Brief Bioinform , IF:8.99 , 2021 Mar doi: 10.1093/bib/bbab029
Current status and future perspectives of computational studies on human-virus protein-protein interactions.
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.; State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
The protein-protein interactions (PPIs) between human and viruses mediate viral infection and host immunity processes. Therefore, the study of human-virus PPIs can help us understand the principles of human-virus relationships and can thus guide the development of highly effective drugs to break the transmission of viral infectious diseases. Recent years have witnessed the rapid accumulation of experimentally identified human-virus PPI data, which provides an unprecedented opportunity for bioinformatics studies revolving around human-virus PPIs. In this article, we provide a comprehensive overview of computational studies on human-virus PPIs, especially focusing on the method development for human-virus PPI predictions. We briefly introduce the experimental detection methods and existing database resources of human-virus PPIs, and then discuss the research progress in the development of computational prediction methods. In particular, we elaborate the machine learning-based prediction methods and highlight the need to embrace state-of-the-art deep-learning algorithms and new feature engineering techniques (e.g. the protein embedding technique derived from natural language processing). To further advance the understanding in this research topic, we also outline the practical applications of the human-virus interactome in fundamental biological discovery and new antiviral therapy development.
PMID: 33693490
Plant Biotechnol J , IF:8.154 , 2021 Mar doi: 10.1111/pbi.13583
KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species.
Rothamsted Research, Harpenden, AL5 2JQ, UK.; IBERS, Aberystwyth University, Aberystwyth, SY23 3DA, UK.
The generation of new ideas and scientific hypotheses is often the result of extensive literature and database searches, but, with the growing wealth of public and private knowledge, the process of searching diverse and interconnected data to generate new insights into genes, gene networks, traits and diseases is becoming both more complex and more time-consuming. To guide this technically challenging data integration task and to make gene discovery and hypotheses generation easier for researchers, we have developed a comprehensive software package called KnetMiner which is open-source and containerised for easy use. KnetMiner is an integrated, intelligent, interactive gene and gene network discovery platform that supports scientists discover and understand the biological stories of complex traits and diseases across species. It features fast algorithms for generating rich interactive gene networks and prioritizing candidate genes based on knowledge mining approaches. KnetMiner is used in many plant science institutions and has been adopted by several plant breeding organisations to accelerate gene discovery. The software is generic and customizable and can therefore be readily applied to new species and data types, for example it has been applied to pest insects and fungal pathogens; and most recently repurposed to support COVID-19 research. Here we give an overview of the main approaches to using KnetMiner and we report plant-centric case studies for identifying genes, gene networks and trait relationships in Triticum aestivum (bread wheat), as well as, an evidence-based approach to rank candidate genes under a large Arabidopsis thaliana QTL. KnetMiner is available at: https://knetminer.org.
PMID: 33750020
Plant J , IF:6.141 , 2021 Mar doi: 10.1111/tpj.15229
Complexity untwined: The structure and function of cucumber (Cucumis sativus L.) shoot phloem.
Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China.; Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
Cucurbit phloem is complex, with large sieve tubes on both sides of the xylem (bicollateral phloem), and extrafascicular elements that form an intricate web linking the rest of the vasculature. Little is known of the physical interconnections between these networks or their functional specialization, largely because the extrafascicular phloem strands branch and turn at irregular angles. Here, export in the phloem from specific regions of the lamina of cucumber (Cucumis sativus L.) was mapped using carboxyfluorescein and (14) C as mobile tracers. We also mapped vascular architecture by conventional microscopy and X-ray computed tomography using optimized whole-tissue staining procedures. Differential gene expression in the internal (IP) and external phloem (EP) was analyzed by laser-capture microdissection followed by RNA-seq. The vascular bundles of the lamina form a nexus at the petiole junction, emerging in a predictable pattern, each bundle conducting photoassimilate from a specific region of the blade. The vascular bundles of the stem interconnect at the node, facilitating lateral transport around the stem. Elements of the extrafascicular phloem traverse the stem and petiole obliquely, joining the IP and EP of adjacent bundles. Using pairwise comparisons and weighted gene coexpression network analysis (WGCNA), we found differences in gene expression patterns between the petiole and stem and between IP and EP, and we identified hub genes of tissue-specific modules. Genes related to transport were expressed primarily in the EP while those involved in cell differentiation and development as well as amino acid transport and metabolism were expressed mainly in the IP.
PMID: 33713355
J Exp Bot , IF:5.908 , 2021 Mar , V72 (7) : P2261-2265 doi: 10.1093/jxb/eraa600
Meeting the complexity of plant nutrient metabolism with multi-omics approaches.
Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany.
PMID: 33779750
J Exp Bot , IF:5.908 , 2021 Mar , V72 (6) : P2011-2013 doi: 10.1093/jxb/erab069
The iron will of the research community: advances in iron nutrition and interactions in lockdown times.
John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.; Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.; Universite Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
PMID: 33728463
J Exp Bot , IF:5.908 , 2021 Mar doi: 10.1093/jxb/erab120
Synonymous mutation of miR396a target sites in Growth Regulating Factor 15 (GRF15) enhances photosynthetic efficiency and heat tolerance in poplar.
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, P. R. China.; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.; State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.; Zhejiang Agriculture & Forestry University, Hangzhou, China.; Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, Canada.
Heat stress damages plant tissues and induces multiple adaptive responses. Complex and spatiotemporally specific interactions among transcription factors (TFs), microRNAs (miRNAs), and their target genes play crucial roles in regulating stress responses. To explore these interactions and identify the regulatory networks in perennial woody plants, we integrated time-course RNA-seq, small RNA-seq, degradome sequencing, weighted gene correlation network analysis, and multi-gene association approaches in poplar. The results allowed for constructing a three-layer, highly interwoven regulatory network involving 15 TFs, 45 miRNAs, and 77 photosynthetic genes. Candidate gene association studies in the population of Populus tomentosa identified 114 significant associations and 696 epistatic SNP-SNP pairs which were linked to 29 photosynthetic and growth traits (P < 0.0001, q < 0.05). Finally, we identified miR396a and its target, Growth-Regulating Factor 15 (GRF15) as an important regulatory module in the heat stress response. Transgenic oxPagGRF15 plants expressing a GRF15 mRNA that lacks miR396a target sites exhibited enhanced heat tolerance and photosynthetic efficiency compared to wild-type plants. Together, these observations demonstrate that GRF15 plays a crucial role in responding to heat stress and validate the power of this new, multifaceted approach for identifying regulatory nodes in plants.
PMID: 33711151
Mol Med , IF:4.096 , 2021 Mar , V27 (1) : P24 doi: 10.1186/s10020-021-00284-5
Modulating brain networks associated with cognitive deficits in Parkinson's disease.
Department of Human Anatomy and Cell Science, University of Manitoba, 130-745 Bannatyne Ave., Winnipeg, MB, R3E 0J9, Canada.; Kleysen Institute for Advanced Medicine, Health Science Centre, Winnipeg, MB, Canada.; Department of Human Anatomy and Cell Science, University of Manitoba, 130-745 Bannatyne Ave., Winnipeg, MB, R3E 0J9, Canada. ji.ko@umanitoba.ca.; Kleysen Institute for Advanced Medicine, Health Science Centre, Winnipeg, MB, Canada. ji.ko@umanitoba.ca.; Graduate Program in Biomedical Engineering, University of Manitoba, Winnipeg, MB, Canada. ji.ko@umanitoba.ca.
Parkinson's disease (PD) is a relatively well characterised neurological disorder that primarily affects motor and cognitive functions. This paper reviews on how transcranial direct current stimulation (tDCS) can be used to modulate brain networks associated with cognitive deficits in PD. We first provide an overview of brain network abnormalities in PD, by introducing the brain network modulation approaches such as pharmacological interventions and brain stimulation techniques. We then present the potential underlying mechanisms of tDCS technique, and specifically highlight how tDCS can be applied to modulate brain network abnormality associated with cognitive dysfunction among PD patients. More importantly, we address the limitations of existing studies and suggest possible future directions, with the aim of helping researchers to further develop the use of tDCS technique in clinical settings.
PMID: 33691622
Expert Rev Proteomics , IF:3.614 , 2021 Mar doi: 10.1080/14789450.2021.1910028
Proteomics and plant biology: contributions to date and a look towards the next decade.
Dpt. Biochemistry and Molecular Biology, Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, ETSIAM, University of Cordoba, UCO-CeiA3, Cordoba 14071 , Spain.
INTRODUCTION: This review presents the view of the author, that is opinionable and even speculative, on the field of proteomics, its application to plant biology knowledge, and translation to biotechnology. Written in a more academic than scientific style, it is based on past original and review articles by the author s group, and those published by leading scientists in the last two years. AREAS COVERED: Starting with a general definition and references to historical milestones, it covers sections devoted to the different platforms employed, the plant biology discourse in the protein language, challenges and future prospects, ending with the author opinion. EXPERT OPINION: In 25 years, five proteomics platform generations have appeared. We are now moving from proteomics to Systems Biology. While feasible with model organisms, proteomics of orphan species remains challenging. Proteomics, even in its simplest approach, sheds light on plant biological processes, central dogma, and molecular bases of phenotypes of interest, and it can be translated to areas such as food traceability and allergen detection. Proteomics should be validated and optimized to each experimental system, objectives, and hypothesis. It has limitations, artefacts, and biases. We should not blindly accept proteomics data and just create a list of proteins, networks, and avoid speculative biological interpretations. From the hundred to thousand proteins identified and quantified it is important to obtain a focus and validate some of them, otherwise it is merely. We are starting to have the protein pieces, so let, from now, build the proteomics and biological puzzle.
PMID: 33770454
Phytopathology , IF:3.234 , 2021 Mar doi: 10.1094/PHYTO-12-20-0536-A
First genomic resource of the Columbia lance nematode Hoplolaimus columbus.
Clemson University College of Agriculture Forestry and Life Sciences, 114625, Plant and Environmental Sciences, 105 Collings St., Clemson, South Carolina, United States, 29634; xm@g.clemson.edu.; Clemson University College of Agriculture Forestry and Life Sciences, 114625, Biological Sciences, Clemson, South Carolina, United States; baeza.antonio@gmail.com.; Clemson University College of Agriculture Forestry and Life Sciences, 114625, Biological Sciences, Clemson, South Carolina, United States; vpricha@clemson.edu.; Clemson University College of Agriculture Forestry and Life Sciences, 114625, Plant and Environmental Sciences, Clemson, South Carolina, United States; pagudel@clemson.edu.
The Columbia lance nematode Hoplolaimus columbus has been reported frequently from North America due to its negative impact on agricultural production. In this study, for the first time, we sequenced the whole genome of a female specimen by using whole-genome-amplification and Illumina MiSeq. Data were de novo assembled to form scaffolds of 205.75 Mbp consisting of 118,374 contigs. The largest scaffold was 636,881 bp. BUSCO completeness was 66.6% (eukaryotic dataset), and over 8,000 unique genes were predicted by GeneMark-ES. A total of 61,855 protein sequences were predicted by AUGUSTUS, and 10,085 of them were annotated by PANNZER2 with at least one function. These data will provide valuable resources for studies focusing on pathogenicity and phylogenomics of plant-parasitic nematodes.
PMID: 33754806
Plant Direct , IF:1.725 , 2021 Mar , V5 (3) : Pe00306 doi: 10.1002/pld3.306
A cellular expression map of epidermal and subepidermal cell layer-enriched transcription factor genes integrated with the regulatory network in Arabidopsis shoot apical meristem.
Department of Biological Sciences Indian Institute of Science Education and Research Mohali Punjab India.; Present address: Department of Biological Sciences University of Pittsburgh Pittsburgh PA USA.
Transcriptional control of gene expression is an exquisitely regulated process in both animals and plants. Transcription factors (TFs) and the regulatory networks that drive the expression of TF genes in epidermal and subepidermal cell layers in Arabidopsis are unexplored. Here, we identified 65 TF genes enriched in the epidermal and subepidermal cell layers of the shoot apical meristem (SAM). To determine the cell type specificity in different stages of Arabidopsis development, we made YFP based transcriptional fusion constructs by taking a 3-kb upstream noncoding region above the translation start site. Here, we report that for ~52% (22/42) TF genes, we detected transcription activity. TF genes derived from epidermis show uniform expression in early embryo development; however, in the late globular stage, their transcription activity is suppressed in the inner cell layers. Expression patterns linked to subepidermal cell layer identity were apparent in the postembryonic development. Potential upstream regulators that could modulate the activity of epidermal and subepidermal cell layer-enriched TF genes were identified using enhanced yeast-one-hybrid (eY1H) assay and validated. This study describes the activation of TF genes in epidermal and subepidermal cell layers in embryonic and postembryonic development of Arabidopsis shoot apex.
PMID: 33748654