering these questions requires distinguishing between local and non-local microorganisms and identifying the source sites for the latter. Predicting the source sites and migration routes of microbiota has been envisioned for decades but was hampered by the lack of data, tools, and understanding of the processes governing biodiversity. State-of-the-art biogeographical tools suffer from low resolution and cannot predict biogeographical patterns at a scale relevant to ecological, medical, or epidemiological applications. Analyzing urban, soil, and marine microorganisms, we found that some taxa exhibit regional-specific composition and abundance, suggesting they can be used as biogeographical biomarkers. We developed the Microbiome Geographic Population Structure (mGPS), a machine-learning-based tool that utilizes microbial relative sequence abundances to yield a fine-scale source site for microorganisms. mGPS predicted the source city for 92% of the samples and the within-city source for 82% of the samples, though they were often only a few hundred meters apart. mGPS also predicted soil and marine sampling sites for 86% and 74% of the samples, respectively. We demonstrated that mGPS differentiated local from non-local microorganisms and used it to trace the global spread of AMR genes. mGPS's ability to localize samples to their waterbody, country, city, and transit stations opens new possibilities in tracing microbiomes and has applications in forensics, medicine, and epidemiology.

Circulation of avian Chlamydia abortus in the Netherlands and community-acquired pneumonia: an outbreak investigation and retrospective cohort study

In 2021, a novel group of Chlamydia strains in wild birds was classified as avian Chlamydia abortus, with unknown zoonotic potential. We report relevant features of avian C abortus infections from a Dutch family cluster and unrelated historical cases using clinical, epidemiological, and microbiological data. An outbreak of avian C abortus started in the Netherlands in December, 2022. Source investigation was done using questionnaires to interview patients and environmental sampling. The outbreak strain of avian C abortus was cultured from three patients from whom sufficient material was available for culture and underwent whole-genome analysis. The outbreak strains and retrospective cohort study strains previously submitted to the National Human Psittacosis surveillance programme in the Netherlands between 2010 and 2022 were typed by partial ompA sequencing. Strains with the same aberrant ompA genotype were further analysed with XerC gene plasmid analysis and compared with closely related Chlamydia sequences available in GenBank. An avian C abortus strain caused a cluster of respiratory illness in four family members. Three patients were hospitalised with community-acquired pneumonia, one of whom was admitted to the intensive care unit. The faeces of wild birds were considered a probable source for the index infection. For two family members, human-to-human transmission was a plausible route. Ten historical cases could be identified with avian C abortus with the same ompA genotype. All patients had been admitted to hospital, at least five developed pneumonia, and one died. This cluster supports that avian C abortus strains can cause human infections and underlines that human-to-human transmission should be considered when tracing the source of such infections. National Institute for Public Health and the Environment and Dutch Ministry of Agriculture, Fisheries, Food Security and Nature. For the Dutch translation of the abstract see Supplementary Materials section.

Rapid genome-wide profiling of DNA methylation and genetic variation using guide positioning sequencing (GPS).

Whole-genome bisulfite sequencing (WGBS) has been extensively utilized for DNA methylation profiling over the past decade. However, it has shown limitations in terms of high costs and inefficiencies. The productivity and accuracy of DNA methylation detection rely critically on the optimization of methodologies and the continuous refinements of related sequencing platforms. Here, we describe a detailed protocol of guide positioning sequencing (GPS), a bisulfite-based, location-specific sequencing technology designed for comprehensive DNA methylation characterization across the genome. The fundamental principle of GPS lies in the substitution of dCTP with 5-methyl-dCTP (5mC) at the 3'-end of DNA fragments by T4 DNA polymerase, which protects cytosines from bisulfite conversion to preserve the integrity of the base composition. This alteration allows the 3'-end to independently facilitate genetic variation profiling and guides the 5'-end, enriched with methylation information, to align more rapidly to the reference genome. Hence, GPS enables the concurrent detection of both genetic and epigenetic variations. Additionally, we provide an accessible description of the data processing, specifically involving certain software and scripts. Overall, the entire GPS procedure can be completed within a maximum of 15days, starting with a low initial DNA input of 100-500ng, followed by 4-5days for library construction, 8-10days for high-throughput sequencing (HTS) and data analysis, which can greatly facilitate the promotion and application of DNA methylation detection, especially for the rapid clinical diagnosis of diverse disease pathologies associated with concurrent genetic and epigenetic variations.

Evaluating the impact of surgery sequence on infection rates in hip or knee arthroplasty: does sequence matter?

The potential influence of surgical sequence of elective hip-and-knee reconstructive surgery in relation to an infection-related procedure on postoperative infection rates is not clearly understood. Therefore, we aimed to examine the impact of surgical sequence on the incidence of postoperative infections within one-year and the longest available follow-up period in patients undergoing hip-and-knee reconstructive surgery. A case-control study with propensity matching was utilized to examine elective surgeries conducted at Sunnybrook Holland Orthopaedic & Arthritic centre, Toronto, Canada between 2015 and 2018. We determined and categorized them based on their operating room (OR) sequence in relation to an infected case; the cases were those performed right after (post-infection cohort), and the controls were those performed before an infection-related procedure in the same OR (pre-infection cohort). We employed survival analysis to compare the infection incidence within one year and at the longest available follow-up among the propensity-matched cohort. A total of 13,651 cases were identified during the four year period. We successfully matched 153 cases (21 post-infection and 132 pre-infection) using propensity scores. Demographic and clinical characteristics were balanced through matching. Kaplan-Meier survival analysis showed no significant difference in infection-free survival within one year and at a median follow-up of 2.2 years [interquartile range 0.9-5.0] between surgeries conducted before and after infected cases (both log-rank p-values = 0.4). The hazard ratios for infection within one year and the longest follow-up period were both 0.37 [95%Confidence Interval 0.03-4.09, p = 0.418], as no more events occurred after one year. The sequence of surgical procedures, whether or not an elective arthroplasty or lower limb reconstructive procedure occurs before or after an infection-related case in the same OR, does not significantly affect postoperative infection rates. This finding supports the efficacy of the current infection control measures and suggests a reconsideration of surgical scheduling standards.

Elastic-Degenerate String Matching with 1 Error or Mismatch

An elastic-degenerate (ED) string is a sequence of n finite sets of strings of total length N, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all occurrences of a pattern of length m in an ED text. The EDSM problem has recently received some attention by the combinatorial pattern matching community, culminating in an O~(nmω-1)+O(N)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathcal {\ ilde{O}}(nm^{\\omega -1})+\\mathcal {O}(N)$$\\end{document}-time algorithm [Bernardini et al., SIAM J. Comput. 2022], where ω\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\omega $$\\end{document} denotes the matrix multiplication exponent and the O~(·)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathcal {\ ilde{O}}(\\cdot )$$\\end{document} notation suppresses polylog factors. In the k-EDSM problem, the approximate version of EDSM, we are asked to report all pattern occurrences with at most k errors. k-EDSM can be solved in O(k2mG+kN)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathcal {O}(k^2mG+kN)$$\\end{document} time, under edit distance, or O(kmG+kN)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathcal {O}(kmG+kN)$$\\end{document} time, under Hamming distance, where G denotes the total number of strings in the ED text [Bernardini et al., Theor. Comput. Sci. 2020]. Unfortunately, G is only bounded by N, and so even for k=1\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$k=1$$\\end{document}, the existing algorithms run in Ω(mN)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\varOmega (mN)$$\\end{document} time in the worst case. In this paper we make progress in this direction. We show that 1-EDSM can be solved in O((nm2+N)logm)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathcal {O}((nm^2 + N)\\log m)$$\\end{document} or O(nm3+N)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathcal {O}(nm^3 + N)$$\\end{document} time under edit distance. For the decision version of the problem, we present a faster O(nm2logm+Nloglogm)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathcal {O}(nm^2\\sqrt{\\log m} + N\\log \\log m)$$\\end{document}-time algorithm. We also show that 1-EDSM can be solved in O(nm2+Nlogm)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathcal {O}(nm^2 + N\\log m)$$\\end{document} time under Hamming distance. Our algorithms for edit distance rely on non-trivial reductions from 1-EDSM to special instances of classic computational geometry problems (2d rectangle stabbing or 2d range emptiness), which we show how to solve efficiently. In order to obtain an even faster algorithm for Hamming distance, we rely on employing and adapting the k-errata trees for indexing with errors [Cole et al., STOC 2004]. This is an extended version of a paper presented at LATIN 2022.

Effects of Microplastic on the Gastrointestinal Tract and Gut microbiome of Sprague Dawley Rats

ABSTRACT Nowadays there is evidence that animals are exposed to microplastics (MPs) via food, however there is not much known about their effect on tissue of gastrointestinal tract and on gut microbiome. In this study, adult male rats were fed with polyethylene MPs, mixed with standard pellet food for 24 days at different concentrations ranging from 0 to 1000 μg/day. At the end of experiment, rats were euthanized and histopathological investigation using light and electron microscopy and the gut microbiome was analyzed using MiSeq 16S rRNA amplicon sequencing. Microscopic analysis revealed significant impact of MPs on the intestine, including visible changes to the crypt area as well as reduction in mucus secretion. Autophagic vacuoles were observed in the livers of the rats fed with MPs at 100 µg/day. Oxidative stress was evident in rats fed with 1000 µg/day of MPs, as indicated by the presence of myeloid bodies in both intestinal and hepatic cells. The gut microbiome was also affected by MPs. Although, no distinct clusters were formed when the bacterial communities in the different treatments were ordinated by multidimensional scaling (NMDS), the diversity indices including operational taxonomic unit (OTU) richness and Chao1 exhibited an increasing trend with increasing MPs concentration. Pearson correlations revealed a linear increase in the relative sequence abundance of Clostridia (R=0.036, P=0.003) with increasing MPs concentration, but not in the case of other bacterial groups,. Lactobacillus faecis was the most abundant OTU in the entire dataset, and its relative abundance decreased significantly with increasing MPs concentration. We conclude that exposure to MPs can disrupt cellular function and disturb microbiome balance, and in the event of prolonged exposure, organisms might experience unpredictable effects.

Chronometric data and stratigraphic evidence support discontinuity between Neanderthals and early Homo sapiens in the Italian Peninsula

The process by which Palaeolithic Europe was transformed from a Neanderthal-dominated region to one occupied exclusively by Homo sapiens has proven challenging to diagnose. A blurred chronology has made it difficult to determine when Neanderthals disappeared and whether modern humans overlapped with them. Italy is a crucial region because here we can identify not only Late Mousterian industries, assumed to be associated with Neanderthals, but also early Upper Palaeolithic industries linked with the appearance of early H. sapiens, such as the Uluzzian and the Aurignacian. Here, we present a chronometric dataset of 105 new determinations (74 radiocarbon and 31 luminescence ages) from four key southern Italian sites: Cavallo, Castelcivita, Cala, and Oscurusciuto. We built Bayesian-based chronometric models incorporating these results alongside the relative stratigraphic sequences at each site. The results suggest; 1) that the disappearance of Neanderthals probably pre-dated the appearance of early modern humans in the region and; 2) that there was a partial overlap in the chronology of the Uluzzian and Protoaurignacian, suggesting that these industries may have been produced by different human groups in Europe.

HEV-3 subtypes and strains detected in cases of HEV infection in central Italy from 2015 to 2023.

HEV is an emerging pathogen in Europe and was previously shown to be hyperendemic in areas of Abruzzo and Lazio, Central Italy. No systematic analysis of the HEV strains responsible for human infections over several years in Central Italy has previously been reported. Aim of the study was the molecular characterization of HEV from autochthonous hepatitis E cases occurred in Abruzzo and Lazio between 2015 and 2023. Samples from 118 cases collected as part of virological surveillance in Abruzzo and Lazio from 2015 to 2023 were subjected to HEV sequencing and phylogenetic analysis. The main observed subtype was 3f, followed by 3c and 3e. The annual subtype distribution was quite stable over the observation period, but 3f cases tended to concentrate in winter/early spring whereas 3e cases in summer. Phylogenetic clusters of highly related sequences (a) highlighted unrecognized "point source outbreaks", (b) provided molecular support to temporally and/or geographically linked cases and (c) provided evidence for transmission of identical/highly related strains up to months/years following their first detection. The data provide an overview of the HEV strains responsible for human infections over eight years in Central Italy. The observed subtype distribution appears to agree better with the subtype distribution reported in Italy in pigs rather than in geographically matched wild boars, suggesting pig and its derivate food was a more frequent source of infection than wild boar in Abruzzo and Lazio. Molecular characterization is essential to recognize "point source outbreaks" and to monitor HEV circulation.

Soil eDNA biomonitoring reveals changes in multitrophic biodiversity and ecological health of agroecosystems

Soil health is integral to sustainable agroecosystem management. Current monitoring and assessment practices primarily focus on soil physicochemical properties, yet the perspective of multitrophic biodiversity remains underexplored. Here we used environmental DNA (eDNA) technology to monitor multitrophic biodiversity in four typical agroecosystems, and analyzed the species composition and diversity changes in fungi, bacteria and metazoan, and combined with the traditional physicochemical variables to establish a soil health assessment framework centered on biodiversity data. First, eDNA technology detected rich multitrophic biodiversity in four agroecosystems, including 100 phyla, 273 classes, 611 orders, 1026 families, 1668 genera and 1146 species with annotated classification, and the relative sequence abundance of dominant taxa fluctuates tens of times across agroecosystems. Second, significant differences in soil physicochemical variables such as organic matter (OM), total nitrogen (TN) and available phosphorus (AP) were observed among different agroecosystems, nutrients were higher in cropland and rice paddies, while heavy metals were higher in fish ponds and lotus ponds. Third, biodiversity metrics, including α and β diversity, also showed significant changes across agroecosystems, the soil biota was generally more sensitive to nutrients (e.g., OM, TN or AP), while the fungal communities were mainly affected by heavy metals in October (e.g., Cu and Cr). Finally, we screened 48 sensitive organismal indicators and found significant positive consistency between the developed eDNA indices and the traditional soil quality index (SQI, reaching up to R2 = 0.58). In general, this study demonstrated the potential of eDNA technology in soil health assessment and underscored the importance of a multitrophic perspective for efficient monitoring and managing agroecosystems.

Molecular similarities between the genes for Trypanosoma cruzi microtubule-associated proteins, mammalian interferons, and TRIMs

Initial studies using bioinformatics analysis revealed DNA sequence similarities between Trypanosoma cruzi GenBank® M21331, coding for Antigen 36 (Ag 36), and tripartite motif (TRIM) genes. TRIM40 showed 9.7% identity to GenBank M21331, and four additional TRIM genes had identities greater than 5.0%. TRIM37 showed a continuous stretch of identity of 12 nucleotides, that is, at least 25% longer than any of the other TRIMs. When we extended our analysis on the relationships of GenBank M21331 to further innate immune genes, using the Needleman-Wunsch (NW) algorithm for alignment, identities to human IFN-α, IFN-β, and IFN-γ genes of 13.6%, 12.6%, and 17.9%, respectively, were found. To determine the minimum number of genes coding for proteins closely related to Ag 36, a BLAST-p search was conducted with it versus the T. cruzi genome. The BLAST-p search revealed that T. cruzi GenBank M21331 had 14 gene sequences homologous to microtubule-associated protein (MAP) genes with 100% amino acid sequence identity. To verify the similarities in non-human genes, a study comparing TRIM21 region sequences among mammalian species to the comparable human TRIM21 region showed that related sequences were also present in 11 mammalian species. The MAP genes homologous to Ag 36 form a family of at least 14 genes which mimic human immune genes in the IFN and TRIM families. This mimicry is of gene sequences and not their protein products or epitopes. These results appear to be the first description of molecular mimicry of immune genes in humans by a protozoan parasite.

Single cell and TCR analysis of immune cells from AAV gene therapy-dosed Duchenne muscular dystrophy patients

Clinical trials for Duchenne muscular dystrophy (DMD) are assessing the therapeutic efficacy of systemically delivered adeno-associated virus (AAV) carrying a modified DMD transgene. High vector doses (>1E14 vg/kg) are needed to globally transduce skeletal muscles; however, such doses trigger immune-related adverse events. Mitigating these immune responses is crucial for widespread application of AAV-based therapies. We used single-cell RNA-sequencing and T-cell receptor (TCR)-sequencing on peripheral blood mononuclear cells from five participants prior to, and after, dosing. One subject in the high-dose cohort experienced thrombotic microangiopathy (TMA). Few changes in cell frequencies occurred after treatment; however, differential gene expression demonstrated induction of interferon response genes in most T-cell types. T-cell clonotype and clumping analysis showed the expansion or appearance of groups of related TCR sequences in the post-treatment samples. Three of these expanded clumps could be assigned to prior Human Herpesvirus infections, two of which were present in the participant that exhibited TMA. These data provide insight on the mechanistic basis of human immune-AAV interactions and lay a foundation for improved understanding of why TMA arises in some patients and not others.

A Novel C-Terminal Truncated Bacteriocin Found by Comparison between Leuconostoc mesenteroides 406 and 213M0 Isolated from Mongolian Traditional Fermented Milk, Airag.

Bacteriocins produced by lactic acid bacteria are known to be useful tools for food biopreservation and fermentation control. Leuconostoc mesenteroides subsp. mesenteroides 406 and 213M0 isolated from different samples of Mongolian traditional fermented milk, airag, had been reported to produce listericidal bacteriocin-like inhibitory substances with similar but slightly different properties. In this study, the antibacterial properties and the related gene sequences of both strains were compared, and then their bacteriocins were purified and identified. Strain 406 was superior to strain 213M0 in cell growth and antibacterial activity against many strains. However, the activity of 213M0 was stronger than that of 406 against a few strains. DNA sequencing revealed two and three plasmids in 406 and 213M0, respectively, and each one of them harbored an almost identical mesentericin Y105-B105 gene cluster. Removal of these plasmids resulted in a complete loss of activity, indicating that the antibacterial activity of both strains was generated by bacteriocins encoded on the plasmids. Mesentericins Y105 and B105 were purified from both cultures, and another novel bacteriocin, named mesentericin M, was identified from the 213M0 culture only. Its structural gene was coded on a 213M0 plasmid and, surprisingly, its C-terminal three amino acid residues were post-translationally cleaved. To our knowledge, this is the first report of a C-terminal truncated bacteriocin. In conclusion, the novel bacteriocin should be mainly responsible for the difference in antibacterial properties between the two strains.

Genetic diversity, virulence profiles, and antimicrobial resistance of Salmonella enterica serovar Typhi isolated from typhoid fever patients in Baghdad, Iraq

Typhoid fever is an important health issue in developing countries, and the pathogenicity of Salmonella enterica serovar Typhi (S. ser. Typhi) depends on the presence of different virulence factors. Therefore, this study aimed to investigate the spread of virulence genes among S. Typhi isolates from patients with typhoid fever in Baghdad, Iraq. Sixty S. Typhi isolates were collected from several hospitals in Baghdad and identified using VITEK-II and confirmed by polymerase chain reaction (PCR) to detect the 16S rRNA gene. After testing their susceptibility to different antimicrobials (via the disk diffusion method), we found the highest resistance rates (100 %) were to ampicillin, piperacillin, cefotaxime, and ceftriaxone. The highest sensitivity rates (100 %) were to ertapenem, imipenem, meropenem, and sulfamethoxazole/trimethoprim. The presence of genes encoding for virulence in S. Typhi isolates was tested by conventional PCR. The results showed that out of 60 isolates, 59 (98.3 %), 59 (98.3 %), 58 (96.7 %), and 60 (100 %) were positive for viaB, staA, cdtB, and orfL genes, respectively. The sequencing of PCR products (viaB, staA, cdtB, and orfL genes) was carried out at the Macrogen Company (Seoul, Korea). The sequences were compared with nucleotide sequences in the BLAST GenBank database, and data obtained from the sequencing of these virulence genes were submitted to GenBank under different accession numbers. A phylogenetic analysis of the 16S rRNA gene sequence found a high similarity between local sequences and the closely related sequences of genes in GenBank. The presence of the viaB, staA, cdtB, and orfL virulence genes in nearly all of the isolates under examination suggests that they play an important role in the pathogenicity of local isolates.

Real-time risk prediction of chemical processes based on attention-based Bi-LSTM

Refined risk prediction must be achieved to guarantee the safe and steady operation of chemical production processes. However, there is high nonlinearity and association coupling among massive, complicated multisource process data, resulting in a low accuracy of existing prediction technology. For that reason, a real-time risk prediction method for chemical processes based on the attention-based bidirectional long short-term memory (Attention-based Bi-LSTM) is proposed in this study. First, multisource process data, such as temperature, pressure, flow rate, and liquid level, are preprocessed for denoising. Data correlation is analyzed in time windows by setting time windows and moving step lengths to explore correlations, thus establishing a complex network model oriented to the chemical production process. Second, network structure entropy is introduced to reduce the dimensions of the multisource process data. Moreover, a 1D relative risk sequence is acquired by max–min deviation standardization to judge whether the chemical process is in a steady state. Finally, an Attention-based Bi-LSTM algorithm is established by integrating the attention mechanism and the Bi-LSTM network to fit and train 1D relative risk sequences. In that way, the proposed algorithm achieves real-time prediction and intelligent perception of risk states during chemical production. A case study based on the Tennessee Eastman process (TEP) is conducted. The validity and reasonability of the proposed method are verified by analyzing distribution laws of relative risks under normal and fault conditions. Also, the proposed algorithm importantly improves the prediction accuracy of chemical process risks relative to that of existing prediction technologies.

A simple method for finding related sequences by adding probabilities of alternative alignments.

The main way of analyzing genetic sequences is by finding sequence regions that are related to each other. There are many methods to do that, usually based on this idea: Find an alignment of two sequence regions, which would be unlikely to exist between unrelated sequences. Unfortunately, it is hard to tell if an alignment is likely to exist by chance. Also, the precise alignment of related regions is uncertain. One alignment does not hold all evidence that they are related. We should consider alternative alignments too. This is rarely done, because we lack a simple and fast method that fits easily into practical sequence-search software. Described here is the simplest-conceivable change to standard sequence alignment, which sums probabilities of alternative alignments and makes it easier to tell if a similarity is likely to occur by chance. This approach is better than standard alignment at finding distant relationships, at least in a few tests. It can be used in practical sequence-search software, with minimal increase in implementation difficulty or run time. It generalizes to different kinds of alignment, for example, DNA-versus-protein with frameshifts. Thus, it can widely contribute to finding subtle relationships between sequences.

Integrative mRNA and miRNA Expression Profiles from Developing Zebrafish Head Highlight Brain-Preference Genes and Regulatory Networks.

Zebrafish is an emerging animal model for studying molecular mechanism underlying neurodevelopmental disorder due to its advantage characters. miRNAs are small non-coding RNAs that play a key role in brain development. Understanding of dynamic transcriptional and post-transcriptional molecules and their regulation during the head development is important for the study of neurodevelopmental disorder. In this study, we performed the high-throughput sequencing of mRNAs and miRNAs in developing zebrafish head from pharyngula to early larval stages and carried out bioinformatic analysis including differential expression and functional enrichment as well as joint analysis of miRNAs and mRNAs, and also compared with other related public sequencing datasets to aid our interpretation. A large number of differential expression genes with a large fold change were detected during the head development. Further clustering and functional enrichment analyses indicated that genes in late stage were most related with synaptic signaling. Overlap test analysis showed a significant enrichment of brain-preference and synapse-associated gene set in the head transcriptome compared with the whole embryo transcriptome. We also constructed miRNA-mRNA network for those brain-preference genes and focused on those densely connected network components. CRISPR-Cas9-mediated snap25b mutants led to embryonic development defects and decreases locomotor activity. Altogether, the present study provides developmental profiles of head-enriched mRNAs and miRNAs at three critical windows for nervous system development, which may contribute to the study of neurodevelopmental disorder.

MARCH1 negatively regulates TBK1-mTOR signaling pathway by ubiquitinating TBK1

BackgroundTBK1 positively regulates the growth factor-mediated mTOR signaling pathway by phosphorylating mTOR. However, it remains unclear how the TBK1-mTOR signaling pathway is regulated. Considering that STING not only interacts with TBK1 but also with MARCH1, we speculated that MARCH1 might regulate the mTOR signaling pathway by targeting TBK1. The aim of this study was to determine whether MARCH1 regulates the mTOR signaling pathway by targeting TBK1.MethodsThe co-immunoprecipitation (Co-IP) assay was used to verify the interaction between MARCH1 with STING or TBK1. The ubiquitination of STING or TBK1 was analyzed using denatured co-immunoprecipitation. The level of proteins detected in the co-immunoprecipitation or denatured co-immunoprecipitation samples were determined by Western blotting. Stable knocked-down cells were constructed by infecting lentivirus bearing the related shRNA sequences. Scratch wound healing and clonogenic cell survival assays were used to detect the migration and proliferation of breast cancer cells.ResultsWe showed that MARCH1 played an important role in growth factor-induced the TBK1- mTOR signaling pathway. MARCH1 overexpression attenuated the growth factor-induced activation of mTOR signaling pathway, whereas its deficiency resulted in the opposite effect. Mechanistically, MARCH1 interacted with and promoted the K63-linked ubiquitination of TBK1. This ubiquitination of TBK1 then attenuated its interaction with mTOR, thereby inhibiting the growth factor-induced mTOR signaling pathway. Importantly, faster proliferation induced by MARCH1 deficiency was weakened by mTOR, STING, or TBK1 inhibition.ConclusionMARCH1 suppressed growth factors mediated the mTOR signaling pathway by targeting the STING-TBK1-mTOR axis.

Jurassic fossil juvenile reveals prolonged life history in early mammals.

Living mammal groups exhibit rapid juvenile growth with a cessation of growth in adulthood1. Understanding the emergence of this pattern in the earliest mammaliaforms (mammals and their closest extinct relatives) is hindered by a paucity of fossils representing juvenile individuals. We report exceptionally complete juvenile and adult specimens of the Middle Jurassic docodontan Krusatodon, providing anatomical data and insights into the life history of early diverging mammaliaforms. We used synchrotron X-ray micro-computed tomography imaging of cementum growth increments in the teeth2-4 to provide evidence of pace of life in a Mesozoic mammaliaform. The adult was about 7 years and the juvenile 7 to 24 months of age at death and in the process of replacing its deciduous dentition with its final, adult generation. When analysed against a dataset of life history parameters for extant mammals5, the relative sequence of adult tooth eruption was already established in Krusatodon and in the range observed in extant mammals but this development was prolonged, taking place during a longer period as part of a significantly longer maximum lifespan than extant mammals of comparable adult body mass (156 g or less). Our findings suggest that early diverging mammaliaforms did not experience the same life histories as extant small-bodied mammals and the fundamental shift to faster growth over a shorter lifespan may not have taken place in mammaliaforms until during or after the Middle Jurassic.