Large-Scale Proteomics of the Cassava Storage Root and Identification of a Target Gene to Reduce Postharvest Deterioration

The Policy Analysis Matrix (PAM) was used to assess the efficiencies and competitiveness of fresh cassava storage root production systems in Sierra Leone. Proportional random sampling was used to select study samples. Information was collected using structured questionnaire from a total of 1,880 producer households. Out of the 36 potential storage root production systems identified, only 6 systems are mainly used by producers. The PAM was based on one hectare of land for production and Leone (SSL) as money to evaluate costs and revenues. The analysis indicates that, all the 6 fresh cassava storage root production systems present a Domestic Resource Cost Ratio of less than 1 (DRC < 1) and Cost-Benefit Ratio (RCB) also less than 1 (RCB within 0.14 to 0.42). Discounting potential revenue from stems and cassava leaves in storage root production systems that use improved varieties and fertilizer have higher comparative and competitive advantages. The systems are also profitable, even though producers are not protected from tradable and taxed inputs. Production systems also remain profitable with 25% and 50% yield loss. This was also confirmed by Abiodun and Adefemi (2016). It is therefore better to produce cassava locally in Sierra Leone than import for processing or consumption. This study proposes recommendations to improve cassava productivity in Sierra Leone.

Download Full-text

FAM129B is a novel regulator of Wnt/β-catenin signal transduction in melanoma cells

F1000Research ◽

10.12688/f1000research.2-134.v2 ◽

2013 ◽

Vol 2 ◽

pp. 134 ◽

Cited By ~ 11

Author(s):

Willliam Conrad ◽

Michael B Major ◽

Michele A Cleary ◽

Marc Ferrer ◽

Brian Roberts ◽

...

Keyword(s):

Large Scale ◽

Target Gene ◽

Mapk Pathway ◽

Melanoma Cells ◽

Luciferase Reporter ◽

Braf Inhibitors ◽

Sirna Screen ◽

Reporter Activity ◽

Fibrosarcoma Cells ◽

Interfering Rna

The inability of targeted BRAF inhibitors to produce long-lasting improvement in the clinical outcome of melanoma highlights a need to identify additional approaches to inhibit melanoma growth. Recent studies have shown that activation of the Wnt/β-catenin pathway decreases tumor growth and cooperates with ERK/MAPK pathway inhibitors to promote apoptosis in melanoma. Therefore, the identification of Wnt/β-catenin regulators may advance the development of new approaches to treat this disease. In order to move towards this goal we performed a large scale small-interfering RNA (siRNA) screen for regulators of β-catenin activated reporter activity in human HT1080 fibrosarcoma cells. Integrating large scale siRNA screen data with phosphoproteomic data and bioinformatics enrichment identified a protein, FAM129B, as a potential regulator of Wnt/β-catenin signaling. Functionally, we demonstrated that siRNA-mediated knockdown of FAM129B in A375 and A2058 melanoma cell lines inhibits WNT3A-mediated activation of a β-catenin-responsive luciferase reporter and inhibits expression of the endogenous Wnt/β-catenin target gene, AXIN2. We also demonstrate that FAM129B knockdown inhibits apoptosis in melanoma cells treated with WNT3A. These experiments support a role for FAM129B in linking Wnt/β-catenin signaling to apoptosis in melanoma.

Download Full-text

Convolutional Neural Net-Based Cassava Storage Root Counting Using Real and Synthetic Images

Frontiers in Plant Science ◽

10.3389/fpls.2019.01516 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 3

Author(s):

John Atanbori ◽

Maria Elker Montoya-P ◽

Michael Gomez Selvaraj ◽

Andrew P. French ◽

Tony P. Pridmore

Keyword(s):

Neural Net ◽

Storage Root ◽

Synthetic Images ◽

Cassava Storage Root ◽

Root Counting

Download Full-text

FAM129B is a novel regulator of Wnt/β-catenin signal transduction in melanoma cells

F1000Research ◽

10.12688/f1000research.2-134.v1 ◽

2013 ◽

Vol 2 ◽

pp. 134 ◽

Cited By ~ 1

Author(s):

Willliam Conrad ◽

Michael B Major ◽

Michele A Cleary ◽

Marc Ferrer ◽

Brian Roberts ◽

...

Keyword(s):

Large Scale ◽

Target Gene ◽

Mapk Pathway ◽

Melanoma Cells ◽

Luciferase Reporter ◽

Braf Inhibitors ◽

Sirna Screen ◽

Reporter Activity ◽

Fibrosarcoma Cells ◽

Interfering Rna

The inability of targeted BRAF inhibitors to produce long-lasting improvement in the clinical outcome of melanoma highlights a need to identify additional approaches to inhibit melanoma growth. Recent studies have shown that activation of the Wnt/β-catenin pathway decreases tumor growth and cooperates with ERK/MAPK pathway inhibitors to promote apoptosis in melanoma. Therefore, the identification of Wnt/β-catenin regulators may advance the development of new approaches to treat this disease. In order to move towards this goal we performed a large scale small-interfering RNA (siRNA) screen for regulators of β-catenin activated reporter activity in human HT1080 fibrosarcoma cells. Integrating large scale siRNA screen data with phosphoproteomic data and bioinformatics enrichment identified a protein, FAM129B, as a potential regulator of Wnt/β-catenin signaling. Functionally, we demonstrated that siRNA-mediated knockdown of FAM129B in A375 and A2058 melanoma cell lines inhibits WNT3A-mediated activation of a β-catenin-responsive luciferase reporter and inhibits expression of the endogenous Wnt/β-catenin target gene, AXIN2. We also demonstrate that FAM129B knockdown inhibits apoptosis in melanoma cells treated with WNT3A. These experiments support a role for FAM129B in linking Wnt/β-catenin signaling to apoptosis in melanoma.

Download Full-text

Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator

eLife ◽

10.7554/elife.23250 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 13

Author(s):

Isabel Nocedal ◽

Eugenio Mancera ◽

Alexander D Johnson

Keyword(s):

Regulatory Networks ◽

Large Scale ◽

Target Gene ◽

Regulatory Function ◽

Transcription Regulator ◽

Ancestral Function ◽

Gene Regulatory ◽

Network Plasticity ◽

Open Question ◽

Phenotypic Novelty

The rewiring of gene regulatory networks can generate phenotypic novelty. It remains an open question, however, how the large number of connections needed to form a novel network arise over evolutionary time. Here, we address this question using the network controlled by the fungal transcription regulator Ndt80. This conserved protein has undergone a dramatic switch in function—from an ancestral role regulating sporulation to a derived role regulating biofilm formation. This switch in function corresponded to a large-scale rewiring of the genes regulated by Ndt80. However, we demonstrate that the Ndt80-target gene connections were undergoing extensive rewiring prior to the switch in Ndt80’s regulatory function. We propose that extensive drift in the Ndt80 regulon allowed for the exploration of alternative network structures without a loss of ancestral function, thereby facilitating the formation of a network with a new function.

Download Full-text

Integration of methylation QTL and enhancer–target gene maps with schizophrenia GWAS summary results identifies novel genes

Bioinformatics ◽

10.1093/bioinformatics/btz161 ◽

2019 ◽

Vol 35 (19) ◽

pp. 3576-3583 ◽

Cited By ~ 7

Author(s):

Chong Wu ◽

Wei Pan

Keyword(s):

Quantitative Trait ◽

Large Scale ◽

Target Gene ◽

Association Studies ◽

Regulatory Elements ◽

Supplementary Information ◽

Genome Wide Association Studies ◽

Novel Genes ◽

Gene Pairs ◽

Genome Wide

Abstract Motivation Most trait-associated genetic variants identified in genome-wide association studies (GWASs) are located in non-coding regions of the genome and thought to act through their regulatory roles. Results To account for enriched association signals in DNA regulatory elements, we propose a novel and general gene-based association testing strategy that integrates enhancer-target gene pairs and methylation quantitative trait locus data with GWAS summary results; it aims to both boost statistical power for new discoveries and enhance mechanistic interpretability of any new discovery. By reanalyzing two large-scale schizophrenia GWAS summary datasets, we demonstrate that the proposed method could identify some significant and novel genes (containing no genome-wide significant SNPs nearby) that would have been missed by other competing approaches, including the standard and some integrative gene-based association methods, such as one incorporating enhancer-target gene pairs and one integrating expression quantitative trait loci. Availability and implementation Software: wuchong.org/egmethyl.html Supplementary information Supplementary data are available at Bioinformatics online.

Download Full-text

An optimized method to obtain high-quality RNA from cassava storage root

3 Biotech ◽

10.1007/s13205-019-1608-9 ◽

2019 ◽

Vol 9 (4) ◽

Author(s):

Lulu Guan ◽

Xiaowen Ma ◽

Xiaoxia Zhou ◽

Bowen Tan ◽

Zhen-Yu Wang

Keyword(s):

Storage Root ◽

High Quality ◽

Cassava Storage Root

Download Full-text

EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species

Nucleic Acids Research ◽

10.1093/nar/gkz980 ◽

2019 ◽

Cited By ~ 8

Author(s):

Tianshun Gao ◽

Jiang Qian

Keyword(s):

Large Scale ◽

Target Gene ◽

Target Genes ◽

Cell Types ◽

Regulatory Elements ◽

Tissue Cell ◽

Normal Tissues ◽

Genome Wide ◽

Wide Range ◽

User Friendly

Abstract Enhancers are distal cis-regulatory elements that activate the transcription of their target genes. They regulate a wide range of important biological functions and processes, including embryogenesis, development, and homeostasis. As more and more large-scale technologies were developed for enhancer identification, a comprehensive database is highly desirable for enhancer annotation based on various genome-wide profiling datasets across different species. Here, we present an updated database EnhancerAtlas 2.0 (http://www.enhanceratlas.org/indexv2.php), covering 586 tissue/cell types that include a large number of normal tissues, cancer cell lines, and cells at different development stages across nine species. Overall, the database contains 13 494 603 enhancers, which were obtained from 16 055 datasets using 12 high-throughput experiment methods (e.g. H3K4me1/H3K27ac, DNase-seq/ATAC-seq, P300, POLR2A, CAGE, ChIA-PET, GRO-seq, STARR-seq and MPRA). The updated version is a huge expansion of the first version, which only contains the enhancers in human cells. In addition, we predicted enhancer–target gene relationships in human, mouse and fly. Finally, the users can search enhancers and enhancer–target gene relationships through five user-friendly, interactive modules. We believe the new annotation of enhancers in EnhancerAtlas 2.0 will facilitate users to perform useful functional analysis of enhancers in various genomes.

Download Full-text

Cloning, Expression, and Purification of Recombinant Mouse Interferon-γ

Research in Molecular Medicine ◽

10.32598/rmm.9.1.1 ◽

2021 ◽

Vol 9 (1) ◽

pp. 1-10

Author(s):

Seyedeh Elham Badiee Kheirabadi ◽

◽

Kazem Mashayekhi ◽

Malihe Moghadam ◽

Mohammad Javad Mousavi ◽

...

Keyword(s):

Western Blotting ◽

Large Scale ◽

Target Gene ◽

Polyacrylamide Gel Electrophoresis ◽

Pcr Amplification ◽

Interferon Γ ◽

Bacterial Cells ◽

Experimental Conditions ◽

Recombinant Mouse ◽

Ifn Γ

Background: Interferon-gamma [IFN-γ) is the most important cytokine in the immune system. This protein has been expressed in bacterial cells. However, bacterial cloning is not an easy task. We aimed to clone, express, and purify recombinant mouse IFN-γ and overcome problems in favor of commercial purposes. Materials and Methods: To amplify the gene product for cloning, we primarily designed two specific primers for the target gene. Following PCR amplification, the amplicon was inserted into the pET-21b[+) vector. The E. coli BL21 [DE3) CodonPlus strain was chosen for the expression of the target gene. Finally, the expressed recombinant mouse IFN-γ was assessed through the western blotting method. Results: We performed a cloning process and produced recombinant mouse IFN-γ in an optimal condition. We also noticed that monomeric protein could be transformed to a homodimeric structure which can be observed using the SDS PAGE [SDS-polyacrylamide gel electrophoresis) and western blotting. Conclusion: Experimental conditions strongly affect the large-scale cloning procedures required to be optimized in each laboratory. The expressed recombinant mouse IFN-γ described here is appropriate for commercial purposes.

Download Full-text

Studies toward the identification of transcription factors in cassava storage root

Brazilian Journal of Plant Physiology ◽

10.1590/s1677-04202003000300006 ◽

2003 ◽

Vol 15 (3) ◽

pp. 167-170 ◽

Cited By ~ 2

Author(s):

Cláudia Regina Batista de Souza ◽

Elionor Rita Pereira de Almeida ◽

Luiz Joaquim Castelo Branco Carvalho ◽

Eugen Silvano Gander

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Manihot Esculenta ◽

Plant Traits ◽

Storage Root ◽

Brazil Nut ◽

Manihot Esculenta Crantz ◽

Physiological Processes ◽

Cassava Storage Root

Transcription factors play important roles in several physiological processes. In recent years many transcription factors have been isolated from plants and they are emerging as powerful tools in the manipulation of plant traits. In this work we initiated studies in order to isolate transcription factors from cassava (Manihot esculenta Crantz), an important tropical and subtropical crop. Our results show three kinds of proteins expressed differentially in cassava storage root and immunologically related to the opaque-2 transcription factor from maize. Southwestern experiments showed two proteins capable of interacting in vitro with the DNA sequence of the be2S1 gene from the Brazil nut tree.

Download Full-text