Growth, yield and fruit quality of Mexican tomato landraces in response to salt stress

The Mexican tomato landraces ‘Campeche’, ‘Oaxaca’, ‘Puebla’, and ‘Veracruz’, and the commercial hybrid ‘Vengador’ were evaluated in response to four levels of NaCl (0, 30, 60 and 90 mM) applied through the nutrient solution in a hydroponic system under greenhouse conditions. Yield and dry biomass weight of roots, stems and leaves were reduced by increasing salinity stress, while fruit quality characteristics were improved, with the magnitude of the changes being genotype-dependent. The landrace ‘Veracruz’ produced the lowest yield, 1.06 t ha-1 under control conditions and 0.59 t ha-1 when treated with 90 mM NaCl, amounting to a 44% reduction that was, however, the lowest yield decrease among all genotypes tested. Paradoxically, ‘Veracruz’ was the only landrace displaying a reduction in the root/shoot ratio when exposed to high salinity, indicating more sensitivity to salinity as compared to the other landraces and the hybrid tested. ‘Campeche’ performed the poorest in response to salinity with the most pronounced yield reductions, recording 71.1%, 80.1% and 89.6% yield decreases when comparing plants exposed to 30, 60 and 90 mM to the control, respectively. Although at each salinity level the ‘Veracruz’ fruits showed the highest °Brix value as compared to the other landraces and the hybrid, ‘Oaxaca’ and ‘Puebla’ fruits had a greater increase in °Brix between the control and 90 mM NaCl (109.2% and 110.4%, respectively). With 90 mM NaCl, ‘Oaxaca’ fruits also registered the highest decrease in pH (6.1%) and the highest increase in total soluble sugars (106.7%) with respect to the control

Ordered three-fold symmetric graphene oxide/buckled graphene/graphene heterostructures on MgO(111) by carbon molecular beam epitaxy

Theory and experiment demonstrate the direct growth of a graphene oxide/buckled graphene/graphene heterostructure on an incommensurate MgO(111) substrate. X-ray photoelectron spectroscopy, electron energy loss, Auger electron spectroscopy, low energy electron diffraction, Raman spectroscopy and first-principles density functional theory (DFT) calculations all demonstrate that carbon molecular beam epitaxy on either a hydroxylated MgO(111) single crystal or a heavily twinned thin film surface at 850 K yields an initial C layer of highly ordered graphene oxide with C_(3v) symmetry. A 5 × 5 unit cell of carbon, with one missing atom, forms on a 4 × 4 unit cell of MgO, with the three C atoms surrounding the C vacancy surface forming covalent C–O bonds to substrate oxide sites. This leads to a bowed graphene-oxide with slightly modified D and G Raman lines and a calculated band gap of 0.36 eV. Continued C growth results in the second layer of graphene that is stacked AB with respect to the first layer and buckled conformably with the first layer while maintaining C_(3v) symmetry, lattice spacing and azimuthal orientation with the first layer. Carbon growth beyond the second layer yields graphene in azimuthal registry with the first two C layers, but with graphene-characteristic lattice spacing and π → π* loss feature. This 3rd layer is also p-type, as indicated by the 5.6 eV energy loss feature. The significant sp^3 character and C_(3v) symmetry of such heterostructures suggest that spin–orbit coupling is enabled, with implications for spintronics and other device applications

GA4GH Phenopackets: A Practical Introduction.

The Global Alliance for Genomics and Health (GA4GH) is developing a suite of coordinated standards for genomics for healthcare. The Phenopacket is a new GA4GH standard for sharing disease and phenotype information that characterizes an individual person, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. A detailed example is presented that illustrates how to use the schema to represent the clinical course of a patient with retinoblastoma, including demographic information, the clinical diagnosis, phenotypic features and clinical measurements, an examination of the extirpated tumor, therapies, and the results of genomic analysis. The Phenopacket Schema, together with other GA4GH data and technical standards, will enable data exchange and provide a foundation for the computational analysis of disease and phenotype information to improve our ability to diagnose and conduct research on all types of disorders, including cancer and rare diseases

GA4GH Phenopackets: A Practical Introduction

The Global Alliance for Genomics and Health (GA4GH) is developing a suite of coordinated standards for genomics for healthcare. The Phenopacket is a new GA4GH standard for sharing disease and phenotype information that characterizes an individual person, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. A detailed example is presented that illustrates how to use the schema to represent the clinical course of a patient with retinoblastoma, including demographic information, the clinical diagnosis, phenotypic features and clinical measurements, an examination of the extirpated tumor, therapies, and the results of genomic analysis. The Phenopacket Schema, together with other GA4GH data and technical standards, will enable data exchange and provide a foundation for the computational analysis of disease and phenotype information to improve our ability to diagnose and conduct research on all types of disorders, including cancer and rare diseases

The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease.

BACKGROUND: Navigating the clinical literature to determine the optimal clinical management for rare diseases presents significant challenges. We introduce the Medical Action Ontology (MAxO), an ontology specifically designed to organize medical procedures, therapies, and interventions. METHODS: MAxO incorporates logical structures that link MAxO terms to numerous other ontologies within the OBO Foundry. Term development involves a blend of manual and semi-automated processes. Additionally, we have generated annotations detailing diagnostic modalities for specific phenotypic abnormalities defined by the Human Phenotype Ontology (HPO). We introduce a web application, POET, that facilitates MAxO annotations for specific medical actions for diseases using the Mondo Disease Ontology. FINDINGS: MAxO encompasses 1,757 terms spanning a wide range of biomedical domains, from human anatomy and investigations to the chemical and protein entities involved in biological processes. These terms annotate phenotypic features associated with specific disease (using HPO and Mondo). Presently, there are over 16,000 MAxO diagnostic annotations that target HPO terms. Through POET, we have created 413 MAxO annotations specifying treatments for 189 rare diseases. CONCLUSIONS: MAxO offers a computational representation of treatments and other actions taken for the clinical management of patients. Its development is closely coupled to Mondo and HPO, broadening the scope of our computational modeling of diseases and phenotypic features. We invite the community to contribute disease annotations using POET (https://poet.jax.org/). MAxO is available under the open-source CC-BY 4.0 license (https://github.com/monarch-initiative/MAxO). FUNDING: NHGRI 1U24HG011449-01A1 and NHGRI 5RM1HG010860-04

Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology.

Technological advances in both genome sequencing and prenatal imaging are increasing our ability to accurately recognize and diagnose Mendelian conditions prenatally. Phenotype-driven early genetic diagnosis of fetal genetic disease can help to strategize treatment options and clinical preventive measures during the perinatal period, to plan in utero therapies, and to inform parental decision-making. Fetal phenotypes of genetic diseases are often unique and at present are not well understood; more comprehensive knowledge about prenatal phenotypes and computational resources have an enormous potential to improve diagnostics and translational research. The Human Phenotype Ontology (HPO) has been widely used to support diagnostics and translational research in human genetics. To better support prenatal usage, the HPO consortium conducted a series of workshops with a group of domain experts in a variety of medical specialties, diagnostic techniques, as well as diseases and phenotypes related to prenatal medicine, including perinatal pathology, musculoskeletal anomalies, neurology, medical genetics, hydrops fetalis, craniofacial malformations, cardiology, neonatal-perinatal medicine, fetal medicine, placental pathology, prenatal imaging, and bioinformatics. We expanded the representation of prenatal phenotypes in HPO by adding 95 new phenotype terms under the Abnormality of prenatal development or birth (HP:0001197) grouping term, and revised definitions, synonyms, and disease annotations for most of the 152 terms that existed before the beginning of this effort. The expansion of prenatal phenotypes in HPO will support phenotype-driven prenatal exome and genome sequencing for precision genetic diagnostics of rare diseases to support prenatal care

The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs

Comparative analysis of the transcriptome across distant species

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters

Central venous oxygen saturation monitoring

It has been established that mixed venous oxygen saturation (SvO2) reflects the balance between systemic oxygen deliver y and consumption. Literature indicates that it is a valuable clinical indicator and has good prognostic value early in patient course. This article aims to establish the usefulness of SvO2 as a clinical indicator. A secondary aim was to determine whether central venous oxygen saturation (ScvO2) and SvO2 are interchangeable. Of particular relevance to cardiac nurses is the link between decreased SvO2 and cardiac failure in patients with myocardial infarction, and with decline in myocardial function, clinical shock and arrhythmias. While absolute values ScvO2 and SvO2 are not interchangeable, ScvO2 and SvO2are equivalent in terms of clinical course. Additionally, ScvO2 monitoring is a safer and less costly alternative to SvO2 monitoring. It can be concluded that continuous ScvO2 monitoring should potentially be undertaken in patients at risk of haemodynamic instability