Potential of Carbofuran Degradation by Soil Bacteria in Malaysia: A Review

Carbofuran is a very toxic and systemic carbamate pesticide which is used as an extensive carbamate insecticide, nematicide andacaricide. It is applied to the soil as a treatment to manage or destroy pests and parasites to improve the quality of agricultural production. It is also an anticholinesterase carbamate which is highly toxic to plants, animals andhumans. The consequences have received great concern as many health-associated problems have still been reported due to pesticide poisoning. In humans, carbofuran is associated with the inhibition of cholinesterase, which could develop a cholinergic crisis known as sludge syndrome. Therefore, it is essential to take quick action to eliminate this pesticide from the environment. Bacterial degradation is a very eco-friendly method for the elimination of carbofuran. Bacterial enzymes and degradation genes play an essential role in catalyzing new biochemical pathways during the bacterial degradation process. A complete screening of bacterial carbofuran metabolic pathway can develop marker genes or enzymes to determine useful bacteria in the contaminated sites capable to degrade carbofuran residues. Therefore, this review focused on the understanding of bacterial degradation of carbofuran in Malaysian soils and to explore the possibility of soil bacteria to degrade carbofuran effectively. Thus, we emphasize on the carbofuran toxicity, bacterial degradation, metabolic and molecular mechanisms of carbofuran's degradation process.

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ClusterMap: Comparing analyses across multiple Single Cell RNA-Seq profiles

10.1101/331330 ◽

2018 ◽

Cited By ~ 3

Author(s):

Xin Gao ◽

Deqing Hu ◽

Madelaine Gogol ◽

Hua Li

Keyword(s):

Single Cell ◽

Molecular Mechanisms ◽

Population Level ◽

Marker Genes ◽

Rna Seq ◽

Matching Problem ◽

Cut Method ◽

Underlying Mechanisms

AbstractSingle cell RNA-Seq facilitates the characterization of cell type heterogeneity and developmental processes. Further study of single cell profiles across different conditions enables the understanding of biological processes and underlying mechanisms at the sub-population level. However, developing proper methodology to compare multiple scRNA-Seq datasets remains challenging. We have developed ClusterMap, a systematic method and workflow to facilitate the comparison of scRNA profiles across distinct biological contexts. Using hierarchical clustering of the marker genes of each sub-group, ClusterMap matches the sub-types of cells across different samples and provides “similarity” as a metric to quantify the quality of the match. We introduce a purity tree cut method designed specifically for this matching problem. We use Circos plot and regrouping method to visualize the results concisely. Furthermore, we propose a new metric “separability” to summarize sub-population changes among all sample pairs. In three case studies, we demonstrate that ClusterMap has the ability to offer us further insight into the different molecular mechanisms of cellular sub-populations across different conditions. ClusterMap is implemented in R and available at https://github.com/xgaoo/ClusterMap.

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The Relationship between the Development of Human Capital and the Agricultural Economy in Rural Areas

Economy of agricultural and processing enterprises ◽

10.31442/0235-2494-2020-0-11-61-65 ◽

2020 ◽

pp. 61-65

Author(s):

B.A. Voronin ◽

◽

I.P. Chupina ◽

Ya.V. Voronina ◽

◽

...

Keyword(s):

Human Capital ◽

Rural Areas ◽

Agricultural Production ◽

Agricultural Sector ◽

Real Life ◽

Standard View ◽

Household Factors ◽

Economic Transformations ◽

The Relationship

The article discusses a non-standard view of the formation of human capital for work in organizations of the agricultural sector of the economy, in the context of modern socio-economic transformations. In the classical sense, human capital for agriculture should be formed and developed in rural areas. But in real life, this is not always the case, because there are many factors that prevent the classical solution of this problem. First, the demographic factor affects, second, social and household factors, and third, in many rural areas there are no working agricultural organizations where qualified agricultural specialists can work. All these and other circumstances actualize the problem of the quality of human capital in rural areas in relation to the development of agricultural production.

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EVALUATING THE CONTRIBUTION OF TOTAL FACTOR PRODUCTIVITY ON AGRICULTURAL GROWTH IN AN GIANG PROVINCE

Scientific Journal of Tra Vinh University ◽

10.35382/18594816.1.29.2018.30 ◽

2018 ◽

Vol 1 (29) ◽

pp. 29-37

Author(s):

Tan Van Truong

Keyword(s):

Total Factor Productivity ◽

Agricultural Production ◽

Science And Technology ◽

Agricultural Labor ◽

Factor Productivity ◽

Agricultural Growth ◽

Regression Approach ◽

Investment Capital ◽

Agricultural Demand

By the growth regression approach, the research has identified that the investment capital contributed 1,939 and agricultural labor contributed 1,291 to the agricultural growth of An Giang province. More specifically, the contribution of TFP (Total Factor Productivity) to the agricultural growth in the period 2000 - 2004 was averagely 0,11%, in 2005 - 2010 was -5,03%, and in period 2011 - 2016 was 0,81%. The total factor productivity contributed to the agricultural growth slowly. In order to raise the contribution of TFP, the research represents 05 solutions including the increase of the effectiveness of using the investment capital, the increase of the quality of labor, the application of the science and technology into agricultural production, agriculturalrestructuring, and the increase of agricultural demand.

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Protective Effect of Psoralea corylifolia L. Seed Extract against Palmitate-Induced Neuronal Apoptosis in PC12 Cells

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2016/5410419 ◽

2016 ◽

Vol 2016 ◽

pp. 1-11 ◽

Cited By ~ 3

Author(s):

Yunkyoung Lee ◽

Hee-Sook Jun ◽

Yoon Sin Oh

Keyword(s):

Pc12 Cells ◽

Molecular Mechanisms ◽

Neuronal Cell ◽

Marker Genes ◽

Heme Oxygenase 1 ◽

Mrna Levels ◽

Protective Effects ◽

Psoralea Corylifolia ◽

Antioxidant Genes ◽

Bax Protein

The extract of Psoralea corylifolia seeds (PCE) has been widely used as a herbal medicine because of its beneficial effect on human health. In this study, we investigated the protective effects and molecular mechanisms of PCE on palmitate- (PA-) induced toxicity in PC12 cells, a neuron-like cell line. PCE significantly increased cell viability in PA-treated PC12 cells and showed antiapoptotic effects, as evidenced by decreased expression of cleaved caspase-3, cleaved poly(ADP-ribose) polymerase, and bax protein as well as increased expression of bcl-2 protein. In addition, PCE treatment reduced PA-induced reactive oxygen species production and upregulated mRNA levels of antioxidant genes such as nuclear factor (erythroid-derived 2)-like 2 and heme oxygenase 1. Moreover, PCE treatment recovered the expression of autophagy marker genes such as beclin-1 and p62, which was decreased by PA treatment. Treatment with isopsoralen, one of the major components of PCE extract, also recovered the expression of autophagy marker genes and reduced PA-induced apoptosis. In conclusion, PCE exerts protective effects against lipotoxicity via its antioxidant function, and this effect is mediated by activation of autophagy. PCE might be a potential pharmacological agent to protect against neuronal cell injury caused by oxidative stress or lipotoxicity.

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Molecular mechanisms of Zika virus teratogenesis from animal studies: a systematic review protocol

Systematic Reviews ◽

10.1186/s13643-021-01713-6 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Gabriela Elis Wachholz ◽

Julia do Amaral Gomes ◽

Juliano André Boquett ◽

Fernanda Sales Luiz Vianna ◽

Lavínia Schuler-Faccini ◽

...

Keyword(s):

Systematic Review ◽

Animal Models ◽

Zika Virus ◽

Methodological Quality ◽

Molecular Mechanisms ◽

Grey Literature ◽

Standard Form ◽

Teratogenic Effect ◽

Control Group

Abstract Background Due to the diversity of studies in animal models reporting that molecular mechanisms are involved in the teratogenic effect of the Zika virus (ZIKV), the objective of the present study is to evaluate the methodological quality of these studies, as well as to demonstrate which genes and which molecular pathways are affected by ZIKV in different animal models. Methods This search will be performed in four databases: PubMed/MEDLINE, EMBASE, Web of Science, and Scopus, as well as in the grey literature. The studies selection process will be reported through the PRISMA Statement diagram model. All studies describing the molecular mechanisms possibly involved in the development of malformations caused by embryonic/fetal ZIKV exposure in animal models with an appropriate control group and methodology will be included (including, for instance, randomized and non-randomized studies). All animals used as experimental models for ZIKV teratogenesis may be included as long as exposure to the virus occurred during the embryonic/fetal period. From the selected studies, data will be extracted using a previously prepared standard form. Bias risk evaluation will be conducted following the SYRCLE’s Risk of Bias tool. All data obtained will be tabulated and organized by outcomes (morphological and molecular). Discussion With the proposed systematic review, we expect to present results about the methodological quality of the published studies with animal models that investigated the molecular mechanisms involved in the teratogenic effect of ZIKV, as well as to show the studies with greater reliability. Systematic review registration PROSPERO CRD42019157316

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Ultrastructural and molecular analysis of the origin and differentiation of cells mediating brittle star skeletal regeneration

BMC Biology ◽

10.1186/s12915-020-00937-7 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Laura Piovani ◽

Anna Czarkwiani ◽

Cinzia Ferrario ◽

Michela Sugni ◽

Paola Oliveri

Keyword(s):

Molecular Mechanisms ◽

Close Contact ◽

Skeletal Development ◽

Morphological Differentiation ◽

Brittle Star ◽

Marker Genes ◽

Body Parts ◽

Coelomic Cavity ◽

Expression Of Genes ◽

Skeletal Regeneration

Abstract Background Regeneration is the ability to re-grow body parts or tissues after trauma, and it is widespread across metazoans. Cells involved in regeneration can arise from a pool of undifferentiated proliferative cells or be recruited from pre-existing differentiated tissues. Both mechanisms have been described in different phyla; however, the cellular and molecular mechanisms employed by different animals to restore lost tissues as well as the source of cells involved in regeneration remain largely unknown. Echinoderms are a clade of deuterostome invertebrates that show striking larval and adult regenerative abilities in all extant classes. Here, we use the brittle star Amphiura filiformis to investigate the origin and differentiation of cells involved in skeletal regeneration using a combination of microscopy techniques and molecular markers. Results Our ultrastructural analyses at different regenerative stages identify a population of morphologically undifferentiated cells which appear in close contact with the proliferating epithelium of the regenerating aboral coelomic cavity. These cells express skeletogenic marker genes, such as the transcription factor alx1 and the differentiation genes c-lectin and msp130L, and display a gradient of morphological differentiation from the aboral coelomic cavity towards the epidermis. Cells closer to the epidermis, which are in contact with developing spicules, have the morphology of mature skeletal cells (sclerocytes), and express several skeletogenic transcription factors and differentiation genes. Moreover, as regeneration progresses, sclerocytes show a different combinatorial expression of genes in various skeletal elements. Conclusions We hypothesize that sclerocyte precursors originate from the epithelium of the proliferating aboral coelomic cavity. As these cells migrate towards the epidermis, they differentiate and start secreting spicules. Moreover, our study shows that molecular and cellular processes involved in skeletal regeneration resemble those used during skeletal development, hinting at a possible conservation of developmental programmes during adult regeneration. Finally, we highlight that many genes involved in echinoderm skeletogenesis also play a role in vertebrate skeleton formation, suggesting a possible common origin of the deuterostome endoskeleton pathway.

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Expression Profile of New Marker Genes Involved in Differentiation of Canine Adipose-Derived Stem Cells into Osteoblasts

International Journal of Molecular Sciences ◽

10.3390/ijms22136663 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6663

Author(s):

Maurycy Jankowski ◽

Mariusz Kaczmarek ◽

Grzegorz Wąsiatycz ◽

Claudia Dompe ◽

Paul Mozdziak ◽

...

Keyword(s):

Stem Cells ◽

In Vitro Culture ◽

Osteogenic Differentiation ◽

Molecular Mechanisms ◽

Marker Genes ◽

P Value ◽

Illumina Platform

Next-generation sequencing (RNAseq) analysis of gene expression changes during the long-term in vitro culture and osteogenic differentiation of ASCs remains to be important, as the analysis provides important clues toward employing stem cells as a therapeutic intervention. In this study, the cells were isolated from adipose tissue obtained during routine surgical procedures and subjected to 14-day in vitro culture and differentiation. The mRNA transcript levels were evaluated using the Illumina platform, resulting in the detection of 19,856 gene transcripts. The most differentially expressed genes (fold change >|2|, adjusted p value < 0.05), between day 1, day 14 and differentiated cell cultures were extracted and subjected to bioinformatical analysis based on the R programming language. The results of this study provide molecular insight into the processes that occur during long-term in vitro culture and osteogenic differentiation of ASCs, allowing the re-evaluation of the roles of some genes in MSC progression towards a range of lineages. The results improve the knowledge of the molecular mechanisms associated with long-term in vitro culture and differentiation of ASCs, as well as providing a point of reference for potential in vivo and clinical studies regarding these cells’ application in regenerative medicine.

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Molecular Mechanisms Associated with ROS-Dependent Angiogenesis in Lower Extremity Artery Disease

Antioxidants ◽

10.3390/antiox10050735 ◽

2021 ◽

Vol 10 (5) ◽

pp. 735

Author(s):

Greg Hutchings ◽

Łukasz Kruszyna ◽

Mariusz J. Nawrocki ◽

Ewa Strauss ◽

Rut Bryl ◽

...

Keyword(s):

Quality Of Life ◽

Blood Vessel ◽

Lower Extremity ◽

Molecular Mechanisms ◽

Lower Extremities ◽

Tissue Response ◽

Peripheral Arteries ◽

Artery Disease ◽

Lower Extremity Artery Disease

Currently, atherosclerosis, which affects the vascular bed of all vital organs and tissues, is considered as a leading cause of death. Most commonly, atherosclerosis involves coronary and peripheral arteries, which results in acute (e.g., myocardial infarction, lower extremities ischemia) or chronic (persistent ischemia leading to severe heart failure) consequences. All of them have a marked unfavorable impact on the quality of life and are associated with increased mortality and morbidity in human populations. Lower extremity artery disease (LEAD, also defined as peripheral artery disease, PAD) refers to atherosclerotic occlusive disease of the lower extremities, where partial or complete obstruction of peripheral arteries is observed. Decreased perfusion can result in ischemic pain, non-healing wounds, and ischemic ulcers, and significantly reduce the quality of life. However, the progressive atherosclerotic changes cause stimulation of tissue response processes, like vessel wall remodeling and neovascularization. These mechanisms of adapting the vascular network to pathological conditions seem to play a key role in reducing the impact of the changes limiting the flow of blood. Neovascularization as a response to ischemia induces sprouting and expansion of the endothelium to repair and grow the vessels of the circulatory system. Neovascularization consists of three different biological processes: vasculogenesis, angiogenesis, and arteriogenesis. Both molecular and environmental factors that may affect the process of development and growth of blood vessels were analyzed. Particular attention was paid to the changes taking place during LEAD. It is important to consider the molecular mechanisms underpinning vessel growth. These mechanisms will also be examined in the context of diseases commonly affecting blood vessel function, or those treatable in part by manipulation of angiogenesis. Furthermore, it may be possible to induce the process of blood vessel development and growth to treat peripheral vascular disease and wound healing. Reactive oxygen species (ROS) play an important role in regulation of essential cellular signaling pathways such as cell differentiation, proliferation, migration and apoptosis. With regard to the repair processes taking place during diseases such as LEAD, prospective therapeutic methods have been described that could significantly improve the treatment of vessel diseases in the future. Summarizing, regenerative medicine holds the potential to transform the therapeutic methods in heart and vessel diseases treatment.

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Comprehensive Analysis of Transcriptome and Metabolome Reveals the Flavonoid Metabolic Pathway Is Associated with Fruit Peel Coloration of Melon

Molecules ◽

10.3390/molecules26092830 ◽

2021 ◽

Vol 26 (9) ◽

pp. 2830

Author(s):

Aiai Zhang ◽

Jing Zheng ◽

Xuemiao Chen ◽

Xueyin Shi ◽

Huaisong Wang ◽

...

Keyword(s):

Molecular Mechanisms ◽

Comprehensive Analysis ◽

Differentially Expressed ◽

Integrated Analysis ◽

Fruit Peel ◽

External Quality ◽

Color Formation ◽

Peel Color ◽

Dark Green

The peel color is an important external quality of melon fruit. To explore the mechanisms of melon peel color formation, we performed an integrated analysis of transcriptome and metabolome with three different fruit peel samples (grey-green ‘W’, dark-green ‘B’, and yellow ‘H’). A total of 40 differentially expressed flavonoids were identified. Integrated transcriptomic and metabolomic analyses revealed that flavonoid biosynthesis was associated with the fruit peel coloration of melon. Twelve differentially expressed genes regulated flavonoids synthesis. Among them, nine (two 4CL, F3H, three F3′H, IFS, FNS, and FLS) up-regulated genes were involved in the accumulation of flavones, flavanones, flavonols, and isoflavones, and three (2 ANS and UFGT) down-regulated genes were involved in the accumulation of anthocyanins. This study laid a foundation to understand the molecular mechanisms of melon peel coloration by exploring valuable genes and metabolites.

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Membrane recruitment of Atg8 by Hfl1 facilitates turnover of vacuolar membrane proteins in yeast cells approaching stationary phase

BMC Biology ◽

10.1186/s12915-021-01048-7 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Cheng-Wen He ◽

Xue-Fei Cui ◽

Shao-Jie Ma ◽

Qin Xu ◽

Yan-Peng Ran ◽

...

Keyword(s):

Membrane Proteins ◽

Membrane Protein ◽

Stationary Phase ◽

Molecular Mechanisms ◽

Multivesicular Body ◽

Degradation Process ◽

Vacuolar Membrane ◽

Yeast Cells ◽

Membrane Structures ◽

Membrane Recruitment

Abstract Background The vacuole/lysosome is the final destination of autophagic pathways, but can also itself be degraded in whole or in part by selective macroautophagic or microautophagic processes. Diverse molecular mechanisms are involved in these processes, the characterization of which has lagged behind those of ATG-dependent macroautophagy and ESCRT-dependent endosomal multivesicular body pathways. Results Here we show that as yeast cells gradually exhaust available nutrients and approach stationary phase, multiple vacuolar integral membrane proteins with unrelated functions are degraded in the vacuolar lumen. This degradation depends on the ESCRT machinery, but does not strictly require ubiquitination of cargos or trafficking of cargos out of the vacuole. It is also temporally and mechanistically distinct from NPC-dependent microlipophagy. The turnover is facilitated by Atg8, an exception among autophagy proteins, and an Atg8-interacting vacuolar membrane protein, Hfl1. Lack of Atg8 or Hfl1 led to the accumulation of enlarged lumenal membrane structures in the vacuole. We further show that a key function of Hfl1 is the membrane recruitment of Atg8. In the presence of Hfl1, lipidation of Atg8 is not required for efficient cargo turnover. The need for Hfl1 can be partially bypassed by blocking Atg8 delipidation. Conclusions Our data reveal a vacuolar membrane protein degradation process with a unique dependence on vacuole-associated Atg8 downstream of ESCRTs, and we identify a specific role of Hfl1, a protein conserved from yeast to plants and animals, in membrane targeting of Atg8.

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