Analysis Of Molecular Data Research Articles

A New Species of Murina (Chiroptera: Vespertilionidae) from Yunnan, China.

During an examination of various specimens previously collected from different locations and times, we discovered seven Murina specimens that had been collected in May 2023 from the Guanyinshan Provincial Nature Reserve, Yuanyang, Yunnan, China. Based on the assessment of morphological characteristics and molecular data analysis, these specimens were determined to represent a previously unidentified species, designated Murina yuanyang sp. nov.

Comparison of population genetic structure of Pinus mugo Turra forest stands in the Giant Mountains by analysis of nSSR molecular marker data

Abstract Pinus mugo (dwarf mountain pine) communities in the protected area of Krkonoše National Park are extremely valuable. After extensive deforestation during the sixteenth to nineteenth centuries, P. mugo recovered naturally in some parts of the Giant Mountains, and in some places imported seeds were likely used for reforestation. To distinguish between native and possibly introduced local P. mugo populations, genetic variations between 12 populations from the Czech Sudeten part of the Giant Mountains and between the two populations from the Tatra Mountains were analysed using 12 nuclear microsatellite markers (nuclear simple sequence repeats). Based on the simple sequence repeat data, 146 alleles were found, and Shannon’s information index, number of private alleles, and expected heterozygosity (HE) of populations averaged 1.12, 0.16, and 0.53, respectively. Analysis of molecular variance indicated that most of the variation was detected within populations. Low levels of genetic differentiation were also observed (average FST = 0.023). The population structure was examined by Bayesian clustering. The results of STRUCTURE analysis confirmed that the introduced populations were different from the autochthonous populations. Some of the introduced Czech Sudeten populations had similar genetic structure as the more distant native populations from the Tatra Mountains. Our results provide important genetic information for the reconstruction of natural communities in the Giant Mountains.

New Myzostomids (Annelida) in Symbiosis with Feather Stars in the Shallow Waters of the South China Sea (Hainan Island).

This research delves into the molecular and morphological characteristics of myzostomid worms associated with common shallow-water feather stars (Echinodermata: Crinoidea: Comatulidae) in the coastal waters near Sanya, Hainan Island. Through the examination of specimens collected at depths of up to 10 m using scuba diving techniques, we describe three new species (Myzostoma ordinatum sp. nov., M. scopus sp. nov., and M. solare sp. nov.) and report the first record of Myzostoma polycyclus Atkins, 1927 in the South China Sea. The absence of overlap with the seven previously documented Myzostomida species in the shallow waters of Hong Kong and Shenzhen reveals significant gaps in our understanding of marine biodiversity in the South China Sea. These findings, combined with an analysis of available molecular data, underscore the potential existence of unexplored and diverse symbiotic relationships among marine invertebrates within the region.

Ontology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine.

Many data resources generate, process, store, or provide kidney related molecular, pathological, and clinical data. Reference ontologies offer an opportunity to support knowledge and data integration. The Kidney Precision Medicine Project (KPMP) team contributed to the representation and addition of 329 kidney phenotype terms to the Human Phenotype Ontology (HPO), and identified many subcategories of acute kidney injury (AKI) or chronic kidney disease (CKD). The Kidney Tissue Atlas Ontology (KTAO) imports and integrates kidney-related terms from existing ontologies (e.g., HPO, CL, and Uberon) and represents 259 kidney-related biomarkers. We have also developed a precision medicine metadata ontology (PMMO) to integrate 50 variables from KPMP and CZ CellxGene data resources and applied PMMO for integrative kidney data analysis. The gene expression profiles of kidney gene biomarkers were specifically analyzed under healthy control or AKI/CKD disease states. This work demonstrates how ontology-based approaches support multi-domain data and knowledge integration in precision medicine.

PIM1 is a potential therapeutic target for the leukemogenic effects mediated by JAK/STAT pathway mutations in T-ALL/LBL

Precursor T-cell neoplasms (T-ALL/LBL) are aggressive hematological malignancies that arise from the malignant transformation of immature thymocytes. Despite the JAK/STAT pathway is recurrently altered in these neoplasms, there are not pharmacological inhibitors officially approved for the treatment of T-ALL/LBL patients that present oncogenic JAK/STAT pathway mutations. In the effort to identify potential therapeutic targets for those patients, we followed an alternative approach and focused on their transcriptional profile. We combined the analysis of molecular data from T-ALL/LBL patients with the generation of hematopoietic cellular models to reveal that JAK/STAT pathway mutations are associated with an aberrant transcriptional profile. Specifically, we demonstrate that JAK/STAT pathway mutations induce the overexpression of the PIM1 gene. Moreover, we show that the pan-PIM inhibitor, PIM447, significantly reduces the leukemogenesis, as well as the aberrant activation of c-MYC and mTOR pathways in cells expressing different JAK/STAT pathway mutations, becoming a potential therapeutic opportunity for a relevant subset of T-ALL/LBL patients.

Morphology and systematics of a new fossil snake from the early Rupelian (Oligocene) White River Formation, Wyoming

Abstract Extinct snake taxa are recognized primarily from isolated vertebrae. A new specimen from the early Oligocene of Wyoming provides a rare opportunity to examine four nearly complete and articulated fossil snakes. Informally assigned previously to the ‘erycine’ vertebral form taxa Ogmophis and Calamagras, a detailed comparison reveals that this fossil snake exhibits vertebral differences from both taxa and is, furthermore, a new taxon, Hibernophis breithaupti gen. et sp. nov., based on a combination of apomorphies such as absence of basal tubera, low subrectangular prootic, low parasphenoid wings obscuring the anterior opening of the Vidian canal, and foramen for the mandibular branch of the trigeminal nerve posteriorly displaced inside the adductor fossa of the compound. Parsimony and Bayesian phylogenetic analysis of combined morphological and molecular data from a broad selection of snakes places Hibernophis breithaupti as sister taxon to all other booids, distant from both Old and New World ‘erycines’. However, an alternative position close to New World ‘erycines’ and ungaliophiines cannot be rejected.

PATH-03. FOXR2-OVEREXPRESSING CENTRAL NERVOUS SYSTEM (CNS) TUMORS EXHIBIT SUBSTANTIAL DIVERSITY ACROSS HISTOLOGICAL, MOLECULAR, AND CLINICAL DIMENSIONS

Abstract BACKGROUND FOXR2 activation is regarded as the pathognomonic molecular signature of CNS neuroblastoma. However, a comprehensive understanding of the landscape for CNS tumors exhibiting FOXR2 activation is lacking. METHODS Integrated histopathologic, molecular, and clinical data analysis of 36 FOXR2-overexpressing CNS tumors identified through screening of an institutional dataset. RESULTS FOXR2-overexpressing CNS tumors showed a broad anatomic distribution throughout the neuraxis. Of the 36 tumors, 17 (47.2%) were gliomas and 17 (47.2%) were embryonal tumors. The gliomas included 16 high-grade gliomas (eight histone H3 K27M-mutant diffuse midline gliomas, seven radiation-associated tumors, and one with MN1::PATZ1 fusion) and one pilocytic astrocytoma. The embryonal tumors included ten CNS neuroblastomas, six pineoblastomas, and one medulloblastoma. Two were difficult-to-classify high-grade neuroepithelial tumors. The gliomas and embryonal tumors demonstrated comparable FOXR2 expression based on normalized RNA-sequencing data. FOXR2-overexpressing gliomas, but not embryonal tumors, displayed diverse concomitant genetic alterations. The most common mechanisms of FOXR2 activation involved structural alterations leading to proximity effects, frequently incorporating non-canonical non-coding exons, followed by activation of the exon -3 promoter. Tumor location, histology, and concomitant alterations correlated with patient outcomes. While FOXR2-overexpressing gliomas were aggressive with a 5-year overall survival of 13.3%, FOXR2-overexpressing embryonal tumors showed a diverse prognosis. FOXR2-activated CNS neuroblastoma showed a 5-year overall survival of 100%. Pineoblastomas with FOXR2 activation in the PB-FOXR2 DNA methylation group showed a 3-year survival of 0% despite multimodal therapy. The one medulloblastoma patient in the cohort is alive at three years post-diagnosis. CONCLUSION FOXR2-overexpressing CNS tumors manifest significant histological, molecular, and clinical diversity and can occur as post-radiation tumors. Glioma histology and concomitant genetic alterations correlate with treatment resistance and inferior prognosis, while FOXR2-overexpressing embryonal tumors show more heterogeneous outcomes. Integrating histologic and molecular diagnostic approaches along with therapeutic interventions and clinical outcomes is imperative for accurate prognostication and optimal therapeutic decision-making.

Genetic spectrum of sarcoglycanopathies in a cohort of Russian patients

Sarcoglycanopathies encompass four distinct forms of limb-girdle muscular dystrophies (LGMD), denoted as LGMD R3-R6, arising from mutations within the SGCA, SGCB, SGCG, and SGCD genes. The global prevalence of sarcoglycanopathies is low, making it challenging to study these diseases. The principal objective of this study was to explore the spectrum of mutations in a cohort of Russian patients with sarcoglycanopathies and to ascertain the frequency of these conditions in the Russian Federation. We conducted a retrospective analysis of clinical and molecular genetic data from 49 Russian patients with sarcoglycan genes variants. The results indicated that variants in the SGCA gene were found in 71.4% of cases, with SGCB and SGCG genes each exhibiting variants in 12.2 % of patients. SGCD gene variants were detected in 4.1% of cases. Bi-allelic pathogenic and likely pathogenic variants were identified in 46 of the 49 cases of sarcoglycanopathies: LGMD R3 (n = 34), LGMD R4 (n = 4), LGMD R5 (n = 6), and LGMD R6 (n = 2). A total of 31 distinct variants were identified, comprising 25 previously reported and 6 novel variants. Two major variants, c.229C>T and c.271G>A, were detected within the SGCA, constituting 61.4% of all mutant alleles in Russian patients with LGMD R3. Both LGMD R6 cases were caused by the homozygous nonsense variant c.493C>T p.(Arg165Ter) in the SGCD gene. The incidence of sarcoglycanopathies in the Russian Federation was estimated to be at least 1 in 4,115,039, which is lower than the reported incidence in other populations.

Molecular insights into fungal diversity reveal three novel species of Leucocoprinus from southern Punjab, Pakistan

ABSTRACT Three novel species of the genus Leucocoprinus, named Lc. cinnamomeodiscus, Lc. dahranwalanus, and Lc. iqbalii, are described from unexplored regions of southern Punjab, Pakistan, based on comprehensive analyses of morphoanatomical characteristics and molecular phylogenetic data. We provide illustrations of freshly collected basidiomata and detailed line drawings highlighting key anatomical features. The molecular phylogenetic analyses, which are based on the internal transcribed spacer (ITS) region and combined ITS-28S sequences, consistently position these newly described species within the genus Leucocoprinus. Additionally, this study also introduces new taxonomic combinations for previously reported Leucoagaricus species.

ITGB6 as an inhibitor of T-cell killing via modulation of paracrine TGFβ signaling in pancreatic ductal adenocarcinoma.

e16334 Background: Immunotherapy has experienced limited success in PDAC, with αPD-1 therapy being approved only in a subset that makes up < 2% of all PDAC cancers. TGFβ is a contributor to T-cell suppression in the PDAC tumor microenvironment. However, the success of blocking TGFβ in preclinical models has failed to translate into the clinic due to the off-target effects of systemic TGFβ blockade. Integrin ITGB6 is an activator of the inert latent TGFβ into the active, immunosuppressive form. Consequently, inhibition of ITGB6 is a potent and targeted therapeutic approach for disrupting TGFβ to overcome T-cell suppression in PDAC. Methods: Analysis of TCGA molecular and survival data was performed to determine the specificity and prognostic value of ITGB6 in PDAC. Subsequently, candidate cell lines were screened for ITGB6 expression using flow cytometry to facilitate an in vitro model. Using a lentiviral system, PDAC cells were transduced with a doxycycline-inducible short hairpin RNA (shRNA) knockdown (KD) of ITGB6. Both KD and control shRNA cell lines were induced with doxycycline and subsequently co-cultured with TALL-104 T-cells. Furthermore, conditioned media was analyzed for secreted active TGFβ levels using a luciferase-based TGFβ reporter cell line. Finally, a clonogenic assay was performed to determine the autocrine effects of TGFβ activation in PDAC. Results: ITGB6 is highly specific to PDAC and also shows upregulation in comparison to normal pancreatic tissue (FC 3.38, p < 0.0001). Capan-2 cells were chosen as a model for high integrin PDAC (Capan-2 99.73% cells ITGB6+, negative control: HCT116WT 0.96% cells ITGB6+). Fluorescent microscopy of the co-culture revealed that the KD of ITGB6 increased T-cell killing over 24 hours (Capan-2 CTRL shRNA 7.71%±3.63 dead vs. Capan-2 ITGB6 shRNA 21.68%±4.57 dead, p < 0.05). Media from ITGB6 KD cells contained significantly decreased TGFβ (+TGFβ: 673000 RLU vs. CTRL: 175500 RLU, p = 0.015). A clonogenic assay of Capan-2 cells treated with active-TGFβ demonstrates that PDAC cells resist the autocrine growth inhibitory effects of TGFβ through loss of SMAD4. TCGA survival data revealed ITGB6 as prognosis marker in PDAC (high ITGB6 median survival 16.79 mos, vs. low ITGB6 21.88 mos, HR = 2.730, p < 0.004). Conclusions: Survival data that clearly demonstrates the poor prognosis of ITGB6 expression, as well as the presently proposed mechanism of immunosuppression, provide ample justification for deploying anti-ITGB6 combination therapies to in vivo studies that facilitate translation of our findings into therapeutic clinical trials.

A taxonomic revision of Arnot’s Chat Myrmecocichla arnotti (family Muscicapidae)

Arnot’s Chat Myrmecocichla arnotti in the family Muscicapidae is largely confined to the woodlands of the Zambezian biome of south-central Africa. This work assesses its taxonomic status, including comments on the so-called Ruaha Chat M. [a.] collaris (also named M. [a.] leucolaema). Based on an analysis of morphology, behaviour and molecular data, we recommend that M. arnotti be considered a single species with two subspecies: M. a. arnotti (including shelleyi, leucolaema and collaris) and M. a. harterti. A restricted type locality is proposed for Saxicola shelleyi Sharpe, 1877: Ngwesi (21°03′ S, 27°50′ E), southwestern Zimbabwe.

Synthesis, Antiproliferative Activity and Molecular Docking Analysis of Both Enantiomerically Pure Decursin Derivatives as Anticancer Agents.

Using (S)-decursinol isolated from root of Angelica gigas Nakai (AGN), we semi-synthesized and evaluated a series of both enantiomerically pure decursin derivatives for their antiproliferative activities against A549 human lung cancer cells. All synthesized compounds showed a broad spectrum of inhibitory activities against the growth of A549 cells. Especially, compound (S)-2d with (E)-(furan-3-yl)acryloyl group showed the most potent activity (IC50: 14.03 µM) against A549 cancer cells as compared with the reference compound, decursin (IC50: 43.55 µM) and its enantiomer, (R)-2d (IC50: 151.59 µM). Western blotting assays indicated that (S)-2d more strongly inhibited Janus kinase 1 (JAK1) and signal transducer and activator of transcription activation 3 (STAT3) phosphorylation than decursin in a dose-dependent manner, while having no effect on CXCR7 overexpression and total STAT3 level. In addition, (S)-2d induced cell cycle arrest at G1 phase and subsequent apoptotic cell death in A549 cancer cells. Our combined analysis of molecular docking studies and biological data suggests that the inhibition of JAK1 with (S)-2d resulted in loss of STAT3 phosphorylation and inhibition of cell growth in A549 cancer cells. These overall results strongly suggest that (S)-2d (MRC-D-004) as a novel JAK1 inhibitor may have therapeutic potential in the treatment of A549 human lung cancers by targeting the JAK1/STAT3 signaling pathway.

A new look at genetic variability in pomegranate: Landscape genetics and structural equation modeling (SEM)

Pomegranate (Punica granatum L.) is an important horticultural plant in Iran and has been a food source since ancient times. Despite several genetic diversity studies conducted on these taxa, there are no reports on the landscape genetics of these important plants in Iran, nor is there any information on the effects of environmental, spatial, and climatic variables on the genetic structure of pomegranate. Therefore, this study used genetics, structural equation modeling (SEM), and species distribution modeling (SDM) approaches to explore the above-mentioned objectives. We used both cytogenetic and molecular analyses (SSR and SCoT markers) of several pomegranate samples along with environmental, spatial, and climatic variables. The redundancy analysis (RDA) analysis showed a significant positive association between terminal chiasmata with the longitudinal distribution of the pomegranate accession, while total chiasma number and interstitial chiasmata have an association with the altitude. The spatial PCA analysis indicated the role played by both global and local spatial variables in the cytogenetic variability like the univalent and terminal chiasmata formation. The Mantel test indicates that the cytogenetic difference in pomegranate plants is not related to their geographical distance, while the Moran I test result shows that geographical regions with similar spatial conditions affect the cytogenetic structuring of pomegranate plants in a similar way. SEM methods showed a strong negative association between bivalent formation and the environmental variables, while they showed both positive and negative associations between some of the environmental variables and different kinds of chiasmata. The sPCA analysis of molecular data showed a significant global, and local, spatial structuring of the molecular data and the genetic cline formation within the pomegranate accessions studied. Similarly, the spatial PCA analysis of climate variables, precipitation, and temperature revealed a significant structuring of genetic diversity and the formation of genetic clines by these factors. RDA analysis identified some of the loci that are significantly associated with temperature and precipitation. Therefore, both geographical/ or spatial variables and climate factors contribute to the genetic structure of the pomegranate accessions studied. SEM models based on genetic data revealed a positive association between environmental and climate variables with genetic diversity parameters and SSR-SCoT molecular loci studied. Climate change is unlikely to hurt pomegranate growing areas due to the high genetic diversity of pomegranate plants and the diverse genetic lineages present in the country.

Unmasking Hidden Threats Global Spread of MBL Resistance Exposed

This study aims to establish a routine monitoring system for MBL enzymes to provide timely data to healthcare professionals and policy makers, enabling informed decision making on antibiotic use and resistance management. Using a combination of molecular biology techniques and data analysis, we monitor MBL activity in various institutional settings. The increasing prevalence of multidrug-resistant (MDR) bacteria is a significant threat to public health globally. Metallo-beta-lactamase (MBL), an enzyme that confers resistance to a wide range of beta-lactam antibiotics, is particularly concerning due to its ability to spread rapidly in healthcare and community settings. Despite the importance of this issue, systematic monitoring and understanding of MBL remains inadequate. Our findings reveal a significant, previously unreported presence of MBLs, underscoring the urgent need for targeted antibiotic stewardship programs. The implications of this study emphasize the importance of integrating enzyme monitoring into standard healthcare practices to reduce the spread of MDR bacteria. Highlights: Regular Monitoring: Essential for tracking MBL enzyme prevalence and guiding antibiotic use. Advanced Techniques: Molecular biology methods enhance MBL detection and analysis. Policy Integration: Crucial for implementing enzyme monitoring in healthcare to combat MDR bacteria spread. Keywords: MBL Enzymes, Antibiotic Resistance, Healthcare Monitoring, Molecular Biology, Stewardship Programs

Molecular evaluation and genetic behavior of white tip nematode resistance against Aphelenchoides besseyi in artificially infected rice plants

Genetic behavior of some morphological, yield and its related traits was studied under nematode infection condition using five rice genotypes which were crossed using complete-diallel analysis to produce 20 rice hybrids. All 25 genotypes were evaluated under both normal and white tip nematode infection conditions. Although, molecular evaluation using simple sequence repeats for characters related to resistance were done. As a result of this study, the parental varieties Giza179, Giza182 and Sakha105 were the best of all parents, since they possessed favorite general combining ability (GCA) effects for many traits. The three crosses Sakha106 × Sakha101, Sakha105 × Sakha101 and Giza182 × Giza179 recorded the desirable values of specific combining ability (SCA) for most of the studied traits. Dominance genetic variance played the most significant role in inheritance of the traits under study. The two crosses Sakha101 × Sakha106 and Sakha105 × Sakha101 were considered the best for yield and its components under affected condition by white tip nematode. RM5526 marker was the best in detecting genetic diversity among the rice accessions for the resistance-associated trait, no. Of Aphelenchoides besseyi (A. besseyi) individuals in 100 grains (NA). While, RM161 marker was the best in detecting genetic diversity among the rice accessions for the resistance-associated trait, loss rate of panicle weight (LRPW). Principal component analysis (PCA) was applied for morpho-physiological characters and molecular data analysis and showed a good separation of the genotypes which was in high agreement with phylogenetic tree clustering and also showed that SSR analysis can be recognized with the help of principal component analysis, which are accountable for the observed genotypic variations presented within each component. Two DNA fragments with molecular size of 165 bp and 146 bp may play an important role in the white tip nematode resistance in rice while they appeared only in the resistant parents and crosses. These bands should be isolated, sequenced and compared with the genes in data base which are responsible for white tip nematode resistance in rice. Both DNA fragments will be of great interest in nematode resistance programs in rice in the future. Finally, we can recommend the farmers to use the two varieties Giza 179 and Giza182 for planting in land affected with white tip nematode. The farmers could also be recommend to use the two hybrids Sakha106 × Sakha105 and Giza179 × Sakha105 when planting in land affected with white tip nematode while they proved to be resistant to white tip nematode by using morphological and molecular analyses. For researchers we can recommend by using the two specific molecular markers, RM5526 and RM161 for fast identification of white tip nematode resistant rice varieties in Egypt.

Morphological and molecular characterization of ‘Saragolla’ wheats (Triticum turgidum subsp. durum from Abruzzo, Italy)

A morphological and genetic characterization of autochthonous ‘Saragolla’ wheats, currently cultivated in Abruzzo Region (Italy), was carried out. Using 15 simple sequence repeat (SSR) markers and 24 UPOV morphological traits we compared: (a) 13 ‘Saragolla’ genotypes with traits of the italicum/apulicum botanical varieties (Saragolla (Sar.) italicum), (b) 26 ‘Saragolla’ genotypes with traits of leucurum/affine botanical varieties (Sar. leucurum), (c) 8 breeding varieties (pure lines), and (d) 5 Italian autochthonous wheats and 1 turanicum line (old wheats). One hundred twenty-six (126) alleles were identified. The number of alleles per locus spanned from 4 to 15 and the number of alleles per genotype varied between 12 and 21. Values of gene diversity (Nei) across the 53 genotypes was 0.17. The groups of Sar. leucurum and Sar. italicum genotypes were morphologically distinguishable from the groups of old wheats and pure lines. Likewise, the analysis of molecular data using the discriminant analysis revealed that genotypes with the Sar. italicum phenotype displayed distinct genetic differences from Sar. leucurum, pure lines and old wheats. These results make Sar. italicum genotypes distinguishable and eligible as a conservation variety. Ward's clustering analysis of the 53-genotype pool showed that the ‘Saragolla’ landrace is a valuable repository of genetic diversity.

Diplostomum cf. vanelli Yamaguti, 1935 (Trematoda: Diplostomidae Poirier, 1886): Morpho-Molecular Data and Life Cycle

Furcocercariae, of the trematodes from the family Diplostomidae, were found in freshwater snails—Radix auricularia, which were collected in a reservoir located on Popov Island (Peter the Great Bay, Sea of Japan). The life cycle was experimentally reproduced for the first time, while morphometric data for the development stages were studied and described for the newly discovered trematode. Moreover, molecular data for nuclear and mitochondrial markers were also obtained. It was determined that the morphometric characteristics of the trematode coincided with the species Diplostomum cf. vanelli, the molecular data analysis validates the species independence. Furthermore, the study highlights the issue of species identification in the Diplostomum genus.

First Report of Postharvest Fruit Rot Caused by Neofusicoccum parvum on Prunus salicina (Nai Plum) in China.

Nai plum (Prunus salicina var. cordata cv. Younai) is one of the most popular fruit crop in South China. In July 2023, a fruit rot of nai plum with about 5 % disease incidence was observed in a fruit market of Changsha city, Hunan Province, China. Initially, small, brown lesions appeared randomly on the fruit surface, with disease progression, the lesions gradually expanded and developed into soft rot. To isolate possible fungi from rotten fruits, small pieces (2 × 2 mm) from the periphery of 10 infected fruits were surface-sterilized using 70% ethanol for 10 s, rinsed three times in sterile distilled water, air dried, and then placed onto potato dextrose agar (PDA) plates and incubated at 28℃ for three days. Emerging colonies were subcultured by hyphal tiptransfer on fresh PDA. A total of ten isolates with similar morphology were obtained. Fungal colonies were initially white, gradually turning gray and eventually becoming black, and aerial hyphae were dense and fluffy. Conidia were hyaline, single celled, ellipsoidal to fusiform, and range from 12.7 to 20.0 μm long (avg. 16.9 ± 2.39 μm) × 5.3 to 7.3 μm wide (avg. 6.3 ± 0.82 μm). These morphological characteristics of these isolates matched those of Neofusicoccum parvum (Phillips et al. 2013). To future confirmation of the identify, the internal transcribed spacer (ITS) region, translation elongation factor 1-alpha (TEF1-a), and beta-tubulin TUB2) genes of two representative isolates (JXNP1 and JXNP2) were amplified and sequenced using primer sets ITS5/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Carbone and Kohn 1999; Phillips et al. 2013), and BT2A/BT2B (Glass and Donaldson 1995), respectively. The sequences of both isolates were deposited in GenBank for the ITS (accession nos. OR899331 and OR899332), TEF1-a gene (accession nos. OR909890 and OR909891) and TUB2 gene (accession nos. OR909892 and OR909893). BLAST analysis showed 99-100% identity with the ex-type strain of N. parvum (CMW9081) for ITS, TEF1-a and TUB2. A maximum likelihood phylogenetic tree was constructed using IQtree web server based on combined ITS, TEF1-a and TUB2 data set. The phylogenetic tree revealed that two isolates clustered with N. parvum in a clade with 90% bootstrap support. Based on morphological and molecular data analysis, the isolates were identified as N. parvum. To confirm the pathogenicity, five healthy nai plum fruits were wounded by using a sterile needle after surface sterilization with 75% ethanol, then a 5-mm-diameter mycelial disc of isolate JXNP1 was taped to the wound, the control fruits were taped with sterile agar plugs. All fruits were incubated at 25 ℃ with 80% humidity. After five days, typical naturally occurring fruit rot symptoms appeared on the fruits which inoculated with N. parvum, whereas control fruits remained asymptomatic. To fulfill Koch's postulates, the pathogen was re-isolated from the inoculated fruits and comfirmed as N. parvum by morphological and molecular analysis. Previous studies reported that N. parvum caused fruit rot on various common fruits in China, including loquat, kiwifruit and citrus (Lei et al. 2013; Zhai et al. 2019; Zhou et al. 2013). To our knowledge, this is the first report of N. parvum causing postharvest fruit rot on nai plum in China. This finding provides critical insights for the management of the high-risk disease on plum in China.

Phylogenetic and molecular dating analyses of Chinese endemic genus Dipelta (Caprifoliaceae) based on nuclear RAD‐Seq and chloroplast genome data

AbstractDipelta Maxim. (Caprifoliaceae) is a Tertiary relic genus endemic to China, which includes three extant species, Dipelta floribunda, Dipelta yunnanensis, and Dipelta elegans. Recent progress in the systematics and phylogeographics of Dipelta has greatly broadened our knowledge about its origin and evolution, however, conflicted phylogenetic relationships and divergence times have been reported and warrant further investigation. Here, we utilized chloroplast genomes and population‐level genomic data restriction site‐associated DNA‐single nucleotide polymorphisms (RAD‐SNPs) to evaluate the interspecific relationships, population genetic structure and demographic histories of this genus. Our results confirmed the sister relationship between D. elegans and the D. yunnanensis–D. floribunda group, but with cyto‐nuclear phylogenetic discordance observed in the latter. Coalescent simulations suggested that this discordance might be attributed to asymmetric “chloroplast capture” through introgressive hybridization between the two parapatric species. Our fossil‐calibrated plastid chronogram of Dipsacales and the coalescent modeling based on nuclear RAD‐SNPs simultaneously suggested that the three species of Dipelta diversified at the late Miocene, which may be related to the uplift of the eastern part of Qinghai–Tibet Plateau (QTP) and adjacent southwest China, and increasing Asian interior aridification since the late Miocene; while in the mid‐Pleistocene, the climatic transition and continuous uplift of the QTP, triggered allopatric speciation via geographical isolation for D. floribunda and D. yunnanensis regardless of bidirectional gene flow. Based on both plastid and nuclear genome‐scale data, our findings provide the most comprehensive and reliable phylogeny and evolutionary histories for Dipelta and enable further understanding of the origin and evolution of floristic endemisms of China.

Vascular Ehlers-Danlos Syndrome: A Comprehensive Natural History Study in a Dutch National Cohort of 142 Patients.

Vascular Ehlers-Danlos syndrome (vEDS) is a rare connective tissue disorder with a high risk for arterial, bowel, and uterine rupture, caused by heterozygous pathogenic variants in COL3A1. The aim of this cohort study is to provide further insights into the natural history of vEDS and describe genotype-phenotype correlations in a Dutch multicenter cohort to optimize patient care and increase awareness of the disease. Individuals with vEDS throughout the Netherlands were included. The phenotype was charted by retrospective analysis of molecular and clinical data, combined with a one-time physical examination. A total of 142 individuals (50% female) participated the study, including 46 index patients (32%). The overall median age at genetic diagnosis was 41.0 years. More than half of the index patients (54.3%) and relatives (53.1%) had a physical appearance highly suggestive of vEDS. In these individuals, major events were not more frequent (P=0.90), but occurred at a younger age (P=0.01). A major event occurred more often and at a younger age in men compared with women (P<0.001 and P=0.004, respectively). Aortic aneurysms (P=0.003) and pneumothoraces (P=0.029) were more frequent in men. Aortic dissection was more frequent in individuals with a COL3A1 variant in the first quarter of the collagen helical domain (P=0.03). Male sex, type and location of the COL3A1 variant, and physical appearance highly suggestive of vEDS are risk factors for the occurrence and early age of onset of major events. This national multicenter cohort study of Dutch individuals with vEDS provides a valuable basis for improving guidelines for the diagnosing, follow-up, and treatment of individuals with vEDS.