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Gruessner BM, Cornet-Vernet L, Desrosiers MR, Lutgen P, Towler MJ, Weathers PJ. It is not just artemisinin: Artemisia sp. for treating diseases including malaria and schistosomiasis. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2019; 18:1509-1527. [PMID: 33911989 PMCID: PMC8078015 DOI: 10.1007/s11101-019-09645-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 09/11/2019] [Indexed: 05/13/2023]
Abstract
Artemisia sp., especially A. annua and A. afra, have been used for centuries to treat many ailments. While artemisinin is the main therapeutically active component, emerging evidence demonstrates that the other phytochemicals in this genus are also therapeutically active. Those compounds include flavonoids, other terpenes, coumarins, and phenolic acids. Artemisia sp. phytochemicals also improve bioavailability of artemisinin and synergistically improve artemisinin therapeutic efficacy, especially when delivered as dried leaf Artemisia as a tea infusion or as powdered dry leaves in a capsule or compressed into a tablet. Here results from in vitro, and in vivo animal and human studies are summarized and critically discussed for mainly malaria, but also other diseases susceptible to artemisinin and Artemisia sp. including schistosomiasis, leishmaniasis, and trypanosomiasis.
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Affiliation(s)
- B M Gruessner
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | | | - M R Desrosiers
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - P Lutgen
- IFVB-BELHERB, Niederanven, Luxembourg
| | - M J Towler
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - P J Weathers
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
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Zwane AA, Schnabel RD, Hoff J, Choudhury A, Makgahlela ML, Maiwashe A, Van Marle-Koster E, Taylor JF. Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa. Front Genet 2019; 10:273. [PMID: 30988672 PMCID: PMC6452414 DOI: 10.3389/fgene.2019.00273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/12/2019] [Indexed: 01/30/2023] Open
Abstract
Single nucleotide polymorphism arrays have created new possibilities for performing genome-wide studies to detect genomic regions harboring sequence variants that affect complex traits. However, the majority of validated SNPs for which allele frequencies have been estimated are limited primarily to European breeds. The objective of this study was to perform SNP discovery in three South African indigenous breeds (Afrikaner, Drakensberger, and Nguni) using whole genome sequencing. DNA was extracted from blood and hair samples, quantified and prepared at 50 ng/μl concentration for sequencing at the Agricultural Research Council Biotechnology Platform using an Illumina HiSeq 2500. The fastq files were used to call the variants using the Genome Analysis Tool Kit. A total of 1,678,360 were identified as novel using Run 6 of 1000 Bull Genomes Project. Annotation of the identified variants classified them into functional categories. Within the coding regions, about 30% of the SNPs were non-synonymous substitutions that encode for alternate amino acids. The study of distribution of SNP across the genome identified regions showing notable differences in the densities of SNPs among the breeds and highlighted many regions of functional significance. Gene ontology terms identified genes such as MLANA, SYT10, and CDC42EP5 that have been associated with coat color in mouse, and ADAMS3, DNAJC3, and PAG5 genes have been associated with fertility in cattle. Further analysis of the variants detected 688 candidate selective sweeps (ZHp Z-scores ≤ -4) across all three breeds, of which 223 regions were assigned as being putative selective sweeps (ZHp scores ≤-5). We also identified 96 regions with extremely low ZHp Z-scores (≤-6) in Afrikaner and Nguni. Genes such as KIT and MITF that have been associated with skin pigmentation in cattle and CACNA1C, which has been associated with biopolar disorder in human, were identified in these regions. This study provides the first analysis of sequence data to discover SNPs in indigenous South African cattle breeds. The information will play an important role in our efforts to understand the genetic history of our cattle and in designing appropriate breed improvement programmes.
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Affiliation(s)
- Avhashoni A. Zwane
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | - Robert D. Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
- Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Jesse Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Ananyo Choudhury
- Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Mahlako Linah Makgahlela
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Azwihangwisi Maiwashe
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Este Van Marle-Koster
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
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Wang X, Cheng D, Jiang W, Ma Y. Mechanisms Underlying Aluminum Neurotoxicity Related to 14-3-3ζ Protein. Toxicol Sci 2018; 163:45-56. [DOI: 10.1093/toxsci/kfy021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Xiaomei Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, People’s Republic of China
| | - Dai Cheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, People’s Republic of China
- College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Weibo Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, People’s Republic of China
| | - Yuxia Ma
- Department of Nutrition and Hygiene, Hebei Medical University, Shijiazhuang, China
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Abstract
p70 S6 kinase (p70S6K), a member of the AGC serine/threonine kinase family, was initially identified as a key player, together with its downstream effector S6, in the regulation of cellular growth and survival. The p70S6K protein has emerged in recent years as a multifunctional protein which also regulates the actin cytoskeleton and thus plays a role in cell migration. This new function is through two important activities of p70S6K, namely actin cross-linking and Rac1 and Cdc42 activation. The testis is critically dependent on an intricate balance of fundamental cellular processes such as adhesion, migration, and differentiation. It is increasingly evident that Rho GTPases and actin binding proteins play fundamental roles in regulating spermatogenesis within the testis. In this review, we will discuss current findings of p70S6K in the control of actin cytoskeleton dynamics. In addition, the potential role of p70S6K in spermatogenesis and testicular function will be highlighted.
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Affiliation(s)
- Carman K M Ip
- School of Biological Sciences; University of Hong Kong; Hong Kong, China
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Bahrami-B F, Ataie-Kachoie P, Pourgholami MH, Morris DL. p70 Ribosomal protein S6 kinase (Rps6kb1): an update. J Clin Pathol 2014; 67:1019-25. [PMID: 25100792 DOI: 10.1136/jclinpath-2014-202560] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Rps6kb1 gene encodes the 70 kDa ribosomal protein S6 kinase (p70S6K), which is a serine/threonine kinase regulated by phosphoinositide 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) pathway. p70S6K plays a crucial role in controlling cell cycle, growth and survival. The PI3K/mTOR signalling pathway is one of the major mechanisms for controlling cell survival, proliferation and metabolism and is the central regulator of translation of some components of protein synthesis system. Upon activation, this kinase phosphorylates S6 protein of ribosomal subunit 40S resulting in selective translation of unique family of mRNAs that contain oligopyrimidine tract on 5' transcriptional site (5'TOP). 5'TOP mRNAs are coding the components of translational apparatus including ribosomal proteins and elongation factors. Due to the role of p70S6K in protein synthesis and also its involvement in a variety of human diseases ranging from diabetes and obesity to cancer, p70S6K is now being considered as a new therapeutic target for drug development. Furthermore, p70S6K acts as a biomarker for response to immunosuppressant as well as anticancer effects of inhibitors of the mTOR. Because of the narrow therapeutic index of mTOR inhibitors, drug monitoring is essential, and this is usually done by measuring blood drug levels, therapeutic response and drug-induced adverse effects. Recent studies have suggested that plasma p70S6K is a reliable index for the monitoring of patient response to mTOR inhibitors. Therefore, a better understanding of p70S6K and its role in various pathological conditions could enable the development of strategies to aid diagnosis, prognosis and treatment schedules.
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Affiliation(s)
- Farnaz Bahrami-B
- Cancer research laboratories, Department of Surgery, St George and Sutherland Clinical School, University of New South Wales, Sydney, Australia
| | | | | | - David L Morris
- Cancer research laboratories, Department of Surgery, St George and Sutherland Clinical School, University of New South Wales, Sydney, Australia
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Bischoff SR, Tsai SQ, Hardison NE, Motsinger-Reif AA, Freking BA, Nonneman DJ, Rohrer GA, Piedrahita JA. Differences in X-chromosome transcriptional activity and cholesterol metabolism between placentae from swine breeds from Asian and Western origins. PLoS One 2013; 8:e55345. [PMID: 23383161 PMCID: PMC3561265 DOI: 10.1371/journal.pone.0055345] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 12/21/2012] [Indexed: 12/19/2022] Open
Abstract
To gain insight into differences in placental physiology between two swine breeds noted for their dissimilar reproductive performance, that is, the Chinese Meishan and white composite (WC), we examined gene expression profiles of placental tissues collected at 25, 45, 65, 85, and 105 days of gestation by microarrays. Using a linear mixed model, a total of 1,595 differentially expressed genes were identified between the two pig breeds using a false-discovery rate q-value ≤0.05. Among these genes, we identified breed-specific isoforms of XIST, a long non-coding RNA responsible X-chromosome dosage compensation in females. Additionally, we explored the interaction of placental gene expression and chromosomal location by DIGMAP and identified three Sus scrofa X chromosomal bands (Xq13, Xq21, Xp11) that represent transcriptionally active clusters that differ between Meishan and WC during placental development. Also, pathway analysis identified fundamental breed differences in placental cholesterol trafficking and its synthesis. Direct measurement of cholesterol confirmed that the cholesterol content was significantly higher in the Meishan versus WC placentae. Taken together, this work identifies key metabolic pathways that differ in the placentae of two swine breeds noted for differences in reproductive prolificacy.
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Affiliation(s)
- Steve R. Bischoff
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Shengdar Q. Tsai
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Nicholas E. Hardison
- Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Alison A. Motsinger-Reif
- Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Bradley A. Freking
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Dan J. Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Gary A. Rohrer
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Jorge A. Piedrahita
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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Dannemann M, Lachmann M, Lorenc A. 'maskBAD'--a package to detect and remove Affymetrix probes with binding affinity differences. BMC Bioinformatics 2012; 13:56. [PMID: 22507266 PMCID: PMC3439685 DOI: 10.1186/1471-2105-13-56] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Accepted: 03/16/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hybridization differences caused by target sequence differences can be a confounding factor in analyzing gene expression on microarrays, lead to false positives and reduce power to detect real expression differences. We prepared an R Bioconductor compatible package to detect, characterize and remove such probes in Affymetrix 3'IVT and exon-based arrays on the basis of correlation of signal intensities from probes within probe sets. RESULTS Using completely mouse genomes we determined type 1 (false negatives) and type 2 (false positives) errors with high accuracy and we show that our method routinely outperforms previous methods. When detecting 76.2% of known SNP/indels in mouse expression data, we obtain at most 5.5% false positives. At the same level of false positives, best previous method detected 72.6%. We also show that probes with differing binding affinity both hinder differential expression detection and introduce artifacts in cancer-healthy tissue comparison. CONCLUSIONS Detection and removal of such probes should be a routine step in Affymetrix data preprocessing. We prepared a user friendly R package, compatible with Bioconductor, that allows the filtering and improving of data from Affymetrix microarrays experiments.
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Affiliation(s)
- Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
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Neuman JA, Isakov O, Shomron N. Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Brief Bioinform 2012; 14:46-55. [PMID: 22707752 DOI: 10.1093/bib/bbs013] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Insertion and deletion (indel) mutations, the most common type of structural variance in the human genome, affect a multitude of human traits and diseases. New sequencing technologies, such as deep sequencing, allow massive throughput of sequence data and greatly contribute to the field of disease causing mutation detection, in general, and indel detection, specifically. In order to infer indel presence (indel calling), the deep-sequencing data have to undergo comprehensive computational analysis. Selecting which indel calling software to use can often skew the results and inherent tool limitations may affect downstream analysis. In order to better understand these inter-software differences, we evaluated the performance of several indel calling software for short indel (1-10 nt) detection. We compared the software's sensitivity and predictive values in the presence of varying parameters such as read depth (coverage), read length, indel size and frequency. We pinpoint several key features that assist successful experimental design and appropriate tool selection. Our study may also serve as a basis for future evaluation of additional indel calling methods.
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Affiliation(s)
- Joseph A Neuman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Xu WW, Cho S, Yang SS, Bolon YT, Bilgic H, Jia H, Xiong Y, Muehlbauer GJ. Single-feature polymorphism discovery by computing probe affinity shape powers. BMC Genet 2009; 10:48. [PMID: 19709416 PMCID: PMC2746803 DOI: 10.1186/1471-2156-10-48] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 08/26/2009] [Indexed: 11/17/2022] Open
Abstract
Background Single-feature polymorphism (SFP) discovery is a rapid and cost-effective approach to identify DNA polymorphisms. However, high false positive rates and/or low sensitivity are prevalent in previously described SFP detection methods. This work presents a new computing method for SFP discovery. Results The probe affinity differences and affinity shape powers formed by the neighboring probes in each probe set were computed into SFP weight scores. This method was validated by known sequence information and was comprehensively compared with previously-reported methods using the same datasets. A web application using this algorithm has been implemented for SFP detection. Using this method, we identified 364 SFPs in a barley near-isogenic line pair carrying either the wild type or the mutant uniculm2 (cul2) allele. Most of the SFP polymorphisms were identified on chromosome 6H in the vicinity of the Cul2 locus. Conclusion This SFP discovery method exhibits better performance in specificity and sensitivity over previously-reported methods. It can be used for other organisms for which GeneChip technology is available. The web-based tool will facilitate SFP discovery. The 364 SFPs discovered in a barley near-isogenic line pair provide a set of genetic markers for fine mapping and future map-based cloning of the Cul2 locus.
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Affiliation(s)
- Wayne Wenzhong Xu
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minnesota, MN 55455, USA.
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Bischoff SR, Tsai S, Hardison N, Motsinger-Reif AA, Freking BA, Nonneman D, Rohrer G, Piedrahita JA. Characterization of conserved and nonconserved imprinted genes in swine. Biol Reprod 2009; 81:906-20. [PMID: 19571260 DOI: 10.1095/biolreprod.109.078139] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
To increase our understanding of imprinted genes in swine, we carried out a comprehensive analysis of this gene family using two complementary approaches: expression and phenotypic profiling of parthenogenetic fetuses, and analysis of imprinting by pyrosequencing. The parthenote placenta and fetus were smaller than those of controls but had no obvious morphological differences at Day 28 of gestation. By Day 30, however, the parthenote placentas had decreased chorioallantoic folding, decreased chorionic ruggae, and reduction of fetal-maternal interface surface in comparison with stage-matched control fetuses. Using Affymetrix Porcine GeneChip microarrays and/or semiquantitative PCR, brain, fibroblast, liver, and placenta of Day 30 fetuses were profiled, and 25 imprinted genes were identified as differentially expressed in at least one of the four tissue types: AMPD3, CDKN1C, COPG2, DHCR7, DIRAS3, IGF2 (isoform specific), IGF2AS, IGF2R, MEG3, MEST, NAP1L5, NDN, NNAT, OSBPL1A, PEG3, APEG3, PEG10, PLAGL1, PON2, PPP1R9A, SGCE, SLC38A4, SNORD107, SNRPN, and TFPI2. For DIRAS3, PLAGL1, SGCE, and SLC38A4, tissue-specific differences were detected. In addition, we examined the imprinting status of candidate genes by quantitative allelic pyrosequencing. Samples were collected from Day 30 pregnancies generated from reciprocal crosses of Meishan and White Composite breeds, and single-nucleotide polymorphisms were identified in candidate genes. Imprinting was confirmed for DIRAS3, DLK1, H19, IGF2AS, NNAT, MEST, PEG10, PHLDA2, PLAGL1, SGCE, and SNORD107. We also found no evidence of imprinting in ASB4, ASCL2, CD81, COMMD1, DCN, DLX5, and H13. Combined, these results represent the most comprehensive survey of imprinted genes in swine to date.
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Affiliation(s)
- Steve R Bischoff
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina 27606, USA
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