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Since 2005, the Pathogen–Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.

A data set of promoter and 5′UTR sequences of homoeo‐alleles of 459 wheat genes that contribute to agriculturally important traits in 95 ancestral and commercial wheat cultivars is presented here. The high‐stringency myBaits technology used made individual capture of homoeo‐allele promoters possible, which is reported here for the first time. Promoters of most genes are remarkably conserved across the 83 hexaploid cultivars used with

Background Knowledge of the clinical and magnetic resonance imaging (MRI) features of intracranial Coccidioides infection in dogs is essential for prompt diagnosis to limit disease‐associated morbidity and death. Objectives To describe the MRI appearance of intracranial coccidioidomycosis in dogs, identify associated clinical and clinicopathologic findings, and report outcomes of medical treatment. Animals Forty‐five client‐owned dogs with presumed intracranial Coccidioides infection. Methods Retrospective case series. Medical records and images were reviewed. Clinical history, examination findings, serology, imaging characteristics, treatment, and outcome were recorded. Included cases had an abnormal brain MRI and positive Coccidioides serology by agar‐gel‐immunodiffusion (AGID). Results Median age was 7‐years. Generalized tonic‐clonic seizures were the most common presenting sign (25/45). Two lesion categories were identified: a granulomatous form with 1 or more distinct, intra‐axial, contrast‐enhancing foci (37/45), and a second variation with diffuse, bilateral, symmetrical lesions of the caudate nuclei and frontal lobes (8/45). Serum IgG titers ranged from 1 : 1 to ≥ 1 : 256; 2 dogs had positive IgM titers at 1 : 2. All dogs with follow‐up serology (34/45) had a reduction in titer. Mean duration of follow‐up was 22.4 ± 20.5 months (median 16 months). Six dogs were lost to follow‐up 1‐year. Of the remaining 34 dogs, 28 (82%) were alive ≥ 1‐year after diagnosis. Thirteen of these dogs had follow‐up times ≥ 2‐years. Conclusions and Clinical Importance The prognosis for intracranial Coccidioides infection is generally more favorable with medical treatment than in earlier reports.

High-risk human papillomaviruses (HPV) cause 5% of all human cancers and are primary etiologic agents of cervical, anal, and oropharyngeal cancer. HPV infection is necessary, but not sufficient per se to produce cancer: additional changes must occur that transform HPV-infected cells to malignancy. The HPV oncoproteins E6 and E7 immortalize human keratinocytes, cervical cells, and fibroblasts in culture. Each oncoprotein interacts with a variety of cellular binding partners; most important for transformation are E6 and E7’s interactions with p53 and RB (respectively) which lead to degradation of p53 and RB through the ubiquitin pathway. Inactivation of p53 and RB leads to inactivation of pivotal cell cycle checkpoints, thereby stimulating cell proliferation and allowing cell division to occur independently of the presence of DNA damage, replicative stress, and other such insults, leading to genome instability. Continuous expression of E6/E7 drives the proliferation and progression of most HPV-mediated cancers of the cervix and a substantial fraction of those of the oropharynx. However, at both cancer sites, “HPV-inactive” tumors that contain HPV DNA, but do not express E6/E7 arise. We propose that these HPV-inactive cancers begin as HPV-driven lesions, but lose E6/E7 expression at some point during progression. We have recently shown that p53 deletion in HPV-immortalized, premalignant cells allows for the emergence of cell populations that no longer express E6/E7. These findings corroborate the notion of a pivotal role of p53 in the context of HPV-mediated transformation, both at the initiation and progression stages of cancer development.

Take-all disease, caused by the fungal root pathogen Gaeumannomyces tritici, is considered to be the most important root disease of wheat worldwide. Here we review the advances in take-all research over the last 15 years, focusing on the identification of new sources of genetic resistance in wheat relatives and the role of the microbiome in disease development. We also highlight recent breakthroughs in the molecular interactions between G. tritici and wheat, including genome and transcriptome analyses. These new findings will aid the development of novel control strategies against take-all disease. In light of this growing understanding, the G. tritici–wheat interaction could provide a model study system for root-infecting fungal pathogens of cereals.

Pediatric therapy-related myeloid neoplasms (tMN) occur in children after exposure to cytotoxic therapy and have a dismal prognosis. The somatic and germline genomic alterations that drive these myeloid neoplasms in children and how they arise have yet to be comprehensively described. We use whole exome, whole genome, and/or RNA sequencing to characterize the genomic profile of 84 pediatric tMN cases (tMDS: n = 28, tAML: n = 56). Our data show that Ras/MAPK pathway mutations, alterations in RUNX1 or TP53, and KMT2A rearrangements are frequent somatic drivers, and we identify cases with aberrant MECOM expression secondary to enhancer hijacking. Unlike adults with tMN, we find no evidence of pre-existing minor tMN clones (including those with TP53 mutations), but rather the majority of cases are unrelated clones arising as a consequence of cytotoxic therapy. These studies also uncover rare cases of lineage switch disease rather than true secondary neoplasms., Paediatric therapy-related myeloid neoplasms (tMN) have a dismal prognosis and have not been comprehensively profiled. Here the authors characterise the molecular landscape of 84 paediatric tMN patients, and find that, unlike adult tMNs, these do not emerge from pre-existing clones and that MECOM dysregulation is frequent.

HPV-inactive head and neck and cervical cancers contain HPV DNA but do not express HPV E6/E7. HPV-positive primary head and neck tumors usually express E6/E7, however they may produce HPV-inactive metastases. These observations led to our hypothesis that HPV-inactive cancers begin as HPV-active lesions, losing dependence on E6/E7 expression during progression. Because HPV-inactive cervical cancers often have mutated p53, we investigated whether p53 loss may play a role in the genesis of HPV-inactive cancers. p53 knockout (p53-KO) by CRISPR-Cas9 resulted in a 5-fold reduction of E7 mRNA in differentiation-resistant HPV16 immortalized human keratinocytes (HKc/DR). E7 expression was restored by 5-Aza-2 deoxycytidine in p53 KO lines, suggesting a role of DNA methylation in this process. In-situ hybridization showed that p53 KO lines consist of mixed populations of E6/E7-positive and negative cells. Hence, loss of p53 predisposes HPV16 transformed cells to losing dependence on the continuous expression of HPV oncogenes for proliferation.

There is growing evidence supporting an inherited basis for susceptibility to acute lymphoblastic leukemia (ALL) in children. In particular, we and others reported recurrent germline ETV6 variants linked to ALL risk, which collectively represent a novel leukemia predisposition syndrome. To understand the influence of ETV6 variation on ALL pathogenesis, we comprehensively characterized a cohort of 32 childhood leukemia cases arising from this rare syndrome. Of 34 nonsynonymous germline ETV6 variants in ALL, we identified 22 variants with impaired transcription repressor activity, loss of DNA binding, and altered nuclear localization. Missense variants retained dimerization with wild-type ETV6 with potentially dominant-negative effects. Whole-transcriptome and whole-genome sequencing of this cohort of leukemia cases revealed a profound influence of germline ETV6 variants on leukemia transcriptional landscape, with distinct ALL subsets invoking unique patterns of somatic cooperating mutations. 70% of ALL cases with damaging germline ETV6 variants exhibited hyperdiploid karyotype with characteristic recurrent mutations in NRAS, KRAS, and PTPN11. In contrast, the remaining 30% cases had a diploid leukemia genome and an exceedingly high frequency of somatic copy-number loss of PAX5 and ETV6, with a gene expression pattern that strikingly mirrored that of ALL with somatic ETV6-RUNX1 fusion. Two ETV6 germline variants gave rise to both acute myeloid leukemia and ALL, with lineage-specific genetic lesions in the leukemia genomes. ETV6 variants compromise its tumor suppressor activity in vitro with specific molecular targets identified by assay for transposase-accessible chromatin sequencing profiling. ETV6-mediated ALL predisposition exemplifies the intricate interactions between inherited and acquired genomic variations in leukemia pathogenesis.

International audience; Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. Previously (Geiser et al. 2013; Phytopathology 103:400-408. 2013), the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani Species Complex (FSSC). Subsequently, this concept was challenged by one research group (Lombard et al. 2015 Studies in Mycology 80: 189-245) who proposed dividing Fusarium into seven genera, including the FSSC as the genus Neocosmospora, with subsequent justification based on claims that the Geiser et al. (2013) concept of Fusarium is polyphyletic (Sandoval-Denis et al. 2018; Persoonia 41:109-129). Here we test this claim, and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species recently described as Neocosmospora were recombined in Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural and practical taxonomic option available.

Background & Aims Congenital tufting enteropathy (CTE) is an intractable diarrheal disease of infancy caused by mutations of epithelial cell adhesion molecule (EpCAM). The cellular and molecular basis of CTE pathology has been elusive. We hypothesized that the loss of EpCAM in CTE results in altered lineage differentiation and defects in absorptive enterocytes thereby contributing to CTE pathogenesis. Methods Intestine and colon from mice expressing a CTE-associated mutant form of EpCAM (mutant mice) were evaluated for specific markers by quantitative real-time polymerase chain reaction, Western blotting, and immunostaining. Body weight, blood glucose, and intestinal enzyme activity were also investigated. Enteroids derived from mutant mice were used to assess whether the decreased census of major secretory cells could be rescued. Results Mutant mice exhibited alterations in brush-border ultrastructure, function, disaccharidase activity, and glucose absorption, potentially contributing to nutrient malabsorption and impaired weight gain. Altered cell differentiation in mutant mice led to decreased enteroendocrine cells and increased numbers of nonsecretory cells, though the hypertrophied absorptive enterocytes lacked key features, causing brush border malfunction. Further, treatment with the Notch signaling inhibitor, DAPT, increased the numbers of major secretory cell types in mutant enteroids (graphical abstract 1). Conclusions Alterations in intestinal epithelial cell differentiation in mutant mice favor an increase in absorptive cells at the expense of major secretory cells. Although the proportion of absorptive enterocytes is increased, they lack key functional properties. We conclude that these effects underlie pathogenic features of CTE such as malabsorption and diarrhea, and ultimately the failure to thrive seen in patients., Graphical abstract

In the present study, we applied a novel high-throughput in vitro gastrointestinal digestion model to phenotype bioaccessibility of phenolics in a diverse germplasm collection representing cultivated highbush blueberries. Results revealed significant (P

Purpose of review This review discusses the current developments on epigenetic inhibition as treatment for atherosclerosis. Recent findings The first phase III clinical trial targeting epigenetics in cardiovascular disease (CVD), BETonMACE, using the bromodomain inhibitor apabetalone (RVX-208) showed no significant effect on major adverse cardiovascular events (MACE) in patients with type II diabetes, low HDL-c and a recent acute coronary artery event compared with its placebo arm. Summary Preclinical and clinical studies suggest that targeting epigenetics in atherosclerosis is a promising novel therapeutic strategy against CVD. Interfering with histone acetylation by targeting histone deacetylates (HDACs) and bromodomain and extraterminal domain (BET) proteins demonstrated encouraging results in modulating disease progression in model systems. Although the first phase III clinical trial targeting BET in CVD showed no effect on MACE, we suggest that there is sufficient potential for future clinical usage based on the outcomes in specific subgroups and the fact that the study was slightly underpowered. Lastly, we propose that there is future window for targeting repressive histone modifications in atherosclerosis.

Beluga whales (Delphinapterus leucas) occur broadly throughout the polar and subpolar regions of the Northern Hemisphere, and as a whole, the species is of low conservation concern. However, some populations, including Alaska’s Cook Inlet beluga whales (CIBW), are in decline for reasons that remain poorly understood. Currently, information on population-specific reproductive parameters of CIBW is non-existent. To address this data gap, we examined long-term photo-identification data of CIBW for insight into the reproductive natural history of this endangered subarctic population. Data are from 438 photo-ID surveys conducted 2005–2017 and over 400 identified individuals, augmented with data from strandings, biopsies, and tagging. During the April–October ice-free field season, we observed neonates July–October but never April-June. We photo-documented three suspected births during July–September. Neonates were present in 30% of groups and encountered and comprised 2% of all belugas observed. Over the course of the 13-year study, the number of calves seen with an individual mother ranged from 1 to 5, with inter-birth intervals ranging from 2 to 13 years. This corresponds to rates of 0.08–0.38 calves per year per mother. Known-aged mothers ranged in age from 13 to 31 years. Skin color was not a reliable indicator of sexual maturity. Calves photographed alongside their mothers were estimated to be 1–8 years old, although most were 1–4 years old. Some mothers (6%) were accompanied by a neonate and an older calf. These summaries of observational data provide critical insight into CIBW reproductive natural history that will inform future population modeling and management decision-making.

Madagascar's ring‐tailed lemurs (Lemur catta) are experiencing rapid population declines due to ongoing habitat loss and fragmentation, as well as increasing exploitation for bushmeat and the illegal pet trade. Despite being the focus of extensive and ongoing behavioral studies, there is comparatively little known about the genetic population structuring of the species. Here, we present the most comprehensive population genetic analysis of ring‐tailed lemurs to date from across their likely remaining geographic range. We assessed levels of genetic diversity and population genetic structure using multilocus genotypes for 106 adult individuals from nine geographically representative localities. Population structure and FST analyses revealed moderate genetic differentiation with localities being geographically partitioned into northern, southern, western and also potentially central clusters. Overall genetic diversity, in terms of allelic richness and observed heterozygosity, was high in the species (AR = 4.74, HO = 0.811). In fact, it is the highest among all published lemur estimates to date. While these results are encouraging, ring‐tailed lemurs are currently affected by ongoing habitat fragmentation and occur at lower densities in poorer quality habitats. The effects of continued isolation and fragmentation, coupled with climate‐driven environmental instability, will therefore likely impede the long‐term viability of the species.

Aims Elevated lipoprotein(a) [Lp(a)] is strongly associated with an increased cardiovascular disease (CVD) risk. We previously reported that pro-inflammatory activation of circulating monocytes is a potential mechanism by which Lp(a) mediates CVD. Since potent Lp(a)-lowering therapies are emerging, it is of interest whether patients with elevated Lp(a) experience beneficial anti-inflammatory effects following large reductions in Lp(a). Methods and results Using transcriptome analysis, we show that circulating monocytes of healthy individuals with elevated Lp(a), as well as CVD patients with increased Lp(a) levels, both have a pro-inflammatory gene expression profile. The effect of Lp(a)-lowering on gene expression and function of monocytes was addressed in two local sub-studies, including 14 CVD patients with elevated Lp(a) who received apolipoprotein(a) [apo(a)] antisense (AKCEA-APO(a)-LRx) (NCT03070782), as well as 18 patients with elevated Lp(a) who received proprotein convertase subtilisin/kexin type 9 antibody (PCSK9ab) treatment (NCT02729025). AKCEA-APO(a)-LRx lowered Lp(a) by 47% and reduced the pro-inflammatory gene expression in monocytes of CVD patients with elevated Lp(a), which coincided with a functional reduction in transendothelial migration capacity of monocytes ex vivo (−17%, P Conclusion Potent Lp(a)-lowering following AKCEA-APO(a)-LRx, but not modest Lp(a)-lowering combined with LDL-C reduction following PCSK9ab treatment, reduced the pro-inflammatory state of circulating monocytes in patients with elevated Lp(a). These ex vivo data support a beneficial effect of large Lp(a) reductions in patients with elevated Lp(a).

The transport of electrolytes and fluid by the intestinal epithelium is critical in health to maintain appropriate levels of fluidity of the intestinal contents. The transport mechanisms that underlie this physiological process are also subject to derangement in various digestive disease states, such as diarrheal illnesses. This article summarizes the 2019 Hans Ussing Lecture of the Epithelial Transport Group of the American Physiological Society and discusses some pathways by which intestinal transport is dysregulated, particularly in the setting of infection with the diarrheal pathogen, Salmonella, and in patients treated with small-molecule inhibitors of the tyrosine kinase activity of the epidermal growth factor receptor (EGFr-TKI). The burdensome diarrhea in patients infected with Salmonella may be attributable to decreased expression of the chloride-bicarbonate exchanger downregulated in adenoma (DRA) that participates in electroneutral NaCl absorption. This outcome is possibly secondary to increased epithelial proliferation and/or decreased epithelial differentiation that occurs following infection. Conversely, the diarrheal side effects of cancer treatment with EGFr-TKI may be related to the known ability of EGFr-associated signaling to reduce calcium-dependent chloride secretion. Overall, the findings described may suggest targets for therapeutic intervention in a variety of diarrheal disease states.

Wilms’ tumor (WT), the most common childhood kidney cancer, develops in association with an underlying germline predisposition in up to 15% of cases. Germline alterations affecting the WT1 gene and epigenetic alterations affecting the 11p15 locus are associated with a selective increase in WT risk. Nevertheless, WT also occurs in the context of more pleiotropic cancer predispositions, such as DICER1, Li-Fraumeni and Bloom syndrome, as well as Fanconi anemia. Recent germline genomic investigations have increased our understanding of the host genetic factors that influence WT risk, with sequencing of rare familial cases and large WT cohorts revealing an expanding array of predisposition genes and associated genetic conditions. Here, we describe evidence implicating WT1, the 11p15 locus, and the recently identified genes CTR9, REST and TRIM28 in WT predisposition. We discuss the clinical features, mode of inheritance and biological aspects of tumorigenesis, when known. Despite these described associations, many cases of familial WT remain unexplained. Continued investigations are needed to fully elucidate the landscape of germline genetic alterations in children with WT. Establishing a genetic diagnosis is imperative for WT families so that individuals harboring a predisposing germline variant can undergo surveillance, which should enable the early detection of tumors and use of less intensive treatments, thereby leading to improved overall outcomes.

The United States Department of Agriculture (USDA)-Agricultural Research Service (ARS)-National Clonal Germplasm Repository (NCGR) in Corvallis Oregon preserves genetic resources of fruit crops. This genebank contains more than 1800 Vaccinium L. accessions from 34 countries. The genotypic identity of the blueberry cultivars in the NCGR collections is critical to genebank management and operations. Previously, identity confirmation was determined through the morphology of key taxonomic traits, but simple sequence repeat (SSR)-based molecular tools have been developed for more thorough “fingerprinting.” We had previously developed a 5-SSR fingerprinting set of tri-nucleotide-containing SSRs in blueberry. The objectives of this study were to use this 5-SSR blueberry test to compare fingerprints of all plants representing the most requested blueberry cultivars in the screenhouse and field collections of the NCGR; conduct parentage analysis to confirm identity; establish reference fingerprints for these cultivars; and expand the fingerprinting set with additional long core repeats, if needed. The SSR-set distinguished all but ‘Lateblue’ and ‘Berkeley’ and was supplemented with five additional SSRs with long core repeats to generate a 10-SSR fingerprinting set. Genotyping 367 samples with one or both of these SSR sets and parentage analysis where possible detected 54 true-to-type (TTT) cultivars, 13 sets of homonyms and ten groups of synonyms. Parentage analysis identified five of the TTT cultivars among the homonyms (‘Bluecrop’, FL 4B, ‘Nelson’ and ‘Clara’) and ‘Elizabeth’ among the synonym sets. A public database of these reference genetic profiles is available on GRIN-Global. We plan to continue adding to this database and eliminate redundant genotypes for more efficient management of blueberry diversity. Confirmed blueberry genotypes will benefit the germplasm community for use in continued breeding and genetic studies.

Fatty alcohols are important products in chemical industry to be used in the formulation of surfactants and lubricants. This work describes a two step approach for the production of myristyl alcohol under neat conditions by combining a lipase catalyzed esterification of myristic acid and myristyl alcohol with a ruthenium catalyzed hydrogenation of the intermediate myristyl myristate. The esterification was carried out in a bubble column reactor with the commercial immobilized lipase B fromCandida antarcticaas a biocatalyst, while the hydrogenation was conducted under pressurized conditions being catalyzed by the homogeneous chemocatalyst Ru-Macho-BH. By investigating the reaction steps separately, comparable reaction rates were found for the esterification of short chain and long chain alcohols. Additionally, the hydrogen pressure could be reduced to 35 bar compared to the current industrial Lurgi process. Characterization of cross interactions by the reactants myristic acid and sodium myristate in the hydrogenation demonstrates that the metal catalyst was completely deactivated, even at a low amount of 0.5 mol% of myristic acid. Complete conversion of myristic acid in the esterification with equal amounts of myristic acid and myristyl alcohol was obtained, overcoming any limitation in the hydrogenation. In comparison to the Lurgi process starting also from fatty acid and fatty alcohols, the chemoenzymatic two step reaction sequence could be realized at lower reaction temperatures of 60 and 100 degrees C as well as lower hydrogen pressures of 35 bar.

Relapse of acute lymphoblastic leukemia (ALL) remains a leading cause of childhood cancer-related death. Prior studies have shown clonal mutations at relapse often arise from relapse-fated subclones that exist at diagnosis. However, the genomic landscape, evolutionary trajectories, and mutational mechanisms driving relapse are incompletely understood. In an analysis of 92 cases of relapsed childhood ALL incorporating multimodal DNA and RNA sequencing, deep digital mutational tracking, and xenografting to formally define clonal structure, we identified 50 significant targets of mutation with distinct patterns of mutational acquisition or enrichment. CREBBP, NOTCH1, and RAS signaling mutations arose from diagnosis subclones, whereas variants in NCOR2, USH2A, and NT5C2 were exclusively observed at relapse. Evolutionary modeling and xenografting demonstrated that relapse-fated clones were minor (50%), major (27%), or multiclonal (18%) at diagnosis. Putative second leukemias, including those with lineage shift, were shown to most commonly represent relapse from an ancestral clone rather than a truly independent second primary leukemia. A subset of leukemias prone to repeated relapse exhibited hypermutation driven by at least three distinct mutational processes, resulting in heightened neoepitope burden and potential vulnerability to immunotherapy. Finally, relapse-driving sequence mutations were detected prior to relapse using droplet digital PCR at levels comparable with orthogonal approaches to monitor levels of measurable residual disease. These results provide a genomic framework to anticipate and circumvent relapse by earlier detection and targeting of relapse-fated clones. Significance: This study defines the landscape of mutations that preexist and arise after commencement of ALL therapy and shows that relapse may be propagated from ancestral, major, or minor clones at initial diagnosis. A subset of cases exhibits hypermutation that results in expression of neoepitopes that may be substrates for immunotherapeutic intervention. See related video: https://vimeo.com/442838617 See related commentary by Ogawa, p. 21. See related article by S. Dobson et al . This article is highlighted in the In This Issue feature, p. 5

OBJECTIVE: This study examined the association between preconception substance use and unintended pregnancy in a large, nationally representative sample of women. METHODS: In this cross-sectional study, we used data from the Pregnancy Risk Assessment Monitoring System (PRAMS) comprising, 74,543 women who had birth during 2016–17. Logistic regression was used to assess the independent association of unintended pregnancy overall and by subtypes to preconception substance use (smoking and other nicotine/tobacco use, alcohol consumption, and use of cannabis, illicit/recreational drugs) and specific medication including prescription opioids, antidepressants and over the counter pain relief. RESULTS: Overall, 41% of pregnancies were unintended. Nearly 57% of participants reported alcohol consumption during the preconception period, with 32% indicating binge drinking, 17% reported preconception smoking, and 10% cannabis use. Unintended pregnancy was significantly associated with substance use, including smoking (adjusted odds ratio [AOR]:1.5, 95% confidence interval [CI]: 1.4–1.6); as well as the use of other nicotine/tobacco (AOR:1.4, 95% CI: 1.3–1.5); cannabis (AOR: 1.9, 95% CI: 1.5–2.3); illicit/recreational drugs (AOR:1.7, 95% CI: 1.2–2.4), prescription opioids (AOR:1.4, 95% CI: 1.02–1.9), and prescription antidepressants (AOR 1.8, 95% CI: 1.1–3.0). The likelihood of unintended pregnancy was significantly elevated with heavy smoking, heavy alcohol consumption, and binge drinking. Analyses by unintended pregnancy subtype yielded similar results. CONCLUSIONS: Preconception substance use was significantly and positively associated with unintended pregnancy. Evidence-based interventions are needed addressing substance use behavior and effective contraceptive use to prevent unintended pregnancy and related adverse effects on maternal and child health.

The conservation status of small cetaceans has significantly worsened since the 1980s, when the baiji was the only species of small cetacean listed as Endangered by IUCN. Now the baiji is almost certainly extinct and 13 other species, subspecies, or populations (hereafter units-to-conserve or units) of small cetaceans are listed as Critically Endangered (CR) on the IUCN Red List. Bycatch is the main threat to 11 of the CR units. Entanglement in gillnets contributed to the extinction of the baiji and is responsible for the imminent extinction of the vaquita. Unfortunately, there is no simple technical solution to the problem of bycatch of small cetaceans. If the 8 CR units with 100 or fewer remaining individuals are to be saved, conservation zones must be established where gillnets are eliminated and bans on their use are strictly enforced. Recent experience with the vaquita in Mexico demonstrates that enforcement of such conservation zones can be very difficult. Ineffective enforcement is also a problem for at least 4 of the other CR units. Time is very short and, unless major efforts are made now to address the bycatch problem, the prospects for CR small cetaceans and other at-risk aquatic megafauna are grim. The ultimate long-term solution to the bycatch problem is the development of efficient, inexpensive, alternative fishing gear that can replace gillnets without jeopardizing the livelihoods of fishermen. Good fishery governance and the direct involvement of fishing communities are also essential to the successful conservation of most threatened populations of small cetaceans.

Hemophagocytic lymphohistiocytosis (HLH) is a hyperinflammatory disorder characterized by the inability to properly terminate an immune response. Familial HLH (FHLH) and related immune dysregulation syndromes are associated with mutations in the genes PRF1, UNC13D, STX11, STXBP2, LYST, AP3B1, and RAB27A, all of which are required for the assembly, exocytosis, and function of cytotoxic granules within CD8+ T cells and natural killer (NK) cells. Loss-of-function mutations in these genes render the cytotoxicity pathway ineffective, thereby failing to eradicate immune stimuli, such as infectious pathogens or malignant cells. The resulting persistent immune system stimulation drives hypercytokinemia, ultimately leading to severe tissue inflammation and end-organ damage. Traditionally, a diagnosis of FHLH requires the identification of biallelic loss-of-function mutations in one of these degranulation pathway genes. However, this narrow definition fails to encompass patients with other genetic mechanisms underlying degranulation pathway dysfunction. In particular, mounting clinical evidence supports a potential digenic mode of inheritance of FHLH in which single loss-of-function mutations in two different degranulation pathway genes cooperate to impair pathway activity. Here, we review the functions of the FHLH-associated genes within the degranulation pathway and summarize clinical evidence supporting a model in which cumulative defects along this mechanistic pathway may underlie HLH.

All cereal crop species are vulnerable to root, stem-base and floral diseases caused by various Fusarium species. Most problematic is Fusarium head blight because grains become contaminated with harmful mycotoxins. Currently Fusarium control using fungicides is only partially effective, whilst cultivars with acceptable resistance levels are scarce. This chapter reviews the recent advances in fundamental knowledge on the cell biology of interactions, the in planta production of trichothecene mycotoxins, Fusarium genomes/pan-genomes, newly discovered Fusarium virulence factors, small secreted effectors, plant defence components and resistance genes underlying major QTLs. These discoveries are discussed in the context of exploiting new intervention targets to achieve control through genetic modification, gene editing and HIGS. Finally, the chapter explores how to develop a more integrated approach that includes marker assisted selection in breeding programmes, removal of susceptibility loci and the inclusion of new approaches arising from plant defence, virulence and effector studies.

BackgroundA profound insight into the immune landscape of vulvar squamous cell carcinoma (VSCC) is lacking. Here, an in-depth interrogation of T cell infiltration, local immune contexture, signaling pathways and checkpoint molecule expression was performed in early-stage and late-stage VSCC.MethodsThe type, location, and infiltration pattern of T cells were studied in 109 patients with primary VSCC FIGO stage I–III. RNA expression of genes involved in immune oncology and oncogenic signaling pathways was analyzed in 40 VSCC, matched for prognostic clinicopathological variables, analyzed for HPV and p53 status, and selected based on T cell infiltration.ResultsHigh intraepithelial infiltration with CD4 or CD8 T cells was associated with longer overall and recurrence-free survival and formed an independent prognostic factor, outperforming molecular subtype and stage of the disease. Strong T cell infiltrated VSCC displayed a coordinated immune response reflected by a positive association between T cells and different lymphocyte and myeloid cell subsets. The expression of genes involved in the migration of T cells and myeloid cells, T cell activation and costimulation, interferon (IFN)-γ signaling, cytotoxicity and apoptosis was higher than in low infiltrated tumors. An active immune signaling profile was observed in all inflamed, part of the altered-excluded and not in altered-immunosuppressed or deserted VSCC. While several checkpoint molecules were overexpressed, only PD-L1 expression displayed discriminatory ability and clinical usefulness. High PD-L1 expression was detected in all inflamed and ~60% of the altered-excluded VSCC.ConclusionAn active immune signaling profile is present in 35% of primary FIGO I–III VSCCs, suggesting potential responsiveness to neoadjuvant PD-1/PD-L1 immunotherapy.

Genetic alterations in the RUNX1 gene are associated with benign and malignant blood disorders, particularly of megakaryocyte and myeloid lineages. The role of RUNX1 in acute lymphoblastic leukemia (ALL) is less clear, particularly in terms of how germline genetic variation influences the predisposition to this type of leukemia. Sequencing DNA of 4836 children with B cell ALL (B-ALL) and 1354 with T cell ALL (T-ALL), we identified 31 and 18 germline RUNX1 variants, respectively. RUNX1 variants in B-ALL consistently showed minimal damaging effects. In contrast, 6 T-ALL–related variants resulted in drastic loss of RUNX1 activity as a transcription activator in vitro. Ectopic expression of dominant-negative RUNX1 variants in human CD34(+) cells repressed differentiation into erythroid cells, megakaryocytes, and T cells, while promoting myeloid cell development. Chromatin immunoprecipitation sequencing of T-ALL models showed distinctive patterns of RUNX1 binding by variant proteins. Further whole-genome sequencing identified the JAK3 mutation as the most frequent somatic genomic abnormality in T-ALL with germline RUNX1 variants. Cointroduction of RUNX1 variant and JAK3 mutation in hematopoietic stem and progenitor cells in mice gave rise to T-ALL with the early T cell precursor phenotype. Taken together, these results indicate that RUNX1 is an important predisposition gene for T-ALL and point to biology of RUNX1-mediated leukemogenesis in the lymphoid lineages.

Genome-wide association studies revealed that loss-of-function mutations in protein tyrosine phosphatase non-receptor type 2 (PTPN2) increase the risk of developing chronic immune diseases, such as inflammatory bowel disease (IBD) and celiac disease. These conditions are associated with increased intestinal permeability as an early etiological event. The aim of this study was to examine the consequences of deficient activity of the PTPN2 gene product, T cell protein tyrosine phosphatase (TCPTP), on intestinal barrier function and tight junction organization in vivo and in vitro. Here, we demonstrate that TCPTP protected against intestinal barrier dysfunction induced by the inflammatory cytokine IFN-γ by 2 mechanisms: it maintained localization of zonula occludens 1 and occludin at apical tight junctions and restricted both expression and insertion of the cation pore-forming transmembrane protein, claudin-2, at tight junctions through upregulation of the inhibitory cysteine protease, matriptase. We also confirmed that the loss-of-function PTPN2 rs1893217 SNP was associated with increased intestinal claudin-2 expression in patients with IBD. Moreover, elevated claudin-2 levels and paracellular electrolyte flux in TCPTP-deficient intestinal epithelial cells were normalized by recombinant matriptase. Our findings uncover distinct and critical roles for epithelial TCPTP in preserving intestinal barrier integrity, thereby proposing a mechanism by which PTPN2 mutations contribute to IBD.

Germline TP53 splicing variants are uncommon, and their clinical relevance is unknown. However, splice-altering variants at exon 4–intron 4 junctions are relatively enriched in pediatric adrenocortical tumors (ACT). Nevertheless, family histories of cancer compatible with classic Li-Fraumeni syndrome are rarely seen in these patients. We used conventional and in silico assays to determine protein stability, splicing, and transcriptional activity of 10 TP53 variants at exon 4–intron 4 junctions and analyzed their clinical correlates. We reviewed public databases that report the impact of TP53 variants in human cancer and examined individual reports, focusing on family history of cancer. TP53 exon 4–intron 4 junction germline variants were identified in 9 of 75 pediatric ACTs enrolled in the International Pediatric Adrenocortical Tumor Registry and Children's Oncology Group ARAR0332 study. An additional eight independent TP53 variants involving exon 4 splicing were identified in the Pediatric Cancer Genome Project (n = 5,213). These variants resulted in improper expression due to ineffective splicing, protein instability, altered subcellular localization, and loss of function. Clinical case review of carriers of TP53 exon 4–intron 4 junction variants revealed a high incidence of pediatric ACTs and atypical tumor types not consistent with classic Li-Fraumeni syndrome. Germline variants involving TP53 exon 4–intron 4 junctions are frequent in ACT and rare in other pediatric tumors. The collective impact of these germline TP53 variants on the fidelity of splicing, protein structure, and function must be considered in evaluating cancer susceptibility. Implications: Taken together, the data indicate that splice variants at TP53 codon 125 and surrounding bases differentially impacted p53 gene expression and function.

Chimeric antigen receptor T-cell (CAR T-cell) therapy is associated with significant toxicities secondary to immune activation, including a rare but increasingly recognised severe toxicity resembling haemophagocytic lymphohistiocytosis (carHLH). We report the development of carHLH in 14·8% of paediatric patients and young adults treated with CD19-specific CAR T-cell therapy with carHLH, occurring most commonly in those with high disease burden. The diagnosis and treatment of carHLH required a high index of suspicion and included multidrug immunomodulation with variable response to therapies. Compared to patients without carHLH, patients with carHLH had both reduced response to CAR T-cell therapy (P-value = 0·018) and overall survival (P-value = < 0·0001).

BackgroundFoeniculum vulgare,F. vulgare, commonly known as fennel, is believed to be one of the world’s oldest medicinal herbs and has been exploited by people for centuries as a nutritional aid for digestive disorders. In many southeast Asian countries it is ingested as an after-meal snack, mukhvas, due to its breath-freshening and digestive aid properties.F. vulgareis used in some countries, such as Iran, as a complementary and alternative treatment for inflammatory bowel disease (IBD).MethodsThis study investigated the effects ofF. vulgareon the barrier function of the intestinal epithelium Signal Transducer and Activator of Transcription (STAT) pathway, which is active in inflammatory bowel disease.To study the protective effects ofF. vulgareextractin vitro, monolayers derived from the T84 colonic cell line were challenged with interferon-gamma (IFN-γ) and monitored with and withoutF. vulgareextract. To complement ourin vitrostudies, the dextran sodium sulfate induced murine colitis model was employed to ascertain whether the protective effect ofF. vulgareextract can be recapitulatedin vivo.ResultsF. vulgareextract was shown to exert a protective effect on TEER in both T84 and murine models and showed increases in tight junction-associated mRNA in T84 cell monolayers. Both models demonstrated significant decreases in phosphorylated STAT1 (pSTAT1), indicating reduced activation of the STAT pathway. Additionally, mice treated withF. vulgareshowed significantly lower ulcer indices than control mice.ConclusionsWe conclude barrier function of the gastrointestinal tract is improved byF. vulgare, suggesting the potential utility of this agent as an alternative or adjunctive therapy in IBD.

Wheat is an economically, socially, and nutritionally important crop, however, aphid infestation can often reduce wheat yield through feeding and virus transmission. Through field phenotyping, we investigated aphid resistance in ancestral wheat Triticum monococcum (L.). Aphid (Rhopalosiphum padi (L.), Sitobion avenae (F.) and Metopolophium dirhodum (Wlk.)) populations and natural enemy presence (parasitised mummified aphids, ladybird adults and larvae and lacewing eggs and larvae) on two naturally susceptible wheat varieties, Triticum aestivum (L.) var. Solstice and T. monococcum MDR037, and three potentially resistant genotypes T. monococcum MDR657, MDR045 and MDR049 were monitored across three years of field trials. Triticum monococcum MDR045 and MDR049 had smaller aphid populations, whereas MDR657 showed no resistance. Overall, natural enemy presence was positively correlated with aphid populations; however, MDR049 had similar natural enemy presence to MDR037 which is susceptible to aphid infestation. It is hypothesised that alongside reducing aphid population growth, MDR049 also confers indirect resistance by attracting natural enemies. The observed resistance to aphids in MDR045 and MDR049 has strong potential for introgression into commercial wheat varieties, which could have an important role in Integrated Pest Management strategies to reduce aphid populations and virus transmission.

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.

Commercial strawberry cultivars are sensitive to salinity. These plants are octoploid (2n = 8x = 56) making analysis of complex traits such as salt tolerance difficult. Hence, the objective of this study was to evaluate eight woodland diploid strawberry genotypes for their physiological and genetic responses under high salinity conditions. Shoot salt tolerance (ST) index of eight genotypes irrigated with water of electrical conductivity (ECiw) of 8 dS m−1 ranged from 0.41 to 0.86. Average Cl concentration in leaves was more than 11-fold higher than Na concentration, indicating that Cl− toxicity is more critical than Na+ for diploid strawberries. Improved water use efficiency (WUE) due to reduced stomatal conductance (gs), intercellular CO2 concentration (Ci), and transpiration rate (Tr) was associated with improved ST index. Expression analyses of eleven genes involved in Na+ and Cl− transport revealed differences in component traits responsible for salt tolerance. Increased expressions of SOS2, NHX1 and NHX2 in salt-tolerant genotypes suggest that Na+ sequestration in vacuoles may play an important role in salt tolerance in strawberry. Additionally, a chloride channel gene (CLC_C) was shown to be critical for salt tolerance. Understanding the genetic mechanisms regulating salt tolerance will be critical in developing strawberry germplasm more tolerant to salinity.

Spitzoid melanoma is a specific morphologic variant of melanoma that most commonly affects children and adolescents, and ranges on the spectrum of malignancy from low grade to overtly malignant. These tumors are generally driven by fusions of ALK, RET, NTRK1/3, MET, ROS1 and BRAF1,2. However, in approximately 50% of cases no genetic driver has been established2. Clinical whole-genome and transcriptome sequencing (RNA-Seq) of a spitzoid tumor from an adolescent revealed a novel gene fusion of MAP3K8, encoding a serine-threonine kinase that activates MEK3,4. The patient, who had exhausted all other therapeutic options, was treated with a MEK inhibitor and underwent a transient clinical response. We subsequently analyzed spitzoid tumors from 49 patients by RNA-Seq and found in-frame fusions or C-terminal truncations of MAP3K8 in 33% of cases. The fusion transcripts and truncated genes all contained MAP3K8 exons 1–8 but lacked the autoinhibitory final exon. Data mining of RNA-Seq from the Cancer Genome Atlas (TCGA) uncovered analogous MAP3K8 rearrangements in 1.5% of adult melanomas. Thus, MAP3K8 rearrangements—uncovered by comprehensive clinical sequencing of a single case—are the most common genetic event in spitzoid melanoma, are present in adult melanomas and could be amenable to MEK inhibition. Rearrangements in MAP3K8 respond to MEK inhibition and represent the most common genetic driver in pediatric spitzoid melanoma, and in some adult melanomas lacking other MAPK alterations and for which clinical testing is warranted.

The Mentha germplasm collection housed at the USDA National Clonal Germplasm Repository is a valuable source of diversity for genetic studies and mint breeding. We surveyed phenotypes and genotypes of accessions belonging to two species ancestral to commercial peppermint: M. aquatica and M. suaveolens. Morphology, ploidy, essential oil composition, and relative Verticillium wilt resistance were assessed. Genotyping with simple sequence repeat (SSR) markers was performed in order to establish a set of informative markers for distinguishing accessions from each other. M. suaveolens accessions were triploid or tetraploid, while M. aquatica accessions were octoploid or nonaploid. Holoploid genome sizes differed significantly among accessions within both species. Half of the M. aquatica accessions had (+)-menthofuran as the primary oil constituent, while other accessions showed atypical oil profiles. Most M. suaveolens accessions had high levels of either piperitenone oxide, (−)-carvone, or trans-piperitenone oxide. M. aquatica accessions showed a range of Verticillium wilt resistance to susceptibility, while most M. suaveolens accessions were highly wilt-resistant. Results from genotyping the accessions with nine SSR markers distinguished three groups: one mainly M. suaveolens, one mostly M. aquatica, and one with a mixture of the species. This study enables updates of accession descriptions in the Germplasm Resources Information Network database, and increases the utility of the Mentha collection to the research community.

The α3 Na+,K+-ATPase (α3NKA) is one of four known α isoforms of the mammalian transporter. A deficiency in α3NKA is linked to severe movement control disorders. Understanding the pathogenesis of these disorders is limited by an incomplete knowledge of α3NKA expression in the brain as well as the challenges associated with identifying living cells that express the isoform for subsequent electrophysiological studies. To address this problem, transgenic mice were generated on the C57BL/6 genetic background, which utilize the mouse α3 subunit gene (Atp1a3) promoter to drive the expression of ZsGreen1 fluorescent protein. Consistent with published results on α3NKA distribution, a ZsGreen1 signal was detected in the brain, but not in the liver, with Atp1a3-ZsGreen1 transgenic mice. The intensity of ZsGreen1 fluorescence in neuronal cell bodies varied considerably in the brain, being highest in the brainstem, deep cerebellar and select thalamic nuclei, and relatively weak in cortical regions. Fluorescence was not detected in astrocytes or white matter areas. ZsGreen1-positive neurons were readily observed in fresh (unfixed) brain sections, which were amenable to patch-clamp recordings. Thus, the α3NKA-ZsGreen1 mouse model provides a powerful tool for studying the distribution and functional properties of α3NKA-expressing neurons in the brain.

Background Hepcidin concentrations measured by various methods differ considerably, complicating interpretation. Here, a previously identified plasma-based candidate secondary reference material (csRM) was modified into a serum-based two-leveled sRM. We validated its functionality to increase the equivalence between methods for international standardization. Methods We applied technical procedures developed by the International Consortium for Harmonization of Clinical Laboratory Results. The sRM, consisting of lyophilized serum with cryolyoprotectant, appeared commutable among nine different measurement procedures using 16 native human serum samples in a first round robin (RR1). Harmonization potential of the sRM was simulated in RR1 and evaluated in practice in RR2 among 11 measurement procedures using three native human plasma samples. Comprehensive purity analysis of a candidate primary RM (cpRM) was performed by state of the art procedures. The sRM was value assigned with an isotope dilution mass spectrometry-based candidate reference method calibrated using the certified pRM. Results The inter-assay CV without harmonization was 42.1% and 52.8% in RR1 and RR2, respectively. In RR1, simulation of harmonization with sRM resulted in an inter-assay CV of 11.0%, whereas in RR2 calibration with the material resulted in an inter-assay CV of 19.1%. Both the sRM and pRM passed international homogeneity criteria and showed long-term stability. We assigned values to the low (0.95±0.11 nmol/L) and middle concentration (3.75±0.17 nmol/L) calibrators of the sRM. Conclusions Standardization of hepcidin is possible with our sRM, which value is assigned by a pRM. We propose the implementation of this material as an international calibrator for hepcidin.

Foliar disease of onion in Michigan, caused by Pantoea agglomerans, Pantoea ananatis, or Enterobacter cowanii, has recently become a concern to producers. The objective of this study was to determine the effect of temperature, relative humidity (RH), and plant age in growth chamber and greenhouse experiments on onion plants inoculated with each pathogen. A significant level of disease resulted from each pathogen at 25 to 30°C, with strong positive associations detected using regression analysis between the area under the disease progress curve (AUDPC) and temperature. RH also significantly influenced symptom development. Foliar disease symptoms developed sooner and were more severe when RH was high (80 to 100%) but was limited at RH < 60%. Significant positive associations between RH and AUDPC, as described by linear regression, were also detected. When 6- to 14-week-old plants were inoculated with each bacterial pathogen, susceptibility increased significantly with age. These results provide insight into the epidemiology of P. agglomerans, P. ananatis, and E. cowanii bacterial pathogens of onions in Michigan and can assist in the development and timing of management strategies.

Bacterial stalk and leaf necrosis of onion, Allium cepa L., is a concern of Michigan producers. Plants with symptoms of bacterial stalk and leaf necrosis were collected in 2013 and 2014 from 17 fields in six Michigan counties. Bacterial isolates were identified using Biolog and confirmed by sequencing the 16s rDNA gene. From a total of 414 isolates, 10 bacterial species were identified. Pantoea agglomerans (42.5%), Pantoea ananatis (17.4%), and Enterobacter cowanii (7.5%) were most prevalent and were tested for pathogenicity on onion foliage and bulbs. More P. ananatis isolates (92%) were pathogenic on seedlings than P. agglomerans or E. cowanii isolates (approximately 50%). When 197 bacterial isolates were tested for sensitivity to copper hydroxide (200 µg/ml), 41% of P. agglomerans isolates were found to be tolerant to copper hydroxide, whereas 19 and 22% of P. ananatis and E. cowanii isolates were tolerant, respectively. Identifying the bacterial species associated with foliar disease symptoms on onions in Michigan, their pathogenicity and tolerance to copper is an important step in developing improved disease management strategies.