bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of the spawning time of Japanese eels in the open ocean
Authors: Higuchi Takatoshi , Yamada Yoshiaki , Watanabe Shun , Kojima Takahito , Tsukamoto Katsumi 
Published: March 2020

AbstractTo understand the spawning ecology of the Japanese eel, the spawning time of this species was estimated based on measurements of the ascending speed of eggs and previously obtained data. Two types of water temperature parameters were calculated assuming an arbitrary spawning time. The ‘incubation temperature’ of 53 eggs collected in the spawning area was estimated based on the developmental stage of each egg and experimentally determined relationships between water temperature and incubation duration. The ‘experienced temperature’ of eggs ascending in the water column after spawning was estimated based on an ascending egg speed of 3.69 m/h and spawning depth of 230 m determined from a pop-up satellite archival tag release experiment on silver eels conducted in the same area. The incubation and experienced temperatures of the eggs coincided only at 20:20–22:30 h, 3 days prior to the new moon. This period is only a few hours after the diel vertical migration of Japanese eels in the evening, when adults move up from a depth of ~800 m (approximately 5 °C) to shallower waters of 200–250 m depth (approximately 20 °C). Our findings will facilitate improvements in aquaculture techniques and the detection of eel spawning events in the open ocean.
Context-dependent selection as the keystone in the somatic evolution of cancer
Authors: Vibishan B. , Watve Milind G. 
Published: March 2020

AbstractSomatic evolution of cancer involves a series of mutations, and attendant changes, in one or more clones of cells. A “bad luck” type model assumes chance accumulation of mutations. The clonal expansion model assumes, on the other hand, that any mutation leading to partial loss of regulation of cell proliferation will give a selective advantage to the mutant. However, a number of experiments show that an intermediate pre-cancer mutant has only a conditional selective advantage. Given that tissue microenvironmental conditions differ across individuals, this selective advantage to a mutant could be widely distributed over the population. We evaluate three models, namely “bad luck”, context-independent, and context-dependent selection, in a comparative framework, on their ability to predict patterns in total incidence, age-specific incidence, stem cell number-incidence relationship and other known phenomena associated with cancers. Results show that among the factors considered in the model, context dependence is necessary and sufficient to explain observed epidemiological patterns, and that cancer evolution is largely selection-limited, rather than mutation-limited. A wide range of physiological, genetic and behavioural factors influence the tissue micro-environment, and could therefore be the source of this context dependence in somatic evolution of cancer. The identification and targeting of these micro-environmental factors that influence the dynamics of selection offer new possibilities for cancer prevention.
Oxygen consumption rate of Caenorhabditis elegans as a high-throughput endpoint of toxicity testing using the Seahorse XFe96 Extracellular Flux Analyzer
Authors: Preez G. Du , Fourie H. , Daneel M. , Miller H. , Höss S. , Ricci C. , Engelbrecht G. , Zouhar M. , Wepener V. 
Published: March 2020

AbstractCaenorhabditis elegans presents functioning, biologically relevant phenotypes and is frequently used as a bioindicator of toxicity. However, most C. elegans in vivo effect-assessment methods are laborious and time consuming. Therefore, we developed a novel method to measure the oxygen consumption rate of C. elegans as a sublethal endpoint of toxicity. This protocol was tested by exposing 50 larval stage one C. elegans individuals for 48 h (at 20 °C) to different concentrations of two toxicants i.e. benzylcetyldimethylammonium chloride (BAC-C16) and cadmium (Cd). Following exposures, the oxygen consumption rate of the C. elegans individuals were measured using the high-throughput functionality of the Seahorse XFe96 Extracellular Flux Analyzer. Dose-response curves for BAC-C16 (R2 = 0.93; P = 0.001) and Cd (R2 = 0.98; P = 0.001) were created. Furthermore, a strong, positive correlation was evidenced between C. elegans oxygen consumption rate and a commonly used, ecologically relevant endpoint of toxicity (growth inhibition) for BAC-C16 (R2 = 0.93; P = 0.0001) and Cd (R2 = 0.91; P = 0.0001). The data presented in this study show that C. elegans oxygen consumption rate can be used as a promising functional measurement of toxicity.
Relationship between Sleep Duration, Sun Exposure, and Serum 25-Hydroxyvitamin D Status: A Cross-sectional Study
Authors: Choi Ji Ho , Lee Bora , Lee Jae Yong , Kim Chang-Hoon , Park Bumhee , Kim Dong Young , Kim Hyun Jun , Park Do-Yang 
Published: March 2020

AbstractNormal-range sleep duration is an important factor for general health and metabolism, and insufficient or excessive sleep is associated with chronic metabolic disease. Among the many factors that affect sleep duration, sun exposure plays an important role in maintaining regular circadian rhythm and is also involved in the production and activation of 25-hydroxyvitamin D [25(OH)D], which regulates various functions in the body. However, 25(OH)D is available through food and various nutritional supplements without sun exposure, so it is important to find out the complex relationship among sun exposure, vitamin D status, and sleep duration. The relationship between sun exposure, vitamin D status, and sleep duration was analyzed in the nationwide survey and examination of 25,534 study populations, after adjusting for demographic characteristics, physical characteristics, lifestyle status, and socio-demographic variables. Vitamin D status alone did not show the relationship with sleep duration, although there were statistical relationships in the various factors including sun exposure with sleep duration. There was a statistical difference in 25(OH)D according to sleep duration, only in low sun exposure group. Subjects with low sun exposure and excessive sleep duration comparatively lower 25(OH)D than those with normal-range sleep, even after adjustment for potentially confounding factors. Individuals with limited exposure to sunlight should maintain adequate vitamin D status to have an appropriate sleep duration for health.
Two-step extinction of Late Cretaceous marine vertebrates in northern Gulf of Mexico prolonged biodiversity loss prior to the Chicxulub impact
Authors: Ikejiri Takehito , Lu YueHan , Zhang Bo 
Published: March 2020

AbstractRecent studies on mass extinctions are often based on the global fossil record, but data from selected paleogeographic regions under a relatively constant paleoenvironmental setting can also provide important information. Eighty-nine marine vertebrate species, including cartilaginous and bony fish and marine reptiles, from northern Gulf of Mexico – located about 500 km from the Chicxulub crater – offer a unique opportunity to determine an extinction process during the last 20 million years of the Late Cretaceous. Our diversity data show two separate extinction events: (i) the ‘Middle Campanian Crisis’ (about 77 Mya) and (ii) the end-Maastrichtian (66 Mya) events. Whether this stepwise pattern of extinctions occurred locally or globally cannot be determined at present due to the lack of a dataset of the marine vertebrate record for reliable comparison. However, this stepwise pattern including the Middle Campanian and end-Maastrichtian events for, at least, a 13 million-year interval indicates long-term global marine environmental changes (e.g., regression, ocean water chemistry change). Because most Cretaceous marine vertebrates already disappeared in the Gulf of Mexico prior to the latest Maastrichtian, the Chicxulub Impact may not be considered as the most devastating extinction event for the community.
Calprotectin, a new biomarker for diagnosis of acute respiratory infections
Authors: Havelka Aleksandra , Sejersen Kristina , Venge Per , Pauksens Karlis , Larsson Anders 
Published: March 2020

AbstractRespiratory tract infections require early diagnosis and adequate treatment. With the antibiotic overuse and increment in antibiotic resistance there is an increased need to accurately distinguish between bacterial and viral infections. We investigated the diagnostic performance of calprotectin in respiratory tract infections and compared it with the performance of heparin binding protein (HBP) and procalcitonin (PCT). Biomarkers were analyzed in patients with viral respiratory infections and patients with bacterial pneumonia, mycoplasma pneumonia and streptococcal tonsillitis (n = 135). Results were compared with values obtained from 144 healthy controls. All biomarkers were elevated in bacterial and viral infections compared to healthy controls. Calprotectin was significantly increased in patients with bacterial infections; bacterial pneumonia, mycoplasma pneumonia and streptococcal tonsillitis compared with viral infections. PCT was significantly elevated in patients with bacterial pneumonia compared to viral infections but not in streptococcal tonsillitis or mycoplasma caused infections. HBP was not able to distinguish between bacterial and viral causes of infections. The overall clinical performance of calprotectin in the distinction between bacterial and viral respiratory infections, including mycoplasma was greater than performance of PCT and HBP. Rapid determination of calprotectin may improve the management of respiratory tract infections and allow more precise diagnosis and selective use of antibiotics.
Detection of the in vitro modulation of Plasmodium falciparum Arf1 by Sec7 and ArfGAP domains using a colorimetric plate-based assay
Authors: Swart Tarryn , Khan Farrah D. , Ntlantsana Apelele , Laming Dustin , Veale Clinton G. L. , Przyborski Jude M. , Edkins Adrienne L. , Hoppe Heinrich C. 
Published: March 2020

AbstractThe regulation of human Arf1 GTPase activity by ArfGEFs that stimulate GDP/GTP exchange and ArfGAPs that mediate GTP hydrolysis has attracted attention for the discovery of Arf1 inhibitors as potential anti-cancer agents. The malaria parasite Plasmodium falciparum encodes a Sec7 domain-containing protein - presumably an ArfGEF - and two putative ArfGAPs, as well as an Arf1 homologue (PfArf1) that is essential for blood-stage parasite viability. However, ArfGEF and ArfGAP-mediated activation/deactivation of PfArf1 has not been demonstrated. In this study, we established an in vitro colorimetric microtiter plate-based assay to detect the activation status of truncated human and P. falciparum Arf1 and used it to demonstrate the activation of both proteins by the Sec7 domain of ARNO, their deactivation by the GAP domain of human ArfGAP1 and the inhibition of the respective reactions by the compounds SecinH3 and QS11. In addition, we found that the GAP domains of both P. falciparum ArfGAPs have activities equivalent to that of human ArfGAP1, but are insensitive to QS11. Library screening identified a novel inhibitor which selectively inhibits one of the P. falciparum GAP domains (IC50 4.7 µM), suggesting that the assay format is suitable for screening compound collections for inhibitors of Arf1 regulatory proteins.
Molecular characteristics of the first case of haloxyfop-resistant Poa annua
Authors: Ghanizadeh H. , Mesarich C. H. , Harrington K. C. 
Published: March 2020

AbstractHaloxyfop is one of two acetyl-coenzyme A carboxylase (ACCase) inhibitors that is recommended for controlling Poa annua. We have characterised a population of P. annua that had developed resistance to haloxyfop. This resistant population was found to be almost 20 times less sensitive to haloxyfop than a susceptible population based on percentage survival of individuals in two dose-response experiments. However, the haloxyfop-resistant population was still susceptible to clethodim. Pre-treatment of resistant individuals with a cytochrome P450 inhibitor, malathion, did not change the sensitivity level of the resistant plants to haloxyfop, suggesting that a non-target site mechanism of resistance involving enhanced metabolism, was not responsible for this resistance in P. annua. Gene sequencing showed that a target site mutation at position 2041, which replaced isoleucine with threonine in the carboxyltransferase (CT) domain of the ACCase enzyme, was associated with resistance to haloxyfop in the resistant population. An evaluation of the 3-D structure of the CT domain suggested that, unlike Asn-2041, which is the most common mutation at this position reported to date, Thr-2041 does not change the conformational structure of the CT domain. This is the first study investigating the molecular mechanism involved with haloxyfop resistance in P. annua.
Pathophysiological changes of the lower urinary tract behind voiding dysfunction in streptozotocin-induced long-term diabetic rats
Authors: Masuda Kazuki , Aizawa Naoki , Watanabe Daiji , Okegawa Takatsugu , Kume Haruki , Igawa Yasuhiko , Fukuhara Hiroshi 
Published: March 2020

AbstractWe evaluated pathophysiological characteristics of the lower urinary tract dysfunction in a streptozotocin (STZ)-induced diabetic rat model. STZ (60 mg/kg) was injected intraperitoneally into male Wistar rats. In vitro bladder muscle strip experiments, in vivo cystometry, and simultaneous recordings of bladder pressure + urethral perfusion pressure (BP + UPP) with or without intravenous administration of L-arginine (300 mg/kg) or tadalafil (0.03 mg/kg) were performed at several time points. In vitro muscle strip experiments demonstrated that diabetic rats had significantly higher contractile responses to carbachol at 4–16 weeks, and a tendency for higher contractile responses to electrical field stimulation at 4–12 weeks, but this was reversed at 16 weeks. Diabetic rats had significant increases in voided volume, residual volume, bladder capacity, maximal voiding pressure, and amplitude and frequency of non-voiding contractions at 16 weeks. Tadalafil decreased the residual volume in diabetic rats. Diabetic rats had significantly higher UPP nadir and mean UPP during high-frequency oscillation at 16 weeks, which were reversed by tadalafil or L-arginine administration. The present results suggest that urethral relaxation failure, probably related to impairment of the NO/cGMP signalling pathway, rather than bladder contractile dysfunction may be a prominent cause for voiding dysfunction in STZ-induced chronic diabetic rats.
Biochemical features of the novel Tail Tubular Protein A of Yersinia phage phiYeO3-12
Authors: Pyra Anna , Urbańska Natalia , Filik Karolina , Tyrlik Katherine , Brzozowska Ewa 
Published: March 2020

AbstractTail Tubular Protein A (TTPA) was long thought to be strictly a structural protein of environmental bacteriophages. However, our recent work has suggested that some TTPAs have additional functional features and thus are dual-function proteins. This study introduces a new TTPA family member, TTPAgp11, which belongs to Yersinia phage phiYeO3-12. We cloned the gene, expressed it and then purified the phage protein. The protein, including its hydrolytic activity, was characterized. Our enzymatic activity tests showed that TTPAgp11 displayed hydrolytic activity towards Red-starch, suggesting that this enzyme could be classified as part as the α − 1, 4-glucosidase family. Protein folding and aggregation tests indicated that TTPAgp11 is a single-domain protein whose aggregation can be induced by maltose or N-acetylglucosamine. The spatial structure of TTPAgp11 seemed to resemble that of the first reported dual-function TTPA, TTPAgp31, which was isolated from Klebsiella pneumoniae phage 32.
The position of the target site for engineered nucleases improves the aberrant mRNA clearance in in vivo genome editing
Authors: Lee Jae Hoon , Yu Sungsook , Nam Tae Wook , Roh Jae-il , Jin Young , Han Jeong Pil , Cha Ji-Young , Kim Yoon Ki , Yeom Su-Cheong , Nam Ki Taek , Lee Han-Woong 
Published: March 2020

AbstractEngineered nucleases are widely used for creating frameshift or nonsense mutations in the target genes to eliminate gene functions. The resulting mRNAs carrying premature termination codons can be eliminated by nonsense-mediated mRNA decay. However, it is unclear how effective this process would be in vivo. Here, we found that the nonsense-mediated decay was unable to remove the mutant mRNAs in twelve out of sixteen homozygous mutant mice with frameshift mutations generated using engineered nucleases, which is far beyond what we expected. The frameshift mutant proteins translated by a single nucleotide deletion within the coding region were also detected in the p53 mutant mice. Furthermore, we showed that targeting the exons present downstream of the exons with a start codon or distant from ATG is relatively effective for eliminating mutant mRNAs in vivo, whereas the exons with a start codon are targeted to express the mutant mRNAs. Of the sixteen mutant mice generated, only four mutant mice targeting the downstream exons exhibited over 80% clearance of mutant mRNAs. Since the abnormal products, either mutant RNAs or mutant proteins, expressed by the target alleles might obscure the outcome of genome editing, these findings will provide insights in the improved performance of engineered nucleases when they are applied in vivo.
Cathepsin g Degrades Both Glycosylated and Unglycosylated Regions of Lubricin, a Synovial Mucin
Authors: Huang Shan , Thomsson Kristina A. , Jin Chunsheng , Alweddi Sally , Struglics André , Rolfson Ola , Björkman Lena I. , Kalamajski Sebastian , Schmidt Tannin A. , Jay Gregory D. , Krawetz Roman , Karlsson Niclas G. , Eisler Thomas 
Published: March 2020

AbstractLubricin (PRG4) is a mucin type protein that plays an important role in maintaining normal joint function by providing lubrication and chondroprotection. Improper lubricin modification and degradation has been observed in idiopathic osteoarthritis (OA), while the detailed mechanism still remains unknown. We hypothesized that the protease cathepsin G (CG) may participate in degrading lubricin in synovial fluid (SF). The presence of endogenous CG in SF was confirmed in 16 patients with knee OA. Recombinant human lubricin (rhPRG4) and native lubricin purified from the SF of patients were incubated with exogenous CG and lubricin degradation was monitored using western blot, staining by Coomassie or Periodic Acid-Schiff base in gels, and with proteomics. Full length lubricin (∼300 kDa), was efficiently digested with CG generating a 25-kDa protein fragment, originating from the densely glycosylated mucin domain (∼250 kDa). The 25-kDa fragment was present in the SF from OA patients, and the amount was increased after incubation with CG. A CG digest of rhPRG4 revealed 135 peptides and 72 glycopeptides, and confirmed that the protease could cleave in all domains of lubricin, including the mucin domain. Our results suggest that synovial CG may take part in the degradation of lubricin, which could affect the pathological decrease of the lubrication in degenerative joint disease.
Identification of the key genes and pathways involved in the tumorigenesis and prognosis of kidney renal clear cell carcinoma
Authors: Cui Hao , Shan Hongjian , Miao Michael Zhe , Jiang Zhiguo , Meng Yuanyuan , Chen Ran , Zhang Longzhen , Liu Yong 
Published: March 2020

AbstractKidney renal clear cell carcinoma (KIRC) is the most common renal cell carcinoma (RCC). However, patients with KIRC usually have poor prognosis due to limited biomarkers for early detection and prognosis prediction. In this study, we analysed key genes and pathways involved in KIRC from an array dataset including 26 tumour and 26 adjacent normal tissue samples. Weighted gene co-expression network analysis (WGCNA) was performed with the WGCNA package, and 20 modules were characterized as having the highest correlation with KIRC. The upregulated genes in the tumour samples are involved in the innate immune response, whereas the downregulated genes contribute to the cellular catabolism of glucose, amino acids and fatty acids. Furthermore, the key genes were evaluated through a protein-protein interaction (PPI) network combined with a co-expression network. The comparatively lower expression of AGXT, PTGER3 and SLC12A3 in tumours correlates with worse prognosis in KIRC patients, while higher expression of ALOX5 predicts reduced survival. Our integrated analysis illustrated the hub genes involved in KIRC tumorigenesis, shedding light on the development of prognostic markers. Further understanding of the function of the identified KIRC hub genes could provide deep insights into the molecular mechanisms of KIRC.
A Novel Fluorescent Reporter System Identifies Laminin-511/521 as Potent Regulators of Cardiomyocyte Maturation
Authors: Chanthra Nawin , Abe Tomoyuki , Miyamoto Matthew , Sekiguchi Kiyotoshi , Kwon Chulan , Hanazono Yutaka , Uosaki Hideki 
Published: March 2020

AbstractPluripotent stem cell-derived cardiomyocytes (PSC-CMs) hold great promise for disease modeling and drug discovery. However, PSC-CMs exhibit immature phenotypes in culture, and the lack of maturity limits their broad applications. While physical and functional analyses are generally used to determine the status of cardiomyocyte maturation, they could be time-consuming and often present challenges in comparing maturation-enhancing strategies. Therefore, there is a demand for a method to assess cardiomyocyte maturation rapidly and reproducibly. In this study, we found that Myomesin-2 (Myom2), encoding M-protein, is upregulated postnatally, and based on this, we targeted TagRFP to the Myom2 locus in mouse embryonic stem cells. Myom2-RFP+ PSC-CMs exhibited more mature phenotypes than RFP- cells in morphology, function and transcriptionally, conductive to sarcomere shortening assays. Using this system, we screened extracellular matrices (ECMs) and identified laminin-511/521 as potent enhancers of cardiomyocyte maturation. Together, we developed and characterized a novel fluorescent reporter system for the assessment of cardiomyocyte maturation and identified potent maturation-enhancing ECMs through this simple and rapid assay. This system is expected to facilitate use of PSC-CMs in a variety of scientific and medical investigations.