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Abstract Background The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Findings Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. Conclusions This indicated that both BAC libraries are valuable tools for molecular studies in chicory, one goal being the positional cloning of the S-locus in this Asteraceae species.

Background: Malignant cardiac neoplasms (MCNs), both primary and metastatic, are rare with few epidemiologic studies., Methods: This retrospective study used the Healthcare Utilization Project/Nationwide Inpatient Sample database from 2002 to 2018 to evaluate the co-occurrences with other malignancies, and mortality of MCNs in the USA., Results: The data contained 7207 weighted discharges of MCN. Median patient age was 51.4 years, 52.29 % were male, in-hospital mortality was 10.51 %, mean cost of hospitalization was $34,280 USD. Lung, mediastinum, and airways were the most common primary cancers associated with metastatic MCN., Conclusions: MCN are rare in the USA, however they carry a high in-hospital mortality, high morbidity, and hospital cost., Competing Interests: Declaration of competing interest The authors have declared that no competing interests exist., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Competing Interests: The authors have declared that no competing interests exist.

The origins and evolution of virulence in amphibian-infecting chytrids Batrachochytrium dendrobatidis ( Bd ) and Batrachochytrium salamandrivorans ( Bsal) are largely unknown. Here, we use deep nanopore sequencing of Bsal and comparative genomics against 21 high-quality genome assemblies that span the fungal Chytridiomycota. We discover that Bsal has the most repeat-rich genome of the Chytridiomycota, comprising 40.9% repetitive elements; this genome has expanded to more than 3× the length of its conspecific Bd , with autonomous and fully functional LTR/Gypsy elements contributing significantly to the expansion. The M36 metalloprotease virulence factors are highly expanded ( n = 177) in Bsal , most of which (53%) are flanked by transposable elements, suggesting they have a repeat-associated expansion. We find enrichment upstream of M36 metalloprotease genes of three novel repeat families belonging to the repeat superfamily of LINEs that are implicated with gene copy number variations. Additionally, Bsal has a highly compartmentalized genome architecture, with virulence factors enriched in gene-sparse/repeat-rich compartments, while core conserved genes are enriched in gene-rich/repeat-poor compartments. Genes upregulated during infection are primarily found in the gene-sparse/repeat-rich compartment in both Bd and Bsal . Furthermore, genes with signatures of positive selection in Bd are enriched in repeat-rich regions, suggesting these regions are a cradle for the evolution of chytrid pathogenicity. These are the hallmarks of two-speed genome evolution, and this study provides evidence of two-speed genomes in an animal pathogen, shedding light on the evolution of fungal pathogens of vertebrates driving global declines and extinctions.

Candida glabrata is the second most common etiological cause of worldwide systemic candidiasis in adult patients. Genome analysis of 68 isolates from 8 hospitals across Scotland, together with 83 global isolates, revealed insights into the population genetics and evolution of C. glabrata. Clinical isolates of C. glabrata from across Scotland are highly genetically diverse, including at least 19 separate sequence types that have been recovered previously in globally diverse locations, and 1 newly discovered sequence type. Several sequence types had evidence for ancestral recombination, suggesting transmission between distinct geographical regions has coincided with genetic exchange arising in new clades. Three isolates were missing MATα1, potentially representing a second mating type. Signatures of positive selection were identified in every sequence type including enrichment for epithelial adhesins thought to facilitate fungal adhesin to human epithelial cells. In patent microevolution was identified from 7 sets of recurrent cases of candidiasis, revealing an enrichment for nonsynonymous and frameshift indels in cell surface proteins. Microevolution within patients also affected epithelial adhesins genes, and several genes involved in drug resistance including the ergosterol synthesis gene ERG4 and the echinocandin target FKS1/2, the latter coinciding with a marked drop in fluconazole minimum inhibitory concentration. In addition to nuclear genome diversity, the C. glabrata mitochondrial genome was particularly diverse, with reduced conserved sequence and conserved protein-encoding genes in all nonreference ST15 isolates. Together, this study highlights the genetic diversity within the C. glabrata population that may impact virulence and drug resistance, and 2 major mechanisms generating this diversity: microevolution and genetic exchange/recombination., (© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.)

Inflammatory bowel disease (IBD), which includes Crohn's disease (CD), is a chronic, immune-mediated disease involving the gastrointestinal tract. Cerebral palsy (CP) has not been associated with IBD aside from a single previously published case series. In this study, we describe two cases of CD in patients with CP. Both patients had global developmental delay. They were also underweight and exclusively gastrostomy tube dependent for nutrition. By detailing their clinical courses, we illustrate the importance of becoming familiar with the extraintestinal manifestations of IBD. In the setting of developmental delay and its associated communication barriers, the evaluation of IBD might shift from assessing subjective symptoms to recognizing the subtle presentations of the disease, including anemia, weight loss, malnutrition, and failure to thrive. We also hypothesize that malnutrition and a change in the gastrointestinal microbiota associated exclusively with enteral nutrition may be linked to the development of CD in patients with CP. Overall, this study provides information for clinicians caring for patients with CP or developmental delay, and how to recognize extraintestinal manifestations of IBD., (© 2021. Japanese Society of Gastroenterology.)

Introduction: Left ventricular thrombus (LVT) is a well-recognised complication of ischaemic and non-ischaemic heart disease. The incidence of this complication has drastically reduced due to reperfusion therapies. Current guidelines recommend using warfarin for at least three months. But, direct-acting oral anticoagulants (DOACs) are increasingly used as an off-label alternative to vitamin K antagonists (VKA) to treat LVT. In this article, we will review the use of DOACs for the treatment of LVT., Methods and Results: We conducted a literature search for published case series, meta-analyses, and review articles in four electronic databases: PubMed, EMBASE, OVID, and Google Scholar from inception until 1 August 2020. Fifteen articles including meta-analyses, review articles and case series were included. A total of 292 patients with LVT from 7 articles are analysed. The majority ( n  = 110) were treated with rivaroxaban followed by apixaban ( n  = 86), and warfarin (60). 26 patients from 292 were not included in the analysis. Of the 206 patients on DOACs, 180 (87.3%) had resolution of LVT. 22 had persistent LVT. Six patients had reported bleeding. Three patients had gastrointestinal (GI) bleeding. One patient had pulmonary haemorrhage while one other had epistaxis requiring blood transfusion. Five of six patients who had bleeding were on either single or dual antiplatelet therapy in addition to DOAC. One patient had reported a cardioembolic stroke while on a DOAC. Median follow-up duration varied from one month to two years., Conclusion: Based on our review, DOACs are likely to be at least as effective and safer as VKA for stroke prevention and thrombus resolution in patients with LVT.

Jamestown Canyon virus (JCV) is a mosquito-borne orthobunyavirus that causes an acute febrile illness, meningitis or meningoencephalitis. Human infections in the USA are rare. A 59-year-old man was admitted with fever, headache and hallucinations and required transfer to intensive care due to worsening agitation. Lumbar puncture was significant for neutrophilic pleocytosis, low glucose and high protein. Cerebral spinal fluid (CSF) bacterial cultures were negative, however, the CSF analysis via ELISA returned positive for JCV IgM. Plaque reduction neutralisation tests on a serum sample revealed IgM for JCV with titres of 1:160, which confirmed the diagnosis of JCV meningoencephalitis as the titres for other arboviruses were low. The patient improved significantly with supportive care. Our case highlights an atypical laboratory presentation of neutrophilic pleocytosis on CSF in a viral meningoencephalitis and draws attention to the potential cross-reactivity with other arboviruses., Competing Interests: Competing interests: None declared., (© BMJ Publishing Group Limited 2021. No commercial re-use. See rights and permissions. Published by BMJ.)

Cardiac neoplasms are uncommon tumors. For epidemiological purposes, they can be divided into benign and malignant subtypes, with the former occurring at a significantly higher rate than the latter. Due to their uncommon nature, there are few data-driven studies examining the characteristics and trends of benign cardiac neoplasms. Our retrospective HCUP-NIS data review purports to illuminate some of the trends surrounding benign cardiac neoplasms and their associated co-occurrences. The data consisted of 482,872,274 weighted discharges. There were 45,568 weighted discharges that included a benign cardiac neoplasm. Benign cardiac neoplasms were more often observed in women (64.33%), and the average age was 63.8 years. The most common cardiovascular co-occurrences in patients with benign cardiac neoplasm were atrial tachyarrhythmias (28.93%), heart failure (19.61%), and embolic events such as stroke, myocardial infarct, or pulmonary embolism (19.82%). Other co-occurrences included pulmonary hypertension (7.55%), ventricular arrhythmias (3.23%), and other EKG abnormalities (3.70%). Procedures were numerous in patients with benign cardiac neoplasms. 43% of patients with this diagnosis had some form of cardiac surgery during their hospitalization. Overall, this study found low incidence of benign cardiac neoplasms in the USA during this 13-year study period. However, in the presence of benign cardiac neoplasms, our study showed that cardiovascular co-occurrences are not uncommon and may help to illuminate this otherwise rare diagnosis., (© 2021 The Author(s). Published by S. Karger AG, Basel.)

We report a case of chronic intestinal pseudo-obstruction due to a generalized visceral autonomic neuropathy in an immune-competent patient infected with Strongyloides stercoralis . The patient had immigrated to the United States from Sierra Leone in childhood but had not returned for decades. His symptoms resolved with ivermectin treatment. Clinicians should have a high index of suspicion for strongyloidiasis in any patient with abdominal complaints and a history of travel to endemic areas, even if the travel history is remote.

The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.

Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are "novel" to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.

Self-incompatibility has been considered by geneticists a model system for reproductive biology and balancing selection, but our understanding of the genetic basis and evolution of this molecular lock-and-key system has remained limited by the extreme level of sequence divergence among haplotypes, resulting in a lack of appropriate genomic sequences. In this study, we report and analyze the full sequence of eleven distinct haplotypes of the self-incompatibility locus (S-locus) in two closely related Arabidopsis species, obtained from individual BAC libraries. We use this extensive dataset to highlight sharply contrasted patterns of molecular evolution of each of the two genes controlling self-incompatibility themselves, as well as of the genomic region surrounding them. We find strong collinearity of the flanking regions among haplotypes on each side of the S-locus together with high levels of sequence similarity. In contrast, the S-locus region itself shows spectacularly deep gene genealogies, high variability in size and gene organization, as well as complete absence of sequence similarity in intergenic sequences and striking accumulation of transposable elements. Of particular interest, we demonstrate that dominant and recessive S-haplotypes experience sharply contrasted patterns of molecular evolution. Indeed, dominant haplotypes exhibit larger size and a much higher density of transposable elements, being matched only by that in the centromere. Overall, these properties highlight that the S-locus presents many striking similarities with other regions involved in the determination of mating-types, such as sex chromosomes in animals or in plants, or the mating-type locus in fungi and green algae., Competing Interests: The authors have declared that no competing interests exist.