Publications by authors named "Baohong Zhang"

229 Publications

Quickomics: exploring omics data in an intuitive, interactive and informative manner.

Bioinformatics 2021 Apr 26. Epub 2021 Apr 26.

Biogen Inc., Cambridge, Massachusetts, USA.

Summary: We developed Quickomics, a feature-rich R Shiny-powered tool to enable biologists to fully explore complex omics statistical analysis results and perform advanced analysis in an easy-to-use interactive interface. It covers a broad range of secondary and tertiary analytical tasks after primary analysis of omics data is completed. Each functional module is equipped with customizable options and generates both interactive and publication-ready plots to uncover biological insights from data. The modular design makes the tool extensible with ease.

Availability: Researchers can experience the functionalities with their own data or demo RNA-Seq and proteomics datasets by using the app hosted at http://quickomics.bxgenomics.com and following the tutorial, https://bit.ly/3rXIyhL. The source code under GPLv3 license is provided at https://github.com/interactivereport/Quickomics for local installation.

Supplementary Information: Supplementary materials are available at https://bit.ly/37HP17g.
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http://dx.doi.org/10.1093/bioinformatics/btab255DOI Listing
April 2021

Genetic variation in the Mauritian cynomolgus macaque population reflects variation in the human population.

Gene 2021 Jun 20;787:145648. Epub 2021 Apr 20.

Preclinical Safety, Research and Development, Sanofi-Aventis US, LLC, Framingham, MA, USA. Electronic address:

The cynomolgus macaque is an important species for preclinical research, however the extent of genetic variation in this population and its similarity to the human population is not well understood. Exome sequencing was conducted for 101 cynomolgus macaques to characterize genetic variation. The variant distribution frequency was 7.81 variants per kilobase across the sequenced regions, with a total of 2,770,009 single nucleotide variants identified from 2,996,041 loci. A large portion (85.6%) had minor allele frequencies greater than 5%. Enriched pathways for genes with high genetic diversity (≥10 variants per kilobase) were those involving signaling peptides and immune response. Compared to human, the variant distribution frequency and nucleotide diversity in the macaque exome was approximately 4 times greater; however the ratio of non-synonymous to synonymous variants was similar (0.735 and 0.831, respectively). Understanding genetic variability in cynomolgus macaques will enable better interpretation and human translation of phenotypic variability in this species.
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http://dx.doi.org/10.1016/j.gene.2021.145648DOI Listing
June 2021

CRISPR/Cas: A powerful tool for gene function study and crop improvement.

J Adv Res 2021 03 21;29:207-221. Epub 2020 Oct 21.

Department of Biology, East Carolina University, Greenville, NC 27858, USA.

Background: It is a long-standing goal of scientists and breeders to precisely control a gene for studying its function as well as improving crop yield, quality, and tolerance to various environmental stresses. The discovery and modification of CRISPR/Cas system, a nature-occurred gene editing tool, opens an era for studying gene function and precision crop breeding.

Aim Of Review: In this review, we first introduce the brief history of CRISPR/Cas discovery followed the mechanism and application of CRISPR/Cas system on gene function study and crop improvement. Currently, CRISPR/Cas genome editing has been becoming a mature cutting-edge biotechnological tool for crop improvement that already used in many different traits in crops, including pathogen resistance, abiotic tolerance, plant development and morphology and even secondary metabolism and fiber development. Finally, we point out the major issues associating with CRISPR/Cas system and the future research directions. CRISPR/Cas9 system is a robust and powerful biotechnological tool for targeting an individual DNA and RNA sequence in the genome. It can be used to target a sequence for gene knockin, knockout and replacement as well as monitoring and regulating gene expression at the genome and epigenome levels by binding a specific sequence. -mediated method is still the major and efficient method for delivering CRISPR/Cas regents into targeted plant cells. However, other delivery methods, such as virus-mediated method, have been developed and enhanced the application potentials of CRISPR/Cas9-based crop improvement. PAM requirement offers the CRISPR/Cas9-targted genetic loci and also limits the application of CRISPR/Cas9. Discovering new Cas proteins and modifying current Cas enzymes play an important role in CRISPR/Cas9-based genome editing. Developing a better CRISPR/Cas9 system, including the delivery system and the methods eliminating off-target effects, and finding key/master genes for controlling crop growth and development is two major directions for CRISPR/Cas9-based crop improvement.
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http://dx.doi.org/10.1016/j.jare.2020.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8020163PMC
March 2021

CRISPR/Cas: a Nobel Prize award-winning precise genome editing technology for gene therapy and crop improvement.

J Zhejiang Univ Sci B 2021 Apr;22(4):253-284

Department of Biology, East Carolina University, Greenville, NC 27858, USA.

Since it was first recognized in bacteria and archaea as a mechanism for innate viral immunity in the early 2010s, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) has rapidly been developed into a robust, multifunctional genome editing tool with many uses. Following the discovery of the initial CRISPR/Cas-based system, the technology has been advanced to facilitate a multitude of different functions. These include development as a base editor, prime editor, epigenetic editor, and CRISPR interference (CRISPRi) and CRISPR activator (CRISPRa) gene regulators. It can also be used for chromatin and RNA targeting and imaging. Its applications have proved revolutionary across numerous biological fields, especially in biomedical and agricultural improvement. As a diagnostic tool, CRISPR has been developed to aid the detection and screening of both human and plant diseases, and has even been applied during the current coronavirus disease 2019 (COVID-19) pandemic. CRISPR/Cas is also being trialed as a new form of gene therapy for treating various human diseases, including cancers, and has aided drug development. In terms of agricultural breeding, precise targeting of biological pathways via CRISPR/Cas has been key to regulating molecular biosynthesis and allowing modification of proteins, starch, oil, and other functional components for crop improvement. Adding to this, CRISPR/Cas has been shown capable of significantly enhancing both plant tolerance to environmental stresses and overall crop yield via the targeting of various agronomically important gene regulators. Looking to the future, increasing the efficiency and precision of CRISPR/Cas delivery systems and limiting off-target activity are two major challenges for wider application of the technology. This review provides an in-depth overview of current CRISPR development, including the advantages and disadvantages of the technology, recent applications, and future considerations.
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http://dx.doi.org/10.1631/jzus.B2100009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042526PMC
April 2021

Subcritical Water Extraction of .

Molecules 2021 Mar 15;26(6). Epub 2021 Mar 15.

Department of Chemistry, East Carolina University, Greenville, NC 27858, USA.

In this work, a green extraction technique, subcritical water extraction (SBWE), was employed to extract active pharmaceutical ingredients (APIs) from an important Chinese medicinal herb, (danshen), at various temperatures. The APIs included tanshinone I, tanshinone IIA, protocatechualdehyde, caffeic acid, and ferulic acid. Traditional herbal decoction (THD) of was also carried out for comparison purposes. Reproduction assay of herbal extracts obtained by both SBWE and THD were then conducted on so that SBWE conditions could be optimized for the purpose of developing efficacious herbal medicine from The extraction efficiency was mostly enhanced with increasing extraction temperature. The quantity of tanshinone I in the herbal extract obtained by SBWE at 150 °C was 370-fold higher than that achieved by THD extraction. Reproduction evaluation revealed that the worm reproduction rate decreased and the reproduction inhibition rate increased with elevated SBWE temperatures. Most importantly, the reproduction inhibition rate of the SBWE herbal extracts obtained at all four temperatures investigated was higher than that of traditional herbal decoction extracts. The results of this work show that there are several benefits of subcritical water extraction of medicinal herbs over other existing herbal medicine preparation techniques. Compared to THD, the thousand-year-old and yet still popular herbal preparation method used in herbal medicine, subcritical water extraction is conducted in a closed system where no loss of volatile active pharmaceutical ingredients occurs, although analyte degradation may happen at higher temperatures. Temperature optimization in SBWE makes it possible to be more efficient in extracting APIs from medicinal herbs than the THD method. Compared to other industrial processes of producing herbal medicine, subcritical water extraction eliminates toxic organic solvents. Thus, subcritical water extraction is not only environmentally friendly but also produces safer herbal medicine for patients.
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http://dx.doi.org/10.3390/molecules26061634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8001979PMC
March 2021

Small RNA and degradome deep sequencing reveals important roles of microRNAs in cotton (Gossypium hirsutum L.) response to root-knot nematode Meloidogyne incognita infection.

Genomics 2021 Mar 3;113(3):1146-1156. Epub 2021 Mar 3.

Department of Biology, East Carolina University, Greenville, NC 27858, USA. Electronic address:

Investigation of cotton response to nematode infection will allow us to better understand the cotton immune defense mechanism and design a better biotechnological approach for efficiently managing pest nematodes in cotton. In this study, we firstly treated cotton by root knot nematode (RKN, Meloidogyne incognita) infections, then we employed the high throughput deep sequencing technology to sequence and genome-widely identify all miRNAs in cotton; finally, we analyzed the functions of these miRNAs in cotton response to RKN infections. A total of 266 miRNAs, including 193 known and 73 novel miRNAs, were identified by deep sequencing technology, which belong to 67 conserved and 66 novel miRNA families, respectively. A majority of identified miRNA families only contain one miRNA; however, miR482 family contains 14 members and some others contain 2-13 members. Certain miRNAs were specifically expressed in RKN-infected cotton roots and others were completely inhibited by RKN infection. A total of 50 miRNAs were differentially expressed after RKN infection, in which 28 miRNAs were up-regulated and 22 were inhibited by RKN treatment. Based on degradome sequencing, 87 gene targets were identified to be targeted by 57 miRNAs. These miRNA-targeted genes are involved in the interaction of cotton plants and nematode infection. Based on GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, 466 genes from all 636 miRNA targets were mapped to 6340 GO terms, 181 genes from 228 targets of differentially expressed miRNAs were mapped to 1588 GO terms. The GO terms were then categorized into the three main GO classes: biological processes, cellular components, and molecular functions. The targets of differentially expressed miRNAs were enriched in 43 GO terms, including 22 biological processes, 10 cellular components, and 11 molecular functions (p < 0.05). Many identified processes were associated with organism responses to the environmental stresses, including regulation of nematode larval development, response to nematode, and response to flooding. Our results will enhance the study and application of developing new cotton cultivars for nematode resistance.
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http://dx.doi.org/10.1016/j.ygeno.2021.02.018DOI Listing
March 2021

Contribution of a European-Prevalent Variant near CD83 and an East Asian-Prevalent Variant near IL17RB to Herpes Zoster Risk in Tofacitinib Treatment: Results of Genome-Wide Association Study Meta-Analyses.

Arthritis Rheumatol 2021 Jan 17. Epub 2021 Jan 17.

Pfizer Inc, Cambridge, Massachusetts, USA.

Objective: Tofacitinib is an oral Janus kinase inhibitor for the treatment of rheumatoid arthritis (RA), psoriatic arthritis, and ulcerative colitis, and has been previously investigated for psoriasis (PsO). Genome-wide association studies (GWAS) were performed to identify genetic factors associated with increased risk/faster onset of herpes zoster (HZ) upon tofacitinib treatment, and potential mechanisms of the varying HZ rate across ethnicities.

Methods: In an ethnicity-/indication-specific and trans-ethnic trans-indication meta-analysis of GWAS in subjects from RA and PsO phase II, III, and long-term extension tofacitinib studies, 8 million genetic variants on time to HZ and HZ event (case versus control) were evaluated via Cox and logistic regression, respectively.

Results: 5,246 subjects were included (RA: 3,168; PsO: 2,078). Adjusting for age, baseline absolute lymphocyte count, genetically-defined ethnicity, and concomitant methotrexate use (RA only), 4 loci were significantly associated with faster HZ onset in Europeans (P < 5×10 ), including a single-nucleotide polymorphism (SNP) near CD83 (risk allele in Europeans ~2%, East Asian ~0.1%). In the trans-ethnic trans-population meta-analysis, the CD83 SNP remained significant, and 4 additional significant loci were identified, among which a SNP near IL17RB was associated with faster HZ onset (meta-analysis hazard ratio [95% confidence interval] 3.6 [2.40, 5.44], P = 7.6×10 ; risk allele in East Asian subjects ~12%, European subjects <0.2%).

Conclusion: Genetic analysis of tofacitinib-treated RA and PsO subjects identified multiple loci associated with increased HZ risk. European or East Asian population-specific prevalent variants near immune-relevant genes of CD83 and IL17RB, respectively, may contribute to HZ risk in tofacitinib-treated subjects.
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http://dx.doi.org/10.1002/art.41655DOI Listing
January 2021

Metabolite Profile of Xylem Sap in Cotton Seedlings Is Changed by K Deficiency.

Front Plant Sci 2020 10;11:592591. Epub 2020 Dec 10.

Department of Biology, East Carolina University, Greenville, NC, United States.

Xylem sap, belonging to the plant apoplast, not only provides plant tissues with inorganic and organic substances but also facilitates communication between the roots and the leaves and coordinates their development. This study investigated the effects of potassium (K) deficiency on the morphology and the physiology of cotton seedlings as well as pH, mineral nutrient contents, and metabolites of xylem sap. In particular, we compared changes in root-shoot communication under low K (LK) and normal K (NK, control) levels. Compared to control, LK stress significantly decreased seedling biomass (leaf, stem, and root dry weight; stem and root length; root surface area and root volume) and the levels of K, Na (sodium), Mg (magnesium), Fe (iron), and Zn (zinc) in xylem sap. A total of 82 metabolites in sap analyzed by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) showed significant differences between the two conditions; among these, 38 were up-regulated more than 2-fold, while the others were down-regulated less than 0.5-fold. In particular, several metabolites found in the cell membrane including three cholines (glycerophosphatecholine, 2-hexenylcholine, and caproylcholine) and desglucocoroloside and others such as malondialdehyde, α-amino acids and derivatives, sucrose, and sugar alcohol significantly increased under LK stress, indicating that cell membranes were damaged and protein metabolism was abnormal. It is worth noting that glycerophosphocholine was up-regulated 29-fold under LK stress, indicating that it can be used as an important signal of root-shoot communication. Furthermore, in pathway analyses, 26 metabolites were matched to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways; L-aspartic acid, which was associated with 10 KEGG pathways, was the most involved metabolite. Overall, K deficiency reduced the antioxidant capacity of cotton seedlings and led to a metabolic disorder including elevated levels of primary metabolites and inhibited production of secondary metabolites. This eventually resulted in decreased biomass of cotton seedlings under LK stress. This study lays a solid foundation for further research on targeted metabolites and signal substances in the xylem sap of cotton plants exposed to K deficiency.
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http://dx.doi.org/10.3389/fpls.2020.592591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758293PMC
December 2020

Reference gene selection for miRNA and mRNA normalization in potato in response to potato virus Y.

Mol Cell Probes 2021 02 25;55:101691. Epub 2020 Dec 25.

Plant Breeding and Acclimatization Institute, National Research Institute, Młochów Research Center, Platanowa 19, Młochów, PL-05-831, Poland.

This was the first report on evaluating candidate reference genes for quantifying the expression profiles of both coding (e.g., mRNA) and non-coding (e.g., miRNA) genes in potato response to potato virus Y (PVY) inoculation. The reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) method was employed to quantify the expression profiles of eight selected candidate reference genes; their expression stability was analyzed by four statistical algorithms, i.e., geNorm, BestKeeper, NormFinder and RefFinder. The most stable reference genes were sEF1a, sTUBb and seIF5 with a high stability. The least stable ones were sPP2A, sSUI1 and sGAPDH. The same reference gene allows for normalization of both miRNA and mRNA levels from a single RNA sample using cDNAs synthesized in a single RT reaction, in which a stem-loop primer was used for miRNAs and the oligo (dT) for mRNAs.
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http://dx.doi.org/10.1016/j.mcp.2020.101691DOI Listing
February 2021

Foxtail Millet: A New Model for C4 Plants.

Trends Plant Sci 2021 03 21;26(3):199-201. Epub 2020 Dec 21.

Department of Biology, East Carolina University, Greenville, NC 27858, USA. Electronic address:

Arabidopsis and rice are major models for C3 plants, but we still lack a model for C4 plants. Recently, Yang and coworkers developed foxtail millet as a C4 plant model; with the rapid development of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas technology, this will open a new era for plant functional studies and crop improvement.
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http://dx.doi.org/10.1016/j.tplants.2020.12.003DOI Listing
March 2021

CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines.

PLoS Comput Biol 2020 12 22;16(12):e1008498. Epub 2020 Dec 22.

Biogen Inc., Cambridge, Massachusetts, United States of America.

Chinese hamster ovary (CHO) cell lines are widely used in industry for biological drug production. During cell culture development, considerable effort is invested to understand the factors that greatly impact cell growth, specific productivity and product qualities of the biotherapeutics. While high-throughput omics approaches have been increasingly utilized to reveal cellular mechanisms associated with cell line phenotypes and guide process optimization, comprehensive omics data analysis and management have been a challenge. Here we developed CHOmics, a web-based tool for integrative analysis of CHO cell line omics data that provides an interactive visualization of omics analysis outputs and efficient data management. CHOmics has a built-in comprehensive pipeline for RNA sequencing data processing and multi-layer statistical modules to explore relevant genes or pathways. Moreover, advanced functionalities were provided to enable users to customize their analysis and visualize the output systematically and interactively. The tool was also designed with the flexibility to accommodate other types of omics data and thereby enabling multi-omics comparison and visualization at both gene and pathway levels. Collectively, CHOmics is an integrative platform for data analysis, visualization and management with expectations to promote the broader use of omics in CHO cell research.
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http://dx.doi.org/10.1371/journal.pcbi.1008498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7790544PMC
December 2020

siRNA Blocks Proliferation in Pancreatic Cancer Cells by Inhibiting DNA Replication and Inducing G1 Arrest and Apoptosis.

Front Oncol 2020 8;10:1730. Epub 2020 Sep 8.

Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.

Background: Our previous study showed that the ribosomal protein L21 (RPL21) may play an important role in the development and survival of pancreatic cancer. In this article, RNA interference (RNAi) experiments were performed with RPL21-specific small interfering RNA (siRNA) to elucidate the mechanism by which RPL21 controls PC PANC-1 and BxPC-3 cell proliferation.

Methods: In the present study, PANC-1, BxPC-3 cells, and BALB/c nude mice were used to investigate antitumor effect and mechanism by which controls cell proliferation and apoptosis and . The effects of knockdown on PANC-1 and BxPC-3 cell proliferation, cell cycle and cell apoptosis were determined using 3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide assays and flow cytometry assay. The mechanism of regulating cell proliferation was investigated using transcriptome sequencing analysis and luciferase reporter assay. The effects of knockdown on PANC-1 and BxPC-3 cell proliferation were determined using BALB/c nude mice tumor model.

Results: In PANC-1 and BxPC-3 cells, the knockdown of RPL21 expression with corresponding siRNA suppressed cell proliferation and , inhibited DNA replication, and induced arrests in the G1 phase of the cell cycle. Further results showed that the mini-chromosome maintenance (MCM) protein family (MCM2-7), CCND1 and CCNE1 were down-regulated significantly in PANC-1 and BxPC-3 cells after transfected with RPL21 siRNA, which suggests that the suppression of DNA replication is due to the reduced expression of MCM2-7 family, and the induction of G1 arrest is correlated with the inhibition of CCND1 and CCNE1. Luciferase reporter assay showed that RPL21 controls the DNA replication and G1-S phase progression possibly through the regulation of E2F1 transcription factor in PC cells. Moreover, RPL21 siRNA showed an apoptosis-inducing effect only in BxPC-3 and PANC-1 cells but not in normal HPDE6-C7 cells. The increase of caspase-8 activities and the loss of mitochondrial membrane potential after RPL21 silencing indicates that the RPL21 gene may be involved in caspase-8-related mitochondrial apoptosis.

Conclusion: Our findings suggest that siRNA against the RPL21 gene possesses a potential anti-cancer activity for PC cells by inhibiting their proliferation and DNA replication, as well as inducing cell cycle G1 arrest and cell apoptosis.
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http://dx.doi.org/10.3389/fonc.2020.01730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509406PMC
September 2020

From Sequencing to Genome Editing for Cotton Improvement.

Trends Biotechnol 2021 Mar 28;39(3):221-224. Epub 2020 Sep 28.

Department of Biology, East Carolina University, Greenville, NC 27858, USA. Electronic address:

Traditional breeding techniques are proven, but additional knowledge learned from genome sequencing provides vast new data that might help identify gene targets for improving cotton sustainability. CRISPR/Cas9 provides a powerful tool for precision cotton breeding. Here, we discuss the opportunities and challenges of genome sequencing and editing for cotton improvement.
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http://dx.doi.org/10.1016/j.tibtech.2020.09.001DOI Listing
March 2021

Edible Plant Oil: Global Status, Health Issues, and Perspectives.

Front Plant Sci 2020 28;11:1315. Epub 2020 Aug 28.

Henan Province Engineering Research Center for Forest Biomass Value-added Products, College of Forestry, Henan Agricultural University, Zhengzhou, China.

Edible plant oil (EPO) is an indispensable nutritional resource for human health. Various cultivars of oil-bearing plants are grown worldwide, and the chemical compositions of different plant oils are diverse. The extremely complex components in oils lead to diverse standards for evaluating the quality and safety of different EPOs. The environment poses great challenges to the EPO safety and quality during the entire industrial chain, including plant cultivation, harvesting, oil processing, and storage. Environmental risk factors include heavy metal or pesticide residue pollution, insect or harmful microbial infestation, and rancidity. Here, the diverse components in oil and various oil-producing processes are discussed, including plant species, oil yield, and composition complexity, environmental factors that degrade oil quality. Additionally, we propose a whole-industrial-chain monitoring system instead of current single-link-monitoring approach by monitoring and tracking the quality and safety of EPOs during the entire process of plant cultivation, raw materials harvest, oil process, and EPOs storage. This will provide guidance for monitoring the quality and safety of EPOs, which were challenged by the deteriorating environment.
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http://dx.doi.org/10.3389/fpls.2020.01315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7485320PMC
August 2020

CRISPR/Cas gene therapy.

Authors:
Baohong Zhang

J Cell Physiol 2021 Apr 22;236(4):2459-2481. Epub 2020 Sep 22.

Department of Biology, East Carolina University, Greenville, North Carolina, USA.

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated enzyme (Cas) is a naturally occurring genome editing tool adopted from the prokaryotic adaptive immune defense system. Currently, CRISPR/Cas9-based genome editing has been becoming one of the most promising tools for treating human genetic diseases, including cardiovascular diseases, neuro-disorders, and cancers. As the quick modification of the CRISPR/Cas9 system, including delivery system, CRISPR/Cas9-based gene therapy has been extensively studied in preclinic and clinic treatments. CRISPR/Cas genome editing is also a robust tool to create animal genetic models for studying and treating human genetic disorders, particularly diseases associated with point mutations. However, significant challenges also remain before CRISPR/Cas technology can be routinely employed in the clinic for treating different genetic diseases, which include toxicity and immune response of treated cells to CRISPR/Cas component, highly throughput delivery method, and potential off-target impact. The off-target effect is one of the major concerns for CRISPR/Cas9 gene therapy, more research should be focused on limiting this impact by designing high specific gRNAs and using high specificity of Cas enzymes. Modifying the CRISPR/Cas9 delivery method not only targets a specific tissue/cell but also potentially limits the off-target impact.
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http://dx.doi.org/10.1002/jcp.30064DOI Listing
April 2021

Potassium Deficiency Significantly Affected Plant Growth and Development as Well as microRNA-Mediated Mechanism in Wheat ( L.).

Front Plant Sci 2020 14;11:1219. Epub 2020 Aug 14.

Department of Biology, East Carolina University, Greenville, NC, United States.

It is well studied that potassium (K) deficiency induced aberrant growth and development of plant and altered the expression of protein-coding genes. However, there are not too many systematic investigations on root development affected by K deficiency, and there is no report on miRNA expression during K deficiency in wheat. In this study, we found that K deficiency significantly affected wheat seedling growth and development, evidenced by reduced plant biomass and small plant size. In wheat cultivar AK-58, up-ground shoots were more sensitive to K deficiency than roots. K deficiency did not significantly affect root vitality but affected root development, including root branching, root area, and root size. K deficiency delayed seminal root emergence but enhanced seminal root elongation, total root length, and correspondingly total root surface area. K deficiency also affected root and leaf respiration at the early exposure stage, but these effects were not observed at the later stage. One potential mechanism causing K deficiency impacts is microRNAs (miRNAs), one important class of small regulatory RNAs. K deficiency induced the aberrant expression of miRNAs and their targets, which further affected plant growth, development, and response to abiotic stresses, including K deficiency. Thereby, this positive root adaption to K deficiency is likely associated with the miRNA-involved regulation of root development.
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http://dx.doi.org/10.3389/fpls.2020.01219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7456879PMC
August 2020

Virus-Based CRISPR/Cas9 Genome Editing in Plants.

Trends Genet 2020 11 19;36(11):810-813. Epub 2020 Aug 19.

Department of Biology, East Carolina University, Greenville, NC 27858, USA. Electronic address:

CRISPR/Cas9 is a versatile tool for plant gene function studies and crop improvement. However, traditional CRISPR/Cas9-mediated genome editing requires plant tissue culture that is both time-consuming and genotype-dependent. Ma et al. recently reported a novel virus-based method for delivering CRISPR/Cas9 into plant cells, and this should further expand the application of CRISPR/Cas9-mediated genome editing.
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http://dx.doi.org/10.1016/j.tig.2020.08.002DOI Listing
November 2020

High throughput deep sequencing elucidates the important role of lncRNAs in Foxtail millet response to herbicides.

Genomics 2020 11 5;112(6):4463-4473. Epub 2020 Aug 5.

College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, Henan 455000, PR China. Electronic address:

Long non-coding RNAs (lncRNAs) play an important function in plant growth and development as well as response to stresses. However, little information was known in foxtail millet; no study was reported on lncRNAs in plant response to herbicide treatment. In this study, by using deep sequencing and advanced bioinformatic analysis, a total of 2547 lncRNAs were identified, including 787 known and 1760 novel lncRNAs. These lncRNAs are distributed across all 9 chromosomes, and the majority were located in the intergenic region with 1-2 exons. These lncRNAs were differentially expressed between different genotypes under different herbicide treatments. lncRNAs regulate plant growth and development as well as response to herbicide treatments through targeting protein-coding genes that directly relate to chemical metabolism and defense system. Multiple potential target genes and lncRNA-mRNA-miRNA gene networks were discovered. These results elucidate the potential roles of lncRNAs in plant response to herbicides.
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http://dx.doi.org/10.1016/j.ygeno.2020.07.045DOI Listing
November 2020

Transcriptome Analysis Provides Insights into Grain Filling in Foxtail Millet ( L.).

Int J Mol Sci 2020 Jul 16;21(14). Epub 2020 Jul 16.

College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China.

Grain filling is an importantly developmental process which is associated with the yield and quality of foxtail millet ( L.). However, the molecular mechanisms of grain filling are rarely reported in foxtail millet. In our study, RNA-seq was performed to investigate the transcriptional dynamics and identify the key genes involved in grain filling in foxtail millet at five different developmental stages. A total of 11,399 differentially expressed genes (DEGs), including 902 transcription factors (TFs), were identified. Certain important genes involved in grain filling were discovered through a function annotation and temporal expression patterns analysis. These genes included genes associated with starch biosynthesis, cell-wall invertases, hormone signal transduction, and polyamine metabolism pathways. The expression levels of seven randomly selected DEGs were validated by a quantitative real-time polymerase chain reaction (qRT-PCR). This study provides the first insight into the changes in the gene expression of grain filling at different developmental stages in foxtail millet. These results could help understand the complex molecular mechanisms of the panicle formation in foxtail millet and other cereal crops.
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http://dx.doi.org/10.3390/ijms21145031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7403974PMC
July 2020

CRISPR/Cas9: A Robust Genome-Editing Tool with Versatile Functions and Endless Application.

Authors:
Baohong Zhang

Int J Mol Sci 2020 Jul 20;21(14). Epub 2020 Jul 20.

Department of Biology, East Carolina University, Greenville, NC 27858, USA.

Since a potential genome editing tool was first recognized in 2012 [...].
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http://dx.doi.org/10.3390/ijms21145111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7404002PMC
July 2020

Effects of preparation method on the biochemical characterization and cytotoxic activity of New Zealand surf clam extracts.

Heliyon 2020 Jul 9;6(7):e04357. Epub 2020 Jul 9.

School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 1010, New Zealand.

Molluscan extracts confer a wide range of health promoting properties, one of them is cytotoxicity. Extraction and processing can affect the efficacy and properties of bioactive molecules. New Zealand (NZ) surf clams have never been thoroughly studied for bioactives until recently. However, the effect of cold and heat extraction procedure on biochemical composition and cytotoxic activities of NZ surf clam remains unanswered. The objective is to compare the effects on cytotoxicity of three NZ surf clams (Diamond shell, ; Storm shell, ; and Deepwater Tua tua, ) extracts via cold or heat process across cancer cell lines to find out which process can preserve bioactivity better. Fractions of extracts prepared via cold or heat procedures were tested for cell growth inhibition, apoptosis induction and cell cycle arrest in seven cancer cell lines. Apoptosis was induced through all cell lines, as further evidenced in Caspase-3/7 activities. Cell cycle arrest was focused on G2/M- and S- phases. Petroleum ether and ethyl acetate fractions, with the greatest bioactivity in this study, are rich in lipids and proteins, indicating likely bioactive sources. Cold preparation was responsible for the lowest cancer cell viability and induced greater apoptosis. Cold process retained better bioactivity/cytotoxicity than that of heat-processed extracts. This information may guide future health/nutraceutical clam product development.
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http://dx.doi.org/10.1016/j.heliyon.2020.e04357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7355998PMC
July 2020

Chilling and Heat Stress-Induced Physiological Changes and MicroRNA-Related Mechanism in Sweetpotato ( L.).

Front Plant Sci 2020 26;11:687. Epub 2020 May 26.

Department of Biology, East Carolina University, Greenville, NC, United States.

Sweetpotato ( (L.) Lam.) is an important industrial and food crop. Both chilling and heat stress inhibits sweetpotato growth and development and then affects yield. However, the physiological and molecular mechanisms of sweetpotato response to chilling and heat stress is unclear. In this study, we investigated the effect of extreme temperature on sweetpotato physiological response, with a focus on oxidative stress and the potential microRNA (miRNA)-mediated molecular mechanism. Our results showed that both chilling and heat stress resulted in accumulation of reactive oxygen species (ROS), including HO and O, and caused oxidative stress in sweetpotato. This further affected the activities of oxidative stress-related enzymes and products, including SOD, POD, and MDA. Both chilling and heat stress inhibited POD activities but induced the enzyme activities of SOD and MDA. This suggests that sweetpotato cells initiated its own defense mechanism to handle extreme temperature-caused oxidative damage. Oxidative damage and repair are one mechanism that sweetpotato plants respond to extreme temperatures. Another potential mechanism is miRNA-mediated gene response. Chilling and heat stress altered the expression of stress-responsive miRNAs in sweetpotato seedlings. These miRNAs regulate sweetpotato response to extreme stress through targeting individual protein-coding genes.
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http://dx.doi.org/10.3389/fpls.2020.00687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7264270PMC
May 2020

Selection of stable reference genes for gene expression analysis in sweet potato (Ipomoea batatas L.).

Mol Cell Probes 2020 10 6;53:101610. Epub 2020 Jun 6.

Department of Biology, East Carolina University, Greenville, NC, 27858, USA. Electronic address:

Gene expression analysis is one of the most common and important studies in biology and biomedicine. No matter for traditional blotting analysis or currently commonly used PCR strategy, all need a stable reference gene for normalizing the gene expression. To screen and select housekeeping genes as the most stable reference genes, quantitative real-time PCR (qRT-PCR) was employed to analyze the expression of sixteen commonly used reference genes (IbelF, Ibα-tubulin, IbHIS, IbCOX, IbGAPDH, IbH2B1, IbARF, IbCYC, Ibβ-tubulin, IbACT, IbEFl-a, IbG14, IbPLD, IbRPL2, IbUBQ, IbUBI) in five different tissues under two different temperature stresses in sweet potato. Data analysis by the Delta CT, geNorm, NormFinder, and BestKeeper programs revealed that IbelF is the most stable gene and IbUBI is the least stable gene as reference. Our study also shows that combination of two or more genes as reference is a better choice, rendering more substantiated expression data for comparison. This study provides evidence for selecting reference genes in sweet potato gene expression analysis.
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http://dx.doi.org/10.1016/j.mcp.2020.101610DOI Listing
October 2020

Pectin Drives Cell Wall Morphogenesis without Turgor Pressure.

Trends Plant Sci 2020 08 5;25(8):719-722. Epub 2020 Jun 5.

Department of Biology, East Carolina University, Greenville, NC 27858, USA. Electronic address:

How the plant cell wall expands and forms shapes is a long-standing mystery. Traditional thought is that turgor pressure drives these processes. However, a recent study by Haas and colleagues shows for the first time that the expansion of pectin homogalacturonan nanofilaments drives morphogenesis without turgor pressure in plant epidermal cells.
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http://dx.doi.org/10.1016/j.tplants.2020.05.007DOI Listing
August 2020

CRISPR/Cas9 genome editing shows the important role of AZC_2928 gene in nitrogen-fixing bacteria of plants.

Funct Integr Genomics 2020 Sep 1;20(5):657-668. Epub 2020 Jun 1.

College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.

AZC_2928 gene (GenBank accession no. BAF88926.1) of Azorhizobium caulinodans ORS571 has sequence homology to 2,3-aminomutases. However, its function is unknown. In this study, we are for the first time to knock out the gene completely in A. caulinodans ORS571 using the current advanced genome editing tool, CRISPR/Cas9. Our results show that the editing efficiency is 34% and AZC_2928 plays an extremely important role in regulating the formation of chemotaxis and biofilm. CRISPR/Cas9 knockout of AZC_2928 (△AZC_2928) significantly enhanced chemotaxis and biofilm formation. Both chemotaxis and biofilm formation play an important role in nitrogen-fixing bacteria and their interaction with their host plants. Interestingly, AZC_2928 did not affect the motility of A. caulinodans ORS571 and the nodulation formation in their natural host plant, Sesbania rostrata. Due to rhizobia needing to form bacteroids for symbiotic nitrogen fixation in mature nodules, AZC_2928 might have a direct influence on nitrogen fixation efficiency rather than the number of nodulations.
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http://dx.doi.org/10.1007/s10142-020-00739-8DOI Listing
September 2020

Impact of potassium deficiency on cotton growth, development and potential microRNA-mediated mechanism.

Plant Physiol Biochem 2020 Aug 25;153:72-80. Epub 2020 May 25.

Department of Biology, East Carolina University, Greenville, NC, 27858, USA. Electronic address:

The goal of this study was to investigate the impact of potassium deficiency on cotton seedling growth and development at the individual, physiological, biochemical, and molecular levels. Potassium is an important plant nutrient; our results show that potassium deficiency significantly affected cotton seedling growth and development, evidenced by reduced plant height, and total areas of the leaves and roots as well as further reduced both fresh and dry biomass of the entire plants. Potassium deficiency also significantly inhibited root and leaf respiration and leaf photosynthesis. Compared with the controls, potassium deficiency significantly inhibited root elongation and total root surface areas that further inhibited cotton seedlings to uptake nutrients from the medium. Potassium deficiency induced aberrant expression of both microRNAs (miRNAs) and their protein-coding targets. These miRNAs regulate plant root development as well as response to abiotic stresses. Potassium deficiency altered the expression of miRNAs that regulate the expression of protein-coding genes controlling root development and response to potassium deficiency. miRNAs regulate root development and further control plant development in cotton seedlings under potassium deficiency. In summary, potassium deficiency significantly affected the cotton seedling photosynthesis and respiration that resulted in inhibition of cotton seedling growth and development potentially due to the miRNA-mediated mechanism.
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http://dx.doi.org/10.1016/j.plaphy.2020.05.006DOI Listing
August 2020

SpRY: Engineered CRISPR/Cas9 Harnesses New Genome-Editing Power.

Trends Genet 2020 08 23;36(8):546-548. Epub 2020 May 23.

Department of Biology, East Carolina University, Greenville, NC 27858, USA. Electronic address:

Due to protospacer adjacent motif (PAM) requirements, CRISPR/Cas9 cannot access many genetic loci. A recent study by Walton et al. structurally engineered Streptococcus pyogenes Cas9 (SpCas9) to near-PAMless SpRY that can target most DNA sequences with high editing efficiency and flexibility. This newly engineered SpRY will potentially expand genome-editing capabilities for basic and applied research.
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http://dx.doi.org/10.1016/j.tig.2020.05.001DOI Listing
August 2020

Integrated small RNA and mRNA expression profiles reveal miRNAs and their target genes in response to Aspergillus flavus growth in peanut seeds.

BMC Plant Biol 2020 May 13;20(1):215. Epub 2020 May 13.

Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.

Background: MicroRNAs are important gene expression regulators in plants immune system. Aspergillus flavus is the most common causal agents of aflatoxin contamination in peanuts, but information on the function of miRNA in peanut-A. flavus interaction is lacking. In this study, the resistant cultivar (GT-C20) and susceptible cultivar (Tifrunner) were used to investigate regulatory roles of miRNAs in response to A. flavus growth.

Results: A total of 30 miRNAs, 447 genes and 21 potential miRNA/mRNA pairs were differentially expressed significantly when treated with A. flavus. A total of 62 miRNAs, 451 genes and 44 potential miRNA/mRNA pairs exhibited differential expression profiles between two peanut varieties. Gene Ontology (GO) analysis showed that metabolic-process related GO terms were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses further supported the GO results, in which many enriched pathways were related with biosynthesis and metabolism, such as biosynthesis of secondary metabolites and metabolic pathways. Correlation analysis of small RNA, transcriptome and degradome indicated that miR156/SPL pairs might regulate the accumulation of flavonoids in resistant and susceptible genotypes. The miR482/2118 family might regulate NBS-LRR gene which had the higher expression level in resistant genotype. These results provided useful information for further understanding the roles of miR156/157/SPL and miR482/2118/NBS-LRR pairs.

Conclusions: Integration analysis of the transcriptome, miRNAome and degradome of resistant and susceptible peanut varieties were performed in this study. The knowledge gained will help to understand the roles of miRNAs of peanut in response to A. flavus.
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http://dx.doi.org/10.1186/s12870-020-02426-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222326PMC
May 2020

A novel bispecific antibody targeting CD3 and prolactin receptor (PRLR) against PRLR-expression breast cancer.

J Exp Clin Cancer Res 2020 May 12;39(1):87. Epub 2020 May 12.

Engineering Research Center of Cell & Therapeutic Antibody, MOE,Shanghai Jiao Tong University, Dongchuan Road, Shanghai, China.

Background: Prolactin receptor (PRLR) is highly expressed in a subset of human breast cancer and prostate cancer, which makes it a potential target for cancer treatment. In clinical trials, the blockade of PRLR was shown to be safe but with poor efficacy. It is therefore urgent to develop new therapies against PRLR target. Bispecific antibodies (BsAbs) could guide immune cells toward tumor cells, and produced remarkable effects in some cancers.

Methods: In this study, a bispecific antibody targeting both tumor antigen PRLR and T cell surface CD3 antigen (PRLR-DbsAb) was constructed by split intein mediated protein transsplicing (BAPTS) system for the first time. Its binding activity was determined by Biacore and Flow cytometry, and target-dependent T cell mediated cytotoxicity was detected using LDH release assay. ELISA was utilized to study the secretion of cytokines by immune cells. Subcutaneous tumor mouse models were used to analyze the in vivo anti-tumor effects of PRLR-DbsAb.

Results: PRLR-DbsAb in vitro could recruit and activate T cells to promote the release of Th1 cytokines IFN- γ and TNF- α, which could kill PRLR expressed breast cancer cells. In xenograft models with breast cancer cell line T47D, NOD/SCID mice intraperitoneally injected with PRLR-DbsAb exhibited significant inhibition of tumor growth and a longer survival compared to mice treated with PRLR monoclonal antibody (PRLR mAb).

Conclusions: Both in vitro and in vivo experiments showed PRLR-DbsAb had a potential therapy of cancer treatment potential therapy for cancer. Immunotherapy may be a promising treatment against the tumor target of PRLR.
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http://dx.doi.org/10.1186/s13046-020-01564-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216678PMC
May 2020

Differential phosphorylation regulates the shear stress-induced polar activity of Rho-specific guanine nucleotide dissociation inhibitor α.

J Cell Physiol 2020 10 31;235(10):6978-6989. Epub 2020 Jan 31.

Liaoning Key Lab of IC & BME System, Dalian University of Technology, Dalian, Liaoning, China.

The activity of Rho-specific guanine nucleotide dissociation inhibitor α (RhoGDIα) is regulated by its own phosphorylation at different amino acid sites. These phosphorylation sites may have a crucial role in local Rho GTPases activation during cell migration. This paper is designed to explore the influence of phosphorylation on shear stress-induced spatial RhoGDIα activation. Based on the fluorescence resonance energy transfer biosensor sl-RhoGDIα, which was constructed to test the RhoGDIα activity in living cells, new RhoGDIα phosphomimetic mutation (sl-S101E/S174E, sl-Y156E, sl-S101E, sl-S174E) and phosphorylation-deficient mutation (sl-S101A/S174A, sl-Y156A, sl-S101A, sl-S174A) biosensors were designed to test their effects on RhoGDIα activation upon shear stress application in human umbilical vein endothelial cells (HUVECs). The results showed lower RhoGDIα activity at the downstream of HUVECs (the region from the edge of the nucleus to the edge of the cell along with the flow). The overall decrease in RhoGDIα activity was inhibited by Y156A-mutant, whereas the polarized RhoGDIα and Rac1 activity were blocked by S101A/S174A mutant. It is concluded that the Tyr156 phosphorylation mainly mediates shear stress-induced overall RhoGDIα activity, while Ser101/Ser174 phosphorylation mediates its polarization. This study demonstrates that differential phosphorylation of RhoGDIα regulates shear stress-induced spatial RhoGDIα activation, which could be a potential target to control cell migration.
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http://dx.doi.org/10.1002/jcp.29594DOI Listing
October 2020