scholarly journals De novo hydroponics system efficiency for the cuttings of alfalfa (Medicago sativa L.)

2021 ◽  
Author(s):  
Zhili Zhao ◽  
Wenyu Zhang ◽  
Yang Liu ◽  
Shuai Li ◽  
Wu Yao ◽  
...  
Keyword(s):  
Medicago Sativa ◽  
De Novo ◽  
Cost Effective ◽  
Breeding Programs ◽  
Ecological Zones ◽  
Cutting Propagation ◽  
Legume Plant ◽  
Propagation Methods ◽  
Incompatible Cross ◽  
Nutrient Solutions

AbstractThe legume plant alfalfa (Medicago sativa L.) is a widely cultivated perennial forage due to its high protein content, palatability, and strong adaptability to diverse agro-ecological zones. Alfalfa is a self-incompatible cross-pollinated autotetraploid species with tetrasomic inheritance. Therefore, maintaining excellent traits through seed reproduction is a prime challenge in alfalfa. However, the cutting propagation technology could enable consistent multiplication of quality plants that are genetically identical to the parent plant. The current study aimed to develop a simple, cost-effective, reproducible, and efficient hydroponic cutting method to preserve alfalfa plants and for molecular research. In this study, alfalfa landrace ‘Wudi’ was grown in hydroponics for 30 days and used as source material for cuttings. The top, middle and bottom sections of its stem were used as cuttings. The rooting rate, root length, and stem height of the different stem sections were compared to determine the best segment for alfalfa propagation in four nutrient treatments (HM, HM + 1/500H, HM + 1/1000H and d HM + 1/2000H). After 21 days of culture, the rooting rates of all the three stem types under four cutting nutrient solutions were above 78%. The rooting rate of the middle and bottom parts in HM + 1/1000 H and HM + 1/2000 H nutrient solutions reached more than 93%, with a higher health survey score (> 4.70). In conclusion, this study developed a de novo cutting propagation method that can be used to conserve and propagate germplasm in breeding programs and research. This method is a new report on the cutting propagation of alfalfa by hydroponics, which could supplement the existing cutting propagation methods.

scholarly journals De novo Propagation of Alfalfa Under Hydroponics

2020 ◽  
Author(s):  
Liu Yang ◽  
Zhang Wenyu ◽  
Li Shuai ◽  
Wu Yao ◽  
Sun Xiaohui ◽  
...  
Keyword(s):  
Root Length ◽  
De Novo ◽  
Cost Effective ◽  
Stem Height ◽  
Poor Growth ◽  
Ecological Zones ◽  
Cutting Propagation ◽  
Protein Levels ◽  
Propagation Methods ◽  
Nutrient Solutions

Abstract Background: The legume plant alfalfa (Medicago sativa L.) is a widely cultivated perennial forage due to its high protein levels, palatability, and strong adaptability to diverse soil types and agro-ecological zones. This forage plant is a self-incompatible, cross-pollinated autotetraploid with tetrasomic inheritance. Therefore, maintaining excellent traits through seed reproduction is challenging in alfalfa. However, the cutting propagation technology could enable consistent multiplication of quality plants that are genetically identical to the parent plant, for use in breeding and other research applications. Most of previous alfalfa omics researches used varieties as material on omics and gene mining experiment due to poor growth consistency of cuttings by existing cutting methods, which generate genetically un-identical cuttings and thus compromise on the reliability of the results. Therefore, this study aimed to develop a simple, cost-effective, reproducible, and efficient hydroponic cutting method for the preservation of alfalfa plants and molecular research applications such as genomic, transcriptomic, and proteomic analyses. Results: Alfalfa cultivar ‘Wudi’ grown under hydroponics for 30 days was used as source material for cuttings. The top, middle and bottom sections of its stem were used as cuttings. The rooting rate, root length, and stem height of the different stem sections were compared to determine the best segment for alfalfa propagation in four nutrient solutions (HM, HM+1/500H, HM+1/1000H and d HM+1/2000H). After 21 days of culture, the rooting rates of all the three stem types under four cutting nutrient solutions were above 78%, The rooting rate of the middle and bottom parts in HM +1/1000 H and HM +1/2000 H nutrient solutions reached more than 93% with higher health survey score (>4.70). Besides, root length and stem height in these two sections was exemplary. Conclusions: This study developed a de novo cutting propagation method that can be used to conserve and propagate germplasm in breeding programs and research. This article is the first report on the cutting propagation of alfalfa by hydroponics, which could supplement the existing cutting propagation methods.

Recent Advances in Drug Repurposing for Parkinson’s Disease

2019 ◽  
Vol 26 (28) ◽  
pp. 5340-5362 ◽  
Author(s):  
Xin Chen ◽  
Giuseppe Gumina ◽  
Kristopher G. Virga
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Drug Discovery ◽  
De Novo ◽  
Drug Repositioning ◽  
Drug Repurposing ◽  
Cost Effective ◽  
New Drugs ◽  
Recent Advances ◽  
Clinical Drugs

:As a long-term degenerative disorder of the central nervous system that mostly affects older people, Parkinson’s disease is a growing health threat to our ever-aging population. Despite remarkable advances in our understanding of this disease, all therapeutics currently available only act to improve symptoms but cannot stop the disease progression. Therefore, it is essential that more effective drug discovery methods and approaches are developed, validated, and used for the discovery of disease-modifying treatments for Parkinson’s disease. Drug repurposing, also known as drug repositioning, or the process of finding new uses for existing or abandoned pharmaceuticals, has been recognized as a cost-effective and timeefficient way to develop new drugs, being equally promising as de novo drug discovery in the field of neurodegeneration and, more specifically for Parkinson’s disease. The availability of several established libraries of clinical drugs and fast evolvement in disease biology, genomics and bioinformatics has stimulated the momentums of both in silico and activity-based drug repurposing. With the successful clinical introduction of several repurposed drugs for Parkinson’s disease, drug repurposing has now become a robust alternative approach to the discovery and development of novel drugs for this disease. In this review, recent advances in drug repurposing for Parkinson’s disease will be discussed.

scholarly journals What Is Known and Unknown About Twice-Weekly Hemodialysis

2015 ◽  
Vol 40 (4) ◽  
pp. 298-305 ◽  
Author(s):  
Yoshitsugu Obi ◽  
Rieko Eriguchi ◽  
Shuo-Ming Ou ◽  
Connie M. Rhee ◽  
Kamyar Kalantar-Zadeh
Keyword(s):  
Quality Of Life ◽  
De Novo ◽  
Urine Volume ◽  
Cost Effective ◽  
Standard Of Care ◽  
Treatment Regimens ◽  
Interdialytic Weight Gain ◽  
Cost Effective Treatment ◽  
Incremental Hemodialysis

Background: The 2006 Kidney Disease Outcomes Quality Initiative guidelines suggest twice-weekly or incremental hemodialysis for patients with substantial residual kidney function (RKF). However, in most affluent nations de novo and abrupt transition to thrice-weekly hemodialysis is routinely prescribed for all dialysis-naïve patients regardless of their RKF. We review historical developments in hemodialysis therapy initiation and revisit twice-weekly hemodialysis as an individualized, incremental treatment especially upon first transitioning to hemodialysis therapy. Summary: In the 1960's, hemodialysis treatment was first offered as a life-sustaining treatment in the form of long sessions (≥10 hours) administered every 5 to 7 days. Twice- and then thrice-weekly treatment regimens were subsequently developed to prevent uremic symptoms on a long-term basis. The thrice-weekly regimen has since become the ‘standard of care' despite a lack of comparative studies. Some clinical studies have shown benefits of high hemodialysis dose by more frequent or longer treatment times mainly among patients with limited or no RKF. Conversely, in selected patients with higher levels of RKF and particularly higher urine volume, incremental or twice-weekly hemodialysis may preserve RKF and vascular access longer without compromising clinical outcomes. Proposed criteria for twice-weekly hemodialysis include urine output >500 ml/day, limited interdialytic weight gain, smaller body size relative to RKF, and favorable nutritional status, quality of life, and comorbidity profile. Key Messages: Incremental hemodialysis including twice-weekly regimens may be safe and cost-effective treatment regimens that provide better quality of life for incident dialysis patients who have substantial RKF. These proposed criteria may guide incremental hemodialysis frequency and warrant future randomized controlled trials.

scholarly journals A practical guide to buildde-novoassemblies for single tissues of non-model organisms: the example of a Neotropical frog

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3702 ◽  
Author(s):  
Santiago Montero-Mendieta ◽  
Manfred Grabherr ◽  
Henrik Lantz ◽  
Ignacio De la Riva ◽  
Jennifer A. Leonard ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Cost Effective ◽  
Model Organisms ◽  
Rna Seq ◽  
Assembly Pipeline ◽  
Wide Variability ◽  
History Of ◽  
Inexperienced User

Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembledde-novo. We used RNA-seq to obtain the transcriptomic profile forOreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome ofO. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating ade-novotranscriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to buildde-novotranscriptome assemblies using readily available software and is freely available at:https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.

scholarly journals Review: Cost-Effective Unmanned Aerial Vehicle (UAV) Platform for Field Plant Breeding Application

2020 ◽  
Vol 12 (6) ◽  
pp. 998 ◽  
Author(s):  
GyuJin Jang ◽  
Jaeyoung Kim ◽  
Ju-Kyung Yu ◽  
Hak-Jin Kim ◽  
Yoonha Kim ◽  
...  
Keyword(s):  
Plant Breeding ◽  
Unmanned Aerial Vehicle ◽  
High Throughput ◽  
New Technologies ◽  
Cost Effective ◽  
New Wave ◽  
Breeding Programs ◽  
Modern Agriculture ◽  
Aerial Vehicle ◽  
High Throughput Phenotyping

Utilization of remote sensing is a new wave of modern agriculture that accelerates plant breeding and research, and the performance of farming practices and farm management. High-throughput phenotyping is a key advanced agricultural technology and has been rapidly adopted in plant research. However, technology adoption is not easy due to cost limitations in academia. This article reviews various commercial unmanned aerial vehicle (UAV) platforms as a high-throughput phenotyping technology for plant breeding. It compares known commercial UAV platforms that are cost-effective and manageable in field settings and demonstrates a general workflow for high-throughput phenotyping, including data analysis. The authors expect this article to create opportunities for academics to access new technologies and utilize the information for their research and breeding programs in more workable ways.

scholarly journals HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C

2020 ◽  
Vol 36 (13) ◽  
pp. 3966-3974
Author(s):  
Ryo Nakabayashi ◽  
Shinichi Morishita
Keyword(s):  
Viterbi Algorithm ◽  
De Novo ◽  
Gene Prediction ◽  
Effective Means ◽  
Cost Effective ◽  
Synteny Block ◽  
Chromosome Length ◽  
Model Organisms ◽  
Contact Frequency ◽  
Reference Quality

Abstract Motivation De novo assembly of reference-quality genomes used to require enormously laborious tasks. In particular, it is extremely time-consuming to build genome markers for ordering assembled contigs along chromosomes; thus, they are only available for well-established model organisms. To resolve this issue, recent studies demonstrated that Hi-C could be a powerful and cost-effective means to output chromosome-length scaffolds for non-model species with no genome marker resources, because the Hi-C contact frequency between a pair of two loci can be a good estimator of their genomic distance, even if there is a large gap between them. Indeed, state-of-the-art methods such as 3D-DNA are now widely used for locating contigs in chromosomes. However, it remains challenging to reduce errors in contig orientation because shorter contigs have fewer contacts with their neighboring contigs. These orientation errors lower the accuracy of gene prediction, read alignment, and synteny block estimation in comparative genomics. Results To reduce these contig orientation errors, we propose a new algorithm, named HiC-Hiker, which has a firm grounding in probabilistic theory, rigorously models Hi-C contacts across contigs, and effectively infers the most probable orientations via the Viterbi algorithm. We compared HiC-Hiker and 3D-DNA using human and worm genome contigs generated from short reads, evaluated their performances, and observed a remarkable reduction in the contig orientation error rate from 4.3% (3D-DNA) to 1.7% (HiC-Hiker). Our algorithm can consider long-range information between distal contigs and precisely estimates Hi-C read contact probabilities among contigs, which may also be useful for determining the ordering of contigs. Availability and implementation HiC-Hiker is freely available at: https://github.com/ryought/hic_hiker.

scholarly journals Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1220
Author(s):  
Roshan Kulkarni ◽  
Ratan Chopra ◽  
Jennifer Chagoya ◽  
Charles E. Simpson ◽  
Michael R. Baring ◽  
...  
Keyword(s):  
Cost Effective ◽  
Amplicon Sequencing ◽  
Routine Practice ◽  
Specific Information ◽  
Illumina Hiseq ◽  
Breeding Programs ◽  
Polymorphic Snps ◽  
Cost Effective Approach ◽  
A Genome ◽  
The Cost

The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost.

scholarly journals A diagnostic marker kit for Fusarium wilt and sterility mosaic diseases resistance in pigeonpea

2020 ◽  
Author(s):  
Rachit K. Saxena ◽  
Anil Hake ◽  
Abhishek Bohra ◽  
Aamir W. Khan ◽  
Anupama Hingane ◽  
...  
Keyword(s):  
Fusarium Wilt ◽  
Diagnostic Marker ◽  
Development Program ◽  
Cost Effective ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
Specific Pcr ◽  
Novel Approach ◽  
Resistant Varieties ◽  
Pathogen Variability

Abstract Fusarium wilt (FW) and sterility mosaic diseases (SMD) are key biotic constraints to pigeonpea production. Occurrence of these two diseases in congenial conditions is reported to cause complete yield loss in susceptible pigeonpea cultivars. Various studies to elucidate genomic architecture of the two traits have revealed significant marker–trait associations for use in breeding programs. However, these DNA markers could not be used effectively in genomics-assisted breeding for developing FW and SMD resistant varieties primarily due to pathogen variability, location or background specificity, lesser phenotypic variance explained by the reported QTL and cost-inefficiency of the genotyping assays. Therefore, in the present study, a novel approach has been used to develop a diagnostic kit for identification of suitable FW and SMD resistant lines. This kit was developed with 10 markers each for FW and SMD resistance. Investigation of the diversity of these loci has shown the role of different alleles in different resistant genotypes. Two genes (C.cajan_03691 and C.cajan_18888) for FW resistance and four genes (C.cajan_07858, C.cajan_20995, C.cajan_21801 and C.cajan_17341) for SMD resistance have been identified. More importantly, we developed a customized and cost-effective Kompetitive allele-specific PCR genotyping assay for the identified genes in order to encourage their downstream applications in pigeonpea breeding programs. The diagnostic marker kit developed here will offer great strength to pigeonpea varietal development program, since the resistance against these two diseases is essentially required for nominating an improved line in varietal release pipeline.

scholarly journals Proposal of De Novo Antigen Test for COVID-19: Ultrasensitive Detection of Spike Proteins of SARS-CoV-2

Diagnostics ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 594 ◽  
Author(s):  
Yuta Kyosei ◽  
Mayuri Namba ◽  
Sou Yamura ◽  
Rikiya Takeuchi ◽  
Noriko Aoki ◽  
...  
Keyword(s):  
De Novo ◽  
Limit Of Detection ◽  
False Negative ◽  
Cost Effective ◽  
Detection Sensitivity ◽  
Enzyme Linked Immunosorbent Assay ◽  
Antigen Test ◽  
Virus Rna ◽  
Antigen Tests ◽  
Spike Proteins

Polymerase chain reaction (PCR)-based antigen tests are technically difficult, time-consuming, and expensive, and may produce false negative results requiring follow-up confirmation with computed tomography. The global coronavirus disease 2019 (COVID-19) pandemic has increased the demand for accurate, easy-to-use, rapid, and cost-effective antigen tests for clinical application. We propose a de novo antigen test for diagnosing COVID-19 using the combination of sandwich enzyme-linked immunosorbent assay and thio-nicotinamide adenine dinucleotide (thio-NAD) cycling. Our test takes advantage of the spike proteins specific to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The limit of detection of our test was 2.3 × 10−18 moles/assay. If the virus has ~25 spike proteins on its surface, our method should detect on the order of 10−20 moles of virus/assay, corresponding to ~104 copies of the virus RNA/assay. The detection sensitivity approaches that of PCR-based assays because the average virus RNA load used for PCR-based assays is ~105 copies per oro- or naso-pharyngeal swab specimen. To our knowledge, this is the first ultrasensitive antigen test for SARS-CoV-2 spike proteins that can be performed with an easy-to-use microplate reader. Sufficient sensitivity can be achieved within 10 min of thio-NAD cycling. Our antigen test allows for rapid, cost-effective, specific, ultrasensitive, and simultaneous multiple measurements of SARS-CoV-2, and has broad application for the diagnosis for COVID-19.

scholarly journals Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (AI-LAMP) for Rapid Detection of SARS-CoV-2

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 972 ◽  
Author(s):  
Mohammed A. Rohaim ◽  
Emily Clayton ◽  
Irem Sahin ◽  
Julianne Vilela ◽  
Manar E. Khalifa ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
De Novo ◽  
Tracking System ◽  
Lamp Assay ◽  
Cost Effective ◽  
Isothermal Amplification ◽  
Analytical Sensitivity ◽  
Diagnostic Device ◽  
Loop Mediated Isothermal Amplification ◽  
Resource Limited

Until vaccines and effective therapeutics become available, the practical solution to transit safely out of the current coronavirus disease 19 (CoVID-19) lockdown may include the implementation of an effective testing, tracing and tracking system. However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2. Here, we report on the development of a de novo, high-resolution and comparative genomics guided reverse-transcribed loop-mediated isothermal amplification (LAMP) assay. To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of results, we engineered a novel hand-held smart diagnostic device. The robust diagnostic device was further furnished with automated image acquisition and processing algorithms and the collated data was processed through artificial intelligence (AI) pipelines to further reduce the assay run time and the subjectivity of the colorimetric LAMP detection. This advanced AI algorithm-implemented LAMP (ai-LAMP) assay, targeting the RNA-dependent RNA polymerase gene, showed high analytical sensitivity and specificity for SARS-CoV-2. A total of ~200 coronavirus disease (CoVID-19)-suspected NHS patient samples were tested using the platform and it was shown to be reliable, highly specific and significantly more sensitive than the current gold standard qRT-PCR. Therefore, this system could provide an efficient and cost-effective platform to detect SARS-CoV-2 in resource-limited laboratories.

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