Biological Functions
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2021 ◽  
Frank Dunemann ◽  
Wanying He ◽  
Christoph Böttcher ◽  
Sven Reichardt ◽  
Thomas Nothnagel ◽  

Abstract Background Falcarinol-type polyacetylenes (PAs) such as falcarinol (FaOH) and falcarindiol (FaDOH) are produced by several Apiaceae vegetables such as carrot, parsnip, celeriac and parsley. They are known for numerous biological functions and contribute to the undesirable bitter off-taste of carrots and their products. Despite their interesting biological functions, the genetic basis of their structural diversity and function is widely unknown. A better understanding of the genetics of the PA levels present in carrot roots might support breeding of carrot cultivars with tailored PA levels for food production or nutraceuticals. Results A large carrot F2 progeny derived from a cross of a cultivated inbred line with an inbred line derived from a Daucus carota ssp. commutatus accession rich in PAs was used for linkage mapping and quantitative trait locus (QTL) analysis. Ten QTLs for FaOH and FaDOH levels in roots were identified in the carrot genome. Major QTLs for FaOH and FaDOH with high LOD values of up to 40 were identified on chromosomes 4 and 9. To discover putative candidate genes from the plant fatty acid metabolism, we examined an extended version of the inventory of the carrot FATTY ACID DESATURASE2 (FAD2) gene family. Additionally, we used the carrot genome sequence for a first inventory of ECERIFERUM1 (CER1) genes possibly involved in PA biosynthesis. We identified genomic regions on different carrot chromosomes around the found QTLs, that contain several FAD2 and CER1 genes within their 2-LOD confidence intervals. With regard to the major QTLs on chromosome 9 three putative CER1 decarbonylase gene models are proposed as candidate genes. Conclusion The present study increases the current knowledge on the genetics of PA accumulation in carrot roots. Our finding, that carrot candidate genes from the fatty acid metabolism are significantly associated with major QTLs for both major PAs, will facilitate future functional gene studies and a further dissection of the genetic factors controlling PA accumulation. Characterization of such candidate genes will have a positive impact on carrot breeding programs aimed at both lowering or increasing PA concentrations in carrot roots.

Emad Alharbi ◽  
Paul Bond ◽  
Radu Calinescu ◽  
Kevin Cowtan

Proteins are macromolecules that perform essential biological functions which depend on their three-dimensional structure. Determining this structure involves complex laboratory and computational work. For the computational work, multiple software pipelines have been developed to build models of the protein structure from crystallographic data. Each of these pipelines performs differently depending on the characteristics of the electron-density map received as input. Identifying the best pipeline to use for a protein structure is difficult, as the pipeline performance differs significantly from one protein structure to another. As such, researchers often select pipelines that do not produce the best possible protein models from the available data. Here, a software tool is introduced which predicts key quality measures of the protein structures that a range of pipelines would generate if supplied with a given crystallographic data set. These measures are crystallographic quality-of-fit indicators based on included and withheld observations, and structure completeness. Extensive experiments carried out using over 2500 data sets show that the tool yields accurate predictions for both experimental phasing data sets (at resolutions between 1.2 and 4.0 Å) and molecular-replacement data sets (at resolutions between 1.0 and 3.5 Å). The tool can therefore provide a recommendation to the user concerning the pipelines that should be run in order to proceed most efficiently to a depositable model.

Cells ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3340
Lena Maltan ◽  
Hadil Najjar ◽  
Adéla Tiffner ◽  
Isabella Derler

Calcium ion channels are involved in numerous biological functions such as lymphocyte activation, muscle contraction, neurotransmission, excitation, hormone secretion, gene expression, cell migration, memory, and aging. Therefore, their dysfunction can lead to a wide range of cellular abnormalities and, subsequently, to diseases. To date various conventional techniques have provided valuable insights into the roles of Ca2+ signaling. However, their limited spatiotemporal resolution and lack of reversibility pose significant obstacles in the detailed understanding of the structure–function relationship of ion channels. These drawbacks could be partially overcome by the use of optogenetics, which allows for the remote and well-defined manipulation of Ca²⁺-signaling. Here, we review the various optogenetic tools that have been used to achieve precise control over different Ca2+-permeable ion channels and receptors and associated downstream signaling cascades. We highlight the achievements of optogenetics as well as the still-open questions regarding the resolution of ion channel working mechanisms. In addition, we summarize the successes of optogenetics in manipulating many Ca2+-dependent biological processes both in vitro and in vivo. In summary, optogenetics has significantly advanced our understanding of Ca2+ signaling proteins and the used tools provide an essential basis for potential future therapeutic application.

2021 ◽  
Vol 12 (12) ◽  
Huan Wang ◽  
Ling Zhang ◽  
Qiuhua Luo ◽  
Jia Liu ◽  
Guiling Wang

AbstractThe microrchidia (MORC) family of proteins is a highly conserved nuclear protein superfamily, whose members contain common domain structures (GHKL-ATPase, CW-type zinc finger and coiled-coil domain) yet exhibit diverse biological functions. Despite the advancing research in previous decades, much of which focuses on their role as epigenetic regulators and in chromatin remodeling, relatively little is known about the role of MORCs in tumorigenesis and pathogenesis. MORCs were first identified as epigenetic regulators and chromatin remodelers in germ cell development. Currently, MORCs are regarded as disease genes that are involved in various human disorders and oncogenes in cancer progression and are expected to be the important biomarkers for diagnosis and treatment. A new paradigm of expanded MORC family function has raised questions regarding the regulation of MORCs and their biological role at the subcellular level. Here, we systematically review the progress of researching MORC members with respect to their domain architectures, diverse biological functions, and distribution characteristics and discuss the emerging roles of the aberrant expression or mutation of MORC family members in human disorders and cancer development. Furthermore, the illustration of related mechanisms of the MORC family has made MORCs promising targets for developing diagnostic tools and therapeutic treatments for human diseases, including cancers.

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 621
Chen-Yang Tang ◽  
Meng-Huan Song ◽  
Zhong-Liang Peng ◽  
Wei Wu ◽  
Changjun Peng ◽  

The visual characteristics of animals with different circadian habits, especially colubrid snakes, exhibit highly variable photoreceptor morphology. While studies have reported on the diversity in retinal cell morphology among snakes with different circadian patterns, few studies have examined the expression of genes related to vision. To explore gene expression patterns in the eyes between diurnal and nocturnal snakes, we carried out RNA sequencing of six tissues (eye, heart, liver, lung, kidney, and muscle) in two colubrids with disparate circadian activities, i.e., diurnal Ahaetulla prasina and nocturnal Lycodon flavozonatum, followed by weighted gene co-expression network analysis (WGCNA). The genes in the two most correlated modules were primarily enriched in different functional pathways, thus suggesting different biological functions. Three opsin genes (RH1, LWS, and SWS) were differentially expressed between the two species. Moreover, in the phototransduction pathway, different genes were highly expressed in the eyes of both species, reflecting specific expression patterns in the eyes of snakes with different circadian activity. We also confirmed the dominance of cone- and rod-related genes in diurnal and nocturnal adaptation, respectively. This work provides an important foundation for genetic research on visual adaptation in snakes and provides further insight into the adaptive evolution of such species.

2021 ◽  
Vol 13 (4) ◽  
pp. 31-37
Tiantian Mao ◽  
Youjian Peng ◽  
Ruobing Peng ◽  
Xiaoying Wei

Human dental pulp stem cells (hDPSCs) are capable of forming mineralized nodules. The proliferation and osteogenic differentiation of hDPSCs are very important for alleviating tooth defects caused by related diseases. Angel-ica polysaccharide (ASP) is the main bioactive ingredient extracted from the angelica root. ASP has a variety of biological functions, including immune regulation, antitumor activity, and hematopoiesis. However, its possible effects on hDPSCs are still unclear. In this study, we aimed to investigate the role of ASP in periodontal diseases. We found that ASP promoted the proliferation of hDPSCs and osteogenic differentiation of hDPSCs. We further found that it promoted the expression of osteogenic-related genes, including ALP, RUNX2, Col1a1, and OCN. Mechanically, we found that ASP activated the Wnt/β-catenin pathway. In conclusion, our results suggested that ASP promoted the proliferation and osteogenic differentiation of hDPSCs via the Wnt/β-catenin pathway.

Biomedicines ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 1768
Kiichi Hirota

Oxygen (O2) is an essential molecule [1] in the production of adenosine triphosphate (ATP) in cells, and a lack of energy due to O2 deficiency makes the maintenance of biological functions and human life improbable. [...]

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3379
Laura Patterson Rosa ◽  
Martha F. Mallicote ◽  
Robert J. MacKay ◽  
Samantha A. Brooks

Macrolide drugs are the treatment of choice for Rhodococcus equi infections, despite severe side-effects temporary anhidrosis as a. To better understand the molecular biology leading to macrolide induced anhidrosis, we performed skin biopsies and Quantitative Intradermal Terbutaline Sweat Tests (QITSTs) in six healthy pony-cross foals for three different timepoints during erythromycin administration—pre-treatment (baseline), during anhidrosis and post-recovery. RNA sequencing of biopsies followed by differential gene expression analysis compared both pre and post normal sweating timepoints to the erythromycin induced anhidrosis episode. After Bonferroni correction for multiple testing, 132 gene transcripts were significantly differentially expressed during the anhidrotic timepoint. Gene ontology analysis of the full differentially expressed gene set identified over-represented biological functions for ubiquitination and ion-channel function, both biologically relevant to sweat production. These same mechanisms were previously implicated in heritable equine idiopathic anhidrosis and sweat gland function and their involvement in macrolide-induced temporary anhidrosis warrants further investigation.

2021 ◽  
Vol 12 (1) ◽  
Qirun Wang ◽  
Jie Lin

AbstractWhile most genes’ expression levels are proportional to cell volumes, some genes exhibit nonlinear scaling between their expression levels and cell volume. Therefore, their mRNA and protein concentrations change as the cell volume increases, which often have crucial biological functions such as cell-cycle regulation. However, the biophysical mechanism underlying the nonlinear scaling between gene expression and cell volume is still unclear. In this work, we show that the nonlinear scaling is a direct consequence of the heterogeneous recruitment abilities of promoters to RNA polymerases based on a gene expression model at the whole-cell level. Those genes with weaker (stronger) recruitment abilities than the average ability spontaneously exhibit superlinear (sublinear) scaling with cell volume. Analysis of the promoter sequences and the nonlinear scaling of Saccharomyces cerevisiae’s mRNA levels shows that motifs associated with transcription regulation are indeed enriched in genes exhibiting nonlinear scaling, in concert with our model.

2021 ◽  
Vol 12 ◽  
Qian Qu ◽  
Yuefei Li ◽  
Qi Dong ◽  
Shupeng Li ◽  
Hongliang Du ◽  

Forsythiae Fructus (FF), the dry fruit of Forsythia suspensa (Thunb.) Vahl, has a long history of use in traditional Chinese Medicine for its heat-clearing and detoxifying properties. It possesses clinical therapeutic effects and biological functions showing efficacy in handling different diseases. To investigate the FF differences in Henan, Shanxi, and Shaanxi in August and October, the surface morphology, mid-infrared and near-infrared spectrums, and HPLC were analyzed. Concurrently, the anti-inflammatory and antioxidant effects on LPS-induced J774A.1 cells were evaluated by western blot and RT-qPCR. The results showed that FF from different Harvest Seasons and Regions are provided with different microstructures and mid-infrared and near-infrared spectrums, and the levels of forsythiaside A and phillyrin of FF from Shanxi in August and phillygenin of FF from Shaanxi in August were the highest. Meanwhile, FF from Shanxi and Shaanxi in August markedly reduced the levels of inflammatory cytokines and mediators (TNF-α, IL-1β, NF-κB, and iNOS) and the protein expression levels of phosphorylated total IKKα/β and nuclear NF-κB. In August, SXFF and SAXFF also promoted the mRNA expression levels of HO-1 and NQO1 and the protein expression levels of HO-1 and nuclear Nrf2 and suppressed the protein expression levels of KEAP1. Spearman correlation analysis showed that phillygenin had a strong correlation with the protein expression on LPS-induced J774A.1 cells. In summary, our results showed that FF from harvest seasons and regions contributed to the distinct differences in microstructure, the mid-infrared and near-infrared spectrums, and compound content. More importantly, FF from Shanxi and Shaanxi in August showed marked anti-inflammatory and antioxidant activities, but with some differences, which may be because of different contents of phillygenin and phillyrin of lignans in FF.

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