A bioinformatic approach to the identification of a conserved domain in a sugarcane legumain that directs GFP to the lytic vacuole

2007 ◽  
Vol 34 (7) ◽  
pp. 633 ◽  
Author(s):  
Mark A. Jackson ◽  
Anne L. Rae ◽  
Rosanne E. Casu ◽  
Christopher P. L. Grof ◽  
Graham D. Bonnett ◽  
...  
Keyword(s):  
Bioinformatic Analysis ◽  
Conserved Domain ◽  
Storage Parenchyma ◽  
High Conservation ◽  
Lytic Vacuole ◽  
The Stability ◽  
Diverse Plant Species ◽  
Bioinformatic Approach ◽  
Diverse Plant ◽  
Novel Products

Sugarcane is an ideal candidate as a biofactory for the production of alternate higher value products. One way of achieving this is to direct useful proteins into the vacuoles within the sugarcane storage parenchyma tissue. By bioinformatic analysis of gene sequences from putative sugarcane vacuolar proteins a motif has been identified that displays high conservation across plant legumain homologues that are known to function within vacuolar compartments. This five amino acid motif, represented by the sequence IRLPS in sugarcane is shown to direct an otherwise secreted GFP fusion protein into a large acidic and proteolytic vacuole in sugarcane callus cells as well as in diverse plant species. In mature sugarcane transgenic plants, the stability of GFP appeared to be dependent on cell type, suggesting that the vacuolar environment can be hostile to introduced proteins. This targeting motif will be a valuable tool for engineering plants such as sugarcane for production of novel products.

Aggregation prone regions in antibody sequences raised against Vibrio cholerae: A bioinformatic approach

2020 ◽  
Vol 15 ◽  
Author(s):  
Zakia Akter ◽  
Anamul Haque ◽  
Md. Sabir Hossain ◽  
Firoz Ahmed ◽  
Md Asiful Islam
Keyword(s):  
Vibrio Cholerae ◽  
Binding Sites ◽  
Bioinformatic Analysis ◽  
Antigen Binding ◽  
Short Term ◽  
Protein Database ◽  
The Stability ◽  
Bioinformatic Approach ◽  
Self Aggregation ◽  
Complementarity Determining Region

Background: Cholera, a diarrheal illness causes millions of deaths worldwide due to large outbreaks. Monoclonal antibody used as therapeutic purposes of cholera are prone to be unstable due to various factors including self-aggregation. Objectives: In this bioinformatic analysis, we identified the aggregation prone regions (APRs) of different immunogens of antibody sequences (i.e., CTB, ZnM-CTB, ZnP-CTB, TcpA-CT-CTB, ZnM-TcpA-CT-CTB, ZnP-TcpA-CT-CTB, ZnM-TcpA, ZnP-TcpA, TcpA-CT-TcpA, ZnM-TcpA-CT-TcpA, ZnP-TcpA-CT-TcpA, Ogawa, Inaba and ZnM-Inaba) raised against Vibrio cholerae. Methods: To determine APRs in antibody sequences that were generated after immunizing Vibrio cholerae immunogens on Mus musculus, a total of 94 sequences were downloaded as FASTA format from a protein database and the algorithms such as Tango, Waltz, PASTA 2.0, and AGGRESCAN were followed to analyze probable APRs in all of the sequences. Results: A remarkably high number of regions in the monoclonal antibodies were identified to be APRs which could explain a cause of instability/short term protection of anticholera vaccine. Conclusion: To increase the stability, it would be interesting to eliminate the APR residues from the therapeutic antibodies in a such way that the antigen binding sites or the complementarity determining region loops involved in antigen recognition are not disrupted.

scholarly journals Phytophthora Diversity in Pennsylvania Nurseries and Greenhouses Inferred from Clinical Samples Collected over Four Decades

2020 ◽  
Vol 8 (7) ◽  
pp. 1056
Author(s):  
Cody Molnar ◽  
Ekaterina Nikolaeva ◽  
Seonghwan Kim ◽  
Tracey Olson ◽  
Devin Bily ◽  
...  
Keyword(s):  
Plant Species ◽  
Morphological Characteristics ◽  
Phytophthora Species ◽  
Clinical Samples ◽  
Department Of Agriculture ◽  
Distinct Subgroup ◽  
Exotic Pathogens ◽  
Diverse Plant Species ◽  
Insight Into ◽  
Diverse Plant

The increasing movement of exotic pathogens calls for systematic surveillance so that newly introduced pathogens can be recognized and dealt with early. A resource crucial for recognizing such pathogens is knowledge about the spatial and temporal diversity of endemic pathogens. Here, we report an effort to build this resource for Pennsylvania (PA) by characterizing the identity and distribution of Phytophthora species isolated from diverse plant species in PA nurseries and greenhouses. We identified 1137 Phytophthora isolates cultured from clinical samples of >150 plant species submitted to the PA Department of Agriculture for diagnosis from 1975 to 2019 using sequences of one or more loci and morphological characteristics. The three most commonly received plants were Abies, Rhododendron, and Pseudotsuga. Thirty-six Phytophthora species identified represent all clades, except 3 and 10, and included a distinct subgroup of a known species and a prospective new species. Prominent pathogenic species such as P. cactorum, P. cinnamomi, P. nicotianae, P. drechsleri, P. pini, P. plurivora, and P. sp. kelmania have been found consistently since 1975. One isolate cultured from Juniperus horizontalis roots did not correspond to any known species, and several other isolates also show considerable genetic variation from any authentic species or isolate. Some species were isolated from never-before-documented plants, suggesting that their host range is larger than previously thought. This survey only provides a coarse picture of historical patterns of Phytophthora encounters in PA nurseries and greenhouses because the isolation of Phytophthora was not designed for a systematic survey. However, its extensive temporal and plant coverage offers a unique insight into the association of Phytophthora with diverse plants in nurseries and greenhouses.

scholarly journals First Report of Tomato chlorotic spot virus in Hoya wayetii and Schlumbergera truncata

2015 ◽  
Vol 16 (1) ◽  
pp. 29-30 ◽  
Author(s):  
Carlye A. Baker ◽  
Scott Adkins
Keyword(s):  
Plant Species ◽  
Vegetable Crops ◽  
Spot Virus ◽  
First Report ◽  
Chlorotic Spot ◽  
Production Space ◽  
Related Plant ◽  
Diverse Plant Species ◽  
Diverse Plant

To the best of our knowledge, this is the first report of TCSV infection of H. wayetii and S. truncata from any location, although other tospoviruses are known to infect these and related plant species. The identification of these two diverse plant species as the first reported natural ornamental hosts of TCSV has implications for TCSV epidemiology and management in ornamental and vegetable crops, which frequently share production space. Accepted by publication 15 January 2015. Published 25 February 2015.

Ecology of the rare but irruptive Pilliga mouse, Pseudomys pilligaensis. III. Dietary ecology

2010 ◽  
Vol 58 (2) ◽  
pp. 85 ◽  
Author(s):  
Hideyuki Tokushima ◽  
Peter J. Jarman
Keyword(s):  
Reproductive Rate ◽  
Wild Fire ◽  
Faecal Samples ◽  
Wide Range ◽  
Different Seasons ◽  
Dietary Ecology ◽  
Protein Rich ◽  
Diverse Plant Species ◽  
Diverse Plant ◽  
Seeds And Fruits

The diet of the Pilliga mouse, Pseudomys pilligaensis, was analysed from 430 faecal samples collected from ~340 individuals across different seasons over a period of five years that included a wild fire and subsequent irruption and sharp decline of the population. The primary food items in all seasons were seeds and fruits from diverse plant species, but the mice also consumed a wide range of other foods, including leaves, invertebrates, fungi and mosses. Invertebrates, the second most abundant type of food item, were eaten in all seasons but, with fungi, increased in winter and spring when consumption of seeds and fruits declined. Mice consumed significantly more fungi and mosses before the wild fire than after it. Diets differed between sites rather little in the proportions of food categories, but greatly in the relative proportions of particular seed types in the seed+fruit category. The population irruption could have been triggered by a high reproductive rate that coincided with higher consumption by females of protein-rich foods such as invertebrates and fungi. Population density collapsed at sites as soil stores of utilisable seeds became depleted, mice surviving where their diet could remain diverse.

scholarly journals Phylogenetic analysis reveals conservation and diversification of micro RNA166 genes among diverse plant species

Genomics ◽  
2014 ◽  
Vol 103 (1) ◽  
pp. 114-121 ◽  
Author(s):  
Suvakanta Barik ◽  
Shabari SarkarDas ◽  
Archita Singh ◽  
Vibhav Gautam ◽  
Pramod Kumar ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Plant Species ◽  
Diverse Plant Species ◽  
Diverse Plant

scholarly journals Green Roof Plant Suitability Analysis for Northern Climates

2013 ◽  
Vol 23 (5) ◽  
pp. 563-574 ◽  
Author(s):  
Katherine L. Vinson ◽  
Youbin Zheng
Keyword(s):  
Plant Species ◽  
Green Roof ◽  
Green Roofs ◽  
Plant Production ◽  
Suitability Analysis ◽  
Production Growth ◽  
Diverse Plant Species ◽  
Extensive Green Roofs ◽  
Different Levels ◽  
Diverse Plant

To select plant species and species combinations for northern climates, mats with different plant species and species combinations were constructed on a green roof plant production farm and later transported and installed on an urban rooftop. There were three treatments: two different planting combinations, which together consisted of 10 diverse plant species [both stonecrop (Sedum) species and nonstonecrop species], and a control, which consisted of 26 stonecrop species used for standard mat production. Growth measurements and observations were made at both sites and special attention was paid to the performance of species during the harvest, transportation, and installation stages, as well as during recovery postinstallation. All species but false rock cress (Aubrieta cultorum) were found to be suitable for extensive green roof applications in northern climates, although there were variations of suitability among the species. Good, mediocre, and poor interactions formed between numerous species, displaying different levels of compatibility. Finally, all species were considered appropriate for a mat production system; species that failed to germinate, species planted postinstallation, the frequently displaced rolling hens and chicks (Jovibarba sobolifera), and false rock cress were exceptions. Overall, many species in this study displayed successful, well-rounded growth. Based on results, species and species combinations were recommended for extensive green roofs in northern climates.

scholarly journals Nanotechnology Approaches for Chloroplast Biotechnology Advancements

2021 ◽  
Vol 12 ◽  
Author(s):  
Gregory M. Newkirk ◽  
Pedro de Allende ◽  
Robert E. Jinkerson ◽  
Juan Pablo Giraldo
Keyword(s):  
Synthetic Biology ◽  
Plant Species ◽  
Targeted Delivery ◽  
Current Knowledge ◽  
Ex Vivo ◽  
Future Research ◽  
Agricultural Field ◽  
Diverse Plant Species ◽  
Diverse Plant

Photosynthetic organisms are sources of sustainable foods, renewable biofuels, novel biopharmaceuticals, and next-generation biomaterials essential for modern society. Efforts to improve the yield, variety, and sustainability of products dependent on chloroplasts are limited by the need for biotechnological approaches for high-throughput chloroplast transformation, monitoring chloroplast function, and engineering photosynthesis across diverse plant species. The use of nanotechnology has emerged as a novel approach to overcome some of these limitations. Nanotechnology is enabling advances in the targeted delivery of chemicals and genetic elements to chloroplasts, nanosensors for chloroplast biomolecules, and nanotherapeutics for enhancing chloroplast performance. Nanotechnology-mediated delivery of DNA to the chloroplast has the potential to revolutionize chloroplast synthetic biology by allowing transgenes, or even synthesized DNA libraries, to be delivered to a variety of photosynthetic species. Crop yield improvements could be enabled by nanomaterials that enhance photosynthesis, increase tolerance to stresses, and act as nanosensors for biomolecules associated with chloroplast function. Engineering isolated chloroplasts through nanotechnology and synthetic biology approaches are leading to a new generation of plant-based biomaterials able to self-repair using abundant CO2 and water sources and are powered by renewable sunlight energy. Current knowledge gaps of nanotechnology-enabled approaches for chloroplast biotechnology include precise mechanisms for entry into plant cells and organelles, limited understanding about nanoparticle-based chloroplast transformations, and the translation of lab-based nanotechnology tools to the agricultural field with crop plants. Future research in chloroplast biotechnology mediated by the merging of synthetic biology and nanotechnology approaches can yield tools for precise control and monitoring of chloroplast function in vivo and ex vivo across diverse plant species, allowing increased plant productivity and turning plants into widely available sustainable technologies.

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