bluuebunny/crossref_metadata_2025 huggingface dataset:
Mythen und Missverständnisse in der Notfall-Labormedizin – Treat the Patient, Not the Blood Test
Authors: Jegerlehner Sabrina , Fiedler Martin , Exadaktylos Aristomenis
Published: November 2017

Zusammenfassung. Verbessertes Verständnis der menschlichen Physiologie und technische Fortschritte haben zu einer breiten Verwendung von Labordiagnostik in der klinischen Aufarbeitung eines Patienten geführt. Diese Entwicklungen gingen jedoch mit der Verbreitung von falschen Mythen und Missverständnissen einher, die humane und ökonomische Ressourcen konsumieren sowie das klinische Denken und – nicht zuletzt – den Patienten gefährden. Das Ziel dieses Artikels ist es daher, eine Übersicht über typische Beispiele von falschen Dogmen über in der Notfallmedizin häufig verwendete Laborwerte zu geben.
Pine Island Glacier and Ice Sheet Stability in West Antarctica
Authors: Smith A.
Published: November 2017

The iSTAR Programme Science Integration Meeting; Leeds, United Kingdom, 18–19 May 2017
Long non-coding RNA LINC00152 promotes cell proliferation, metastasis, and confers 5-FU resistance in colorectal cancer by inhibiting miR-139-5p
Authors: Bian Zehua , Zhang Jiwei , Li Min , Feng Yuyang , Yao Surui , Song Mingxun , Qi Xiaowei , Fei Bojian , Yin Yuan , Hua Dong , Huang Zhaohui
Published: November 2017

Long intergenic non-coding RNA 152 (LINC00152) is a recently identified tumor-promoting long non-coding RNA. However, the biological functions of LINC00152 in colorectal cancer (CRC) remain unclear and require further research. The aim of the present study is to explore the roles of LINC00152 in cellular function and its possible molecular mechanism. In this study, we discovered that LINC00152 was overexpressed in CRC tissues and negatively related to the survival time of CRC patients. Functional analyses revealed that LINC00152 could promote cell proliferation. Furthermore, LINC00152 could increase the resistance of CRC cells to 5-fluorouracil (5-FU) by suppressing apoptosis. We also discovered that LINC00152 could enhance cell migration and invasion. Mechanistic studies demonstrated that LINC00152 could regulate the expression of NOTCH1 through sponging miR-139-5p and inhibiting its activity from promoting CRC progression and development. Altogether, our work points out a novel LINC00152/miR-139-5p/NOTCH1 regulatory axis in CRC progression and development.
Noninvasive liquid diet delivery of stable isotopes into mouse models for deep metabolic network tracing
Authors: Sun Ramon C. , Fan Teresa W.-M. , Deng Pan , Higashi Richard M. , Lane Andrew N. , Le Anh-Thu , Scott Timothy L. , Sun Qiushi , Warmoes Marc O. , Yang Ye
Published: November 2017

Delivering isotopic tracers for metabolic studies in rodents without overt stress is challenging. Current methods achieve low label enrichment in proteins and lipids. Here, we report noninvasive introduction of13C6-glucose via a stress-free, ad libitum liquid diet. Using NMR and ion chromatography-mass spectrometry, we quantify extensive13C enrichment in products of glycolysis, the Krebs cycle, the pentose phosphate pathway, nucleobases, UDP-sugars, glycogen, lipids, and proteins in mouse tissues during 12 to 48 h of13C6-glucose feeding. Applying this approach to patient-derived lung tumor xenografts (PDTX), we show that the liver supplies glucose-derived Gln via the blood to the PDTX to fuel Glu and glutathione synthesis while gluconeogenesis occurs in the PDTX. Comparison of PDTX with ex vivo tumor cultures and arsenic-transformed lung cells versus xenografts reveals differential glucose metabolism that could reflect distinct tumor microenvironment. We further found differences in glucose metabolism between the primary PDTX and distant lymph node metastases.
Structure-based design of native-like HIV-1 envelope trimers to silence non-neutralizing epitopes and eliminate CD4 binding
Authors: Kulp Daniel W. , Steichen Jon M. , Pauthner Matthias , Hu Xiaozhen , Schiffner Torben , Liguori Alessia , Cottrell Christopher A. , Havenar-Daughton Colin , Ozorowski Gabriel , Georgeson Erik , Kalyuzhniy Oleksandr , Willis Jordan R. , Kubitz Michael , Adachi Yumiko , Reiss Samantha M. , Shin Mia , de Val Natalia , Ward Andrew B. , Crotty Shane , Burton Dennis R. , Schief William R.
Published: November 2017

Elicitation of broadly neutralizing antibodies (bnAbs) is a primary HIV vaccine goal. Native-like trimers mimicking virion-associated spikes present nearly all bnAb epitopes and are therefore promising vaccine antigens. However, first generation native-like trimers expose epitopes for non-neutralizing antibodies (non-nAbs), which may hinder bnAb induction. We here employ computational and structure-guided design to develop improved native-like trimers that reduce exposure of non-nAb epitopes in the V3-loop and trimer base, minimize both CD4 reactivity and CD4-induced non-nAb epitope exposure, and increase thermal stability while maintaining bnAb antigenicity. In rabbit immunizations with native-like trimers of the 327c isolate, improved trimers suppress elicitation of V3-directed and tier-1 neutralizing antibodies and induce robust autologous tier-2 neutralization, unlike a first-generation trimer. The improved native-like trimers from diverse HIV isolates, and the design methods, have promise to assist in the development of a HIV vaccine.
A multiplexable TALE-based binary expression system for in vivo cellular interaction studies
Authors: Toegel Markus , Azzam Ghows , Lee Eunice Y. , Knapp David J. H. F. , Tan Ying , Fa Ming , Fulga Tudor A.
Published: November 2017

Binary expression systems have revolutionised genetic research by enabling delivery of loss-of-function and gain-of-function transgenes with precise spatial-temporal resolution in vivo. However, at present, each existing platform relies on a defined exogenous transcription activator capable of binding a unique recognition sequence. Consequently, none of these technologies alone can be used to simultaneously target different tissues or cell types in the same organism. Here, we report a modular system based on programmable transcription activator-like effector (TALE) proteins, which enables parallel expression of multiple transgenes in spatially distinct tissues in vivo. Using endogenous enhancers coupled to TALE drivers, we demonstrate multiplexed orthogonal activation of several transgenes carrying cognate variable activating sequences (VAS) in distinct neighbouring cell types of the Drosophila central nervous system. Since the number of combinatorial TALE–VAS pairs is virtually unlimited, this platform provides an experimental framework for highly complex genetic manipulation studies in vivo.
UNC93B1 interacts with the calcium sensor STIM1 for efficient antigen cross-presentation in dendritic cells
Authors: Maschalidi Sophia , Nunes-Hasler Paula , Nascimento Clarissa R , Sallent Ignacio , Lannoy Valérie , Garfa-Traore Meriem , Cagnard Nicolas , Sepulveda Fernando E. , Vargas Pablo , Lennon-Duménil Ana-Maria , van Endert Peter , Capiod Thierry , Demaurex Nicolas , Darrasse-Jèze Guillaume , Manoury Bénédicte
Published: November 2017

Dendritic cells (DC) have the unique ability to present exogenous antigens via the major histocompatibility complex class I pathway to stimulate naive CD8+ T cells. In DCs with a non-functional mutation in Unc93b1 (3d mutation), endosomal acidification, phagosomal maturation, antigen degradation, antigen export to the cytosol and the function of the store-operated-Ca2+-entry regulator STIM1 are impaired. These defects result in compromised antigen cross-presentation and anti-tumor responses in 3d-mutated mice. Here, we show that UNC93B1 interacts with the calcium sensor STIM1 in the endoplasmic reticulum, a critical step for STIM1 oligomerization and activation. Expression of a constitutively active STIM1 mutant, which no longer binds UNC93B1, restores antigen degradation and cross-presentation in 3d-mutated DCs. Furthermore, ablation of STIM1 in mouse and human cells leads to a decrease in cross-presentation. Our data indicate that the UNC93B1 and STIM1 cooperation is important for calcium flux and antigen cross-presentation in DCs.
DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes
Authors: Nothjunge Stephan , Nührenberg Thomas G. , Grüning Björn A. , Doppler Stefanie A. , Preissl Sebastian , Schwaderer Martin , Rommel Carolin , Krane Markus , Hein Lutz , Gilsbach Ralf
Published: November 2017

Storage of chromatin in restricted nuclear space requires dense packing while ensuring DNA accessibility. Thus, different layers of chromatin organization and epigenetic control mechanisms exist. Genome-wide chromatin interaction maps revealed large interaction domains (TADs) and higher order A and B compartments, reflecting active and inactive chromatin, respectively. The mutual dependencies between chromatin organization and patterns of epigenetic marks, including DNA methylation, remain poorly understood. Here, we demonstrate that establishment of A/B compartments precedes and defines DNA methylation signatures during differentiation and maturation of cardiac myocytes. Remarkably, dynamic CpG and non-CpG methylation in cardiac myocytes is confined to A compartments. Furthermore, genetic ablation or reduction of DNA methylation in embryonic stem cells or cardiac myocytes, respectively, does not alter genome-wide chromatin organization. Thus, DNA methylation appears to be established in preformed chromatin compartments and may be dispensable for the formation of higher order chromatin organization.
Switching between H- and J-type electronic coupling in single conjugated polymer aggregates
Authors: Eder Theresa , Stangl Thomas , Gmelch Max , Remmerssen Klaas , Laux Dirk , Höger Sigurd , Lupton John M. , Vogelsang Jan
Published: November 2017

The aggregation of conjugated polymers and electronic coupling of chromophores play a central role in the fundamental understanding of light and charge generation processes. Here we report that the predominant coupling in isolated aggregates of conjugated polymers can be switched reversibly between H-type and J-type coupling by partially swelling and drying the aggregates. Aggregation is identified by shifts in photoluminescence energy, changes in vibronic peak ratio, and photoluminescence lifetime. This experiment unravels the internal electronic structure of the aggregate and highlights the importance of the drying process in the final spectroscopic properties. The electronic coupling after drying is tuned between H-type and J-type by changing the side chains of the conjugated polymer, but can also be entirely suppressed. The types of electronic coupling correlate with chain morphology, which is quantified by excitation polarization spectroscopy and the efficiency of interchromophoric energy transfer that is revealed by the degree of single-photon emission.
Biosynthesis of helvolic acid and identification of an unusual C-4-demethylation process distinct from sterol biosynthesis
Authors: Lv Jian-Ming , Hu Dan , Gao Hao , Kushiro Tetsuo , Awakawa Takayoshi , Chen Guo-Dong , Wang Chuan-Xi , Abe Ikuro , Yao Xin-Sheng
Published: November 2017

Fusidane-type antibiotics represented by helvolic acid, fusidic acid and cephalosporin P1 are a class of bacteriostatic agents, which have drawn renewed attention because they have no cross-resistance to commonly used antibiotics. However, their biosynthesis is poorly understood. Here, we perform a stepwise introduction of the nine genes from the proposed gene cluster for helvolic acid into Aspergillus oryzae NSAR1, which enables us to isolate helvolic acid (~20 mg L−1) and its 21 derivatives. Anti-Staphylococcus aureus assay reveals that the antibacterial activity of three intermediates is even stronger than that of helvolic acid. Notably, we observe an unusual C-4 demethylation process mediated by a promiscuous short-chain dehydrogenase/reductase (HelC) and a cytochrome P450 enzyme (HelB1), which is distinct from the common sterol biosynthesis. These studies have set the stage for using biosynthetic approaches to expand chemical diversity of fusidane-type antibiotics.
Cisplatin is retained in the cochlea indefinitely following chemotherapy
Authors: Breglio Andrew M. , Rusheen Aaron E. , Shide Eric D. , Fernandez Katharine A. , Spielbauer Katie K. , McLachlin Katherine M. , Hall Matthew D. , Amable Lauren , Cunningham Lisa L.
Published: November 2017

Cisplatin chemotherapy causes permanent hearing loss in 40–80% of treated patients. It is unclear whether the cochlea has unique sensitivity to cisplatin or is exposed to higher levels of the drug. Here we use inductively coupled plasma mass spectrometry (ICP-MS) to examine cisplatin pharmacokinetics in the cochleae of mice and humans. In most organs cisplatin is detected within one hour after injection, and is eliminated over the following days to weeks. In contrast, the cochlea retains cisplatin for months to years after treatment in both mice and humans. Using laser ablation coupled to ICP-MS, we map cisplatin distribution within the human cochlea. Cisplatin accumulation is consistently high in the stria vascularis, the region of the cochlea that maintains the ionic composition of endolymph. Our results demonstrate long-term retention of cisplatin in the human cochlea, and they point to the stria vascularis as an important therapeutic target for preventing cisplatin ototoxicity.
Selenoprotein P-neutralizing antibodies improve insulin secretion and glucose sensitivity in type 2 diabetes mouse models
Authors: Mita Yuichiro , Nakayama Kaho , Inari Shogo , Nishito Yukina , Yoshioka Yuya , Sakai Naoko , Sotani Kanade , Nagamura Takahiro , Kuzuhara Yuki , Inagaki Kumi , Iwasaki Miki , Misu Hirofumi , Ikegawa Masaya , Takamura Toshinari , Noguchi Noriko , Saito Yoshiro
Published: November 2017

Selenoprotein P (SeP) functions as a selenium (Se)-supply protein. SeP is identified as a hepatokine, promoting insulin resistance in type 2 diabetes. Thus, the suppression of Se-supply activity of SeP might improve glucose metabolism. Here, we develop an anti-human SeP monoclonal antibody AE2 as with neutralizing activity against SeP. Administration of AE2 to mice significantly improves glucose intolerance and insulin resistance that are induced by human SeP administration. Furthermore, excess SeP administration significantly decreases pancreas insulin levels and high glucose-induced insulin secretion, which are improved by AE2 administration. Epitope mapping reveals that AE2 recognizes a region of human SeP adjacent to the first histidine-rich region (FHR). A polyclonal antibody against the mouse SeP FHR improves glucose intolerance and insulin secretion in a mouse model of diabetes. This report describes a novel molecular strategy for the development of type 2 diabetes therapeutics targeting SeP.
DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle
Authors: Mikheikin Andrey , Olsen Anita , Leslie Kevin , Russell-Pavier Freddie , Yacoot Andrew , Picco Loren , Payton Oliver , Toor Amir , Chesney Alden , Gimzewski James K. , Mishra Bud , Reed Jason
Published: November 2017

Progress in whole-genome sequencing using short-read (e.g., <150 bp), next-generation sequencing technologies has reinvigorated interest in high-resolution physical mapping to fill technical gaps that are not well addressed by sequencing. Here, we report two technical advances in DNA nanotechnology and single-molecule genomics: (1) we describe a labeling technique (CRISPR-Cas9 nanoparticles) for high-speed AFM-based physical mapping of DNA and (2) the first successful demonstration of using DVD optics to image DNA molecules with high-speed AFM. As a proof of principle, we used this new “nanomapping” method to detect and map precisely BCL2–IGH translocations present in lymph node biopsies of follicular lymphoma patents. This HS-AFM “nanomapping” technique can be complementary to both sequencing and other physical mapping approaches.
Optically driven ultra-stable nanomechanical rotor
Authors: Kuhn Stefan , Stickler Benjamin A. , Kosloff Alon , Patolsky Fernando , Hornberger Klaus , Arndt Markus , Millen James
Published: November 2017

Nanomechanical devices have attracted the interest of a growing interdisciplinary research community, since they can be used as highly sensitive transducers for various physical quantities. Exquisite control over these systems facilitates experiments on the foundations of physics. Here, we demonstrate that an optically trapped silicon nanorod, set into rotation at MHz frequencies, can be locked to an external clock, transducing the properties of the time standard to the rod’s motion with a remarkable frequency stability fr/Δfr of 7.7 × 1011. While the dynamics of this periodically driven rotor generally can be chaotic, we derive and verify that stable limit cycles exist over a surprisingly wide parameter range. This robustness should enable, in principle, measurements of external torques with sensitivities better than 0.25 zNm, even at room temperature. We show that in a dilute gas, real-time phase measurements on the locked nanorod transduce pressure values with a sensitivity of 0.3%.
Intranasal infection and contact transmission of Zika virus in guinea pigs
Authors: Deng Yong-Qiang , Zhang Na-Na , Li Xiao-Feng , Wang Ya-Qing , Tian Min , Qiu Ye-Feng , Fan Jun-Wan , Hao Jia-Nan , Huang Xing-Yao , Dong Hao-Long , Fan Hang , Wang Yu-Guang , Zhang Fu-Chun , Tong Yi-Gang , Xu Zhiheng , Qin Cheng-Feng
Published: November 2017

Zika virus (ZIKV) is primarily transmitted to humans through mosquito bites or sexual contact. The excretion and persistence of contagious ZIKV in various body fluids have been well documented in ZIKV patients; however, the risk of direct contact exposure remains unclear. Here, we show that guinea pigs are susceptible to ZIKV infection via subcutaneous inoculation route; infected guinea pigs exhibit seroconversion and significant viral secretion in sera, saliva, and tears. Notably, ZIKV is efficiently transmitted from infected guinea pigs to naïve co-caged animals. In particular, intranasal inoculation of ZIKV is fully capable of establishing infection in guinea pigs, and viral antigens are detected in multiple tissues including brain and parotid glands. Cynomolgus macaques also efficiently acquire ZIKV infection via intranasal and intragastric inoculation routes. These collective results from animal models highlight the risk of exposure to ZIKV contaminants and raise the possibility of close contact transmission of ZIKV in humans.
Outcomes of patients with sarcoma enrolled in clinical trials of pazopanib combined with histone deacetylase, mTOR, Her2, or MEK inhibitors
Authors: Dembla Vikas , Groisberg Roman , Hess Ken , Fu Siqing , Wheler Jennifer , Hong David S. , Janku Filip , Zinner Ralph , Piha-Paul Sarina Anne , Ravi Vinod , Benjamin Robert S. , Patel Shreyaskumar , Somaiah Neeta , Herzog Cynthia E. , Karp Daniel D. , Roszik Jason , Meric-Bernstam Funda , Subbiah Vivek
Published: November 2017

Pazopanib is US FDA approved for the treatment of advanced soft tissue sarcomas. All patients with this disease ultimately develop resistance to therapy. Mechanisms of resistance include activation of the mTOR, histone deacetylase (HDAC), MAPK, and ERBB4 pathways. We hypothesized that combining pazopanib with other targeted agents inhibiting these pathways would increase response rates. We retrospectively evaluated the safety and efficacy of pazopanib plus vorinostat, everolimus, lapatinib or trastuzumab, and MEK inhibitor in patients with advanced sarcoma. The Cancer Geneome Atlas (TCGA) data was analyzed for HDAC, PI3K, HER2, and MAPK/RAS/RAF gene alterations from sarcoma TCGA. Of the 44 advanced sarcoma patients in these trials, 27 (61%) were male; 18 (41%) had bone sarcoma, and 26 (59%) had soft tissue sarcoma. Best response was partial response (PR) in four patients [(overall response rate (ORR) = 9%, 95% confidence interval [CI] 3% to 22%)]. The median progression-free survival (PFS) for all patients was 9.6 weeks (95% CI 8.0 to 15.7 weeks). Analysis of TCGA data revealed HDAC, PI3K, HER2, and MAPK/RAS/RAF gene alterations in 112/243 (46%) of patients predominantly HDAC1–11 (41%) alterations. Pazopanib combinations did demonstrate safety in combination with other agents. TCGA data suggests further evaluation of epigenetic pathway inhibitors in sarcoma.
Whey Protein Concentrate Renders MDA-MB-231 Cells Sensitive to Rapamycin by Altering Cellular Redox State and Activating GSK3β/mTOR Signaling
Authors: Cheng Shih-Hsuan , Tseng Yang-Ming , Wu Szu-Hsien , Tsai Shih-Meng , Tsai Li-Yu
Published: November 2017

Whey protein concentrate (WPC) is an amino acid-rich supplement that has been shown to increase cellular antioxidant capacity. Mammalian target of rapamycin (mTOR) is a crucial regulator of signaling in mammalian cells, and serves as a therapeutic target for triple-negative breast cancer (TNBC). This study was designed to investigate the effect of combining WPC with rapamycin on MDA-MB-231 human breast cancer cells. These cells were found to be insensitive to rapamycin and exhibited higher glutathione (GSH) and reactive oxygen species levels than non-tumorigenic MCF-10A cells. However, for MDA-MB-231 cells, the half maximal inhibitory concentration of rapamycin was lower when this drug was administered in combination with WPC than when used alone. Furthermore, combining WPC with rapamycin depleted GSH levels and reduced Nrf2 nuclear accumulation. In addition, WPC activated GSK3β/mTOR signaling, and GSK3β appeared to be involved in the WPC-mediated Nrf2 reduction and mTOR activation. In conclusion, WPC induced rapamycin sensitivity in MDA-MB-231 cells by altering their redox state and activating GSK3β/mTOR signaling. These results not only suggest a novel therapeutic approach for breast cancer treatment, but also provide insight into the critical pathways affecting the resistance to mTOR inhibition observed in a subgroup of TNBC patients.
Detection of Somatic Mutations in Exome Sequencing of Tumor-only Samples
Authors: Hsu Yu-Chin , Hsiao Yu-Ting , Kao Tzu-Yuan , Chang Jan-Gowth , Shieh Grace S.
Published: November 2017

Due to lack of normal samples in clinical diagnosis and to reduce costs, detection of small-scale mutations from tumor-only samples is required but remains relatively unexplored. We developed an algorithm (GATKcan) augmenting GATK with two statistics and machine learning to detect mutations in cancer. The averaged performance of GATKcan in ten experiments outperformed GATK in detecting mutations of randomly sampled 231 from 241 TCGA endometrial tumors (EC). In external validations, GATKcan outperformed GATK in TCGA breast cancer (BC), ovarian cancer (OC) and melanoma tumors, in terms of Matthews correlation coefficient (MCC) and precision, where MCC takes both sensitivity and specificity into account. Further, GATKcan reduced high fractions of false positives detected by GATK. In mutation detection of somatic variants, classified commonly by VarScan 2 and MuTect from the called variants in BC, OC and melanoma, ranked by adjusted MCC (adjusted precision) GATKcan was the top 1, followed by MuTect, VarScan 2 and GATK. Importantly, GATKcan enables detection of mutations when alternate alleles exist in normal samples. These results suggest that GATKcan trained by a cancer is able to detect mutations in future patients with the same type of cancer and is likely applicable to other cancers with similar mutations.
Predicting nosocomial lower respiratory tract infections by a risk index based system
Authors: Chen Yong , Shan Xue , Zhao Jingya , Han Xuelin , Tian Shuguang , Chen Fangyan , Su Xueting , Sun Yansong , Huang Liuyu , Grundmann Hajo , Wang Hongyuan , Han Li
Published: November 2017

Although belonging to one of the most common type of nosocomial infection, there was currently no simple prediction model for lower respiratory tract infections (LRTIs). This study aims to develop a risk index based system for predicting nosocomial LRTIs based on data from a large point-prevalence survey. Among the 49328 patients included, the prevalence of nosocomial LRTIs was 1.70% (95% confidence interval [CI], 1.64% to 1.76%). The areas under the receiver operating characteristic (ROC) curve for logistic regression and fisher discriminant analysis were 0.907 (95% CI, 0.897 to 0.917) and 0.902 (95% CI, 0.892 to 0.912), respectively. The constructed risk index based system also displayed excellent discrimination (area under the ROC curve: 0.905 [95% CI, 0.895 to 0.915]) to identify LRTI in internal validation. Six risk levels were generated according to the risk score distribution of study population, ranging from 0 to 5, the corresponding prevalence of nosocomial LRTIs were 0.00%, 0.39%, 3.86%, 12.38%, 28.79% and 44.83%, respectively. The sensitivity and specificity of prediction were 0.87 and 0.79, respectively, when the best cut-off point of risk score was set to 14. Our study suggested that this newly constructed risk index based system might be applied to boost more rational infection control programs in clinical settings.
Rapid in situ imaging and whole genome sequencing of biofilm in neonatal feeding tubes: A clinical proof of concept
Authors: Ogrodzki Pauline , Cheung Chi Shing , Saad Mohamed , Dahmani Khaled , Coxill Rebecca , Liang Haida , Forsythe Stephen j.
Published: November 2017

The bacterial flora of nasogastric feeding tubes and faecal samples were analysed for a low-birth weight (725 g) neonate EGA 25 weeks in intensive care. Samples were collected at age 6 and 8 weeks of life. Optical coherence tomography (OCT) was used to visualise bacterial biofilms inside the nasogastric feeding tubes. The biofilm was heterogeneously distributed along the tube lumen wall, and had a depth of up to 500 µm. The bacterial biofilm and faecal samples included Enterococcus faecalis and Enterobacter hormaechei. Representative strains, recovered from both feeding tubes and faecal samples, were whole genome sequenced using Illumina, Mi-Seq, which revealed indistinguishable strains, each with less than 28 SNP differences, of E. faecalis and E. hormaechei. The E. faecalis strains were from two sequence types (ST191 and ST211) and encoded for a number of traits related to biofilm formation (BopD), adherence (Epb pili), virulence (cps loci, gelatinase, SprE) and antibiotic resistances (IsaA, tetM). The E. hormaechei were all ST106, and encoded for blaACT-15 β–lactamase and fosfomycin resistance (fosA). This proof of concept study demonstrates that bacterial flora within the neonatal feeding tubes may influence the bacterial colonisation of the intestinal tract and can be visualised non-destructively using OCT.
Partial loss-of-function of NAL1 alters canopy photosynthesis by changing the contribution of upper and lower canopy leaves in rice
Authors: Hirotsu Naoki , Ujiie Kazuhiro , Perera Ishara , Iri Ayano , Kashiwagi Takayuki , Ishimaru Ken
Published: November 2017

Little is known about the genetic basis of leaf and canopy photosynthesis. Here we aimed to detect novel quantitative trait loci (QTL) controlling photosynthesis by increasing leaf nitrogen content (LNC) per leaf area and analysed its effect on leaf and canopy photosynthesis. To identify QTL that increase photosynthetic rate in leaves, we screened chromosome segment substitution lines (CSSLs) of Oryza sativa ssp. japonica cultivar Koshihikari and O. sativa ssp. indica cultivar Nona Bokra using LNC per leaf area as the phenotype indicator. Locus leaf nitrogen content on chromosome four (qLNC4) is associated with increased LNC and photosynthetic rate per leaf area. Moreover, a non-synonymous amino acid substitution was identified in the NARROW LEAF 1 (NAL1) gene located in the qLNC4 region. This NAL1 allele increases LNC and photosynthetic rate per leaf area in flag leaves but does not increase whole-leaf photosynthesis. This NAL1 allele also increases light capture and whole-leaf nitrogen content of the lower leaves and is associated with slower senescence in flag leaves. These results suggest that this NAL1 allele does not increase whole-leaf photosynthesis but plays a role in regulating spatial and temporal trade-offs among traits at the whole-plant level.
TYK2-induced phosphorylation of Y640 suppresses STAT3 transcriptional activity
Authors: Mori Raffaele , Wauman Joris , Icardi Laura , Van der Heyden José , De Cauwer Lode , Peelman Frank , De Bosscher Karolien , Tavernier Jan
Published: November 2017

STAT3 is a pleiotropic transcription factor involved in homeostatic and host defense processes in the human body. It is activated by numerous cytokines and growth factors and generates a series of cellular effects. Of the STAT-mediated signal transduction pathways, STAT3 transcriptional control is best understood. Jak kinase dependent activation of STAT3 relies on Y705 phosphorylation triggering a conformational switch that is stabilized by intermolecular interactions between SH2 domains and the pY705 motif. We here show that a second tyrosine phosphorylation within the SH2 domain at position Y640, induced by Tyk2, negatively controls STAT3 activity. The Y640F mutation leads to stabilization of activated STAT3 homodimers, accelerated nuclear translocation and superior transcriptional activity following IL-6 and LIF stimulation. Moreover, it unlocks type I IFN-dependent STAT3 signalling in cells that are normally refractory to STAT3 transcriptional activation.
Temporal expression pattern of genes during the period of sex differentiation in human embryonic gonads
Authors: Mamsen Linn S. , Ernst Emil H. , Borup Rehannah , Larsen Agnete , Olesen Rasmus H. , Ernst Erik , Anderson Richard A. , Kristensen Stine G. , Andersen Claus Y.
Published: November 2017

The precise timing and sequence of changes in expression of key genes and proteins during human sex-differentiation and onset of steroidogenesis was evaluated by whole-genome expression in 67 first trimester human embryonic and fetal ovaries and testis and confirmed by qPCR and immunohistochemistry (IHC).SRY/SOX9expression initiated in testis around day 40 pc, followed by initiation ofAMHand steroidogenic genes required for androgen production at day 53 pc. In ovaries, gene expression ofRSPO1, LIN28,FOXL2, WNT2B, andETV5, were significantly higher than in testis, whereasGLI1was significantly higher in testis than ovaries. Gene expression was confirmed by IHC for GAGE, SOX9, AMH, CYP17A1, LIN28, WNT2B, ETV5 and GLI1. Gene expression was not associated with the maternal smoking habits. Collectively, a precise temporal determination of changes in expression of key genes involved in human sex-differentiation is defined, with identification of new genes of potential importance.
HDL particles incorporate into lipid bilayers – a combined AFM and single molecule fluorescence microscopy study
Authors: Plochberger Birgit , Röhrl Clemens , Preiner Johannes , Rankl Christian , Brameshuber Mario , Madl Josef , Bittman Robert , Ros Robert , Sezgin Erdinc , Eggeling Christian , Hinterdorfer Peter , Stangl Herbert , Schütz Gerhard J.
Published: November 2017

The process, how lipids are removed from the circulation and transferred from high density lipoprotein (HDL) – a main carrier of cholesterol in the blood stream – to cells, is highly complex. HDL particles are captured from the blood stream by the scavenger receptor, class B, type I (SR-BI), the so-called HDL receptor. The details in subsequent lipid-transfer process, however, have not yet been completely understood. The transfer has been proposed to occur directly at the cell surface across an unstirred water layer, via a hydrophobic channel in the receptor, or after HDL endocytosis. The role of the target lipid membrane for the transfer process, however, has largely been overlooked. Here, we studied at the single molecule level how HDL particles interact with synthetic lipid membranes. Using (high-speed) atomic force microscopy and fluorescence correlation spectroscopy (FCS) we found out that, upon contact with the membrane, HDL becomes integrated into the lipid bilayer. Combined force and single molecule fluorescence microscopy allowed us to directly monitor the transfer process of fluorescently labelled amphiphilic lipid probe from HDL particles to the lipid bilayer upon contact.
Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum
Authors: Naqvi Rubab Zahra , Zaidi Syed Shan-e-Ali , Akhtar Khalid Pervaiz , Strickler Susan , Woldemariam Melkamu , Mishra Bharat , Mukhtar M. Shahid , Scheffler Brian E. , Scheffler Jodi A. , Jander Georg , Mueller Lukas A. , Asif Muhammad , Mansoor Shahid
Published: November 2017

Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most devastating diseases in cotton. While the widely cultivated cotton speciesGossypium hirsutumis generally susceptible, the diploid speciesG. arboreumis a natural source for resistance against CLCuD. However, the influence of CLCuD on theG. arboreumtranscriptome and the interaction of CLCuD withG. arboreumremains to be elucidated. Here we have used an RNA-Seq based study to analyze differential gene expression inG. arboreumunder CLCuD infestation.G. arboreumplants were infested by graft inoculation using a CLCuD infected scion ofG. hirsutum. CLCuD infested asymptomatic and symptomatic plants were analyzed with RNA-seq using an Illumina HiSeq. 2500. Data analysis revealed 1062 differentially expressed genes (DEGs) inG. arboreum. We selected 17 genes for qPCR to validate RNA-Seq data. We identified several genes involved in disease resistance and pathogen defense. Furthermore, a weighted gene co-expression network was constructed from the RNA-Seq dataset that indicated 50 hub genes, most of which are involved in transport processes and might have a role in the defense response ofG. arboreumagainst CLCuD. This fundamental study will improve the understanding of virus-host interaction and identification of important genes involved inG. arboreumtolerance against CLCuD.
Radioligand binding analysis of α2 adrenoceptors with [11C]yohimbine in brain in vivo: Extended Inhibition Plot correction for plasma protein binding
Authors: Phan Jenny-Ann , Landau Anne M. , Jakobsen Steen , Wong Dean F. , Gjedde Albert
Published: November 2017

We describe a novel method of kinetic analysis of radioligand binding to neuroreceptors in brain in vivo, here applied to noradrenaline receptors in rat brain. The method uses positron emission tomography (PET) of [11C]yohimbine binding in brain to quantify the density and affinity of α2 adrenoceptors under condition of changing radioligand binding to plasma proteins. We obtained dynamic PET recordings from brain of Spraque Dawley rats at baseline, followed by pharmacological challenge with unlabeled yohimbine (0.3 mg/kg). The challenge with unlabeled ligand failed to diminish radioligand accumulation in brain tissue, due to the blocking of radioligand binding to plasma proteins that elevated the free fractions of the radioligand in plasma. We devised a method that graphically resolved the masking of unlabeled ligand binding by the increase of radioligand free fractions in plasma. The Extended Inhibition Plot introduced here yielded an estimate of the volume of distribution of non-displaceable ligand in brain tissue that increased with the increase of the free fraction of the radioligand in plasma. The resulting binding potentials of the radioligand declined by 50–60% in the presence of unlabeled ligand. The kinetic unmasking of inhibited binding reflected in the increase of the reference volume of distribution yielded estimates of receptor saturation consistent with the binding of unlabeled ligand.
The effects of diets enriched in omega-3 polyunsaturated fatty acids on systemic vaccinia virus infection
Authors: Jones Gwendolyn J. B. , Roper Rachel L.
Published: November 2017

Omega-3 polyunsaturated fatty acids (PUFA, n-3 fatty acids), the key components of fish and flaxseed oils, are increasingly consumed by the public because of their potential health benefits and are available by prescription for hypertriglyceridemia. However, numerous studies have shown that these compounds are immunoregulatory and immunosuppressive and thus may increase susceptibility to infection. In this study, we tested the effects of the amount of fat and the types of fatty acid in the diet on infection by vaccinia virus, an acute infection that begins in the respiratory tract and spreads by viremia to internal organs. Male C57Bl6 mice (~5 week old) were fed for 3 weeks prior to infection and continuing during infection and recovery one of the following: 1) a normal low fat (13% kcal) diet, 2) a low fat diet containing n-3 PUFAs, 3) a high fat (41% kcal) diet rich in n-3 PUFAs, 4) a high fat n-6 PUFA diet, or 5) a high fat monounsaturated diet. We found no statistically significant differences in the susceptibility of mice to viral infection, morbidity, viral organ titers, recovery time, or mortality with these diets, indicating that, over this approximately 6-week time period, dietary fats did not substantially affect responses to poxviral infection.
Intrinsic short-tailed azole resistance in mucormycetes is due to an evolutionary conserved aminoacid substitution of the lanosterol 14α-demethylase
Authors: Caramalho Rita , Tyndall Joel D. A. , Monk Brian C. , Larentis Thomas , Lass-Flörl Cornelia , Lackner Michaela
Published: November 2017

Mucormycoses are emerging and potentially lethal infections. An increase of breakthrough infections has been found in cohorts receiving short-tailed azoles prophylaxis (e.g. voriconazole (VCZ)). Although VCZ is ineffective in vitro and in vivo, long-tailed triazoles such as posaconazole remain active against mucormycetes. Our goal was to validate the molecular mechanism of resistance to short-tailed triazoles in Mucorales. The paralogous cytochrome P450 genes (CYP51 F1 and CYP51 F5) of Rhizopus arrhizus, Rhizopus microsporus, and Mucor circinelloides were amplified and sequenced. Alignment of the protein sequences of the R. arrhizus, R. microsporus, and M. circinelloides CYP51 F1 and F5 with additional Mucorales species (n = 3) and other fungi (n = 16) confirmed the sequences to be lanosterol 14α-demethylases (LDMs). Sequence alignment identified a pan-Mucorales conservation of a phenylalanine129 substitution in all CYP51 F5s analyzed. A high resolution X-ray crystal structure of Saccharomyces cerevisiae LDM in complex with VCZ was used for generating a homology model of R. arrhizus CYP51 F5. Structural and functional knowledge of S. cerevisiae CYP51 shows that the F129 residue in Mucorales CYP51 F5 is responsible for intrinsic resistance of Mucorales against short-tailed triazoles, with a V to A substitution in Helix I also potentially playing a role.
Broad-spectrum antiviral agents: secreted phospholipase A2 targets viral envelope lipid bilayers derived from the endoplasmic reticulum membrane
Authors: Chen Ming , Aoki-Utsubo Chie , Kameoka Masanori , Deng Lin , Terada Yutaka , Kamitani Wataru , Sato Kei , Koyanagi Yoshio , Hijikata Makoto , Shindo Keiko , Noda Takeshi , Kohara Michinori , Hotta Hak
Published: November 2017

Hepatitis C virus (HCV), dengue virus (DENV) and Japanese encephalitis virus (JEV) belong to the family Flaviviridae. Their viral particles have the envelope composed of viral proteins and a lipid bilayer acquired from budding through the endoplasmic reticulum (ER). The phospholipid content of the ER membrane differs from that of the plasma membrane (PM). The phospholipase A2 (PLA2) superfamily consists of a large number of members that specifically catalyse the hydrolysis of phospholipids at a particular position. Here we show that the CM-II isoform of secreted PLA2 obtained from Naja mossambica mossambica snake venom (CM-II-sPLA2) possesses potent virucidal (neutralising) activity against HCV, DENV and JEV, with 50% inhibitory concentrations (IC50) of 0.036, 0.31 and 1.34 ng/ml, respectively. In contrast, the IC50 values of CM-II-sPLA2 against viruses that bud through the PM (Sindbis virus, influenza virus and Sendai virus) or trans-Golgi network (TGN) (herpes simplex virus) were >10,000 ng/ml. Moreover, the 50% cytotoxic (CC50) and haemolytic (HC50) concentrations of CM-II-sPLA2 were >10,000 ng/ml, implying that CM-II-sPLA2 did not significantly damage the PM. These results suggest that CM-II-sPLA2 and its derivatives are good candidates for the development of broad-spectrum antiviral drugs that target viral envelope lipid bilayers derived from the ER membrane.
Novel, one-step synthesis of zwitterionic polymer nanoparticles via distillation-precipitation polymerization and its application for dye removal membrane
Authors: Ibrahim G. P. Syed , Isloor Arun M. , Inamuddin  , Asiri Abdullah M. , Ismail Norafiqah , Ismail Ahmed Fauzi , Ashraf Ghulam Md
Published: November 2017

In this work, poly(MBAAm-co-SBMA) zwitterionic polymer nanoparticles were synthesized in one-step via distillation-precipitation polymerization (DPP) and were characterized. [2-(methacryloyloxy)ethyl]dimethyl-(3-sulfopropyl)ammonium hydroxide (SBMA) as monomer and N, N′-methylene bis(acrylamide) (MBAAm) as cross-linker are used for the synthesis of nanoparticles. As  far as our knowledge, this is the first such report on the synthesis of poly(MBAAm-co-SBMA) nanoparticles via DPP. The newly synthesized nanoparticles were further employed for the surface modification of polysulfone (PSF) hollow fiber membranes for dye removal. The modified hollow fiber membrane exhibited the improved permeability (56 L/ m2 h bar) and dye removal (>98% of Reactive Black 5 and >80.7% of Reactive orange 16) with the high permeation of salts. Therefore, the as-prepared membrane can have potential application in textile and industrial wastewater treatment.
Information processing in the NF-κB pathway
Authors: Tudelska Karolina , Markiewicz Joanna , Kochańczyk Marek , Czerkies Maciej , Prus Wiktor , Korwek Zbigniew , Abdi Ali , Błoński Sławomir , Kaźmierczak Bogdan , Lipniacki Tomasz
Published: November 2017

The NF-κB pathway is known to transmit merely 1 bit of information about stimulus level. We combined experimentation with mathematical modeling to elucidate how information about TNF concentration is turned into a binary decision. Using Kolmogorov-Smirnov distance, we quantified the cell’s ability to discern 8 TNF concentrations at each step of the NF-κB pathway, to find that input discernibility decreases as signal propagates along the pathway. Discernibility of low TNF concentrations is restricted by noise at the TNF receptor level, whereas discernibility of high TNF concentrations it is restricted by saturation/depletion of downstream signaling components. Consequently, signal discernibility is highest between 0.03 and 1 ng/ml TNF. Simultaneous exposure to TNF or LPS and a translation inhibitor, cycloheximide, leads to prolonged NF-κB activation and a marked increase of transcript levels of NF-κB inhibitors, IκBα and A20. The impact of cycloheximide becomes apparent after the first peak of nuclear NF-κB translocation, meaning that the NF-κB network not only relays 1 bit of information to coordinate the all-or-nothing expression of early genes, but also over a longer time course integrates information about other stimuli. The NF-κB system should be thus perceived as a feedback-controlled decision-making module rather than a simple information transmission channel.
Human canonical CD157/Bst1 is an alternatively spliced isoform masking a previously unidentified primate-specific exon included in a novel transcript
Authors: Ferrero Enza , Lo Buono Nicola , Morone Simona , Parrotta Rossella , Mancini Cecilia , Brusco Alfredo , Giacomino Alice , Augeri Stefania , Rosal-Vela Antonio , García-Rodríguez Sonia , Zubiaur Mercedes , Sancho Jaime , Fiorio Pla Alessandra , Funaro Ada
Published: November 2017

CD157/Bst1 is a dual-function receptor and β-NAD+-metabolizing ectoenzyme of the ADP-ribosyl cyclase family. Expressed in human peripheral blood neutrophils and monocytes, CD157 interacts with extracellular matrix components and regulates leukocyte diapedesis via integrin-mediated signalling in inflammation. CD157 also regulates cell migration and is a marker of adverse prognosis in epithelial ovarian cancer and pleural mesothelioma. One form of CD157 is known to date: the canonical sequence of 318 aa from a 9-exon transcript encoded by BST1 on human chromosome 4. Here we describe a second BST1 transcript, consisting of 10 exons, in human neutrophils. This transcript includes an unreported exon, exon 1b, located between exons 1 and 2 of BST1. Inclusion of exon 1b in frame yields CD157-002, a novel proteoform of 333 aa: exclusion of exon 1b by alternative splicing generates canonical CD157, the dominant proteoform in neutrophils and other tissues analysed here. In comparative functional analyses, both proteoforms were indistinguishable in cell surface localization, specific mAb binding, and behaviour in cell adhesion and migration. However, NAD glycohydrolase activity was detected in canonical CD157 alone. Comparative phylogenetics indicate that exon 1b is a genomic innovation acquired during primate evolution, pointing to the importance of alternative splicing for CD157 function.
Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism
Authors: Botta Cristian , Acquadro Alberto , Greppi Anna , Barchi Lorenzo , Bertolino Marta , Cocolin Luca , Rantsiou Kalliopi
Published: November 2017

The butyrogenic capability of Lactobacillus (L.) plantarum is highly dependent on the substrate type and so far not assigned to any specific metabolic pathway. Accordingly, we compared three genomes of L. plantarum that showed a strain-specific capability to produce butyric acid in human cells growth media. Based on the genomic analysis, butyric acid production was attributed to the complementary activities of a medium-chain thioesterase and the fatty acid synthase of type two (FASII). However, the genomic islands of discrepancy observed between butyrogenic L. plantarum strains (S2T10D, S11T3E) and the non-butyrogenic strain O2T60C do not encompass genes of FASII, but several cassettes of genes related to sugar metabolism, bacteriocins, prophages and surface proteins. Interestingly, single amino acid substitutions predicted from SNPs analysis have highlighted deleterious mutations in key genes of glutamine metabolism in L. plantarum O2T60C, which corroborated well with the metabolic deficiency suffered by O2T60C in high-glutamine growth media and its consequent incapability to produce butyrate. In parallel, the increase of glutamine content induced the production of butyric acid by L. plantarum S2T10D. The present study reveals a previously undescribed metabolic route for butyric acid production in L. plantarum, and a potential involvement of the glutamine uptake in its regulation.
Cartilage intermediate layer protein 1 (CILP1): A novel mediator of cardiac extracellular matrix remodelling
Authors: van Nieuwenhoven Frans A. , Munts Chantal , op’t Veld Roel C. , González Arantxa , Díez Javier , Heymans Stephane , Schroen Blanche , van Bilsen Marc
Published: November 2017

Heart failure is accompanied by extracellular matrix (ECM) remodelling, often leading to cardiac fibrosis. In the present study we explored the significance of cartilage intermediate layer protein 1 (CILP1) as a novel mediator of cardiac ECM remodelling. Whole genome transcriptional analysis of human cardiac tissue samples revealed a strong association of CILP1 with many structural (e.g. COL1A2 r2 = 0.83) and non-structural (e.g. TGFB3 r2 = 0.75) ECM proteins. Gene enrichment analysis further underscored the involvement of CILP1 in human cardiac ECM remodelling and TGFβ signalling. Myocardial CILP1 protein levels were significantly elevated in human infarct tissue and in aortic valve stenosis patients. CILP1 mRNA levels markedly increased in mouse heart after myocardial infarction, transverse aortic constriction, and angiotensin II treatment. Cardiac fibroblasts were found to be the primary source of cardiac CILP1 expression. Recombinant CILP1 inhibited TGFβ-induced αSMA gene and protein expression in cardiac fibroblasts. In addition, CILP1 overexpression in HEK293 cells strongly (5-fold p < 0.05) inhibited TGFβ signalling activity. In conclusion, our study identifies CILP1 as a new cardiac matricellular protein interfering with pro-fibrotic TGFβ signalling, and as a novel sensitive marker for cardiac fibrosis.