bluuebunny/crossref_metadata_2025 huggingface dataset:
Whole genome sequencing revealed host adaptation-focused genomic plasticity of pathogenic Leptospira
Authors: Xu Yinghua , Zhu Yongzhang , Wang Yuezhu , Chang Yung-Fu , Zhang Ying , Jiang Xiugao , Zhuang Xuran , Zhu Yongqiang , Zhang Jinlong , Zeng Lingbing , Yang Minjun , Li Shijun , Wang Shengyue , Ye Qiang , Xin Xiaofang , Zhao Guoping , Zheng Huajun , Guo Xiaokui , Wang Junzhi
Published: February 2016

Leptospirosis, caused by pathogenic Leptospira spp., has recently been recognized as an emerging infectious disease worldwide. Despite its severity and global importance, knowledge about the molecular pathogenesis and virulence evolution of Leptospira spp. remains limited. Here we sequenced and analyzed 102 isolates representing global sources. A high genomic variability were observed among different Leptospira species, which was attributed to massive gene gain and loss events allowing for adaptation to specific niche conditions and changing host environments. Horizontal gene transfer and gene duplication allowed the stepwise acquisition of virulence factors in pathogenic Leptospira evolved from a recent common ancestor. More importantly, the abundant expansion of specific virulence-related protein families, such as metalloproteases-associated paralogs, were exclusively identified in pathogenic species, reflecting the importance of these protein families in the pathogenesis of leptospirosis. Our observations also indicated that positive selection played a crucial role on this bacteria adaptation to hosts. These novel findings may lead to greater understanding of the global diversity and virulence evolution of Leptospira spp.
Installing amino acids and peptides on N-heterocycles under visible-light assistance
Authors: Jin Yunhe , Jiang Min , Wang Hui , Fu Hua
Published: February 2016

Readily available natural α-amino acids are one of nature’s most attractive and versatile building blocks in synthesis of natural products and biomolecules. Peptides and N-heterocycles exhibit various biological and pharmaceutical functions. Conjugation of amino acids or peptides with N-heterocycles provides boundless potentiality for screening and discovery of diverse biologically active molecules. However, it is a great challenge to install amino acids or peptides on N-heterocycles through formation of carbon-carbon bonds under mild conditions. In this article, eighteen N-protected α-amino acids and three peptides were well assembled on phenanthridine derivatives via couplings of N-protected α-amino acid and peptide active esters with substituted 2-isocyanobiphenyls at room temperature under visible-light assistance. Furthermore, N-Boc-proline residue was successfully conjugated with oxindole derivatives using similar procedures. The simple protocol, mild reaction conditions, fast reaction and high efficiency of this method make it an important strategy for synthesis of diverse molecules containing amino acid and peptide fragments.
Universal anyons at the irradiated surface of topological insulator
Authors: Wang Rui , Chen Wei , Wang Baigeng , Xing D. Y.
Published: February 2016

Anyons have recently received great attention due to their promising application in topological quantum computation. The best validated system that enjoys the anyonic excitations are the Laughlin states. The quasi-particles in Laughlin states are neither fermions nor bosons but possess the discrete statistical angle θ = π/m, with m being an integer. Here we report a possible realization of the universal Abelian anyons, whose statistical angle can be tuned continuously by external parameters and can take any arbitrary values interpolating θ = 0 and θ = π. The proposed setup is the surface state of a three dimensional topological insulator driven by an amplitude-modulated circularly-polarized light. It is found that the external field leads to a particular Floquet phase, which is a two-spatial-dimensional analogy of the Weyl semimetal phase in the Floquet first Brillouin zone. The chiral anomaly of this phase results in a U(1) Chern-Simons gauge theory with a tunable Floquet Chern number. Owing to this underlying gauge field theory, the irradiated surface of topological insulator constitutes a promising platform for the observation of the universal anyons.
Multiple exciton generation induced enhancement of the photoresponse of
pulsed-laser-ablation synthesized single-wall-carbon-nanotube/PbS-quantum-dots
nanohybrids
Authors: Ka Ibrahima , Le Borgne Vincent , Fujisawa Kazunori , Hayashi Takuya , Kim Yoong Ahm , Endo Morinobu , Ma Dongling , El Khakani My Ali
Published: February 2016

The pulsed laser deposition method was used to decorate appropriately single wall
carbon nanotubes (SWCNTs) with PbS quantum dots (QDs), leading to the formation of a
novel class of SWCNTs/PbS-QDs nanohybrids (NHs), without resorting to any ligand
engineering and/or surface functionalization. The number of laser ablation pulses
(NLp) was used to control the average size of the PbS-QDs and their
coverage on the SWCNTs’ surface. Photoconductive (PC) devices fabricated
from these SWCNTs/PbS-QDs NHs have shown a significantly enhanced photoresponse,
which is found to be PbS-QD size dependent. Wavelength-resolved photocurrent
measurements revealed a strong photoconductivity of the NHs in the UV-visible
region, which is shown to be due to multiple exciton generation (MEG) in the
PbS-QDs. For the 6.5 nm-diameter PbS-QDs (with a bandgap
(Eg) = 0.86 eV), the MEG contribution of the NHs
based PC devices was shown to lead to a normalized internal quantum efficiency in
excess of 300% for photon energies ≥4.5Eg. While the lowest MEG
threshold in our NHs based PC devices is found to be of ~2.5Eg, the MEG
efficiency reaches values as high as
0.9 ± 0.1.
Distinct Reward Properties are Encoded via Corticostriatal Interactions
Authors: Smith David V. , Rigney Anastasia E. , Delgado Mauricio R.
Published: February 2016

The striatum serves as a critical brain region for reward processing. Yet, understanding the link between striatum and reward presents a challenge because rewards are composed of multiple properties. Notably, affective properties modulate emotion while informative properties help obtain future rewards. We approached this problem by emphasizing affective and informative reward properties within two independent guessing games. We found that both reward properties evoked activation within the nucleus accumbens, a subregion of the striatum. Striatal responses to informative, but not affective, reward properties predicted subsequent utilization of information for obtaining monetary reward. We hypothesized that activation of the striatum may be necessary but not sufficient to encode distinct reward properties. To investigate this possibility, we examined whether affective and informative reward properties were differentially encoded in corticostriatal interactions. Strikingly, we found that the striatum exhibited dissociable connectivity patterns with the ventrolateral prefrontal cortex, with increasing connectivity for affective reward properties and decreasing connectivity for informative reward properties. Our results demonstrate that affective and informative reward properties are encoded via corticostriatal interactions. These findings highlight how corticostriatal systems contribute to reward processing, potentially advancing models linking striatal activation to behavior.
Inhibition of lysosomal protease cathepsin D reduces renal fibrosis in murine chronic kidney disease
Authors: Fox Christopher , Cocchiaro Pasquale , Oakley Fiona , Howarth Rachel , Callaghan Krystena , Leslie Jack , Luli Saimir , Wood Katrina M. , Genovese Federica , Sheerin Neil S. , Moles Anna
Published: February 2016

During chronic kidney disease (CKD) there is a dysregulation of extracellular matrix (ECM) homeostasis leading to renal fibrosis. Lysosomal proteases such as cathepsins (Cts) regulate this process in other organs, however, their role in CKD is still unknown. Here we describe a novel role for cathepsins in CKD. CtsD and B were located in distal and proximal tubular cells respectively in human disease. Administration of CtsD (Pepstatin A) but not B inhibitor (Ca074-Me), in two mouse CKD models, UUO and chronic ischemia reperfusion injury, led to a reduction in fibrosis. No changes in collagen transcription or myofibroblasts numbers were observed. Pepstatin A administration resulted in increased extracellular urokinase and collagen degradation. In vitro and in vivo administration of chloroquine, an endo/lysosomal inhibitor, mimicked Pepstatin A effect on renal fibrosis. Therefore, we propose a mechanism by which CtsD inhibition leads to increased collagenolytic activity due to an impairment in lysosomal recycling. This results in increased extracellular activity of enzymes such as urokinase, triggering a proteolytic cascade, which culminates in more ECM degradation. Taken together these results suggest that inhibition of lysosomal proteases, such as CtsD, could be a new therapeutic approach to reduce renal fibrosis and slow progression of CKD.
Hierarchy of cellular decisions in collective behavior: Implications for wound healing
Authors: Wickert Lisa E. , Pomerenke Shaun , Mitchell Isaiah , Masters Kristyn S. , Kreeger Pamela K.
Published: February 2016

Collective processes such as wound re-epithelialization result from the integration of individual cellular decisions. To determine which individual cell behaviors represent the most promising targets to engineer re-epithelialization, we examined collective and individual responses of HaCaT keratinocytes seeded upon polyacrylamide gels of three stiffnesses (1, 30 and 100 kPa) and treated with a range of epidermal growth factor (EGF) doses. Wound closure was found to increase with substrate stiffness, but was responsive to EGF treatment only above a stiffness threshold. Individual cell behaviors were used to create a partial least squares regression model to predict the hierarchy of factors driving wound closure. Unexpectedly, cell area and persistence were found to have the strongest correlation to the observed differences in wound closure. Meanwhile, the model predicted a relatively weak correlation between wound closure with proliferation and the unexpectedly minor input from proliferation was successfully tested with inhibition by aphidicolin. Combined, these results suggest that the poor clinical results for growth factor-based therapies for chronic wounds may result from a disconnect between the individual cellular behaviors targeted in these approaches and the resulting collective response. Additionally, the stiffness-dependency of EGF sensitivity suggests that therapies matched to microenvironmental characteristics will be more efficacious.
Post-floral Erection of Stalks Provides Insight into the Evolution of Fruit Orientation and Its Effects on Seed Dispersal
Authors: Niu Yang , Zhou Zhuo , Sha Wen , Sun Hang
Published: February 2016

That stalks reorient after flowering to face upwards is a common phenomenon in many flowering plants, indicating the potential importance of fruit orientation on seed dispersal. But this idea has not been subject to an empirical test. We examined this hypothesis by analysing the evolutionary correlation between fruit orientation and other characters and by investigating the effects of fruit orientation on seed dispersal. We found that 1) in a sub-alpine plant community, upward fruit orientation strongly correlates with fruits that act as seed containers, which are often of dry type and are dispersed by non-animal vectors; 2) as exemplified by the Campanulaceae s. str., fruit orientation strongly correlates with dehiscence position. Upwardly-oriented capsules dehisce at the apex, whereas pendent ones dehisce at the base, in both cases ensuring that seeds are released from an upright position; 3) in manipulation experiments on Silene chungtienensis, upward fruits (the natural state) exhibit much greater dispersal distances and more dispersive pattern than pendent ones and have a more even distribution of dispersal direction than horizontal ones. Our results suggest that fruit orientation may have important function in seed dispersal, which may be the reason why the phenomenon that stalk erection after flowering occurs widely.
Novel functional microRNAs from virus-free and infected Vitis vinifera plants under water stress
Authors: Pantaleo Vitantonio , Vitali Marco , Boccacci Paolo , Miozzi Laura , Cuozzo Danila , Chitarra Walter , Mannini Franco , Lovisolo Claudio , Gambino Giorgio
Published: February 2016

MicroRNAs (miRNAs) are small non-coding RNAs that regulate the post-transcriptional control of several pathway intermediates, thus playing pivotal roles in plant growth, development and response to biotic and abiotic stresses. In recent years, the grapevine genome release, small(s)-RNAseq and degradome-RNAseq together has allowed the discovery and characterisation of many miRNA species, thus rendering the discovery of additional miRNAs difficult and uncertain. Taking advantage of the miRNA responsiveness to stresses and the availability of virus-free Vitis vinifera plants and those infected only by a latent virus, we have analysed grapevines subjected to drought in greenhouse conditions. The sRNA-seq and other sequence-specific molecular analyses have allowed us to characterise conserved miRNA expression profiles in association with specific eco-physiological parameters. In addition, we here report 12 novel grapevine-specific miRNA candidates and describe their expression profile. We show that latent viral infection can influence the miRNA profiles of V. vinifera in response to drought. Moreover, study of eco-physiological parameters showed that photosynthetic rate, stomatal conductance and hydraulic resistance to water transport were significantly influenced by drought and viral infection. Although no unequivocal cause–effect explanation could be attributed to each miRNA target, their contribution to the drought response is discussed.
Changes in intestinal microflora of Caenorhabditis elegans following Bacillus nematocida B16 infection
Authors: Niu Qiuhong , Zhang Lin , Zhang Keqin , Huang Xiaowei , Hui Fengli , Kan Yunchao , Yao Lunguang
Published: February 2016

The effect of pathogenic bacteria on a host and its symbiotic microbiota is vital and widespread in the biotic world. The soil-dwelling opportunistic bacterium Bacillus nematocida B16 uses a “Trojan horse” mechanism to kill Caenorhabditis elegans. The alterations in the intestinal microflora that occur after B16 infection remain unknown. Here, we analyzed the intestinal bacteria presented in normal and infected worms. The gut microbial community experienced a complex change after B16 inoculation, as determined through marked differences in species diversity, structure, distribution and composition between uninfected and infected worms. Regardless of the worm’s origin (i.e., from soil or rotten fruits), the diversity of the intestinal microbiome decreased after infection. Firmicutes increased sharply, whereas Proteobacteria, Actinobacteria, Cyanobacteria and Acidobacteria decreased to different degrees. Fusobacteria was only present 12 h post-infection. After 24 h of infection, 1228 and 1109 bacterial species were identified in the uninfected and infected groups, respectively. The shared species reached 21.97%. The infected group had a greater number of Bacillus species but a smaller number of Pediococcus, Halomonas, Escherichia and Shewanella species (P < 0.01). Therefore, this study provides the first evaluation of the alterations caused by pathogenic bacteria on symbiotic microbiota using C. elegans as the model species.
Age-dependent inverse correlations in CSF and plasma amyloid-β(1–42) concentrations prior to amyloid plaque deposition in the brain of 3xTg-AD mice
Authors: Cho Soo Min , Lee Sejin , Yang Seung-Hoon , Kim Hye Yun , Lee Michael Jisoo , Kim Hyunjin Vincent , Kim Jiyoon , Baek Seungyeop , Yun Jin , Kim Dohee , Kim Yun Kyung , Cho Yakdol , Woo Jiwan , Kim Tae Song , Kim YoungSoo
Published: February 2016

Amyloid-β (Aβ) plays a critical role as a biomarker in Alzheimer’s disease (AD) diagnosis. In addition to its diagnostic potential in the brain, recent studies have suggested that changes of Aβ level in the plasma can possibly indicate AD onset. In this study, we found that plasma Aβ(1–42) concentration increases with age, while the concentration of Aβ(1–42) in the cerebrospinal fluid (CSF) decreases in APPswe, PS1M146V and TauP301L transgenic (3xTg-AD) mice, if measurements were made before formation of ThS-positive plaques in the brain. Our data suggests that there is an inverse correlations between the plasma and CSF Aβ(1–42) levels until plaques form in transgenic mice’s brains and that the plasma Aβ concentration possesses the diagnostic potential as a biomarker for diagnosis of early AD stages.
Reversible interconversion and maintenance of mammary epithelial cell characteristics by the ligand-regulated EGFR system
Authors: Fukuda Shinji , Nishida-Fukuda Hisayo , Nanba Daisuke , Nakashiro Koh-ichi , Nakayama Hironao , Kubota Hiroyuki , Higashiyama Shigeki
Published: February 2016

Epithelial cell plasticity is controlled by extracellular cues, but the underlying mechanisms remain to be fully understood. Epidermal growth factor (EGF) and amphiregulin (AREG) are high- and low-affinity ligands for EGF receptor (EGFR), respectively. EGFR signaling is known to promote epithelial-mesenchymal transition (EMT) by the activation of ERK and the induction of an EMT transcription factor, ZEB1. Here, we demonstrate that ligand-switching between EGF and AREG at equivalent molarity reversibly interconverts epithelial and mesenchymal-like states of EGFR signal-dependent mammary epithelial cells. The EGF- and AREG-cultured cells also differ in their epithelial characteristics, including the expression of cell surface markers, the mode of migration and the ability for acinus-formation. The ligand-switching between EGF and AREG temporally alters strength of the shared EGFR-ERK signaling. This alteration inverts relative expression levels of ZEB1 and its antagonizing microRNAs, miR-205 and miR-200c, those are critical determinants of the epithelial phenotype. Further, AREG-induced EGFR accumulation on the plasma membrane compensates for the weak association between AREG and EGFR. The EGFR dynamics enables AREG to support proliferation as efficiently as EGF at equivalent molarity and to maintain epithelial characteristics. Our findings reveal a role of EGFR ligands-generated signal strength in the regulation of mammary epithelial cell plasticity.
Grafting cucumber onto luffa improves drought tolerance by increasing ABA biosynthesis and sensitivity
Authors: Liu Shanshan , Li Hao , Lv Xiangzhang , Ahammed Golam Jalal , Xia Xiaojian , Zhou Jie , Shi Kai , Asami Tadao , Yu Jingquan , Zhou Yanhong
Published: February 2016

Balancing stomata-dependent CO2 assimilation and transpiration is a key challenge for increasing crop productivity and water use efficiency under drought stress for sustainable crop production worldwide. Here, we show that cucumber and luffa plants with luffa as rootstock have intrinsically increased water use efficiency, decreased transpiration rate and less affected CO2 assimilation capacity following drought stress over those with cucumber as rootstock. Drought accelerated abscisic acid (ABA) accumulation in roots, xylem sap and leaves and induced the transcript of ABA signaling genes, leading to a decreased stomatal aperture and transpiration in the plants grafted onto luffa roots as compared to plants grafted onto cucumber roots. Furthermore, stomatal movement in the plants grafted onto luffa roots had an increased sensitivity to ABA. Inhibition of ABA biosynthesis in luffa roots decreased the drought tolerance in cucumber and luffa plants. Our study demonstrates that the roots of luffa have developed an enhanced ability to sense the changes in root-zone moisture and could eventually deliver modest level of ABA from roots to shoots that enhances water use efficiency under drought stress. Such a mechanism could be greatly exploited to benefit the agricultural production especially in arid and semi-arid areas.
Human X-linked Intellectual Disability Factor CUL4B Is Required for Post-meiotic Sperm Development and Male Fertility
Authors: Lin Chien-Yu , Chen Chun-Yu , Yu Chih-Hsiang , Yu I-Shing , Lin Shu-Rung , Wu June-Tai , Lin Ying-Hung , Kuo Pao-Lin , Wu Jui-Ching , Lin Shu-Wha
Published: February 2016

In this study, we demonstrate that an E3-ubiquitin ligase associated with human X-linked intellectual disability, CUL4B, plays a crucial role in post-meiotic sperm development. Initially, Cul4bΔ/Y male mice were found to be sterile and exhibited a progressive loss in germ cells, thereby leading to oligoasthenospermia. Adult Cul4b mutant epididymides also contained very low numbers of mature spermatozoa and these spermatazoa exhibited pronounced morphological abnormalities. In post-meiotic spermatids, CUL4B was dynamically expressed and mitosis of spermatogonia and meiosis of spermatocytes both appeared unaffected. However, the spermatids exhibited significantly higher levels of apoptosis during spermiogenesis, particularly during the acrosome phase through the cap phase. Comparative proteomic analyses identified a large-scale shift between wild-type and Cul4b mutant testes during early post-meiotic sperm development. Ultrastructural pathology studies further detected aberrant acrosomes in spermatids and nuclear morphology. The protein levels of both canonical and non-canonical histones were also affected in an early spermatid stage in the absence of Cul4b. Thus, X-linked CUL4B appears to play a critical role in acrosomal formation, nuclear condensation and in regulating histone dynamics during haploid male germ cell differentiation in relation to male fertility in mice. Thus, it is possible that CUL4B-selective substrates are required for post-meiotic sperm morphogenesis.
Deficiency in DGCR8-dependent canonical microRNAs causes infertility due to multiple abnormalities during uterine development in mice
Authors: Kim Yeon Sun , Kim Hye-Ryun , Kim Hyongbum , Yang Seung Chel , Park Mira , Yoon Jung Ah , Lim Hyunjung J. , Hong Seok-Ho , DeMayo Francesco J. , Lydon John P. , Choi Youngsok , Lee Dong Ryul , Song Haengseok
Published: February 2016

DGCR8 is an RNA-binding protein that interacts with DROSHA to produce pre-microRNA in the nucleus, while DICER generates not only mature microRNA, but also endogenous small interfering RNAs in the cytoplasm. Here, we produced Dgcr8 conditional knock-out mice using progesterone receptor (PR)-Cre (Dgcr8d/d) and demonstrated that canonical microRNAs dependent on the DROSHA-DGCR8 complex are required for uterine development as well as female fertility in mice. Adult Dgcr8d/d females neither underwent regular reproductive cycles nor produced pups, whereas administration of exogenous gonadotropins induced normal ovulation in these mice. Interestingly, immune cells associated with acute inflammation aberrantly infiltrated into reproductive organs of pregnant Dgcr8d/d mice. Regarding uterine development, multiple uterine abnormalities were noticeable at 4 weeks of age when PR is significantly increased and the severity of these deformities increased over time. Gland formation and myometrial layers were significantly reduced and the stromal cell compartment did not expand and became atrophic during uterine development in these mice. These results were consistent with aberrantly reduced stromal cell proliferation and completely failed decidualization. Collectively, we suggest that DGCR8-dependent canonical microRNAs are essential for uterine development and physiological processes such as proper immune modulation, reproductive cycle and steroid hormone responsiveness in mice.
The phylogeny and evolutionary history of tyrannosauroid dinosaurs
Authors: Brusatte Stephen L. , Carr Thomas D.
Published: February 2016

Tyrannosauroids—the group of carnivores including Tyrannosaurs rex—are some of the most familiar dinosaurs of all. A surge of recent discoveries has helped clarify some aspects of their evolution, but competing phylogenetic hypotheses raise questions about their relationships, biogeography and fossil record quality. We present a new phylogenetic dataset, which merges published datasets and incorporates recently discovered taxa. We analyze it with parsimony and, for the first time for a tyrannosauroid dataset, Bayesian techniques. The parsimony and Bayesian results are highly congruent and provide a framework for interpreting the biogeography and evolutionary history of tyrannosauroids. Our phylogenies illustrate that the body plan of the colossal species evolved piecemeal, imply no clear division between northern and southern species in western North America as had been argued and suggest that T. rex may have been an Asian migrant to North America. Over-reliance on cranial shape characters may explain why published parsimony studies have diverged and filling three major gaps in the fossil record holds the most promise for future work.
A universal probe design for colorimetric detection of single-nucleotide variation with visible readout and high specificity
Authors: Chen Xueping , Zhou Dandan , Shen Huawei , Chen Hui , Feng Wenli , Xie Guoming
Published: February 2016

Single-nucleotide variation (SNV) is a crucial biomarker for drug resistance-related detection in cancer and bacterial infection. However, the unintended binding of DNA probes limits the specificity of SNV detection and the need for redesigned sequences compromise the universality of SNV assay. Herein, we demonstrated a universal and low-cost assay for the colorimetric discrimination of drug-resistance related point mutation. By the use of a universal DNA probe and a split G-quadruplex, the signal could be recognized by naked eye at room temperature. The DNA probe was used as a signal reporter which not only improved the universality, but also enabled high specificity of probe hybridization. This assay was successfully applied in the detection of cancer-related SNV in the epidermal growth factor receptor (EGFR) gene, kirsten rat sarcoma viral oncogene homologue (KRAS) and tuberculosis drug-resistance related point mutation in RNA polymerase beta subunit gene (rpoB) with high specificity and visible readout. This method was simple, rapid, high-throughput and effective, which was suitable for point-of-care applications.
Bacterial Muramyl Dipeptide (MDP) Restricts Human Cytomegalovirus Replication via an IFN-β-Dependent Pathway
Authors: Kapoor Arun , Fan Yi-Hsin , Arav-Boger Ravit
Published: February 2016

We recently reported that induction of NOD2 by human Cytomegalovirus (HCMV) resulted in virus inhibition and upregulation of antiviral and inflammatory cytokines. Here we investigated the effects of muramyl dipeptide (MDP), a bacterial cell wall component that activates NOD2, on HCMV replication and antiviral responses. HCMV infection of human foreskin fibroblasts induced NOD2, the downstream receptor-interacting serine/threonine-protein kinase 2 (RIPK2), resulting in phosphorylation of TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3). MDP treatment following infection at low multiplicity (MOI = 0.1 PFU/cell) inhibited HCMV in a dose-dependent manner and further induced phosphorylation of TBK1, IRF3 and expression of IFN-β. None of these effects of MDP were observed following infection at multiplicity of 1. In infected NOD2 knocked-down cells MDP did not induce IFN-β, irrespective of MOI. Treatment with MDP before infection also inhibited HCMV, an effect augmented with treatment duration. Treatment with an IFN-β receptor blocking antibody or knockdown of IFN-β significantly attenuated the inhibitory effect of MDP on HCMV. MDP treatment before or after infection with herpesvirus 1 did not inhibit its replication. Summarized, NOD2 activation exerts anti-HCMV activities predominantly via IFN-β. Since MDP is a bacterial cell wall component, ongoing microbial exposure may influence HCMV replication.
An integrated multi-electrode-optrode array for in vitro optogenetics
Authors: Welkenhuysen Marleen , Hoffman Luis , Luo Zhengxiang , De Proft Anabel , Van den Haute Chris , Baekelandt Veerle , Debyser Zeger , Gielen Georges , Puers Robert , Braeken Dries
Published: February 2016

Modulation of a group of cells or tissue needs to be very precise in order to exercise effective control over the cell population under investigation. Optogenetic tools have already demonstrated to be of great value in the study of neuronal circuits and in neuromodulation. Ideally, they should permit very accurate resolution, preferably down to the single cell level. Further, to address a spatially distributed sample, independently addressable multiple optical outputs should be present. In current techniques, at least one of these requirements is not fulfilled. In addition to this, it is interesting to directly monitor feedback of the modulation by electrical registration of the activity of the stimulated cells. Here, we present the fabrication and characterization of a fully integrated silicon-based multi-electrode-optrode array (MEOA) for in vitro optogenetics. We demonstrate that this device allows for artifact-free electrical recording. Moreover, the MEOA was used to reliably elicit spiking activity from ChR2-transduced neurons. Thanks to the single cell resolution stimulation capability, we could determine spatial and temporal activation patterns and spike latencies of the neuronal network. This integrated approach to multi-site combined optical stimulation and electrical recording significantly advances today’s tool set for neuroscientists in their search to unravel neuronal network dynamics.
Comparison of Particle-Associated Bacteria from a Drinking Water Treatment Plant and Distribution Reservoirs with Different Water Sources
Authors: Liu G. , Ling F. Q. , van der Mark E. J. , Zhang X. D. , Knezev A. , Verberk J. Q. J. C. , van der Meer W. G. J. , Medema G. J. , Liu W. T. , van Dijk J. C.
Published: February 2016

This study assessed the characteristics of and changes in the suspended particles and the associated bacteria in an unchlorinated drinking water distribution system and its reservoirs with different water sources. The results show that particle-associated bacteria (PAB) were present at a level of 0.8–4.5 × 103 cells ml−1 with a biological activity of 0.01–0.04 ng l−1 ATP. Different PAB communities in the waters produced from different sources were revealed by a 16S rRNA-based pyrosequencing analysis. The quantified biomass underestimation due to the multiple cells attached per particle was ≥ 85%. The distribution of the biologically stable water increased the number of cells per particle (from 48 to 90) but had minor effects on the PAB community. Significant changes were observed at the mixing reservoir. Our results show the characteristics of and changes in suspended PAB during distribution and highlight the significance of suspended PAB in the distribution system, because suspended PAB can lead to a considerable underestimation of biomass and because they exist as biofilm, which has a greater mobility than pipe-wall biofilm and therefore presents a greater risk, given the higher probability that it will reach the customers’ taps and be ingested.
Sorting of Single Biomolecules based on Fourier Polar Representation of Surface Enhanced Raman Spectra
Authors: Leray Aymeric , Brulé Thibault , Buret Mickael , Colas des Francs Gérard , Bouhelier Alexandre , Dereux Alain , Finot Eric
Published: February 2016

Surface enhanced Raman scattering (SERS) spectroscopy becomes increasingly used in biosensors for its capacity to detect and identify single molecules. In practice, a large number of SERS spectra are acquired and reliable ranking methods are thus essential for analysing all these data. Supervised classification strategies, which are the most effective methods, are usually applied but they require pre-determined models or classes. In this work, we propose to sort SERS spectra in unknown groups with an alternative strategy called Fourier polar representation. This non-fitting method based on simple Fourier sine and cosine transforms produces a fast and graphical representation for sorting SERS spectra with quantitative information. The reliability of this method was first investigated theoretically and numerically. Then, its performances were tested on two concrete biological examples: first with single amino-acid molecule (cysteine) and then with a mixture of three distinct odorous molecules. The benefits of this Fourier polar representation were highlighted and compared to the well-established statistical principal component analysis method.
Partitioned airs at microscale and nanoscale: thermal diffusivity in ultrahigh porosity solids of nanocellulose
Authors: Sakai Koh , Kobayashi Yuri , Saito Tsuguyuki , Isogai Akira
Published: February 2016

High porosity solids, such as plastic foams and aerogels, are thermally insulating. Their insulation performance strongly depends on their pore structure, which dictates the heat transfer process in the material. Understanding such a relationship is essential to realizing highly efficient thermal insulators. Herein, we compare the heat transfer properties of foams and aerogels that have very high porosities (97.3–99.7%) and an identical composition (nanocellulose). The foams feature rather closed, microscale pores formed with a thin film-like solid phase, whereas the aerogels feature nanoscale open pores formed with a nanofibrous network-like solid skeleton. Unlike the aerogel samples, the thermal diffusivity of the foam decreases considerably with a slight increase in the solid fraction. The results indicate that for suppressing the thermal diffusion of air within high porosity solids, creating microscale spaces with distinct partitions is more effective than directly blocking the free path of air molecules at the nanoscale.
Detecting O2 binding sites in protein cavities
Authors: Kitahara Ryo , Yoshimura Yuichi , Xue Mengjun , Kameda Tomoshi , Mulder Frans A. A.
Published: February 2016

Internal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O2) to cavities in a well-studied model for ligand binding, the L99A mutant of T4 lysozyme. On increasing the O2 concentration to 8.9 mM, changes in 1H, 15N and 13C chemical shifts and signal broadening were observed specifically for backbone amide and side chain methyl groups located around the two hydrophobic cavities of the protein. O2-induced longitudinal relaxation enhancements for amide and methyl protons could be adequately accounted for by paramagnetic dipolar relaxation. These data provide the first experimental demonstration that O2 binds specifically to the hydrophobic and not the hydrophilic cavities, in a protein. Molecular dynamics simulations visualized the rotational and translational motions of O2 in the cavities, as well as the binding and egress of O2, suggesting that the channel consisting of helices D, E, G, H and J could be the potential gateway for ligand binding to the protein. Due to strong paramagnetic relaxation effects, O2 gas-pressure NMR measurements can detect hydrophobic cavities when populated to as little as 1% and thereby provide a general and highly sensitive method for detecting oxygen binding in proteins.
Resistance switching behavior of atomic layer deposited SrTiO3 film through possible formation of Sr2Ti6O13 or Sr1Ti11O20 phases
Authors: Lee Woongkyu , Yoo Sijung , Yoon Kyung Jean , Yeu In Won , Chang Hye Jung , Choi Jung-Hae , Hoffmann-Eifert Susanne , Waser Rainer , Hwang Cheol Seong
Published: February 2016

Identification of microstructural evolution of nanoscale conducting phase, such as conducting filament (CF), in many resistance switching (RS) devices is a crucial factor to unambiguously understand the electrical behaviours of the RS-based electronic devices. Among the diverse RS material systems, oxide-based redox system comprises the major category of these intriguing electronic devices, where the local, along both lateral and vertical directions of thin films, changes in oxygen chemistry has been suggested to be the main RS mechanism. However, there are systems which involve distinctive crystallographic phases as CF; the Magnéli phase in TiO2 is one of the very well-known examples. The current research reports the possible presence of distinctive local conducting phase in atomic layer deposited SrTiO3 RS thin film. The conducting phase was identified through extensive transmission electron microscopy studies, which indicated that oxygen-deficient Sr2Ti6O13 or Sr1Ti11O20 phase was presumably present mainly along the grain boundaries of SrTiO3 after the unipolar set switching in Pt/TiN/SrTiO3/Pt structure. A detailed electrical characterization revealed that the samples showed typical bipolar and complementary RS after the memory cell was unipolar reset.
Short environmental enrichment in adulthood reverses anxiety and basolateral amygdala hypertrophy induced by maternal separation
Authors: Koe A S , Ashokan A , Mitra R
Published: February 2016

Maternal separation during early childhood results in greater sensitivity to stressors later in adult life. This is reflected as greater propensity to develop stress-related disorders in humans and animal models, including anxiety and depression. Environmental enrichment (EE) reverses some of the damaging effects of maternal separation in rodent models when provided during peripubescent life, temporally proximal to the separation. It is presently unknown if EE provided outside this critical window can still rescue separation-induced anxiety and neural plasticity. In this report we use a rat model to demonstrate that a single short episode of EE in adulthood reduced anxiety-like behaviour in maternally separated rats. We further show that maternal separation resulted in hypertrophy of dendrites and increase in spine density of basolateral amygdala neurons in adulthood, long after initial stress treatment. This is congruent with prior observations showing centrality of basolateral amygdala hypertrophy in anxiety induced by stress during adulthood. In line with the ability of the adult enrichment to rescue stress-induced anxiety, we show that enrichment renormalized stress-induced structural expansion of the amygdala neurons. These observations argue that behavioural plasticity induced by early adversity can be rescued by environmental interventions much later in life, likely mediated by ameliorating effects of enrichment on basolateral amygdala plasticity.
Neuroplasticity in response to cognitive behavior therapy for social anxiety disorder
Authors: Månsson K N T , Salami A , Frick A , Carlbring P , Andersson G , Furmark T , Boraxbekk C-J
Published: February 2016

Patients with anxiety disorders exhibit excessive neural reactivity in the amygdala, which can be normalized by effective treatment like cognitive behavior therapy (CBT). Mechanisms underlying the brain’s adaptation to anxiolytic treatments are likely related both to structural plasticity and functional response alterations, but multimodal neuroimaging studies addressing structure–function interactions are currently missing. Here, we examined treatment-related changes in brain structure (gray matter (GM) volume) and function (blood–oxygen level dependent, BOLD response to self-referential criticism) in 26 participants with social anxiety disorder randomly assigned either to CBT or an attention bias modification control treatment. Also, 26 matched healthy controls were included. Significant time × treatment interactions were found in the amygdala with decreases both in GM volume (family-wise error (FWE) corrected PFWE=0.02) and BOLD responsivity (PFWE=0.01) after successful CBT. Before treatment, amygdala GM volume correlated positively with anticipatory speech anxiety (PFWE=0.04), and CBT-induced reduction of amygdala GM volume (pre–post) correlated positively with reduced anticipatory anxiety after treatment (PFWE⩽0.05). In addition, we observed greater amygdala neural responsivity to self-referential criticism in socially anxious participants, as compared with controls (PFWE=0.029), before but not after CBT. Further analysis indicated that diminished amygdala GM volume mediated the relationship between decreased neural responsivity and reduced social anxiety after treatment (P=0.007). Thus, our results suggest that improvement-related structural plasticity impacts neural responsiveness within the amygdala, which could be essential for achieving anxiety reduction with CBT.
MAP training: combining meditation and aerobic exercise reduces depression and rumination while enhancing synchronized brain activity
Authors: Alderman B L , Olson R L , Brush C J , Shors T J
Published: February 2016

Mental and physical (MAP) training is a novel clinical intervention that combines mental training through meditation and physical training through aerobic exercise. The intervention was translated from neuroscientific studies indicating that MAP training increases neurogenesis in the adult brain. Each session consisted of 30 min of focused-attention (FA) meditation and 30 min of moderate-intensity aerobic exercise. Fifty-two participants completed the 8-week intervention, which consisted of two sessions per week. Following the intervention, individuals with major depressive disorder (MDD;n=22) reported significantly less depressive symptoms and ruminative thoughts. Typical healthy individuals (n=30) also reported less depressive symptoms at follow-up. Behavioral and event-related potential indices of cognitive control were collected at baseline and follow-up during a modified flanker task. Following MAP training, N2 and P3 component amplitudes increased relative to baseline, especially among individuals with MDD. These data indicate enhanced neural responses during the detection and resolution of conflicting stimuli. Although previous research has supported the individual beneficial effects of aerobic exercise and meditation for depression, these findings indicate that a combination of the two may be particularly effective in increasing cognitive control processes and decreasing ruminative thought patterns.
Sample preparation protocol for bottom-up proteomic analysis of the secretome of the islets of Langerhans
Authors: Schmudlach Andrew , Felton Jeremy , Cipolla Cynthia , Sun Liangliang , Kennedy Robert T. , Dovichi Norman J.
Published: February 2016

We evaluate a set of protocols for preparation of the secretome from murine islets of Langerhans for bottom-up proteomic analysis.
Highly luminescent nanoscale quasi-2D layered lead bromide perovskites with tunable emissions
Authors: Yuan Zhao , Shu Yu , Xin Yan , Ma Biwu
Published: February 2016

Herein, we report a new color tuning approach for highly luminescent nanoscale lead(ii) bromide perovskites with a quasi-2D layered structure.
Aquatic ecotoxicity of personal care products: QSAR models and ranking for prioritization and safer alternatives’ design
Authors: Gramatica Paola , Cassani Stefano , Sangion Alessandro
Published: February 2016

New externally validated QSAR models for aquatic toxicity of PCPs are proposed and applicable in QSARINS for thea priorichemical design of environmentally safer PCPs.
An efficient synthesis of N-nitrosamines under solvent, metal and acid free conditions using tert-butyl nitrite
Authors: Chaudhary Priyanka , Gupta Surabhi , Muniyappan Nalluchamy , Sabiah Shahulhameed , Kandasamy Jeyakumar
Published: February 2016

N-Nitrosation of secondary amines was accomplished in an efficient manner using tert-butyl nitrite under solvent, metal and acid free conditions.
Roles of a hydrogen bond donor and a hydrogen bond acceptor in the extraction of toluene from n-heptane using deep eutectic solvents
Authors: Wang Yan , Hou Yucui , Wu Weize , Liu Dongdong , Ji Youan , Ren Shuhang
Published: February 2016

As analogues of ionic liquids, deep eutectic solvents (DESs) have attracted considerable attention in the field of separating aromatics from aromatics/aliphatics mixtures.
Directional liquefaction coupling fractionation of lignocellulosic biomass for platform chemicals
Authors: Xu Junming , Xie Xinfeng , Wang Jingxin , Jiang Jianchun
Published: February 2016

Conventional thermochemical liquefaction of lignocellulosic biomass produces an unpredictable complex mixture of oxygenated products, which creates techno-economic barriers during subsequent upgrading processes.
Statistics, damned statistics and nanoscience – using data science to meet the challenge of nanomaterial complexity
Authors: Sun Baichuan , Fernandez Michael , Barnard Amanda S.
Published: February 2016

Combining advances in digital technology and modern methods in statistics with a detailed understanding of nano-structure/property relationships can pave the way for more realistic predictions of nanomaterials performance.
High resolution atomic force microscopy of double-stranded RNA
Authors: Ares Pablo , Fuentes-Perez Maria Eugenia , Herrero-Galán Elías , Valpuesta José M. , Gil Adriana , Gomez-Herrero Julio , Moreno-Herrero Fernando
Published: February 2016

Imaging double-stranded RNA at sub-helical pitch resolution with atomic force microscopy in liquid.
Ultratrace level determination and quantitative analysis of kidney injury biomarkers in patient samples attained by zinc oxide nanorods
Authors: Singh Manpreet , Alabanza Anginelle , Gonzalez Lorelis E. , Wang Weiwei , Reeves W. Brian , Hahm Jong-in
Published: February 2016

A ZnO NRs-based approach is employed in the rapid, quantitative, and simultaneous detection of multiple biomarkers directly in patient samples, providing an unparalleled detection capability.
I2 mediated synthesis of 5-substituted-3-methyl/benzyl-1,3,4-oxadiazol-2(3H)-ones via sequential condensation/oxidative cyclization and rearrangement
Authors: Patel Shyam Sunder , Chandna Nisha , Kumar Shreemoyee , Jain Nidhi
Published: February 2016

A simple and efficient iodine-assisted protocol for synthesis of 5-substituted-3-methyl/benzyl-1,3,4-oxadiazol-2(3H)-ones has been developed.
A remarkable solvent effect of fluorinated alcohols on transition metal catalysed C–H functionalizations
Authors: Wencel-Delord J. , Colobert F.
Published: February 2016

Fluorinated solvents like 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) and trifluoroethanol (TFE) have recently emerged as a remarkable synthetic hint allowing challenging C–H activation reactions.
Effect of crystallographic orientation on the tribological behavior of electrodeposited Zn coatings
Authors: Sriraman K. R. , Manimunda P. , Chromik R. R. , Yue S.
Published: February 2016

Tribo/transfer film evolution during sliding wear of steel contact on oriented Zn coatings.
Nucleophilicity of normal and abnormal N-heterocyclic carbenes at DFT: steric effects on tetrazole-5-ylidenes
Authors: Rezaee Nasibeh , Ahmadi Aliakbar , Kassaee Mohammad Zaman
Published: February 2016

Nucleophilicity of both normal (1R) and abnormal (2R) N-heterocyclic carbene (NHC); every 2R showing a higher nucleophilicity than its corresponding 1R isomer (R = H, methyl, ethyl, i-propyl, and t-butyl).
Enhanced biocompatibility in poly(3-hexylthiophene)-based organic thin-film transistors upon blending with poly(2-(2-acetoxyacetyl)ethyl methacrylate)
Authors: Kim Na Kyung , Bae Jin Woo , Jang Hyeon-Ki , Lee Jong-Chan , Song Kigook , Kim Byung-Soo , Park In Jun , Ha Jong-Wook , Lee Soo-Bok , Sohn Eun-Ho
Published: February 2016

Polymer blends with both biocompatibility and OTFT characteristics are developed by mixing a biocompatible polymer, PHEMAAA and a conducting polymer, P3HT at different weight ratios (i.e. P3HT/PHEMAAA = 75/25, 50/50, 25/75).
Activated carbon from Luffa cylindrica doped chitosan for mitigation of lead(ii) from an aqueous solution
Authors: Gedam Asha H. , Dongre Rajendra S.
Published: February 2016

The present study is concerned with the batch adsorption of toxic lead(ii) ions from an aqueous solution using activated carbon from a Luffa cylindrica fibers doped chitosan (ACLFCS) biocomposite as an adsorbent.