bluuebunny/crossref_metadata_2025_split huggingface dataset:
The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain
Authors: Mandad Sunit , Rahman Raza-Ur , Centeno Tonatiuh Pena , Vidal Ramon O. , Wildhagen Hanna , Rammner Burkhard , Keihani Sarva , Opazo Felipe , Urban Inga , Ischebeck Till , Kirli Koray , Benito Eva , Fischer André , Yousefi Roya Y. , Dennerlein Sven , Rehling Peter , Feussner Ivo , Urlaub Henning , Bonn Stefan , Rizzoli Silvio O. , Fornasiero Eugenio F. 
Published: November 2018

AbstractThe homeostasis of the proteome depends on the tight regulation of the mRNA and protein abundances, of the translation rates, and of the protein lifetimes. Results from several studies on prokaryotes or eukaryotic cell cultures have suggested that protein homeostasis is connected to, and perhaps regulated by, the protein and the codon sequences. However, this has been little investigated for mammalsin vivo. Moreover, the link between the coding sequences and one critical parameter, the protein lifetime, has remained largely unexplored, bothin vivoandin vitro. We tested this in the mouse brain, and found that the percentages of amino acids and codons in the sequences could predict all of the homeostasis parameters with a precision approaching experimental measurements. A key predictive element was the wobble nucleotide. G-/C-ending codons correlated with higher protein lifetimes, protein abundances, mRNA abundances and translation rates than A-/U-ending codons. Modifying the proportions of G-/C-ending codons could tune these parameters in cell cultures, in a proof-of-principle experiment. We suggest that the coding sequences are strongly linked to protein homeostasisin vivo, albeit it still remains to be determined whether this relation is causal in nature.
Smallest known raptor tracks suggest microraptorine activity in lakeshore setting
Authors: Kim Kyung Soo , Lim Jong Deock , Lockley Martin G. , Xing Lida , Kim Dong Hee , Piñuela Laura , Romilio Anthony , Yoo Jae Sang , Kim Jin Ho , Ahn Jaehong 
Published: November 2018

AbstractOngoing studies of a multiple track-bearing horizons from massive excavations in the Jinju Formation (Lower Cretaceous) of South Korea have yielded a remarkable diversity of avian, non-avian dinosaur, pterosaur, crocodilian and mammal tracks, many very small and well preserved. Here we report diminutive, didactyl tracks (~1.0 cm long) assigned to a new dromaeosaurid ichnogenus Dromaeosauriformipes, which resembles the larger, but still quite small, ichnogenus Dromaeosauripus, also from the same formation only 30 km away. These diminutive tracks are consistent with the foot size of smaller dromaeosaurid taxa like Early Cretaceous Microraptor from China, and may represent diminutive species or juveniles of larger species. The association of tracks with lakeshore sediments is consistent with the evidence that Microraptor was a fish eater. Two trackways and isolated tracks indicate variable trackmaker gaits and speeds. If oviparous, as assumed for most non-avian dinosaur neonates, the trackmakers must have hatched from tiny eggs. Previous studies of the Korean Cretaceous indicate the presence of other diminutive (~1.0 cm long) theropod tracks (Minisauripus). Such occurrences strongly suggest that small tracks attributed to juveniles, or very small tetrapod species, are more common than previously supposed especially where suitable preservation conditions prevailed.
Asymmetric flows and drivers of herbaceous plant invasion success among Mediterranean-climate regions
Authors: Casado Miguel A. , Martín-Forés Irene , Castro Isabel , de Miguel José M. , Acosta-Gallo Belén 
Published: November 2018

AbstractUnderstanding the mechanisms that support the arrival, establishment and spread of species over an introduced range is crucial in invasion ecology. We analysed the unintentionally introduced herbaceous species that are naturalised in the five Mediterranean-climate regions. There is an asymmetry in the species flows among regions, being the Iberian Peninsula the main donor to the other regions. At interregional scale, the species’ capacity to spread among regions is related to the ecological versatility of the species in the donor area (Iberian Peninsula). At intraregional scale, the species’ capacity to successfully occupy a complete region first depends on the time elapsed from its introduction and afterwards on the degree of occurrence in the region of origin, which is commonly related to its chance of coming into contact with humans. Information on exotic species in their origin region provides insights into invasion process and decision-making to reduce the risks of future invasions.
Responses to climatic and pathogen threats differ in biodynamic and conventional vines
Authors: Soustre-Gacougnolle Isabelle , Lollier Marc , Schmitt Carine , Perrin Mireille , Buvens Estelle , Lallemand Jean-François , Mermet Mélanie , Henaux Mélanie , Thibault-Carpentier Christelle , Dembelé Doulaye , Steyer Damien , Clayeux Céline , Moneyron Anne , Masson Jean E. 
Published: November 2018

AbstractViticulture is of high socio-economic importance; however, its prevalent practices severely impact the environment and human health, and criticisms from society are raising. Vine managements systems are further challenged by climatic changes. Of the 8 million hectares grown worldwide, conventional and organic practices cover 90% and 9% of acreage, respectively. Biodynamic cultivation accounts for 1%. Although economic success combined with low environmental impact is widely claimed by biodynamic winegrowers from California, to South Africa, and France, this practice is still controversial in viticulture and scientific communities. To rethink the situation, we encouraged stakeholders to confront conventional and biodynamic paradigms in a Participative-Action-Research. Co-designed questions were followed up by holistic comparison of conventional and biodynamic vineyard managements. Here we show that the amplitude of plant responses to climatic threats was higher in biodynamic than conventional management. The same stood true for seasonal trends and pathogens attacks. This was associated with higher expression of silencing and immunity genes, and higher anti-oxidative and anti-fungal secondary metabolite levels. This suggests that sustainability of biodynamic practices probably relies on fine molecular regulations. Such knowledge should contribute to resolving disagreements between stakeholders and help designing the awaited sustainable viticulture at large.
A standardized herbal extract PM014 ameliorates pulmonary fibrosis by suppressing the TGF-β1 pathway
Authors: Kim Kyung Hwa , Lee Sujin , Lee Hyunji , Shin Dasom , Min Daeun , Kim Miran , Ryu Byeol , Kim Hyeon Woo , Bae Hyunsu 
Published: November 2018

AbstractIdiopathic pulmonary fibrosis (IPF) is a devastating and common chronic lung disease pathologically characterized by loss of epithelial cells and activation of fibroblasts and myofibroblasts. The etiology of IPF remains unclear and the disease pathology is poorly understood with no known efficacious therapy. PM014 is an herbal extract that has been shown to have beneficial effects in pulmonary diseases, which are likely to exert anti-inflammatory bioactions. In the present study, we observed that bleomycin (BLM) caused increased inflammatory infiltration as well as collagen deposition in lungs of mice on day 14 after treatment. Administration of PM014 suppressed BLM-induced inflammatory responses and fibrotic changes in dose-dependent manner in mice. Additionally, we provided in vitro evidence suggesting that PM014 inhibited TGF-β1-induced epithelial-mesenchymal transition (EMT) and fibroblast activation in alveolar epithelial cells and human lung fibroblasts from healthy donor and IPF patients. PM014 appeared to target TGF-β1 signaling via Smad-dependent pathways and p38 mitogen-activated protein kinases (MAPKs) pathways. Taken together, our data suggest that PM014 administration exerts a protective effect against lung fibrosis and highlight PM014 as a viable treatment option that may bring benefits to patient with IPF.
Liver-specific Repin1 deficiency impairs transient hepatic steatosis in liver regeneration
Authors: Abshagen Kerstin , Degenhardt Bastian , Liebig Marie , Wendt Anna , Genz Berit , Schaeper Ute , Stumvoll Michael , Hofmann Ute , Frank Marcus , Vollmar Brigitte , Klöting Nora 
Published: November 2018

AbstractTransient hepatic steatosis upon liver resection supposes functional relationships between lipid metabolism and liver regeneration. Repin1 has been suggested as candidate gene for obesity and dyslipidemia by regulating key genes of lipid metabolism and lipid storage. Herein, we characterized the regenerative potential of mice with a hepatic deletion of Repin1 (LRep1−/−) after partial hepatectomy (PH) in order to determine the functional significance of Repin1 in liver regeneration. Lipid dynamics and the regenerative response were analyzed at various time points after PH. Hepatic Repin1 deficiency causes a significantly decreased transient hepatic lipid accumulation. Defects in lipid uptake, as analyzed by decreased expression of the fatty acid transporter Cd36 and Fatp5, may contribute to attenuated and shifted lipid accumulation, accompanied by altered extent and chronological sequence of liver cell proliferation in LRep1−/− mice. In vitro steatosis experiments with primary hepatocytes also revealed attenuated lipid accumulation and occurrence of smaller lipid droplets in Repin1-deficient cells, while no direct effect on proliferation in HepG2 cells was observed. Based on these results, we propose that hepatocellular Repin1 might be of functional significance for early accumulation of lipids in hepatocytes after PH, facilitating efficient progression of liver regeneration.
Characterization of human breast tissue microbiota from core needle biopsies through the analysis of multi hypervariable 16S-rRNA gene regions
Authors: Costantini Lara , Magno Stefano , Albanese Davide , Donati Claudio , Molinari Romina , Filippone Alessio , Masetti Riccardo , Merendino Nicolò 
Published: November 2018

AbstractBreast microbiota compositions are not well understood, and a few recent reports have begun to explore the correlation between breast tissue dysbiosis and cancer. Given that various methods for breast microbiota detection were used, the aim of the present paper was to clarify which hypervariable region of the 16S-rRNA gene (V2, V3, V4, V6 + 7, V8, and V9) is the most informative for breast tissue microbiota. Core needle biopsies (CNBs) were compared with surgical excision biopsies (SEBs) to find a less invasive form of recovery useful for the analysis of a larger statistical population and potentially for diagnostic use of breast tissue microbiota. Finally, this study was the first to analyse the breast microbiota of tumours and paired normal tissues of a Mediterranean population. Our findings showed that the V3 region is the most informative for breast tissue microbiota, accounting for 45% of all reads. No significant differences were found between CNB and SEB specimens in terms of total reads and numbers of Operational Taxonomic Units (OTUs). Moreover, we find that more similarities than differences exist between tumours and adjacent normal tissues. Finally, the presence of the Ralstonia genus is associated with breast tissue.
Identification of soybean peptide leginsulin variants in different cultivars and their insulin-like activities
Authors: Hashidume Tsutomu , Sakano Taiken , Mochizuki Ayaka , Ito Keisuke , Ito Sohei , Kawarasaki Yasuaki , Miyoshi Noriyuki 
Published: November 2018

AbstractWe have recently reported that green soybean cultivar, echigomidori, and not the yellow cultivar, fukuyutaka, is a rich source of hormone-like peptide leginsulin consisting of 37 amino acids (Leg_1_37, PDB 1JU8A) and its C-terminal glycine deletant, Leg_1_36. Green soybean is mature, but the color of the seedcoat and cotyledon remains green. Therefore, in this study, we examined the leginsulin content in different varieties of 11 colored soybeans (including green, yellow, red, brown and black) and edamame (immature soybean). Profile analysis of soybean constituents by LC-MS showed that Leg_1 (36 + 37) detected as a prominent peak in 3 green and 1 yellow soybean cultivar was the strongest contributor in principal component analysis, indicating Leg_1 is the most characteristic feature for distinguishing soybean cultivars. However, smaller amounts of leginsulin-like peptides, defined as Leg_2 and Leg_3, were detected in other samples. The cDNA sequences and LC-MS/MS analyses revealed that Leg_2 was a homologue of Leg_1 with three amino acid substitutions derived from SNPs, while Leg_3 was a Leg_1/Leg_2 paralog. Expression levels of Leg_1 were markedly higher than Leg_2 and Leg_3. Additionally, in glucose uptake assay, purified TRX-His-tag fused recombinant Leg_1_37 prepared by bacterial expression showed stronger insulin-like activities than other variants including Leg_2, Leg_3, and their Gly deletants in myotube-like differentiated L6 and C2C12 cells. These results suggest that dietary consumption of soybean seed, especially including a higher amount of Leg_1_37, could be useful for lowering of blood glucose.
Co-expression of the Hemagglutinin and Neuraminidase by Heterologous Newcastle Disease Virus Vectors Protected Chickens against H5 Clade 2.3.4.4 HPAI Viruses
Authors: Cho Yeonwoo , Lamichhane Barisha , Nagy Abdou , Chowdhury Ishita Roy , Samal Siba K. , Kim Shin-Hee 
Published: November 2018

AbstractAvian influenza remains an important zoonotic disease with a significant global impact. The spread of H5 highly pathogenic avian influenza (HPAI) viruses (clade 2.3.4.4) by migratory birds has caused outbreaks in wide geographic regions (Asia, Europe, and North America) with great economic losses during 2014–2015. Efficient vaccines and vaccination approaches are needed to enhance protective immunity against HPAI viruses. Although several vaccination strategies have been developed, none has been satisfactory. Our strategy has been to use avirulent vaccine strain of Newcastle disease virus (NDV) as a vaccine vector for HPAI viruses. For poultry vaccination, we previously generated a new platform of chimeric NDV vector to overcome preexisting maternal antibodies to NDV in poultry. In this study, we have generated vaccine candidates targeting H5 clade 2.3.4.4 HPAI viruses by using our chimeric NDV and conventional NDV strain LaSota vectors for a heterologous prime-boost immunization approach. Co-expression of the HA and NA proteins by our vaccine vectors induced enhanced HPAI virus specific immune responses in specific-pathogen free and broiler chickens prior to challenge. Further, these vaccine candidates efficiently protected broiler chickens from mortality, clinical signs, and shedding of homologous and heterologous H5 HPAI viruses and highly virulent NDV, thus providing a dual vaccination approach in the field.
Pre-existing Symptoms and Healthcare Utilization Prior to Diagnosis of Neuroendocrine Tumors: A SEER-Medicare Database Study
Authors: Shen C. , Dasari A. , Xu Y. , Zhou S. , Gu D. , Chu Y. , Halperin D. M. , Shih Y. T. , Yao J. C. 
Published: November 2018

AbstractThe incidence and prevalence of neuroendocrine tumors (NETs) are continually increasing. While it is known that NET symptoms often predate diagnosis, their prevalence and impact on resource utilization and costs are largely unknown. We identified 9,319 elderly patients diagnosed with NETs between 1/2003 and 12/2011 from the Surveillance, Epidemiology and End Results (SEER)-Medicare. We examined the patients’ conditions potentially associated with NET, resource utilization and costs during the year before diagnosis. We found that NET patients were more likely to have diagnoses of hypertension (63.8% vs. 53.3%), abdominal pain (22.2% vs. 7.6%), heart failure (11.7% vs. 8.0%), diarrhea (5.8% vs. 1.8%), peripheral edema (5.4% vs. 3.8%) and irritable bowel syndrome (1.2% vs. 0.5%) compared to the non-cancer control group. They also had much higher resource utilization including number of outpatient visits (mean: 22.1 vs. 17.2), percentage with ER visits (20.9% vs. 11.6%), and hospitalizations (28.4% vs. 17.0%). Similarly, NET patients incurred significantly higher total (mean: $14602 vs. $9464), outpatient (mean: $5987 vs. $4253), and inpatient costs (mean: $8615 vs. $5211). This first population-based study on the pre-diagnosis symptoms and healthcare utilization found that NET patients were more likely to have certain conditions and incur higher resource utilizations and costs.
Cerebrospinal Fluid Levels of Autophagy-related Proteins Represent Potentially Novel Biomarkers of Early-Stage Parkinson’s Disease
Authors: Youn Jinyoung , Lee Sang-Bin , Lee Hyo Sang , Yang Hyun Ok , Park Jinse , Kim Ji Sun , Oh Eungseok , Park Suyeon , Jang Wooyoung 
Published: November 2018

AbstractThe roles of autophagy-related proteins as diagnostic or monitoring biomarkers in Parkinson’s disease (PD) have not been clearly elucidated. We recruited 32 patients with early-stage PD and 28 control subjects, and evaluated parkinsonian motor symptoms and dopamine transporter imaging data. Cerebrospinal fluid (CSF) levels of LC3B, Beclin1, and LAMP-2 were estimated using ELISAs, and CSF levels of ATG5, ATG7, and p62 were examined by immunoblotting. Additionally, we also assessed the levels of α-synuclein, total tau, and phosphorylated tau in CSF using ELISAs. Significant differences in the levels of LC3B, LAMP-2, and Beclin1 were observed between the PD and control groups. Using 29.8 pg/mL as the cut-off value for a diagnostic biomarker of PD, CSF LC3B levels exhibited high sensitivity (96.9%) and specificity (89.3%) with an area under the curve of 0.982. Furthermore, LC3B was significantly correlated with the asymmetry index in the caudate and putamen, as estimated by a semi-quantitative analysis of [18F] N-(3-fluoropropyl)-2β-carbon ethoxy-3β-(4-iodophenyl) nortropane (FP-CIT) positron emission tomography (PET). CSF levels of LC3B represented a potential diagnostic and prognostic biomarker of early-stage PD in patients. Based on our findings, molecular biological changes in PD are associated with dysregulation of the lysosomal autophagy pathway.
Deciphering the molecular basis of mycobacteria and lipoglycan recognition by the C-type lectin Dectin-2
Authors: Decout Alexiane , Silva-Gomes Sandro , Drocourt Daniel , Blattes Emilyne , Rivière Michel , Prandi Jacques , Larrouy-Maumus Gérald , Caminade Anne-Marie , Hamasur Beston , Källenius Gunilla , Kaur Devinder , Dobos Karen M. , Lucas Megan , Sutcliffe Iain C. , Besra Gurdyal S. , Appelmelk Ben J. , Gilleron Martine , Jackson Mary , Vercellone Alain , Tiraby Gérard , Nigou Jérôme 
Published: November 2018

AbstractDectin-2 is a C-type lectin involved in the recognition of several pathogens such as Aspergillus fumigatus, Candida albicans, Schistosoma mansonii, and Mycobacterium tuberculosis that triggers Th17 immune responses. Identifying pathogen ligands and understanding the molecular basis of their recognition is one of the current challenges. Purified M. tuberculosis mannose-capped lipoarabinomannan (ManLAM) was shown to induce signaling via Dectin-2, an activity that requires the (α1 → 2)-linked mannosides forming the caps. Here, using isogenic M. tuberculosis mutant strains, we demonstrate that ManLAM is a bona fide and actually the sole ligand mediating bacilli recognition by Dectin-2, although M. tuberculosis produces a variety of cell envelope mannoconjugates, such as phosphatidyl-myo-inositol hexamannosides, lipomannan or manno(lipo)proteins, that bear (α1 → 2)-linked mannosides. In addition, we found that Dectin-2 can recognize lipoglycans from other bacterial species, such as Saccharotrix aerocolonigenes or the human opportunistic pathogen Tsukamurella paurometabola, suggesting that lipoglycans are prototypical Dectin-2 ligands. Finally, from a structure/function relationship perspective, we show, using lipoglycan variants and synthetic mannodendrimers, that dimannoside caps and multivalent interaction are required for ligand binding to and signaling via Dectin-2. Better understanding of the molecular basis of ligand recognition by Dectin-2 will pave the way for the rational design of potent adjuvants targeting this receptor.
RanBP2 regulates the anti-retroviral activity of TRIM5α by SUMOylation at a predicted phosphorylated SUMOylation motif
Authors: Maarifi Ghizlane , Fernandez Juliette , Portilho Débora M. , Boulay Aude , Dutrieux Jacques , Oddos Stéphane , Butler-Browne Gillian , Nisole Sébastien , Arhel Nathalie J. 
Published: November 2018

AbstractTRIM5α is a cytoplasmic restriction factor that blocks post-entry retroviral infection. Evidence suggests that its antiviral activity can be regulated by SUMO, but how this is achieved remains unknown. Here, we show that TRIM5α forms a complex with RanGAP1, Ubc9, and RanBP2 at the nuclear pore, and that RanBP2 E3 SUMO ligase promotes the SUMOylation of endogenous TRIM5α in the cytoplasm. Loss of RanBP2 blocked SUMOylation of TRIM5α, altered its localization in primary cells, and suppressed the antiviral activity of both rhesus and human orthologs. In cells, human TRIM5α is modified on K84 within a predicted phosphorylated SUMOylation motif (pSUM) and not on K10 as found in vitro. Non-modified TRIM5α lacked antiviral activity, indicating that only SUMOylated TRIM5α acts as a restriction factor. This work illustrates the importance of the nuclear pore in intrinsic antiviral immunity, acting as a hub where virus, SUMO machinery, and restriction factors can meet.
Dandelion-shaped manganese sulfide in ether-based electrolyte for enhanced performance sodium-ion batteries
Authors: Pham Duong Tung , Sambandam Balaji , Kim Sungjin , Jo Jeonggeun , Kim Seokhun , Park Sohyun , Mathew Vinod , Sun Yang-Kook , Kim Kwangho , Kim Jaekook 
Published: November 2018

AbstractMetal sulfide materials serve as environment-friendly, sustainable, and effective electrode materials for green-energy storage systems. However, their capacity-fading issues related to low electrical conductivity and drastic volume changes during electrochemical cycling have generally limited their application to sodium ion batteries. Here we show that with the combination of an ether-based NaPF6/diglyme electrolyte, the dandelion-shaped manganese sulfide electrode displays enhanced reversible capacity, cycle life, and rate capability. The capacity of 340 mAh g−1 is maintained over more than 1000 cycles at a current density of 5.0 A g−1. Furthermore, discharge capacities of 277 and 230 mAh g−1 at 10 and 20 A g−1 current densities, respectively, are obtained. Our work demonstrates the formation of a protective solid electrolyte interface layer along the surface of the primary seed particle that limits polysulfide dissolution and hence the preservation of the active material during reaction with sodium.