bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and characterization of pineapple leaf lncRNAs in crassulacean acid metabolism (CAM) photosynthesis pathway
Authors: Bai Youhuang , Dai Xiaozhuan , Li Yi , Wang Lulu , Li Weimin , Liu Yanhui , Cheng Yan , Qin Yuan 
Published: April 2019

AbstractLong noncoding RNAs (lncRNAs) have been identified in many mammals and plants and are known to play crucial roles in multiple biological processes. Pineapple is an important tropical fruit and a good model for studying the plant evolutionary adaptation to the dry environment and the crassulacean acid metabolism (CAM) photosynthesis strategy; however, the lncRNAs involved in CAM pathway remain poorly characterized. Here, we analyzed the available RNA-seq data sets derived from 26 pineapple leaf samples at 13 time points and identified 2,888 leaf lncRNAs, including 2,046 long intergenic noncoding RNAs (lincRNAs) and 842 long noncoding natural antisense transcripts (lncNATs). Pineapple leaf lncRNAs are expressed in a highly tissue-specific manner. Co-expression analysis of leaf lncRNA and mRNA revealed that leaf lncRNAs are preferentially associated with photosynthesis genes. We further identified leaf lncRNAs that potentially function as competing endogenous RNAs (ceRNAs) of two CAM photosynthesis pathway genes, PPCK and PEPC, and revealed their diurnal expression pattern in leaves. Moreover, we found that 48% of lncRNAs exhibit diurnal expression patterns in leaves, suggesting their important roles in CAM. This study conducted a comprehensive genome-wide analysis of leaf lncRNAs and identified their role in gene expression regulation of the CAM photosynthesis pathway in pineapple.
DNAH11 variants and its association with congenital heart disease and heterotaxy syndrome
Authors: Liu Sida , Chen Weicheng , Zhan Yongkun , Li Shuolin , Ma Xiaojing , Ma Duan , Sheng Wei , Huang Guoying 
Published: April 2019

AbstractCongenital heart diseases (CHDs) are the most common types of birth defects, affecting approximately 1% of live births and remaining the leading cause of mortality. CHD patients often show a higher incidence of heterotaxy syndrome. However, the exact aetiology of CHD and heterotaxy syndrome remains unclear. In this study, targeted sequencing and Sanger sequencing were performed to analyze the exonic regions of 37 primary ciliary dysfunction (PCD)- related candidate genes in 42 CHD patients with heterotaxy syndrome. Variants affecting protein-coding regions were filtered according to databases of known variants and predicted in silico using functional prediction program. Thirty-four potential disease-causing heterozygous variants in 11 genes were identified in the 19 CHD patients with heterotaxy syndrome (45.2%, 19/42). The DNAH11 gene showed the highest mutation rate (16.7%; 14 of 84 alleles) among the CHD patients with heterotaxy. Fisher’s exact test revealed a significant association of DNAH11 variants with CHD and heterotaxy (P = 0.0001). In families, six different compound heterozygous variants of DNAH11 were validated in family 1-5031 (p.W802X/p.M282I), family 2-5045 (p.T3460K/p.G4425S), family 3-5065 (p.G447R/p.L1157R), family 4-5130 (p.I2262T/p.D3800H), family 5-5707 (p.S1823fs/p.F2759L/p.R4395X) and family 6-5062 (p.D3610V/p.I243V). These findings suggest that the DNAH11 variants are significantly associated with CHD and heterotaxy syndrome and that compound heterozygous DNAH11 variants may be the common genetic cause of the development of familial CHD and heterotaxy syndrome.
UPF1 inhibits the hepatocellular carcinoma progression by targeting long non-coding RNA UCA1
Authors: Zhou Yongli , Li Yandong , Wang Na , Li Xiuying , Zheng Jianyun , Ge Liqiao 
Published: April 2019

AbstractHepatocellular carcinoma (HCC) is one of the major causes of cancer-related death worldwide. However, the molecular mechanism underlying HCC carcinogenesis remains to be further elucidated. Up-frameshift protein 1 (UPF1) is a RNA/DNA-dependent ATPase and ATP-dependent RNA helicase. Here, we explored the expression and function of UPF1 in HCC. In this study, we demonstrated that UPF1 expression was significantly reduced in hepatocellular carcinoma (HCC) tissues compared with the adjacent normal tissues. And further functional assays revealed that knockdown of UPF1 promoted HCC cells growth and invasion. Furthermore, we found that UPF1 could bind to long non-coding RNA urothelial cancer associated 1 (UCA1) and was negatively correlated with UCA1. UCA1 expression also affected HCC growth and invasion. Knockdown of UCA1 ameliorated the effect of UPF1 knock down on HCC growth and invasion. Knockdown of UPF1 enhances glycolysis in HCC. Taken together, our results provided new insights for finding novel therapeutic targets for hepatocellular carcinoma progression.
Besnoitia besnoiti infection alters both endogenous cholesterol de novo synthesis and exogenous LDL uptake in host endothelial cells
Authors: Silva Liliana M. R. , Lütjohann Dieter , Hamid Penny , Velasquez Zahady D. , Kerner Katharina , Larrazabal Camilo , Failing Klaus , Hermosilla Carlos , Taubert Anja 
Published: April 2019

AbstractBesnoitia besnoiti, an apicomplexan parasite of cattle being considered as emergent in Europe, replicates fast in host endothelial cells during acute infection and is in considerable need for energy, lipids and other building blocks for offspring formation. Apicomplexa are generally considered as defective in cholesterol synthesis and have to scavenge cholesterol from their host cells for successful replication. Therefore, we here analysed the influence of B. besnoiti on host cellular endogenous cholesterol synthesis and on sterol uptake from exogenous sources. GC-MS-based profiling of cholesterol-related sterols revealed enhanced cholesterol synthesis rates in B. besnoiti-infected cells. Accordingly, lovastatin and zaragozic acid treatments diminished tachyzoite production. Moreover, increased lipid droplet contents and enhanced cholesterol esterification was detected and inhibition of the latter significantly blocked parasite proliferation. Furthermore, artificial increase of host cellular lipid droplet disposability boosted parasite proliferation. Interestingly, lectin-like oxidized low density lipoprotein receptor 1 expression was upregulated in infected endothelial hostcells, whilst low density lipoproteins (LDL) receptor was not affected by parasite infection. However, exogenous supplementations with non-modified and acetylated LDL both boosted B. besnoiti proliferation. Overall, current data show that B. besnoiti simultaneously exploits both, endogenous cholesterol biosynthesis and cholesterol uptake from exogenous sources, during asexual replication.
An Integrated Chemical Proteomics Approach for Quantitative Profiling of Intracellular ADP-Ribosylation
Authors: Kalesh Karunakaran , Lukauskas Saulius , Borg Aaron J. , Snijders Ambrosius P. , Ayyappan Vinay , Leung Anthony K. L. , Haskard Dorian O. , DiMaggio Peter A. 
Published: April 2019

AbstractADP-ribosylation is integral to a diverse range of cellular processes such as DNA repair, chromatin regulation and RNA processing. However, proteome-wide investigation of its cellular functions has been limited due to numerous technical challenges including the complexity of the poly(ADP-ribose) (PAR) chains, low abundance of the modification and lack of sensitive enrichment methods. We herein show that an adenosine analogue with a terminal alkyne functionality at position 2 of the adenine (2-alkyne adenosine or 2YnAd) is suitable for selective enrichment, fluorescence detection and mass spectrometry proteomics analysis of the candidate ADP-ribosylome in mammalian cells. Although similar labelling profiles were observed via fluorescence imaging for 2YnAd and 6YnAd, a previously reported clickable NAD+ precursor, quantitative mass spectrometry analysis of the two probes in MDA-MB-231 breast cancer cells revealed a significant increase in protein coverage of the 2YnAd probe. To facilitate global enrichment of ADP-ribosylated proteins, we developed a dual metabolic labelling approach that involves simultaneous treatment of live cells with both 2YnAd and 6YnAd. By combining this dual metabolic labelling strategy with highly sensitive tandem mass tag (TMT) isobaric mass spectrometry and hierarchical Bayesian analysis, we have quantified the responses of thousands of endogenous proteins to clinical PARP inhibitors Olaparib and Rucaparib.
Temperature-dependent increase in the calcium sensitivity and acceleration of activation of ANO6 chloride channel variants
Authors: Lin Haiyue , Jun Ikhyun , Woo Joo Han , Lee Min Goo , Kim Sung Joon , Nam Joo Hyun 
Published: April 2019

AbstractAnoctamin-6 (ANO6) belongs to a family of calcium (Ca2+)-activated chloride channels (CaCCs), with three splicing variants (V1, V2, and V5) showing plasma membrane expression. Unlike other CaCCs, ANO6 requires a non-physiological intracellular free calcium concentration ([Ca2+]i > 1 μM) and several minutes for full activation under a whole-cell patch clamp. Therefore, its physiological role as an ion channel is uncertain and it is more commonly considered a Ca2+-dependent phospholipid scramblase. Here, we demonstrate that physiological temperature (37 °C) increases ANO6 Ca2+ sensitivity under a whole-cell patch clamp; V1 was activated by 1 μM [Ca2+]i, whereas V2 and V5 were activated by 300 nM [Ca2+]i. Increasing the temperature to 42 °C led to activation of all ANO6 variants by 100 nM [Ca2+]i. The delay time for activation of the three variants was significantly shortened at 37 °C. Notably, the temperature-dependent Ca2+-sensitisation of ANO6 became insignificant under inside-out patch clamp, suggesting critical roles of unknown cytosolic factors. Unlike channel activity, 27 °C but not 37 °C (physiological temperature) induced the scramblase activity of ANO6 at submicromolar [Ca2+]i (300 nM), irrespective of variant type. Our results reveal a physiological ion conducting property of ANO6 at 37 °C and suggest that ANO6 channel function acts separately from its scramblase activity.
Competitive non-SELEX for the selective and rapid enrichment of DNA aptamers and its use in electrochemical aptasensor
Authors: Kushwaha Ankita , Takamura Yuzuru , Nishigaki Koichi , Biyani Manish 
Published: April 2019

AbstractThe SELEX (Systematic Evolution of Ligands by EXponential enrichment) method has been used successfully since 1990, but work is still required to obtain highly specific aptamers. Here, we present a novel approach called ‘Competitive non-SELEX’ (and termed as ‘SELCOS’ (Systematic Evolution of Ligands by COmpetitive Selection)) for readily obtaining aptamers that can discriminate between highly similar targets. This approach is based on the theoretical background presented here, in which under the co-presence of two similar targets, a specific binding type can be enriched more than a nonspecifically binding one during repetitive steps of partitioning with no PCR amplification between them. This principle was experimentally confirmed by the selection experiment for influenza virus subtype-specific DNA aptamers. Namely, the selection products (pools of DNA aptamers) obtained by SELCOS were subjected to a DEPSOR-mode electrochemical sensor, enabling the method to select subtype-specific aptamer pools. From the clonal analysis of these pools, only a few rounds of in vitro selection were sufficient to achieve the surprisingly rapid enrichment of a small number of aptamers with high selectivity, which could be attributed to the SELCOS principle and the given selection pressure program. The subtype-specific aptamers obtained in this manner had a high affinity (e.g., KD = 82 pM for H1N1; 88 pM for H3N2) and negligible cross-reactivity. By making the H1N1-specific DNA aptamer a sensor unit of the DEPSOR electrochemical detector, an influenza virus subtype-specific and portable detector was readily constructed, indicating how close it is to the field application goal.
Efficacy of vector control tools against malaria-infected mosquitoes
Authors: Mulatier Margaux , Camara Soromane , Koffi Alphonsine , Carrasco David , Porciani Angélique , Chandre Fabrice , Moiroux Nicolas , Lefevre Thierry , Dabiré Roch , Assi Serge , Ahoua Alou Ludovic Phamien , Dormont Laurent , Pennetier Cédric , Cohuet Anna 
Published: April 2019

AbstractWithin mosquito vector populations, infectious mosquitoes are the ones completing the transmission of pathogens to susceptible hosts and they are, consequently, of great epidemiological interest. Mosquito infection by malaria parasites has been shown to affect several traits of mosquito physiology and behavior, and could interplay with the efficacy of control tools. In this study, we evaluated, in pyrethroid resistant Anopheles gambiae, the effect of mosquito infection with the human malaria parasite Plasmodium falciparum on the efficacy of nets treated with either the insecticide deltamethrin or the repellent DEET, measuring (i) mosquito success to pass through the net, (ii) blood-feeding on a host and (iii) chemicals-induced mortality. Infection of mosquitoes at non-infectious stage did not affect their success to pass through the net, to blood-feed, nor chemicals-induced mortality. At infectious stage, depending on replicates, infected mosquitoes had higher mortality rates than uninfected mosquitoes, with stronger effect in presence of DEET. This data evidenced a cost of infection on mosquito survival at transmissible stages of infection, which could have significant consequences for both malaria epidemiology and vector control. This stresses the need for understanding the combined effects of insecticide resistance and infection on the efficacy on control tools.
Western corn rootworm pyrethroid resistance confirmed by aerial application simulations of commercial insecticides
Authors: Souza Dariane , Vieira Bruno C. , Fritz Bradley K. , Hoffmann Wesley C. , Peterson Julie A. , Kruger Greg R. , Meinke Lance J. 
Published: April 2019

AbstractThe western corn rootworm (Diabrotica virgifera virgifera LeConte) (WCR) is a major insect pest of corn (Zea mays L.) in the United States (US) and is highly adaptable to multiple management tactics. A low level of WCR field-evolved resistance to pyrethroid insecticides has been confirmed in the US western Corn Belt by laboratory dose-response bioassays. Further investigation has identified detoxification enzymes as a potential part of the WCR resistance mechanism, which could affect the performance of insecticides that are structurally related to pyrethroids, such as organophosphates. Thus, the responses of pyrethroid-resistant and -susceptible WCR populations to the commonly used pyrethroid bifenthrin and organophosphate dimethoate were compared in active ingredient bioassays. Results revealed a relatively low level of WCR resistance to both active ingredients. Therefore, a simulated aerial application bioassay technique was developed to evaluate how the estimated resistance levels would affect performance of registered rates of formulated products. The simulated aerial application technique confirmed pyrethroid resistance to formulated rates of bifenthrin whereas formulated dimethoate provided optimal control. Results suggest that the relationship between levels of resistance observed in dose-response bioassays and actual efficacy of formulated product needs to be further explored to understand the practical implications of resistance.
Heterogeneous Nuclear Ribonucleoprotein F Mediates Insulin Inhibition of Bcl2-Modifying Factor Expression and Tubulopathy in Diabetic Kidney
Authors: Ghosh Anindya , Zhao Shuiling , Lo Chao-Sheng , Maachi Hasna , Chenier Isabelle , Lateef Muhammad Abdul , Abdo Shaaban , Filep Janos G. , Ingelfinger Julie R. , Zhang Shao-Ling , Chan John S. D. 
Published: April 2019

AbstractWe investigated the molecular mechanism(s) by which insulin prevents Bcl2-modifying factor (Bmf)-induced renal proximal tubular cell (RPTC) apoptosis and loss in diabetic mice. Transgenic mice (Tg) mice specifically overexpressing human BMF in RPTCs and non-Tg littermates were studied at 10 to 20 weeks of age. Non-diabetic littermates, diabetic Akita mice +/− insulin implant, Akita Tg mice specifically overexpressing heterogeneous nuclear ribonucleoprotein F (hnRNP F) in their RPTCs and immortalized rat renal proximal tubular cells (IRPTCs) were also studied. BMF-Tg mice exhibited higher systolic blood pressure, urinary albumin/creatinine ratio, RPTC apoptosis and urinary RPTCs than non-Tg mice. Insulin treatment in Akita mice and Akita mice overexpressing hnRNP F suppressed Bmf expression and RPTC apoptosis. In hyperinsulinemic-euglycemic wild type mice, renal Bmf expression was down-regulated with up-regulation of hnRNP F. In vitro, insulin inhibited high glucose-stimulation of Bmf expression, predominantly via p44/42 mitogen-activated protein kinase (MAPK) signaling. Transfection of p44/42 MAPK or hnRNP F small interfering RNA (siRNA) prevented insulin inhibition of Bmf expression. HnRNP F inhibited Bmf transcription via hnRNP F-responsive element in the Bmf promoter. Our results demonstrate that hnRNP F suppression of Bmf transcription is an important mechanism by which insulin protects RPTCs from apoptosis in diabetes.
HMGB1 promotes hair growth via the modulation of prostaglandin metabolism
Authors: Hwang Ji-Hye , Chu Howard , Ahn Yuri , Kim Jino , Kim Do-Young 
Published: April 2019

AbstractUnexpected hair growth can occur after tissue injury. The pathogenic mechanism for this phenomenon is unknown but is likely related to inflammatory mediators. One such mediator is high-mobility group box 1 (HMGB1), a ubiquitous nuclear protein that is released from cell nuclei after tissue damage. To elucidate the effect of HMGB1 on hair growth and understand its mechanism of action, we evaluated the effect of HMGB1 treatment on hair shaft elongation and on mRNA and protein expression in cultured human dermal papilla cells (hDPCs). HMGB1 enhanced hair shaft elongation in an ex vivo hair organ culture. In hDPCs, HMGB1 treatment significantly increased mRNA and protein expression levels of prostagladin E synthases. HMGB1 also stimulated prostaglandin E2 (PGE2) secretion from hDPCs. Finally, blocking the receptor for advanced glycation end-products, a canonical HMGB1 receptor, inhibited HMGB1-induced PGE2 production and hair shaft elongation. Our results suggest that HMGB1 promotes hair growth via PGE2 secretion from hDPCs. This mechanism can explain the paradoxical phenomenon of trauma-induced hair growth. Thus, HGMB1 can be a viable therapeutic target for the treatment of alopecia.
Targeting GPER1 to suppress autophagy as a male-specific therapeutic strategy for iron-induced striatal injury
Authors: Chen Tzu-Yun , Lin Chih-Lung , Wang Li-Fang , Tsai Ke-Li , Lin Jun-Yu , Hsu Chin 
Published: April 2019

AbstractThe functional outcome of intracerebral hemorrhage (ICH) in young male patients are poor than in premenopausal women. After ICH, ferrous iron accumulation causes a higher level of oxidative injury associated with autophagic cell death in striatum of male mice than in females. In rodent model of ferrous citrate (FC)-infusion that simulates iron accumulation after ICH, female endogenous estradiol (E2) suppresses autophagy via estrogen receptor α (ERα) and contributes to less injury severity. Moreover, E2 implantation diminished the FC-induced autophagic cell death and injury in males, whose ERα in the striatum is less than females. Since, no sex difference of ERβ was observed in striatum, we delineated whether ERα and G-protein-coupled estrogen receptor 1 (GPER1) mediate the suppressions of FC-induced autophagy and oxidative injury by E2 in a sex-dimorphic manner. The results showed that the ratio of constitutive GPER1 to ERα in striatum is higher in males than in females. The GPER1 and ERα predominantly mediated suppressive effects of E2 on FC-induced autophagy in males and antioxidant effect of E2 in females, respectively. This finding opens the prospect of a male-specific therapeutic strategy targeting GPER1 for autophagy suppression in patients suffering from iron overload after hemorrhage.
Testing relationship recognition in wild jackdaws (Corvus monedula)
Authors: Lee Victoria E. , McIvor Guillam E. , Thornton Alex 
Published: April 2019

AbstractAccording to the social intelligence hypothesis, understanding the challenges faced by social animals is key to understanding the evolution of cognition. In structured social groups, recognising the relationships of others is often important for predicting the outcomes of interactions. Third-party relationship recognition has been widely investigated in primates, but studies of other species are limited. Furthermore, few studies test for third-party relationship recognition in the wild, where cognitive abilities are deployed in response to natural socio-ecological pressures. Here, we used playback experiments to investigate whether wild jackdaws (Corvus monedula)track changes in their own relationships and the relationships of others. Females were presented with ‘infidelity simulations’: playbacks of their male partner copulating with a neighbouring female, and their male neighbour copulating with another female, against a congruent control. Our results showed substantial inter-individual variation in responses, but females did not respond more strongly to infidelity playbacks, indicating that jackdaws may not attend and/or respond to relationship information in this experimental context. Our results highlight the need for further study of relationship recognition and other cognitive traits that facilitate group-living in the wild, particularly in non-primates and in a wider range of social systems.
Transcriptomic profiling identifies novel mechanisms of transcriptional regulation of the cytochrome P450 (Cyp)3a11 gene
Authors: Taneja Guncha , Maity Suman , Jiang Weiwu , Moorthy Bhagavatula , Coarfa Cristian , Ghose Romi 
Published: April 2019

AbstractCytochrome P450 (CYP)3A is the most abundant CYP enzyme in the human liver, and a functional impairment of this enzyme leads to unanticipated adverse reactions and therapeutic failures; these reactions result in the early termination of drug development or the withdrawal of drugs from the market. The transcriptional regulation mechanism of the Cyp3a gene is not fully understood and requires a thorough investigation. We mapped the transcriptome of the Cyp3a gene in a mouse model. The Cyp3a gene was induced using the mPXR activator pregnenolone-16alpha-carbonitrile (PCN) and was subsequently downregulated using lipopolysaccharide (LPS). Our objective was to identify the transcription factors (TFs), epigenetic modulators and molecular pathways that are enriched or repressed by PCN and LPS based on a gene set enrichment analysis. Our analysis shows that 113 genes were significantly upregulated (by at least 1.5-fold) with PCN treatment, and that 834 genes were significantly downregulated (by at least 1.5-fold) with LPS treatment. Additionally, the targets of the 536 transcription factors were enriched by a combined treatment of PCN and LPS, and among these, 285 were found to have binding sites on Cyp3a11. Moreover, the repressed targets of the epigenetic markers HDAC1, HDAC3 and EZH2 were further suppressed by LPS treatment and were enhanced by PCN treatment. By identifying and contrasting the transcriptional regulators that are altered by PCN and LPS, our study provides novel insights into the transcriptional regulation of CYP3A in the liver.