bluuebunny/crossref_metadata_2025 huggingface dataset:
ASF1a inhibition induces p53-dependent growth arrest and senescence of cancer cells
Authors: Wu Yujiao , Li Xidan , Yu Jingya , Björkholm Magnus , Xu Dawei
Published: January 2019

Anti-silencing function 1a (ASF1a) is a histone H3–H4 chaperone isoform involved in chromatin assembling and transcription regulation. Recently, ASF1a has been shown to be up-regulated in certain human malignancies and required for the expression of telomerase reverse transcriptase (TERT), a factor essential for the immortal phenotype of cancer cells; however, its role in oncogenesis remains poorly defined. In the present study, we determine whether ASF1a is required for the unlimited proliferation of cancer cells, a key cancer hallmark. Elevated ASF1a mRNA expression was observed in hepatocellular carcinoma (HCC) tumors. The overexpression of ASF1a was similarly found in 20 cancer types contained in TCGA and GTEx datasets. ASF1a knockdown led to growth arrest and senescence of wild-type (wt) p53-carrying HCC and prostate cancer cells. Cellular senescence mediated by ASF1a inhibition resulted from the robust up-regulation of p53 and p21cip1 expression, but without detectable changes in TERT expression. p53 inhibition attenuated p21cip1 induction caused by ASF1a depletion. Mechanistically, ASF1a-knocked down cells displayed widespread DNA damage. The TCGA dataset analysis revealed a negative correlation between ASF1a and p21cip1 expression in multiple types of primary tumors, including HCC, prostate, gastric, and breast cancer. Higher ASF1a and lower p21cip1 expression predicted a poor outcome in patients with HCC. Our results reveal that ASF1a overexpression is widespread in human malignancies and is required for the infinite proliferation of cancer cells, whereas its inhibition induces DNA damage and subsequent up-regulation of p53-p21cip1 expression, thereby triggering cellular senescence. Thus, ASF1a may serve as a potential target in cancer therapy.
Hypoxia-induced 26S proteasome dysfunction increases immunogenicity of mesenchymal stem cells
Authors: Abu-El-Rub Ejlal , Sequiera Glen Lester , Sareen Niketa , Yan Weiang , Moudgil Meenal , Sabbir Mohammad Golam , Dhingra Sanjiv
Published: January 2019

Bone marrow-derived allogeneic (donor derived) mesenchymal stem cells (MSCs) are immunoprivileged and are considered to be prominent candidates for regenerative therapy for numerous degenerative diseases. Even though the outcome of initial allogeneic MSCs based clinical trials was encouraging, the overall enthusiasm, of late, has dimmed down. This is due to failure of long-term survival of transplanted cells in the recipient. In fact, recent analyses of allogeneic MSC-based studies demonstrated that cells after transplantation turned immunogenic and were subsequently rejected by host immune system. The current study reveals a novel mechanism of immune switch in MSCs. We demonstrate that hypoxia, a common denominator of ischemic tissues, induces an immune shift in MSCs from immunoprivileged to immunogenic state. The immunoprivilege of MSCs is preserved by downregulation or the absence of major histocompatibility complex class II (MHC-II) molecules. We found that 26S proteasome-mediated intracellular degradation of MHC-II helps maintain the absence of MHC-II expression on cell surface in normoxic MSCs and preserves their immunoprivilege. The exposure to hypoxia leads to dissociation of 19S and 20S subunits, and inactivation of 26S proteasome. This prevented the degradation of MHC-II and, as a result, the MSCs became immunogenic. Furthermore, we found that hypoxia-induced decrease in the levels of a chaperon protein HSP90α is responsible for inactivation of 26S proteasome. Maintaining HSP90α levels in hypoxic MSCs preserved the immunoprivilege of MSCs. Therefore, hypoxia-induced inactivation of 26S proteasome assembly instigates loss of immunoprivilege of allogeneic mesenchymal stem cells. Maintaining 26S proteasome activity in mesenchymal stem cells preserves their immunoprivilege.
Differential effects of N-acetylcysteine on retinal degeneration in two mouse models of normal tension glaucoma
Authors: Sano Hiroki , Namekata Kazuhiko , Kimura Atsuko , Shitara Hiroshi , Guo Xiaoli , Harada Chikako , Mitamura Yoshinori , Harada Takayuki
Published: January 2019

N-acetylcysteine (NAC) is widely used as a mucolytic agent and as an antidote to paracetamol overdose. NAC serves as a precursor of cysteine and stimulates the synthesis of glutathione in neural cells. Suppressing oxidative stress in the retina may be an effective therapeutic strategy for glaucoma, a chronic neurodegenerative disease of the retinal ganglion cells (RGCs) and optic nerves. Here we examined the therapeutic potential of NAC in two mouse models of normal tension glaucoma, in which excitatory amino-acid carrier 1 (EAAC1) or glutamate/aspartate transporter (GLAST) gene was deleted. EAAC1 is expressed in retinal neurons including RGCs, whereas GLAST is mainly expressed in Müller glial cells. Intraperitoneal administration of NAC prevented RGC degeneration and visual impairment in EAAC1-deficient (knockout; KO) mice, but not in GLAST KO mice. In EAAC1 KO mice, oxidative stress and autophagy were suppressed with increased glutathione levels by NAC treatment. Our findings suggest a possibility that systemic administration of NAC may be available for some types of glaucoma patients.
Cancer cell-derived immunoglobulin G activates platelets by binding to platelet FcγRIIa
Authors: Miao Shuo , Shu Dan , Zhu Ying , Lu Meng , Zhang Qingsong , Pei Youliang , He Ao-Di , Ma Rong , Zhang Bixiang , Ming Zhang-Yin
Published: January 2019

Tumor-associated thrombosis is the second leading risk factor for cancer patient death, and platelets activity is abnormal in cancer patients. Discovering the mechanism of platelet activation and providing effective targets for therapy are urgently needed. Cancer cell- derived IgG has been reported to regulate development of tumors. However, studies on the functions of cancer cell-derived IgG are quite limited. Here we investigated the potential role of cancer cell-derived IgG in platelet activation. We detected the expression of CD62P on platelets by flow cytometry and analyzed platelet function by platelets aggregation and ATP release. The content of IgG in cancer cell supernatants was detected by enzyme-linked immune sorbent assay. The distribution of cancer-derived IgG in cancer cells was analyzed by immunofluorescence assay. Western blot was performed to quantify the relative expression of FcγRIIa, syk, PLCγ2. The interaction between cancer cell-derived IgG and platelet FcγRIIa was analyzed by co-immunoprecipitation. The results showed that higher levels of CD62P were observed in cancer patients’ platelets compared with that of healthy volunteers. Cancer cell culture supernatants increased platelet CD62P and PAC-1 expression, sensitive platelet aggregation and ATP release in response to agonists, while blocking FcγRIIa or knocking down IgG reduced the activation of platelets. Coimmunoprecipitation results showed that cancer cell-derived IgG interacted directly with platelet FcγRIIa. In addition, platelet FcγRIIa was highly expressed in liver cancer patients. In summary, cancer cell-derived IgG interacted directly with FcγRIIa and activated platelets; targeting this interaction may be an approach to prevent and treat tumor-associated thrombosis.
TMEM97 and PGRMC1 do not mediate sigma-2 ligand-induced cell death
Authors: Zeng Chenbo , Weng Chi-Chang , Schneider Mark E. , Puentes Laura , Riad Aladdin , Xu Kuiying , Makvandi Mehran , Jin Linda , Hawkins William G. , Mach Robert H.
Published: January 2019

Sigma-2 receptors have been implicated in both tumor proliferation and neurodegenerative diseases. Recently the sigma-2 receptor was identified as transmembrane protein 97 (TMEM97). Progesterone receptor membrane component 1 (PGRMC1) was also recently reported to form a complex with TMEM97 and the low density lipoprotein (LDL) receptor, and this trimeric complex is responsible for the rapid internalization of LDL. Sigma-2 receptor ligands with various structures have been shown to induce cell death in cancer cells. In the current study, we examined the role of TMEM97 and PGRMC1 in mediating sigma-2 ligand-induced cell death. Cell viability and caspase-3 assays were performed in control, TMEM97 knockout (KO), PGRMC1 KO, and TMEM97/PGRMC1 double KO cell lines treated with several sigma-2 ligands. The data showed that knockout of TMEM97, PGRMC1, or both did not affect the concentrations of sigma-2 ligands that induced 50% of cell death (EC50), suggesting that cytotoxic effects of these compounds are not mediated by TMEM97 or PGRMC1. Sigma-1 receptor ligands, (+)-pentazocine and NE-100, did not block sigma-2 ligand cytotoxicity, suggesting that sigma-1 receptor was not responsible for sigma-2 ligand cytotoxicity. We also examined whether the alternative, residual binding site (RBS) of 1,3-Di-o-tolylguanidine (DTG) could be responsible for sigma-2 ligand cytotoxicity. Our data showed that the binding affinities (Ki) of sigma-2 ligands on the DTG RBS did not correlate with the cytotoxicity potency (EC50) of these ligands, suggesting that the DTG RBS was not fully responsible for sigma-2 ligand cytotoxicity. In addition, we showed that knocking out TMEM97, PGRMC1, or both reduced the initial internalization rate of a sigma-2 fluorescent ligand, SW120. However, concentrations of internalized SW120 became identical later in the control and knockout cells. These data suggest that the initial internalization process of sigma-2 ligands does not appear to mediate the cell-killing effect of sigma-2 ligands. In summary, we have provided evidence that sigma-2 receptor/TMEM97 and PGRMC1 do not mediate sigma-2 ligand cytotoxicity. Our work will facilitate elucidating mechanisms of sigma-2 ligand cytotoxicity.
The prodomain of caspase-3 regulates its own removal and caspase activation
Authors: Ponder Katelyn G. , Boise Lawrence H.
Published: January 2019

Caspase-3 is a cysteine–aspartic acid protease that cleaves cellular targets and executes cell death. Our current understanding is caspase-3 is activated by the cleavage of the interdomain linker and then subsequent cleavage of the N-terminal prodomain. However, previous reports have suggested that removal of the prodomain can result in the constitutive activation of caspase-3, although other studies have not observed this. To address this question in a more physiological setting, we developed an inducible doxycycline system to express a mutant form of caspase-3 that lacks the prodomain (∆28). We found that the removal of the prodomain renders the cells more susceptible to death signals, but the caspase is not constitutively active. To elucidate the regions of the prodomain that regulate activity, we created deletion constructs that remove 10 and 19 N-terminal amino acids. Surprisingly, removal of the first 10 amino acids renders caspase-3 inactive. Following serum withdrawal, the interdomain linker is cleaved, however, the remaining prodomain is not removed. Therefore, there is a specific amino acid or stretch of amino acids within the first 10 that are important for prodomain removal and caspase-3 function. We created different point mutations within the prodomain and found amino acid D9 is vital for caspase-3 function. We hypothesize that an initial cleavage event at D9 is required to allow cleavage at D28 that causes the complete removal of the prodomain allowing for full caspase activation. Together these findings demonstrate a previously unknown role of the prodomain in caspase activation.
The biochemical and electrophysiological profiles of amniotic fluid-derived stem cells following Wnt signaling modulation cardiac differentiation
Authors: Liu Yen-Wen , Fang Yi-Hsein , Su Chi-Ting , Hwang Shiaw-Min , Liu Ping-Yen , Wu Sheng-Nan
Published: January 2019

Owing to the beneficial properties of amniotic fluid-derived stem cells (AFSCs), including pluripotency and the lack of ethical issues associated with embryonic stem cells (ESCs), they should be a promising cell source for regenerative medicine. However, how to differentiate AFSCs into contracting cardiomyocytes has not been established. In this study, a well-established, direct cardiac differentiation protocol involving the modulation of Wnt signaling was used to differentiate Oct 3/4+ AFSCs into cardiomyocytes. By day 14 of cardiomyocyte differentiation, these AFSCs expressed cardiac-specific genes (i.e., cardiac troponin T and myosin light chain 2v) and proteins but could not spontaneously contract. Using the patch-clamp technique, we further characterized the electrophysiological properties of human ESC-derived cardiomyocytes (hESC-CMs) and differentiated AFSCs. We used different configurations to investigate membrane potentials and ion currents in differentiated AFSCs and hESC-CMs. Under cell-attached voltage- or whole-cell current-clamp modes, we recorded spontaneous action currents (ACs) or action potentials (APs) in hESC-CMs but not in differentiated AFSCs. Compared to hESC-CMs, differentiated AFSCs showed significantly diminished activity of both BKCa and IKCa channels, which might lead to a lack of spontaneous ACs and APs in differentiated AFSCs. These results indicated that this well-established Wnt signaling modulating cardiac differentiation protocol was insufficient to induce the differentiation of functional cardiomyocytes from Oct 3/4+ AFSCs. Therefore, AFSC may not be an ideal candidate for cardiomyocyte differentiation.
Intestinal epithelial N-acylphosphatidylethanolamine phospholipase D links dietary fat to metabolic adaptations in obesity and steatosis
Authors: Everard Amandine , Plovier Hubert , Rastelli Marialetizia , Van Hul Matthias , de Wouters d’Oplinter Alice , Geurts Lucie , Druart Céline , Robine Sylvie , Delzenne Nathalie M. , Muccioli Giulio G. , de Vos Willem M. , Luquet Serge , Flamand Nicolas , Di Marzo Vincenzo , Cani Patrice D.
Published: January 2019

Variations in N-acylethanolamines (NAE) levels are associated with obesity and metabolic comorbidities. Their role in the gut remains unclear. Therefore, we generated a mouse model of inducible intestinal epithelial cell (IEC)-specific deletion of N-acylphosphatidylethanolamine phospholipase D (NAPE-PLD), a key enzyme involved in NAE biosynthesis (Napepld∆IEC). We discovered that Napepld∆IEC mice are hyperphagic upon first high-fat diet (HFD) exposure, and develop exacerbated obesity and steatosis. These mice display hypothalamic Pomc neurons dysfunctions and alterations in intestinal and plasma NAE and 2-acylglycerols. After long-term HFD, Napepld∆IEC mice present reduced energy expenditure. The increased steatosis is associated with higher gut and liver lipid absorption. Napepld∆IEC mice display altered gut microbiota. Akkermansia muciniphila administration partly counteracts the IEC NAPE-PLD deletion effects. In conclusion, intestinal NAPE-PLD is a key sensor in nutritional adaptation to fat intake, gut-to-brain axis and energy homeostasis and thereby constitutes a novel target to tackle obesity and related disorders.
Experimental time-reversed adaptive Bell measurement towards all-photonic quantum repeaters
Authors: Hasegawa Yasushi , Ikuta Rikizo , Matsuda Nobuyuki , Tamaki Kiyoshi , Lo Hoi-Kwong , Yamamoto Takashi , Azuma Koji , Imoto Nobuyuki
Published: January 2019

An all-optical network is identified as a promising infrastructure for fast and energy-efficient communication. Recently, it has been shown that its quantum version based on ‘all-photonic quantum repeaters’—inheriting, at least, the same advantages—expands its possibility to the quantum realm, that is, a global quantum internet with applications far beyond the conventional Internet. Here we report a proof-of-principle experiment for a key component for the all-photonic repeaters—called all-photonic time-reversed adaptive (TRA) Bell measurement, with a proposal for the implementation. In particular, our TRA measurement—based only on optical devices without any quantum memories and any quantum error correction—passively but selectively performs the Bell measurement only on single photons that have successfully survived their lossy travel over optical channels. In fact, our experiment shows that only the survived single-photon state is faithfully teleported without the disturbance from the other lost photons, as the theory predicts.
Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria
Authors: Matheus Carnevali Paula B. , Schulz Frederik , Castelle Cindy J. , Kantor Rose S. , Shih Patrick M. , Sharon Itai , Santini Joanne M. , Olm Matthew R. , Amano Yuki , Thomas Brian C. , Anantharaman Karthik , Burstein David , Becraft Eric D. , Stepanauskas Ramunas , Woyke Tanja , Banfield Jillian F.
Published: January 2019

The evolution of aerobic respiration was likely linked to the origins of oxygenic Cyanobacteria. Close phylogenetic neighbors to Cyanobacteria, such as Margulisbacteria (RBX-1 and ZB3), Saganbacteria (WOR-1), Melainabacteria and Sericytochromatia, may constrain the metabolic platform in which aerobic respiration arose. Here, we analyze genomic sequences and predict that sediment-associated Margulisbacteria have a fermentation-based metabolism featuring a variety of hydrogenases, a streamlined nitrogenase, and electron bifurcating complexes involved in cycling of reducing equivalents. The genomes of ocean-associated Margulisbacteria encode an electron transport chain that may support aerobic growth. Some Saganbacteria genomes encode various hydrogenases, and others may be able to use O2 under certain conditions via a putative novel type of heme copper O2 reductase. Similarly, Melainabacteria have diverse energy metabolisms and are capable of fermentation and aerobic or anaerobic respiration. The ancestor of all these groups may have been an anaerobe in which fermentation and H2 metabolism were central metabolic features. The ability to use O2 as a terminal electron acceptor must have been subsequently acquired by these lineages.
A five-residue motif for the design of domain swapping in proteins
Authors: Nandwani Neha , Surana Parag , Negi Hitendra , Mascarenhas Nahren M. , Udgaonkar Jayant B. , Das Ranabir , Gosavi Shachi
Published: January 2019

Domain swapping is the process by which identical monomeric proteins exchange structural elements to generate dimers/oligomers. Although engineered domain swapping is a compelling strategy for protein assembly, its application has been limited due to the lack of simple and reliable design approaches. Here, we demonstrate that the hydrophobic five-residue ‘cystatin motif’ (QVVAG) from the domain-swapping protein Stefin B, when engineered into a solvent-exposed, tight surface loop between two β-strands prevents the loop from folding back upon itself, and drives domain swapping in non-domain-swapping proteins. High-resolution structural studies demonstrate that engineering the QVVAG stretch independently into various surface loops of four structurally distinct non-domain-swapping proteins enabled the design of different modes of domain swapping in these proteins, including single, double and open-ended domain swapping. These results suggest that the introduction of the QVVAG motif can be used as a mutational approach for engineering domain swapping in diverse β-hairpin proteins.
Cycles of protein condensation and discharge in nuclear organelles studied by fluorescence lifetime imaging
Authors: Pliss Artem , Levchenko Svitlana M. , Liu Lixin , Peng Xiao , Ohulchanskyy Tymish Y. , Roy Indrajit , Kuzmin Andrey N. , Qu Junle , Prasad Paras N.
Published: January 2019

Nuclear organelles are viscous droplets, created by concentration-dependent condensation and liquid–liquid phase separation of soluble proteins. Nuclear organelles have been actively investigated for their role in cellular regulation and disease. However, these studies are highly challenging to perform in live cells, and therefore, their physico-chemical properties are still poorly understood. In this study, we describe a fluorescence lifetime imaging approach for real-time monitoring of protein condensation in nuclear organelles of live cultured cells. This approach unravels surprisingly large cyclic changes in concentration of proteins in major nuclear organelles including nucleoli, nuclear speckles, Cajal bodies, as well as in the clusters of heterochromatin. Remarkably, protein concentration changes are synchronous for different organelles of the same cells. We propose a molecular mechanism responsible for synchronous accumulations of proteins in the nuclear organelles. This mechanism can serve for general regulation of cellular metabolism and contribute to coordination of gene expression.
2600-years of stratospheric volcanism through sulfate isotopes
Authors: Gautier E. , Savarino J. , Hoek J. , Erbland J. , Caillon N. , Hattori S. , Yoshida N. , Albalat E. , Albarede F. , Farquhar J.
Published: January 2019

High quality records of stratospheric volcanic eruptions, required to model past climate variability, have been constructed by identifying synchronous (bipolar) volcanic sulfate horizons in Greenland and Antarctic ice cores. Here we present a new 2600-year chronology of stratospheric volcanic events using an independent approach that relies on isotopic signatures (Δ33S and in some cases Δ17O) of ice core sulfate from five closely-located ice cores from Dome C, Antarctica. The Dome C stratospheric reconstruction provides independent validation of prior reconstructions. The isotopic approach documents several high-latitude stratospheric events that are not bipolar, but climatically-relevant, and diverges deeper in the record revealing tropospheric signals for some previously assigned bipolar events. Our record also displays a collapse of the Δ17O anomaly of sulfate for the largest volcanic eruptions, showing a further change in atmospheric chemistry induced by large emissions. Thus, the refinement added by considering both isotopic and bipolar correlation methods provides additional levels of insight for climate-volcano connections and improves ice core volcanic reconstructions.
Hierarchical composition of reliable recombinase logic devices
Authors: Guiziou Sarah , Mayonove Pauline , Bonnet Jerome
Published: January 2019

A major goal of synthetic biology is to reprogram living organisms to solve pressing challenges in manufacturing, environmental remediation, and healthcare. Recombinase devices can efficiently encode complex logic in many species, yet current designs are performed on a case-by-case basis, limiting their scalability and requiring time-consuming optimization. Here we provide a systematic framework for engineering reliable recombinase logic devices by hierarchical composition of well-characterized, optimized recombinase switches. We apply this framework to build a recombinase logic device family supporting up to 4-input Boolean logic within a multicellular system. This work enables straightforward implementation of multicellular recombinase logic and will support the predictable engineering of several classes of recombinase devices to reliably control cellular behavior.
Author Correction: Hysteresis control of epithelial-mesenchymal transition dynamics conveys a distinct program with enhanced metastatic ability
Authors: Celià-Terrassa Toni , Bastian Caleb , Liu Daniel D. , Ell Brian , Aiello Nicole M. , Wei Yong , Zamalloa Jose , Blanco Andres M. , Hang Xiang , Kunisky Dmitriy , Li Wenyang , Williams Elizabeth D. , Rabitz Herschel , Kang Yibin
Published: January 2019

The original version of this Article contained an error in the spelling of the author Daniel D. Liu, which was incorrectly given as Daniel Liu. This has now been corrected in both the PDF and HTML versions of the Article.
Effect of continuous and intermittent electric current on lignin wastewater treatment and microbial community structure in electro-microbial system
Authors: Zhang Lulu , Ding Lili , He Xuemeng , Ma Haijun , Fu Huimin , Wang Jinfeng , Ren Hongqiang
Published: January 2019

In this study, complex structured soluble lignin wastewater was treated by electro-microbial system (EMS) using different direct current (DC) application modes (CR (continuous ON), IR12h (12 h-ON/12 h-OFF) and IR2h (2 h-ON/2 h-OFF)), and physiological characteristics and microbial communities were investigated. Results showed that CR, IR12h and IR2h had higher lignin removals, which were almost two times that of the control reactor (R0′, no current), and IR2h performed best and stably. Furthermore, IR2h exhibited the lowest ohmic resistance (Rs) of electrode biofilms, which could be explained by its higher abundance of electroactive bacteria. In the activated sludge of EMS, the concentration of dehydrogenase activity (DHA) and electronic transport system (ETS) in IR2h were the highest (1.48 and 1.28 times of R0′), which contributed to its high content of adenosine triphosphate (ATP). The viability of activated sludge was not affected by different DC application modes. Phospholipid fatty acids (PLFA) analysis indicated that IR2h had the maximum content of C15:1 anteiso A, C16:0 and C18:0; CR increased the content of C15:0 anteiso and decreased the content of saturated fatty acids. Genus-level results revealed that lignin-degrading bacteria, Pseudoxanthomonas and Mycobacterium, could be enriched in IR2h and CR, respectively.
Variants in ABCG8 and TRAF3 genes confer risk for gallstone disease in admixed Latinos with Mapuche Native American ancestry
Authors: Bustos Bernabé I. , Pérez-Palma Eduardo , Buch Stephan , Azócar Lorena , Riveras Eleodoro , Ugarte Giorgia D. , Toliat Mohammad , Nürnberg Peter , Lieb Wolfgang , Franke Andre , Hinz Sebastian , Burmeister Greta , von Schönfels Witigo , Schafmayer Clemens , Völzke Henry , Völker Uwe , Homuth Georg , Lerch Markus M. , Santos José Luis , Puschel Klaus , Bambs Claudia , Roa Juan Carlos , Gutiérrez Rodrigo A. , Hampe Jochen , De Ferrari Giancarlo V. , Miquel Juan Francisco
Published: January 2019

Latin Americans and Chilean Amerindians have the highest prevalence of gallstone disease (GSD) and gallbladder cancer (GBC) in the world. A handful of loci have been associated with GSD in populations of predominantly European ancestry, however, they only explain a small portion of the genetic component of the disease. Here, we performed a genome-wide association study (GWAS) for GSD in 1,095 admixed Chilean Latinos with Mapuche Native American ancestry. Disease status was assessed by cholecystectomy or abdominal ultrasonography. Top-10 candidate variants surpassing the suggestive cutoff of P < 1 × 10−5 in the discovery cohort were genotyped in an independent replication sample composed of 1,643 individuals. Variants with positive replication were further examined in two European GSD populations and a Chilean GBC cohort. We consistently replicated the association of ABCG8 gene with GSD (rs11887534, P = 3.24 × 10−8, OR = 1.74) and identified TRAF3 (rs12882491, P = 1.11 × 10−7, OR = 1.40) as a novel candidate gene for the disease in admixed Chilean Latinos. ABCG8 and TRAF3 variants also conferred risk to GBC. Gene expression analyses indicated that TRAF3 was significantly decreased in gallbladder (P = 0.015) and duodenal mucosa (P = 0.001) of GSD individuals compared to healthy controls, where according to GTEx data in the small intestine, the presence of the risk allele contributes to the observed effect. We conclude that ABCG8 and TRAF3 genes are associated with GSD and GBC in admixed Latinos and that decreased TRAF3 levels could enhance gallbladder inflammation as is observed in GSD and GSD-associated GBC.
Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow
Authors: Li Wenli , Edwards Andrea , Riehle Christina , Cox Madison S. , Raabis Sarah , Skarlupka Joseph H. , Steinberger Andrew J. , Walling Jason , Bickhart Derek , Suen Garret
Published: January 2019

In mammals, microbial colonization of the digestive tract (GIT) occurs right after birth by several bacterial phyla. Numerous human and mouse studies have reported the importance of early gut microbial inhabitants on host health. However, few attempts have been undertaken to directly interrogate the role of early gut/rumen microbial colonization on GIT development or host health in neonatal ruminants through artificial manipulation of the rumen microbiome. Thus, the molecular changes associated with bacterial colonization are largely unknown in cattle. In this study, we dosed young calves with exogenous rumen fluid obtained from an adult donor cow, starting at birth, and repeated every other week until six weeks of age. Eight Holstein bull calves were included in this study and were separated into two groups of four: the first group was treated with rumen content freshly extracted from an adult cow, and the second group was treated with sterilized rumen content. Using whole-transcriptome RNA-sequencing, we investigated the transcriptional changes in the host liver, which is a major metabolic organ and vital to the calf’s growth performance. Additionally, the comparison of rumen epimural microbial communities between the treatment groups was performed using the rRNA reads generated by sequencing. Liver transcriptome changes were enriched with genes involved in cell signaling and protein phosphorylation. Specifically, up-regulation of SGPL1 suggests a potential increase in the metabolism of sphingolipids, an essential molecular signal for bacterial survival in digestive tracts. Notably, eight genera, belonging to four phyla, had significant increases in abundance in treated calves. Our study provides insight into host liver transcriptome changes associated with early colonization of the microbial communities in neonatal calves. Such knowledge provides a foundation for future probiotics-based research in microbial organism mediated rumen development and nutrition in ruminants.
Quantitative analysis of melanin content in a three-dimensional melanoma cell culture
Authors: Chung Soobin , Lim Gippeum J. , Lee Ji Youn
Published: January 2019

Reliable measurement of the amount of melanin produced by melanocytes is essential to study various skin disorders and to evaluate the efficacy of candidate reagents for such disorders or for whitening purposes. Conventional melanin quantification methods are based on absorption spectroscopy, which measures the melanin from lysed cells grown on two-dimensional (2D) surfaces. The 2D culture environment is intrinsically different from in vivo systems though, and therefore cells often lose their original phenotypes. Melanocytes in particular lose their ability to synthesize melanin, thereby requiring melanogenesis stimulators such as alpha-melanocyte stimulating hormone (α-MSH) to promote melanin synthesis. In this study, we compared melanin synthesis in B16 murine melanoma cells grown in 2D and three-dimensional culture environments. B16 cells instantly formed an aggregate in a hanging-drop culture, and synthesized melanin efficiently without treatment of α-MSH. We were able to measure the melanin secreted from a single melanocyte aggregate, indicating that our method enables non-invasive long-term monitoring of melanin synthesis and secretion in a high-throughput format. We successfully tested the developed platform by quantifying the depigmenting effects of arbutin and kojic acid.
Dispositional Gratitude Moderates the Association between Socioeconomic Status and Interleukin-6
Authors: Hartanto Andree , Lee Sean T. H. , Yong Jose C.
Published: January 2019

Socioeconomic disparities in health are prevalent and growing in importance as a concern among academics, policymakers, and the general public. However, psychological resources that can narrow such disparities have not been well-examined. The current study examined the moderating role of dispositional gratitude in the relationship between socioeconomic status (SES) and inflammation risk as an index of health. Participants consisted of 1,054 midlife adults from the biomarker project of the Midlife in the United States. Inflammation risk was measured by interleukin-6 biomarker and SES was operationalized by education attainment and income. We found that dispositional gratitude significantly moderated the relationships between SES and interleukin-6. Among individuals with low dispositional gratitude, higher SES was significantly associated with lower levels of interleukin-6. However, the association between SES and interleukin-6 was not significant among individuals with high dispositional gratitude. More importantly, the findings remained robust after controlling for demographic characteristics, health status, health behaviours, and personality traits. Our findings suggest that gratitude may serve as an important psychological resource in attenuating health-related risk from socioeconomic stressors.
Nano-to-Submicron Hydroxyapatite Coatings for Magnesium-based Bioresorbable Implants – Deposition, Characterization, Degradation, Mechanical Properties, and Cytocompatibility
Authors: Tian Qiaomu , Lin Jiajia , Rivera-Castaneda Laura , Tsanhani Amit , Dunn Zachary S. , Rodriguez Alexis , Aslani Arash , Liu Huinan
Published: January 2019

Magnesium (Mg) and its alloys have shown attractive biocompatibility and mechanical strength for medical applications, but low corrosion resistance of Mg in physiological environment limits its broad clinical translation. Hydroxyapatite (HA) nanoparticles (nHA) are promising coating materials for decreasing degradation rates and prolonging mechanical strength of Mg-based implants while enhancing bone healing due to their osteoconductivity and osteoinductivity. Conformal HA coatings with nano-to-submicron structures, namely nHA and mHA coatings, were deposited successfully on Mg plates and rods using a transonic particle acceleration (TPA) process under two different conditions, characterized, and investigated for their effects on Mg degradation in vitro. The nHA and mHA coatings enhanced corrosion resistance of Mg and retained 86–90% of ultimate compressive strength after in vitro immersion in rSBF for 6 weeks, much greater than non-coated Mg that only retained 66% of strength. Mg-based rods with or without coatings showed slower degradation than the respective Mg-based plates in rSBF after 6 weeks, likely because of the greater surface-to-volume ratio of Mg plates than Mg rods. This indicates that Mg-based plate and screw devices may undergo different degradation even when they have the same coatings and are implanted at the same or similar anatomical locations. Therefore, in addition to locations of implantation, the geometry, dimension, surface area, volume, and mass of Mg-based implants and devices should be carefully considered in their design and processing to ensure that they not only provide adequate structural and mechanical stability for bone fixation, but also support the functions of bone cells, as clinically required for craniomaxillofacial (CMF) and orthopedic implants. When the nHA and mHA coated Mg and non-coated Mg plates were cultured with bone marrow derived mesenchymal stem cells (BMSCs) using the in vitro direct culture method, greater cell adhesion densities were observed under indirect contact conditions than that under direct contact conditions for the nHA and mHA coated Mg. In comparison with non-coated Mg, the nHA and mHA coated Mg reduced BMSC adhesion densities directly on the surface, but increased the average BMSC adhesion densities under indirect contact. Further long-term studies in vitro and in vivo are necessary to elucidate the effects of nHA and mHA coatings on cell functions and tissue healing.
Isophorone derivatives as a new structural motif of aggregation pheromones in Curculionidae
Authors: Vidal Diogo Montes , Moreira Marcos Antonio Barbosa , Coracini Miryan Denise Araujo , Zarbin Paulo Henrique Gorgatti
Published: January 2019

The beetle Homalinotus depressus (Coleoptera: Curculionidae) is a major pest of coconuts in the Northern region of Brazil, for which environmentally friendly methods of control are desired. Behavioral responses of H. depressus to airborne volatile extracts from conspecifics suggested the presence of a male-produced aggregation pheromone. GC analyses of these extracts showed the presence of four male-specific compounds. Analytical data in combination with the synthesis of standards led to the identification of the male-released semiochemicals as epoxyisophorone (1), isophorone (2), homalinol (3), and 2-hydroxyisophorone (4), of which (3) was the major constituent. The configuration of homalinol was determined to be cis on the basis of retention times of synthetic cis and trans synthetic standards. Enantiomers of cis-homalinol were obtained in high enantiomeric excess by using biocatalysis. Their separation on a GC enantioselective column (β-Dex325®), allowed us to unambiguously determine that the absolute configuration of natural homalinol was (1R,2R,6S). Field bioassays demonstrated that both the synthetic major compound per se and mixtures of all four male-specific compounds were attractive to H. depressus.
Modeling Oral Multispecies Biofilm Recovery After Antibacterial Treatment
Authors: Jing Xiaobo , Huang Xiangya , Haapasalo Markus , Shen Ya , Wang Qi
Published: January 2019

Recovery of multispecies oral biofilms is investigated following treatment by chlorhexidine gluconate (CHX), iodine-potassium iodide (IPI) and Sodium hypochlorite (NaOCl) both experimentally and theoretically. Experimentally, biofilms taken from two donors were exposed to the three antibacterial solutions (irrigants), respectively, for 10 minutes. We observe that (a) live bacterial cell ratios decline for a week after the exposure and the trend then reverses beyond the week; after fifteen weeks, live bacterial cell ratios in biofilms fully return to their pretreatment levels; (b) NaOCl is shown as the strongest antibacterial agent for the oral biofilms; (c) multispecies oral biofilms from different donors showed no difference in their susceptibility to all the bacterial solutions. Guided by the experiment, a mathematical model for biofilm dynamics is developed, accounting for multiple bacterial phenotypes, quorum sensing, and growth factor proteins, to describe the nonlinear time evolutionary behavior of the biofilms. The model captures time evolutionary dynamics of biofilms before and after antibacterial treatment very well. It reveals the important role played by quorum sensing molecules and growth factors in biofilm recovery and verifies that the source of biofilms has a minimal effect to their recovery. The model is also applied to describe the state of biofilms of various ages treated respectively by CHX, IPI and NaOCl, taken from different donors. Good agreement with experimental data predicted by the model is obtained as well, confirming its applicability to modeling biofilm dynamics in general.
Directed evolution of super-secreted variants from phage-displayed human Interleukin-2
Authors: Rojas Gertrudis , Carmenate Tania , Santo-Tomás Julio Felipe , Valiente Pedro A. , Becker Marlies , Pérez-Riverón Annia , Tundidor Yaima , Ortiz Yaquelín , Fernandez de Cossio-Diaz Jorge , Graça Luis , Dübel Stefan , León Kalet
Published: January 2019

Selection from a phage display library derived from human Interleukin-2 (IL-2) yielded mutated variants with greatly enhanced display levels of the functional cytokine on filamentous phages. Introduction of a single amino acid replacement selected that way (K35E) increased the secretion levels of IL-2-containing fusion proteins from human transfected host cells up to 20-fold. Super-secreted (K35E) IL-2/Fc is biologically activein vitroandin vivo, has anti-tumor activity and exhibits a remarkable reduction in its aggregation propensity- the major manufacturability issue limiting IL-2 usefulness up to now. Improvement of secretion was also shown for a panel of IL-2-engineered variants with altered receptor binding properties, including a selective agonist and a super agonist that kept their unique properties. Our findings will improve developability of the growing family of IL-2-derived immunotherapeutic agents and could have a broader impact on the engineering of structurally related four-alpha-helix bundle cytokines.
HRGPred: Prediction of herbicide resistant genes with k-mer nucleotide compositional features and support vector machine
Authors: Meher Prabina Kumar , Sahu Tanmaya Kumar , Raghunandan K. , Gahoi Shachi , Choudhury Nalini Kanta , Rao Atmakuri Ramakrishna
Published: January 2019

Herbicide resistance (HR) is a major concern for the agricultural producers as well as environmentalists. Resistance to commonly used herbicides are conferred due to mutation(s) in the genes encoding herbicide target sites/proteins (GETS). Identification of these genes through wet-lab experiments is time consuming and expensive. Thus, a supervised learning-based computational model has been proposed in this study, which is first of its kind for the prediction of seven classes of GETS. The cDNA sequences of the genes were initially transformed into numeric features based on the k-mer compositions and then supplied as input to the support vector machine. In the proposed SVM-based model, the prediction occurs in two stages, where a binary classifier in the first stage discriminates the genes involved in conferring the resistance to herbicides from other genes, followed by a multi-class classifier in the second stage that categorizes the predicted herbicide resistant genes in the first stage into any one of the seven resistant classes. Overall classification accuracies were observed to be ~89% and >97% for binary and multi-class classifications respectively. The proposed model confirmed higher accuracy than the homology-based algorithms viz., BLAST and Hidden Markov Model. Besides, the developed computational model achieved ~87% accuracy, while tested with an independent dataset. An online prediction server HRGPred (http://cabgrid.res.in:8080/hrgpred) has also been established to facilitate the prediction of GETS by the scientific community.
mmSTORM: Multimodal localization based super-resolution microscopy
Authors: Gajdos Tamás , Cserteg Zsófia , Szikora Szilárd , Novák Tibor , H. Kovács Bálint Barna , Szabó Gábor , Mihály József , Erdélyi Miklós
Published: January 2019

Super-resolution localization microscopy provides a powerful tool to study biochemical mechanisms at single molecule level. Although the lateral position of the fluorescent dye molecules can be determined routinely with high precision, measurement of other modalities such as 3D and multicolor without the degradation of the original super-resolved image is still in the focus. In this paper a dual-objective multimodal single molecule localization microscopy (SMLM) technique has been developed, optimized and tested. The proposed optical arrangement can be implemented onto a conventional inverted microscope without serious system modification. The performance of the method was tested using fluorescence beads, F-actin filaments and sarcomere structures. It was shown that the proposed imaging method does not degrade the image quality of the original SMLM 2D image but could provide information on the axial position or emission spectra of the dye molecules.
Overcoming NADPH product inhibition improves D-sorbitol conversion to L-sorbose
Authors: Kim Tae-Su , Gao Hui , Li Jinglin , Kalia Vipin C. , Muthusamy Karthikeyan , Sohng Jae Kyung , Kim In-Won , Lee Jung-Kul
Published: January 2019

Gluconobacter oxydans sorbitol dehydrogenase (GoSLDH) exhibits a higher catalytic efficiency than other l-sorbose producing enzymes. During the reaction catalysed by GoSLDH, NADP+ is reduced to NADPH and d-sorbitol is oxidized to l-sorbose. However, GoSLDH activity is inhibited by the NADPH (Ki = 100 μM) formed during the enzymatic reaction. Therefore, Escherichia coligosldh-lrenox producing both GoSLDH for d-sorbitol oxidation and LreNOX (NAD(P)H oxidase from Lactobacillus reuteri) for NADP+ regeneration was generated and used for l-sorbose production. Whole cell biocatalysts with the LreNOX cofactor recycling system showed a high conversion rate (92%) of d-sorbitol to l-sorbose in the presence of low concentration of NADP+ (0.5 mM). By alleviating NADPH accumulation during the catalytic reactions, E. coligosldh-lrenox exhibited 23-fold higher conversion rate of d-sorbitol than E. coligosldh. l-Sorbose production by E. coligosldh-lrenox reached 4.1 g/L after 40 min, which was 20.5-fold higher than that of E. coligosldh. We also constructed G. oxydansgosldh and G. oxydansgosldh-lrenox strains, and they exhibited 1.2- and 2.9-fold higher conversion rates than the wild-type G. oxydans KCTC 1091. The results indicate that overcoming NADPH product inhibition using LreNOX improves chemical production in NADP+-dependent enzymatic reactions.
A Comparative Analysis of the Status Anxiety Hypothesis of Socio-economic Inequalities in Health Based on 18,349 individuals in Four Countries and Five Cohort Studies
Authors: Layte Richard , McCrory Cathal , Cheallaigh Cliona Ni , Bourke Nollaig , Kivimaki Mika , Ribeiro Ana Isabel , Stringhini Silvia , Vineis Paolo
Published: January 2019

The status anxiety hypothesis proposes that systematic inflammation as a consequence of chronic psycho-social stress is a possible pathway linking socio-economic position (SEP) to premature ageing and is a possible explanation for cross-national variation in patterns of health and well-being. Harmonised data from the LIFEPATH consortium on 18,349 individuals aged 50 to 75 and 30,632 observations are used to measure variation in the association between inflammation measured as C-reactive protein and SEP across four countries (Britain, Ireland, Portugal and Switzerland) and five studies (ELSA, Whitehall II, TILDA, EPIPorto and SKIPOGH). Adjusting for population composition, mean concentrations of CRP are highest in Portugal, the country with the highest income inequality and lowest in Switzerland, a lower income inequality country. Across all of the studies, lower SEP groups have higher mean concentrations of CRP and, as predicted by the theory, absolute differentials between SEP groups reflect the pattern of societal income inequality. Adjustment for lifestyle indicators reduces SEP differentials by between 45% and 52% but cannot account for country variation in mean inflammation.
Identification of microbiota in peri-implantitis pockets by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Authors: Yeh Hwey-Chin , Lu Jang-Jih , Chang Shih-Cheng , Ge Mao-Cheng
Published: January 2019

The purpose of this study was to identify the microbial communities that colonize peri-implantitis pockets using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Subjects having at least one implant with peri-implantitis, no diabetes, and not taking antibiotics in the previous 3 months were selected. Peri-implantitis was defined when surrounding bone loss ≥0.5 mm and bleeding on probing was found. Microbial samples were collected from peri-implantitis pockets using paper points. After incubation and isolation, the colonies were analyzed by MALDI-TOF MS. A total of 126 isolates were cultivated and identified from 12 samples, in identification rates of 82.5% at the species level and 12.72% at the genus level. Although the compositions were highly variable, major habitants in different peri-implant pockets could be identified. Among them the most distinguished were Neisseria flavescens (87%), Streptococcus constellatus (56%), Slackia exigua (46%), Streptococcus intermedius (45%), Fusobacterium nucleatum (45%) and Gemella morbillorum (43%). This preliminary study provides comprehensive and reliable data for future study designs involving MALDI-TOF MS and peri-implantitis in a more specific, easy, rapid and economical way. MALDI-TOF MS could be a new clinical method to evaluate and monitor oral microbiota associated with the disease.