bluuebunny/crossref_metadata_2025 huggingface dataset:
Trends in the prevalence of elevated skinfold thickness among children and adolescents in Shandong Province, China, 1995–2014
Authors: Wang Shu-Rong , Cheng Yan , Chen Min , Zhang Ying-Xiu
Published: April 2018

Objective

There are abundant data on secular trends in BMI; however, information on the change in subcutaneous fat is limited. The present study examined the trends in the prevalence of elevated skinfold thickness among children and adolescents over the past 19 years (1995–2014) in Shandong Province, China.

Design

Data for the study were obtained from two cross-sectional surveys of schoolchildren carried out in 1995 and 2014. Triceps and subscapular skinfold thicknesses (SFT) of all participants were measured. The sum of triceps and subscapular SFT (SSFT) was applied. Children and adolescents with SSFT above or equal to the national age- and sex-specific 85th percentile were defined as ‘high SFT’.

Setting

Shandong Province, China.

Subjects

A total of 16 917 students aged 7–18 years were included.

Results

For both boys and girls, an increasing trend in ‘high SFT’ was observed between 1995 and 2014. The overall prevalence of ‘high SFT’ increased from 10·31 % for boys and 13·40 % for girls in 1995 to 33·94 % for boys and 29·30 % for girls in 2014 (P<0·01).

Conclusions

There are more children and adolescents with very high levels of SFT. These trends describe very unfavourable changes in the body composition and should give cause for concern.
Subsurface exolife
Authors: Lingam Manasvi , Loeb Abraham
Published: April 2018

We study the prospects for life on planets with subsurface oceans, and find that a wide range of planets can exist in diverse habitats with ice envelopes of moderate thickness. We quantify the energy sources available to these worlds, the rate of production of prebiotic compounds, and assess their potential for hosting biospheres. Life on these planets is likely to face challenges, which could be overcome through a combination of different mechanisms. We estimate the number of such worlds, and find that they may outnumber rocky planets in the habitable zone of stars by a few orders of magnitude.
New design for highly durable infrared-reflective coatings
Authors: Hu Chaoquan , Liu Jian , Wang Jianbo , Gu Zhiqing , Li Chao , Li Qian , Li Yuankai , Zhang Sam , Bi Chaobin , Fan Xiaofeng , Zheng Weitao
Published: April 2018

The fundamental challenge in designing durable infrared-reflective coatings is achieving the ideal combination of both high reflectivity and durability. Satisfying these competing demands is traditionally achieved by deposition of durable layers on highly reflective metals. We overturn the traditional logic of ‘first reflectivity and then durability’ and propose an alternative of ‘first durability and then reflectivity’: First, a transition-metal compound is selected as a durable base; then its reflectivity is improved by incorporating silver/gold to form an alloy or by overcoating a multilayer stack. Two validation experiments prove that the new strategy works extremely well: the coatings thus obtained have infrared reflectivities close to that of aluminum, and their hardness and acid and salt corrosion resistances are 27–50, 400–1 500 and 7 500–25 000 times that of aluminum. The traditional mirror coating (e.g., Al/SiO2 films) is more suitable for moderate environments, while our mirror coating that was obtained by the new strategy (e.g., an Ag-doped hafnium nitride film) is more suitable for harsh environments, such as ones with dust, windblown sand, moisture, acid rain or salt fog. This work opens up new opportunities for highly durable infrared-reflective coatings and rejuvenates the study of transition metal compounds in a completely new area of optics.
Persistent urine leakage around a suprapubic catheter: the experience of a person with chronic tetraplegia
Authors: Vaidyanathan Subramanian , Ward Jerry , Soni Bakul M. , Hughes Peter , Oo Tun
Published: April 2018

Introduction

Persistent urine leakage after suprapubic cystostomy in tetraplegic subjects occurs due to shrinkage of the urinary bladder and bladder spasms. The patient’s social life is adversely affected as clothes become wet, smelly, and require frequent changing, thus increasing the workload of carers.

Case presentation

A 48-year-old male sustained C-4 complete (AIS:A) tetraplegia while swimming in 2007. Suprapubic cystostomy was performed in 2009. From 2012, this patient had urine leakage around the suprapubic catheter, which became progressively more frequent. Propiverine, then oxybutynin tablets instead of propiverine, oxybutynin transdermal patches, and mirabegron in addition to oxybutynin were tried. An indwelling urethral catheter was used in addition to the suprapubic catheter to alleviate urine leakage when the bladder was undergoing spasms. This patient continued to have leakage around the suprapubic catheter. Leakage of urine was occasionally accompanied by autonomic dysreflexia. Leakage of urine caused huge amounts of extra work for carers, and family. Furthermore, leakage of urine had a significant impact on quality of life, and going out with friends and family. Bladder wall injection of Botox was performed in 2015 and in 2016, which reduced urine leakage.

Discussion

Bladder wall injection of Botox to treat persistent urine leakage around the suprapubic catheter in spinal cord injury patients with suprapubic cystostomy has not been mentioned in NICE guidelines or publications indexed in PubMed. While recommending suprapubic cystostomy to subjects with tetraplegia, leakage of urine around the suprapubic catheter, which may occur sometime after suprapubic cystostomy, should be included in the conversation so that patients and carers become aware of this potential complication.
CHIP regulates bone mass by targeting multiple TRAF family members in bone marrow stromal cells
Authors: Wang Tingyu , Li Shan , Yi Dan , Zhou Guang-Qian , Chang Zhijie , Ma Peter X. , Xiao Guozhi , Chen Di
Published: April 2018

Carboxyl terminus of Hsp70-interacting protein (CHIP or STUB1) is an E3 ligase and regulates the stability of several proteins which are involved in different cellular functions. Our previous studies demonstrated that Chip deficient mice display bone loss phenotype due to increased osteoclast formation through enhancing TRAF6 activity in osteoclasts. In this study we provide novel evidence about the function of CHIP. We found that osteoblast differentiation and bone formation were also decreased in Chip KO mice. In bone marrow stromal (BMS) cells derived from Chip−/− mice, expression of a panel of osteoblast marker genes was significantly decreased. ALP activity and mineralized bone matrix formation were also reduced in Chip-deficient BMS cells. We also found that in addition to the regulation of TRAF6, CHIP also inhibits TNFα-induced NF-κB signaling through promoting TRAF2 and TRAF5 degradation. Specific deletion of Chip in BMS cells downregulated expression of osteoblast marker genes which could be reversed by the addition of NF-κB inhibitor. These results demonstrate that the osteopenic phenotype observed in Chip−/− mice was due to the combination of increased osteoclast formation and decreased osteoblast differentiation. Taken together, our findings indicate a significant role of CHIP in bone remodeling.
Enhancer variants reveal a conserved transcription factor network governed by PU.1 during osteoclast differentiation
Authors: Carey Heather A. , Hildreth Blake E. , Geisler Jennifer A. , Nickel Mara C. , Cabrera Jennifer , Ghosh Sankha , Jiang Yue , Yan Jing , Lee James , Makam Sandeep , Young Nicholas A. , Valiente Giancarlo R. , Jarjour Wael N. , Huang Kun , Rosol Thomas J. , Toribio Ramiro E. , Charles Julia F. , Ostrowski Michael C. , Sharma Sudarshana M.
Published: April 2018

Genome-wide association studies (GWASs) have been instrumental in understanding complex phenotypic traits. However, they have rarely been used to understand lineage-specific pathways and functions that contribute to the trait. In this study, by integrating lineage-specific enhancers from mesenchymal and myeloid compartments with bone mineral density loci, we were able to segregate osteoblast- and osteoclast (OC)-specific functions. Specifically, in OCs, a PU.1-dependent transcription factor (TF) network was revealed. Deletion of PU.1 in OCs in mice resulted in severe osteopetrosis. Functional genomic analysis indicated PU.1 and MITF orchestrated a TF network essential for OC differentiation. Several of these TFs were regulated by cooperative binding of PU.1 with BRD4 to form superenhancers. Further, PU.1 is essential for conformational changes in the superenhancer region of Nfatc1. In summary, our study demonstrates that combining GWASs with genome-wide binding studies and model organisms could decipher lineage-specific pathways contributing to complex disease states.
Omentin-1 prevents inflammation-induced osteoporosis by downregulating the pro-inflammatory cytokines
Authors: Rao Shan-Shan , Hu Yin , Xie Ping-Li , Cao Jia , Wang Zhen-Xing , Liu Jiang-Hua , Yin Hao , Huang Jie , Tan Yi-Juan , Luo Juan , Luo Ming-Jie , Tang Si-Yuan , Chen Tuan-Hui , Yuan Ling-Qing , Liao Er-Yuan , Xu Ran , Liu Zheng-Zhao , Chen Chun-Yuan , Xie Hui
Published: April 2018

Osteoporosis is a frequent complication of chronic inflammatory diseases and increases in the pro-inflammatory cytokines make an important contribution to bone loss by promoting bone resorption and impairing bone formation. Omentin-1 is a newly identified adipocytokine that has anti-inflammatory effects, but little is known about the role of omentin-1 in inflammatory osteoporosis. Here we generated global omentin-1 knockout (omentin-1−/−) mice and demonstrated that depletion of omentin-1 induces inflammatory bone loss-like phenotypes in mice, as defined by abnormally elevated pro-inflammatory cytokines, increased osteoclast formation and bone tissue destruction, as well as impaired osteogenic activities. Using an inflammatory cell model induced by tumor necrosis factor-α (TNF-α), we determined that recombinant omentin-1 reduces the production of pro-inflammatory factors in the TNF-α-activated macrophages, and suppresses their anti-osteoblastic and pro-osteoclastic abilities. In the magnesium silicate-induced inflammatory osteoporosis mouse model, the systemic administration of adenoviral-delivered omentin-1 significantly protects from osteoporotic bone loss and inflammation. Our study suggests that omentin-1 can be used as a promising therapeutic agent for the prevention or treatment of inflammatory bone diseases by downregulating the pro-inflammatory cytokines.
Quantitative proteomic profiling of primary cancer-associated fibroblasts in oesophageal adenocarcinoma
Authors: Manousopoulou Antigoni , Hayden Annette , Mellone Massimiliano , Garay-Baquero Diana J. , White Cory H. , Noble Fergus , Lopez Monette , Thomas Gareth J. , Underwood Timothy J. , Garbis Spiros D.
Published: April 2018

Background

Cancer-associated fibroblasts (CAFs) form the major stromal component of the tumour microenvironment (TME). The present study aimed to examine the proteomic profiles of CAFs vs. normal fibroblasts (NOFs) from patients with oesophageal adenocarcinoma to gain insight into their pro-oncogenic phenotype.

Methods

CAFs/NOFs from four patients were sub-cultured and analysed using quantitative proteomics. Differentially expressed proteins (DEPs) were subjected to bioinformatics and compared with published proteomics and transcriptomics  datasets.

Results

Principal component analysis of all profiled proteins showed that CAFs had high heterogeneity and clustered separately from NOFs. Bioinformatics interrogation of the DEPs demonstrated inhibition of adhesion of epithelial cells, adhesion of connective tissue cells and cell death of fibroblast cell lines in CAFs vs. NOFs (p < 0.0001). KEGG pathway analysis showed a significant enrichment of the insulin-signalling pathway (p = 0.03). Gene ontology terms related with myofibroblast phenotype, metabolism, cell adhesion/migration, hypoxia/oxidative stress, angiogenesis, immune/inflammatory response were enriched in CAFs vs. NOFs. Nestin, a stem-cell marker up-regulated in CAFs vs. NOFs, was confirmed to be expressed in the TME with immunohistochemistry.

Conclusions

The identified pathways and participating proteins may provide novel insight on the tumour-promoting properties of CAFs and unravel novel adjuvant therapeutic targets in the TME.
Use of the XRCC2 promoter for in vivo cancer diagnosis and therapy
Authors: Chen Yu , Li Zhen , Xu Zhu , Tang Huanyin , Guo Wenxuan , Sun Xiaoxiang , Zhang Wenjun , Zhang Jian , Wan Xiaoping , Jiang Ying , Mao Zhiyong
Published: April 2018

The homologous recombination (HR) pathway is a promising target for cancer therapy as it is frequently upregulated in tumors. One such strategy is to target tumors with cancer-specific, hyperactive promoters of HR genes including RAD51 and RAD51C. However, the promoter size and the delivery method have limited its potential clinical applications. Here we identified the ~2.1 kb promoter of XRCC2, similar to ~6.5 kb RAD51 promoter, as also hyperactivated in cancer cells. We found that XRCC2 expression is upregulated in nearly all types of cancers, to a degree comparable to RAD51 while much higher than RAD51C. Further study demonstrated that XRCC2 promoter is hyperactivated in cancer cell lines, and diphtheria toxin A (DTA) gene driven by XRCC2 promoter specifically eliminates cancer cells. Moreover, lentiviral vectors containing XRCC2 promoter driving firefly luciferase or DTA were created and applied to subcutaneous HeLa xenograft mice. We demonstrated that the pXRCC2-luciferase lentivirus is an effective tool for in vivo cancer visualization. Most importantly, pXRCC2-DTA lentivirus significantly inhibited the growth of HeLa xenografts in comparison to the control group. In summary, our results strongly indicate that virus-mediated delivery of constructs built upon the XRCC2 promoter holds great potential for tumor diagnosis and therapy.
β2 spectrin-mediated differentiation repressed the properties of liver cancer stem cells through β-catenin
Authors: Chen Yuhua , Meng Lingling , Shang Haitao , Dou Qian , Lu Zhiwen , Liu Liping , Wang Zhijun , He Xingxing , Song Yuhu
Published: April 2018

βII-Spectrin (β2SP), a Smad3/4 adaptor protein during transforming growth factor (TGF) β/Smad signal pathway, plays a critical role in suppressing hepatocarcinogenesis. Dedifferentiation is a distinctive feature of cancer progression. Therefore, we investigated whether the disruption of β2SP contributed to tumorigenesis of hepatocellular carcinoma (HCC) through the dedifferentiation. Down-regulation of β2SP in hepatocytes was observed in cirrhotic liver and HCC. The level of β2SP expression was closely associated with the differentiation status of hepatocytes in rat model of hepatocarcinogenesis and clinical specimens. Transgenic expression of β2SP in HCC cells promoted the differentiation of HCC cells and suppressed the growth of HCC cells in vitro. Efficient transduction of β2SP into liver CSCs resulted in a reduction in colony formation ability, spheroid formation capacity, invasive activity, chemo-resistance properties, tumorigenicity in vivo. In addition, β2 spectrin exerted its effect through β catenin in liver CSCs. In conclusion, β2 spectrin repressed the properties of liver CSCs through inducing differentiation; thus, strategies to restore its levels and activities would be a novel strategy for HCC prevention and differentiation therapy
Endogenous c-Jun N-terminal kinase (JNK) activity marks the boundary between normal and malignant granulosa cells
Authors: Bildik Gamze , Akin Nazli , Senbabaoglu Filiz , Esmalian Yashar , Sahin Gizem Nur , Urman Defne , Karahuseyinoglu Sercin , Ince Umit , Palaoglu Erhan , Taskiran Cagatay , Arvas Macit , Guzel Yilmaz , Yakin Kayhan , Oktem Ozgur
Published: April 2018

Granulosa cell tumor of the ovary (GCT) is a very rare tumor, accounting for only 2% of all ovarian tumors. It originates from sex cords in the ovary and can be divided into adult (95%) and juvenile (5%) types based on histologic findings. To date, no clear etiologic process has been identified other than a missense point mutation in the FOXL2 gene. Our previous works showed that c-Jun N-terminal kinase (JNK) pathway plays critical role in cell cycle progression and mitosis of normal and immortalized granulosa cells and follicle growth in rodent ovaries. These findings led us to investigate the role of JNK pathway in the granulosa cell tumor of the ovary. We used two different GCT cell lines (COV434 and KGN) and fresh GCT samples of adult and juvenile types obtained from the patients during surgery. We have discovered that endogenous kinase activity of JNK is markedly enhanced in the GCT samples and cell lines, whereas it was almost undetectable in mitotic non-malignant human granulosa cells. The inhibition of JNK pathway in GCT cell lines with two different pharmacologic inhibitors (SP600125 and AS601245) or siRNA resulted in a dose-dependent reduction in in vitro cell growth, increased apoptosis and diminished estradiol and AMH productions. JNK inhibition was also associated with a decrease in the number of cells positive for mitosis marker phospho-histone H3Ser 10 in the asynchronous cells; and diminished EdU uptake during S phase and cell cycle arrest at G2/M-phase transition in the synchronized cells. Ex vivo treatment of patient-derived GCT samples with JNK inhibitors for 24 h significantly decreased their in vitro growth and estradiol and AMH productions. Furthermore, in human GCT xenograft model, in vivo tumor growth was significantly reduced and plasma AMH levels were significantly decreased in SCID mice after administration of JNK inhibitors and siRNA. These findings suggest that targeting JNK pathway may provide therapeutic benefit in the treatment of granulosa cell tumors for which currently no curative therapy exists beyond surgery.
Bax retrotranslocation potentiates Bcl-xL’s antiapoptotic activity and is essential for switch-like transitions between MOMP competency and resistance
Authors: Hantusch Annika , Das Kushal K. , García-Sáez Ana J. , Brunner Thomas , Rehm Markus
Published: April 2018

The rapid, typically all-or-none process of mitochondrial outer membrane permeabilization (MOMP) constitutes a primary cell death decision that is controlled by the Bcl-2 family interactome. However, how strict all-or-none MOMP decisions are governed by and emanate from the dynamic interplay of pro- and antiapoptotic Bcl-2 family members remains incompletely understood. In particular, it is unclear to which extent the shuttling of Bcl-2 family species between lipid and aqueous phases contributes to regulating MOMP sensitivity. Here, we studied the interplay of tBid, Bax, and Bcl-xL, using a combined approach of deterministic mathematical modeling and retrospective as well as prospective experimental testing of model predictions. Systems modeling of the tBid–Bax interplay and their fluxes between cytosol and mitochondrial membranes reproduced experimental data on tBid-triggered Bax activation and oligomerization highly accurately. Extending these studies to analyze the cell-protective role of Bcl-xLstrikingly revealed that the activity of Bcl-xLto retrotranslocate activated Bax from membranes back into the cytosol is essential to reproduce or correctly predict experimental outcomes. These included the potency of Bcl-xLin suppressing Bax oligomerization, its role in limiting Bax membrane recruitment, the resistance threshold to low concentrations of MOMP triggers as well as a response potentiaton arising from combinations of tBid and sensitizer BH3-only peptides. Importantly, retrotranslocation activity of Bcl-xLis necessary to strictly separate conditions of MOMP competency and resistance. Our results therefore identify Bax retrotranslocation by Bcl-xLas an indispensable component of the molecular switch by which Bcl-2 family members govern cellular death decisions.
Klf4 glutamylation is required for cell reprogramming and early embryonic development in mice
Authors: Ye Buqing , Liu Benyu , Hao Lu , Zhu Xiaoxiao , Yang Liuliu , Wang Shuo , Xia Pengyan , Du Ying , Meng Shu , Huang Guanling , Qin Xiwen , Wang Yanying , Yan Xinlong , Li Chong , Hao Junfeng , Zhu Pingping , He Luyun , Tian Yong , Fan Zusen
Published: April 2018

Temporal and spatial-specific regulation of pluripotency networks is largely dependent on the precise modifications of core transcription factors. Misregulation of glutamylation is implicated in severe physiological abnormalities. However, how glutamylation regulates cell reprogramming and pluripotency networks remains elusive. Here we show that cytosolic carboxypeptidases 1 (CCP1) or CCP6 deficiency substantially promotes induced pluripotent cell (iPSC) induction and pluripotency of embryonic stem cells (ESCs). Klf4 polyglutamylation at Glu381 by tubulin tyrosine ligase-like 4 (TTLL4) and TTLL1 during cell reprogramming impedes its lysine 48-linked ubiquitination and sustains Klf4 stability. Klf4-E381A knockin mice display impaired blastocyst development and embryonic lethality. Deletion of TTLL4 or TTLL1 abrogates cell reprogramming and early embryogenesis. Thus, Klf4 polyglutamylation plays a critical role in the regulation of cell reprogramming and pluripotency maintenance.
Genome-wide association study identifies susceptibility loci for B-cell childhood acute lymphoblastic leukemia
Authors: Vijayakrishnan Jayaram , Studd James , Broderick Peter , Kinnersley Ben , Holroyd Amy , Law Philip J. , Kumar Rajiv , Allan James M. , Harrison Christine J. , Moorman Anthony V. , Vora Ajay , Roman Eve , Rachakonda Sivaramakrishna , Kinsey Sally E. , Sheridan Eamonn , Thompson Pamela D. , Irving Julie A. , Koehler Rolf , Hoffmann Per , Nöthen Markus M. , Heilmann-Heimbach Stefanie , Jöckel Karl-Heinz , Easton Douglas F. , Pharaoh Paul D. P. , Dunning Alison M. , Peto Julian , Canzian Frederico , Swerdlow Anthony , Eeles Rosalind A. , Kote-Jarai ZSofia , Muir Kenneth , Pashayan Nora ,   The PRACTICAL Consortium, Henderson Brian E. , Haiman Christopher A. , Benlloch Sara , Schumacher Fredrick R. , Olama Ali Amin Al , Berndt Sonja I. , Conti David V. , Wiklund Fredrik , Chanock Stephen , Stevens Victoria L. , Tangen Catherine M. , Batra Jyotsna , Clements Judith , Gronberg Henrik , Schleutker Johanna , Albanes Demetrius , Weinstein Stephanie , Wolk Alicja , West Catharine , Mucci Lorelei , Cancel-Tassin Géraldine , Koutros Stella , Sorensen Karina Dalsgaard , Maehle Lovise , Neal David E. , Travis Ruth C. , Hamilton Robert J. , Ingles Sue Ann , Rosenstein Barry , Lu Yong-Jie , Giles Graham G. , Kibel Adam S. , Vega Ana , Kogevinas Manolis , Penney Kathryn L. , Park Jong Y. , Stanford Janet L. , Cybulski Cezary , Nordestgaard Børge G. , Brenner Hermann , Maier Christiane , Kim Jeri , John Esther M. , Teixeira Manuel R. , Neuhausen Susan L. , De Ruyck Kim , Razack Azad , Newcomb Lisa F. , Lessel Davor , Kaneva Radka , Usmani Nawaid , Claessens Frank , Townsend Paul A. , Gago-Dominguez Manuela , Roobol Monique J. , Menegaux Florence , Greaves Mel , Zimmerman Martin , Bartram Claus R. , Schrappe Martin , Stanulla Martin , Hemminki Kari , Houlston Richard S.
Published: April 2018

Genome-wide association studies (GWAS) have advanced our understanding of susceptibility to B-cell precursor acute lymphoblastic leukemia (BCP-ALL); however, much of the heritable risk remains unidentified. Here, we perform a GWAS and conduct a meta-analysis with two existing GWAS, totaling 2442 cases and 14,609 controls. We identify risk loci for BCP-ALL at 8q24.21 (rs28665337,P = 3.86 × 10−9, odds ratio (OR) = 1.34) and forETV6-RUNX1fusion-positive BCP-ALL at 2q22.3 (rs17481869,P = 3.20 × 10−8, OR = 2.14). Our findings provide further insights into genetic susceptibility to ALL and its biology.
The global distribution and spread of the mobilized colistin resistance gene mcr-1
Authors: Wang Ruobing , van Dorp Lucy , Shaw Liam P. , Bradley Phelim , Wang Qi , Wang Xiaojuan , Jin Longyang , Zhang Qing , Liu Yuqing , Rieux Adrien , Dorai-Schneiders Thamarai , Weinert Lucy Anne , Iqbal Zamin , Didelot Xavier , Wang Hui , Balloux Francois
Published: April 2018

Colistin represents one of the few available drugs for treating infections caused by carbapenem-resistant Enterobacteriaceae. As such, the recent plasmid-mediated spread of the colistin resistance gene mcr-1 poses a significant public health threat, requiring global monitoring and surveillance. Here, we characterize the global distribution of mcr-1 using a data set of 457 mcr-1-positive sequenced isolates. We find mcr-1 in various plasmid types but identify an immediate background common to all mcr-1 sequences. Our analyses establish that all mcr-1 elements in circulation descend from the same initial mobilization of mcr-1 by an ISApl1 transposon in the mid 2000s (2002–2008; 95% highest posterior density), followed by a marked demographic expansion, which led to its current global distribution. Our results provide the first systematic phylogenetic analysis of the origin and spread of mcr-1, and emphasize the importance of understanding the movement of antibiotic resistance genes across multiple levels of genomic organization.
A loop region of BAFF controls B cell survival and regulates recognition by different inhibitors
Authors: Vigolo Michele , Chambers Melissa G. , Willen Laure , Chevalley Dehlia , Maskos Klaus , Lammens Alfred , Tardivel Aubry , Das Dolon , Kowalczyk-Quintas Christine , Schuepbach-Mallepell Sonia , Smulski Cristian R. , Eslami Mahya , Rolink Antonius , Hummler Edith , Samy Eileen , Fomekong Nanfack Yves , Mackay Fabienne , Liao Maofu , Hess Henry , Jiang Xuliang , Schneider Pascal
Published: April 2018

The B cell survival factor (TNFSF13B/BAFF) is often elevated in autoimmune diseases and is targeted in the clinic for the treatment of systemic lupus erythematosus. BAFF contains a loop region designated the flap, which is dispensable for receptor binding. Here we show that the flap of BAFF has two functions. In addition to facilitating the formation of a highly active BAFF 60-mer as shown previously, it also converts binding of BAFF to TNFRSF13C (BAFFR) into a signaling event via oligomerization of individual BAFF-BAFFR complexes. Binding and activation of BAFFR can therefore be targeted independently to inhibit or activate the function of BAFF. Moreover, structural analyses suggest that the flap of BAFF 60-mer temporarily prevents binding of an anti-BAFF antibody (belimumab) but not of a decoy receptor (atacicept). The observed differences in profiles of BAFF inhibition may confer distinct biological and clinical efficacies to these therapeutically relevant inhibitors.
Surface tension-assisted additive manufacturing
Authors: Ragelle Héloïse , Tibbitt Mark W. , Wu Shang-Yun , Castillo Michael A. , Cheng George Z. , Gangadharan Sidharta P. , Anderson Daniel G. , Cima Michael J. , Langer Robert
Published: April 2018

The proliferation of computer-aided design and additive manufacturing enables on-demand fabrication of complex, three-dimensional structures. However, combining the versatility of cell-laden hydrogels within the 3D printing process remains a challenge. Herein, we describe a facile and versatile method that integrates polymer networks (including hydrogels) with 3D-printed mechanical supports to fabricate multicomponent (bio)materials. The approach exploits surface tension to coat fenestrated surfaces with suspended liquid films that can be transformed into solid films. The operating parameters for the process are determined using a physical model, and complex geometric structures are successfully fabricated. We engineer, by tailoring the window geometry, scaffolds with anisotropic mechanical properties that compress longitudinally (~30% strain) without damaging the hydrogel coating. Finally, the process is amenable to high cell density encapsulation and co-culture. Viability (>95%) was maintained 28 days after encapsulation. This general approach can generate biocompatible, macroscale devices with structural integrity and anisotropic mechanical properties.
Chronic nicotinamide riboside supplementation is well-tolerated and elevates NAD+ in healthy middle-aged and older adults
Authors: Martens Christopher R. , Denman Blair A. , Mazzo Melissa R. , Armstrong Michael L. , Reisdorph Nichole , McQueen Matthew B. , Chonchol Michel , Seals Douglas R.
Published: April 2018

Nicotinamide adenine dinucleotide (NAD+) has emerged as a critical co-substrate for enzymes involved in the beneficial effects of regular calorie restriction on healthspan. As such, the use of NAD+ precursors to augment NAD+ bioavailability has been proposed as a strategy for improving cardiovascular and other physiological functions with aging in humans. Here we provide the evidence in a 2 × 6-week randomized, double-blind, placebo-controlled, crossover clinical trial that chronic supplementation with the NAD+ precursor vitamin, nicotinamide riboside (NR), is well tolerated and effectively stimulates NAD+ metabolism in healthy middle-aged and older adults. Our results also provide initial insight into the effects of chronic NR supplementation on physiological function in humans, and suggest that, in particular, future clinical trials should further assess the potential benefits of NR for reducing blood pressure and arterial stiffness in this group.
An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations
Authors: Liu Xiaonan , Salokas Kari , Tamene Fitsum , Jiu Yaming , Weldatsadik Rigbe G. , Öhman Tiina , Varjosalo Markku
Published: April 2018

Protein-protein interactions govern almost all cellular functions. These complex networks of stable and transient associations can be mapped by affinity purification mass spectrometry (AP-MS) and complementary proximity-based labeling methods such as BioID. To exploit the advantages of both strategies, we here design and optimize an integrated approach combining AP-MS and BioID in a single construct, which we term MAC-tag. We systematically apply the MAC-tag approach to 18 subcellular and 3 sub-organelle localization markers, generating a molecular context database, which can be used to define a protein’s molecular location. In addition, we show that combining the AP-MS and BioID results makes it possible to obtain interaction distances within a protein complex. Taken together, our integrated strategy enables the comprehensive mapping of the physical and functional interactions of proteins, defining their molecular context and improving our understanding of the cellular interactome.
A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons
Authors: Södersten Erik , Toskas Konstantinos , Rraklli Vilma , Tiklova Katarina , Björklund Åsa K. , Ringnér Markus , Perlmann Thomas , Holmberg Johan
Published: April 2018

The brain is composed of hundreds of different neuronal subtypes, which largely retain their identity throughout the lifespan of the organism. The mechanisms governing this stability are not fully understood, partly due to the diversity and limited size of clinically relevant neuronal populations, which constitute a technical challenge for analysis. Here, using a strategy that allows for ChIP-seq combined with RNA-seq in small neuronal populations in vivo, we present a comparative analysis of permissive and repressive histone modifications in adult midbrain dopaminergic neurons, raphe nuclei serotonergic neurons, and embryonic neural progenitors. Furthermore, we utilize the map generated by our analysis to show that the transcriptional response of midbrain dopaminergic neurons following 6-OHDA or methamphetamine injection is characterized by increased expression of genes with promoters dually marked by H3K4me3/H3K27me3. Our study provides an in vivo genome-wide analysis of permissive/repressive histone modifications coupled to gene expression in these rare neuronal subtypes.
Publisher Correction: Ultrafast quantum beats of anisotropic excitons in atomically thin ReS2
Authors: Sim Sangwan , Lee Doeon , Trifonov Artur V. , Kim Taeyoung , Cha Soonyoung , Sung Ji Ho , Cho Sungjun , Shim Wooyoung , Jo Moon-Ho , Choi Hyunyong
Published: April 2018

In the originally published HTML and PDF versions of this article, Figs. 3g and 4d contained typesetting errors affecting the way the data points were displayed. This has now been corrected in the HTML and PDF versions.
uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins
Authors: Maticzka Daniel , Ilik Ibrahim Avsar , Aktas Tugce , Backofen Rolf , Akhtar Asifa
Published: April 2018

RNA-binding proteins (RBPs) play important and essential roles in eukaryotic gene expression regulating splicing, localization, translation, and stability of mRNAs. We describe ultraviolet crosslinking and affinity purification (uvCLAP), an easy-to-use, robust, reproducible, and high-throughput method to determine in vivo targets of RBPs. uvCLAP is fast and does not rely on radioactive labeling of RNA. We investigate binding of 15 RBPs from fly, mouse, and human cells to test the method’s performance and applicability. Multiplexing of signal and control libraries enables straightforward comparison of samples. Experiments for most proteins achieve high enrichment of signal over background. A point mutation and a natural splice isoform that change the RBP subcellular localization dramatically alter target selection without changing the targeted RNA motif, showing that compartmentalization of RBPs can be used as an elegant means to generate RNA target specificity.
Quantum probe hyperpolarisation of molecular nuclear spins
Authors: Broadway David A. , Tetienne Jean-Philippe , Stacey Alastair , Wood James D. A. , Simpson David A. , Hall Liam T. , Hollenberg Lloyd C. L.
Published: April 2018

Hyperpolarisation of nuclear spins is important in overcoming sensitivity and resolution limitations of magnetic resonance imaging and nuclear magnetic resonance spectroscopy. Current hyperpolarisation techniques require high magnetic fields, low temperatures, or catalysts. Alternatively, the emergence of room temperature spin qubits has opened new pathways to achieve direct nuclear spin hyperpolarisation. Employing a microwave-free cross-relaxation induced polarisation protocol applied to a nitrogen vacancy qubit, we demonstrate quantum probe hyperpolarisation of external molecular nuclear spins to ~50% under ambient conditions, showing a single qubit increasing the polarisation of ~106 nuclear spins by six orders of magnitude over the thermal background. Results are verified against a detailed theoretical treatment, which also describes how the system can be scaled up to a universal quantum hyperpolarisation platform for macroscopic samples. Our results demonstrate the prospects for this approach to nuclear spin hyperpolarisation for molecular imaging and spectroscopy and its potential to extend beyond into other scientific areas.
Dynamical origins of heat capacity changes in enzyme-catalysed reactions
Authors: van der Kamp Marc W. , Prentice Erica J. , Kraakman Kirsty L. , Connolly Michael , Mulholland Adrian J. , Arcus Vickery L.
Published: April 2018

Heat capacity changes are emerging as essential for explaining the temperature dependence of enzyme-catalysed reaction rates. This has important implications for enzyme kinetics, thermoadaptation and evolution, but the physical basis of these heat capacity changes is unknown. Here we show by a combination of experiment and simulation, for two quite distinct enzymes (dimeric ketosteroid isomerase and monomeric alpha-glucosidase), that the activation heat capacity change for the catalysed reaction can be predicted through atomistic molecular dynamics simulations. The simulations reveal subtle and surprising underlying dynamical changes: tightening of loops around the active site is observed, along with changes in energetic fluctuations across the whole enzyme including important contributions from oligomeric neighbours and domains distal to the active site. This has general implications for understanding enzyme catalysis and demonstrating a direct connection between functionally important microscopic dynamics and macroscopically measurable quantities.
Opn5L1 is a retinal receptor that behaves as a reverse and self-regenerating photoreceptor
Authors: Sato Keita , Yamashita Takahiro , Ohuchi Hideyo , Takeuchi Atsuko , Gotoh Hitoshi , Ono Katsuhiko , Mizuno Misao , Mizutani Yasuhisa , Tomonari Sayuri , Sakai Kazumi , Imamoto Yasushi , Wada Akimori , Shichida Yoshinori
Published: April 2018

Most opsins are G protein-coupled receptors that utilize retinal both as a ligand and as a chromophore. Opsins’ main established mechanism is light-triggered activation through retinal 11-cis-to-all-trans photoisomerization. Here we report a vertebrate non-visual opsin that functions as a Gi-coupled retinal receptor that is deactivated by light and can thermally self-regenerate. This opsin, Opn5L1, binds exclusively to all-trans-retinal. More interestingly, the light-induced deactivation through retinal trans-to-cis isomerization is followed by formation of a covalent adduct between retinal and a nearby cysteine, which breaks the retinal-conjugated double bond system, probably at the C11 position, resulting in thermal re-isomerization to all-trans-retinal. Thus, Opn5L1 acts as a reverse photoreceptor. We conclude that, like vertebrate rhodopsin, Opn5L1 is a unidirectional optical switch optimized from an ancestral bidirectional optical switch, such as invertebrate rhodopsin, to increase the S/N ratio of the signal transduction, although the direction of optimization is opposite to that of vertebrate rhodopsin.
BEARscc determines robustness of single-cell clusters using simulated technical replicates
Authors: Severson D. T. , Owen R. P. , White M. J. , Lu X. , Schuster-Böckler B.
Published: April 2018

Single-cell messenger RNA sequencing (scRNA-seq) has emerged as a powerful tool to study cellular heterogeneity within complex tissues. Subpopulations of cells with common gene expression profiles can be identified by applying unsupervised clustering algorithms. However, technical variance is a major confounding factor in scRNA-seq, not least because it is not possible to replicate measurements on the same cell. Here, we present BEARscc, a tool that uses RNA spike-in controls to simulate experiment-specific technical replicates. BEARscc works with a wide range of existing clustering algorithms to assess the robustness of clusters to technical variation. We demonstrate that the tool improves the unsupervised classification of cells and facilitates the biological interpretation of single-cell RNA-seq experiments.
Designed heterogeneous palladium catalysts for reversible light-controlled bioorthogonal catalysis in living cells
Authors: Wang Faming , Zhang Yan , Du Zhi , Ren Jinsong , Qu Xiaogang
Published: April 2018

As a powerful tool for chemical biology, bioorthogonal chemistry broadens the ways to explore the mystery of life. In this field, transition metal catalysts (TMCs) have received much attention because TMCs can rapidly catalyze chemical transformations that cannot be accomplished by bio-enzymes. However, fine controlling chemical reactions in living systems like bio-enzymes is still a great challenge. Herein, we construct a versatile light-controlled bioorthogonal catalyst by modifying macroporous silica-Pd0 with supramolecular complex of azobenzene (Azo) and β-cyclodextrin (CD). Its catalytic activity can be regulated by light-induced structural changes, mimicking allosteric regulation mechanism of bio-enzymes. The light-gated heterogeneous TMCs are important for in situ controlling bioorthogonal reactions and have been successfully used to synthesize a fluorescent probe for cell imaging and mitochondria-specific targeting agent by Suzuki–Miyaura cross-coupling reaction. Endowing the bioorthogonal catalyst with new functions is highly valuable for realizing more complex researches in biochemistry.
The role of CSF1R-dependent macrophages in control of the intestinal stem-cell niche
Authors: Sehgal Anuj , Donaldson David S. , Pridans Clare , Sauter Kristin A. , Hume David A. , Mabbott Neil A.
Published: April 2018

Colony-stimulating factor 1 (CSF1) controls the growth and differentiation of macrophages.CSF1R signaling has been implicated in the maintenance of the intestinal stem cell niche and differentiation of Paneth cells, but evidence of expression of CSF1R within the crypt is equivocal. Here we show that CSF1R-dependent macrophages influence intestinal epithelial differentiation and homeostasis. In the intestinal lamina propria CSF1R mRNA expression is restricted to macrophages which are intimately associated with the crypt epithelium, and is undetectable in Paneth cells. Macrophage ablation following CSF1R blockade affects Paneth cell differentiation and leads to a reduction ofLgr5+intestinal stem cells. The disturbances to the crypt caused by macrophage depletion adversely affect the subsequent differentiation of intestinal epithelial cell lineages. Goblet cell density is enhanced, whereas the development of M cells in Peyer’s patches is impeded. We suggest that modification of the phenotype or abundance of macrophages in the gut wall alters the development of the intestinal epithelium and the ability to sample gut antigens.
Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation
Authors: Marteil Gaëlle , Guerrero Adan , Vieira André F. , de Almeida Bernardo P. , Machado Pedro , Mendonça Susana , Mesquita Marta , Villarreal Beth , Fonseca Irina , Francia Maria E. , Dores Katharina , Martins Nuno P. , Jana Swadhin C. , Tranfield Erin M. , Barbosa-Morais Nuno L. , Paredes Joana , Pellman David , Godinho Susana A. , Bettencourt-Dias Mónica
Published: April 2018

Centrosomes are the major microtubule organising centres of animal cells. Deregulation in their number occurs in cancer and was shown to trigger tumorigenesis in mice. However, the incidence, consequence and origins of this abnormality are poorly understood. Here, we screened the NCI-60 panel of human cancer cell lines to systematically analyse centriole number and structure. Our screen shows that centriole amplification is widespread in cancer cell lines and highly prevalent in aggressive breast carcinomas. Moreover, we identify another recurrent feature of cancer cells: centriole size deregulation. Further experiments demonstrate that severe centriole over-elongation can promote amplification through both centriole fragmentation and ectopic procentriole formation. Furthermore, we show that overly long centrioles form over-active centrosomes that nucleate more microtubules, a known cause of invasiveness, and perturb chromosome segregation. Our screen establishes centriole amplification and size deregulation as recurrent features of cancer cells and identifies novel causes and consequences of those abnormalities.
Compositional heterogeneity near the base of the mantle transition zone beneath Hawaii
Authors: Yu Chunquan , Day Elizabeth A. , de Hoop Maarten V. , Campillo Michel , Goes Saskia , Blythe Rachel A. , van der Hilst Robert D.
Published: April 2018

Global seismic discontinuities near 410 and 660 km depth in Earth’s mantle are expressions of solid-state phase transitions. These transitions modulate thermal and material fluxes across the mantle and variations in their depth are often attributed to temperature anomalies. Here we use novel seismic array analysis of SS waves reflecting off the 410 and 660 below the Hawaiian hotspot. We find amplitude–distance trends in reflectivity that imply lateral variations in wavespeed and density contrasts across 660 for which thermodynamic modeling precludes a thermal origin. No such variations are found along the 410. The inferred 660 contrasts can be explained by mantle composition varying from average (pyrolitic) mantle beneath Hawaii to a mixture with more melt-depleted harzburgite southeast of the hotspot. Such compositional segregation was predicted, from petrological and numerical convection studies, to occur near hot deep mantle upwellings like the one often invoked to cause volcanic activity on Hawaii.
Beclin1 restricts RNA virus infection in plants through suppression and degradation of the viral polymerase
Authors: Li Fangfang , Zhang Changwei , Li Yinzi , Wu Guanwei , Hou Xilin , Zhou Xueping , Wang Aiming
Published: April 2018

Autophagy emerges as an essential immunity defense against intracellular pathogens. Here we report that turnip mosaic virus (TuMV) infection activates autophagy in plants and that Beclin1 (ATG6), a core component of autophagy, inhibits virus replication. Beclin1 interacts with NIb, the RNA-dependent RNA polymerase (RdRp) of TuMV, via the highly conserved GDD motif and the interaction complex is targeted for autophagic degradation likely through the adaptor protein ATG8a. Beclin1-mediated NIb degradation is inhibited by autophagy inhibitors. Deficiency of Beclin1 or ATG8a enhances NIb accumulation and promotes viral infection and vice versa. These data suggest that Beclin1 may be a selective autophagy receptor. Overexpression of a Beclin1 truncation mutant that binds to NIb but lacks the ability to mediate NIb degradation also inhibits virus replication. The Beclin1–RdRp interaction further extends to several RNA viruses. Thus Beclin1 restricts viral infection through suppression and also likely autophagic degradation of the viral RdRp.
A vaccinia-based single vector construct multi-pathogen vaccine protects against both Zika and chikungunya viruses
Authors: Prow Natalie A. , Liu Liang , Nakayama Eri , Cooper Tamara H. , Yan Kexin , Eldi Preethi , Hazlewood Jessamine E. , Tang Bing , Le Thuy T. , Setoh Yin Xiang , Khromykh Alexander A , Hobson-Peters Jody , Diener Kerrilyn R. , Howley Paul M. , Hayball John D. , Suhrbier Andreas
Published: April 2018

Zika and chikungunya viruses have caused major epidemics and are transmitted by Aedes aegypti and/or Aedes albopictus mosquitoes. The “Sementis Copenhagen Vector” (SCV) system is a recently developed vaccinia-based, multiplication-defective, vaccine vector technology that allows manufacture in modified CHO cells. Herein we describe a single-vector construct SCV vaccine that encodes the structural polyprotein cassettes of both Zika and chikungunya viruses from different loci. A single vaccination of mice induces neutralizing antibodies to both viruses in wild-type and IFNAR−/− mice and protects against (i) chikungunya virus viremia and arthritis in wild-type mice, (ii) Zika virus viremia and fetal/placental infection in female IFNAR−/− mice, and (iii) Zika virus viremia and testes infection and pathology in male IFNAR−/− mice. To our knowledge this represents the first single-vector construct, multi-pathogen vaccine encoding large polyproteins, and offers both simplified manufacturing and formulation, and reduced “shot burden” for these often co-circulating arboviruses.
The RNA-binding protein ARPP21 controls dendritic branching by functionally opposing the miRNA it hosts
Authors: Rehfeld Frederick , Maticzka Daniel , Grosser Sabine , Knauff Pina , Eravci Murat , Vida Imre , Backofen Rolf , Wulczyn F. Gregory
Published: April 2018

About half of mammalian miRNA genes lie within introns of protein-coding genes, yet little is known about functional interactions between miRNAs and their host genes. The intronic miRNA miR-128 regulates neuronal excitability and dendritic morphology of principal neurons during mouse cerebral cortex development. Its conserved host genes, R3hdm1 and Arpp21, are predicted RNA-binding proteins. Here we use iCLIP to characterize ARPP21 recognition of uridine-rich sequences with high specificity for 3′UTRs. ARPP21 antagonizes miR-128 activity by co-regulating a subset of miR-128 target mRNAs enriched for neurodevelopmental functions. Protein–protein interaction data and functional assays suggest that ARPP21 acts as a positive post-transcriptional regulator by interacting with the translation initiation complex eIF4F. This molecular antagonism is reflected in inverse activities during dendritogenesis: miR-128 overexpression or knockdown of ARPP21 reduces dendritic complexity; ectopic ARPP21 leads to an increase. Thus, we describe a unique example of convergent function by two products of a single gene.