bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species
Authors: Zhang Wei‐Ping , Ding Ya‐Mei , Cao Yu , Li Pan , Yang Yang , Pang Xiao‐Xu , Bai Wei‐Ning , Zhang Da‐Yong 
Published: June 2024

SUMMARYGhost introgression, or the transfer of genetic material from extinct or unsampled lineages to sampled species, has attracted much attention. However, conclusive evidence for ghost introgression, especially in plant species, remains scarce. Here, we newly assembled chromosome‐level genomes for both Carya sinensis and Carya cathayensis, and additionally re‐sequenced the whole genomes of 43 C. sinensis individuals as well as 11 individuals representing 11 diploid hickory species. These genomic datasets were used to investigate the reticulation and bifurcation patterns within the genus Carya (Juglandaceae), with a particular focus on the beaked hickory C. sinensis. By combining the D‐statistic and BPP methods, we obtained compelling evidence that supports the occurrence of ghost introgression in C. sinensis from an extinct ancestral hickory lineage. This conclusion was reinforced through the phylogenetic network analysis and a genome scan method VolcanoFinder, the latter of which can detect signatures of adaptive introgression from unknown donors. Our results not only dispel certain misconceptions about the phylogenetic history of C. sinensis but also further refine our understanding of Carya's biogeography via divergence estimates. Moreover, the successful integration of the D‐statistic and BPP methods demonstrates their efficacy in facilitating a more precise identification of introgression types.
Integrative taxonomy of an East Asian songbird indicates rapid dwarfism after island colonization
Authors: Wei Chentao , Peng Lanhui , Zhang Yanyun , Nishiumi Isao , Carey Geoff J. , Liu Zongzhuang , Alström Per , Dong Lu , Liu Yang 
Published: June 2024

AbstractAnimals that colonize islands often undergo significant evolutionary changes in comparison with their continental counterparts as a response to specific island conditions. The pace of such changes can be relatively fast, which poses challenges in the evaluation of the taxonomic status of island taxa. The Japanese and Manchurian Bush Warbler species complex (Horornis diphone–canturians), which breeds in East Asia and the Japanese Archipelago, is such an avian example. This species complex exhibits significant morphological differentiation between different taxa, and the taxonomic status and phylogenetic relationships within the complex are debated. Here, we updated the taxonomy of this species complex and shed insight on its evolutionary history using multi‐locus phylogeographic and acoustic analyses. Our results support the conventional treatment of the two continental taxa borealis and canturians as subspecies of H. canturians, contrary to some recent proposals that they are affiliated to H. diphone. We also document a reduction in body size, that is dwarfism, and vocal divergence in the nominate subspecies H. d. diphone, which is endemic to the remote and isolated Ogasawara Islands. These changes may have happened following colonization of these islands, which was estimated to have taken place approximately 0.2 million years ago. Although H. d. diphone is clearly distinctive and deserves recognition as an evolutionarily significant unit, H. d. diphone and other H. diphone samples were not reciprocally monophyletic. Because of this lack of reciprocal monophyly and a relatively recent divergence time, we advocate maintaining its current subspecies status. We also detected reduced genetic diversity, measured as heterozygosity, in H. d. diphone. We suggest that conservation efforts in the Ogasawara Islands should prioritize the protection of this endemic subspecies. Collectively, our findings suggest that the separation between the populations on the East Asian continent and the Japanese Archipelago, followed by colonization of remote oceanic islands through long‐distance dispersal, underlie rapid phenotypic and genetic diversification of the Horornis diphone–canturians species complex.
Study on the alleviative effect of
Lactobacillus plantarum
on
Eimeria falciformis
infection
Authors: Sun Yufei , Liu Pufang , Guo Wenhui , Guo Jun , Chen Jia , Xue Xinyu , Duan Chao , Wang Zixuan , Yan Xinlei 
Published: June 2024

ABSTRACT

Coccidia of the genus
Eimeria
are specialized intracellular parasitic protozoa that cause severe coccidiosis when they infect their hosts. Animals infected with
Eimeria
develop clinical symptoms, such as anorexia, diarrhea, and hematochezia, which can even cause death. Although the current preferred regimen for the treatment of coccidiosis is antibiotics, this treatment strategy is limited by the ban on antibiotics and the growing problem of drug resistance. Therefore, the exploration of alternative methods for controlling coccidiosis has attracted much attention.
Lactobacillus plantarum
has been shown to have many beneficial effects. In this study,
L. plantarum
M2 was used as a research object to investigate the effect of
L. plantarum
on intestinal inflammation induced by infection with
Eimeria falciformis
in mice by detecting indicators, such as oocyst output, serum cytokines, and the intestinal microbiota. Compared with that in the infection group, the percent weight loss of the mice that were administered with
L. plantarum
M2 was significantly reduced (
P
< 0.05). Supplemented
L. plantarum
M2 and probiotics combined with diclazuril can reduce the total oocyst output significantly (
P
< 0.05,
P
< 0.001).
L. plantarum
M2 had outstanding performance in maintaining intestinal barrier function, and the levels of the mucin MUC1 and the tight junction protein E-cadherin were significantly elevated (
P
< 0.01,
P
< 0.05). Studies have shown that probiotic supplementation can alleviate adverse reactions after infection and significantly improve intestinal barrier function. In addition, probiotics combined with diclazuril could optimize the partial efficacy of diclazuril, which not only enhanced the effect of antibiotics but also alleviated their adverse effects. This study expands the application of probiotics, provides new ideas for alternative strategies for coccidia control, and suggests a basis for related research on lactobacilli antagonizing intracellular pathogen infection.

IMPORTANCE

Coccidia of the genus
Eimeria
are specialized intracellular parasitic protozoa, and the current preferred regimen for the treatment of coccidiosis is antibiotics. However, due to antibiotic bans and drug resistance, the exploration of alternative methods for controlling coccidiosis has attracted much attention. In this work, we focused on
Lactobacillus plantarum
M2 and found that probiotic supplementation can alleviate adverse reactions after infection and improve intestinal barrier function. This study proposes the possibility of using lactic acid bacteria to control coccidiosis, and its potential mechanism needs further exploration.
Complete genome sequence of
Peptostreptococcus porci
isolated from porcine endocarditis in Japan
Authors: Hayashi Masahiro , Yonetamari Jun , Muto Yoshinori , Tanaka Kaori 
Published: June 2024

ABSTRACT

Peptostreptococcus porci
is a recently described bacterium belonging to the
Peptostreptococcaceae
family, which was isolated in 2016 from pig intestine. Herein, we report the complete genome sequence of a clinical isolate of
P. porci
(GAI11004) obtained from porcine endocarditis in Japan. The genome contains a 2.4-Mb circular chromosome.
Whole-genome sequence of
Streptomyces
sp. F41, a potent insecticidal
Streptomyces
isolated from soil in Sichuan, China
Authors: Du Shige , Guo Cheng , Wei Junhong , Li Chunfeng , Zhou Zeyang 
Published: June 2024

ABSTRACT

Streptomyces
sp. F41 is a potent insecticidal metabolite producing actinomycetes isolated from the topsoil, and the complete genome sequence was determined. The genome consists of 8,343,496 bp, with 7,221 genes and a GC content of 71.84%.
Genetic architecture of heritable leaf microbes
Authors: Boyle Julia A. , Frederickson Megan E. , Stinchcombe John R. 
Published: June 2024

ABSTRACT

Host-associated microbiomes are shaped by both their environment and host genetics, and often impact host performance. The scale of host genetic variation important to microbes is largely unknown yet fundamental to the community assembly of host-associated microbiomes, with implications for the eco-evolutionary dynamics of microbes and hosts. Using
Ipomoea hederacea
, ivyleaf morning glory, we generated matrilines differing in quantitative genetic variation and leaf shape, which is controlled by a single Mendelian locus. We then investigated the relative roles of Mendelian and quantitative genetic variation in structuring the leaf microbiome and how these two sources of genetic variation contributed to microbe heritability. We found that despite large effects of the environment, both Mendelian and quantitative genetic host variation contribute to microbe heritability and that the cumulative small effect genomic differences due to matriline explained as much or more microbial variation than a single large effect Mendelian locus. Furthermore, our results are the first to suggest that leaf shape itself contributes to variation in the abundances of some phyllosphere microbes.

IMPORTANCE

We investigated how host genetic variation affects the assembly of
Ipomoea hederacea
’s natural microbiome. We found that the genetic architecture of leaf-associated microbiomes involves both quantitative genetic variation and Mendelian traits, with similar contributions to microbe heritability. The existence of Mendelian and quantitative genetic variation for host-associated microbes means that plant evolution at the leaf shape locus or other quantitative genetic loci has the potential to shape microbial abundance and community composition.
Antibacterial efficacy and membrane mechanism of action of the
Serratia
-derived non-ionic lipopeptide, serrawettin W2-FL10
Authors: Decker Tanya , Rautenbach Marina , Khan Sehaam , Khan Wesaal 
Published: June 2024

ABSTRACT

The study aimed to investigate the antibacterial activity, cytotoxicity, and mechanism of action of the non-ionic, cyclic lipopeptide, serrawettin W2-FL10 against
Staphylococcus aureus
. W2-FL10 exhibited potent activity against the Gram-positive bacteria
S. aureus
,
Enterococcus faecalis
,
Enterococcus faecium
,
Listeria monocytogenes,
and
Bacillus subtilis
, with minimum inhibitory concentration (MIC) values ranging from 6.3 to 31.3 μg/mL, while no activity was observed against Gram-negative bacteria. Broth microdilution assays showed that W2-FL10 interacted with key cell membrane components, such as lipid phosphatidyl glycerol and lipoteichoic acid of
S. aureus
. Upon membrane interaction, W2-FL10 dissipated membrane potential within 12 min and increased
S. aureus
membrane permeability within 28–40 min, albeit at slower rates and higher concentrations than the lytic peptide melittin. The observed membrane permeability, as detected with propidium iodide (PI), may be attributed to transmembrane pores/lesions, possibly dependent on dimer-driven lipopeptide oligomerization in the membrane. Scanning electron microscopy (SEM) imaging also visually confirmed the formation of lesions in the cell wall of one of the
S. aureus
strains, and cell damage within 1 h of exposure to W2-FL10, corroborating the rapid time-kill kinetics of the
S. aureus
strains. This bactericidal action against the
S. aureus
strains corresponded to membrane permeabilization by W2-FL10, indicating that self-promoted uptake into the cytosol may be part of the mode of action. Finally, this lipopeptide exhibited low to moderate cytotoxicity to the Chinese hamster ovarian (CHO) cell line in comparison to the control (emetine) with an optimal lipophilicity range (log D value of 2.5), signifying its potential as an antibiotic candidate.

IMPORTANCE

Antimicrobial resistance is a major public health concern, urgently requiring antibacterial compounds exhibiting low adverse health effects. In this study, a novel antibacterial lipopeptide analog is described, serrawettin W2-FL10 (derived from
Serratia marcescens
), with potent activity displayed against
Staphylococcus aureus
. Mechanistic studies revealed that W2-FL10 targets the cell membrane of
S. aureus
, causing depolarization and permeabilization because of transmembrane lesions/pores, resulting in the leakage of intracellular components, possible cytosolic uptake of W2-FL10, and ultimately cell death. This study provides the first insight into the mode of action of a non-ionic lipopeptide. The low to moderate cytotoxicity of W2-FL10 also highlights its application as a promising therapeutic agent for the treatment of bacterial infections.
Urbanization in a karst terrane, Springfield, Missouri, USA
Authors: Barner Wendell , Gouzie Douglas 
Published: June 2024

ABSTRACT
Springfield, Greene County, Missouri, is the third largest city in Missouri and is located within the Springfield Plateau, a subregion of the Ozark Physiographic Region of the United States. This region is underlain by the Burlington-Keokuk Limestone, which is highly susceptible to solution and is host to more than 2500 sinkholes within Greene County. Springfield, as well as the surrounding communities, has been growing in recent years. Prime areas for development are scarce, thus, leaving more areas that are vulnerable to sinkholes targeted for development. Development next to, and sometimes within, a sinkhole has exacerbated flooding problems, caused structural damage to homes and businesses, and is prone to increasing pollution into the underlying shallow aquifer. Control of stormwater in and around sinkhole areas typically involved the use of several standard approaches: concrete-lined channels draining into sinkholes; installation of pipes into the sinkhole “eye” (swallow hole); filling of sinkholes; elaborate drain or pump systems to remove stormwater from one sinkhole and discharge into another basin or sinkhole; and enlargement of swallow holes by excavation to increase drainage capacity. In an effort to remedy these issues, the City of Springfield adopted a Sinkhole Ordinance around 1990, requiring a permit if a development will encroach upon a sinkhole, sinkhole drainage area, or impact a sinkhole area. This field trip will review examples of pre-ordinance and post-ordinance practices of development in and around sinkholes and sinkhole areas, view recent investigations within this karst area, and discuss approaches to matching geologic knowledge with urbanization in a karst area.
Evidence for sodium valproate toxicity in mitochondrial diseases: a systematic analysis
Authors: Ratnaike Thiloka E , Elkhateeb Nour , Lochmüller Angela , Gilmartin Christopher , Schon Katherine , Horváth Rita , Chinnery Patrick F 
Published: June 2024

BackgroundWe aimed to determine whether sodium valproate (VPA) should be contraindicated in all mitochondrial diseases, due to known VPA-induced severe hepatotoxicity in some mitochondrial diseases.MethodsWe systematically reviewed the published literature for mitochondrial DNA (mtDNA) and common nuclear genotypes of mitochondrial diseases using PubMed, Ovid Embase, Ovid Medline and MitoPhen databases. We extracted patient-level data from peer-reviewed articles, published until July 2022, using the Human Phenotype Ontology to manually code clinical presentations for 156 patients with genetic diagnoses from 90 publications.ResultsThere were no fatal adverse drug reactions (ADRs) in the mtDNA disease group (35 patients), and only 1 out of 54 patients with a non-POLGmitochondrial disease developed acute liver failure. There were fatal outcomes in 53/102 (52%)POLGVPA-exposed patients who all harboured recessive mutations.ConclusionsOur findings confirm the high risk of severe ADRs in any patient with recessivePOLGvariants irrespective of the phenotype, and therefore recommend that VPA is contraindicated in this group. However, there was limited evidence of toxicity to support a similar recommendation in other genotypes of mitochondrial diseases.
CSF sphingolipids are correlated with neuroinflammatory cytokines and differentiate neuromyelitis optica spectrum disorder from multiple sclerosis
Authors: Shi Lisa , Ghezzi Laura , Fenoglio Chiara , Pietroboni Anna Margherita , Galimberti Daniela , Pace Francesca , Hardy Todd A , Piccio Laura , Don Anthony S 
Published: June 2024

BackgroundThere is a need for biomarkers of disease progression and therapeutic response in multiple sclerosis (MS). This study aimed to identify cerebrospinal fluid (CSF) lipids that differentiate MS from other neuroinflammatory conditions and correlate with Expanded Disability Status Scale (EDSS) scores, gadolinium-enhancing lesions or inflammatory mediators.MethodsLipids and inflammatory cytokines/chemokines were quantified with liquid chromatography-tandem mass spectrometry and multiplex ELISA, respectively, in CSF from people with untreated MS, neuromyelitis optica spectrum disorder (NMOSD), other inflammatory neurological diseases and non-inflammatory neurological diseases (NIND). Analytes were compared between groups using analysis of variance, and correlations were assessed with Pearson’s analysis.ResultsTwenty-five sphingolipids and four lysophosphatidylcholines were significantly higher in NMOSD compared with MS and NIND cases, whereas no lipids differed significantly between MS and NIND. A combination of three sphingolipids differentiated NMOSD from MS with the area under the curve of 0.92 in random forest models. Ninety-four lipids, including those that differentiated NMOSD from MS, were positively correlated with macrophage migration inhibitory factor (MIF) and 37 lipids were positively correlated with CSF protein in two independent MS cohorts. EDSS was inversely correlated with cholesterol ester CE(16:0) in both MS cohorts. In contrast, MIF and soluble triggering receptor expressed on myeloid cells 2 were positively associated with EDSS.ConclusionsCSF sphingolipids are positively correlated with markers of neuroinflammation and differentiate NMOSD from MS. The inverse correlation between EDSS and CE(16:0) levels may reflect poor clearance of cholesterol released during myelin break-down and warrants further investigation as a biomarker of therapeutic response.
Tripartite entanglement and Bell non-locality in loop-induced Higgs boson decays
Authors: Morales R. A. 
Published: June 2024

AbstractIn this article, we study quantum entanglement properties of the three-body $$H\rightarrow \gamma l{\bar{l}}$$

H
→
γ
l

l

¯

decays (for $$l=e,\mu ,\tau $$

l
=
e
,
μ
,
τ

) within the context of the Standard Model augmented with CP-violating interactions in the lepton Yukawa sector. Our aim is to elucidate the distribution of entanglement between the final photon, lepton and antilepton across the phase-space. These rare Higgs boson decays occur at 1-loop level, presenting a unique opportunity to scrutinize quantum correlations of fundamental interactions in tripartite systems by computing concurrence measures and investigating Bell non-locality. Moreover, we explore post-decay and autodistillation phenomena. Multipartite entanglement measures have much richer structure than those in the bipartite case, thus deserve more attention in collider phenomenology. In this line, we analyze here novel observables for these three-body Higgs boson decays, which can be extended to other multiparticle systems within the high-energy regime. We found that entanglement manifests among final particles, occasionally achieving a maximally entangled state in specific kinematical configurations. Also, these decay channels are promising for Bell non-locality tests but CP-effects are suppressed by lepton masses in this kind of observables.
Dynamical photon spheres in charged black holes and naked singularities
Authors: Heydarzade Yaghoub , Vertogradov Vitalii 
Published: June 2024

AbstractTo understand the nature of a black hole shadow in dynamical spacetimes, we construct an analytical model of a dynamical photon sphere in the context of the Bonnor–Vaidya spacetime. Comparing the resulting photon sphere radius with the one in Vaidya spacetime, we find that the charge always decreases the radius of the photon sphere. We also prove that a naked singularity in Bonnor–Vaidya spacetime, unlike the static Reissner–Nordstrom naked singularity, may cast a shadow, and as a result, it cannot be distinguished from a black hole through its shadow.
Ubiquitin Ligase TRIM22 Inhibits Ovarian Cancer Malignancy via TCF4 Degradation
Authors: Tao Tao , Zhang Yongqi , Guan Chunyan , Wang Shuxiang , Liu Xiaoli , Wang Min 
Published: June 2024

Abstract
Ovarian cancer is one of the most common malignancies in women. Tripartite motif-containing protein 22 (TRIM22) plays an important role in the initiation and progression of malignant tumors. Similarly, the transcription factor 4 (TCF4) is an essential factor involved in the initiation and progression of many tumors. However, it is still unclear whether TRIM22 can affect TCF4 in ovarian cancer. Therefore, this study aims to investigate the mechanism related to TRIM22 and TCF4 in ovarian cancer. TRIM22 protein and mRNA levels were analyzed in samples from clinical and cell lines. The effects of TRIM22 knockdown and overexpression on cell proliferation, colony formation, migration, invasion, and related biomarkers were evaluated. In addition, the role of ubiquitination-mediated degradation of TCF4 was investigated by qRT-PCR and Western blotting. The association between TRIM22 and TCF4 was evaluated by Western blotting, coimmunoprecipitation, proliferation, colony formation, invasion, migration, and related biomarkers. The results showed that the expression of TRIM22 was minimal in ovarian cancer tissues. Furthermore, upregulation of TRIM22 significantly inhibited ovarian cancer cell proliferation, colony formation, migration, and invasion. In addition, TRIM22 was observed to regulate the degradation of TCF4 through the ubiquitination pathway. TCF4 can reverse the effects of TRIM22 on proliferation, colony formation, migration, and invasion in ovarian cancer cells. TRIM22-mediated ubiquitination of TCF4 at K48 is facilitated by the RING domain.
Implications: In conclusion, ubiquitination of TCF4 protein in ovarian cancer is regulated by TRIM22, which has the potential to limit the proliferation, migration, and invasion of ovarian cancer.