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Open Biology

Thomas G McWilliams, Erica Barini, Risto Pohjolan-Pirhonen, Simon P Brooks, François Singh, Sophie Burel, Kristin Balk, Atul Kumar, Lambert Montava-Garriga, Alan R Prescott, Sidi Mohamed Hassoun, François Mouton-Liger, Graeme Ball, Rachel Hills, Axel Knebel, Ayse Ulusoy, Donato A Di Monte, Jevgenia Tamjar, Odetta Antico, Kyle Fears, Laura Smith, Riccardo Brambilla, Eino Palin, Miko Valori, Johanna Eerola-Rautio, Pentti Tienari, Olga Corti, Stephen B Dunnett, Ian G Ganley, Anu Suomalainen, Miratul M K Muqit
Mutations in PINK1 and Parkin result in autosomal recessive Parkinson's disease (PD). Cell culture and in vitro studies have elaborated the PINK1-dependent regulation of Parkin and defined how this dyad orchestrates the elimination of damaged mitochondria via mitophagy. PINK1 phosphorylates ubiquitin at serine 65 (Ser65) and Parkin at an equivalent Ser65 residue located within its N-terminal ubiquitin-like domain, resulting in activation; however, the physiological significance of Parkin Ser65 phosphorylation in vivo in mammals remains unknown...
November 7, 2018: Open Biology
Akpéli V Nordor, Dominique Bellet, Geoffrey H Siwo
Cancer and malaria exemplify two maladies historically assigned to separated research spaces. Cancer, on the one hand, ranks among the top priorities in the research agenda of developed countries. Its rise is mostly explained by the ageing of these populations and linked to environment and lifestyle. Malaria, on the other hand, represents a major health burden for developing countries in the Southern Hemisphere. These two diseases also belong to separate fields of medicine: non-communicable diseases for cancer and communicable diseases for malaria...
October 31, 2018: Open Biology
Nadia C Abascal, Lynne Regan
Protein-based materials are finding new uses and applications after millennia of impacting the daily life of humans. Some of the earliest uses of protein-based materials are still evident in silk and wool textiles and leather goods. Today, even as silks, wools and leathers are still be used in traditional ways, these proteins are now seen as promising materials for biomaterials, vehicles of drug delivery and components of high-tech fabrics. With the advent of biosynthetic methods and streamlined means of protein purification, protein-based materials-recombinant and otherwise-are being used in a host of applications at the cutting edge of medicine, electronics, materials science and even fashion...
October 31, 2018: Open Biology
Elisabetta Onelli, Monica Scali, Marco Caccianiga, Nadia Stroppa, Piero Morandini, Giulio Pavesi, Alessandra Moscatelli
Fine regulation of exocytosis and endocytosis plays a basic role in pollen tube growth. Excess plasma membrane secreted during pollen tube elongation is known to be retrieved by endocytosis and partially reused in secretory pathways through the Golgi apparatus. Dissection of endocytosis has enabled distinct degradation pathways to be identified in tobacco pollen tubes and has shown that microtubules influence the transport of plasma membrane internalized in the tip region to vacuoles. Here, we used different drugs affecting the polymerization state of microtubules together with SYP21, a marker of prevacuolar compartments, to characterize trafficking of prevacuolar compartments in Nicotiana tabacum pollen tubes...
October 31, 2018: Open Biology
Thomas F Chartier, Joran Deschamps, Wiebke Dürichen, Gáspár Jékely, Detlev Arendt
Chemical detection is key to various behaviours in both marine and terrestrial animals. Marine species, though highly diverse, have been underrepresented so far in studies on chemosensory systems, and our knowledge mostly concerns the detection of airborne cues. A broader comparative approach is therefore desirable. Marine annelid worms with their rich behavioural repertoire represent attractive models for chemosensation. Here, we study the marine worm Platynereis dumerilii to provide the first comprehensive investigation of head chemosensory organ physiology in an annelid...
October 31, 2018: Open Biology
Feng Wang, Weihua Zhang, Tianfeng Wu, Heying Chu
Lung cancer continues to be the leading cause of cancer-related deaths worldwide due to its high incidence, malignant behaviour and lack of major advancements in treatment strategy. The occurrence and development of lung cancer is closely related to inflammation. Thus, we conducted the present study to investigate the effects of IL-38 (interleukin-38), a newly identified anti-inflammatory factor, on non-small cell lung cancer (NSCLC), which accounts for about 85% of all lung cancers. We first evaluated the IL-38 expression in 384 pairs of NSCLC samples and their adjacent normal mucosa by real-time PCR, ELISA (enzyme-linked immunoassay) and tissue microarrays...
October 31, 2018: Open Biology
Rongsong Luo, Chunling Bai, Lei Yang, Zhong Zheng, Guanghua Su, Guangqi Gao, Zhuying Wei, Yongchun Zuo, Guangpeng Li
DNA methylation has been investigated for many years, but recent technologies have allowed for single-cell- and single-base-resolution DNA methylation datasets and more accurate assessment of DNA methylation dynamics at the key genomic regions that regulate gene expression in human early embryonic development. In this study, the region from upstream 20 kb to downstream 20 kb of RefSeq gene was selected and divided into 12 distinct regions (up20, up10, up5, up2, 5'UTR, exon, intron, 3'UTR, down2, down5, down10 and down20)...
October 31, 2018: Open Biology
Le Shu, Zhe Wang, Qizhi Wang, Yumeng Wang, Xiaobo Zhang
The dysregulation of microRNAs (miRNAs), key posttranscriptional regulators of gene expression, is closely associated with cancer development. However, the miRNAs of monocytes, important cells of tumour immunity, have not been extensively explored. In the present study, the differentially expressed miRNAs of blood monocytes derived from gastric and breast cancer patients and healthy donors were characterized. The results indicated that 74 miRNAs were upregulated and 46 miRNAs were downregulated in monocytes of patients with breast or gastric cancers compared with the healthy donors, suggesting that these 120 miRNAs from transformed monocytes were associated with cancers...
October 31, 2018: Open Biology
Shinichi Nakagawa, Tomohiro Yamazaki, Tetsuro Hirose
Paraspeckles are nuclear bodies built on an architectural long noncoding RNA, NEAT1, and a series of studies have revealed their molecular components, fine internal structures and cellular and physiological functions. Emerging lines of evidence suggest that paraspeckle formation is elicited by phase separation of associating RNA-binding proteins containing intrinsically disordered regions, which induce ordered arrangement of paraspeckle components along NEAT1. In this review, we will summarize the history of paraspeckle research over the last couple of decades, especially focusing on the function and structure of the nuclear bodies...
October 24, 2018: Open Biology
Stephanie Sefried, Hans-Ulrich Häring, Cora Weigert, Sabine S Eckstein
Immortal hepatocyte cell lines are widely used to elucidate insulin-dependent signalling pathways and regulation of hepatic metabolism, although the often tumorigenic origin might not represent the metabolic state of healthy hepatocytes. We aimed to investigate if murine cell line AML12 and human cell line THLE-2, which are derived from healthy liver cells, are comparable to hepatoma cell line HepG2 for studying acute insulin signalling and expression of gluconeogenic enzymes and hepatokines. Insulin responsiveness of AML12 and THLE-2 cells was impaired when cells were cultured in the recommended growth medium, but comparable with HepG2 cells by using insulin-deficient medium...
October 24, 2018: Open Biology
Ana Lopez, Angeleen Fleming, David C Rubinsztein
Autophagy is an intracellular clearance pathway that delivers cytoplasmic contents to the lysosome for degradation. It plays a critical role in maintaining protein homeostasis and providing nutrients under conditions where the cell is starved. It also helps to remove damaged organelles and misfolded or aggregated proteins. Thus, it is not surprising that defects in this pathway are associated with a variety of pathological conditions, such as neurodegeneration, cancer and infection. Pharmacological upregulation of autophagy is considered a promising therapeutic strategy for the treatment of neurodegenerative and infectious diseases...
October 24, 2018: Open Biology
Natacha Raich, Souhir Mahmoudi, Doruk Emre, Roger E Karess
The Drosophila Mad1 spindle checkpoint protein helps organize several nucleoplasmic components, and flies lacking Mad1 present changes in gene expression reflecting altered chromatin conformation. In interphase, checkpoint protein Mad1 is usually described as localizing to the inner nuclear envelope by binding the nucleoporin Tpr, an interaction believed to contribute to proper mitotic regulation. Whether Mad1 has other nuclear interphase functions is unknown. We found in Drosophila that Mad1 is present in nuclei of both mitotic and postmitotic tissues...
October 17, 2018: Open Biology
Hongxu Liu, Yegang Ma, Changhao Liu, Pengfei Li, Tao Yu
Emerging evidence suggests that microRNAs (miRNAs) serve an important role in tumourigenesis and development. Although the low expression of miR-125a-5p in non-small-cell lung cancer (NSCLC) has been reported, the underlying mechanism remains unknown. In the current study, the low expression of miR-125a-5p in NSCLC was verified in paired cancer tissues and adjacent non-tumour tissues. Furthermore, the CpG island in the miR-125a-5p region was hypermethylated in the tumour tissues, and the hypermethylation was negatively correlated with miR-125a-5p expression...
October 10, 2018: Open Biology
Bingdi Yan, Yanbing Hu, Tiangang Ma, Yanjun Wang
Mutation in isocitrate dehydrogenase ( IDH ) leads to an aberrant function of the enzyme, leading to the production of hydroxyglutarate, as well as changes in cellular metabolism, DNA methylation and histone modification. Previous studies uncovered mutations in IDH1 in several malignancies, with the most frequent mutation being IDH1 R132H. It has been demonstrated that IDH1 expression is induced in non-small-cell lung cancer (NSCLC). However, the contribution of IDH1 mutation in the malignant transformation and development of NSCLC is unclear...
October 10, 2018: Open Biology
Yanhong Wei, Jie Zhang, Shenhui Xu, Xin Peng, Xia Yan, Xiaoyu Li, Huiping Wang, Hui Chang, Yunfang Gao
Mammalian hibernators experience repeated hypoxic ischaemia and reperfusion during the torpor-arousal cycle. We investigated levels of oxidative stress, antioxidant capacity, and the underlying mechanism in heart, liver, brain and kidney tissue as well as plasma during different periods of hibernation in Daurian ground squirrels ( Spermophilus dauricus ). Our data showed that the levels of hydrogen peroxide significantly increased in the heart and brain during late torpor (LT) compared with levels during the summer active (SA) state...
October 10, 2018: Open Biology
Mitsutoshi Nakamura, Andrew N M Dominguez, Jacob R Decker, Alexander J Hull, Jeffrey M Verboon, Susan M Parkhurst
Repair of wounds to individual cells is crucial for organisms to survive daily physiological or environmental stresses, as well as pathogen assaults, which disrupt the plasma membrane. Sensing wounds, resealing membranes, closing wounds and remodelling plasma membrane/cortical cytoskeleton are four major steps that are essential to return cells to their pre-wounded states. This process relies on dynamic changes of the membrane/cytoskeleton that are indispensable for carrying out the repairs within tens of minutes...
October 3, 2018: Open Biology
Chun-Wei He, Chien-Po Liao, Chun-Liang Pan
Wnts are a highly conserved family of secreted glycoproteins that play essential roles in the morphogenesis and body patterning during the development of metazoan species. In recent years, mounting evidence has revealed important functions of Wnt signalling in diverse aspects of neural development, including neuronal polarization, guidance and branching of the axon and dendrites, as well as synapse formation and its structural remodelling. In contrast to Wnt signalling in cell proliferation and differentiation, which mostly acts through β-catenin-dependent pathways, Wnts engage a diverse array of non-transcriptional cascades in neuronal development, such as the planar cell polarity, cytoskeletal or calcium signalling pathways...
October 3, 2018: Open Biology
Logan George, Fred E Indig, Kotb Abdelmohsen, Myriam Gorospe
RNA tracking allows researchers to visualize RNA molecules in cells and tissues, providing important spatio-temporal information regarding RNA dynamics and function. Methods such as fluorescent in situ hybridization (FISH) and molecular beacons rely on complementary oligonucleotides to label and view endogenous transcripts. Other methods create artificial chimeric transcripts coupled with bacteriophage-derived coat proteins (e.g. MS2, λN) to tag molecules in live cells. In other approaches, endogenous RNAs are recognized by complementary RNAs complexed with noncatalytic Cas proteins...
October 3, 2018: Open Biology
Robert G Smock, Rob Meijers
Glycosaminoglycans (GAGs) play a widespread role in embryonic development, as deletion of enzymes that contribute to GAG synthesis lead to deficiencies in cell migration and tissue modelling. Despite the biochemical and structural characterization of individual protein/GAG interactions, there is no concept available that links the molecular mechanisms of GAG/protein engagements to tissue development. Here, we focus on the role of GAG polymers in mediating interactions between cell surface receptors and their ligands...
October 3, 2018: Open Biology
Trevor D Lamb, David M Hunt
We examined the genes encoding the proteins that mediate the Ca-feedback regulatory system in vertebrate rod and cone phototransduction. These proteins comprise four families: recoverin/visinin, the guanylyl cyclase activating proteins (GCAPs), the guanylyl cyclases (GCs) and the sodium/calcium-potassium exchangers (NCKXs). We identified a paralogon containing at least 36 phototransduction genes from at least fourteen families, including all four of the families involved in the Ca-feedback loop (recoverin/visinin, GCAPs, GCs and NCKXs)...
September 26, 2018: Open Biology
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