151 results
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2. Descriptions of Centrifugation Manipulations in the Literature Illustrate the Need for Better Laboratory Training of Biologists
- Author
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Rioux, Pierre and Blier, Pierre
- Abstract
Students in environmental sciences, ecology, or wildlife management are often reluctant to acquire training in basic laboratory techniques. To advocate the importance of this training, we reviewed literature in the fields of biological and environmental science for one frequently used technique--centrifugation--and evaluated whether centrifugation parameters are properly expressed. Centrifugation is used to extract and purify different types of biomolecules for further characterization or quantification. The repeatability of the procedure depends on the proper identification of parameters defining the gravitational force applied to a solution, for example the duration, distance from central axis, and angular velocity. Correctly expressing rotation velocity--the "speed"--is therefore crucial to ensuring repeatability and the possibility of using the same protocols in different laboratories. When scrutinizing the materials and methods sections of publications in ecology, zoology, botany, or general biology journals, we noticed that velocity is expressed in different ways and essential information is often missing. We sampled 2000 articles in different fields of biological sciences that recorded centrifugation as a technique in the materials and methods section. We found centrifugation velocity to be properly expressed in gravitational force "g" in only 47.8% of the papers. The score dropped to 40.4% in journals specialized in ecology. We use this analysis to advocate for a minimum of training in the techniques of biochemistry that are of common use in environmental sciences. Better training would allow higher reproducibility of results in scientific publications.
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- 2021
3. Phylogenetic Analysis and Molecular Evolution (PAME)
- Author
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Yoshida, R. and Page, R.
- Abstract
In the fall of 2009 and in the spring of 2012, supported by the National Institute of General Medical Sciences (NIGMS) in the National Institutes of Health (NIH), we designed a course "Phylogenetic Analysis and Molecular Evolution" (PAME), the first cross-listed course across three different colleges (College of Arts and Sciences, College of Engineering, and College of Agriculture). This course was the first at the author's university. The course will be made available to graduate students and advanced undergraduate students in biology and computer science, and undergraduate student in statistics and mathematics at regional universities and colleges. The graduate students will learn how to gather sequence data, use bioinformatics tools, and analyze biological data using mathematics and statistics throughout the project. In this paper, we propose an online course on PAME facilitated with the statistical software RStudio on Amazon Web Service (AWS).
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- 2022
- Full Text
- View/download PDF
4. From sequence to structure to mechanism to phenotype: The new frontiers of structural biology.
- Author
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Pastore A and Shakhnovitch E
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- Phenotype, Molecular Biology, Biology
- Abstract
Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
- Published
- 2023
- Full Text
- View/download PDF
5. Comparative examination of pinniped craniofacial musculature and its role in aquatic feeding
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Joy S. Reidenberg, Roxanne D. Cuthbertson, and Sarah S. Kienle
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Histology ,Seals, Earless ,Zoology ,adaptation ,Biology ,Predation ,foraging ,Tongue ,morphology ,medicine ,Animals ,Craniofacial ,marine mammals ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Key innovation ,Mammals ,Original Paper ,suction ,Skull ,Cell Biology ,Feeding Behavior ,Hyoid Muscle ,Original Papers ,biting ,Caniformia ,Sea Lions ,medicine.anatomical_structure ,Biting ,Underwater habitat ,Anatomy ,Developmental Biology - Abstract
Secondarily aquatic tetrapods have many unique morphologic adaptations for life underwater compared with their terrestrial counterparts. A key innovation during the land‐to‐water transition was feeding. Pinnipeds, a clade of air‐breathing marine carnivorans that include seals, sea lions, and walruses, have evolved multiple strategies for aquatic feeding (e.g., biting, suction feeding). Numerous studies have examined the pinniped skull and dental specializations for underwater feeding. However, data on the pinniped craniofacial musculoskeletal system and its role in aquatic feeding are rare. Therefore, the objectives of this study were to conduct a comparative analysis of pinniped craniofacial musculature and examine the function of the craniofacial musculature in facilitating different aquatic feeding strategies. We performed anatomic dissections of 35 specimens across six pinniped species. We describe 32 pinniped craniofacial muscles—including facial expression, mastication, tongue, hyoid, and soft palate muscles. Pinnipeds broadly conform to mammalian patterns of craniofacial muscle morphology. Pinnipeds also exhibit unique musculoskeletal morphologies—in muscle position, attachments, and size—that likely represent adaptations for different aquatic feeding strategies. Suction feeding specialists (bearded and northern elephant seals) have a significantly larger masseter than biters. Further, northern elephant seals have large and unique tongue and hyoid muscle morphologies compared with other pinniped species. These morphologic changes likely help generate and withstand suction pressures necessary for drawing water and prey into the mouth. In contrast, biting taxa (California sea lions, harbor, ringed, and Weddell seals) do not exhibit consistent craniofacial musculoskeletal adaptations that differentiate them from suction feeders. Generally, we discover that all pinnipeds have well‐developed and robust craniofacial musculature. Pinniped head musculature plays an important role in facilitating different aquatic feeding strategies. Together with behavioral and kinematic studies, our data suggest that pinnipeds’ robust facial morphology allows animals to switch feeding strategies depending on the environmental context—a critical skill in a heterogeneous and rapidly changing underwater habitat., Pinnipeds (seals, sea lions, and walruses) have strong, powerful craniofacial muscles that reflect their aquatic habitat and underwater feeding strategies. Their well‐developed facial expression, mastication, tongue, and hyoid muscles allow pinnipeds to successfully capture prey in dynamic marine ecosystems across the globe.
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- 2021
6. Long non-coding RNA 00960 promoted the aggressiveness of lung adenocarcinoma via the miR-124a/SphK1 axis
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Pengchong Zhu, Qiaoling Liu, Tao Ji, Lulu Zhang, Liang Li, Liangming Zhu, Zhipeng Ge, and Haibo Liu
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Male ,Lung Neoplasms ,Bioengineering ,Adenocarcinoma of Lung ,Applied Microbiology and Biotechnology ,Mice ,Downregulation and upregulation ,Cell Movement ,Cell Line, Tumor ,microRNA ,Animals ,Humans ,Luciferase ,Neoplasm Metastasis ,linc00960 ,Cell Proliferation ,sphk1 ,Gene knockdown ,biology ,Chemistry ,RNA ,General Medicine ,aggressiveness ,lung adenocarcinoma ,Molecular biology ,Long non-coding RNA ,Up-Regulation ,Gene Expression Regulation, Neoplastic ,MicroRNAs ,Phosphotransferases (Alcohol Group Acceptor) ,Sphingosine kinase 1 ,Cell culture ,A549 Cells ,Gene Knockdown Techniques ,biology.protein ,mir-124a ,Female ,RNA, Long Noncoding ,Neoplasm Transplantation ,TP248.13-248.65 ,Research Article ,Research Paper ,Biotechnology - Abstract
Long non-coding RNAs (lncRNAs) are closely associated with the development of lung adenocarcinoma (LADC). The present study focused on the role of LINC00960 in LADC. miRNA and mRNA expression levels were detected using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Cellular functions were evaluated by MTT, colony formation, and Transwell assays, respectively. LINC00960 Luciferase and RNA pull-down assays were performed to clarify the interaction between miR-124a and LINC00960 or Recombinant Sphingosine Kinase 1 (SphK1). We observed that LINC00960 was overexpressed in LADC tumor tissues and cell lines. LINC00960 knockdown suppressed the proliferation, migration, and invasion of LADC cells. Moreover, LINC00960 sponged miR-124a to inhibit the SphK1/S1P pathway in LADC cells. LINC00960 knockdown markedly reduced the rate of tumor growth. The luciferase reporter assay results demonstrated an interaction between miR-124a and LINC00960 or SphK1. This interaction was confirmed using the RNA pull-down assay. In addition, miR-124a downregulation or SphK1 upregulation reversed the inhibitory effects of LINC00960 knockdown on cellular functions of LADC cells, suggesting that LINC00960 may be a potential therapeutic biomarker for LADC via the miR-124a/SphK1 axis. Accordingly, LINC00960 may be a potential therapeutic biomarker for LADC.
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- 2022
7. Curcumin protection against ultraviolet-induced photo-damage in Hacat cells by regulating nuclear factor erythroid 2-related factor 2
- Author
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Runxiang Li, Huilan Zhu, Miaojian Wan, Huiyan Deng, Huaping Li, Quan Chen, and Bihua Liang
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Keratinocytes ,skin ,Cell Survival ,NF-E2-Related Factor 2 ,Ultraviolet Rays ,Apoptosis ,Bioengineering ,medicine.disease_cause ,Applied Microbiology and Biotechnology ,Antioxidants ,Superoxide dismutase ,chemistry.chemical_compound ,ultraviolet ,medicine ,HaCaT Cells ,Humans ,oxidative stress ,curcumin ,Cell Proliferation ,Cell Nucleus ,biology ,integumentary system ,Cell growth ,Chemistry ,photo-damage ,General Medicine ,respiratory system ,Molecular biology ,Heme oxygenase ,HaCaT ,nuclear factor erythroid 2-related factor 2 ,Cytoprotection ,Catalase ,biology.protein ,Curcumin ,Oxidative stress ,TP248.13-248.65 ,Research Article ,Research Paper ,Biotechnology - Abstract
Curcumin suppressed ultraviolet (UV) induced skin carcinogenesis and activated the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway. However, whether curcumin protects skin injury caused by UV is still unknown. A vitro model was established and curcumin effects on Hacat cells were detected. Nrf2 was knocked down in Hacat cells to verify the Nrf2 role in the protective effect of curcumin. Results indicated that ultraviolet A (UVA) (or ultraviolet B (UVB)) irradiation would lead to decreased cell proliferation, increased cell apoptosis, decreased catalase, heme oxygenase 1, and superoxide dismutase expression, and increased levels of protein carbonylation and malondialdehyde (p
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- 2021
8. Maturation of 23S rRNA includes removal of helix H1 in many bacteria
- Author
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Ralf Bundschuh, Elan A Shatoff, Bryan T Gemler, and Kurt Fredrick
- Subjects
Models, Molecular ,Biology ,Bacterial Physiological Phenomena ,Ribosome ,Ribosome assembly ,5S ribosomal RNA ,Structure-Activity Relationship ,RRNA modification ,Ribosomal protein ,23S ribosomal RNA ,Escherichia coli ,5S rRNA ,16S rRNA ,RNA Processing, Post-Transcriptional ,RRNA processing ,Molecular Biology ,Genetics ,Base Sequence ,SMART-seq ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,23S rRNA ,Cell Biology ,Gene Expression Regulation, Bacterial ,Ribosomal RNA ,50S subunit maturation ,RNA, Bacterial ,RNA, Ribosomal, 23S ,Nucleic Acid Conformation ,RNA-seq ,Research Article ,Research Paper - Abstract
In most bacteria, the three ribosomal RNAs (rRNAs) are encoded together in each of several near-identical operons. As soon as the nascent precursor rRNA emerges from RNA polymerase, ribosome assembly begins. This process entails ribosomal protein binding, rRNA folding, rRNA modification, and rRNA processing. In the model organisms Escherichia coli and Bacillus subtilis, rRNA processing results in similar mature rRNAs, despite substantial differences in the cohort of RNAses involved. A recent study of Flavobacterium johnsoniae, a member of the phylum Bacteroidota (formerly Bacteroidetes), revealed that helix H1 of 23S rRNA is absent from ribosomes, apparently a consequence of rRNA maturation. In this work, we mined RNA-seq data from 19 individual organisms and ocean metatranscriptomic samples to compare rRNA processing across diverse bacterial lineages. We found that mature ribosomes from multiple clades lack H1, and typically these ribosomes also lack an encoded H98. For all groups analysed, H1 is predicted to form in precursor rRNA as part of a longer leader-trailer helix. Hence, we infer that evolutionary loss of H98 sets the stage for H1 removal during 50S subunit maturation.
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- 2021
9. Spatiotemporal expression of long noncoding RNA Moshe modulates heart cell lineage commitment
- Author
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Young Jae Lee, Jung-Hoon Pyun, Na-Jung Kim, Jong-Sun Kang, Kang-Hoon Lee, YeonSung Son, Jinyoung Park, Eun-Hye Moon, Je-Yoel Cho, and A-Reum Nam
- Subjects
Organogenesis ,Cell Line ,Mesoderm ,Mice ,GATA6 Transcription Factor ,Gene expression ,Animals ,Humans ,Cell Lineage ,Myocytes, Cardiac ,RNA, Antisense ,atrial septal defect ,Promoter Regions, Genetic ,Molecular Biology ,Gene ,Transcription factor ,GATA6 ,biology ,Heart development ,Gene Expression Profiling ,Gene Expression Regulation, Developmental ,Cell Differentiation ,Cell Biology ,heart development ,second heart field ,Chromatin ,Cell biology ,Gata6 antisense transcript ,Enhancer Elements, Genetic ,Gene Knockdown Techniques ,Long non-coding RNA ,ISL1 ,biology.protein ,cardiovascular system ,RNA Interference ,RNA, Long Noncoding ,HAND2 ,Myoblasts, Cardiac ,Research Article ,Research Paper - Abstract
The roles of long non-coding RNA (LncRNA) have been highlighted in various development processes including congenital heart defects (CHD). Here, we characterized the molecular function of LncRNA, Moshe (1010001N08ik-203), one of the Gata6 antisense transcripts located upstream of Gata6, which is involved in both heart development and the most common type of congenital heart defect, atrial septal defect (ASD). During mouse embryonic development, Moshe was first detected during the cardiac mesoderm stage (E8.5 to E9.5) where Gata6 is expressed and continues to increase at the atrioventricular septum (E12.5), which is involved in ASD. Functionally, the knock-down of Moshe during cardiogenesis caused significant repression of Nkx2.5 in cardiac progenitor stages and resulted in the increase in major SHF lineage genes, such as cardiac transcriptional factors (Isl1, Hand2, Tbx2), endothelial-specific genes (Cd31, Flk1, Tie1, vWF), a smooth muscle actin (a-Sma) and sinoatrial node-specific genes (Shox2, Tbx18). Chromatin Isolation by RNA Purification showed Moshe activates Nkx2.5 gene expression via direct binding to its promoter region. Of note, Moshe was conserved across species, including human, pig and mouse. Altogether, this study suggests that Moshe is a heart-enriched lncRNA that controls a sophisticated network of cardiogenesis by repressing genes in SHF via Nkx2.5 during cardiac development and may play an important role in ASD.
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- 2021
10. Circular RNA_0037128 aggravates high glucose-induced damage in HK-2 cells via regulation of microRNA-497-5p/nuclear factor of activated T cells 5 axis
- Author
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Sufang Chen, Tianyi Li, Wenjun Jiao, Tao Feng, and Weifang Li
- Subjects
Down-Regulation ,Bioengineering ,Diabetic nephropathy ,Kidney ,Applied Microbiology and Biotechnology ,Proinflammatory cytokine ,Cell Line ,Superoxide dismutase ,Downregulation and upregulation ,NFAT5 ,miR-497-5p ,microRNA ,medicine ,Humans ,Diabetic Nephropathies ,Cell damage ,chemistry.chemical_classification ,Reactive oxygen species ,biology ,Base Sequence ,Chemistry ,Cell growth ,General Medicine ,RNA, Circular ,medicine.disease ,Molecular biology ,high glucose ,MicroRNAs ,Glucose ,Gene Knockdown Techniques ,biology.protein ,circ_0037128 ,TP248.13-248.65 ,Biotechnology ,Research Article ,Research Paper ,Transcription Factors - Abstract
Circular RNAs (CircRNAs) were reported to play vital roles in the progression of DN. Herein, the action of circular RNA_0037128 (circ_0037128) was investigated in DN. The level of circ_0037128, microRNA-497-5p (miR-497-5p) and nuclear factor of activated T cells 5 (NFAT5) was determined using quantitative real-time polymerase chain reaction (qRT-PCR). The feature of circ_0037128 was tested by RNase R and Actinomycin D treatment assays. Cell Counting Kit-8 (CCK-8) and 5-ethynyl-2ʹ-deoxyuridine (EdU) staining assays were conducted to evaluate the proliferation ability. The relative protein expression was determined via Western blot analysis. Levels of the inflammatory cytokines, like tumor necrosis factor α (TNF-α), interleukin-1β (IL-1β) and interleukin-6 (IL-6), were assessed by enzyme-linked immunosorbent assay (ELISA). Reactive oxygen species (ROS) production, lactate dehydrogenase (LDH) and superoxide dismutase (SOD) activity were determined by the matched kits. Dual-luciferase reporter and RNA immunoprecipitation (RIP) assays were conducted for evaluating the correlation between miR-497-5p and circ_0037128 or NFAT5. Circ_0037128 and NFAT5 were enhanced, while miR-497-5p was weakened in kidney tissues of DN patients and high glucose (HG)-cultured HK-2 cells. Circ_0037128 inhibition bated HG-caused inhibition effect on cell proliferation and promotion effects on oxidative stress, inflammation and fibrosis in HK-2 cells. Moreover, circ_0037128 knockdown alleviated HG-caused cell damage via regulating miR-497-5p. In addition, NFAT5 overexpression could reverse the influence of miR-497-5p on HG-induced injury in HK-2 cells. Mechanically, circ_0037128 sponged miR-497-5p to modulate NFAT5. Circ_0037128 downregulation could mitigate HG-stimulated cell damage via regulating the miR-497-5p/NFAT5 axis in HK-2 cells in vitro, providing a possible therapy target for DN.
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- 2021
11. Single-cell RNA sequencing deconvolutes the in vivo heterogeneity of human bone marrow-derived mesenchymal stem cells
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Hong-Wen Deng, Yun Gong, Zun Wang, Li-Jun Tan, Yang Junxiao, Yiping Chen, Xiang Qiu, Cui Zhou, Liang Cheng, Jonathan Greenbaum, Siyuan Tang, Hong-Mei Xiao, Yusheng Li, Martin R. Schiller, Xiaohua Li, Yu Chen, Huixi Zhang, Yihe Hu, Hui Shen, Yang Xucheng, Ying Liu, and Jie Xie
- Subjects
Male ,Stromal cell ,bone marrow ,Bone Marrow Cells ,Nerve Tissue Proteins ,Receptors, Nerve Growth Factor ,Biology ,Muscle Development ,Applied Microbiology and Biotechnology ,Chondrocyte ,osteogenesis ,adipogenesis ,Mice ,Chondrocytes ,Bone Density ,chondrogenesis ,medicine ,Animals ,Cluster Analysis ,Humans ,Molecular Biology ,single-cell RNA sequencing (scRNA-seq) ,Ecology, Evolution, Behavior and Systematics ,Aged ,Aged, 80 and over ,Cluster of differentiation ,mesenchymal stem cell (MSC) ,Sequence Analysis, RNA ,Mesenchymal stem cell ,Osteoblast ,Cell Differentiation ,Mesenchymal Stem Cells ,Cell Biology ,CD56 Antigen ,Cell biology ,Mice, Inbred C57BL ,Haematopoiesis ,medicine.anatomical_structure ,Gene Expression Regulation ,Osteocyte ,Female ,Bone marrow ,Single-Cell Analysis ,Developmental Biology ,Research Paper - Abstract
Bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stromal cells that have a critical role in the maintenance of skeletal tissues such as bone, cartilage, and the fat in bone marrow. In addition to providing microenvironmental support for hematopoietic processes, BM-MSCs can differentiate into various mesodermal lineages including osteoblast/osteocyte, chondrocyte, and adipocyte that are crucial for bone metabolism. While BM-MSCs have high cell-to-cell heterogeneity in gene expression, the cell subtypes that contribute to this heterogeneity in vivo in humans have not been characterized. To investigate the transcriptional diversity of BM-MSCs, we applied single-cell RNA sequencing (scRNA-seq) on freshly isolated CD271+ BM-derived mononuclear cells (BM-MNCs) from two human subjects. We successfully identified LEPRhiCD45low BM-MSCs within the CD271+ BM-MNC population, and further codified the BM-MSCs into distinct subpopulations corresponding to the osteogenic, chondrogenic, and adipogenic differentiation trajectories, as well as terminal-stage quiescent cells. Biological functional annotations of the transcriptomes suggest that osteoblast precursors induce angiogenesis coupled with osteogenesis, and chondrocyte precursors have the potential to differentiate into myocytes. We also discovered transcripts for several clusters of differentiation (CD) markers that were either highly expressed (e.g., CD167b, CD91, CD130 and CD118) or absent (e.g., CD74, CD217, CD148 and CD68) in BM-MSCs, representing potential novel markers for human BM-MSC purification. This study is the first systematic in vivo dissection of human BM-MSCs cell subtypes at the single-cell resolution, revealing an insight into the extent of their cellular heterogeneity and roles in maintaining bone homeostasis.
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- 2021
12. Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples
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Frank P.H.A. Vandenbussche, Thierry van den Berg, Steven Van Borm, Bénédicte Lambrecht, Elisabeth Mathijs, and Mieke Steensels
- Subjects
Next-Generation Sequencing ,animal structures ,Coronaviridae ,viruses ,Sicinivirus ,Infectious bronchitis virus ,Gallus gallus ,Biology ,medicine.disease_cause ,Virus ,Leucosis ,Astrovirus ,Infectious bursal disease ,03 medical and health sciences ,Virology ,Genetics ,medicine ,Animals ,Molecular Biology ,Poultry Diseases ,030304 developmental biology ,Coronavirus ,2. Zero hunger ,0303 health sciences ,Original Paper ,030306 microbiology ,Virome ,RNA virus ,General Medicine ,Genomics ,biology.organism_classification ,medicine.disease ,Avian orthoreovirus ,embryonic structures ,Metagenomics ,Igacovirus ,Chickens - Abstract
Infectious bronchitis virus (IBV, genus Gammacoronavirus) causes an economically important and highly contagious disease in chicken. Random primed RNA sequencing was applied to two IBV positive clinical samples and one in ovo-passaged virus. The virome of a cloacal swab pool was dominated by IBV (82% of viral reads) allowing de novo assembly of a GI-13 lineage complete genome with 99.95% nucleotide identity to vaccine strain 793B. In addition, substantial read counts (16% of viral reads) allowed the assembly of a near-complete chicken astrovirus genome, while lower read counts identified the presence of chicken calicivirus and avian leucosis virus. Viral reads in a respiratory/intestinal tissue pool were distributed between IBV (22.53%), Sicinivirus (Picornaviridae, 24%), and avian leucosis virus (37.04%). A complete IBV genome with 99.95% nucleotide identity to vaccine strain H120 (lineage GI-1), as well as a near-complete avian leucosis virus genome and a partial Sicinivirus genome were assembled from the tissue sample data. Lower read counts identified chicken calicivirus, Avibirnavirus (infectious bursal disease virus, assembling to 98.85% of segment A and 69.66% of segment B closely related to D3976/1 from Germany, 2017) and avian orthoreovirus, while three avian orthoavulavirus 1 reads confirmed prior real-time RT-PCR result. IBV sequence variation analysis identified both fixed and minor frequency variations in the tissue sample compared to its in ovo-passaged virus. Metagenomic methods allow the determination of complete coronavirus genomes from clinical chicken samples while providing additional insights in RNA virus sequence diversity and coinfecting viruses potentially contributing to pathogenicity. Supplementary Information The online version contains supplementary material available at 10.1007/s11262-021-01872-7.
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- 2021
13. Integrated multi-omics reveals common properties underlying stress granule and P-body formation
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Chris M. Grant, Mark P. Ashe, Michael G. Nelson, Martin D. Jennings, Christopher J. Kershaw, Christian Bates, Jennifer Lui, and Simon J. Hubbard
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Proteomics ,Proteome ,RNA-binding protein ,Biology ,Low complexity ,Stress granule ,stomatognathic system ,Stress, Physiological ,Gene Expression Regulation, Fungal ,Yeasts ,P-bodies ,Humans ,Molecular Biology ,Regulation of gene expression ,Messenger RNA ,Chemistry ,RNA fate ,Gene Expression Profiling ,RNA ,translational control ,Cell Biology ,glucose depletion yeast ,Genomics ,Processing Bodies ,Stress Granules ,Cell biology ,Glucose ,p-bodies ,Multi omics ,Stress conditions ,Research Article ,Research Paper - Abstract
Non-membrane-bound compartments such as P-bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. We have systematically and quantitatively determined the protein and mRNA composition of PBs and SGs formed before and after nutrient stress. We find that high molecular weight (HMW) complexes exist prior to glucose depletion that we propose may act as seeds for further condensation of proteins forming mature PBs and SGs. We identify an enrichment of proteins with low complexity and RNA binding domains, as well as long, structured mRNAs that are poorly translated following nutrient stress. Many proteins and mRNAs are shared between PBs and SGs including several multivalent RNA binding proteins that promote condensate interactions during liquid-liquid phase separation. We uncover numerous common protein and RNA components across PBs and SGs that support a complex interaction profile during the maturation of these biological condensates. These interaction networks represent a tuneable response to stress, highlighting previously unrecognized condensate heterogeneity. These studies therefore provide an integrated and quantitative understanding of the dynamic nature of key biological condensates.
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- 2021
14. A novel mutation in PCK2 gene causes primary angle-closure glaucoma
- Author
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Tao Liu, Menghan Xu, Zheng Liu, Xuemei Xing, Jin Yang, and Jia-Yue Sun
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Adult ,Male ,Aging ,China ,Glaucoma ,Biology ,Cell Line ,medicine ,Missense mutation ,Animals ,Humans ,Genetic Predisposition to Disease ,Disease-causing Mutation ,primary angle closure glaucoma ,Gene ,Protein kinase B ,disease-causing mutation ,Whole Genome Sequencing ,apoptosis ,Cell Biology ,Transfection ,Middle Aged ,medicine.disease ,Molecular biology ,Pedigree ,Rats ,medicine.anatomical_structure ,PCK2 ,whole-genome sequencing ,Mutation (genetic algorithm) ,Mutation ,Female ,Trabecular meshwork ,sense organs ,Glaucoma, Angle-Closure ,Phosphoenolpyruvate Carboxykinase (ATP) ,Research Paper - Abstract
Primary angle-closure glaucoma (PACG) is an ophthalmic genetic disease characterized by direct contact between the iris and trabecular meshwork, resulting in an obstructed outflow of aqueous humor from the eye. However, it is unclear as to what role genetics plays in the development of PACG. The present study investigated the disease-causing mutation in a five-generation Chinese PACG family using whole-genome sequencing. A novel heterozygous missense mutation c.977C>T in PCK2 gene was identified in five affected family members, but not in any unaffected and 86 unrelated healthy individuals. This nucleotide substitute is predicted to result in a proline to leucine substitution p.Pro326Leu. Furthermore, the function of this mutation was analyzed through various in vitro assays using the RGC-5 cell line. Our results demonstrate that the p.Pro326Leu mutation induces RGC-5 cell cycle arrest and apoptosis with a decreased BcL-XL. The increasing P53, P27, P21, AKT, and P-GSK3α were also detected in the cells transfected with c.977C>T mutation, suggesting that this mutation within PCK2 gene cause PACG through impairment of AKT/GSK3α signaling pathway.
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- 2021
15. Targeted Inhibition of LPL/FABP4/CPT1 fatty acid metabolic axis can effectively prevent the progression of nonalcoholic steatohepatitis to liver cancer
- Author
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Qingmei Deng, Hongzhi Wang, Haoran Yang, Yu liu, Li Lu, Tun Ni, Haiming Dai, and Wulin Yang
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Carcinoma, Hepatocellular ,Hepatocellular carcinoma ,Cell ,Biology ,Fatty Acid-Binding Proteins ,Applied Microbiology and Biotechnology ,Malignant transformation ,chemistry.chemical_compound ,Mice ,Downregulation and upregulation ,Non-alcoholic Fatty Liver Disease ,Cell Line, Tumor ,Nonalcoholic fatty liver disease ,Databases, Genetic ,medicine ,Animals ,Humans ,Nonalcoholic steatohepatitis ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Gene differential expression ,Fatty acid metabolism ,Carnitine O-Palmitoyltransferase ,Transdifferentiation ,Liver Neoplasms ,Metabolic reprogramming ,food and beverages ,nutritional and metabolic diseases ,Computational Biology ,Cell Biology ,medicine.disease ,digestive system diseases ,Up-Regulation ,Mice, Inbred C57BL ,Lipoprotein Lipase ,medicine.anatomical_structure ,chemistry ,Gene Expression Regulation ,Cancer research ,Neoplastic Stem Cells ,Stem cell ,Liver cancer ,Developmental Biology ,Research Paper - Abstract
Rationale: Nonalcoholic steatohepatitis (NASH), as one of the key stages in the development of nonalcoholic fatty liver disease (NAFLD), can directly progress to HCC, but the underlying mechanism is not fully understood. Methods: Differentially expressed genes (DEGs) in each stage of disease development were studied through a GEO dataset deriving from a Stelic Animal Model (STAM), which can simulate the evolution of NAFLD/NASH to HCC in humans. GSVA analysis was performed to analyze the differentially expressed oncogenic signatures in each stage. A human NAFLD-related dataset from GEO database was utilized for gene expression verification and further validated in the protein level in STAM mice. Small molecule inhibitors were applied to STAM mice for investigating whether inhibition of the LPL/FABP4/CPT1 axis could prevent the occurrence of NASH-related HCC in vivo. Microsphere formation and clonal formation assays in vitro were applied to study if inhibition of the LPL/FABP4/CPT1 axis can reduce the viability of liver cancer stem cells (LCSCs). Results: We found that upregulation of the LPL/FABP4/CPT1 molecular axis, as a fatty acid metabolic reprogramming process, occurred specifically during the NASH phase. GSVA analysis showed widespread activation of a large number of oncogenic signals, which may contribute to malignant transformation during NASH. Furthermore, inhibition of the LPL/FABP4/CPT1 axis could effectively delay the tumor growth in STAM mice. Cell assays revealed inhibitors targeting this axis can significantly reduce the sphere-forming, proliferation, and clonality of LCSCs. Conclusion: These results suggest that activation of the LPL/FABP4/CPT1 axis is essential for LCSCs maintenance, which acts synergistically with a variety of up-regulated oncogenic signals that drive the hepatocyte-LCSCs transdifferentiation during NASH to HCC progression. Thus, targeting the LPL/FABP4/CPT1 axis may provide a potential direction for NASH-related HCC prevention.
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- 2021
16. Co-targeting BET bromodomain BRD4 and RAC1 suppresses growth, stemness and tumorigenesis by disrupting the c-MYC-G9a-FTH1axis and downregulating HDAC1 in molecular subtypes of breast cancer
- Author
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Nour Al-Jabi, Amjad Ali, Khuloud Bajbouj, Rola Abu Jabal, Hema Unnikannan, Jasmin Shafarin, Jibran Sualeh Muhammad, and Mawieh Hamad
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rac1 GTP-Binding Protein ,Carcinogenesis ,Cell Cycle Proteins ,Histone Deacetylase 1 ,medicine.disease_cause ,Applied Microbiology and Biotechnology ,Metastasis ,Mice ,Breast cancer ,Histocompatibility Antigens ,Cell migration ,Azepines ,Gene Expression Regulation, Neoplastic ,c-MYC ,FTH1 ,Aminoquinolines ,BRD4 ,Female ,Oxidoreductases ,BET bromodomain ,RAC1 ,Research Paper ,G9a ,JQ1 ,Mice, Nude ,Breast Neoplasms ,Biology ,Proto-Oncogene Proteins c-myc ,Cell Line, Tumor ,medicine ,Animals ,Humans ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,NSC23766 ,Cell Proliferation ,Cell growth ,Cancer ,Cell Biology ,Histone-Lysine N-Methyltransferase ,Triazoles ,medicine.disease ,Xenograft Model Antitumor Assays ,HDAC1 ,Pyrimidines ,Ferritins ,Cancer research ,Developmental Biology ,Transcription Factors - Abstract
BET bromodomain BRD4 and RAC1 oncogenes are considered important therapeutic targets for cancer and play key roles in tumorigenesis, survival and metastasis. However, combined inhibition of BRD4-RAC1 signaling pathways in different molecular subtypes of breast cancer including luminal-A, HER-2 positive and triple-negative breast (TNBC) largely remains unknown. Here, we demonstrated a new co-targeting strategy by combined inhibition of BRD4-RAC1 oncogenic signaling in different molecular subtypes of breast cancer in a context-dependent manner. We show that combined treatment of JQ1 (inhibitor of BRD4) and NSC23766 (inhibitor of RAC1) suppresses cell growth, clonogenic potential, cell migration and mammary stem cells expansion and induces autophagy and cellular senescence in molecular subtypes of breast cancer cells. Mechanistically, JQ1/NSC23766 combined treatment disrupts MYC/G9a axis and subsequently enhances FTH1 to exert antitumor effects. Furthermore, combined treatment targets HDAC1/Ac-H3K9 axis, thus suggesting a role of this combination in histone modification and chromatin modeling. C-MYC depletion and co-treatment with vitamin-C sensitizes different molecular subtypes of breast cancer cells to JQ1/NSC23766 combination and further reduces cell growth, cell migration and mammosphere formation. Importantly, co-targeting RAC1-BRD4 suppresses breast tumor growth in vivo using xenograft mouse model. Clinically, RAC1 and BRD4 expression positively correlates in breast cancer patient's samples and show high expression patterns across different molecular subtypes of breast cancer. Both RAC1 and BRD4 proteins predict poor survival in breast cancer patients. Taken together, our results suggest that combined inhibition of BRD4-RAC1 pathways represents a novel and potential therapeutic approach in different molecular subtypes of breast cancer and highlights the importance of co-targeting RAC1-BRD4 signaling in breast tumorigenesis via disruption of C-MYC/G9a/FTH1 axis and down regulation of HDAC1.
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- 2021
17. 40th Anniversary Virtual Issues: Genomic Innovations in Extremophiles.
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McGrath, Casey L
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MOLECULAR evolution ,BIOLOGICAL evolution ,MOLECULAR biology ,PERIODICAL publishing ,BIOLOGY - Abstract
To celebrate the 40th anniversary of Molecular Biology and Evolution, the Society for Molecular Biology and Evolution (SMBE) is publishing a series of virtual issues in 2024. These virtual issues feature selected papers from the society's journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue is accompanied by a Perspective that highlights the contributions of the journals to a specific topic in molecular evolution. The August Perspective, titled "Lessons from extremophiles: genomic innovations and functional adaptations across the eukaryotic tree of life," was written by H.B. Rappaport and Angela M. Oliverio and appears in Genome Biology and Evolution. The virtual issues include noteworthy papers on Genomic Innovations in Extremophiles and can be found on SMBE's 40th anniversary site. [Extracted from the article]
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- 2024
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18. Cranial shape variation in mink: separating two highly similar species
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Brandon M. Kilbourne, Eloy Gálvez-López, and Philip G. Cox
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Male ,Histology ,Zoology ,Bite Force ,Neovison ,cranium ,shape variation ,biology.animal ,medicine ,Animals ,Humans ,Mink ,American mink ,geometric morphometrics ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,European mink ,Morphometrics ,Original Paper ,Sex Characteristics ,biology ,Skull ,Mustela lutreola ,Cell Biology ,biology.organism_classification ,Original Papers ,Sexual dimorphism ,medicine.anatomical_structure ,Neurocranium ,sexual dimorphism ,Female ,Allometry ,Anatomy ,Head ,Developmental Biology - Abstract
European and American minks (Mustela lutreola and Neovison vison, respectively) are very similar in their ecology, behavior, and morphology. However, the American mink is a generalist predator and seems to adapt better to anthropized environments, allowing it to outcompete the European mink in areas where it has been introduced, threatening the survival of the native species. To assess whether morphological differences may be contributing to the success of the American mink relative to the European mink, we analyzed shape variation in the cranium of both species using 3D geometric morphometrics. A set of 38 landmarks and 107 semilandmarks was used to study shape variation between and within species, and to assess how differences in size factored into that variation. Sexual dimorphism in both size and shape was also studied. Significant differences between species were found in cranial shape, but not in size. Relative to American mink, European mink have a shorter facial region with a rounder forehead and wider orbits, a longer neurocranium with less developed crests and processes, and an antero‐medially placed tympanic bullae with an anteriorly expanded cranial border. Within species, size‐related sexual dimorphism is highly significant, but sexual dimorphism in shape is only significant in American mink, not in European mink. Additionally, two trends common to both species were discovered, one related to allometric changes and another to sexual size dimorphism. Shape changes related to increasing size can be subdivided into two, probably related, groups: increased muscle force and growth. The first group somewhat parallels the differences between both mink species, while the second group of traits includes an anterodorsal expansion of the face, and the neurocranium shifting from a globous shape in small individuals to a dorsoventrally flattened ellipse in the largest ones. Finally, the sexual dimorphism trend, while also accounting for differences in muscle force, seems to be related to the observed dietary differences between males and females. Overall, differences between species and sexes, and shape changes with increasing size, seem to mainly relate to differences in masticatory‐muscle volume and therefore muscle force and bite force, which, in turn, relate to a wider range of potential prey (bigger prey, tougher shells). Thus, muscle force (and dietary range) would be larger in American mink than in European mink, in males than in females, and in larger individuals than in smaller ones., Cranial shape and size variation in European (Mlu) and American minks (Nvi) were studied. Both species differed in shape but not size, while sexes within each differed in size but in shape only for Nvi. Allometric shape changes were related to growth and sexual dimorphism. Overall, differences among species, sexes, and sizes related to masticatory‐muscle volume, which suggests that muscle force (and dietary range) would be larger in Nvi than in Mlu, in males than in females, and in larger mink.
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- 2022
19. Deletion of Smad3 protects against C-reactive protein-induced renal fibrosis and inflammation in obstructive nephropathy
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Hai-Di Li, Jin-Cheng Zeng, Wei-Feng Wu, Hui Y. Lan, Yong-Ke You, Ye-Ping Ren, Hai-Yong Chen, and Xiao-Ru Huang
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Male ,medicine.medical_specialty ,Inflammation ,urologic and male genital diseases ,Applied Microbiology and Biotechnology ,NF-κB ,C-reactive protein ,Cell Line ,chemistry.chemical_compound ,Mice ,Fibrosis ,Internal medicine ,medicine ,Renal fibrosis ,Animals ,Smad3 Protein ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Mice, Knockout ,Kidney ,UUO ,biology ,business.industry ,urogenital system ,Cell Biology ,medicine.disease ,Obstructive Nephropathy ,Rats ,Disease Models, Animal ,medicine.anatomical_structure ,Endocrinology ,chemistry ,renal fibrosis and inflammation ,biology.protein ,Kidney Diseases ,medicine.symptom ,business ,Gene Deletion ,Developmental Biology ,Kidney disease ,Research Paper ,TGF-β/Smad3 ,Ureteral Obstruction - Abstract
Introduction and Aims: Elevated plasma levels of C-reactive protein (CRP) are closely associated with progressive renal injury in patients with chronic kidney disease (CKD). Here, we tested a hypothesis that CRP may promote renal fibrosis and inflammation via a TGF-β/Smad3-dependent mechanism. Methods: Role and mechanisms of TGF-β/Smad3 in CRP-induced renal fibrosis and inflammation were examined in a mouse model of unilateral ureteral obstruction (UUO) induced in CRP Tg/Smad3 KO mice and in a rat tubular epithelial cell line in which Smad3 gene is stably knocked down (S3KD-NRK52E). Results: We found that mice overexpressing the human CRP gene were largely promoted renal inflammation and fibrosis as evidenced by increasing IL-1β, TNF-α, MCP-1 expression, F4/80+ macrophages infiltration, and marked accumulation of α-smooth muscle actin (α-SMA), collagen I and fibronectin in the UUO kidney, which were blunted when Smad3 gene was deleted in CRPtg-Smad3KO. Mechanistically, we found that the protection of renal inflammation and fibrosis in the UUO kidney of CRPtg-Smad3KO mice was associated with the inactivation of CD32-NF-κB and TGF-β/Smad3 signaling. Conclusion: In conclusion, Smad3 deficiency protects against CRP-mediated renal inflammation and fibrosis in the UUO kidney by inactivating CD32-NF-κB and TGF-β/Smad3 signaling.
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- 2021
20. Cohnella cholangitidis sp. nov., a novel species of the genus Cohnella isolated from a clinical specimen in Korea
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Young Sill Choi, Min Kyoung Shin, Kyu Jam Hwang, Myunghwan Jung, Su Yeon Kim, Woo-Kon Lee, Chi-Hwan Choi, Joon Ki Kim, and Dae Won Kim
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DNA, Bacterial ,Sequence analysis ,Biochemistry ,Microbiology ,Complete genome ,Human blood ,chemistry.chemical_compound ,RNA, Ribosomal, 16S ,Genotype ,Cohnella cholangitidis ,Republic of Korea ,Genetics ,Humans ,Molecular Biology ,Gene ,Phospholipids ,Phylogeny ,Taxonomy ,Original Paper ,Bacillales ,biology ,Strain (chemistry) ,Fatty Acids ,Vitamin K 2 ,General Medicine ,Sequence Analysis, DNA ,16S ribosomal RNA ,biology.organism_classification ,Novel species ,Bacterial Typing Techniques ,chemistry ,Taxonomy (biology) ,Peptidoglycan ,Bacteria - Abstract
A Gram-positive, aerobic, rod-shaped bacterium, designated as strain 1605-214T, was isolated from the blood sample of a patient with cholangitis. Based on its 16S rRNA gene sequence, the strain 1605-214T belonged to the genus Cohnella and exhibited 97.9% sequence identity with Cohnella luojiensis DSM 24270T (GQ214052). DNA–DNA hybridization, digital DNA–DNA hybridization, and average nucleotide identity values between the two species were 23% ± 1.9, 21.1%, and 77.2%, respectively. The cellular fatty acids of strain 1605-214T were mainly comprised of anteiso-C15:0 (36.1%), iso-C16:0 (16.5%), and C16:0 (15.1%). The predominant quinone was menaquinone-7; predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and aminophospholipid-1. The cell wall peptidoglycan of strain 1605-214T contained meso-diaminopimelic acid. DNA G + C content of strain 1605-214T was 50.6 mol%. 5187 genes out of a total of 5413 (94.6%) were assigned putative functions using eggNOG v5.0. Based on genotypic characteristics and genomic sequence analysis results, strain 1605-214T was confirmed to represent a novel species of genus Cohnella, for which the name Cohnella cholangitidis sp. nov., was proposed.
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- 2021
21. Anaerobic 3-methylhopanoid production by an acidophilic photosynthetic purple bacterium
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M. N. Parenteau, Linda L. Jahnke, Michael T. Madigan, Megan L. Kempher, Paula V. Welander, and Marisa H. Mayer
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Hopanoids ,Aerobic bacteria ,Photosynthesis ,Biochemistry ,Microbiology ,Anoxygenic phototrophs ,Microbial ecology ,RNA, Ribosomal, 16S ,Botany ,Genetics ,Anaerobiosis ,Molecular Biology ,Phylogeny ,Original Paper ,Base Composition ,biology ,Phototroph ,Chemistry ,Rhodopila globiformis ,General Medicine ,Sequence Analysis, DNA ,biology.organism_classification ,Anoxic waters ,Warm thermal springs ,Acetobacteraceae ,Anaerobic exercise ,Bacteria - Abstract
Bacterial lipids are well-preserved in ancient rocks and certain ones have been used as indicators of specific bacterial metabolisms or environmental conditions existing at the time of rock deposition. Here we show that an anaerobic bacterium produces 3-methylhopanoids, pentacyclic lipids previously detected only in aerobic bacteria and widely used as biomarkers for methane-oxidizing bacteria. Both Rhodopila globiformis, a phototrophic purple nonsulfur bacterium isolated from an acidic warm spring in Yellowstone, and a newly isolated Rhodopila species from a geochemically similar spring in Lassen Volcanic National Park (USA), synthesized 3-methylhopanoids and a suite of related hopanoids and contained the genes encoding the necessary biosynthetic enzymes. Our results show that 3-methylhopanoids can be produced under anoxic conditions and challenges the use of 3-methylhopanoids as biomarkers of oxic conditions in ancient rocks and as prima facie evidence that methanotrophic bacteria were active when the rocks were deposited.
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- 2021
22. ATF4 links ER stress with reticulophagy in glioblastoma cells
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Sjoerd J L van Wijk, Nina Meyer, Donat Kögel, Muriel Mari, Svenja Zielke, Laura Zein, Simon Kardo, Fulvio Reggiori, Adriana Covarrubias-Pinto, Alexandra Stolz, Maximilian N. Kinzler, Simone Fulda, Center for Liver, Digestive and Metabolic Diseases (CLDM), and Microbes in Health and Disease (MHD)
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0301 basic medicine ,RETREG1 ,STIMULATION ,loperamide ,ENDOPLASMIC-RETICULUM TURNOVER ,Eukaryotic translation initiation factor 2A ,PATHWAY ,EIF2AK3 ,Endoribonucleases/metabolism ,education.field_of_study ,UNFOLDED PROTEIN RESPONSE ,DEATH ,Endoplasmic Reticulum Stress ,Cell biology ,autophagic cell death ,p-eIF2α ,AUTOPHAGY ,Autophagy/physiology ,FAM134B ,Research Paper ,PERK ,MZ-54 ,BiP ,CARGO RECOGNITION ,Reticulophagy ,Biology ,Protein Serine-Threonine Kinases ,03 medical and health sciences ,Endoribonucleases ,Humans ,HSPA5 ,education ,Molecular Biology ,selective autophagy ,030102 biochemistry & molecular biology ,ATF6 ,Endoplasmic reticulum ,PHAGY ,ATF4 ,Cell Biology ,Activating Transcription Factor 4/metabolism ,Activating Transcription Factor 4 ,ERN1 ,Glioblastoma/pathology ,TEX264 ,030104 developmental biology ,Unfolded protein response ,MEFs ,Glioblastoma ,RESISTANCE - Abstract
Selective degradation of the endoplasmic reticulum (ER; reticulophagy) is a type of autophagy involved in the removal of ER fragments. So far, amino acid starvation as well as ER stress have been described as inducers of reticulophagy, which in turn restores cellular energy levels and ER homeostasis. Here, we explored the autophagy-inducing mechanisms that underlie the autophagic cell death (ACD)-triggering compound loperamide (LOP) in glioblastoma cells. Interestingly, LOP triggers upregulation of the transcription factor ATF4, which is accompanied by the induction of additional ER stress markers. Notably, knockout of ATF4 significantly attenuated LOP-induced autophagy and ACD. Functionally, LOP also specifically induces the engulfment of large ER fragments within autophagosomes and lysosomes as determined by electron and fluorescence microscopy. LOP-induced reticulophagy and cell death are predominantly mediated through the reticulophagy receptor RETREG1/FAM134B and, to a lesser extent, TEX264, confirming that reticulophagy receptors can promote ACD. Strikingly, apart from triggering LOP-induced autophagy and ACD, ATF4 is also required for LOP-induced reticulophagy. These observations highlight a key role for ATF4, RETREG1 and TEX264 in response to LOP-induced ER stress, reticulophagy and ACD, and establish a novel mechanistic link between ER stress and reticulophagy, with possible implications for additional models of drug-induced ER stress. Abbreviations: ACD: autophagic cell death; ATF6: activating transcription factor 6; ATL3: atlastin 3; BafA 1: bafilomycin A 1; CCPG1: cell cycle progression gene 1; co-IP: co-immunoprecipitation; DDIT3/CHOP: DNA damage inducible transcript 3; ER: endoplasmic reticulum; EIF2A/eIF2α: eukaryotic translation initiation factor 2A; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; ERN1/IRE1α: endoplasmic reticulum to nucleus signaling 1; GABARAP: GABA type A receptor-associated protein; GBM: glioblastoma multiforme; HSPA5/BiP: heat shock protein family (Hsp70) member 5; LOP: loperamide; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; RETREG1/FAM134B: reticulophagy regulator 1; RTN3L: reticulon 3 long; SEC62: SEC62 homolog, protein translocation factor; TEX264: testis-expressed 264, reticulophagy receptor; UPR: unfolded protein response.
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- 2021
23. Evaluating the estimation of genetic correlation and heritability using summary statistics
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Fredrick R. Schumacher and Ju Zhang
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Genetic correlation ,Population ,Methods Paper ,Single-nucleotide polymorphism ,Biology ,Polymorphism, Single Nucleotide ,Heritability ,Quantitative Trait, Heritable ,Neoplasms ,Statistics ,Genetics ,Humans ,Generalizability theory ,Computer Simulation ,Genetic Predisposition to Disease ,education ,Evaluation ,Molecular Biology ,Estimation ,education.field_of_study ,Models, Genetic ,General Medicine ,Summary statistics ,Sample size determination ,Genetic Background ,Genome-Wide Association Study - Abstract
While novel statistical methods quantifying the shared heritability of traits and diseases between ancestral distinct populations have been recently proposed, a thorough evaluation of these approaches under differing circumstances remain elusive. Brown et al.2016 proposed the method Popcorn to estimate the shared heritability, i.e. genetic correlation, using only summary statistics. Here, we evaluate Popcorn under several parameters and circumstances: sample size, number of SNPs, sample size of external reference panel, various population pairs, inappropriate external reference panel, and admixed population involved. Our results determined the minimum sample size of the external reference panel, summary statistics, and number of SNPs required to accurately estimate both the genetic correlation and heritability. Moreover, the number of individuals and SNPs required to produce accurate and stable estimates was directly proportional with heritability in Popcorn. Misrepresentation of the reference panel overestimated the genetic correlation by 20% and heritability by 60%. Lastly, applying Popcorn to homogeneous (EUR) and admixed (ASW) populations underestimated the genetic correlation by 15%. Although statistical approaches estimating the shared heritability between ancestral populations will provide novel etiologic insight, caution is required ensuring results are based on the appropriate sample size, number of SNPs, and the generalizability of the reference panel to the discovery populations.
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- 2021
24. Comprehensive landscape of the renin-angiotensin system in Pan-cancer: a potential downstream mediated mechanism of SARS-CoV-2
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Liying Shan, Yuqing Cui, Fengzhi Chen, Yan Guo, Dandan Wang, Xiaoying Jin, Jiayi Gao, Xuesong Chen, and Mengxia Lei
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medicine.medical_treatment ,ACE2 ,Pan-cancer ,RAS family ,Applied Microbiology and Biotechnology ,Proto-Oncogene Mas ,Renin-Angiotensin System ,Ubiquitin ,Downregulation and upregulation ,Neoplasms ,medicine ,Humans ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,Tumor microenvironment ,biology ,SARS-CoV-2 ,Cancer ,COVID-19 ,Cell Biology ,Immunotherapy ,DNA Methylation ,medicine.disease ,Immune checkpoint ,Immune infiltration ,Gene Expression Regulation, Neoplastic ,DNA methylation ,Cancer research ,biology.protein ,Protein Processing, Post-Translational ,Developmental Biology ,Research Paper - Abstract
Background: SARS-CoV-2, the cause of the worldwide COVID-19 pandemic, utilizes the mechanism of binding to ACE2 (a crucial component of the renin-angiotensin system [RAS]), subsequently mediating a secondary imbalance of the RAS family and leading to severe injury to the host. However, very few studies have been conducted to reveal the mechanism behind the effect of SARS-CoV-2 on tumors. Methods: Demographic data extracted from 33 cancer types and over 10,000 samples were employed to determine the comprehensive landscape of the RAS. Expression distribution, pretranscriptional and posttranscriptional regulation and posttranslational modifications (PTMs) as well as genomic alterations, DNA methylation and m6A modification were analyzed in both tissue and cell lines. The clinical phenotype, prognostic value and significance of the RAS during immune infiltration were identified. Results: Low expression of AGTR1 was common in tumors compared to normal tissues, while very low expression of AGTR2 and MAS1 was detected in both tissues and cell lines. Differential expression patterns of ACE in ovarian serous cystadenocarcinoma (OV) and kidney renal clear cell carcinoma (KIRC) were correlated with ubiquitin modification involving E3 ligases. Genomic alterations of the RAS family were infrequent across TCGA pan-cancer program, and ACE had the highest alteration frequency compared with other members. Low expression of AGTR1 may result from hypermethylation in the promoter. Downregulation of RAS family was linked to higher clinical stage and worse survival (as measured by disease-specific survival [DSS], overall survival [OS] or progression-free interval [PFI]), especially for ACE2 and AGTR1 in KIRC. ACE-AGTR1, a classical axis of the RAS family related to immune infiltration, was positively correlated with M2-type macrophages, cancer-associated fibroblasts (CAFs) and immune checkpoint genes in most cancers. Conclusion: ACE, ACE2, AGT and AGTR1 were differentially expressed in 33 types of cancers. PTM of RAS family was found to rely on ubiquitination. ACE2 and AGTR1 might serve as independent prognostic factors for LGG and KIRC. SARS-CoV-2 might modify the tumor microenvironment by regulating the RAS family, thus affecting the biological processes of cancer.
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- 2021
25. Kinetics of alpha-synuclein depletion in three brain regions following conditional pan-neuronal inactivation of the encoding gene (Snca) by tamoxifen-induced Cre-recombination in adult mice
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Kirill D. Chaprov, Vladimir L. Buchman, Ekaterina V. Teterina, and Ekaterina A. Lysikova
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Male ,Enolase ,Mice, Transgenic ,Striatum ,Biology ,Midbrain ,Alpha-synuclein ,chemistry.chemical_compound ,Mice ,Conditional gene knockout ,Genetics ,medicine ,Recombinase ,Animals ,Gene ,Recombination, Genetic ,Original Paper ,Integrases ,Brain ,Cerebral cortex ,Molecular biology ,Tamoxifen-induced Cre-recombination ,Kinetics ,Tamoxifen ,medicine.anatomical_structure ,chemistry ,nervous system ,Animal Science and Zoology ,Female ,Agronomy and Crop Science ,Biotechnology - Abstract
Conditional pan-neuronal inactivation of the Snca gene in 2-month old male and female mice causes dramatic decrease in the level of the encoded protein, alpha-synuclein, in three studied brain regions, namely cerebral cortex, midbrain and striatum, 12 weeks after the last injection of tamoxifen. Kinetics of alpha-synuclein depletion is different in these brain regions with a longer lag period in the cerebral cortex where this protein is normally most abundant. Our results suggest that efficient post-developmental pan-neuronal knockout of alpha-synuclein in adult, i.e. 5- to 6-month old, animals, could be achieved by tamoxifen treatment of 2-month old mice carrying loxP-flanked Snca gene and expressing inducible Cre-ERT2 recombinase under control of the promoter of neuron-specific enolase (NSE) gene. Supplementary Information The online version contains supplementary material available at 10.1007/s11248-021-00286-3.
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- 2021
26. Editorial: Special Issue—Understanding and Targeting Heart Failure: From Biology to Therapeutics.
- Author
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Pu, Jun, Zhu, Wuqiang, and Ye, Lei
- Subjects
HEART failure ,BIOLOGY ,CYTOLOGY ,MANGANESE porphyrins ,THERAPEUTICS ,MOLECULAR biology - Abstract
This editorial discusses the prevalence of heart failure worldwide and the advancements in molecular and cellular biology that are transforming our understanding and treatment of the condition. The special issue includes nine papers that highlight recent advances in understanding the transcriptome profile in cardiovascular diseases and providing novel treatments for promoting cardiac repair. The papers cover topics such as the transcriptomic profile of endothelial cells in Duchenne muscular dystrophy, the impact of inflammation in remote zones after myocardial infarction, the effectiveness of manganese porphyrin compound for cardiac arrest, the role of HIF2α and ARNT signaling in endothelial cells, strategies to induce cardiomyocyte proliferation, the characterization of the common marmoset as a primate model for cardiovascular disease, and the link between heart failure and cognitive impairment. The authors express their gratitude to the contributors and reviewers of the special issue. [Extracted from the article]
- Published
- 2023
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- View/download PDF
27. Roars, groans and moans: anatomical correlates of vocal diversity in polygynous deer
- Author
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Yann Locatelli, Michael Schofield, David Reby, Megan T. Wyman, Malcolm Johnston, and Roland Frey
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Larynx ,Male ,Histology ,Range (biology) ,red deer ,sika deer ,Zoology ,descended larynx ,Vocal Cords ,vocal anatomy ,medicine ,otorhinolaryngologic diseases ,Animals ,sexual selection ,Molecular Biology ,male sexual calls ,Ecology, Evolution, Behavior and Systematics ,vocal repertoire ,Original Paper ,Cervus ,biology ,Deer ,source‐filter theory ,female contact calls ,vocal production ,Cell Biology ,Acoustics ,polygynous deer ,biology.organism_classification ,acoustic variation ,Original Papers ,Sexual dimorphism ,medicine.anatomical_structure ,Formant ,source-filter theory ,sexual dimorphism ,fallow deer ,Vocal folds ,Sexual selection ,Female ,Anatomy ,Vocalization, Animal ,Vocal tract ,Developmental Biology - Abstract
Eurasian deer are characterized by the extraordinary diversity of their vocal repertoires. Male sexual calls range from roars with relatively low fundamental frequency (hereafter f o) in red deer Cervus elaphus, to moans with extremely high f o in sika deer Cervus nippon, and almost infrasonic groans with exceptionally low f o in fallow deer Dama dama. Moreover, while both red and fallow males are capable of lowering their formant frequencies during their calls, sika males appear to lack this ability. Female contact calls are also characterized by relatively less pronounced, yet strong interspecific differences. The aim of this study is to examine the anatomical bases of these inter‐specific and inter‐sexual differences by identifying if the acoustic variation is reflected in corresponding anatomical variation. To do this, we investigated the vocal anatomy of male and female specimens of each of these three species. Across species and sexes, we find that the observed acoustic variability is indeed related to expected corresponding anatomical differences, based on the source‐filter theory of vocal production. At the source level, low f o is associated with larger vocal folds, whereas high f o is associated with smaller vocal folds: sika deer have the smallest vocal folds and male fallow deer the largest. Red and sika deer vocal folds do not appear to be sexually dimorphic, while fallow deer exhibit strong sexual dimorphism (after correcting for body size differences). At the filter level, the variability in formants is related to the configuration of the vocal tract: in fallow and red deer, both sexes have evolved a permanently descended larynx (with a resting position of the larynx much lower in males than in females). Both sexes also have the potential for momentary, call‐synchronous vocal tract elongation, again more pronounced in males than in females. In contrast, the resting position of the larynx is high in both sexes of sika deer and the potential for further active vocal tract elongation is virtually absent in both sexes. Anatomical evidence suggests an evolutionary reversal in larynx position within sika deer, that is, a secondary larynx ascent. Together, our observations confirm that the observed diversity of vocal behaviour in polygynous deer is supported by strong anatomical differences, highlighting the importance of anatomical specializations in shaping mammalian vocal repertoires. Sexual selection is discussed as a potential evolutionary driver of the observed vocal diversity and sexual dimorphisms., The comparison of three species of acoustically diverse polygynous deer suggests that acoustic variability is related to corresponding anatomical differences of the vocal organs.
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- 2021
28. Structural basis for the recognition of deaminated nucleobases by an archaeal DNA polymerase
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Karin Betz, Heike M. Kropp, Andreas Marx, Kay Diederichs, and Samra Ludmann
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DNA Replication ,Models, Molecular ,crystal structure ,DNA polymerase ,DNA damage ,DNA-Directed DNA Polymerase ,Biochemistry ,DNA polymerases ,chemistry.chemical_compound ,ddc:570 ,uracil ,Molecular Biology ,Full Paper ,biology ,DNA synthesis ,Organic Chemistry ,DNA replication ,Uracil ,Full Papers ,Thermococcus ,deaminated base recognition ,DNA, Archaeal ,chemistry ,Deamination ,hypoxanthine ,biology.protein ,Nucleic Acid Conformation ,Molecular Medicine ,Primer (molecular biology) ,Cytosine ,DNA - Abstract
With increasing temperature, nucleobases in DNA become increasingly damaged by hydrolysis of exocyclic amines. The most prominent damage includes the conversion of cytosine to uracil and adenine to hypoxanthine. These damages are mutagenic and put the integrity of the genome at risk if not repaired appropriately. Several archaea live at elevated temperatures and thus, are exposed to a higher risk of deamination. Earlier studies have shown that DNA polymerases of archaea have the property of sensing deaminated nucleobases in the DNA template and thereby stalling the DNA synthesis during DNA replication providing another layer of DNA damage recognition and repair. However, the structural basis of uracil and hypoxanthine sensing by archaeal B‐family DNA polymerases is sparse. Here we report on three new crystal structures of the archaeal B‐family DNA polymerase from Thermococcus kodakarensis (KOD) DNA polymerase in complex with primer and template strands that have extended single stranded DNA template 5’‐overhangs. These overhangs contain either the canonical nucleobases as well as uracil or hypoxanthine, respectively, and provide unprecedented structural insights into their recognition by archaeal B‐family DNA polymerases., Due to their life in hot environments, archaea are increasingly affected by deamination of the bases cytosine and adenine. To prevent mutations, archaeal DNA polymerases seem to recognize these base changes by a so‐called “read‐ahead” mechanism and react accordingly. Here we show by means of crystal structures how Thermococcus kodakarensis (KOD) DNA polymerase binds uracil and hypoxanthine in a special binding pocket and thus can recognize these bases on the single stranded template overhang already six nucleotides before the active site.
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- 2021
29. Disentangling tumorigenesis-associated DNA methylation changes in colorectal tissues from those associated with ageing
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Mark D. Robinson, Hannah R Parker, Matthias Sauter, Federico Buffoli, Fabrizio Cereatti, Giancarlo Marra, Stephany Orjuela, Sija Sajibu, University of Zurich, and Marra, Giancarlo
- Subjects
Aging ,Cancer Research ,Carcinogenesis ,Bisulfite sequencing ,Colorectal adenoma ,Biology ,medicine.disease_cause ,Biomarkers, Tumor ,medicine ,1312 Molecular Biology ,Humans ,1306 Cancer Research ,Promoter Regions, Genetic ,Molecular Biology ,Epigenomics ,10061 Institute of Molecular Cancer Research ,Methylation ,DNA Methylation ,medicine.disease ,10124 Institute of Molecular Life Sciences ,Chromatin ,Gene Expression Regulation, Neoplastic ,CpG site ,DNA methylation ,Cancer research ,570 Life sciences ,biology ,CpG Islands ,Female ,Colorectal Neoplasms ,Research Paper - Abstract
Physiological ageing and tumorigenesis are both associated with epigenomic alterations in human tissue cells, the most extensively investigated of which entails de novo cytosine methylation (i.e., hypermethylation) within the CpG dinucleotides of CpG islands. Genomic regions that become hypermethylated during tumorigenesis are generally believed to overlap regions that acquire methylation in normal tissues as an effect of ageing. To define the extension of this overlap, we analysed the DNA methylomes of 48 large-bowel tissue samples taken from women of different ages during screening colonoscopy: 18 paired samples of normal and lesional tissues from donors harbouring a precancerous lesion and 12 samples of normal mucosa from tumour-free donors. Each sample was subjected to targeted, genome-wide bisulphite sequencing of ~2.5% of the genome, including all CpG islands. In terms of both its magnitude and extension along the chromatin, tumour-associated DNA hypermethylation in these regions was much more conspicuous than that observed in the normal mucosal samples from older (vs. younger) tumour-free donors. 83% of the ageing-associated hypermethylated regions (n = 2501) coincided with hypermethylated regions observed in tumour samples. However, 86% of the regions displaying hypermethylation in precancerous lesions (n = 16,772) showed no methylation changes in the ageing normal mucosa. The tumour-specificity of this latter hypermethylation was validated using published sets of data on DNA methylation in normal and neoplastic colon tissues. This extensive set of genomic regions displaying tumour-specific hypermethylation represents a rich vein of putative biomarkers for the early, non-invasive detection of colorectal tumours in women of all ages.
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- 2022
30. Idéfix
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Pauline Lanting, Robert Warmerdam, Lude Franke, Patrick Deelen, Stem Cell Aging Leukemia and Lymphoma (SALL), and Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
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Statistics and Probability ,Supplementary data ,education.field_of_study ,AcademicSubjects/SCI01060 ,Computer science ,Concordance ,Genetics and Population Analysis ,Population ,Sample (statistics) ,Genome-wide association study ,Computational biology ,Biology ,Original Papers ,Biochemistry ,Biobank ,Computer Science Applications ,Computational Mathematics ,Identification (information) ,Computational Theory and Mathematics ,Set (psychology) ,education ,Molecular Biology ,Repurposing ,Pharmacogenetics - Abstract
Motivation Identifying sample mix-ups in biobanks is essential to allow the repurposing of genetic data for clinical pharmacogenetics. Pharmacogenetic advice based on the genetic information of another individual is potentially harmful. Existing methods for identifying mix-ups are limited to datasets in which additional omics data (e.g. gene expression) is available. Cohorts lacking such data can only use sex, which can reveal only half of the mix-ups. Here, we describe Idéfix, a method for the identification of accidental sample mix-ups in biobanks using polygenic scores. Results In the Lifelines population-based biobank, we calculated polygenic scores (PGSs) for 25 traits for 32 786 participants. We then applied Idéfix to compare the actual phenotypes to PGSs, and to use the relative discordance that is expected for mix-ups, compared to correct samples. In a simulation, using induced mix-ups, Idéfix reaches an AUC of 0.90 using 25 polygenic scores and sex. This is a substantial improvement over using only sex, which has an AUC of 0.75. Subsequent simulations present Idéfix’s potential in varying datasets with more powerful PGSs. This suggests its performance will likely improve when more highly powered GWASs for commonly measured traits will become available. Idéfix can be used to identify a set of high-quality participants for whom it is very unlikely that they reflect sample mix-ups, and for these participants we can use genetic data for clinical purposes, such as pharmacogenetic profiles. For instance, in Lifelines, we can select 34.4% of participants, reducing the sample mix-up rate from 0.15% to 0.01%. Availabilityand implementation Idéfix is freely available at https://github.com/molgenis/systemsgenetics/wiki/Idefix. The individual-level data that support the findings were obtained from the Lifelines biobank under project application number ov16_0365. Data is made available upon reasonable request submitted to the LifeLines Research office (research@lifelines.nl, https://www.lifelines.nl/researcher/how-to-apply/apply-here). Supplementary information Supplementary data are available at Bioinformatics online.
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- 2022
31. Dysregulation of Transglutaminase type 2 through GATA3 defines aggressiveness and Doxorubicin sensitivity in breast cancer
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Silvia Grassilli, Jeffrey W. Keillor, Cristian Taccioli, Stefano Volinia, Gianluca Aguiari, Linda Minotti, Fabio Corrà, Francesca Crudele, Nicoletta Bianchi, Carlo M. Bergamini, and Carlo Cervellati
- Subjects
Tissue transglutaminase ,Socio-culturale ,Breast Neoplasms ,GATA3 Transcription Factor ,Applied Microbiology and Biotechnology ,Cell Line ,Breast cancer ,breast cancer ,Antibiotics ,Cell Line, Tumor ,GATA3 ,medicine ,Humans ,Doxorubicin ,Protein Glutamine gamma Glutamyltransferase 2 ,Sensitivity (control systems) ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,drug resistance ,NC9 ,Transglutaminase variants ,Antibiotics, Antineoplastic ,Disease Progression ,Female ,MCF-7 Cells ,Up-Regulation ,Tumor ,biology ,business.industry ,Cell Biology ,medicine.disease ,Antineoplastic ,biology.protein ,Cancer research ,business ,Developmental Biology ,medicine.drug ,Research Paper - Abstract
The role of transglutaminase type 2 in cell physiology is related to protein transamidation and signal transduction (affecting extracellular, intracellular and nuclear processes) aided by the expression of truncated isoforms and of two lncRNAs with regulatory functions. In breast cancer TG2 is associated with disease progression supporting motility, epithelial-mesenchymal transition, invasion and drug resistance. The aim of his work is to clarify these issues by emphasizing the interconnections among TGM2 variants and transcription factors associated with an aggressive phenotype, in which the truncated TGH isoform correlates with malignancy. TGM2 transcripts are upregulated by several drugs in MCF-7, but only Doxorubicin is effective in MDA-MB-231 cells. These differences reflect the expression of GATA3, as demonstrated by silencing, suggesting a link between this transcription factor and gene dysregulation. Of note, NC9, an irreversible inhibitor of enzymatic TG2 activities, emerges to control NF-ĸB and apoptosis in breast cancer cell lines, showing potential for combination therapies with Doxorubicin.
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- 2022
32. Hypermethylation of the oxytocin receptor gene (OXTR) in obsessive-compulsive disorder: further evidence for a biomarker of disease and treatment response
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Alfredo Ramirez, Norbert Kathmann, Michael Wagner, Rosa Grützmann, Benedikt Reuter, Katharina Bey, Anja Riesel, Rafael Campos-Martin, and Julia Klawohn
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Oncology ,Cancer Research ,Mediation (statistics) ,medicine.medical_specialty ,Obsessive-Compulsive Disorder ,genetics [Receptors, Oxytocin] ,OXTR ,therapy [Obsessive-Compulsive Disorder] ,Disease ,Biology ,Affect (psychology) ,Oxytocin ,behavioral disciplines and activities ,Internal medicine ,mental disorders ,medicine ,Obsessive-compulsive disorder ,Humans ,Epigenetics ,ddc:610 ,Molecular Biology ,genetics [Obsessive-Compulsive Disorder] ,treatment response ,Methylation ,DNA Methylation ,Oxytocin receptor ,Receptors, Oxytocin ,DNA methylation ,Biomarker (medicine) ,methylation ,Biomarkers ,epigenetic ,Research Paper - Abstract
Obsessive-compulsive disorder (OCD) has recently been linked to increased methylation levels in the oxytocin receptor (OXTR) gene, and OXTR hypermethylation has predicted a worse treatment response to cognitive-behavioural therapy (CBT). Furthermore, OCD is associated with childhood trauma and stressful life events, which have both been shown to affect OXTR methylation. Here, we aimed to replicate findings of increased OXTR methylation as a predictor of disease and worse treatment response in an independent sample that received treatment within the public health care system. In addition, we aimed to extend previous findings by examining associations between OXTR hypermethylation, environmental stressors, OCD diagnosis, and treatment response. Methylation levels at two CpGs within OXTR exon III were compared between n = 181 OCD patients and n = 199 healthy controls using linear regression analysis. In a subsample of OCD patients (n = 98) with documented treatment data, we examined associations between methylation and treatment response to CBT. Childhood adversity and stressful life events were assessed using Childhood Trauma Questionnaire and Life Experience Survey, respectively. OCD patients exhibited significant hypermethylation at CpG site cg04523291 compared to controls, and increased methylation was associated with impaired treatment response. Moreover, hypermethylation at cg04523291 was associated with stressful life events in OCD patients, and with childhood adversity in controls. Yet, there were no significant mediation effects. In conclusion, we replicated the association between OXTR hypermethylation and OCD in the largest sample, so far. Furthermore, our findings support the role of OXTR methylation as a promising biomarker for treatment response in OCD.
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- 2022
33. The effect of experimental lead pollution on DNA methylation in a wild bird population
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Hannu Mäkinen, Suvi Ruuskanen, Tapio Eeva, Kees van Oers, and Animal Ecology (AnE)
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Cancer Research ,environmental epigenetics ,Population ,Zoology ,Genome ,Epigenesis, Genetic ,ecotoxicology ,raskasmetallit ,Metals, Heavy ,Animals ,pollution ,Epigenetics ,Passeriformes ,ympäristömyrkyt ,education ,Molecular Biology ,Gene ,Organism ,Pb ,parus major ,Parus ,education.field_of_study ,biology ,Methylation ,Plan_S-Compliant_NO ,talitiainen ,DNA Methylation ,biology.organism_classification ,DNA-metylaatio ,ekotoksikologia ,Lead ,epigenetiikka ,international ,DNA methylation ,ecological epigenetics ,saastuminen ,Environmental Pollutants ,lyijy ,Research Paper - Abstract
Anthropogenic pollution is known to negatively influence an organism’s physiology, behaviour, and fitness. Epigenetic regulation, such as DNA methylation, has been hypothesized as a potential mechanism to mediate such effects, yet studies in wild species are lacking. We first investigated the effects of early-life exposure to the heavy metal lead (Pb) on DNA methylation levels in a wild population of great tits (Parus major), by experimentally exposing nestlings to Pb at environmentally relevant levels. Secondly, we compared nestling DNA methylation from a population exposed to long-term heavy metal pollution (close to a copper smelter), where birds suffer from pollution-related decrease in food quality, and a control population. For both comparisons, the analysis of about one million CpGs covering most of the annotated genes revealed that pollution-related changes in DNA methylation were not genome wide, but enriched for genes underlying developmental processes. However, the results were not consistent when using binomial or beta binomial regression highlighting the difficulty of modelling variance in CpGs. Our study indicates that post-natal anthropogenic heavy metal exposure can affect methylation levels of development related genes in a wild bird population. peerReviewed
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- 2022
34. Exploring the impact of night shift work on methylation of circadian genes
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Francine Durocher, Joan Tranmer, Parveen Bhatti, Qing Ling Duan, Lisa Flaten, Jennifer Ritonja, Danai G. Topouza, and Kristan J. Aronson
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Cancer Research ,Candidate gene ,Physiology ,ARNTL Transcription Factors ,Shift Work Schedule ,Methylation ,DNA ,Biology ,DNA Methylation ,Circadian Rhythm ,ARNTL ,Cross-Sectional Studies ,CSNK1E ,CpG site ,DNA methylation ,Humans ,Female ,Circadian rhythm ,5' Untranslated Regions ,Molecular Biology ,Gene ,Research Paper - Abstract
Night shift work is associated with increased breast cancer risk, but the molecular mechanisms are not well-understood. The objective of this study was to explore the relationship between night shift work parameters (current status, duration/years, and intensity) and methylation in circadian genes as a potential mechanism underlying the carcinogenic effects of night shift work. A cross-sectional study was conducted among 74 female healthcare employees (n = 38 day workers, n = 36 night shift workers). The Illumina Infinium MethylationEPIC beadchip was applied to DNA extracted from blood samples to measure methylation using a candidate gene approach at 1150 CpG loci across 22 circadian genes. Linear regression models were used to examine the association between night shift work parameters and continuous methylation measurements (β-values) for each CpG site. The false-discovery rate (q = 0.2) was used to account for multiple comparisons. Compared to day workers, current night shift workers demonstrated hypermethylation in the 5'UTR region of CSNK1E (q = 0.15). Individuals that worked night shifts for ≥10 years exhibited hypomethylation in the gene body of NR1D1 (q = 0.08) compared to those that worked
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- 2021
35. miR-222-3p is involved in neural tube closure by directly targeting Ddit4 in RA induced NTDs mouse model
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Hong Zhao, Jun Xie, Juan Zhang, Li Zhang, Qiwei He, Tian'e Luo, Yufei Wang, Yuqing Sun, Meining Li, Zhizhen Liu, Meiyan Song, Xianghui Xie, Ajab Khan, Bo Niu, and Lei Wang
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Neural Tube ,Tretinoin ,Biology ,Transcriptome ,Mice ,Cell Movement ,Cell Line, Tumor ,medicine ,Animals ,Neural Tube Defects ,Molecular Biology ,Wnt Signaling Pathway ,beta Catenin ,Cell Proliferation ,Cell growth ,Wnt signaling pathway ,Neural tube ,Cell Biology ,Cell cycle ,Cell biology ,Gene Expression Regulation, Neoplastic ,MicroRNAs ,medicine.anatomical_structure ,Cell culture ,Apoptosis ,Signal transduction ,Developmental Biology ,Research Paper ,DNA Damage ,Transcription Factors - Abstract
Previously our results showed miR-222-3p was significantly downregulated in retinoic acid-induced neural tube defect (NTD) mouse model through transcriptome. Down-regulation of miR-222-3p may be a causative biomarker in NTDs. In this study, RNA was extracted from mouse embryos at E8.5, E9.5 and E10.5, and the expression level of miR-222-3p was measured by quantitative real-time PCR analysis. The preliminary mechanism of miR-222-3p in NTDs involved in cell proliferation, apoptosis and migration was investigated in mouse HT-22 cell line. The expression of miR-222-3p was significantly decreased at E8.5, E9.5 and E10.5 developed in mouse embryos which were consistent with our transcriptome sequencing. Suppression of miR-222-3p in HT-22 cells resulted in the inhibition of cell proliferation and migration, cell cycle and apoptosis. Moreover, DNA damage transcript 4 (Ddit4) was identified as a direct and functional target of miR-222-3p. miR-222-3p is negatively regulated by Ddit4. The mutation of binding site of Ddit4 3ʹUTR abrogated the responsiveness of luciferase reporters to miR-222-3p and showed that Ddit4 expression partially attenuated the function of miR-222-3p. We preliminatively confirmed that low expression of miR-222-3p has reduced the expression of β-catenin, TCF4 and other related genes in the Wnt/β-catenin signaling pathway. Collectively, these results demonstrated that miR-222-3p regulates the Wnt/β-catenin signaling pathway through Ddit4 inhibition in HT-22 cells, resulted in cell proliferation and apoptosis imbalance, and thus led to neural tube defects.
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- 2021
36. Substitutions at a rheostat position in human aldolase A cause a shift in the conformational population
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Tiffany Wu, Kathleen M. Meneely, Kathryn D. Fenton, Liskin Swint-Kruse, Aron W. Fenton, Audrey L. Lamb, and Tyler A. Martin
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chemistry.chemical_classification ,education.field_of_study ,Binding Sites ,biology ,Stereochemistry ,Protein Conformation ,Protein subunit ,Full‐Length Papers ,Aldolase A ,Population ,Wild type ,Mutation, Missense ,Active site ,Cooperativity ,Biochemistry ,Amino acid ,chemistry ,Amino Acid Substitution ,Catalytic Domain ,Fructose-Bisphosphate Aldolase ,biology.protein ,Humans ,Isoleucine ,education ,Molecular Biology - Abstract
Some protein positions play special roles in determining the magnitude of protein function: at such “rheostat” positions, varied amino acid substitutions give rise to a continuum of functional outcomes, from wild type (or enhanced), to intermediate, to loss of function. This observed range raises interesting questions about the biophysical bases by which changes at single positions have such varied outcomes. Here, we assessed variants at position 98 in human aldolase A (“I98X”). Despite being ~17 Å from the active site and far from subunit interfaces, substitutions at position 98 have rheostatic contributions to the apparent cooperativity (n ( H )) associated with fructose‐1,6‐bisphosphate substrate binding and moderately affected binding affinity. Next, we crystallized representative I98X variants to assess structural consequences. Residues smaller than the native isoleucine (cysteine and serine) were readily accommodated, and the larger phenylalanine caused only a slight separation of the two parallel helixes. However, the diffraction quality was reduced for I98F, and further reduced for I98Y. Intriguingly, the resolutions of the I98X structures correlated with their n ( H ) values. We propose that substitution effects on both n ( H ) and crystal lattice disruption arise from changes in the population of aldolase A conformations in solution. In combination with results computed for rheostat positions in other proteins, the results from this study suggest that rheostat positions accommodate a wide range of side chains and that structural consequences manifest as shifted ensemble populations and/or dynamics changes.
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- 2021
37. Role of unique loops in oligomerization and ATPase function of Plasmodium falciparum gyrase B
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Ramanathan Natesh, Monica Purushothaman, and Suman Kumar Dhar
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chemistry.chemical_classification ,Adenosine Triphosphatases ,biology ,Topoisomerase ,ATPase ,Protein subunit ,Full‐Length Papers ,Plasmodium falciparum ,Protozoan Proteins ,Isothermal titration calorimetry ,biology.organism_classification ,Biochemistry ,DNA gyrase ,Enzyme ,Adenosine Triphosphate ,chemistry ,ATP hydrolysis ,DNA Gyrase ,biology.protein ,Molecular Biology ,Dimerization - Abstract
DNA gyrase is an ATP dependent Type IIA topoisomerase that is unique to prokaryotes. Interestingly DNA gyrase has also been found in the apicoplasts of apicomplexan parasites like Plasmodium falciparum (Pf) the causative agent of Malaria. Gyrase B (GyrB), a subunit of gyrase A(2)B(2) complex has an N‐terminal domain (GyrBN) which is endowed with ATPase activity. We reported earlier that PfGyrB exhibits ATP‐independent dimerization unlike its bacterial counterparts. Here we report the role of two unique regions (L1 and L2) identified in PfGyrBN. Deletions of L1 alone (PfGyrBNΔL1), or L1 and L2 together (PfGyrBNΔL1ΔL2) have indicated that these regions may play an important role in ATPase activity and the oligomeric state of PfGyrBN. Our experiments show that the deletion of L1 region disrupts the dimer interface of PfGyrBN and reduces its ATPase activity. Further through ITC experiments we show that the binding affinity of ATP to PfGyrBN is reduced upon the deletion of L1 region. We have observed a reduction in ATPase activity for of all three proteins PfGyrBN, PfGyrBNΔL1, and PfGyrBNΔL1ΔL2 in presence of coumermycin. Our results suggests that L1 region of PfGyrBN is likely to be functionally important and may provide a unique dimer interface that affects its enzymatic activity. Since deletion of L1 region decreases the affinity of ATP to the protein, this region can be targeted toward designing novel inhibitors of ATP hydrolysis.
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- 2021
38. A noncanonical autophagy is involved in the transfer of Plasmodium -microvesicles to astrocytes
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Sophie Salomé Desnoulez, Priscille Brodin, Sylviane Pied, Nasreddine Saidi, Frank Lafont, Inès Leleu, Stanislas Tomavo, Delphine Genete, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Lille, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Réseau International des Instituts Pasteur (RIIP), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Pied, Sylviane, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL], and Institut de Biologie Intégrative de la Cellule [I2BC]
- Subjects
Plasmodium ,autophagy ,Plasmodium berghei ,[SDV]Life Sciences [q-bio] ,ATG5 ,Malaria, Cerebral ,Inflammation ,Biology ,parasite microvesicles ,Proinflammatory cytokine ,03 medical and health sciences ,Mice ,0302 clinical medicine ,parasitic diseases ,medicine ,Animals ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,Molecular Biology ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,0303 health sciences ,Innate immune system ,Autophagy ,Cell Biology ,Astrocyte ,cerebral malaria ,inflammation ,Microvesicles ,3. Good health ,Cell biology ,Mice, Inbred C57BL ,[SDV] Life Sciences [q-bio] ,medicine.anatomical_structure ,Cerebral Malaria ,Astrocytes ,medicine.symptom ,030217 neurology & neurosurgery ,[SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,Research Paper - Abstract
International audience; Cerebral malaria is a neuroinflammatory disease induced by P. falciparum infection. In animal models, the neuro-pathophysiology of cerebral malaria results from the sequestration of infected red blood cells (iRBCs) in microvessels that promotes the activation of glial cells in the brain. This activation provokes an exacerbated inflammatory response characterized by the secretion of proinflammatory cytokines and chemokines, leading to brain infiltration by pathogenic CD8+ T lymphocytes. Astrocytes are a major subtype of brain glial cells that play an important role in maintaining the homeostasis of the central nervous system, the integrity of the brain-blood barrier and in mounting local innate immune responses. We have previously shown that parasitic microvesicles (PbA-MVs) are transferred from iRBCs to astrocytes. The present study shows that an unconventional LC3-mediated autophagy pathway independent of ULK1 is involved in the transfer and degradation of PbA-MVs inside the astrocytes. We further demonstrate that inhibition of the autophagy process by treatment with 3-methyladenine blocks the transfer of PbA-MVs, which remain localized in the astrocytic cell membrane and are not internalized. Moreover, bafilomycin A1, another drug against autophagy promotes the accumulation of PbA-MVs inside the astrocytes by inhibiting the fusion with lysosomes, and prevents ECM in mice infected with PbA. Finally, we establish that RUBCN/rubicon or ATG5 silencing impede astrocyte production in CCL2 and CXCL10 chemokines induced by PbA stimulation. Altogether, our data suggest that a non-canonical autophagy-lysosomal pathway may play a key role in cerebral malaria through regulation of brain neuro-inflammation by astrocytes.
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- 2021
39. Exosomal lncAY927529 enhances prostate cancer cell proliferation and invasion through regulating bone microenvironment
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Xiaoyan Li, Tianxiang Bi, Mulun Xiao, Jinhao Hu, Yibo Shi, Chaoliang Wang, Liang Yan, and Qi Li
- Subjects
Male ,Prostatic Hyperplasia ,Biology ,urologic and male genital diseases ,Exosomes ,Bone and Bones ,Flow cytometry ,DU145 ,Cell Movement ,Cell Line, Tumor ,LNCaP ,medicine ,Tumor Microenvironment ,Humans ,CXCL14 ,Molecular Biology ,Cell Proliferation ,medicine.diagnostic_test ,Cell growth ,Prostate ,Prostatic Neoplasms ,Cell Biology ,Microvesicles ,MicroRNAs ,Cell culture ,Cancer cell ,Cancer research ,RNA, Long Noncoding ,Developmental Biology ,Research Paper - Abstract
Exosomes mediate the interaction between cancer cells and their microenvironment, and play a key role in tumor development. Although exosomes can package lncRNAs to mediate extracellular communication, the role of exosomal lncRNA AY927529 in prostate cancer (PCa) remains unclear. Exosomes were extracted from normal human prostatic epithelial cell lines (BPH-1 and RWPE-1) and PCa cell lines (VCaP and LNCaP, DU145, PC3) by ultrahigh speed centrifugation. Results of Western blot indicated that Alix, HSC70 and TSGl01 protein levels were upregulated in exosomes derived from PCa cells. LncAY927529 level was upregulated in PCa cells and exosomes derived from PCa patient serum and human PCa cells. CCK-8, Transwell and Flow cytometry assays demonstrated that bone marrow stromal cell line (ST2) conditioned medium (ST2-CM), treated with exosomes derived from PCa cells with high lncAY927529 level, promoted proliferation and invasion of PC3 and DU145 cells, and inhibited cell apoptosis. RT-qPCR assay indicated that lncAY927529 level was downregulated in PC3 and DU145 cells, exosomes derived from PCa cells (PCa-Exo) and ST2-CM treated with PCa-Exo with low expression of lncAY927529, and overexpression of lncAY927529 had the opposite results. In addition, Western blot assay showed that the autophagy related protein LC3II level was increased in ST2 cells treated with exosomes derived from DU145 cells with high expression of lncAY927529, and LC3I protein level was decreased. CXCL14 acted as a RNA-binding protein of lncAY927529, and exosome-mediated lncAY927529 positively regulated CXCL14 levels in ST2 cells. In general, exosome-mediated lncAY927529 could promote PCa cell proliferation and invasion by regulating bone microenvironment, suggesting that exosomal lncAY927529 may be a potential molecular diagnostic marker of PCa.
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- 2021
40. Differential transcription profiling of the phage LUZ19 infection process in different growth media
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Joana Azeredo, Rob Lavigne, Diana Priscila Penso Pires, Lucas Coppens, Ana Catarina Brandão, Marleen Voet, and Universidade do Minho
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viruses ,Cell Culture Techniques ,RNA-Seq ,Computational biology ,Bacteriophage ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Bacterial Proteins ,Gene expression ,Humans ,Bacteriophages ,Molecular Biology ,Differential transcription ,030304 developmental biology ,0303 health sciences ,Science & Technology ,biology ,RNA ,Gene Expression Regulation, Bacterial ,Cell Biology ,biology.organism_classification ,Culture Media ,3. Good health ,P. aeruginosa ,030220 oncology & carcinogenesis ,Host-Pathogen Interactions ,Pseudomonas aeruginosa ,RNA-seq ,Research Paper - Abstract
RNA sequencing of phage-infected bacterial cultures offers a snapshot of transcriptional events occurring during the infection process, providing insights into the phage transcriptional organization as well as the bacterial response. To better mimic real environmental contexts, we performed RNA-seq of Pseudomonas aeruginosa PAO1 cultures infected with phage LUZ19 in a mammalian cell culture medium to better simulate a phage therapy event and the data were compared to lysogeny broth medium. Regardless of the media, phage LUZ19 induces significant transcriptional changes in the bacterial host over time, particularly during early infection (t= 5 min) and gradually shuts down bacterial transcription. In a common response in both media, 56 P. aeruginosa PAO1 genes are differentially transcribed and clustered into several functional categories such as metabolism, translation and transcription. Our data allowed us to tease apart a medium-specific response during infection from the identified infection-associated responses. This reinforces the concept that phages overtake bacterial transcriptome in a strict manner to gain control of the bacterial machinery and reallocate resources for infection, in this case overcoming the nutritional limitations of the mammalian cell culture medium. From a phage therapy perspective, this study contributes towards a better understanding of phagehost interaction in human physiological conditions and demonstrates the versatility of phage LUZ19 to adapt to different environments., This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the project PTDC/BBB-BSS/6471/ 2014 (POCI-01-0145-FEDER-016643) and the strategic funding of UIDB/04469/2020 unit. AB is supported by FCT through the grant SFRH/BD/133193/2017. This research was supported by funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 819800) awarded to RL., info:eu-repo/semantics/publishedVersion
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- 2021
41. WIPI1 promotes fission of endosomal transport carriers and formation of autophagosomes through distinct mechanisms
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Philipp Berger, Maria Giovanna De Leo, and Andreas Mayer
- Subjects
0301 basic medicine ,Autophagosome ,Endosome ,Fission ,WIPI ,autophagosome ,Autophagy-Related Proteins ,Vacuole ,Biology ,complex mixtures ,Cell Line ,03 medical and health sciences ,EGF receptor ,Lysosome ,CRISPR-Associated Protein 9 ,parasitic diseases ,medicine ,Autophagy ,Humans ,Molecular Biology ,endosome ,endosomal transport carrier ,Gene Editing ,Microscopy, Confocal ,030102 biochemistry & molecular biology ,vacuole ,Autophagosomes ,Multivesicular Bodies ,Membrane Proteins ,Cell Biology ,transferrin receptor ,Endocytosis ,Cell biology ,030104 developmental biology ,medicine.anatomical_structure ,Endosomal transport ,WIPI proteins ,Mutagenesis, Site-Directed ,lysosome ,PROPPIN ,CRISPR-Cas Systems ,Research Article ,Research Paper - Abstract
Autophagosome formation requires PROPPIN/WIPI proteins and monophosphorylated phosphoinositides, such as phosphatidylinositol-3-phosphate (PtdIns3P) or PtdIns5P. This process occurs in association with mammalian endosomes, where the PROPPIN WIPI1 has additional, undefined roles in vesicular traffic. To explore whether these functions are interconnected, we dissected routes and subreactions of endosomal trafficking requiring WIPI1. WIPI1 specifically acts in the formation and fission of tubulo-vesicular endosomal transport carriers. This activity supports the PtdIns(3,5)P 2 -dependent transport of endosomal cargo toward the plasma membrane, Golgi, and lysosomes, suggesting a general role of WIPI1 in endosomal protein exit. Three features differentiate the endosomal and macroautophagic/autophagic activities of WIPI1: phosphoinositide binding site II, the requirement for PtdIns(3,5)P 2 , and bilayer deformation through a conserved amphipathic α-helix. Their inactivation preserves autophagy but leads to a strong enlargement of endosomes, which accumulate micrometer-long endosomal membrane tubules carrying cargo proteins. WIPI1 thus supports autophagy and protein exit from endosomes by different modes of action. We propose that the type of phosphoinositides occupying its two lipid binding sites, the most unusual feature of PROPPIN/WIPI family proteins, switches between these effector functions.Abbreviations: EGF: epidermal growth factorEGFR: epidermal growth factor receptorKD: knockdownKO: knockoutPtdIns3P: phosphatidylinositol-3-phosphatePtdIns5P: phosphatidylinositol-5-phosphatePtdIns(3,5)P 2 : phosphatidylinositol-3,5-bisphosphateTF: transferrinTFRC: transferrin receptorWT: wildtype.
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- 2021
42. SHISA5/SCOTIN restrains spontaneous autophagy induction by blocking contact between the ERES and phagophores
- Author
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Joo-Yeon Yoo, Min Kyo Jung, Ji-Young Mun, Nari Kim, and Jee-Eun Lee
- Subjects
Endoplasmic reticulum ,Autophagy ,Autophagosomes ,Vesicular Transport Proteins ,Golgi Apparatus ,Cell Biology ,Proximity ligation assay ,Biology ,ULK1 ,Endoplasmic Reticulum ,Class III Phosphatidylinositol 3-Kinases ,Transmembrane protein ,Cell biology ,Cytosol ,chemistry.chemical_compound ,chemistry ,Phosphatidylinositol ,Streptavidin ,Molecular Biology ,COPII ,hormones, hormone substitutes, and hormone antagonists ,Research Paper - Abstract
The phagophore expands into autophagosomes in close proximity to endoplasmic reticulum (ER) exit sites (ERESs). Here, we propose that a single-pass ER transmembrane protein, SHISA5/SCOTIN, acts as an autophagy suppressor under basal condition by blocking the contact between the phagophore and ERES. HeLa cells lacking SHISA5 displayed higher levels of macroautophagy/autophagy. The enhanced autophagy in SHISA5 KO cells requires class III phosphatidylinositol 3-kinase complex I (PtdIns3K-C1) activity and functional assembly of ERES, but not ULK1 activity. A proximity ligation assay (PLA) of SEC16A (Sec16 homolog A, endoplasmic reticulum export factor)-WIPI2 (WD repeat domain, phosphoinositide interacting 2) and SEC31A (Sec31 homolog A, COPII coat complex component)-MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3 beta) demonstrated that contact between the ERES and phagophore increased in SHISA5 KO cells, and the cytosolic domain of SHISA5 was sufficient to rescue this phenotype. Close proximity between ERES and phagophore in SHISA5 KO cells was also visualized by performing an ultrastructure correlative image analysis of SEC31A associated with LC3-positive membranes. Furthermore, we observed that SHISA5 was located near ERES under basal conditions, but displaced away from ERES under autophagy-inducing conditions. These data suggest that SHISA5 functions to block spontaneous contact between ERES and phagophore, and the blockage effect of SHISA5 should be relieved for the proper induction of autophagy. ABBREVIATIONS: ATG2: autophagy related 2; BECN1: beclin 1; COPII: coat protein II; DMSO: dimethyl sulfoxide; EBSS: Earle’s balanced salt solution; EGFP: enhanced green fluorescent protein; ER: endoplasmic reticulum; ERES: ER exit site(s); GFP: green fluorescent protein; H89: H-89 dihydrochloride hydrate; LAMP1: lysosomal-associated membrane protein 1; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTORC1: mechanistic target of rapamycin kinase complex 1; NS5A: nonstructural protein 5A; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PLA: proximity ligation assay; PtdIns3P: phosphatidylionositol-3-phosphate; RB1CC1/FIP200: RB1 inducible coiled-coil 1; RFP: red fluorescent protein; RPS6KB1/S6K: ribosomal protein S6 kinase B1; SBP: streptavidin binding protein; SEC16A: SEC16 homolog A, endoplasmic reticulum export factor; SEC31A: SEC31 homolog A, COPII coat complex component; siRNA: small interfering RNA; Str: streptavidin; ULK1: unc-51-like autophagy activating kinase 1; VSVG: vesicular stomatitis virus glycoprotein; WIPI2: WD repeat domain, phosphoinositide interacting 2; WT: wild type
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- 2021
43. Tumour suppressor TET2 safeguards enhancers from aberrant DNA methylation and epigenetic reprogramming in ERα-positive breast cancer cells
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Li Tan, Feizhen Wu, Christian Argueta, Ruitu Lyu, Lu Liu, Hang Liu, Xuguo Zhu, Lijun Xiong, and Yinghui Shen
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Cancer Research ,Methyltransferase ,Breast Neoplasms ,Biology ,medicine.disease_cause ,Dioxygenases ,Epigenesis, Genetic ,Breast cancer ,Proto-Oncogene Proteins ,medicine ,Biomarkers, Tumor ,Humans ,Epigenetics ,RNA, Messenger ,Enhancer ,Molecular Biology ,Transcription factor ,Estradiol ,Estrogen Receptor alpha ,Estrogens ,DNA ,Methyltransferases ,DNA Methylation ,medicine.disease ,DNA-Binding Proteins ,Enhancer Elements, Genetic ,DNA methylation ,Cancer research ,Female ,Carcinogenesis ,Reprogramming ,Research Paper - Abstract
Aberrant DNA methylation is an epigenetic hallmark of malignant tumours. The DNA methylation level is regulated by not only DNA methyltransferases (DNMTs) but also Ten-Eleven Translocation (TET) family proteins. However, the exact role of TET genes in breast cancer remains controversial. Here, we uncover that the ERα-positive breast cancer patients with high TET2 mRNA expression had better overall survival rates. Consistently, knockout of TET2 promotes the tumorigenesis of ERα-positive MCF7 breast cancer cells. Mechanistically, TET2 loss leads to aberrant DNA methylation (gain of 5mC) at a large proportion of enhancers, accompanied by significant reduction in H3K4me1 and H3K27ac enrichment. By analysing the epigenetically reprogrammed enhancers, we identify oestrogen responsive element (ERE) as one of the enriched motifs of transcriptional factors. Importantly, TET2 loss impairs 17beta-oestradiol (E2)-induced transcription of the epigenetically reprogrammed EREs-associated genes through attenuating the binding of ERα. Taken together, these findings shed light on our understanding of the epigenetic mechanisms underlying the enhancer reprogramming during breast cancer pathogenesis.
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- 2021
44. Urinary metals and maternal circulating extracellular vesicle microRNA in the MADRES pregnancy cohort
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John D. Meeker, Caitlin G. Howe, Thomas Chavez, Carrie V. Breton, Mark C. Johnson, Theresa M. Bastain, Shohreh F. Farzan, Helen B. Foley, and Carmen J. Marsit
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Cancer Research ,Urinary system ,Placenta ,Early pregnancy factor ,Biology ,Andrology ,Extracellular Vesicles ,Pregnancy ,microRNA ,medicine ,Humans ,Circulating MicroRNA ,Thallium ,Molecular Biology ,Bayes Theorem ,Extracellular vesicle ,Cobalt ,Mercury ,DNA Methylation ,medicine.disease ,Late pregnancy ,Pregnancy Complications ,MicroRNAs ,Barium ,Metals ,Cohort ,biology.protein ,Gestation ,Female ,Research Paper - Abstract
Background: Exposure to metals increases risk for pregnancy complications. Extracellular vesicle (EV) miRNA contribute to maternal-fetal communication and are dysregulated in pregnancy complications. However, metal impacts on maternal circulating EV miRNA during pregnancy are unknown. Our objective was to investigate the impact of multiple metal exposures on EV miRNA in maternal circulation during pregnancy in the MADRES Study.Methods: Associations between urinary concentrations of nine metals and 106 EV miRNA in maternal plasma during pregnancy were investigated using robust linear regression (N=231). Primary analyses focused on metal-miRNA associations in early pregnancy (median: 12.3 weeks gestation). In secondary analyses, we investigated associations with late pregnancy miRNA counts in a smaller subset of participants (N=184) with paired data in the third trimester (median: 31.8 weeks gestation). MiRNA associated with three or more metals (PFDR
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- 2021
45. Draft genome and description of Waterburya agarophytonicola gen. nov. sp. nov. (Pleurocapsales, Cyanobacteria): a seaweed symbiont
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Florian Weinberger, Sergei Shalygin, Till Bayer, and Guido Bonthond
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Cyanobacteria ,DNA, Bacterial ,Pleurocapsales ,Biology ,Microbiology ,Genome ,Holobiont ,03 medical and health sciences ,Symbiosis ,Genus ,RNA, Ribosomal, 16S ,Molecular Biology ,Gene ,Phylogeny ,030304 developmental biology ,Genetics ,0303 health sciences ,Original Paper ,Vitamin B12 ,030306 microbiology ,Gracilaria vermiculophylla ,General Medicine ,Sequence Analysis, DNA ,biology.organism_classification ,Seaweed ,Cobalamin ,Rhodophyta ,Cyanobiont - Abstract
This work introduces Waterburya agarophytonicola Bonthond and Shalygin gen. nov., sp. nov, a baeocyte producing cyanobacterium that was isolated from the rhodophyte Agarophyton vermiculophyllum (Ohmi) Gurgel et al., an invasive seaweed that has spread across the northern hemisphere. The new species genome reveals a diverse repertoire of chemotaxis and adhesion related genes, including genes coding for type IV pili assembly proteins and a high number of genes coding for filamentous hemagglutinin family (FHA) proteins. Among a genetic basis for the synthesis of siderophores, carotenoids and numerous vitamins, W. agarophytonicola is potentially capable of producing cobalamin (vitamin B12), for which A. vermiculophyllum is an auxotroph. With a taxonomic description of the genus and species and a draft genome, this study provides as a basis for future research, to uncover the nature of this geographically independent association between seaweed and cyanobiont.
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- 2021
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46. A genetic variant alters the secondary structure of the lncRNA H19 and is associated with dilated cardiomyopathy
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Moritz F. Sinner, Anika Witten, Frank Rühle, Sabine Pankuweit, Hugo A. Katus, Leonie Martens, Stefan Kääb, Gerd Hasenfuß, Benjamin Meder, Christiane E. Angermann, Erich Bornberg-Bauer, Monika Stoll, Eloisa Arbustini, Biochemie, RS: FHML MaCSBio, and RS: Carim - B01 Blood proteins & engineering
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Male ,Genome-wide association study ,030204 cardiovascular system & hematology ,Genome ,DISEASE ,0302 clinical medicine ,lncRNA ,cardiovascular disease ,SHAPE-Seq ,AXIS ,RNA structure ,Base Pairing ,Aged, 80 and over ,Regulation of gene expression ,0303 health sciences ,minimum free energy ,LONG NONCODING RNA ,Middle Aged ,Long non-coding RNA ,Female ,RNA, Long Noncoding ,Boltzmann ensemble ,Research Paper ,Adult ,Cardiomyopathy, Dilated ,Genotype ,SNP ,Single-nucleotide polymorphism ,Computational biology ,Biology ,Polymorphism, Single Nucleotide ,Young Adult ,03 medical and health sciences ,Humans ,Genetic Predisposition to Disease ,Nucleic acid structure ,Molecular Biology ,Gene ,Aged ,030304 developmental biology ,RiboSNitch ,Base Sequence ,H19 ,LANDSCAPE ,Point mutation ,RNA ,Cell Biology ,rs217727 ,EVOLUTION ,Case-Control Studies ,Nucleic Acid Conformation ,Function (biology) - Abstract
lncRNAs are at the core of many regulatory processes and have also been recognized to be involved in various complex diseases. They affect gene regulation through direct interactions with RNA, DNA or proteins. Accordingly, lncRNAs structure is likely to be essential for their regulatory function. Point mutations, which manifest as SNPs (single nucleotide polymorphisms) in genome screens, can substantially alter their function and, subsequently, the expression of their down-stream regulated genes. To test the effect of SNPs on structure, we investigated lncRNAs associated with dilated cardiomyopathy. Among 322 human candidate lncRNAs we demonstrate first the significant association of a SNP located in lncRNA H19 using data from 1084 diseased and 751 control patients. H19 is generally highly expressed in the heart, with a complex expression pattern during heart development. Next, we used MFE (minimum free energy) folding to demonstrate a significant refolding in the secondary structure of this 861 nt long lncRNA. Since MFE folding may overlook the importance of sub-optimal structures, we showed that this refolding also manifests in the overall Boltzmann structure ensemble. There, the composition of structures is tremendously affected in their thermodynamic probabilities through the genetic variant. Finally, we confirmed these results experimentally, using SHAPE-Seq, corroborating that SNPs affecting such structures may explain hidden genetic variance not accounted for through genome wide association studies. Our results suggest that structural changes in lncRNAs, and lncRNA H19 in particular, affect regulatory processes and represent optimal targets for further in-depth studies probing their molecular interactions.
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- 2021
47. Inferring gene targets of drugs and chemical compounds from gene expression profiles
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Heeju Noh and Rudiyanto Gunawan
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0301 basic medicine ,Statistics and Probability ,Underdetermined system ,0206 medical engineering ,Gene regulatory network ,Inference ,02 engineering and technology ,Saccharomyces cerevisiae ,Biology ,computer.software_genre ,Biochemistry ,03 medical and health sciences ,Lasso (statistics) ,Escherichia coli ,Animals ,Humans ,Gene Regulatory Networks ,Molecular Targeted Therapy ,Molecular Biology ,Drug discovery ,Least-angle regression ,Gene Expression Profiling ,Linear model ,Computational Biology ,Original Papers ,Computer Science Applications ,Gene expression profiling ,Computational Mathematics ,030104 developmental biology ,Computational Theory and Mathematics ,Genome Expression ,Linear Models ,Drosophila ,Data mining ,Transcriptome ,computer ,020602 bioinformatics ,Algorithms - Abstract
Motivation: Finding genes which are directly perturbed or targeted by drugs is of great interest and importance in drug discovery. Several network filtering methods have been created to predict the gene targets of drugs from gene expression data based on an ordinary differential equation model of the gene regulatory network (GRN). A critical step in these methods involves inferring the GRN from the expression data, which is a very challenging problem on its own. In addition, existing network filtering methods require computationally intensive parameter tuning or expression data from experiments with known genetic perturbations or both. Results: We developed a method called DeltaNet for the identification of drug targets from gene expression data. Here, the gene target predictions were directly inferred from the data without a separate step of GRN inference. DeltaNet formulation led to solving an underdetermined linear regression problem, for which we employed least angle regression (DeltaNet-LAR) or LASSO regularization (DeltaNet-LASSO). The predictions using DeltaNet for expression data of Escherichia coli , yeast, fruit fly and human were significantly more accurate than those using network filtering methods, namely mode of action by network identification (MNI) and sparse simultaneous equation model (SSEM). Furthermore, DeltaNet using LAR did not require any parameter tuning and could provide computational speed-up over existing methods. Conclusion: DeltaNet is a robust and numerically efficient tool for identifying gene perturbations from gene expression data. Importantly, the method requires little to no expert supervision, while providing accurate gene target predictions., Bioinformatics, 32 (14), ISSN:1367-4803, ISSN:1460-2059
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- 2021
48. Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin‐like mediator
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Maria G. Rivas, Pablo J. González, Diederik J. Opperman, Carlos D. Brondino, Carmien Tolmie, Felix Martín Ferroni, and Cintia S. Ramírez
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Sinorhizobium meliloti ,Nitrite Reductases ,biology ,Chemistry ,Stereochemistry ,Full‐Length Papers ,Denitrification pathway ,Structural alignment ,Kinetics ,Substrate (chemistry) ,biology.organism_classification ,Nitrite reductase ,Crystallography, X-Ray ,Biochemistry ,Electron transfer ,Bacterial Proteins ,Protein Domains ,Docking (molecular) ,Azurin ,Molecular Biology - Abstract
We report the crystal structure of the copper-containing nitrite reductase (NirK) from the Gram-negative bacterium Sinorhizobium meliloti 2011 (Sm), together with complex structural alignment and docking studies with both non-cognate and the physiologically related pseudoazurins, SmPaz1 and SmPaz2, respectively. S. meliloti is a rhizobacterium used for the formulation of Medicago sativa bionoculants, and SmNirK plays a key role in this symbiosis through the denitrification pathway. The structure of SmNirK, solved at a resolution of 2.5 A, showed a striking resemblance with the overall structure of the well-known Class I NirKs composed of two Greek key β-barrel domains. The activity of SmNirK is ~12% of the activity reported for classical NirKs, which could be attributed to several factors such as subtle structural differences in the secondary proton channel, solvent accessibility of the substrate channel, and that the denitrifying activity has to be finely regulated within the endosymbiont. In vitro kinetics performed in homogenous and heterogeneous media showed that both SmPaz1 and SmPaz2, which are coded in different regions of the genome, donate electrons to SmNirK with similar performance. Even though the energetics of the interprotein electron transfer (ET) process is not favorable with either electron donors, adduct formation mediated by conserved residues allows minimizing the distance between the copper centers involved in the interprotein ET process.
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- 2021
49. Cdc25C/cdc2/cyclin B, raf/MEK/ERK and PERK/eIF2α/CHOP pathways are involved in forskolin-induced growth inhibition of MM.1S cells by G2/M arrest and mitochondrion-dependent apoptosis
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Pei-Wen Jiang, Dan-Ying Zhang, Ping Yang, Yan Li, Li Cheng, Wen-Qian Du, Yi-Song Sun, Min-Hui Li, Chen Li, Jing Zhao, Tai Yang, Song-Ting Shi, and Ming-Xiang Gao
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MAPK/ERK pathway ,Eukaryotic Initiation Factor-2 ,Cyclin B ,Apoptosis ,CHOP ,chemistry.chemical_compound ,Cell Line, Tumor ,Humans ,Cyclin B1 ,Molecular Biology ,Mitogen-Activated Protein Kinase Kinases ,Cyclin-dependent kinase 1 ,Forskolin ,biology ,Colforsin ,Cell Biology ,Mitochondria ,G2 Phase Cell Cycle Checkpoints ,chemistry ,biology.protein ,Cancer research ,Growth inhibition ,Developmental Biology ,Research Paper - Abstract
Multiple myeloma (MM) remains an incurable hematological malignancy characterized by proliferation and accumulation of plasma cells in the bone marrow. Innovative and effective therapeutic approaches that are able to improve the outcome and the survival of MM sufferers, especially the identification of novel natural compounds and investigation of their anti-MM mechanisms, are needed. Here, we investigated the effects and the potential mechanisms against MM of forskolin, a diterpene derived from the medicinal plant Coleus forskohlii, in MM cell line MM.1S. CCK-8 assay showed that forskolin significantly inhibited MM.1S cells viability in a time- and dose-dependent manner. Furthermore, we demonstrated that forskolin induced G2/M phase arrest with a remarkable increase of p-cdc25c, p-cdc2, and a decrease of cyclin B1, indicating the suppression of cdc25C/cdc2/cyclin B pathway. Moreover, we found that forskolin induced mitochondrion-dependent apoptosis which was accompanied by the increase of pro-apoptotic proteins Bax, Bad, Bim and Bid, the decrease of anti-apoptotic proteins Bcl-2 and Bcl-xl, the changes of the mitochondrial membrane potential (MMP) and increase of cleaved caspase-9, cleaved caspase-3 and cleaved PARP. Of note, we demonstrated that forskolin induced a decrease of p-C-Raf, p-MEK, p-ERK1/2 and p-p90Rsk, and an increase of p-PERK, p-eIF2α and CHOP, which indicated that the inhibition of Raf/MEK/ERK pathway and activation of PERK/eIF2α/CHOP pathway were involved, at least partially, in forskolin-induced MM.1S cells apoptosis. These findings confirm the anti-MM action of forskolin and extend the understanding of its anti-MM mechanism in MM.1S cells, as well as reinforcing the evidence for forskolin as a natural chemotherapeutic compound against MM.
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- 2021
50. Coffee Pulp, a By-Product of Coffee Production, Modulates Gut Microbiota and Improves Metabolic Syndrome in High-Carbohydrate, High-Fat Diet-Fed Rats
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Marwan E Majzoub, Nikhil S. Bhandarkar, Lindsay Brown, Torsten Thomas, Sunil K. Panchal, and Peter Mouatt
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Microbiology (medical) ,obesity ,chlorogenic acid ,Gut flora ,engineering.material ,Feed conversion ratio ,Article ,metabolic syndrome ,chemistry.chemical_compound ,Functional food ,Chlorogenic acid ,stomatognathic system ,Trigonelline ,coffee pulp ,medicine ,Immunology and Allergy ,Food science ,high-fat ,Molecular Biology ,General Immunology and Microbiology ,biology ,gut microbiota ,Pulp (paper) ,medicine.disease ,biology.organism_classification ,Infectious Diseases ,chemistry ,engineering ,high-carbohydrate ,Medicine ,Metabolic syndrome ,Caffeine - Abstract
Waste from food production can be re-purposed as raw material for usable products to decrease industrial waste. Coffee pulp is 29% of the dry weight of coffee cherries and contains caffeine, chlorogenic acid, trigonelline, diterpenes and fibre. We investigated the attenuation of signs of metabolic syndrome induced by high-carbohydrate, high-fat diet in rats by dietary supplementation with 5% freeze-dried coffee pulp for the final 8 weeks of a 16-week protocol. Coffee pulp decreased body weight, feed efficiency and abdominal fat, normalised systolic blood pressure, left ventricular diastolic stiffness, and plasma concentrations of triglycerides and non-esterified fatty acids, and improved glucose tolerance in rats fed high-carbohydrate, high-fat diet. Further, the gut microbiota was modulated with high-carbohydrate, high-fat diet and coffee pulp supplementation and 14 physiological parameters were correlated with the changes in bacterial community structures. This study suggested that coffee pulp, as a waste from the coffee industry, is useful as a functional food for improving obesity-associated metabolic, cardiovascular and liver structure and function, and gut microbiota.
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- 2021
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