13 research outputs found
Improved annotation of the insect vector of citrus greening disease: Biocuration by a diverse genomics community
The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the D. citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in D. citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models.Peer reviewedBiochemistry and Molecular BiologyEntomology and Plant Patholog
Models of classroom assessment for course-based research experiences
Course-based research pedagogy involves positioning students as contributors to authentic research projects as part of an engaging educational experience that promotes their learning and persistence in science. To develop a model for assessing and grading students engaged in this type of learning experience, the assessment aims and practices of a community of experienced course-based research instructors were collected and analyzed. This approach defines four aims of course-based research assessment—(1) Assessing Laboratory Work and Scientific Thinking; (2) Evaluating Mastery of Concepts, Quantitative Thinking and Skills; (3) Appraising Forms of Scientific Communication; and (4) Metacognition of Learning—along with a set of practices for each aim. These aims and practices of assessment were then integrated with previously developed models of course-based research instruction to reveal an assessment program in which instructors provide extensive feedback to support productive student engagement in research while grading those aspects of research that are necessary for the student to succeed. Assessment conducted in this way delicately balances the need to facilitate students’ ongoing research with the requirement of a final grade without undercutting the important aims of a CRE education
Genome characterization of brugmansia latent virus, a novel tobamovirus
A novel tobamovirus, brugmansia latent virus (BrLV), was discovered during a study of brugmansia (Brugmansia spp.) in the living collections held at the Royal Botanic Gardens, Kew. Here, we report the complete genome sequence of BrLV, which is 6,397 nucleotides long and contains the four open reading frames (RNA-dependent RNA polymerase, methyltransferase/helicase, movement, and coat proteins) typical of tobamoviruses. The complete genome sequence of BrLV shares 69.7% nucleotide sequence identity with brugmansia mild mottle virus (BrMMV) and 66.7 to 68.7% identity with other tobamoviruses naturally infecting members of the Solanaceae plant family. Phylogenetic analysis of the complete genome nucleotide sequence and the deduced amino acid sequences of the four tobamovirus proteins place BrLV in a subcluster with BrMMV within the Solanaceae-infecting tobamovirus subgroup as a new species
Perceptions on artificial intelligence-based decision-making for coexisting multiple long-term health conditions: protocol for a qualitative study with patients and healthcare professionals
Introduction Coexisting multiple health conditions is common among older people, a population that is increasing globally. The potential for polypharmacy, adverse events, drug interactions and development of additional health conditions complicates prescribing decisions for these patients. Artificial intelligence (AI)-generated decision-making tools may help guide clinical decisions in the context of multiple health conditions, by determining which of the multiple medication options is best. This study aims to explore the perceptions of healthcare professionals (HCPs) and patients on the use of AI in the management of multiple health conditions.Methods and analysis A qualitative study will be conducted using semistructured interviews. Adults (≥18 years) with multiple health conditions living in the West Midlands of England and HCPs with experience in caring for patients with multiple health conditions will be eligible and purposively sampled. Patients will be identified from Clinical Practice Research Datalink (CPRD) Aurum; CPRD will contact general practitioners who will in turn, send a letter to patients inviting them to take part. Eligible HCPs will be recruited through British HCP bodies and known contacts. Up to 30 patients and 30 HCPs will be recruited, until data saturation is achieved. Interviews will be in-person or virtual, audio recorded and transcribed verbatim. The topic guide is designed to explore participants’ attitudes towards AI-informed clinical decision-making to augment clinician-directed decision-making, the perceived advantages and disadvantages of both methods and attitudes towards risk management. Case vignettes comprising a common decision pathway for patients with multiple health conditions will be presented during each interview to invite participants’ opinions on how their experiences compare. Data will be analysed thematically using the Framework Method.Ethics and dissemination This study has been approved by the National Health Service Research Ethics Committee (Reference: 22/SC/0210). Written informed consent or verbal consent will be obtained prior to each interview. The findings from this study will be disseminated through peer-reviewed publications, conferences and lay summaries
In silico characterization of chitin deacetylase genes in the Diaphorina citri genome
Chitin deacetylases (CDAs) are one of the least understood components of insect chitin metabolism. The partial deacetylation of chitin polymers appears to be important for the proper formation of higher order chitin structures, such as long fibers and bundles, which contribute to the integrity of the insect exoskeleton and other structures. Some CDAs may also be involved in bacterial defense. Here, we report the manual annotation of four CDA genes from the Asian citrus psyllid, Diaphorina citri, laying the groundwork for future study of these genes
Subglacial Lake Vostok (Antarctica) Accretion Ice Contains a Diverse Set of Sequences from Aquatic, Marine and Sediment-Inhabiting Bacteria and Eukarya
<div><p>Lake Vostok, the 7<sup>th</sup> largest (by volume) and 4<sup>th</sup> deepest lake on Earth, is covered by more than 3,700 m of ice, making it the largest subglacial lake known. The combination of cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier), limited nutrients and complete darkness presents extreme challenges to life. Here, we report metagenomic/metatranscriptomic sequence analyses from four accretion ice sections from the Vostok 5G ice core. Two sections accreted in the vicinity of an embayment on the southwestern end of the lake, and the other two represented part of the southern main basin. We obtained 3,507 unique gene sequences from concentrates of 500 ml of 0.22 µm-filtered accretion ice meltwater. Taxonomic classifications (to genus and/or species) were possible for 1,623 of the sequences. Species determinations in combination with mRNA gene sequence results allowed deduction of the metabolic pathways represented in the accretion ice and, by extension, in the lake. Approximately 94% of the sequences were from Bacteria and 6% were from Eukarya. Only two sequences were from Archaea. In general, the taxa were similar to organisms previously described from lakes, brackish water, marine environments, soil, glaciers, ice, lake sediments, deep-sea sediments, deep-sea thermal vents, animals and plants. Sequences from aerobic, anaerobic, psychrophilic, thermophilic, halophilic, alkaliphilic, acidophilic, desiccation-resistant, autotrophic and heterotrophic organisms were present, including a number from multicellular eukaryotes.</p></div
Annotation of chitin biosynthesis genes in Diaphorina citri, the Asian citrus psyllid
The polysaccharide chitin is critical for the formation of many insect structures, including the exoskeleton, and is required for normal development. Here we report the annotation of three genes from the chitin synthesis pathway in the Asian citrus psyllid, Diaphorina citri (Hemiptera: Liviidae), the vector of Huanglongbing (citrus greening disease). Most insects have two chitin synthase (CHS) genes but, like other hemipterans, D. citri has only one. In contrast, D. citri is unusual among insects in having two UDP-N-acetylglucosamine pyrophosphorylase (UAP) genes. One of the D. citri UAP genes is broadly expressed, while the other is expressed predominantly in males. Our work helps pave the way for potential utilization of these genes as pest control targets to reduce the spread of Huanglongbing
A Systematic Review and Meta-Analysis on the Association Between Driving Ability and Neuropsychological Test Performances after Moderate to Severe Traumatic Brain Injury
Summary of proportions of sequences in V5 (left) and V6 (right) categorized by habitat (upper row) and growth conditions (lower row) based on species with highest sequence identities.
<p>Each pie chart is comprised of sequences that were either ≥97% identity or ≥99% identity, and also could be classified by habitat (above) or growth conditions (below). Habitat abbreviations: An = animal associated (most are also found in soils and/or water); Aq = aquatic; I = ice, glaciers and/or polar; M = marine; Pl = plant associated (most are also found in soils and water); S = soils or sediments. Growth conditions abbreviations: Ac = acidophilic or acid tolerant; Al = alkaliphilic or alkali tolerant; D = desiccation resistant; H = halophilic or halotolerant; Ps = psychrophilic or psychrotolerant; T = thermophilic or thermotolerant. Number of sequences (N) used for each is indicated below each pie chart.</p
Summary of broad taxonomic proportions based on the metagenomic and metatranscriptomic data.
<p>The first column presents the proportion of unique sequences from all sequences in the entire data set, regardless of percent identity to sequences deposited in the NCBI nucleotide database. The upper row represents data from V5, and the lower row represents data from V6. The totals are represented in the bar graph on the left in each box, with numerical totals at the top. There were 3,507 unique sequences (3,369+138) in the entire data set, including 3,169 from Bacteria, 2 from Archaea and 198 from Eukarya in V5; and 114 Bacteria and 24 from Eukarya in V6. The middle column includes sequences that have identities between 97 and 100% with sequences in the NCBI database. There were 1,911 unique sequences, including 1,724 from Bacteria, 2 from Archaea and 105 from Eukarya in V5; and 61 from Bacteria and 19 from Eukarya in V6. The final column includes sequences that have identities between 99 and 100% with sequences in the NCBI database. There were 1,102 Bacteria, 2 Archaea and 64 Eukarya in V5; and 36 Bacteria and 11 Eukarya in V6. Scales (in number of sequences) are at the bottom right of each bar graph. Abbreviations: Ac = Actinobacteria; Ad = Acidobacteria; Am = Amoebozoa; An = Animalia; Ap = Archaeplastida; Greek alpha = Alphaproteobacteria; Ar = Archaea; Ba = Bacteroidetes; Greek beta = Betaproteobacteria; Ca = Chromalveolata; CDF = Chlorobi/Deferribacteres/Fibrobacteres; Ch = Chloroflexi; Cy = Cyanobacteria; Greek delta = Deltaproteobacteria; DT = Deinococcus/Thermus; Greek εpsilon = Epsilonproteobacteria; Eu = Eukarya; Ex = Excavata; Fi = Firmicutes; Fs = Fusobacteria; Fu = Fungi; Greek gamma = Gammaproteobacteria; Pl = Planctomyces; Pr = Proteobacteria; Rh = Rhizaria; Sp = Spirochaetes; Te = Tenericutes; u = uncultured/unidentified; Ve = Verrucomicrobia.</p