bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered brain ion gradients following compensation for elevated CO2 are linked to behavioural alterations in a coral reef fish
Authors: Heuer R. M. , Welch M. J. , Rummer J. L. , Munday P. L. , Grosell M. 
Published: September 2016

AbstractNeurosensory and behavioural disruptions are some of the most consistently reported responses upon exposure to ocean acidification-relevant CO2 levels, especially in coral reef fishes. The underlying cause of these disruptions is thought to be altered current across the GABAA receptor in neuronal cells due to changes in ion gradients (HCO3− and/or Cl−) that occur in the body following compensation for elevated ambient CO2. Despite these widely-documented behavioural disruptions, the present study is the first to pair a behavioural assay with measurements of relevant intracellular and extracellular acid-base parameters in a coral reef fish exposed to elevated CO2. Spiny damselfish (Acanthochromis polyacanthus) exposed to 1900 μatm CO2 for 4 days exhibited significantly increased intracellular and extracellular HCO3− concentrations and elevated brain pHi compared to control fish, providing evidence of CO2 compensation. As expected, high CO2 exposed damselfish spent significantly more time in a chemical alarm cue (CAC) than control fish, supporting a potential link between behavioural disruption and CO2 compensation. Using HCO3− measurements from the damselfish, the reversal potential for GABAA (EGABA) was calculated, illustrating that biophysical properties of the brain during CO2 compensation could change GABAA receptor function and account for the behavioural disturbances noted during exposure to elevated CO2.
Fluorescence imaging of chromosomal DNA using click chemistry
Authors: Ishizuka Takumi , Liu Hong Shan , Ito Kenichiro , Xu Yan 
Published: September 2016

AbstractChromosome visualization is essential for chromosome analysis and genetic diagnostics. Here, we developed a click chemistry approach for multicolor imaging of chromosomal DNA instead of the traditional dye method. We first demonstrated that the commercially available reagents allow for the multicolor staining of chromosomes. We then prepared two pro-fluorophore moieties that served as light-up reporters to stain chromosomal DNA based on click reaction and visualized the clear chromosomes in multicolor. We applied this strategy in fluorescence in situ hybridization (FISH) and identified, with high sensitivity and specificity, telomere DNA at the end of the chromosome. We further extended this approach to observe several basic stages of cell division. We found that the click reaction enables direct visualization of the chromosome behavior in cell division. These results suggest that the technique can be broadly used for imaging chromosomes and may serve as a new approach for chromosome analysis and genetic diagnostics.
Reproducible Ultrahigh SERS Enhancement in Single Deterministic Hotspots Using Nanosphere-Plane Antennas Under Radially Polarized Excitation
Authors: Long Jing , Yi Hui , Li Hongquan , Lei Zeyu , Yang Tian 
Published: September 2016

AbstractSurface enhanced Raman scattering (SERS) in a nanometer size hotspot has empowered the investigation of chemical structures and dynamic behaviors of one and a few molecules. However, further advancement is hindered by lack of large enough yet reproducible enhancement in single deterministic hotspots. To resolve this problem, here we introduce a nanosphere-plane antenna under radially polarized laser excitation experiment, which provides an electromagnetic enhancement of 109~10 at the gap of each individual nanosphere-plane antenna and a root-mean-square error down to 100.08 between them. The experiment also reveals a nonlinear SERS behavior with less than one plasmon, which is also observed within a single hotspot. The unprecedented simultaneous achievement of ultrahigh enhancement and reproducibility in deterministic individual hotspots is attributed to the combination of a well-controlled hotspot geometry, the efficient coupling between vertical antenna and laser which produces orders of magnitude higher enhancement than previous excitation methods, and low power operation which is critical for high reproducibility. Our method opens a path for systematic studies on single and few molecule SERS and their surface chemistry in an in-situ and well-controlled manner.
Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area
Authors: Cao Chen , Xu Shutan 
Published: September 2016

AbstractProtein ligand-binding site prediction is highly important for protein function determination and structure-based drug design. Over the past twenty years, dozens of computational methods have been developed to address this problem. Soga et al. identified ligand cavities based on the preferences of amino acids for the ligand-binding site (RA) and proposed the propensity for ligand binding (PLB) index to rank the cavities on the protein surface. However, we found that residues exhibit different RAs in response to changes in solvent exposure. Furthermore, previous studies have suggested that some dihedral angles of amino acids in specific regions of the Ramachandran plot are preferred at the functional sites of proteins. Based on these discoveries, the amino acid solvent-accessible surface area and dihedral angles were combined with the RA and PLB to obtain two new indexes, multi-factor RA (MF-RA) and multi-factor PLB (MF-PLB). MF-PLB, PLB and other methods were tested using two benchmark databases and two particular ligand-binding sites. The results show that MF-PLB can improve the success rate of PLB for both ligand-bound and ligand-unbound structures, particularly for top choice prediction.
Sub-CMC solubilization of dodecane by rhamnolipid in saturated porous media
Authors: Zhong Hua , Zhang Hui , Liu Zhifeng , Yang Xin , Brusseau Mark L. , Zeng Guangming 
Published: September 2016

AbstractExperiments were conducted with a two-dimensional flow cell to examine the effect of monorhamnolipid surfactant at sub-CMC concentrations on solubilization of dodecane in porous media under dynamic flow conditions. Quartz sand was used as the porous medium and artificial groundwater was used as the background solution. The effectiveness of the monorhamnolipid was compared to that of SDBS, Triton X-100, and ethanol. The results demonstrated the enhancement of dodecane solubility by monorhamnolipid surfactant at concentrations lower than CMC. The concentrations (50–210 μM) are sufficiently low that they do not cause mobilization of the dodecane. Retention of rhamnolipid in the porous medium and detection of nano-size aggregates in the effluent show that the solubilization is based on a sub-CMC aggregate-formation mechanism, which is significantly stronger than the solubilization caused by the co-solvent effect. The rhamnolipid biosurfactant is more efficient for the solubilization compared to the synthetic surfactants. These results indicate a strategy of employing low concentrations of rhamnolipid for surfactant-enhanced aquifer remediation (SEAR), which may overcome the drawbacks of using surfactants at hyper-CMC concentrations.
A polymorphic (GA/CT)n- SSR influences promoter activity of Tryptophan decarboxylase gene in Catharanthus roseus L. Don
Authors: Kumar Santosh , Bhatia Sabhyata 
Published: September 2016

AbstractSimple Sequence Repeats (SSRs) of polypurine-polypyrimidine type motifs occur very frequently in the 5′ flanks of genes in plants and have recently been implicated to have a role in regulation of gene expression. In this study, 2 accessions of Catharanthus roseus having (CT)8 and (CT)21 varying motifs in the 5′UTR of Tryptophan decarboxylase (Tdc) gene, were investigated for its role in regulation of gene expression. Extensive Tdc gene expression analysis in the 2 accessions was carried out both at the level of transcription and translation. Transcript abundance was estimated using Northern analysis and qRT-PCR, whereas the rate of Tdc gene transcription was assessed using in-situ nuclear run-on transcription assay. Translation status of Tdc gene was monitored by quantification of polysome associated Tdc mRNA using qRT-PCR. These observations were validated through transient expression analysis using the fusion construct [CaM35S:(CT)8–21:GUS]. Our study demonstrated that not only does the length of (CT)n -SSRs influences the promoter activity, but the presence of SSRs per se in the 5′-UTR significantly enhances the level of gene expression. We termed this phenomenon as “microsatellite mediated enhancement” (MME) of gene expression. Results presented here will provide leads for engineering plants with enhanced amounts of medicinally important alkaloids.
Optimized holographic femtosecond laser patterning method towards rapid integration of high-quality functional devices in microchannels
Authors: Zhang Chenchu , Hu Yanlei , Du Wenqiang , Wu Peichao , Rao Shenglong , Cai Ze , Lao Zhaoxin , Xu Bing , Ni Jincheng , Li Jiawen , Zhao Gang , Wu Dong , Chu Jiaru , Sugioka Koji 
Published: September 2016

AbstractRapid integration of high-quality functional devices in microchannels is in highly demand for miniature lab-on-a-chip applications. This paper demonstrates the embellishment of existing microfluidic devices with integrated micropatterns via femtosecond laser MRAF-based holographic patterning (MHP) microfabrication, which proves two-photon polymerization (TPP) based on spatial light modulator (SLM) to be a rapid and powerful technology for chip functionalization. Optimized mixed region amplitude freedom (MRAF) algorithm has been used to generate high-quality shaped focus field. Base on the optimized parameters, a single-exposure approach is developed to fabricate 200 × 200 μm microstructure arrays in less than 240 ms. Moreover, microtraps, QR code and letters are integrated into a microdevice by the advanced method for particles capture and device identification. These results indicate that such a holographic laser embellishment of microfluidic devices is simple, flexible and easy to access, which has great potential in lab-on-a-chip applications of biological culture, chemical analyses and optofluidic devices.
Voluntary movement affects simultaneous perception of auditory and tactile stimuli presented to a non-moving body part
Authors: Hao Qiao , Ora Hiroki , Ogawa Ken-ichiro , Ogata Taiki , Miyake Yoshihiro 
Published: September 2016

AbstractThe simultaneous perception of multimodal sensory information has a crucial role for effective reactions to the external environment. Voluntary movements are known to occasionally affect simultaneous perception of auditory and tactile stimuli presented to the moving body part. However, little is known about spatial limits on the effect of voluntary movements on simultaneous perception, especially when tactile stimuli are presented to a non-moving body part. We examined the effect of voluntary movement on the simultaneous perception of auditory and tactile stimuli presented to the non-moving body part. We considered the possible mechanism using a temporal order judgement task under three experimental conditions: voluntary movement, where participants voluntarily moved their right index finger and judged the temporal order of auditory and tactile stimuli presented to their non-moving left index finger; passive movement; and no movement. During voluntary movement, the auditory stimulus needed to be presented before the tactile stimulus so that they were perceived as occurring simultaneously. This subjective simultaneity differed significantly from the passive movement and no movement conditions. This finding indicates that the effect of voluntary movement on simultaneous perception of auditory and tactile stimuli extends to the non-moving body part.
Metabolic engineering of cottonseed oil biosynthesis pathway via RNA interference
Authors: Xu Zhongping , Li Jingwen , Guo Xiaoping , Jin Shuangxia , Zhang Xianlong 
Published: September 2016

AbstractCottonseed oil is recognized as an important oil in food industry for its unique characters: low flavor reversion and the high level of antioxidants (VitaminE) as well as unsaturated fatty acid. However, the cottonseed oil content of cultivated cotton (Gossypium hirsutum) is only around 20%. In this study, we modified the accumulation of oils by the down-regulation of phosphoenolpyruvate carboxylase 1 (GhPEPC1) via RNA interference in transgenic cotton plants. The qRT-PCR and enzyme activity assay revealed that the transcription and expression of GhPEPC1 was dramatically down-regulated in transgenic lines. Consequently, the cottonseed oil content in several transgenic lines showed a significant (P < 0.01) increase (up to 16.7%) without obvious phenotypic changes under filed condition when compared to the control plants. In order to elucidate the molecular mechanism of GhPEPC1 in the regulation of seed oil content, we quantified the expression of the carbon metabolism related genes of transgenic GhPEPC1 RNAi lines by transcriptome analysis. This analysis revealed the decrease of GhPEPC1 expression led to the increase expression of triacylglycerol biosynthesis-related genes, which eventually contributed to the lipid biosynthesis in cotton. This result provides a valuable information for cottonseed oil biosynthesis pathway and shows the potential of creating high cottonseed oil germplasm by RNAi strategy for cotton breeding.
Pits, a protein interacting with Ttk69 and Sin3A, has links to histone deacetylation
Authors: Liaw Gwo-Jen 
Published: September 2016

AbstractHistone deacetylation plays an important role in transcriptional repression. Previous results showed that the genetic interaction between ttk and rpd3, which encodes a class I histone deacetylase, is required for tll repression. This study investigated the molecular mechanism by which Ttk69 recruits Rpd3. Using yeast two-hybrid screening and datamining, one novel protein was found that weakly interacts with Ttk69 and Sin3A, designated as Protein interacting with Ttk69 and Sin3A (Pits). Pits protein expressed in the early stages of embryos and bound to the region of the tor response element in vivo. Expanded tll expression patterns were observed in embryos lacking maternal pits activity and the expansion was not widened by reducing either maternal ttk or sin3A activity. However, in embryos with simultaneously reduced maternal pits and sin3A activities or maternal pits, sin3A and ttk activities, the proportions of the embryos with expanded tll expression were significantly increased. These results indicate that all three gene activities are involved in tll repression. Level of histone H3 acetylation in the tll proximal region was found to be elevated in embryo with reduced these three gene activities. In conclusion, Ttk69 causes the histone deacetylation-mediated repression of tll via the interaction of Pits and Sin3A.
Evidence that COMT genotype and proline interact on negative-symptom outcomes in schizophrenia and bipolar disorder
Authors: Clelland C L , Drouet V , Rilett K C , Smeed J A , Nadrich R H , Rajparia A , Read L L , Clelland J D 
Published: September 2016

AbstractElevated peripheral proline is associated with psychiatric disorders, and there is evidence that proline is a neuromodulator. The proline dehydrogenase (PRODH) gene, which encodes the enzyme that catalyzes proline catabolism, maps to human chromosome 22q11.2, a region conferring risk of schizophrenia. In the Prodh-null mouse, an interaction between elevated peripheral proline and another 22q11.2 gene, catechol-O-methyltransferase (COMT), on neurotransmission and behavior has been reported. We explored the relationship between fasting plasma proline levels and COMT Val158Met genotype on symptoms (positive, negative and total) in schizophrenia patients. In an exploratory study we also examined symptom change in patients with bipolar disorder. There was a significant interaction between peripheral proline and COMT on negative symptoms in schizophrenia (P<0.0001, n=95). In COMT Val/Val patients, high proline was associated with low Scale for the Assessment of Negative Symptom (SANS) scores. In contrast, high proline was associated with high SANS scores in patients carrying a Met allele. The relationship between proline and COMT also appears to modify negative symptoms across psychiatric illness. In bipolar disorder, a significant interaction was also observed on negative-symptom change (P=0.007, n=43). Negative symptoms are intractable and largely unaddressed by current medications. These data indicate a significant interaction between peripheral proline and COMT genotype, influencing negative symptoms in schizophrenia and bipolar disorder. That high proline has converse effects on symptoms by COMT genotype, may have implications for therapeutic decisions.
Biological risk factors for suicidal behaviors: a meta-analysis
Authors: Chang B P , Franklin J C , Ribeiro J D , Fox K R , Bentley K H , Kleiman E M , Nock M K 
Published: September 2016

AbstractPrior studies have proposed a wide range of potential biological risk factors for future suicidal behaviors. Although strong evidence exists for biological correlates of suicidal behaviors, it remains unclear if these correlates are also risk factors for suicidal behaviors. We performed a meta-analysis to integrate the existing literature on biological risk factors for suicidal behaviors and to determine their statistical significance. We conducted a systematic search of PubMed, PsycInfo and Google Scholar for studies that used a biological factor to predict either suicide attempt or death by suicide. Inclusion criteria included studies with at least one longitudinal analysis using a biological factor to predict either of these outcomes in any population through 2015. From an initial screen of 2541 studies we identified 94 cases. Random effects models were used for both meta-analyses and meta-regression. The combined effect of biological factors produced statistically significant but relatively weak prediction of suicide attempts (weighted mean odds ratio (wOR)=1.41; CI: 1.09–1.81) and suicide death (wOR=1.28; CI: 1.13–1.45). After accounting for publication bias, prediction was nonsignificant for both suicide attempts and suicide death. Only two factors remained significant after accounting for publication bias—cytokines (wOR=2.87; CI: 1.40–5.93) and low levels of fish oil nutrients (wOR=1.09; CI: 1.01–1.19). Our meta-analysis revealed that currently known biological factors are weak predictors of future suicidal behaviors. This conclusion should be interpreted within the context of the limitations of the existing literature, including long follow-up intervals and a lack of tests of interactions with other risk factors. Future studies addressing these limitations may more effectively test for potential biological risk factors.
Consistently altered expression of gene sets in postmortem brains of individuals with major psychiatric disorders
Authors: Darby M M , Yolken R H , Sabunciyan S 
Published: September 2016

AbstractThe measurement of gene expression in postmortem brain is an important tool for understanding the pathogenesis of serious psychiatric disorders. We hypothesized that major molecular deficits associated with psychiatric disease would affect the entire brain, and such deficits may be shared across disorders. We performed RNA sequencing and quantified gene expression in the hippocampus of 100 brains in the Stanley Array Collection followed by replication in the orbitofrontal cortex of 57 brains in the Stanley Neuropathology Consortium. We then identified genes and canonical pathway gene sets with significantly altered expression in schizophrenia and bipolar disorder in the hippocampus and in schizophrenia, bipolar disorder and major depression in the orbitofrontal cortex. Although expression of individual genes varied, gene sets were significantly enriched in both of the brain regions, and many of these were consistent across diagnostic groups. Further examination of core gene sets with consistently increased or decreased expression in both of the brain regions and across target disorders revealed that ribosomal genes are overexpressed while genes involved in neuronal processes, GABAergic signaling, endocytosis and antigen processing have predominantly decreased expression in affected individuals compared to controls without a psychiatric disorder. Our results highlight pathways of central importance to psychiatric health and emphasize messenger RNA processing and protein synthesis as potential therapeutic targets for all three of the disorders.
Loss of RIG-I leads to a functional replacement with MDA5 in the Chinese tree shrew
Authors: Xu Ling , Yu Dandan , Fan Yu , Peng Li , Wu Yong , Yao Yong-Gang 
Published: September 2016

Significance
RIG-I-like receptors (RLRs) belong to a family of DExD/H box RNA helicases and comprise three members: RIG-I, MDA5, and LGP2. The function of RLRs as key cytoplasmic sensors of pathogen-associated molecular patterns has been subjected to numerous pathogenic challenges and undergone dynamic evolution, making it an excellent example for studying innate immunity evolution. We characterized the loss of RIG-I and found that tMDA5 acted as the pattern-recognition receptor responsible for sensing Sendai virus infection in the tree shrew, with an involvement of tLGP2 and tMITA. The positively selective sites in tMDA5 were crucial for the tMDA5-mediated antiviral signaling pathway. Our results provided insights into the evolutionary adaptation and functional diversity of antiviral activity in vertebrates.
Fluids by design using chaotic surface waves to create a metafluid that is Newtonian, thermal, and entirely tunable
Authors: Welch Kyle J. , Liebman-Peláez Alexander , Corwin Eric I. 
Published: September 2016

Significance
The flow properties of conventional fluids are inextricably linked with their molecular composition; to make water flow like wine would require changing water’s molecular identity. In this paper, we show that nonequilibrium chaotic waves excited on the surface of a fluid form a “metafluid,” so called because its constitutive dynamics are derived not from the properties of molecules but rather the macroscopic waves. Unlike in conventional fluids, the viscosity and temperature of this metafluid are independently tunable. Despite this unconventional property, our system surprisingly satisfies the Einstein relation, a fundamental characteristic of equilibrium thermal systems. Our metafluid naturally emerges as the result of an external input of energy, thus representing a significant advance in the pursuit of programmable matter.
Functional polyesters enable selective siRNA delivery to lung cancer over matched normal cells
Authors: Yan Yunfeng , Liu Li , Xiong Hu , Miller Jason B. , Zhou Kejin , Kos Petra , Huffman Kenneth E. , Elkassih Sussana , Norman John W. , Carstens Ryan , Kim James , Minna John D. , Siegwart Daniel J. 
Published: September 2016

Significance
Ideal cancer therapeutics accurately hit tumors and avoid side effects on healthy cells. We used a patient-derived pair of matched cancer/normal cell lines to discover selective nanoparticles that could deliver a cytotoxic siRNA to kill cancer cells and not normal cells. The finding that cells respond differently to the same nanoparticle has profound implications for gene therapy because cell-type specificity of drug carriers in vivo could alter clinical patient outcomes. Our data suggest that selectivity is an underappreciated reality that should be carefully considered when evaluating drug carriers. The combination of both well-defined molecular targets and nanoparticle delivery to targeted cells is likely required to improve cancer drug accuracy in the clinic.