Genetic Lineages Research Articles

Biological properties of foot-and-mouth disease virus А 2205/G-IV strain

According to the World Organisation for Animal Health, foot-and-mouth disease (FMD) is regularly reported in domestic and wild cloven-hoofed animals in Africa. G-I, G-IV, G-VI, G-VII, ASIA/Iran-05 genetic lineages of serotype А FMD virus are considered to be the most widespread on the African continent. Given the close economic and trade relations maintained by the Russian Federation with the countries of North Africa, of particular interest for us is studying the FMD virus of serotype A G-IV genetic lineage, which has been responsible for the infection outbreaks in the naturally susceptible animal population of the said region every year since 2012, and there is a risk of introduction of this virus genotype in to the Russian Federation. Therefore, the issues of FMD introduction risk assessment and timely diagnosis are relevant for the Veterinary Service of Russia. FMD virus A 2205/G-IV strain tested for its biological and antigenic properties in cell cultures and naturally susceptible animals (cattle and pigs) was adapted for its reproduction in initially trypsinized porcine kidney (PK) cell culture, continuous monolayer cell cultures (IB-RS-2, PSGK-30, YaDK-04, ВНК-21) by five serial passages. The virus was considered to be adapted when 90–95% cytopathic effect developed within 14–19 hours after the cell culture infection. The virus adapted to the cell cultures was tested for its infectivity with microtitration in IB-RS-2 cell culture. The virus strain tested for vaccine matching with microneutralization test (MNT) demonstrated significant difference from production A/Turkey/06, А22 No. 550/Azerbaijan/64, A22/Iraq/64, A/Iran/97, A No. 2155/Zabaikalsky/2013, A No. 2166/Krasnodarsky/2013, A No. 2269/ARRIAH/2015 strains of FMD virus.

Unraveling the evolutionary dynamics of toxin-antitoxin systems in diverse genetic lineages of Escherichia coli including the high-risk clonal complexes.

Large-scale genomic studies of E. coli provide an invaluable opportunity to understand how genomic fine-tuning contributes to the transition of bacterial lifestyle from being commensals to mutualists or pathogens. Within this context, through machine learning-based studies, it appears that TA systems play an important role in the classification of high-risk clonal lineages and could be attributed to their epidemiological success. Due to these profound indications and assumptions, we attempted to provide unique insights into the ordered world of TA systems at the population level by investigating the diversity and evolutionary patterns of TA genes across 19 different STs of E. coli. Further in-depth analysis of ST-specific TA structures and associated genetic coordinates holds the potential to elucidate the functional implications of TA systems in bacterial cell survival and persistence, by and large.

First Molecular Evidence of Seewis Virus in Croatia.

Orthohantaviruses are mainly carried and transmitted by wild rodents, although during the last decade, they have also been identified in multiple species of shrews and moles. Orthohantavirus, Orthohantavirus seewisense (Seewis virus, SWSV), first detected in Switzerland in a single Sorex araneus (Eurasian common shrew) specimen, has been further described in several European countries, including Croatia's neighboring Slovenia and Hungary. Croatia is a well-known endemic region for several zoonotic agents including three different orthohantaviruses: Orthohantavirus puumalaense (PUUV), Orthohantavirus dobravaense (DOBV), and Orthohantavirus tulaense (TULV). In this study, nine shrews were tested and SWSV RNA was detected in liver, lung, and kidney belonging to two shrews (22.22%), one collected on Medvednica mountain in Zagreb County, and the other in the Stara Gradiška area in lowland Croatia. The phylogenetic analysis of the complete S segment's open reading frame (ORF) and partial L-segment revealed that the Croatian sequences, when compared to sequences from the adjacent geographic regions, form a specific genetic lineage. Two SWSV-positive shrew species-Sorex araneus and Neomys milleri (Mediterranean water shrew)-were identified using barcode-based sequence analysis. Therefore, the SWSV detection in N. milleri throughout the course of this study is seen as a rare find in this shrew species. To our knowledge, this is the first molecular and phylogenetic analysis of SWSV in Croatia.

Genetic Lineage Traces the Differentiation Fate of Epicardial Cells during Heart Development

Objective: The genetic lineage tracing method was used to examine the Epithelial-Mesenchymal Transition (EMT) process and the contribution of epicardial cells to mesenchymal cells at various stages of fetal heart development. Methods: In Wt1-CreER; R26-tdTomato transgenic mice, tamoxifen was utilized to promote the tagging of epicardial cells with tdTomato fluorescence at E10. At E11.5, E12.5, and E16.5, embryonic hearts were harvested and photographed using confocal fluorescence microscopy and stereomicroscopy. Results: According to the findings, the tdTomato+ cells at E11.5 were still in the epicardium and had not yet moved into the myocardium. Epicardial cells began to separate from the epicardium and give rise to epicardial-derived cells at embryonic day 12.5 (E12.5). On the valve primordium, fibroblasts generated from epicardium have been found. By E16.5, many epicardial cells had moved into the myocardium and formed fibroblasts, mesenchymal cells, vascular smooth muscle cells, as well as migrated into the ventricular septum and valves, contributing to their growth and creation. Conclusions: The contribution of epicardial cells to mesenchymal cells during development is shown by genetic lineage tracing, opening up possibilities and offering references for creating relevant treatment approaches based on epicardial cells.

Pleistocene climatic oscillations influenced the emergence of geographically widespread and restricted genetic lineages in an Andean grasshopper species group

Abstract The grasshopper Trimerotropis pallidipennis species complex is distributed across arid and semi-arid environments from North to South America, reaching high altitudes along the Andes Mountain range. Currently, there are four valid species of Trimerotropis in South America. However, some species were found to comprise several genetic lineages. Here, we describe the genetic structure, lineage diversification, and environmental requirements within the Trimerotropis species complex in South America based on sequences from the mitochondrial COI gene, 4048 single nucleotide polymorphisms, and ecological niche modelling. The analyses revealed the existence of at least five lineages: two with a restricted geographical distribution and three with a very wide one. The results provide evidence that glacial cycles promoted not only the presence of refuge areas but also the isolation of widely distributed lineages on the eastern and western sides of the southern Andes, potentially driving the emergence of the Trimerotropis sp. lineage, which can tolerate more temperate habitats. Our results provide evidence for the effects of Pleistocene climatic changes on the diversification history of a South American grasshopper species complex.

Genetic diversity and evolutionary patterns of SARS-CoV-2 among the Bhutanese population during the pandemic.

The coronavirus disease 2019 (COVID-19) pandemic, caused by a dynamic virus, has had a profound global impact. Despite declining global COVID-19 cases and mortality rates, the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants remains a major concern. This study provides a comprehensive analysis of the genomic sequences of SARS-CoV-2 within the Bhutanese population during the pandemic. The primary aim was to elucidate the molecular epidemiology and evolutionary patterns of SARS-CoV-2 in Bhutan, with a particular focus on genetic variations and lineage dynamics. Whole-genome sequences of SARS-CoV-2 collected from Bhutan between May 2020 and February 2023 (n=135) were retrieved from the Global Initiative on Sharing All Influenza Database. The SARS-CoV-2 variants in Bhutan were predominantly classified within the Nextstrain clade 20A (31.1%), followed by clade 21L (20%) and clade 22D (15.6%). We identified 26 Pangolin lineages with variations in their spatial and temporal distribution. Bayesian time-scaled phylogenetic analysis estimated the time to the most recent common ancestor as February 15, 2020, with a substitution rate of 0.97×10-3 substitutions per site per year. Notably, the spike glycoprotein displayed the highest mutation frequency among major viral proteins, with 116 distinct mutations, including D614G. The Bhutanese isolates also featured mutations such as E484K, K417N, and S477N in the spike protein, which have implications for altered viral properties. This is the first study to describe the genetic diversity of SARS-CoV-2 circulating in Bhutan during the pandemic, and this data can inform public health policies and strategies for preventing future outbreaks in Bhutan.

Genomic analysis of lineage-specific transmission of multidrug resistance tuberculosis in China

ABSTRACT Objectives We investigated the genetic diversities and lineage-specific transmission dynamics of multidrug-resistant tuberculosis (MDR-TB), with the goal of determining the potential factors driving the MDR epidemics in China. Methods We curated a large nationwide Mycobacterium tuberculosis (M. tuberculosis) whole genome sequence data set, including 1313 MDR strains. We reconstructed the phylogeny and mapped the transmission networks of MDR-TB across China using Bayesian inference. To identify drug-resistance variants linked to enhanced transmissibility, we employed ordinary least-squares (OLS) regression analysis. Result The majority of MDR-TB strains in China belong to lineage 2.2.1. Transmission chain analysis has indicated that the repeated and frequent transmission of L2.2.1 plays a central role in the establishment of MDR epidemic in China, but no occurrence of a large predominant MDR outbreak was detected. Using OLS regression, the most common single nucleotide polymorphisms (SNPs) associated with resistance to isoniazid (katG_p.Ser315Thr and katG_p.Ser315Asn) and rifampicin (rpoB_p.Ser450Leu, rpoB_p.His445Tyr, rpoB_p.His445Arg, rpoB_p.His445Asp, and rpoB_p.His445Asn) were more likely to be found in L2 clustered strains. Several putative compensatory mutations in rpoA, rpoC, and katG were significantly associated with clustering. The eastern, central, and southern regions of China had a high level of connectivity for the migration of L2 MDR strains throughout the country. The skyline plot showed distinct population size expansion dynamics for MDR-TB lineages in China. Conclusion MDR-TB epidemic in China is predominantly driven by the spread of highly transmissible Beijing strains. A range of drug-resistance mutations of L2 MDR-TB strains displayed minimal fitness costs and may facilitate their transmission.

Sequence capture identifies fastidious chytrid fungi directly from host tissue

The chytrid fungus Batrachochytrium dendrobatidis (Bd) was discovered in 1998 as the cause of chytridiomycosis, an emerging infectious disease causing mass declines in amphibian populations worldwide. The rapid population declines of the 1970s-1990s were likely caused by the spread of a highly virulent lineage belonging to the Bd-GPL clade that was introduced to naïve susceptible populations. Multiple genetically distinct and regional lineages of Bd have since been isolated and sequenced, greatly expanding the known biological diversity within this fungal pathogen. To date, most Bd research has been restricted to the limited number of samples that could be isolated using culturing techniques, potentially causing a selection bias for strains that can grow on media and missing other unculturable or fastidious strains that are also present on amphibians. We thus attempted to characterize potentially non-culturable genetic lineages of Bd from distinct amphibian taxa using sequence capture technology on DNA extracted from host tissue and swabs. We focused our efforts on host taxa from two different regions that likely harbored distinct Bd clades: (1) wild-caught leopard frogs (Rana) from North America, and (2) a Japanese Giant Salamander (Andrias japonicus) at the Smithsonian Institution’s National Zoological Park that exhibited signs of disease and tested positive for Bd using qPCR, but multiple attempts failed to isolate and culture the strain for physiological and genetic characterization. We successfully enriched for and sequenced thousands of fungal genes from both host clades, and Bd load was positively associated with number of recovered Bd sequences. Phylogenetic reconstruction placed all the Rana-derived strains in the Bd-GPL clade. In contrast, the A. japonicus strain fell within the Bd-Asia3 clade, expanding the range of this clade and generating additional genomic data to confirm its placement. The retrieved ITS locus matched public barcoding data from wild A. japonicus and Bd infections found on other amphibians in India and China, suggesting that this uncultured clade is widespread across Asia. Our study underscores the importance of recognizing and characterizing the hidden diversity of fastidious strains in order to reconstruct the spatiotemporal and evolutionary history of Bd. The success of the sequence capture approach highlights the utility of directly sequencing pathogen DNA from host tissue to characterize cryptic diversity that is missed by culture-reliant approaches.

Co-occurrence of dual lineages within Simulium (Gomphostilbia) atratum De Meijere in the Indonesian Archipelago along Wallace's Line

Mitochondrial cytochrome c oxidase subunit I (COI) sequences were utilized to infer the population genetic structure of Simulium (Gomphostilbia) atratum De Meijere, an endemic simulid species to Indonesia. Both median-joining haplotype network and maximum-likelihood tree revealed two genetic lineages (A and B) within the species, with an overlap distribution in Lombok, which is situated along Wallace's line. Genetic differentiation and gene flow with varying frequencies (FST = 0.02–0.967; Nm = 0.01–10.58) were observed between populations of S. (G.) atratum, of which population pairs of different lineages showed high genetic differentiation. Notably, the high genetic distance of up to 5.92 % observed within S. (G.) atratum in Lombok was attributed to the existence of two genetically distinct lineages. The co-occurrence of distinct lineages in Lombok indicated that Wallace's line did not act as faunistic border for S. (G.) atratum in the present study. Moreover, both lineages also exhibited unimodal distributions and negative values of neutrality tests, suggesting a pattern of population expansion. The expansion and divergence time estimation suggested that the two lineages of S. (G.) atratum diverged and expanded during the Pleistocene era in Indonesia.

Repopulating Kupffer cells originate directly from hematopoietic stem cells

BackgroundKupffer cells (KCs) originate from yolk-sac progenitors before birth. Throughout adulthood, they self-maintain independently from the input of circulating monocytes (MOs) at a steady state and are replenished within 2 weeks after having been depleted, but the origin of repopulating KCs in adults remains unclear. The current paradigm dictates that repopulating KCs originate from preexisting KCs or monocytes, but there remains a lack of fate-mapping evidence.MethodsWe first traced the fate of preexisting KCs and that of monocytic cells with tissue-resident macrophage-specific and monocytic cell-specific fate-mapping mouse models, respectively. Secondly, we performed genetic lineage tracing to determine the type of progenitor cells involved in response to KC-depletion in mice. Finally, we traced the fate of hematopoietic stem cells (HSCs) in an HSC-specific fate-mapping mouse model, in the context of chronic liver inflammation induced by repeated carbon tetrachloride treatment.ResultsBy using fate-mapping mouse models, we found no evidence that repopulating KCs originate from preexisting KCs or MOs and found that in response to KC-depletion, HSCs proliferated in the bone marrow, mobilized into the blood, adoptively transferred into the liver and differentiated into KCs. Then, in the chronic liver inflammation context, we confirmed that repopulating KCs originated directly from HSCs.ConclusionTaken together, these findings provided in vivo fate-mapping evidence that repopulating KCs originate directly from HSCs, which presents a completely novel understanding of the cellular origin of repopulating KCs and shedding light on the divergent roles of KCs in liver homeostasis and diseases.

Molecular population genetics and phylogeographic studies of Ligia exotica and Ligia cinerascens in East Asia

IntroductionSea slater, in the genus Ligia, is widespread in rocky shore habitats, and the taxon is easily isolated due to its limited dispersal capacity. Therefore, most Ligia species exhibit an allopatric distribution, but Ligia exotica and L. cinerascens exhibit an overlapping distribution distribution in East Asia. Previous studies on both species have confirmed the existence of highly divergent lineages based on 16S rRNA.MethodsIn the present study, 282 Ligia individuals were collected at ten, three, and three sites in South Korea, Japan, and Vietnam, respectively, and 41 haplotypes were observed based on 16S rRNA.Results and discussionThe results of phylogeny, phylogenetic network, and TCS network, Principal Coordinates Analysis, and four Molecular Species Delimitation Analyses revealed that six genetic lineages including L. cinerascens, Lineages N and S of L. exotica, Ligia sp. 1, sp.2 and sp.3 were present. The three genetic lineages, including L. cinerascens, Lineage N of L. exotica, and Lineage S of L. exotica, were also identified in the phylogeny based on a nuclear gene of the sodium–potassium ATPase α-subunit (Nak). Phylogeographic analysis revealed that L. cinerascens and Lineage N of L. exotica were distributed overlappingly in South Korea, Japan, and the northern region of China. Generally, the two lineages of L. exotica were distributed allopatrically, which was more evident along the coastline of mainland China than that of Japan. The results of time-calibrated phylogeny suggested that the speciation events of Ligia species might be associated with Japanese mainland formation from Oligocene to Miocene (approximately 30-5 million years ago, Mya). The results of the present study provide insights that could facilitate the understanding of the evolutionary history of Ligia, tracking of geological processes, and evolutionary effects of palaeogeographical events at the population level.

Differential changes in body size and stoichiometry in genetic lineages of the earthworm Eisenia nordenskioldi with elevation

Exploring species and their functional diversity is of fundamental importance in biology and ecology. Many earthworm species comprise a wide range of genetic lineages/cryptic species, but it remains unclear whether these lineages/cryptic species represent distinct ecological entities that differ in traits. We barcoded 280 individuals of the earthworm species Eisenia nordenskioldi from 42 forest plots across seven elevations (800–1700 m) on Changbai Mountain, northeast China, and found them to comprise two genetic lineages with a p-distance in the COI gene of 16.7%. We evaluated whether the two distinct lineages differ in morphological (body length, body with, body mass and length:width ratio) and stoichiometric traits (C, N and P concentrations and C:N, C:P and N:P ratios), and whether these traits vary with elevation. At elevations where lineages co-existed, we further evaluated their ecological niche overlap. When co-existing, the two lineages of E. nordenskioldi significantly differed in body length, body mass, length:width ratio, and C and N concentrations as well as C:N and N:P ratios. With increasing elevation, body length, body mass and the length:width ratio of the two lineages linearly increased, whereas body width and C:N ratio linearly decreased; while C and N concentrations as well as C:P and N:P ratios showed a hump-shaped relationship with elevation. Across elevations trait distribution overlapped by 29%–100%, but the overlap in body mass, body length and length:width ratio decreased to 0%–15% when the two lineages co-existed. The significant differences in multiple traits indicate that the two lineages have different physiologies, supporting their status as cryptic species. The documented variations in morphological and stoichiometric traits of the two lineages/cryptic species call for integration of genetics and ecology for understanding biodiversity and ecological functioning of soil animal species.

Natural Vector of Avian Haemoproteus asymmetricus Parasite and Factors Altering the Spread of Infection.

Avian haemosporidians (Apicomplexa, Haemosporida) are widespread blood protists, often causing severe haemosporidiosis, pathology, or even mortality in their hosts. Migrant birds regularly bring various haemosporidian parasites from wintering grounds to European breeding areas. Some haemosporidian parasites are prevalent in breeding sites and complete their life cycles in temperate climate zones and can be transmitted, but others do not. The factors altering the spread of these haemosporidians are not fully understood. Culicoides biting midges (Diptera: Ceratopogonidae) play an important role in the transmission of worldwide distributed avian haemosporidian parasites belonging to the genus Haemoproteus, but this information is particularly scarce and insufficient. The key factors limiting the spread of these pathogens in temperate climate zones, which we suspect and aim to study, are the absence of susceptible vectors and the ecological isolation of birds from vectors during the breeding period when transmission occurs. The primary objective of this study was to evaluate how the habitats of biting midges and bird breeding sites influence parasite transmission while also seeking to expand our understanding of the natural vectors for these parasites. Biting midges were collected using UV traps on the Curonian Spit, Lithuania, in different habitats, such as woodland and reeds, from May to September. Parous Culicoides females were identified, dissected, and investigated for the presence of Haemoproteus parasites using both microscopy and PCR-based tools. Among the dissected 1135 parous Culicoides females, the sporozoites of Haemoproteus asymmetricus (genetic lineage hTUPHI01) have been detected for the first time in the salivary glands of Culicoides festivipennis. The sporozoites of four Haemoproteus lineages were detected in Culicoides segnis, C. festivipennis, and Culicoides kibunensis biting midges. PCR-based screening showed that the females of seven Culicoides species were naturally infected with Haemoproteus parasites. The DNA of the parasite of owls, Haemoproteus syrnii (hSTAL2), was detected for the first time in Culicoides punctatus. The highest abundance of collected Culicoides females was in June, but the highest prevalence of Haemoproteus parasites in biting midges was in July. The abundance of Culicoides was higher in the woodland compared with reeds during the season. The acquired findings indicate the varied abundance and diversity of biting midges throughout the season and across distinct habitats. This variability could potentially impact the transmission of Haemoproteus parasites among birds with diverse breeding site ecologies. These outcomes hold the potential to enhance our understanding of the epizootiology of Haemoproteus infections within temperate climatic zones.

Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population.

Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment. Because the gut microbiome supports host immune function, understanding the effects of animal ecology and evolution on the gut microbiome and immune phenotypes is critical. We investigated how domestication affects the gut microbiome and host immune state in multiple pig populations across five domestication contexts representing domestication status and current living conditions: free-ranging wild, captive wild, free-ranging domestic, captive domestic in research or industrial settings. We observed that domestication context explained much of the variation in gut microbiome composition, pathogen abundances and immune markers, yet the main differences in the repertoire of metabolic genes found in the gut microbiome were between the wild and domestic genetic lineages. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding which gut microbiome and immune traits respond to host genetic lineage and/or scales of local ecology could inform targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes.

Nuclear and chloroplast DNA phylogeography reveals high genetic diversity and postglacial range expansion in Quercus mexicana.

Phylogeographical studies are fundamental for understanding factors that influence the spatial distribution of genetic lineages within species. Population expansions and contractions, distribution shifts, and climate changes are among the most important factors shaping the genetic compositions of populations. We investigated the phylogeography of an endemic oak, Quercus mexicana (Fagaceae), which has a restricted distribution in northeastern Mexico along the Sierra Madre Oriental and adjacent areas. Nuclear and chloroplast DNA microsatellite markers were used to describe the genetic diversity and structure of 39 populations of Q. mexicana along its entire distribution area. We tested whether population expansion or contraction events influenced the genetic diversity and structure of the species. We also modeled the historical distributional range of Q. mexicana (for the Mid Holocene, the Last Glacial Maximum, and the Last Interglacial) to estimate the extent to which climate fluctuations have impacted the distribution of this oak species. Our results revealed high genetic diversity and low genetic structure in Q. mexicana populations. Ecological niche models suggested historical fluctuations in the distributional range of Q. mexicana. Historical range changes, gene flow, and physical barriers seem to have played an important role in shaping the phylogeographic structure of Q. mexicana. Our study indicates that the genetic structure of Q. mexicana may have been the result of responses of oak trees not only to heterogeneous environments present in the Sierra Madre Oriental and adjacent areas, but also to elevational and latitudinal shifts in response to climate changes in the past.

Genetic characterization and lineage analysis of Pasundan (Rancah) cattle in West Java, Indonesia: Insights from ZFY gene sequencing

<p class="MDPI17abstract"><strong>Objective: </strong>This study was carried out to characterize Pasundan (Rancah) cattle from West Java of Indonesia based on a partial Zinc Finger Y-linked (ZFY) gene sequence.</p><p class="MDPI17abstract"><strong>Methods:</strong> Total of fourteen (14) DNA samples of unrelated Pasundan bulls at the breeding station (BPPIBT-SP Ciamis, West Java) were used for sequencing analysis. The blood samples were collected from jugular vein of each bull for the DNA extraction analysis. Along 979 bp of ZFY gene was amplified using primer pairs of forward: 5’- GGT GAG GGC ACA TGA GTT C -3’and reverse: 5’- CTC TGC AGG TGG TTG TGT AA -3’. Therefore, a forward sequencing method was performed in the present study to obtain the ZFY gene sequences. Along 714 bp of <em>bovine </em>ZFY gene sequences were used for determining the Neighbor-Joining (NJ) tree for Pasundan bulls with 1000 × bootstrap replications using a MEGA computer program. The genetic diversity parameters of haplotype diversity (H<sub>d</sub>), nucleotide diversity (p<sub>i</sub>), Tajima’s D test and Fu’s Fs statistics were calculated using a DNAsp computer program.</p><p class="MDPI17abstract"><strong>Results:</strong> Total of fourteen (14) haplotypes of ZFY gene and seventy (70) mutation sites were detected in the Pasundan bulls. The haplotype diversity (H<sub>d</sub>) and nucleotide diversity (p<sub>i</sub>) in Pasundan’s ZFY gene diversity were 1.00 (high) and 0.01 (low), respectively. The neutrality test of Tajima’s D and Fu’s Fs statistic values were -1.42 and -6.47, respectively. <em>Bovine </em>ZFY gene can be classified into two clades of ZFY-1 and ZFY-2. Therefore, the Neighbor-joining (NJ) tree (1000×bootstrap) revealed that the Pasundan cattle are classified into clade ZFY-1 together with <em>Bos taurus </em>(AF241273, AF465179). Meanwhile, a clade ZFY-2 consisted of <em>Bos taurus </em>(AF465181, DQ336536), <em>Bos indicus </em>(DQ336537), and <em>Bos javanicus </em>(DQ336578).</p><p class="MDPI17abstract"><strong>Conclusion:</strong> The ZFY gene of Pasundan bulls were polymorphic with seventy mutation sites. Therefore, Pasundan bulls were characterized into ZFY-1 clade or <em>Taurine </em>lineage based on ZFY gene sequence variaton. The crossbreeding program with <em>Bos taurus</em> straw to increase meat production of cattle may affecting the genetic structure of Pasundan bulls since this program is widely applied in West Java through many years ago.</p>

Terbutaline Modulates Macrophage Homeostasis and Macrophage-T-Cell Interactions in Immune Thrombocytopenia

Background: Increased platelet destruction by macrophage phagocytosis contributes to immune thrombocytopenia (ITP). Neural immune modulation in autoimmune diseases has been given considerable interest. Our preliminary studies showed a decreased sympathetic innervation in the bone marrow and spleen of ITP mice and that abnormal T cell immunity caused by sympathetic modulation promoted the progression of ITP ( Blood Advances 2019; J Thromb Haemost, 2023). Moreover, previous studies indicated a potential interaction between T cells and macrophages ( Immunity, 2017). However, the regulation of spleen sympathetic denervation on macrophage function and the interaction between splenic macrophages and T cells under the sympathetic modulation in ITP remain unknown. Methods: Whole-tissue immunolabeling and 3D imaging of the human spleen were performed to compare the sympathetic distribution between ITP with splenectomy and non-ITP with traumatic splenectomy. RNA sequencing was used to detect the transcriptional changes and metabolomics and seahorse extracellular flux analyses were carried out to determine the metabolic reprogramming in splenic macrophages of ITP mice. The expression of cell surface markers of macrophages and T cells and cytokines was assessed by flow cytometry, western blot, and enzyme-linked immunosorbent assay. Chemical sympathectomy with 6-hydroxydopamine (6-OHDA), a β2-AR agonist terbutaline, and a β2-AR antagonist ICI 118,551 were used to detect the sympathetic modulation. Genetic lineage tracing was used to compare serum norepinephrine (NE) and its origin in the spleen of WT mice with or without chemical sympathectomy. Results: A panicle-shaped sympathetic neural architecture was revealed in the spleen of both ITP and non-ITP patients. The distribution of sympathetic nerves in the spleen and the level of serum NE were both significantly decreased in ITP patients. Immunofluorescence staining revealed an anatomical colocalization between sympathetic nerves, macrophages, and T cells in the spleen, suggesting potential sympathetic modulation of macrophages and a potential interaction between splenic macrophages and T cells. RNA-sequencing data of splenic macrophages in ITP mice compared with wild type (WT) mice revealed higher expression of M1-specific genes, including IL1b, Tnf and IL6, and lower expression of M2-specific genes, including IL10 and Arg1, indicating an M1 polarization tendency. In splenic macrophages isolated from ITP mice, we observed an enrichment of glycolysis pathway genes compared to WT mice, including Hk2, Pkm2and Ldha. An increase in the extracellular acidification rate and a decrease in the oxygen consumption rate were also found in splenic macrophages of ITP mice, indicating a switch to glycolysis. To investigate the interaction between splenic macrophages and T cells under sympathetic modulation in ITP, we measured the expression of cytokines that might have an influence on macrophage polarization and T cell differentiation and observed upregulation of interleukin (IL)-12, IL-18 and interferon (IFN)-γ. We also used macrophages from ITP mice and WT mice as antigen-presenting cells for naïve CD4 + T cells, which were interrogated for IFN-γ production following stimulation with OVA 323-339. We observed increased IFN-γ production and upregulation of IL-12 and IL-18 in response to macrophages from ITP mice, and we also observed diminished production of IL-12, IL-18 and IFN-γ when pretreated with aIL-12 mAb and aIL-18 mAb. Moreover, chemical sympathectomy with 6-OHDA was carried out in WT mice and significantly decreased serum NE and platelet counts at D7 and D14 were observed. Increased expression of M1-specific markers and upregulation of IL-12, IL-18 and IFN-γ were also determined. The β2-AR agonist terbutaline was shown to decrease the expression of proinflammatory factors and inhibit M1 polarization, and its effects were reversed by the β2-AR antagonist ICI 118,551. Conclusions: Splenic sympathetic denervation-mediated proinflammatory M1 polarization, metabolic alterations, and proinflammatory interactions between macrophages and T cells were involved in ITP pathogenesis. The β2-AR agonist terbutaline was demonstrated to restore the homeostasis of splenic macrophages, indicating a novel potential ITP treatment strategy.

Nasal staphylococci microbiota and resistome in healthy adults in La Rioja, northern Spain: High frequency of toxigenic S. aureus and MSSA-CC398 subclade

This study determined the nasal staphylococci diversity and characterized their resistome, with a focus on the mobilome of methicillin-susceptible Staphylococcus aureus (MSSA)-CC398 subclade from healthy adults in La Rioja (northern Spain). Nasal staphylococci recovered from 57 healthy individuals (HI) were identified (MALDI-TOF-MS) and their antimicrobial resistance, virulence determinants and genetic lineages were studied. The relatedness of MSSA-CC398 isolates was assessed by core-genome single-nucleotide-polymorphisms (SNPs). One-hundred-forty-three non-repetitive staphylococci were obtained from most HI (98.2%), of which S. epidermidis (87.7%) and S. aureus (36.8%) were the predominant species. About 15% of the 27 S. aureus and 30.1% of the 116 coagulase-negative staphylococci (CoNS) isolates presented a multidrug resistance (MDR) phenotype. All S. aureus isolates were MSSA but 30.2% of CoNS isolates were mecA-positive and carried SCCmec types III, IV, and V. The highest non-beta-lactam resistance (frequency/genes) in S. aureus and CoNS were: erythromycin-clindamycin-inducible (25.9%/ermT, ermC) and mupirocin (30.1%/mupA), respectively. About 85% of S. aureus isolates carried relevant virulence genes. Eight clonal complexes (CCs) of MSSA were identified, of which CC398 was the predominant (33.3%). About 78% of the CC398 isolates harboured rep13-bound ermT gene, however, one carried a rep10-bound ermC gene. Only the ermT-positive MSSA-CC398 isolates were closely related (<50 SNPs) and carried the φSa3. Diverse MDR-S. epidermidis isolates were identified which included the lineages ST59 and ST210. The high rate of toxigenic S. aureus and of MSSA-CC398 subclade highlight the ability of HI to carry and transmit virulent isolates. Moreover, the high frequency of MDR-CoNS, often linked with SCCmec, needs to be monitored for their potential human health implications.

Genetic diversity and population differentiation of wild and domesticated banana shrimp Fenneropenaeus merguiensis: Applications for development of its breeding program

The basic information on genetic diversity is important for the construction of a breeding scheme leading to the sustainable farming activity of banana shrimp Fenneropenaeus merguiensis. Here, its genetic variability was examined (N = 584). Species authentication was performed by cytochrome oxidase subunit I (COI) polymorphism (N = 77). Microsatellite analysis revealed limited genetic diversity (average no. of alleles per locus, NA = 4.857-5.571) in the previous domesticated stocks. Subsequently, specimens from different geographic locations including Trat, Rayong, Chonburi, Pattani and Nakhon Si Thammarat on the Gulf of Thailand (east) and Trang and Krabi on the Andaman Sea (west) were genetically analyzed. Relatively high levels of genetic diversity (NA = 7.857–23.429) and heterozygosity (Ho = 0.500–0.733) were observed. Genetic differentiation was found between all pairwise comparisons (P < 0.001) except Trat-Nakhon Si Thammarat (P > 0.0071). Phylogenetic analysis allocated wild F. merguiensis to three groups, A (Gulf of Thailand), B (Trang) and C (Krabi). Admixture analysis did not reveal large mixing between different lineages of genotypes in each population. However, the Krabi population (west) mainly showed the eastern genetic lineage. A new domestication program was established by selecting shrimp from different genetic groups. High genetic diversity was found in founders (NA = 27.714 and AR = 14.137) and brooders of the second generation (NA = 24.571 and AR = 12.835). Currently, genome-wide association study (GWAS) of G2 shrimp exhibiting large and small sizes from four families is being carried out to analyze growth-related SNPs in this species.

Transracial Adoption, Memory, and Mobile, Processual Identity in Jackie Kay’s Red Dust Road

Representations of adoptions tend to concentrate on normatively conceived forms of identity, which prioritize the genetic lineage of adoptees. In contrast, scholarship on autobiographical writing emphasizes that identities are not fixed but are always in process and intersectional because they are formed in within inequal power relations. Kay’s experimental, autobiographical narrative Red Dust Road (2010) tackles the themes of adoption, the search for close relatives, and reunion. Many scholars of her autobiographical writings describe the fluidity of the diasporic adoptee identities created by her. My aim is more specific: I examine what I call Kay’s continuously mobile, processual identity construction as a transracial adoptee in Red Dust Road. I argue that her identity formation, which is also intersectional, is interconnected with her multidirectional networks of attachments and the experimental form of her adoption narrative. In addition to an intersectional approach and autobiographical studies, I draw on insights from adoption studies. In my reading of Kay’s work, I pay special attention to the inequalities derived from the intersecting vectors of adoption and race, which also intersect with other dimensions of difference, such as nation, gender, class, and sexual orientation. I employ the notion of the multidirectional in the sense in which McLeod applies it to the study of adoption writing. As I demonstrate, multidirectionality and the complex form of Red Dust Road provide versatile means of conveying Kay’s fragmented acts of memory, which assist her ongoing mobile, processual identity construction. Her multidirectional lines of transformative attachments finally bond her to her adoptive and biogenetic families as well as other affective connections. While Kay’s socially significant narrative indicates, amongst other adoption issues, that transracial adoptions can be successful, it is significant that it has no closure. The last chapter gestures toward potential new beginnings, which indicates that the story of adoption has no end.