bluuebunny/crossref_metadata_2025_split huggingface dataset:
PCR under Low Ionic Concentration Buffer Conditions
Authors: Takei Fumie , Akiyama Misaki , Nobusawa Kazuyuki , Sabani Norhayati Binti , Han Huanwen , Nakatani Kazuhiko , Yamashita Ichiro 
Published: January 2018

AbstractA new polymerase chain reaction (PCR) system using a low‐salt concentration buffer was developed, which is suitable for electrical PCR process monitoring. Using Taq polymerase in 10 mM of Tris‐HCl buffer without KCl, the PCR progressed and the target DNA PCR products were produced. As the ionic concentration in PCR buffer solution decreased, the quantity of PCR products decreased, but the PCR products could be detected down to a total ion concentration of 5 mM. Single nucleotide polymorphism typing was also successful under 10 mM of Tris‐HCl without KCl. Both alleles (G or T) were detected clearly.
In vitro to in vivo benchmark dose comparisons to inform risk assessment of quantum dot nanomaterials
Authors: Weldon Brittany A. , Griffith William C. , Workman Tomomi , Scoville David K. , Kavanagh Terrance J. , Faustman Elaine M. 
Published: January 2018

Engineered nanomaterials are currently under review for their potential toxicity; however, their use in consumer/commercial products has continued to outpace risk assessments. In vitro methods may be utilized as tools to improve the efficiency of risk assessment approaches. We propose a framework to compare relationships between previously published in vitro and in vivo toxicity assessments of cadmium‐selenium containing quantum dots (QDs) using benchmark dose (BMD) and dosimetric assessment methods. Although data were limited this approach was useful for identifying sensitive assays and strains. In vitro studies assessed effects of QDs in three pulmonary cell types across two mouse strains. Significant dose–response effects were modeled and a standardized method of BMD analysis was performed as a function of both exposure dose and dosimetric dose. In vivo studies assessed pulmonary effects of QD exposure across eight mouse strains. BMD analysis served as a basis for relative comparison with in vitro studies. We found consistent responses in common endpoints between in vitro and in vivo studies. Strain sensitivity was consistent between in vitro and in vivo studies, showing A/J mice more sensitive to QDs. Cell types were found to differentially take up QDs. Dosimetric adjustments identified similar sensitivity among cell types. Thus, BMD analysis can be used as an effective tool to compare the sensitivity of different strains, cell types, and assays to QDs. These methods allow for in vitro assays to be used to predict in vivo responses, improve the efficiency of in vivo studies, and allow for prioritization of nanomaterial assessments.This article is categorized under:

Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials
Toxicology and Regulatory Issues in Nanomedicine > Regulatory and Policy Issues in Nanomedicine
Hydrothermal Fracture Controlled Vein Type Uranium Mineralization in the Paleoproterozoic Bijawar Group of Rocks, Sonrai Basin, Lalitpur District, U.P. – Fresh Findings from Subsurface Borehole Data
Authors: Rawat T. P. S. , Roy Madhuparna , Joshi G. B. 
Published: January 2018

ABSTRACT
Sonrai basin, located along the southwestern margin of Bundelkhand Granite-Gneiss Complex (BGC) is known for its base metal and phosphorite mineralization. Uranium mineralization of appreciable grade and thickness was reported in Pisnari block in the northern part of this basin during sub-surface exploration activity in 1976-97. This was in the form of uranium-bitumin association within fractures in the carbonate-terrigenous sediments of Gorakalan shale, Rohini carbonate and Bandai sandstone of Sonrai Formation of Bijawar Group. Similar mineralization was also noted within the lower chloritic shale member of Solda Formation of the same Group. During subsequent drilling activity at a later phase (2005-09), uranium rich zones within Rohini carbonate and chloritic shale members were corroborated by the interception of mineralized bands in two boreholes drilled near Pisnari. Petrographic study of radioactive core samples reveal that uranium mineralization is closely associated with globular carbonaceous matter and sulphides along the fractures. Uranium is either adsorbed in carbonaceous matter or occurs as ultrafine inclusions of coffinite within carbonaceous matter. An additional phase of secondary uranium mineral (uranophane) is also noted in one of the boreholes. The uranium minerals, in association with sulphides, fill up moderately dipping fractures (approximately 15° towards North) which are oblique to the core axis of the inclined borehole and thus, the mineralization is characterized as hydrothermal fracture-controlled vein type mineralisation. C-H-N-S analysis of carbonaceous matter occurring in close association with the uranium minerals reveal heterogeneity in composition with respect to carbon and sulfur. The present paper aims at discussing the geological, petrological and radiometric aspects of this mineralization, so as to enhance the understanding of the same.
Application of Multivariate Statistical Techniques for the Characterization of Groundwater Quality of Bacheli and Kirandul Area, Dantewada District, Chattisgarh
Authors: Behera Bhagirathi , Das Mira 
Published: January 2018

ABSTRACT
Either naturally occurring process or human activities may have a significant impact on the quality of sub-surface waters which further limit its use. Multivariate statistical techniques such as factor analysis (FA), cluster analysis (CA) were applied for the evaluation of spatial variations and the interpretation of ground water quality data around Bacheli and Kirandul area. The major anions, cations and heavy metals were determined for each of 20 samples collected in pre-monsoon seasons. Hydrochemical parameters like EC, pH, TDS, TH, TA, Na+, K+, Ca2+, Cl−, F−, SO42−, As, Sb, Se, Pb, Cd, Zn, Cu were estimated in pre monsoon and post monsoon seasons. Different geochemical controls of the investigated parameters were also assessed. Factor 1 explains 33.47% of the total variance and indicates atmospheric controls and silicate mineral weathering process. Factor 2 explains 13.83% of total variance, indicating silicate mineral weathering process resulting in elevated pH. Generally, water types tend towards magnesium-bicarbonate-chloride.
Expression and significance of ASPP2 in squamous carcinoma of esophagus
Authors: Liu Bo , Yang Lv , Li Xiu‐Juan , Li Rou , Sun Wei , Chen Xiao‐Yi , Liu Jun‐Chao 
Published: January 2018

AbstractTo study the significance of apoptosis stimulating protein of P53 2 (ASPP2) expression in esophageal squamous cell carcinoma (ESCC), immunohistochemistry S‐P method was used to examine the expression of ASPP2 in 136 cases of ESCC, 35 cases of high grade intraepithelial neoplasia (HGIN), 29 cases of low grade intraepithelial neoplasia (LGIN) and 37 cases of normal esophageal epithelium (NEE). The associations of ASPP2 expression with clinicopathological data and overall survival (OS) were also analyzed. Quantitative real‐time polymerase chain reaction (qRT‐PCR) was performed to evaluate ASPP2 expression in a total of 20 matched human ESCC tumor tissues and normal adjacent tissues (NAT). In addition, EC109 cells were treated with cisplatin (CDDP) in vitro for 24 h (the intervention group) and the control group was set up at the same time. Western blot was used to examine the expression of ASPP2 protein between the two groups. The expression of ASPP2 decreased progressively from NEE to LGIN, to HGIN, and to ESCC, and it was related to TNM stage, histological differentiation and lymph node metastasis in ESCC (P < 0.05). ASPP2 was a protective factor of patients with ESCC (P = 0.008). The relative expression of ASPP2 mRNA was markedly downregulated in ESCC compared with the paired NAT (P < 0.01). Western blot results showed that cells in the intervention group could express ASPP2 while there was no expression of ASPP2 in the control group. Taken together, these results indicate that the abnormal expression of ASPP2 may play an important role for development and metastasis in ESCC.
Eldonioids with associated trace fossils from the lower Cambrian Emu Bay Shale Konservat-Lagerstätte of South Australia
Authors: Schroeder Natalie I. , Paterson John R. , Brock Glenn A. 
Published: January 2018

AbstractRare specimens of eldonioids recovered from the lower Cambrian (Series 2, Stage 4) Emu Bay Shale (EBS) Konservat-Lagerstätte represent the first record of the group for the Cambrian of East Gondwana. The disc-shaped body of the EBS taxon bears fine concentric corrugations on the dorsal surface and, ventrally, a series of internal lobes that have primary and secondary bifurcations, as well as a coiled sac. It appears to be most similar toRotadiscusandPararotadiscusof the Cambrian Chengjiang and Kaili biotas of South China, respectively. While the structure of the internal lobes would indicate that this occurrence in the EBS represents a new taxon within the Rotadiscidae, lack of detail regarding the precise number of internal lobes and the condition of the circumoral tentacles warrants a more conservative approach in leaving the genus and species under open nomenclature. The EBS specimens also host trace fossils, including the remains of a burrow, which are generally lacking in the body-fossil-bearing layers of the Konservat-Lagerstätte interval. These traces appear to have been made by small organisms and are similar to traces associated with the discs ofPararotadiscus guizhouensis(Zhao and Zhu, 1994) from the Kaili Biota. The available taphonomic, paleoenvironmental, and ichnological evidence indicates that the EBS eldonioids are most likely vagrants that were transported or settled into the ‘preservational trap’ and subsequently exposed on the substrate for a brief period before burial, thereby allowing organisms to exploit their carcasses for nutrients or other purposes.
Getting Along or Going Alone: Understanding Collaboration Between Local Governments and NGOs in Bolivia
Authors: Nelson-Nuñez Jami , Cartwright Kate 
Published: January 2018

AbstractWhat explains mayors’ collaboration with nongovernmental organizations in delivering public goods and services? While some successful collaborations are established, in other cases the call for NGOs to coordinate with governments goes unheeded. Collaboration minimizes the duplication of effort, maximizes information sharing, and builds capacity. Given the scholarly consensus on the importance of collaboration, we know little about it at local levels, where it may matter most. This article focuses on Bolivia, a country with deep decentralization reforms and an active NGO sector. It utilizes survey data on mayors from 2007 to provide insight into the variation in NGO–local government collaboration across a country. It argues that political context is important: mayoral turnover, greater community group engagement, and more municipal resources deter collaboration. The findings illustrate the strategic interplay between state and nonstate actors and explain the uneven geographies of partnerships in governance.
Igf1 and Pacap rescue cerebellar granule neurons from apoptosis via a common transcriptional program
Authors: Maino B , D’Agata V , Severini C , Ciotti MT , Calissano P , Copani A , Chang Y-C , DeLisi C , Cavallaro S 
Published: January 2018

AbstractA shift of the delicate balance between apoptosis and survival-inducing signals determines the fate of neurons during the development of the central nervous system and its homeostasis throughout adulthood. Both pathways, promoting or protecting from apoptosis, trigger a transcriptional program. We conducted whole-genome expression profiling to decipher the transcriptional regulatory elements controlling the apoptotic/survival switch in cerebellar granule neurons following the induction of apoptosis by serum and potassium deprivation or their rescue by either insulin-like growth factor-1 (Igf1) or pituitary adenylyl cyclase-activating polypeptide (Pacap). Although depending on different upstream signaling pathways, the survival effects of Igf1 and Pacap converged into common transcriptional cascades, thus suggesting the existence of a general transcriptional program underlying neuronal survival.
Shifting priorities: highly conserved behavioral and brain network adaptations to chronic stress across species
Authors: Nikolova Yuliya S. , Misquitta Keith A. , Rocco Brad R. , Prevot Thomas D. , Knodt Annchen R. , Ellegood Jacob , Voineskos Aristotle N. , Lerch Jason P. , Hariri Ahmad R. , Sibille Etienne , Banasr Mounira 
Published: January 2018

AbstractParallel clinical and preclinical research have begun to illuminate the biological basis of stress-related disorders, including major depression, but translational bridges informing discrete mechanistic targets for intervention are missing. To address this critical need, we used structural MRI in a mouse model and in a large human sample to examine stress effects on brain structure that may be conserved across species. Specifically, we focused on a previously unexplored approach, whole-brain structural covariance, as it reflects synchronized changes in neuroanatomy, potentially due to mutual trophic influences or shared plasticity across regions. Using the unpredictable chronic mild stress (UCMS) paradigm in mouse we first demonstrate that UCMS-induced elevated behavioral emotionality correlates with increased size of the amygdala and other corticolimbic regions. We further identify focal increases in the amygdala’s ‘hubness’ (degree and strength) set against the background of a global stress-related loss of network clustering and modularity. These macroscopic changes are supported on the molecular level by increased postsynaptic density-95 protein in the amygdala, consistent with stress-induced plastic changes and synaptic strengthening. Finally, we provide clinical evidence that strikingly similar structural network reorganization patterns exist in young adults reporting high childhood trauma and increased mood symptoms. Collectively, we provide initial translational evidence for a conserved stress-related increase in amygdala-centered structural synchrony, as measured by enhanced structural covariance, which is paralleled by a decrease in global structural synchrony. This putative trade-off reflected in increased amygdala-centered plastic changes at the expense of global structural dedifferentiation may represent a mechanistic pathway for depression and related psychopathology.
Insight into the role of PIKK family members and NF-кB in DNAdamage-induced senescence and senescence-associated secretory phenotype of colon cancer cells
Authors: Strzeszewska Anna , Alster Olga , Mosieniak Grażyna , Ciolko Agata , Sikora Ewa 
Published: January 2018

AbstractSenescence of cancer cells is an important outcome of treatment of many cancer types. Cell senescence is a permanent cell cycle arrest induced by stress conditions, including DNA damage. DNA damage activates DNA damage response (DDR), which involves members of the phosphatidylinositol 3-kinase-related kinase (PIKK) superfamily: protein kinases ATM, ATR, and DNA-PKcs. The so-far collected data indicate that ATM, with its downstream targets CHK2, p53, and p21, is the key protein involved in DDR-dependent senescence. It was also documented that the so-called senescence-associated secretory phenotype-SASP relies on ATM/CHK2, and not on p53 signaling. Moreover, genotoxic agents used in cancer treatment can activate NF-κB, which also induces transcription of SASP genes. In this paper, we have studied the involvement of three PIKK family members in colon cancer cell senescence and connection between DNA-damage-induced senescence and NF-κB-regulated SASP in p53-proficient and p53-deficient colon cancer cells treated with doxorubicin. We showed that doxorubicin induced cell senescence in both p53+/+ and p53−/− HCT116 cells, proving that this process is p53-independent. Senescence was successfully abrogated by a PIKK inhibitor, caffeine, or by simultaneous silencing of three PIKKs by specific siRNAs. By silencing individual members of PIKK family and analyzing common markers of senescence, the level of p21 and SA-β-Gal activity, we came to the conclusion that ATR kinase is crucial for the onset of senescence as, in contrast to ATM and DNA-PKsc, it could not be fully substituted by other PIKKs. Moreover, we showed that in case of silencing the three PIKKs, there was no SASP reduction accompanying the decrease in the level of p21 and SA-β-Gal (Senescence-Associated-β-Galactosidase) activity; whereas knocking down the NF-κB component, p65, abrogated SASP, but did not affect other markers of senescence, proving that DNA damage regulated senescence independently and NF-κB evoked SASP.
Molecular and physiological roles of the adaptor protein CARD9 in immunity
Authors: Zhong Xiaoming , Chen Bin , Yang Liang , Yang Zhiwen 
Published: January 2018

AbstractCARD9 is a caspase recruitment domain-containing signaling protein that plays a critical role in innate and adaptive immunity. It has been widely demonstrated that CARD9 adaptor allows pattern recognition receptors to induce NF-κB and MAPK activation, which initiates a “downstream” inflammation cytokine cascade and provides effective protection against microbial invasion, especially fungal infection. Here our aim is to update existing paradigms and summarize the most recent findings on the CARD9 signaling pathway, revealing significant mechanistic insights into the pathogenesis of CARD9 deficiency. We also discuss the effect of CARD9 genetic mutations on the in vivo immune response, and highlight clinical advances in non-infection inflammation.
Sirt6 overexpression suppresses senescence and apoptosis of nucleus pulposus cells by inducing autophagy in a model of intervertebral disc degeneration
Authors: Chen Jian , Xie Jun-Jun , Jin Meng-Yun , Gu Yun-Tao , Wu Cong-Cong , Guo Wei-Jun , Yan Ying-Zhao , Zhang Zeng-Jie , Wang Jian-Le , Zhang Xiao-Lei , Lin Yan , Sun Jia-Li , Zhu Guang-Hui , Wang Xiang-Yang , Wu Yao-Sen 
Published: January 2018

AbstractTreatment of intervertebral disc degeneration (IDD) seeks to prevent senescence and death of nucleus pulposus (NP) cells. Previous studies have shown that sirt6 exerts potent anti-senescent and anti-apoptotic effects in models of age-related degenerative disease. However, it is not known whether sirt6 protects against IDD. Here, we explored whether sirt6 influenced IDD. The sirt6 level was reduced in senescent human NP cells. Sirt6 overexpression protected against apoptosis and both replicative and stress-induced premature senescence. Sirt6 also activated NP cell autophagy both in vivo and in vitro. 3-methyladenine (3-MA) and chloroquine (CQ)-mediated inhibition of autophagy partially reversed the anti-senescent and anti-apoptotic effects of sirt6, which regulated the expression of degeneration-associated proteins. In vivo, sirt6 overexpression attenuated IDD. Together, the data showed that sirt6 attenuated cell senescence, and reduced apoptosis, by triggering autophagy that ultimately ameliorated IDD. Thus, sirt6 may be a novel therapeutic target for IDD treatment.
2,5-Hexanedione induces dopaminergic neurodegeneration through integrin αMβ2/NADPH oxidase axis-mediated microglial activation
Authors: Zhang Cong , Hou Liyan , Yang Jie , Che Yuning , Sun Fuqiang , Li Huihua , Wang Qingshan 
Published: January 2018

AbstractRecent study demonstrated that chronic exposure to solvents increases the risk of Parkinson’s disease (PD), the second most common neurodegenerative disorder characterized by progressive dopaminergic neurodegeneration in the substantia nigra (SN). n-Hexane, a widely used organic solvent, displays central-peripheral neurotoxicity, which is mainly mediated by its active metabolite, 2,5-hexanedione (HD). However, whether HD exposure contributes to PD remains unclear. In this study, we found that rats exposed to HD displayed progressive dopaminergic neurodegeneration in the nigrostriatal system. Microglial activation was also detected in HD-treated rats, which occurred prior to degeneration of dopaminergic neurons. Moreover, depletion of microglia markedly reduced HD-induced dopaminergic neurotoxicity. Mechanistic study revealed an essential role of microglial integrin αMβ2-NADPH oxidase (NOX2) axis in HD-elicited neurotoxicity. HD activated NOX2 by inducing membrane translocation of NOX2 cytosolic subunit, p47phox. Integrin αMβ2 was critical for HD-induced NOX2 activation since inhibition or genetic deletion of αMβ2 attenuated NOX2-generated superoxide and p47phox membrane translocation in response to HD. Src and Erk, two downstream signals of αMβ2, were recognized to bridge HD/αMβ2-mediated NOX2 activation. Finally, pharmacological inhibition of αMβ2-NOX2 axis attenuated HD-induced microglial activation and dopaminergic neurodegeneration. Our findings revealed that HD exposure damaged nigrostriatal dopaminergic system through αMβ2-NOX2 axis-mediated microglial activation, providing, for the first time, experimental evidence for n-hexane exposure contributing to the etiology of PD.
Loss of ASXL1 in the bone marrow niche dysregulates hematopoietic stem and progenitor cell fates
Authors: Zhang Peng , Chen Zizhen , Li Rong , Guo Ying , Shi Hui , Bai Jie , Yang Hui , Sheng Mengyao , Li Zhaomin , Li Zhuo , Li Jianping , Chen Shi , Yuan Weiping , Cheng Tao , Xu Mingjiang , Zhou Yuan , Yang Feng-Chun 
Published: January 2018

AbstractSomatic or de novo mutations of Additional sex combs-like 1 (ASXL1) frequently occur in patients with myeloid malignancies or Bohring-Opitz syndrome, respectively. We have reported that global loss of Asxl1 leads to the development of myeloid malignancies and impairs bone marrow stromal cell (BMSC) fates in mice. However, the impact of Asxl1 deletion in the BM niche on hematopoiesis remains unclear. Here, we showed that BMSCs derived from chronic myelomonocytic leukemia patients had reduced expression of ASXL1, which impaired the maintaining cord blood CD34+ cell colony-forming capacity with a myeloid differentiation bias. Furthermore, Asxl1 deletion in the mouse BMSCs altered hematopoietic stem and progenitor cell (HSC/HPC) pool and a preferential myeloid lineage increment. Immunoprecipitation and ChIP-seq analyses demonstrated a novel interaction of ASXL1 with the core subunits of RNA polymerase II (RNAPII) complex. Convergent analyses of RNA-seq and ChIP-seq data revealed that loss of Asxl1 deregulated RNAPII transcriptional function and altered the expression of genes critical for HSC/HPC maintenance, such as Vcam1. Altogether, our study provides a mechanistic insight into the function of ASXL1 in the niche to maintain normal hematopoiesis; and ASXL1 alteration in, at least, a subset of the niche cells induces myeloid differentiation bias, thus, contributes the progression of myeloid malignancies.
Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli
Authors: Bohl Heather O. , Shi Ke , Lee John K. , Aihara Hideki 
Published: January 2018

AbstractMost Gram-negative bacteria are surrounded by a glycolipid called lipopolysaccharide (LPS), which forms a barrier to hydrophobic toxins and, in pathogenic bacteria, is a virulence factor. During LPS biosynthesis, a membrane-associated glycosyltransferase (LpxB) forms a tetra-acylated disaccharide that is further acylated to form the membrane anchor moiety of LPS. Here we solve the structure of a soluble and catalytically competent LpxB by X-ray crystallography. The structure reveals that LpxB has a glycosyltransferase-B family fold but with a highly intertwined, C-terminally swapped dimer comprising four domains. We identify key catalytic residues with a product, UDP, bound in the active site, as well as clusters of hydrophobic residues that likely mediate productive membrane association or capture of lipidic substrates. These studies provide the basis for rational design of antibiotics targeting a crucial step in LPS biosynthesis.