Sequence Analysis Research Articles

Algebraic Gestalt-archetypes of Probabilities in Genomic DNAs, Cyclic Gray Codes, Quantum Bioinformatics

The article is devoted to the study of the regularities of the statistical organization of nucleotide sequences of single-stranded DNAs in genomes of higher and lower organisms, as well as their connections with cyclic Gray codes and the problem of holistic structures (gestalts) in physiology. The author presents stable statistical structures of an algebraic nature, which are found in many genomic DNAs and are called algebraic gestalt-archetypes of probabilities in genomic DNAs. They are discussed as a possible basis for several genetically inherited physiological and psychophysical properties. The numerical rules of these genomic archetypes realized in nature for a representative class of genomic DNAs, whose initial data were taken by the author from the publicly available genomic data bank “GenBank”, are formulated. The analysis of single-stranded genomic DNAs was carried out using the author's method of "hierarchies of multilayer statistics", representing the nucleotide sequence of DNA as a multilayer text structure, in which each n-th layer is a sequence of n-plets (that is, of monoplets, or duplets, or triplets, etc.). In each such layer, the percentages of each of the types of its n-plets are calculated, the values of which are inserted into the so-called genetic (2n∙2n) Karnaugh matrices, whose columns and rows are numbered by n-bit Gray codes by analogy with Karnaugh maps from the Boolean algebra of logic. The data of the analysis of the nucleotide sequence of DNA of the human chromosome № 1, containing about 250 million nucleotides, are represented as an example. The obtained data are discussed in light of the problem of genetically inherited holistic structures in biology and the tasks of developing algebraic biology, genetic biomechanics, quantum bioinformatics, artificial intelligence, and genetic algorithms.

Pervasive mitochondrial tRNA gene loss in the clade B of haplosclerid sponges (Porifera, Demospongiae)

Abstract Mitochondrial tRNA gene loss and cytosolic tRNA import are two common phenomena in mitochondrial biology, but their importance is often under-appreciated in animals. This is because the mitochondrial DNA (mtDNA) of most bilaterally symmetrical animals (Bilateria) encodes a complete set of tRNAs required for mitochondrial translation. By contrast, the mtDNA of non-bilaterian animals (phyla Cnidaria, Ctenophora, Porifera, and Placozoa) often contains a reduced set of tRNA genes, necessitating tRNA import from the cytosol. Interestingly, in many non-bilaterian lineages, tRNA gene content appears to be set early in evolution and remains conserved thereafter. Here, we report that Clade B of Haplosclerid Sponges (CBHS) represents an exception to this pattern, displaying considerable variation in tRNA gene content even among relatively closely related species. We determined mt-genome sequences for eight CBHS species and analyzed them in conjunction with six previously available sequences. Additionally, we sequenced mt-genomes for two species of haplosclerid sponges outside the CBHS and used eight previously available sequences as outgroups. We found that tRNA gene content varied widely within CBHS, ranging from three in an undescribed Haliclona species (Haliclona sp. TLT785) to 25 in Xestospongia muta and X. testudinaria. Furthermore, we found that all CBHS species outside the genus Xestospongia lacked the atp9 gene, with some also lacking atp8. Analysis of nuclear sequences from Niphates digitalis revealed that both atp8 and atp9 had transferred to the nuclear genome, while the absence of mt-tRNA genes indicated their genuine loss. We argue that CBHS can serve as a valuable system for studying mt-tRNA gene loss, mitochondrial import of cytosolic tRNAs, and the impact of these processes on mitochondrial evolution.

Molecular prevalence and associated risk factors of Entamoeba spp. in donkeys in Shanxi Province, North China

BackgroundThe intestinal protozoa Entamoeba spp. can infect humans and various animals, including donkeys, causing diarrhea and malabsorption and presenting significant risks to animal husbandry and public health. Most Entamoeba species are not pathogenic except for Entamoeba histolytica. China has among the highest rates of donkey farming worldwide. Donkey (Equus asinus) farming is increasingly important in China because of their draft and medicinal value; however, epidemiological data on Entamoeba spp. in donkeys remains limited globally. This study aimed to investigate the prevalence of Entamoeba in donkeys in Shanxi Province, North China, and assess associated risk factors using a molecular approach.MethodsFecal samples of 815 donkeys from three representative geographical locations in Shanxi Province were collected to investigate the presence of Entamoeba spp. A portion of the small-subunit rRNA gene (SSU rRNA) was amplified and sequenced to determine the prevalence and species/genotypes of Entamoeba spp. Statistical analysis of possible risk factors was performed using Statistical Product and Service Solutions (SPSS) 26.0 software. The phylogenetic relationship of Entamoeba spp. was reconstructed using the neighbor-joining (NJ) method in Molecular Evolutionary Genetics Analysis (Mega) 7.0 software.ResultsThe overall prevalence of Entamoeba spp. in donkeys in Shanxi Province was 7.12% (58/815). Two species (Entamoeba sp. RL9 and Entamoeba equi) were identified by sequence analysis; of these, Entamoeba sp. RL9 was the most prevalent species in donkeys in this study. Statistical analysis revealed that the donkeys' sex, region, age, and altitude are the risk factors associated with Entamoeba spp. prevalence (P < 0.05). Phylogenetic analysis indicated that the sequences of Entamoeba sp. RL9 and E. equi isolated from donkeys in this study were clustered with previously reported animal-derived Entamoeba sp. RL9 and E. equi sequences, respectively.ConclusionsThis study reports the occurrence and prevalence of Entamoeba spp. in donkeys worldwide for the first time to our knowledge. This not only expands the geographical distribution but also broadens the host range of Entamoeba spp., addressing the knowledge gap regarding the prevalence of Entamoeba spp. in donkeys, providing baseline data for carrying out prevention and control of Entamoeba spp. in donkeys in China.Graphical

First Report of Lasiodiplodia theobromae Causing Wilt and Fruit Rot of Pepper in Hainan Province, China.

Ornamental pepper (Capsicum annuum L.) is an economically important plant with extensive genetic diversity (Zhang et al. 2020). In September 2022, symptoms of wilt and fruit rot were identified in approximately 0.02 hectares of an ornamental pepper plantation in Haikou, Hainan Province, China (110°32' E, 20°06' N). Disease severity reached 85%, with an incidence rate of 90%. Symptoms started as black foliar spots that expanded into large lesions, spreading to fruits and stems, causing wilting (Fig. S1). Samples from symptomatic leaves, fruits, and stems of 27 plants were surface-sterilized with 75% ethanol for 30 s, rinsed five times with sterile water, air-dried, plated on potato dextrose agar (PDA), and incubated at 28°C for 5 to 6 days. To obtain pure fungal cultures, initial isolates were subcultured onto fresh PDA. Among the 27 fungal cultures, 11 isolates from leaves and fruits consistently formed gray to olivaceous colonies. Isolate LJY224 initially produced grayish-white, fluffy mycelia with radiating aerial hyphae. Over time, the colony became grayish-black and produced black, nearly spherical pycnidia. The conidia were oval, initially transparent, and single-celled. Mature conidia were dark brown, septate, with longitudinal striations, averaging 11.55 ± 0.75 µm in width and 24.93 ± 1.50 µm in length (n=35) (Fig. S2), indicating Lasiodiplodia spp. Genomic DNA was extracted using a fungal DNA extraction kit (OMEGA BIO-TEK, GZ Feiyang Biotech Co., Ltd., Guangzhou, China). Molecular identification involved sequencing the rRNA internal transcribed spacer (ITS) region and genes encoding β-tubulin (TUB) and translation elongation factor 1-α (TEF1) with primers ITS1/ITS4, Bt2a/Bt2b, and EF1-983F/EF1-2218R, respectively (White et al. 1990; Rosado et al. 2016; Rehner and Buckley 2005). BLASTn searches with the obtained ITS, TUB, and TEF1 sequences (GenBank accessions OQ612711, OR039814, OR039813) revealed 98% to 100% identity with Lasiodiplodia theobromae reference sequences from the NCBI database (OR018404, KR260830, MN461169), matching 541/548, 446/446, and 947/955 base pairs, respectively. A phylogenetic tree was constructed using concatenated multi-locus sequence analysis (MLSA) of ITS, TUB, and TEF1 (Fig. S3). To fulfill Koch's postulates, healthy 3-month-old ornamental pepper plants were inoculated by spraying the entire plant with a conidial suspension (50 ml, 107 conidia/L) of LJY224, using sterile water as a negative control. Each treatment included three replicates. Plants were maintained at 25°C, 75% humidity, under a 12-h light/dark cycle, and monitored daily. After 14 days, inoculated plants developed black foliar spots that expanded into large lesions, spreading to fruits and stems, and causing wilting, consistent with initial symptoms, while control plants remained healthy (Fig. S4). The re-isolated pathogen showed identical morphology to the original strain. In contrast, no fungi were isolated or recovered from the plants inoculated with water. Results from disease symptoms, colony and spore morphology, pathogenicity tests, and multi-locus DNA sequence analysis suggest that L. theobromae was the pathogen responsible for the disease symptoms on ornamental peppers. L. theobromae is closely related to Botryosphaeria dothidea, both of which cause fruit rot in peppers (Rui et al. 2023). To our knowledge, this is the first report of L. theobromae causing leaf wilt and fruit rot in ornamental pepper in Hainan Province, China, offering insights to mitigate crop losses.

Description of two new species of the genus Hemicycliophora (Nematoda: Hemicycliophoridae) from the USA

Summary Two species of sheath nematodes were studied using an integrative approach, combining morphological and molecular analyses. The first species was collected from an oak tree (Quercus sp.) imported from Texas into Florida, while the second one was obtained from the ornamental palm Phoenix sylvestris in a Florida nursery. These species were compared to a closely related species, Hemicaloosia uarki, which was originally described in Arkansas. Phylogenetic analyses using partial 18S rRNA, D2-D3 expansion segments of 28S rRNA, ITS rRNA, and COI gene sequences revealed that sheath nematodes from Texas and Florida represent two new species of the genus Hemicycliophora, which are described here as Hemicycliophora ornata sp. n. and H. silvestris sp. n., respectively. In the phylogenetic tree based on ITS rRNA gene sequences, Hemicaloosia uarki grouped within a clade of other Hemicycliophora species rather than within the Hemicaloosia species clade, indicating that this species belongs to the genus Hemicycliophora rather than to Hemicaloosia. Consequently, this species was reclassified as Hemicycliophora uarki comb. n. These findings confirmed that morphological characters traditionally used to distinguish Hemicaloosia species from those of Hemicycliophora are valid but insufficient for reliable identification when some life stages, such as males, are absent. The presence of males with straight spicules is a very useful character to validate the morphological identification of Hemicaloosia species. In absence of this life stage, phylogenetic analysis of gene sequences is the only reliable method to accurately differentiate sheath nematodes resembling Hemicaloosia from Hemicycliophora.

Characterization of Begomovirus Isolates Causing YMD in soybean and Analyzing the Relation with Early Reported Strains of Begomovirus from New Delhi Region

This work was focused on the exact characterization of begomovirus correlated with yellow mosaic disease (YMD) in soybean during the monsoon season. This information helped to understand the time-bound status of the viral group. Augmented design and was carried out at the research field. Starting material source for pure viral DNA Initial source material consisted of soybean plants (JS335) with a prominent yellow mosaic symptom that were grown in sick plots under controlled conditions in order to obtain a DNA samples that also contained the genomes of begomovirus. The experiment used an augmented design and was carried out at the research field in New Delhi during the 2018 kharif season. In each replication, the susceptible cultivar (JS335) genotypes were planted for the establishment of a sick soybean plot for YMD development purposes. A limited number of MYMIV DNA-A sequences was used to create the phylogenetic tree. Cluster W was used to align the sequences, with the default gap penalty values of gap opening 10 and extension 0.2. A neighbor-joining tree was built using MEGA 11.0, a p-distance model, and pairwise gap deletion. The viral genome was amplified and sequenced. The sequence analysis revealed that the viral genome is 2747 nucleotides long, similar to monopartite begomoviruses, and has seven conserved ORFs. Further nucleotide (nts) sequence comparisons revealed that the genome had the maximum sequence identity of 99%, which is identical to the previously reported sequence. The DNA-A of MYMIV (GenBank accession number: OQ473638) was made from 2747 nucleotides that were 99% the same as the sequence that had already been reported. Previously, that Mungbean yellow mosaic virus (MYMV) and Mungbean yellow mosaic India virus (MYMIV) are the primary begomoviruses causing yellow mosaic disease (YMD) in soybeans in India. This study also demonstrated that our isolate of MYMIV was more similar to the one that was already recognized to be Mu2 New Delhi isolate. This information would be useful in more detailed screening processes under controlled condition and evaluation of soybean genotypes as part of variety development for sustainable cultivation of soybean.

Isolation, Characterization, and Anti-Biofilm Activity of a Novel Kaypoctavirus Against K24 Capsular Type, Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates

Background/Objectives: The significant outbreak of multidrug-resistant Klebsiella pneumoniae has emerged as a primary global concern associated with high morbidity and mortality rates. Certain strains of K. pneumoniae are highly resistant to most antibiotics available in clinical practice, exacerbating the challenge of bacterial infections. Methods: Phage vB_KpnP_PW7 (vKPPW7) was isolated and characterized. Its morphology, stability, adsorption rate, one-step growth curve, lytic activity, whole-genome sequence analysis, and antibacterial and antibiofilm activities were evaluated. Results: The virulent phage has a 73,658 bp linear dsDNA genome and was classified as a new species of the genus Kaypoctavirus, subfamily Enquatrovirinae, and family Schitoviridae. Phage vKPPW7 has a high adsorption rate, a short latent period, and a large burst size. The phage showed activity against 18 K. pneumoniae isolates with the K24 capsular type but was unable to lyse K. pneumoniae isolates whose capsular type was not classified as K24. Additionally, phage vKPPW7 demonstrated strong stability across various temperatures and pH values. The phage exhibited antibacterial activity, and scanning electron microscopy (SEM) confirmed its ability to lyse MDR K. pneumoniae with the K24 capsular type. Furthermore, phage vKPPW7 effectively removed preformed biofilm and prevented biofilm formation, resulting in reduced biofilm biomass and biofilm viability compared to controls. The architecture of phage-treated biofilms was confirmed under SEM. Conclusions: These findings suggest that phage vKPPW7 holds promise for development as a therapeutic or biocontrol agent.

Combined metabolomics and 16S rDNA sequence analyses of the gut microbiome reveal the action mechanism of Fructus Akebiae against hepatic fibrosis

ObjectivesTo explore the mechanism underlying the effect of Fructus Akebiae (FAE) against hepatic fibrosis in mice through combined network pharmacology, liver metabolomics, and 16S rDNA analyses of the gut microbiota.MethodsIn this study, we randomly divided mice into the control, model, FAE high-dose, FAE medium-dose, and FAE low-dose groups to analyze the pathological changes in the hepatic fibrosis and levels of the α-SMA, collagen 1, Nuclear Factor Kappa B (NF-κ B), Toll Like Receptor 4 (TLR4). The gut microbiota was analyzed through 16S rDNA sequencing analysis of liver metabolites using liquid chromatography-mass spectrometry. Furthermore, network pharmacology was used to determine the specific molecular regulation mechanism of FAE in hepatic fibrosis treatment.ResultsFAE treatment markedly improved the pathological changes in the hepatic fibrosis. Analysis revealed that FAE administration reversed the carbon tetrachloride (CCl4)-induced dysbiosis by increasing the abundance of Akkermansia and reducing that of Cyanobacteria. Additionally, metabolomic analysis showed that FAE treatment reversed the CCl4-induced metabolic disorders by regulating amino and nucleotide sugar metabolism. Furthermore, correlation analysis showed that Akkermansia and Verrucomicobiota were closely related to D-tolasaccharide and maltotetraose saccharide. Moreover, network pharmacology indicated that FAE might regulate the signaling pathway through the JUN/CASP3/NOS3/PTGS2/HSP90AA1 during treatment.ConclusionFAE may be a promising treatment for hepatic fibrosis, and its protective effects are associated with improvements in the microbiome and metabolic disorders.

First detection and molecular characterization of Jingmen tick virus with a high occurrence in Rhipicephalus (Boophilus) microplus collected from livestock in Cameroon (2024)

BackgroundJingmen tick virus (JMTV) is a novel tick-borne virus detected for the first time in Rhipicephalus (Boophilus) microplus in China. To date, there is no information regarding the circulation of JMTV in ticks collected from livestock in Cameroon. As part of the surveillance for arboviral circulation, this study aimed to assess the presence of JMTV in ticks collected from livestock (cattle and sheep) in an area of the Akonolinga health district, Center Region, Cameroon.MethodsA cross sectional study was carried out during the dry season between 5 and 14 March 2024. Ticks were collected from cattle and sheep in six sampling sites in an area approximately 30 km long and 18 km wide along the Nyong River, in central Cameroon. Ticks were identified morphologically and molecularly. Total RNA/DNA was extracted from tick pools and screened for JMTV RNA using a segment 2 RT-qPCR system. Positive JMTV pools were sequenced for partial JMTV-Segment 1 and full genome analyses.ResultsA total of 622 ticks, organized into 251 pools were collected from 155 cattle and nine sheep. They consisted of five species covering three genera: R. (B.) microplus (472; 75.9%), Amblyomma variegatum (118; 19.0%), Hyalomma truncatum (13; 2.1%), Hyalomma rufipes (2; 0.3%), and other Rhipicephalus spp. (17; 2.7%). The quantitative reverse transcription polymerase chain reaction (qRT-PCR) screening of 251 tick pools yielded 61 JMTV-positive pools, of which 58 corresponded to R. (B.) microplus. Multiple sequence analysis revealed that JMTV from the Akonolinga area shared > 95% identity with strains from Guinea, and that these strains clustered phylogenetically together.ConclusionsWe provide molecular evidence of the presence of JMTV in R. (B.) microplus and A. variegatum collected from cattle and sheep from an area not yet recognized as endemic for this virus, confirming its wide geographical distribution.Graphical

A Review Article: Mitigation Strategies for Seismic Damage in Structures

This in-depth review article provides a comprehensive analysis of mitigation strategies for seismic damage in structures, focusing on the importance of understanding seismic properties and implementing advanced analysis techniques. The review underscores the critical role of structural properties, including stiffness, strength, and ductility, in designing earthquake-resistant structures. By exploring a range of seismic analysis methods, such as force-based, displacement-based, and numerical approaches, the review highlights the significance of a holistic approach in assessing structural response to seismic events. Moreover, the review delves into innovative methods like subspace system identification for damage detection and statistical analysis of seismic sequences, offering promising avenues for future research. The adoption of passive energy dissipation systems and base isolation techniques emerges as key strategies in reducing seismic damage and enhancing structural resilience. Additionally, the review discusses the potential of machine learning techniques in predicting seismicity rates and improving risk management in seismic-prone areas. By combining traditional and advanced methods, this review sets the stage for further developments in seismic damage mitigation strategies. The integration of technological expertise, scientific aptitude, and interdisciplinary approaches is highlighted as essential in ensuring the built environment adapts to unforeseeable natural forces. Ultimately, this review provides a foundational resource for academics, policymakers, and practitioners in the field of earthquake mitigation and structural safety.

New species and new records of the basidiolichen Sulzbacheromyces (Lepidostromataceae) from India

The basidiolichens in India are rare and prior to this study, only three species were known. A detailed study of basidiolichen specimens freshly collected and some already available at herbarium LWG resulted in interesting species of Sulzbacheromyces. Notably, all these specimens were collected from northeastern states of India. Sulzbacheromyces arunachalensis is described as new to science which is characterized by its terricolous and crustose thallus; chlorococcoidal photobiont; terete to fusiform, unbranched, white to off-white basidiomata; reniform, 7.1–8.9 × 3.0–3.9 µm basidiospores. The novelty of the species is further confirmed by phylogenetic analysis of the nrITS sequence. In addition, S. bicolor and S. yunnanensis are reported for the first time in India. A key to all known species of Sulzbacheromyces from the world is provided. The discovery of the new species from northeastern India once agin proves it to be a lichen diversity hotspot. The present communication emphasises the need for special focus on basidiolichen study in India.

First detection and phylogenetic analysis of Trypanosoma species in European wolves and bears: discovery of novel haplotypes.

Wild carnivores may be important sources of emerging zoonotic pathogens worldwide, however, specific data concerning their presence in large carnivores are limited. The genus Trypanosoma (protozoan parasites) comprises numerous species adapted to all classes of vertebrates. This genus includes highly pathogenic species, such as T. brucei ssp., T. congolense or T. vivax. The aim of this study was to expand on the ecological or zoonotic significance of detecting Trypanosoma in large carnivores. Samples from free-living carnivores (n = 26) were collected. The diversity and occurrence of Trypanosoma species among wildlife in Europe were investigated through the analysis of 18S rRNA gene sequences. The phylogenetic analysis showed three new haplotypes of the 18S rRNA gene of Trypanosoma sp. isolated from two grey wolves (Canis lupus) and two brown bears (Ursus arctos). To the best of our knowledge, this this study represents the first detection of trypanosomes in large carnivores in Europe. The detection of Trypanosoma sp. was achieved through nested- PCR amplification. Furthermore, the identification of new haplotypes of these protozoan highlights variability within Trypanosoma sp., which could lead to the emergence of new, potentially more virulent variants of these parasites in wild animal populations, posing a potential threat to their health. Moreover, these findings underscore the need for further research to comprehensively understand the diversity, distribution, and potential impact of Trypanosoma species on the populations of large carnivores.

Molecular characterization, chemical profile and biological properties of essential oils from Chamaemelum nobile (L.) flowers of Morocco: in vitro and in silico studies

IntroductionThis study investigated the antioxidant, antimicrobial, and insecticidal properties of Chamaemelum nobile (L.) essential oil (CN-EO), harvested in Taounate, Morocco. The molecular composition and chemical profile of CN-EO were also characterized.MethodsThe CN-EO was extracted using a Clevenger apparatus. Its chemical composition was analyzed using gas chromatography-mass spectrometry (GC-MS). Antioxidant activity was evaluated using the DPPH assay, while antimicrobial properties were assessed via the disk diffusion method to measure inhibition zones against various bacterial and fungal strains. Insecticidal activity was tested through bioassays to determine insect mortality and repellency rates. Phylogenetic analysis of DNA sequences was conducted to confirm the species identity.ResultsGC-MS analysis identified 24 compounds in CN-EO, with β-Oplopenone (18.66%), Spathulenol (14.90%), and Himachalene (12.47%) as major constituents. CN-EO exhibited strong antioxidant activity (IC50 = 135.8 ± 1.03 μg/mL). Antimicrobial assays revealed inhibition zones of up to 20.67 ± 0.58 mm (Staphylococcus aureus) and antifungal inhibition of 40.42% ± 2.82% against Aspergillus flavus. Insecticidal tests showed total insect mortality at 166 µL/L within 48 h and a 60% repellent effect. Phylogenetic analysis of the DNA sequence revealed a 99.22% similarity with Chamaemelum nobile (L.).ConclusionThese results demonstrate the significant potential of Moroccan CN-EO in phytomedicine. It exhibits a wide range of biological activities and shows great promise as a natural antioxidant, antimicrobial agent, antifungal, and insecticide.

Characteristics of Plasmodium vivax apicomplexan amino acid transporter 8 (PvApiAT8) in the cationic amino acid transport.

Plasmodium vivax is the most widespread malaria parasite affecting humans, and its eradication is challenging due to the spread of drug-resistant parasites and their ability to remain in liver as a dormant stage. These parasites invade and multiply extensively within hepatocytes and erythrocytes in the host, relying on nutrient acquisition for their growth and replication. A promising new treatment aimed at targeting P. vivax involves blocking cationic amino acid uptake, which is a biological source of nutrients for the parasite. Novel Putative Transporter 1 (NPT1), identified as a cationic amino acid transporter in Apicomplexan, has a homologue in Plasmodium species known as apicomplexan amino acid transporter 8 (ApiAT8). This study focuses on P. vivax ApiAT8 to understand its precise role. PvApiAT8 was expressed in Xenopus laevisoocytes and shown to selectively uptake cationic amino acids. The uptake activity of [3H] L-arginine was shown to depend on PvApiAT8 expression time and substrate incubation time. PvApiAT8 was sodium-independent and functioned at pH levels between 6.5 and 8.5, with no efflux activity observed. Kinetic analysis showed saturable uptake for L-arginine consistent with Michaelis-Menten kinetics, with a Km of 1.5 ± 0.3 µM and a Vmax of 25.0 ± 4.8 pmol/oocyte/hr. Inhibition assays further confirmed its selectivity for cationic amino acids such as L-arginine, L-lysine, L-histidine, and L-ornithine. Sequence and structural analyses revealed a conserved binding pocket for cationic amino acids in Plasmodium species, distinct from that in Toxoplasma gondii NPT1. These findings highlight the potential of targeting PvApiAT8 in developing new treatments for P. vivax malaria.

Isolation, Identification and Phylogeny of Actinobacteria from Island Soils Using Different Isolation Methods

Actinobacteria are one of the most frequently studied prokaryotic groups within the Bacteria domain. In this study, soil samples collected from the islands of Burgazada, Büyükada, Gökçeada, Heybeliada, and Kınalıada were used to isolate, identify, and analyze the phylogeny of Actinobacteria. For the isolation studies, three different isolation methods and 11 different selective media were employed. As a result, a total of 103 bacterial strains were isolated. The molecular identification of the isolated strains was conducted using 16S rRNA gene region sequence analyses. These analyses revealed that the isolates belonged to 12 different genera within the Actinobacteria phylum. Comparison of the 16S rRNA gene sequences of the isolates with their closest relatives in the EzBioCloud database indicated a sequence similarity ranging between 95.76% and 100%. The isolation studies demonstrated that the standard dilution plate method was more effective for isolating both diverse genera and potential novel species. The data obtained through this method showed that 22 of the isolated strains, belonging to 8 different genera, have the potential to represent novel species. In conclusion, this study highlights that island soils are an important source for the discovery of new Actinobacteria species. Furthermore, it emphasizes the significance of such isolation studies in uncovering the rich biotechnological potential of Actinobacteria.

Antimicrobial Resistance in Pasteurella multocida Isolates from Bovine Mastitis Can Be Associated with Multidrug-Resistance-Mediating Integrative and Conjugative Elements (ICEs)

Background/Objectives: Pasteurella multocida commonly colonizes the bovine respiratory tract and can occasionally cause intramammary infections. Here, eight P. multocida isolates from clinical cases of bovine mastitis were investigated for their molecular characteristics as well as phenotypic and genotypic antimicrobial resistance (AMR) properties. Methods: The isolates originated from quarter milk samples obtained in Germany for diagnostic purposes. Antimicrobial susceptibility testing (AST) by broth microdilution was performed according to the Clinical and Laboratory Standards Institute. Closed whole-genome sequences were generated by hybrid assembly of Illumina MiSeq short-reads and Oxford Nanopore MinION long-reads, followed by consecutive sequence analysis. Results: The P. multocida isolates belonged either to capsular:lipopolysaccharide type A:3 (n = 7) or A:6 (n = 1), and multi-locus sequence types 1 (n = 7) or 7 (n = 1). Seven isolates carried AMR genes, such as mef(C), mph(G), strA, strB, aphA1, aadA31, tet(H), tet(Y), floR, catA3, and sul2, as part of an integrative and conjugative element (ICE). These mobile genetic elements, 58,382–78,401 bp in size, were highly similar to the ICEs Tn7406 or Tn7407 that have been previously described in bovine Mannheimia haemolytica and P. multocida, respectively. Moreover, the isolates showed elevated minimal inhibitory concentrations corresponding to the identified AMR determinants. Conclusions: Molecular typing and ICE organization suggest the bovine respiratory tract as reservoir of the investigated mastitis-associated P. multocida. Horizontal cross-genus transfer of multidrug-resistance-mediating ICEs seems to occur under in vivo conditions among different pathogens from cattle in Germany, which underlines the importance of pathogen identification followed by AST for successful bovine mastitis therapy.

Identification and management of a novel Danshen leaf anthracnose caused by Colletotrichum karstii in Salvia miltiorrhiza Bunge in China

Danshen (Salvia miltiorrhiza Bunge), a member of the genus Salvia within the Lamiaceae family, holds significant economic and medicinal value. Regrettably, the emergence of a novel leaf anthracnose in 2020 has significantly impacted its cultivation, leading to decreased yield and compromised quality. This newly identified pathogen was meticulously isolated from affected leaves, employing meticulous single conidia isolation techniques. Subsequent confirmation of pathogenicity was achieved through strict adherence of Koch’s postulates. To ensure precise identification, morphological characteristics were supplemented with tandem sequence analysis targeting the rDNA internal transcribed spacer (ITS), β-tubulin (TUB), and histone (His3) regions. Combining molecular biology techniques with morphological observation and Koch’s postulates, the pathogen was conclusively identified as Colletotrichum karstii. Further investigations focused on understanding the environmental factors influencing the mycelial growth and sporulation of the pathogen. The optimum temperature for the growth of C.karstii is 25°C, the suitable light conditions are 12h light/12h dark or 24h dark, and the suitable pH is 5 to 9. Utilizing BIOLOG phenotypic analysis technique, the metabolic utilization of carbon and nitrogen sources by the pathogen was assessed across different temperatures (20°C, 25°C, and 30°C). Results indicated the highest utilization rates at 25°C, particularly for arbutin and L-tryptophan. Lastly, the efficacy of 15 chemical fungicides and six botanical fungiticide against C. karstii was evaluated in vitro, revealing fluazinam as the most potent inhibitor against mycelial growth with EC50 of 0.0725 mg/mL for mycelium and 0.0378 mg/mL for spore germination, respectively. The 1 % osthole emulsion in water was found to have the strongest inhibitory effect on the growth of mycelium, with an EC50 value of 4.8984 µg/mL. Spore germination was most strongly inhibited by the 80 % ethylicin EC, which had an EC50 value of 0.5541 µg/mL. This study represents the first documentation of C. karstii as a causative agent of anthrax in Danshen, underscoring the significance of these findings for agricultural management and disease control strategies.

Longitudinal wave propagation determination in concrete specimen under impact loading by ultrahigh-speed camera image sequence and strain gauge data analysis

Abstract To demonstrate the potential of an ultrahigh-speed camera with frame rates beyond a million images per second for high dynamic material analysis, cylindrical concrete specimens are tested under compression at strain rates up to 164.3 s-1 in a split Hopkinson pressure bar facility. The evaluation includes the determination of the actual longitudinal wave propagation velocity and the induced longitudinal deformations. The results obtained from image sequence analysis are validated with those obtained by the well-established strain gauge measuring technique that estimate the specimen deformation in the same facility. Data analysis for both measuring techniques is based on the one-dimensional wave theory. Image quality challenges affecting the material analysis are overcome by applying a Bézier fitting filter to the image sequences. Using the image-sequence-based approach to select stress-wave-induced motion points, different wave characteristics are acquired. Subsequently, selecting the points in compression during the first stress wave transit yields longitudinal wave propagation velocities up to 2995 m/s with a standard deviation of 265 m/s. From the validation results, first, an observed bilateral complementarity of both techniques enables a comprehensive analysis of the specimen deformation. Second, individual discrepancies between the material properties obtained from both techniques up to ultimate compressive strength for deformation, velocity, strain, and stress of 20.8 %, 14.4 %, 8.3 %, and 10.0 %, respectively, are achieved.

Integrated analysis of M2 macrophage-related gene prognostic model and single-cell sequence to predict immunotherapy response in lung adenocarcinoma

BackgroundLung adenocarcinoma (LUAD) patients have high heterogeneity. The significance and clinical value of M2 macrophage-related genes in LUAD require further exploration. We aimed to construct a prognostic signature to predict the immunotherapy efficacy and prognosis in LUAD.MethodsGSE26939 and GSE19188 chips were downloaded from the Gene Expression Omnibus (GEO). Weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) analysis were used to screen M2 macrophage-related prognostic genes. A signature based on M2 macrophage-related prognostic genes was established and used to predict the prognosis and immunotherapy efficacy in LUAD.ResultsTwenty-two M2 macrophage-related genes associated with the prognosis of LUAD were confirmed using WGCNA, and then two molecular subtypes were identified with significantly different survival, gene expressions, and clinic characteristics were classified. LASSO analysis identified nine M2 macrophage-related prognostic genes to establish a risk signature, classifying patients into low- and high-risk groups. Data indicated that low-risk patients had better survival. Moreover, the signature was an independent prognostic factor for LUAD and a potential biomarker for patients receiving immunotherapy. Single-cell transcriptome analysis may provide important information on molecular subtypes and heterogeneity.ConclusionRisk signature based on M2 macrophage-related genes is a valuable tool for predicting prognosis and immunotherapy response in patients with LUAD.

Three new asexual Kirschsteiniothelia species from Guizhou Province, China

During our investigation of saprobic fungi in southwestern China, three micro-hyphomycetous fungi were isolated from dead wood in freshwater and terrestrial habitats in Guizhou Province. Phylogenetic analyses of ITS, LSU, and SSU sequences, performed using Maximum Likelihood and Bayesian Inference methods, confirmed that these isolates belong to Kirschsteiniothelia. Based on distinct morphological characteristics and molecular phylogenetic evidence, we describe three new species: Kirschsteiniothelia guizhouensis, K. weiningensis, and K. xishuiensis. Furthermore, the effectiveness of three DNA markers for species-level identification within Kirschsteiniothelia was evaluated using Assemble Species by Automatic Partitioning (ASAP) analysis, which identified the ITS nucleotide sequences as the most reliable marker for species differentiation within the genus.