Biotechnol Adv , IF:14.227 , 2022 Oct , V59 : P107969 doi: 10.1016/j.biotechadv.2022.107969
Current status, and the developments of hosts and expression systems for the production of recombinant human cytokines.
Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.; Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India. Electronic address: veeranki@iitg.ac.in.
Cytokines consist of peptides, proteins and glycoproteins, which are biological signaling molecules, and boost cell-cell communication in immune reactions to stimulate cellular movements in the place of trauma, inflammation and infection. Recombinant cytokines are designed in such a way that they have generalized immunostimulation action or stimulate specific immune cells when the body encounters immunosuppressive signals from exogenous pathogens or other tumor microenvironments. Recombinant cytokines have improved the treatment processes for numerous diseases. They are also beneficial against novel toxicities that arise due to pharmacologic immunostimulators that lead to an imbalance in the regulation of cytokine. So, the production and use of recombinant human cytokines as therapeutic proteins are significant for medical treatment purposes. For the improved production of recombinant human cytokines, the development of host cells such as bacteria, yeast, fungi, insect, mammal and transgenic plants, and the specific expression systems for individual hosts is necessary. The recent advancements in the field of genetic engineering are beneficial for easy and efficient genetic manipulations for hosts as well as expression cassettes. The use of metabolic engineering and systems biology approaches have tremendous applications in recombinant protein production by generating mathematical models, and analyzing complex biological networks and metabolic pathways via simulations to understand the interconnections between metabolites and genetic behaviors. Further, the bioprocess developments and the optimization of cell culture conditions would enhance recombinant cytokines productivity on large scales.
PMID: 35525478
New Phytol , IF:10.151 , 2022 Jun doi: 10.1111/nph.18255
Trihelix transcription factors GTL1 and DF1 prevent aberrant root hair formation in an excess nutrient condition.
RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan.; Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan.; KU Leuven Plant Institute (LPI), KU Leuven, Kasteelpark Arenberg 31, Leuven, B-3001, Belgium.; Department of Biological Sciences, University of Tokyo, Tokyo, 119-0033, Japan.
Root hair growth is tuned in response to the environment surrounding plants. While most previous studies focused on the enhancement of root hair growth during nutrient starvation, few studies investigated the root hair response in the presence of excess nutrients. We report that the post-embryonic growth of wild-type Arabidopsis plants is strongly suppressed with increasing nutrient availability, particularly in the case of root hair growth. We further used gene expression profiling to analyze how excess nutrient availability affects root hair growth, and found that RHD6 subfamily genes, which are positive regulators of root hair growth, are downregulated in this condition. However, defects in GTL1 and DF1, which are negative regulators of root hair growth, cause frail and swollen root hairs to form when excess nutrients are supplied. Additionally, we observed that the RHD6 subfamily genes are mis-expressed in gtl1-1 df1-1. Furthermore, overexpression of RSL4, an RHD6 subfamily gene, induces swollen root hairs in the face of a nutrient overload, while mutation of RSL4 in gtl1-1 df1-1 restore root hair swelling phenotype. In conclusion, our data suggest that GTL1 and DF1 prevent unnecessary root hair formation by repressing RSL4 under excess nutrient conditions.
PMID: 35713645
Plant Biotechnol J , IF:9.803 , 2022 May doi: 10.1111/pbi.13833
Two high hierarchical regulators, PuMYB40 and PuWRKY75, control the low phosphorus driven adventitious root formation in Populus ussuriensis.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.; College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, China.; College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
Adventitious rooting is an essential biological process in the vegetative propagation of economically important horticultural and forest tree species. It enables utilization of the elite genotypes in breeding programmes and production. Promotion of adventitious root (AR) formation has been associated with starvation of inorganic phosphate and some factors involved in low phosphorus (LP) signalling. However, the regulatory mechanism underlying LP-mediated AR formation remains largely elusive. We established an efficient experimental system that guaranteed AR formation through short-term LP treatment in Populus ussuriensis. We then generated a time-course RNA-seq data set to recognize key regulatory genes and regulatory cascades positively regulating AR formation through data analysis and gene network construction, which were followed by experimental validation and characterization. We constructed a multilayered hierarchical gene regulatory network, from which PuMYB40, a typical R2R3-type MYB transcription factor (TF), and its interactive partner, PuWRKY75, as well as their direct targets, PuLRP1 and PuERF003, were identified to function upstream of the known adventitious rooting genes. These regulatory genes were functionally characterized and proved their roles in promoting AR formation in P. ussuriensis. In conclusion, our study unveiled a new hierarchical regulatory network that promoted AR formation in P. ussuriensis, which was activated by short-term LP stimulus and primarily governed by PuMYB40 and PuWRKY75.
PMID: 35514032
Environ Pollut , IF:8.071 , 2022 Aug , V307 : P119516 doi: 10.1016/j.envpol.2022.119516
Effects of soil protists on the antibiotic resistome under long term fertilization.
Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China.; Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China. Electronic address: dongzhu@rcees.ac.cn.; Key Laboratory for Humid Subtropical Ecogeographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China.; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871, Frederiksberg, Denmark; Sino-Danish Center for Education and Research, Beijing, China.; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
Soil protists are key in regulating soil microbial communities. However, our understanding on the role of soil protists in shaping antibiotic resistome is limited. Here, we considered the diversity and composition of bacteria, fungi and protists in arable soils collected from a long-term field experiment with multiple fertilization treatments. We explored the effects of soil protists on antibiotic resistome using high-throughput qPCR. Our results showed that long term fertilization had stronger effect on the composition of protists than those of bacteria and fungi. The detected number and relative abundance of antibiotic resistance genes (ARGs) were elevated in soils amended with organic fertilizer. Co-occurrence network analysis revealed that changes in protists may contribute to the changes in ARGs composition, and the application of different fertilizers altered the communities of protistan consumers, suggesting that effects of protistan communities on ARGs might be altered by the top-down impact on bacterial composition. This study demonstrates soil protists as promising agents in monitoring and regulating ecological risk of antibiotic resistome associated with organic fertilizers.
PMID: 35609845
Sci Total Environ , IF:7.963 , 2022 Sep , V838 (Pt 3) : P156426 doi: 10.1016/j.scitotenv.2022.156426
The combined effect of an integrated reclaimed water system on the reduction of antibiotic resistome.
Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing 100875, China.; Beijing BHZQ Environmental Engineering Technology Co., LTD, Beijing 100176, China.; Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing 100875, China. Electronic address: chen.haiyang@bnu.edu.cn.
The reuse of urban reclaimed water is conducive to alleviate the current serious shortage of water resources. However, antibiotic resistance genes (ARGs) in reclaimed water have received widespread attention due to their potential risks to public health. Deciphering the fate of ARGs in reclaimed water benefits the development of effective strategies to control resistome risk and guarantees the safety of water supply of reclaimed systems. In this study, the characteristics of ARGs in an integrated reclaimed water system (sewage treatment plant-constructed wetland, STP-CW) in Beijing (China) have been identified using metagenomic assembly-based analysis, as well as the combined effect of the STP-CW system on the reduction of antibiotic resistome. Results showed a total of 29 ARG types and 813 subtypes were found in the reclaimed water system. As expected, the STP-CW system improved the removal of ARGs, and about 58% of ARG subtypes were removed from the effluent of the integrated STP-CW system, which exceeded 43% for the STP system and 37% for the CW system. Although the STP-CW system had a great removal on ARGs, abundant and diverse ARGs were still found in the downstream river. Importantly, network analysis revealed the co-occurrence of ARGs, mobile genetic elements and virulence factors in the downstream water, implying potential resistome dissemination risk in the environment. Source identification with SourceTracker showed the STP-effluent was the largest contributor of ARGs in the downstream river, with a contribution of 45%. Overall, the integrated STP-CW system presented a combined effect on the reduction of antibiotic resistome, however, the resistome dissemination risk was still non-negligible in the downstream reclaimed water. This study provides a comprehensive analysis on the fate of ARGs in the STP-CW-river system, which would benefit the development of effective strategies to control resistome risk for the reuse of reclaimed water.
PMID: 35660592
Plant J , IF:6.417 , 2022 May doi: 10.1111/tpj.15838
CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice.
UMR DIADE, Universite de Montpellier, IRD, CIRAD, 911 Avenue Agropolis, 34394, Montpellier, France.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, CNRS, INRAE, INRIA, UCB Lyon 1, Lyon, 69007, France.; Agricultural Genetic Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE2, 11300, Hanoi, Vietnam.; CIRAD, UMR AGAP, F-34398, Montpellier, France.; Universite de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.; University of Science and Technology of Hanoi, LMIRICE2, Vietnam Academy of Science and Technology, 11300.; Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052, Ghent, Belgium.; VIB Center for Plant Systems Biology, 9052, Ghent, Belgium.; Palacky University Olomouc, Czech Advanced Technology and Research Institute, Centre of Region Hana for Biotechnological and Agricultural Research.; Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain-Centre de Recherche, Route d'Ennezat, Chappes, France.
In cereals, the root system is mainly composed of postembryonic shoot borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family is a key regulator of crown root initiation in rice. Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or a LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and a LBD -box in their promoter show that CRL1 binds preferentially the LBD-box in these promoter contexts. CRISPR-Cas9 targeted mutation of these two CRL1-regulated genes, that encode a plant Rho GTPase (OsROP) and a basic helix-loop-helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.
PMID: 35596715
Int J Mol Sci , IF:5.923 , 2022 May , V23 (11) doi: 10.3390/ijms23116192
Exosome Carrier Effects; Resistance to Digestion in Phagolysosomes May Assist Transfers to Targeted Cells; II Transfers of miRNAs Are Better Analyzed via Systems Approach as They Do Not Fit Conventional Reductionist Stoichiometric Concepts.
Section of Rheumatology, Allergy and Clinical Immunology, Department of Internal Medicine, School of Medicine, Yale University, 217 TAC Building South, 333 Cedar Street, New Haven, CT 06520, USA.
Carrier effects of extracellular vesicles (EV) like exosomes refer to properties of the vesicles that contribute to the transferred biologic effects of their contents to targeted cells. This can pertain to ingested small amounts of xenogeneic plant miRNAs and oral administration of immunosuppressive exosomes. The exosomes contribute carrier effects on transfers of miRNAs by contributing both to the delivery and the subsequent functional intracellular outcomes. This is in contrast to current quantitative canonical rules that dictate just the minimum copies of a miRNA for functional effects, and thus successful transfers, independent of the EV carrier effects. Thus, we argue here that transfers by non-canonical minute quantities of miRNAs must consider the EV carrier effects of functional low levels of exosome transferred miRNA that may not fit conventional reductionist stoichiometric concepts. Accordingly, we have examined traditional stoichiometry vs. systems biology that may be more appropriate for delivered exosome functional responses. Exosome carrier properties discussed include; their required surface activating interactions with targeted cells, potential alternate targets beyond mRNAs, like reaching a threshold, three dimensional aspects of the RNAs, added EV kinetic dynamic aspects making transfers four dimensional, and unique intracellular release from EV that resist intracellular digestion in phagolysosomes. Together these EV carrier considerations might allow systems analysis. This can then result in a more appropriate understanding of transferred exosome carrier-assisted functional transfers. A plea is made that the miRNA expert community, in collaboration with exosome experts, perform new experiments on molecular and quantitative miRNA functional effects in systems that include EVs, like variation in EV type and surface constituents, delivery, dose and time to hopefully create more appropriate and truly current canonical concepts of the consequent miRNA functional transfers by EVs like exosomes.
PMID: 35682875
Int J Mol Sci , IF:5.923 , 2022 May , V23 (11) doi: 10.3390/ijms23115983
Insights into the Transcriptional Reprogramming in Tomato Response to PSTVd Variants Using Network Approaches.
Centro de Investigacion y de Estudios Avanzados del I.P.N Unidad Irapuato, Irapuato 36821, Mexico.; Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.; Center for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London WC2R 2LS, UK.; Centro de Investigacion en Computacion, Instituto Politecnico Nacional, Mexico City 07738, Mexico.; USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA.
Viroids are the smallest pathogens of angiosperms, consisting of non-coding RNAs that cause severe diseases in agronomic crops. Symptoms associated with viroid infection are linked to developmental alterations due to genetic regulation. To understand the global mechanisms of host viroid response, we implemented network approaches to identify master transcription regulators and their differentially expressed targets in tomato infected with mild and severe variants of PSTVd. Our approach integrates root and leaf transcriptomic data, gene regulatory network analysis, and identification of affected biological processes. Our results reveal that specific bHLH, MYB, and ERF transcription factors regulate genes involved in molecular mechanisms underlying critical signaling pathways. Functional enrichment of regulons shows that bHLH-MTRs are linked to metabolism and plant defense, while MYB-MTRs are involved in signaling and hormone-related processes. Strikingly, a member of the bHLH-TF family has a specific potential role as a microprotein involved in the post-translational regulation of hormone signaling events. We found that ERF-MTRs are characteristic of severe symptoms, while ZNF-TF, tf3a-TF, BZIP-TFs, and NAC-TF act as unique MTRs. Altogether, our results lay a foundation for further research on the PSTVd and host genome interaction, providing evidence for identifying potential key genes that influence symptom development in tomato plants.
PMID: 35682662
J Fungi (Basel) , IF:5.816 , 2022 Jun , V8 (6) doi: 10.3390/jof8060631
Leaf-Associated Epiphytic Fungi of Gingko biloba, Pinus bungeana and Sabina chinensis Exhibit Delicate Seasonal Variations.
Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.; School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 102616, China.; State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Taipa 999078, Macao.; Xiongan Institute of Innovation, Baoding 071000, China.
Plant-leaf surface on Earth harbors complex microbial communities that influence plant productivity and health. To gain a detailed understanding of the assembly and key drivers of leaf microbial communities, especially for leaf-associated fungi, we investigated leaf-associated fungal communities in two seasons for three plant species at two sites by high-throughput sequencing. The results reveal a strong impact of growing season and plant species on fungal community composition, exhibiting clear temporal patterns in abundance and diversity. For the deciduous tree Gingko biloba, the number of enriched genera in May was much higher than that in October. The number of enriched genera in the two evergreen trees Pinus bungeana and Sabina chinensis was slightly higher in October than in May. Among the genus-level biomarkers, the abundances of Alternaria, Cladosporium and Filobasidium were significantly higher in October than in May in the three tree species. Additionally, network correlations between the leaf-associated fungi of G. biloba were more complex in May than those in October, containing extra negative associations, which was more obvious than the network correlation changes of leaf-associated fungi of the two evergreen plant species. Overall, the fungal diversity and community composition varied significantly between different growing seasons and host plant species.
PMID: 35736114
Front Plant Sci , IF:5.753 , 2022 , V13 : P915400 doi: 10.3389/fpls.2022.915400
Dynamic Transcriptome-Based Weighted Gene Co-expression Network Analysis Reveals Key Modules and Hub Genes Associated With the Structure and Nutrient Formation of Endosperm for Wax Corn.
Tobacco Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China.
The endosperm of corn kernel consists of two components, a horny endosperm, and a floury endosperm. In the experiment, a kind of floury endosperm corn was identified. The result of phenotypic trait analysis and determination of amino acid content showed that the floury endosperm filled with the small, loose, and scattered irregular spherical shape starch granules and contained higher content of amino acid. The starch biochemical properties are similar between floury corns and regular flint corn. By using dynamically comparative transcriptome analysis of endosperm at 20, 25, and 30 DAP, a total of 113.42 million raw reads and 50.508 thousand genes were obtained. By using the weighted gene co-expression network analysis, 806 genes and six modules were identified. And the turquoise module with 459 genes was proved to be the key module closely related to the floury endosperm formation. Nine zein genes in turquoise module, including two zein-alpha A20 (Zm00001d019155 and Zm00001d019156), two zein-alpha A30 (Zm00001d048849 and Zm00001d048850), one 50 kDa gamma-zein (Zm00001d020591), one 22 kDa alpha-zein 14 (Zm00001d048817), one zein-alpha 19D1 (Zm00001d030855), one zein-alpha 19B1 (Zm00001d048848), and one FLOURY 2 (Zm00001d048808) were identified closely related the floury endosperm formation. Both zein-alpha 19B1 (Zm00001d048848) and zein-alpha A30 (Zm00001d048850) function as source genes with the highest expression level in floury endosperm. These results may provide the supplementary molecular mechanism of structure and nutrient formation for the floury endosperm of maize.
PMID: 35755662
Front Plant Sci , IF:5.753 , 2022 , V13 : P876371 doi: 10.3389/fpls.2022.876371
Transcriptomic Analysis Reveals the Regulatory Networks and Hub Genes Controlling the Unsaturated Fatty Acid Contents of Developing Seed in Soybean.
School of Agriculture, Yunnan University, Kunming, China.; Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.
Soybean [Glycine max (L.) Merr.] is one of the most important crops, which produces about 25% of the world's edible oil. The nutritional value of soybean oil depends mostly on the relative contents of three unsaturated fatty acids (UFAs), i.e., oleic acid, linoleic acid (LA), and linolenic acid. However, the biosynthetic mechanism of UFAs remains largely unknown, and there are few studies on RNA-seq analysis of developing seeds. To identify the candidate genes and related pathways involved in the regulation of UFA contents during seed development in soybean, two soybean lines with different UFA profiles were selected from 314 cultivars and landraces originated from Southern China, and RNA-seq analysis was performed in soybean seeds at three developmental stages. Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, a series of genes and pathways related to fatty acid metabolism were identified, and 40 days after flowering (DAF) was found to be the crucial period in the formation of UFA profiles. Further, weighted gene co-expression network analysis identified three modules with six genes whose functions were highly associated with the contents of oleic and LA. The detailed functional investigation of the networks and hub genes could further improve the understanding of the underlying molecular mechanism of UFA contents and might provide some ideas for the improvement in fatty acids profiles in soybean.
PMID: 35646018
Front Plant Sci , IF:5.753 , 2022 , V13 : P848474 doi: 10.3389/fpls.2022.848474
The Construction and Exploration of a Comprehensive MicroRNA Centered Regulatory Network in Foxtail Millet (Setaria italica L.).
Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing, China.; College of Life Science, Shanghai Normal University, Shanghai, China.; College of Agricultural, Shanxi Agricultural University, Jinzhong, China.; Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Jinzhong, China.
MicroRNA (miRNA) is an essential endogenous post-transcriptional regulatory factor, and foxtail millet (Setaria italica L.) is an ideal C4 model cereal that is a highly valuable crop in semiarid and arid areas. The Research on comprehensive and high confidence identification and annotation of foxtail millet miRNAs needs to be strengthened, and to our knowledge, there is no information on the regulatory network of foxtail millet miRNA. In this study, 136 high confidence miRNAs were identified through high-throughput sequencing of the small RNAs in seven tissues at the shooting and grain filling stages of foxtail millet. A total of 2,417 target genes were obtained by combining computational biology software and degradome sequencing methods. Furthermore, an analysis using transcriptome sequencing revealed the relationships between miRNAs and their target genes and simultaneously explored key regulatory modules in panicles during the grain filling stage. An miRNA regulatory network was constructed to explore the functions of miRNA in more detail. This network, centered on miRNAs and combining upstream transcriptional factors and downstream target genes, is primarily composed of feed forward loop motifs, which greatly enhances our knowledge of the potential functions of miRNAs and uncovers numerous previously unknown regulatory links. This study provides a solid foundation for research on the function and regulatory network of miRNAs in foxtail millet.
PMID: 35599893
Front Plant Sci , IF:5.753 , 2022 , V13 : P852511 doi: 10.3389/fpls.2022.852511
Analysis of the Expression and Function of Key Genes in Pepper Under Low-Temperature Stress.
College of Horticulture, Hunan Agricultural University, Changsha, China.; Longping Branch, Graduate School of Hunan University, Changsha, China.; ERC for Germplasm Innovation and New Variety, Breeding of Horticultural Crops, Changsha, China.; Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China.
The mechanism of resistance of plants to cold temperatures is very complicated, and the molecular mechanism and related gene network in pepper are largely unknown. Here, during cold treatment, we used cluster analysis (k-means) to classify all expressed genes into 15 clusters, 3,680 and 2,405 differentially expressed genes (DEGs) were observed in the leaf and root, respectively. The DEGs associated with certain important basic metabolic processes, oxidoreductase activity, and overall membrane compositions were most significantly enriched. In addition, based on the homologous sequence alignment of Arabidopsis genes, we identified 14 positive and negative regulators of the ICE-CBF-COR module in pepper, including CBF and ICE, and compared their levels in different data sets. The correlation matrix constructed based on the expression patterns of whole pepper genes in leaves and roots after exposure to cold stress showed the correlation between 14 ICE-CBF-COR signaling module genes, and provided insight into the relationship between these genes in pepper. These findings not only provide valuable resources for research on cold tolerance, but also lay the foundation for the genetic modification of cold stress regulators, which would help us achieve improved crop tolerance. To our knowledge, this is the first study to demonstrate the relationship between positive and negative regulators related to the ICE-CBF-COR module, which is of great significance to the study of low-temperature adaptive mechanisms in plants.
PMID: 35599873
Front Microbiol , IF:5.64 , 2022 , V13 : P864619 doi: 10.3389/fmicb.2022.864619
Bacteria Community Inhabiting Heterobasidion Fruiting Body and Associated Wood of Different Decay Classes.
Department of Forest Sciences, University of Helsinki, Helsinki, Finland.; Natural Resources Institute of Finland (Luke), Helsinki, Finland.
The microbiome of Heterobasidion-induced wood decay of living trees has been previously studied; however, less is known about the bacteria biota of its perennial fruiting body and the adhering wood tissue. In this study, we investigated the bacteria biota of the Heterobasidion fruiting body and its adhering deadwood. Out of 7,462 operational taxonomic units (OTUs), about 5,918 OTUs were obtained from the fruiting body and 5,469 OTUs were obtained from the associated dead wood. Interestingly, an average of 52.6% of bacteria biota in the fruiting body was shared with the associated dead wood. The overall and unique OTUs had trends of decreasing from decay classes 1 to 3 but increasing in decay class 4. The fruiting body had the highest overall and unique OTUs number in the fourth decay class, whereas wood had the highest OTU in decay class 1. Sphingomonas spp. was significantly higher in the fruiting body, and phylum Firmicutes was more dominant in wood tissue. The FAPROTAX functional structure analysis revealed nutrition, energy, degradation, and plant-pathogen-related functions of the communities. Our results also showed that bacteria communities in both substrates experienced a process of a new community reconstruction through the various decay stages. The process was not synchronic in the two substrates, but the community structures and functions were well-differentiated in the final decay class. The bacteria community was highly dynamic; the microbiota activeness, community stability, and functions changed with the decay process. The third decay class was an important turning point for community restructuring. Host properties, environmental factors, and microbial interactions jointly influenced the final community structure. Bacteria community in the fruiting body attached to the living standing tree was suppressed compared with those associated with dead wood. Bacteria appear to spread from wood tissue of the standing living tree to the fruiting body, but after the tree is killed, bacteria moved from fruiting body to wood. It is most likely that some of the resident endophytic bacteria within the fruiting body are either parasitic, depending on it for their nutrition, or are mutualistic symbionts.
PMID: 35591994
Microbiol Res , IF:5.415 , 2022 Jun , V262 : P127084 doi: 10.1016/j.micres.2022.127084
Effect of the mineral-microbial complexes on the quality, soil nutrients, and microbial community of tailing substrates for growing potted Rorippa.
Key Laboratory of Ministry of Education on Safe Mining of Deep Metal Mines, Northeastern University, Shenyang 110819, PR China.; School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, PR China.; College of Architecture and Environment, Ningxia Institute of Science and Technology, Shizuishan 753000, PR China.; Institute for Frontier Technologies of Low-Carbon Steelmaking, Northeastern University, Shenyang 110819, PR China.; Key Laboratory of Ministry of Education on Safe Mining of Deep Metal Mines, Northeastern University, Shenyang 110819, PR China. Electronic address: hxmin_jj@163.com.
With China's industrialization and a rapidly developing coal industry, tailings have become one of the most widely distributed solid wastes, responsible for degrading available land and damaging the surrounding ecological environment. This study investigated the effect of adding mineral-microbial complexes to tailing substrates for the improvement of plant growth and substrate microbial community. The results revealed that compared with other treatments, the growth of Rorippa was considerably better after the addition of mineral-microbial complexes to the substrate, indicating that the mineral-microbial complexes promoted plant growth. After the addition of mineral-microbial complexes, the fertility indicators of the substrate showed a substantial improvement, in addition to the pH and organic matter (OM). The addition of fertilizers to the substrate plays a key role in plant growth, whereas the addition of microbial supplements to the substrate alone has little effect on plant growth. The results of high-throughput sequencing showed that the main microbial communities present in the substrate were Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Nitrospirae. The results of the microbial community alpha-diversity analysis showed that the addition of the mineral-microbial complexes improved the abundance and diversity of the substrate microbial community. Results of the microbial community beta-diversity analysis indicated that the experimental group showed a higher correlation with the microbial community relative to the background group. Network analysis revealed similar correlations between microbial communities and environmental factors, and total phosphorous (TP)-pH-available potassium (AK)-available nitrogen (AN) and TP-electronic conductivity (EC)-AK-AN were the main drivers of microbial communities in the background and experimental groups, respectively. The findings of this study provide a theoretical basis for the resource utilization of tailings and vegetation restoration using tailings.
PMID: 35690045
Front Genet , IF:4.599 , 2022 , V13 : P921096 doi: 10.3389/fgene.2022.921096
Genome-Wide Identification and Characterization of CPR5 Genes in Gossypium Reveals Their Potential Role in Trichome Development.
State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.; National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China.; Hainan Yazhou Bay Seed Laboratory, Sanya, China.; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
Trichomes protect plants against insects, microbes, herbivores, and abiotic damages and assist seed dispersal. The function of CPR5 genes have been found to be involved in the trichome development but the research on the underlying genetic and molecular mechanisms are extremely limited. Herein, genome wide identification and characterization of CPR5 genes was performed. In total, 26 CPR5 family members were identified in Gossypium species. Phylogenetic analysis, structural characteristics, and synteny analysis of CPR5s showed the conserved evolution relationships of CPR5. The promoter analysis of CPR5 genes revealed hormone, stress, and development-related cis-elements. Gene ontology (GO) enrichment analysis showed that the CPR5 genes were largely related to biological regulation, developmental process, multicellular organismal process. Protein-protein interaction analysis predicted several trichome development related proteins (SIM, LGO, and GRL) directly interacting with CPR5 genes. Further, nine putative Gossypium-miRNAs were also identified, targeting Gossypium CPR5 genes. RNA-Seq data of G. arboreum (with trichomes) and G. herbaceum (with no trichomes) was used to perform the co-expression network analysis. GheCPR5.1 was identified as a hub gene in a co-expression network analysis. RT-qPCR of GheCPR5.1 gene in different tissues suggests that this gene has higher expressions in the petiole and might be a key candidate involved in the trichome development. Virus induced gene silencing of GheCPR5.1 (Ghe02G17590) confirms its role in trichome development and elongation. Current results provide proofs of the possible role of CPR5 genes and provide preliminary information for further studies of GheCPR5.1 functions in trichome development.
PMID: 35754813
Genetics , IF:4.562 , 2022 May , V221 (2) doi: 10.1093/genetics/iyac056
An interolog-based barley interactome as an integration framework for immune signaling.
Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA 50011, USA.; Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA.; Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA.
The barley MLA nucleotide-binding leucine-rich-repeat (NLR) receptor and its orthologs confer recognition specificity to many fungal diseases, including powdery mildew, stem-, and stripe rust. We used interolog inference to construct a barley protein interactome (Hordeum vulgare predicted interactome, HvInt) comprising 66,133 edges and 7,181 nodes, as a foundation to explore signaling networks associated with MLA. HvInt was compared with the experimentally validated Arabidopsis interactome of 11,253 proteins and 73,960 interactions, verifying that the 2 networks share scale-free properties, including a power-law distribution and small-world network. Then, by successive layering of defense-specific "omics" datasets, HvInt was customized to model cellular response to powdery mildew infection. Integration of HvInt with expression quantitative trait loci (eQTL) enabled us to infer disease modules and responses associated with fungal penetration and haustorial development. Next, using HvInt and infection-time-course RNA sequencing of immune signaling mutants, we assembled resistant and susceptible subnetworks. The resulting differentially coexpressed (resistant - susceptible) interactome is essential to barley immunity, facilitates the flow of signaling pathways and is linked to mildew resistance locus a (Mla) through trans eQTL associations. Lastly, we anchored HvInt with new and previously identified interactors of the MLA coiled coli + nucleotide-binding domains and extended these to additional MLA alleles, orthologs, and NLR outgroups to predict receptor localization and conservation of signaling response. These results link genomic, transcriptomic, and physical interactions during MLA-specified immunity.
PMID: 35435213
Plant Dis , IF:4.438 , 2022 Jun : PPDIS09211974RE doi: 10.1094/PDIS-09-21-1974-RE
Differential Microbial Communities in Paddy Soils Between Guiyang Plateaus and Chengdu Basins Drive the Incidence of Rice Bacterial Diseases.
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.; Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China.
Southwest China has the most complex rice-growing regions in China. With great differences in topography, consisting mainly of basins and plateaus, ecological factors differ greatly between regions. In this study, bulk paddy soils collected from long-term rice fields in Chengdu (basins) and Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared >70% of the dominant genera (abundance >1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites, especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively correlated with the higher incidence of rice bacterial foot rot in Guiyang, whereas temperature had a greater effect on soil microbial functions and positively correlated with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.
PMID: 35021874
BMC Plant Biol , IF:4.215 , 2022 May , V22 (1) : P247 doi: 10.1186/s12870-022-03641-6
Systematic identification of miRNA-regulatory networks unveils their potential roles in sugarcane response to Sorghum mosaic virus infection.
Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.; Fuzhou Institute of Agricultural Sciences, Fuzhou, 350018, Fujian, China.; College of Agriculture, Yulin Normal University, Yulin, 537000, Guangxi,, China.; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. xlpmail@126.com.; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. queyouxiong@126.com.
BACKGROUND: Sugarcane mosaic disease (SMD) is a major viral disease of sugarcane (Saccharum spp.) worldwide. Sorghum mosaic virus (SrMV) is the dominant pathogen of SMD in the sugarcane planting areas of China. There is no report on miRNAs and their regulatory networks in sugarcane response to SrMV infection. RESULTS: In this study, small RNA sequencing (sRNA-seq) of samples from the leaves of SMD-susceptible variety ROC22 and -resistant variety FN39 infected by SrMV was performed. A total of 132 mature miRNAs (55 known miRNAs and 77 novel miRNAs) corresponding to 1,037 target genes were identified. After the SrMV attack, there were 30 differentially expressed miRNAs (17 up-regulated and 13 down-regulated) in FN39 and 19 in ROC22 (16 up-regulated and 3 down-regulated). Besides, there were 18 and 7 variety-specific differentially expressed miRNAs for FN39 and ROC22, respectively. KEGG enrichment analysis showed that the differentially expressed miRNAs targeted genes involved in several disease resistance-related pathways, such as mRNA surveillance, plant pathway interaction, sulfur metabolism, and regulation of autophagy. The reliability of sequencing data, and the expression patterns / regulation relationships between the selected differentially expressed miRNAs and their target genes in ROC22 and FN39 were confirmed by quantitative real-time PCR. A regulatory network diagram of differentially expressed miRNAs and their predicted target genes in sugarcane response to SrMV infection was sketched. In addition, precursor sequences of three candidate differentially expressed novel miRNAs (nov_3741, nov_22650 and nov_40875) were cloned from the ROC22 leaf infected by SrMV. Transient overexpression demonstrated that they could induce the accumulation of hydrogen peroxide and the expression level of hypersensitive response marker genes, salicylic acid-responsive genes and ethylene synthesis-depended genes in Nicotiana benthamiana. It is thus speculated that these three miRNAs may be involved in regulating the early immune response of sugarcane plants following SrMV infection. CONCLUSIONS: This study lays a foundation for revealing the miRNA regulation mechanism in the interaction of sugarcane and SrMV, and also provides a resource for miRNAs and their predicted target genes for SrMV resistance improvement in sugarcane.
PMID: 35585486
Phytopathology , IF:4.025 , 2022 May doi: 10.1094/PHYTO-02-22-0053-SYM
Why do plant pathogenic fungi produce mycotoxins? Potential roles for mycotoxins in the plant ecosystem.
USDA Agricultural Research Service, 17123, Food and Feed Safety Research Unit, Southern Regional Research Center, New Orleans, Louisiana, United States; rebecca.sweany@usda.gov.; Michigan State College of Agriculture and Applied Science, 3078, Department of Plant, Soil, and Microbial Sciences, East Lansing, Michigan, United States; mikaela.breunig@bayer.com.; USDA Agricultural Research Service, 17123, Pest Management and Biological Control Research Unit, US Arid-land Agricultural Research Center, Tucson, Arizona, United States; Joseph.Opoku@usda.gov.; Tulane University, 5783, Department of Ecology and Evolutionary Biology, New Orleans, Louisiana, United States; clay@tulane.edu.; Oregon State University, 2694, Botany and Plant Pathology, Corvallis, Oregon, United States; joseph.spatafora@oregonstate.edu.; University of Wisconsin-Madison, 5228, Department of Medical Microbiology and Immunology, Madison, Wisconsin, United States; mdrott@wisc.edu.; North Dakota State University, 3323, Department of Plant Pathology, Fargo, North Dakota, United States; thomas.t.baldwin@ndsu.edu.; Mississippi State University, 5547, Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Starkville, Mississippi, United States; jcf416@msstate.edu.
For many plant pathogenic or endophytic fungi, production of mycotoxins, which are toxic to humans, may present a fitness gain. However, associations between mycotoxin production and plant pathogenicity or virulence is inconsistent and difficult due to the complexity of these host-pathogen interactions and the influences of environmental and insect factors. Aflatoxin receives a lot of attention due to its potent toxicity and carcinogenicity, but the connection between aflatoxin production and pathogenicity is complicated by the pathogenic ability and prevalence of n on-aflatoxigenic isolates in crops. Other toxins directly aid fungi in planta, trichothecenes are important virulence factors and ergot alkaloids limit herbivory and fungal consumption due to insect toxicity. We review a panel discussion at Amercian Phytopathological Society's Plant Health 2021 conference, which gathered diverse experts representing different research sectors, career stages, ethnicities and genders to discuss the diverse roles of mycotoxins in the lifestyles of filamentous fungi of the families: Clavicipitaceae, Trichocomaceae (Eurotiales), Nectriaceae (Hypocreales).
PMID: 35502928
Plants (Basel) , IF:3.935 , 2022 May , V11 (10) doi: 10.3390/plants11101344
Secondary Succession Altered the Diversity and Co-Occurrence Networks of the Soil Bacterial Communities in Tropical Lowland Rainforests.
Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing 100102, China.; National Positioning and Monitoring Station for Ecosystem of Bamboo and Rattan, Sanya 572000, China.; Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100089, China.; Shaanxi Academy of Forestry, Xi'an 710082, China.
The characteristics of plant and soil bacterial communities in forest ecosystems have been reported, but our understanding of the relationship between plant communities and soil bacteria in different stages of secondary tropical rainforest succession is still poor. In June 2018, three different natural successional stages of tropical lowland rainforests, early (33 years), early-mid (60 years), and mid successional stage (73 years), in Hainan Island, China, were selected for this study. By conducting field investigation and 16S rRNA gene high-throughput sequencing, the composition and diversity of tree communities, the niche overlap of tree species with legumes among tree species, and the diversity and composition of soil bacterial communities and co-occurrence networks within communities across the successional stages were investigated. The results showed that plant richness and species diversity increased significantly during the secondary succession of tropical lowland rainforests. The order of positive correlations between nitrogen-fixing legumes and other species in plant communities was early-mid > mid > early successional stage. Soil nutrient content and soil bacterial richness were highest in the early-mid stages of succession, followed by mid and early stages of succession. Organic matter (OM), total nitrogen (TN), alkali nitrogen (AN), and available phosphorus (AP) had a stronger positive impact on soil bacterial communities. Co-occurrence network analysis showed that with the advancement of rainforests succession, the negative correlation between soil bacterial species decreased, and the community stability increased. Overall, as a result of tropical lowland rainforest secondary natural succession, the richness and diversity of plant communities increased, which altered the living conditions of nitrogen-fixing legumes and the soil properties, and the network complexity of soil bacterial communities increased with the rising of rainforest soil nutrient content.
PMID: 35631769
BMC Bioinformatics , IF:3.169 , 2022 May , V23 (1) : P165 doi: 10.1186/s12859-022-04696-w
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique.
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. zhangxj@wbgcas.cn.; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China. zhangxj@wbgcas.cn.
BACKGROUND: Current gene regulatory network (GRN) inference methods are notorious for a great number of indirect interactions hidden in the predictions. Filtering out the indirect interactions from direct ones remains an important challenge in the reconstruction of GRNs. To address this issue, we developed a redundancy silencing and network enhancement technique (RSNET) for inferring GRNs. RESULTS: To assess the performance of RSNET method, we implemented the experiments on several gold-standard networks by using simulation study, DREAM challenge dataset and Escherichia coli network. The results show that RSNET method performed better than the compared methods in sensitivity and accuracy. As a case of study, we used RSNET to construct functional GRN for apple fruit ripening from gene expression data. CONCLUSIONS: In the proposed method, the redundant interactions including weak and indirect connections are silenced by recursive optimization adaptively, and the highly dependent nodes are constrained in the model to keep the real interactions. This study provides a useful tool for inferring clean networks.
PMID: 35524190
3 Biotech , IF:2.406 , 2022 Jun , V12 (6) : P127 doi: 10.1007/s13205-022-03182-7
Identification of major candidate genes for multiple abiotic stress tolerance at seedling stage by network analysis and their validation by expression profiling in rice (Oryza sativa L.).
ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012 India.grid.418105.90000 0001 0643 7375; Department of Botany, National College, Tiruchirapalli, Tamil Nadu 620001 India.; Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India.grid.418196.30000 0001 2172 0814; Tamil Nadu Agricultural University, Coimbatore, India.grid.412906.80000 0001 2155 9899
A wealth of microarray and RNA-seq data for studying abiotic stress tolerance in rice exists but only limited studies have been carried out on multiple stress-tolerance responses and mechanisms. In this study, we identified 6657 abiotic stress-responsive genes pertaining to drought, salinity and heat stresses from the seedling stage microarray data of 83 samples and used them to perform unweighted network analysis and to identify key hub genes or master regulators for multiple abiotic stress tolerance. Of the total 55 modules identified from the analysis, the top 10 modules with 8-61 nodes comprised 239 genes. From these 10 modules, 10 genes common to all the three stresses were selected. Further, based on the centrality properties and highly dense interactions, we identified 7 intra-modular hub genes leading to a total of 17 potential candidate genes. Out of these 17 genes, 15 were validated by expression analysis using a panel of 4 test genotypes and a pair of standard check genotypes for each abiotic stress response. Interestingly, all the 15 genes showed upregulation under all stresses and in all the genotypes, suggesting that they could be representing some of the core abiotic stress-responsive genes. More pertinently, eight of the genes were found to be co-localized with the stress-tolerance QTL regions. Thus, in conclusion, our study not only provided an effective approach for studying abiotic stress tolerance in rice, but also identified major candidate genes which could be further validated by functional genomics for abiotic stress tolerance. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03182-7.
PMID: 35573803
J Comput Biol , IF:1.479 , 2022 May doi: 10.1089/cmb.2021.0600
Extracting Information from Gene Coexpression Networks of Rhizobium leguminosarum.
Department of Statistics, University of Oxford, Oxford, United Kingdom.; Department of Plant Sciences, University of Oxford, Oxford, United Kingdom.; Department of the Mathematical Institute, University of Oxford, Oxford, United Kingdom.
Nitrogen uptake in legumes is facilitated by bacteria such as Rhizobium leguminosarum. For this bacterium, gene expression data are available, but functional gene annotation is less well developed than for other model organisms. More annotations could lead to a better understanding of the pathways for growth, plant colonization, and nitrogen fixation in R. leguminosarum. In this study, we present a pipeline that combines novel scores from gene coexpression network analysis in a principled way to identify the genes that are associated with certain growth conditions or highly coexpressed with a predefined set of genes of interest. This association may lead to putative functional annotation or to a prioritized list of genes for further study.
PMID: 35588362
Clin Nutr ESPEN , 2022 Jun , V49 : P425-435 doi: 10.1016/j.clnesp.2022.03.010
Attenuation of low-grade chronic inflammation by phytonutrients: A computational systems biology analysis.
Systems Biology Group, CytoSolve Research Division, CytoSolve, Inc., Cambridge, MA, USA. Electronic address: vashiva@cytosolve.com.; Systems Biology Group, CytoSolve Research Division, CytoSolve, Inc., Cambridge, MA, USA.; Center for Treatment Comparison and Integrative Analysis (CTCIA), Division of Rheumatology, Tufts Medical Center, Boston, MA, USA.
BACKGROUND: Low-grade chronic inflammation (LGCI) is a strong and independent risk factor for many chronic diseases, like cardiovascular, musculoskeletal, metabolic, and neurological conditions. Dietary intervention studies have reported evidence for the role of plant-derived flavonoids in modulation of LGCI. This research explores the efficacy of Fruit/Berry/Vegetable (FBV) juice powder on LGCI. METHODS: The study employs computational systems biology: 1) to identify biomolecular mechanisms of LGCI; 2) to identify the bioactive compounds of FBV juice powder and their specific effects on mechanisms of LGCI; and, 3) to predict the quantitative effects of those bioactive compounds on LGCI. RESULTS: Four molecular pathways that are affected by the compounds of FBV include: 1) TNF-alpha production; 2) CCL2 production; 3) IL-1beta production; and 4) reactive oxygen species production. The bioactive compounds including luteolin, epicatechin, epigallocatechin gallate, lycopene, quercetin, vitamin A, vitamin C and vitamin E in FBV significantly lowered TNF-alpha production, CCL2 production, IL-1beta production, and reactive oxygen species production. CONCLUSION: FBV provides a combination of active ingredients that synergistically affect multiple modalities of low grade chronic inflammation to help improve blood circulation and energy levels, and lower muscle soreness.
PMID: 35623848
Soil Biol Biochem , 2022 Jun , V169 : P108604 doi: 10.1016/j.soilbio.2022.108604
From diversity to complexity: Microbial networks in soils.
Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.; Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.; Centro de Investigaciones sobre Desertificacion (CIDE, CSIC-UV-GV), Carretera de Moncada-Naquera Km 4.5, 46113, Moncada, Valencia, Spain.
Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research. Analysing microbial networks in soils opens a window to a better understanding of the complexity of microbial communities. However, this approach is unfortunately often used to draw conclusions which are far beyond the scientific evidence it can provide, which has damaged its reputation for soil microbial analysis. In this Perspectives Paper, we would like to sharpen the view for the real potential of microbial co-occurrence analysis in soils, and at the same time raise awareness regarding its limitations and the many ways how it can be misused or misinterpreted.
PMID: 35712047
Energy Nexus , 2022 Jun , V6 : P100080 doi: 10.1016/j.nexus.2022.100080
Plant-Based Natural Bioactive Compounds 2,4-Ditert-Butylphenolas: A Potential Candidates Against SARS-Cov-2019.
Department of Botany, Periyar University, Periyar Palkalai Nagar, Salem 636011, Tamil Nadu, India.; Department of Plant Biology and Plant Biotechnology, Guru Nanak College (Autonomous) Chennai 600 042.; Department of Biotechnology, Rathinam College of Arts and Science(Autonomous), Coimbatore 641021, Tamil Nadu, India.; Department of Botany, Thiru Kolanjiyapper Government Arts College, Virudhachalam, Cuddalore 606001, Tamil Nadu, India.; Department of Biotechnology, St Joseph's College (Arts & Science), Kovur, Chennai, Tamil Nadu, India.; Department of Botany, Shri Sakthikailassh Women's college, Salem 636003, Tamil Nadu, India.
The novel coronavirus 2019 is spreading around the world and causing serious concern. However, there is limited information about novel coronavirus that hinders the design of effective drug. Bioactive compounds are rich source of chemo preventive ingredients. In our present research focuses on identifying and recognizing bioactive chemicals in Lantana camara, by evaluating their potential toward new coronaviruses and confirming the findings using molecular docking, ADMET, network analysis and dynamics investigations.. The spike protein receptor binding domain were docked with 25 identified compounds and 2,4-Ditertbutyl-phenol (-6.3kcal/mol) shows highest docking score, its interactions enhances the increase in binding and helps to identify the biological activity. The ADME/toxicity result shows that all the tested compounds can serve as inhibitors of the enzymes CYP1A2 and CYP2D6. In addition, Molecular dynamics simulations studies with reference inhibitors were carried out to test the stability. This study identifies the possible active molecules against the receptor binding domain of spike protein, which can be further exploited for the treatment of novel coronavirus 2019. The results of the toxicity risk for phytocompounds and their active derivatives showed a moderate to good drug score.
PMID: 35578668