bluuebunny/crossref_metadata_2025 huggingface dataset:
Aboriginal Australian mitochondrial genome variation – an increased understanding of population antiquity and diversity
Authors: Nagle Nano , van Oven Mannis , Wilcox Stephen , van Holst Pellekaan Sheila , Tyler-Smith Chris , Xue Yali , Ballantyne Kaye N. , Wilcox Leah , Papac Luka , Cooke Karen , van Oorschot Roland A. H. , McAllister Peter , Williams Lesley , Kayser Manfred , Mitchell R. John ,   The Genographic Consortium, Adhikarla Syama , Adler Christina J. , Balanovska Elena , Balanovsky Oleg , Bertranpetit Jaume , Clarke Andrew C. , Comas David , Cooper Alan , Der Sarkissian Clio S. I. , Dulik Matthew C. , Gaieski Jill B. , GaneshPrasad ArunKumar , Haak Wolfgang , Haber Marc , Hobbs Angela , Javed Asif , Jin Li , Kaplan Matthew E. , Li Shilin , Martínez-Cruz Begoña , Matisoo-Smith Elizabeth A. , Melé Marta , Merchant Nirav C. , Owings Amanda C. , Parida Laxmi , Pitchappan Ramasamy , Platt Daniel E. , Quintana-Murci Lluis , Renfrew Colin , Royyuru Ajay K. , Santhakumari Arun Varatharajan , Santos Fabrício R. , Schurr Theodore G. , Soodyall Himla , Soria Hernanz David F. , Swamikrishnan Pandikumar , Vilar Miguel G. , Wells R. Spencer , Zalloua Pierre A. , Ziegle Janet S.
Published: March 2017

Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian genomes. We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians. In particular, the more common haplogroups observed in our dataset included M42a, M42c, S, P5 and P12, followed by rarer haplogroups M15, M16, N13, O, P3, P6 and P8. We propose some major phylogenetic rearrangements, such as in haplogroup P where we delinked P4a and P4b and redefined them as P4 (New Guinean) and P11 (Australian), respectively. Haplogroup P2b was identified as a novel clade potentially restricted to Torres Strait Islanders. Nearly all Aboriginal Australian mitochondrial haplogroups detected appear to be ancient, with no evidence of later introgression during the Holocene. Our findings greatly increase knowledge about the geographic distribution and phylogenetic structure of mitochondrial lineages that have survived in contemporary descendants of Australia’s first settlers.
Using Delaunay triangulation and Voronoi tessellation to predict the toxicities of binary mixtures containing hormetic compound
Authors: Qu Rui , Liu Shu-Shen , Zheng Qiao-Feng , Li Tong
Published: March 2017

Concentration addition (CA) was proposed as a reasonable default approach for the ecological risk assessment of chemical mixtures. However, CA cannot predict the toxicity of mixture at some effect zones if not all components have definite effective concentrations at the given effect, such as some compounds induce hormesis. In this paper, we developed a new method for the toxicity prediction of various types of binary mixtures, an interpolation method based on the Delaunay triangulation (DT) and Voronoi tessellation (VT) as well as the training set of direct equipartition ray design (EquRay) mixtures, simply IDVequ. At first, the EquRay was employed to design the basic concentration compositions of five binary mixture rays. The toxic effects of single components and mixture rays at different times and various concentrations were determined by the time-dependent microplate toxicity analysis. Secondly, the concentration-toxicity data of the pure components and various mixture rays were acted as a training set. The DT triangles and VT polygons were constructed by various vertices of concentrations in the training set. The toxicities of unknown mixtures were predicted by the linear interpolation and natural neighbor interpolation of vertices. The IDVequ successfully predicted the toxicities of various types of binary mixtures.
Influence of substrate modulus on gecko adhesion
Authors: Klittich Mena R. , Wilson Michael C. , Bernard Craig , Rodrigo Rochelle M. , Keith Austin J. , Niewiarowski Peter H. , Dhinojwala Ali
Published: March 2017

The gecko adhesion system fascinates biologists and materials scientists alike for its strong, reversible, glue-free, dry adhesion. Understanding the adhesion system’s performance on various surfaces can give clues as to gecko behaviour, as well as towards designing synthetic adhesive mimics. Geckos encounter a variety of surfaces in their natural habitats; tropical geckos, such as Gekko gecko, encounter hard, rough tree trunks as well as soft, flexible leaves. While gecko adhesion on hard surfaces has been extensively studied, little work has been done on soft surfaces. Here, we investigate for the first time the influence of macroscale and nanoscale substrate modulus on whole animal adhesion on two different substrates (cellulose acetate and polydimethylsiloxane) in air and find that across 5 orders of magnitude in macroscale modulus, there is no change in adhesion. On the nanoscale, however, gecko adhesion is shown to depend on substrate modulus. This suggests that low surface-layer modulus may inhibit the gecko adhesion system, independent of other influencing factors such as macroscale composite modulus and surface energy. Understanding the limits of gecko adhesion is vital for clarifying adhesive mechanisms and in the design of synthetic adhesives for soft substrates (including for biomedical applications and wearable electronics).
Plumbagin sensitizes breast cancer cells to tamoxifen-induced cell death through GRP78 inhibition and Bik upregulation
Authors: Kawiak Anna , Domachowska Anna , Jaworska Anna , Lojkowska Ewa
Published: March 2017

The glucose regulated protein 78 (GRP78) is a major chaperone of the endoplasmic reticulum, and a prosurvival component of the unfolded protein response. GRP78 is upregulated in many types of cancers, including breast cancer. Research has suggested that GRP78 overexpression confers chemoresistance to anti-estrogen agents through a mechanism involving the inhibition of a pro-apoptotic BH3-only protein, Bik. In the present research the role of plumbagin, a naturally occurring naphthoquinone, in GRP78-associated cell death inhibition was examined. The results demonstrated that plumbagin inhibits GRP78 activity and GRP78 inhibition contributes to plumbagin-mediated cell death induction. Furthermore, Bik upregulation was associated with plumbagin-induced cell death and an increase in plumbagin-mediated Bik induction was observed upon GRP78 downregulation. Plumbagin sensitized estrogen-positive breast cancer cells to tamoxifen and the association of GRP78 inhibition and Bik upregulation in plumbagin-mediated cell sensitization was shown. Collectively, the results of this research suggest that plumbagin inhibits the antiapoptotic activity of GRP78 leading to Bik upregulation and apoptosis induction, which contributes to the sensitization of breast cancer cells to tamoxifen.
Optimizing non-invasive radiofrequency hyperthermia treatment for improving drug delivery in 4T1 mouse breast cancer model
Authors: Ware Matthew J. , Krzykawska-Serda Martyna , Chak-Shing Ho Jason , Newton Jared , Suki Sarah , Law Justin , Nguyen Lam , Keshishian Vazrik , Serda Maciej , Taylor Kimberly , Curley Steven A. , Corr Stuart J.
Published: March 2017

Interactions of high-frequency radio waves (RF) with biological tissues are currently being investigated as a therapeutic platform for non-invasive cancer hyperthermia therapy. RF delivers thermal energy into tissues, which increases intra-tumoral drug perfusion and blood-flow. Herein, we describe an optical-based method to optimize the short-term treatment schedules of drug and hyperthermia administration in a 4T1 breast cancer model via RF, with the aim of maximizing drug localization and homogenous distribution within the tumor microenvironment. This method, based on the analysis of fluorescent dyes localized into the tumor, is more time, cost and resource efficient, when compared to current analytical methods for tumor-targeting drug analysis such as HPLC and LC-MS. Alexa-Albumin 647 nm fluorphore was chosen as a surrogate for nab-paclitaxel based on its similar molecular weight and albumin driven pharmacokinetics. We found that RF hyperthermia induced a 30–40% increase in Alexa-Albumin into the tumor micro-environment 24 h after treatment when compared to non-heat treated mice. Additionally, we showed that the RF method of delivering hyperthermia to tumors was more localized and uniform across the tumor mass when compared to other methods of heating. Lastly, we provided insight into some of the factors that influence the delivery of RF hyperthermia to tumors.
Enhanced osteogenesis and angiogenesis by mesoporous hydroxyapatite microspheres-derived simvastatin sustained release system for superior bone regeneration
Authors: Yu Wei-Lin , Sun Tuan-Wei , Qi Chao , Zhao Hua-Kun , Ding Zhen-Yu , Zhang Zhi-Wang , Sun Ben-Ben , Shen Ji , Chen Feng , Zhu Ying-Jie , Chen Dao-Yun , He Yao-Hua
Published: March 2017

Biomaterials with both excellent osteogenic and angiogenic activities are desirable to repair massive bone defects. In this study, simvastatin with both osteogenic and angiogenic activities was incorporated into the mesoporous hydroxyapatite microspheres (MHMs) synthesized through a microwave-assisted hydrothermal method using fructose 1,6-bisphosphate trisodium salt (FBP) as an organic phosphorous source. The effects of the simvastatin-loaded MHMs (S-MHMs) on the osteogenic differentiation of rat bone marrow mesenchymal stem cells (rBMSCs) and angiogenesis in EA.hy926 cells were investigated. The results showed that the S-MHMs not only enhanced the expression of osteogenic markers in rBMSCs but also promoted the migration and tube formation of EA.hy926 cells. Furthermore, the S-MHMs were incorporated into collagen matrix to construct a novel S-MHMs/collagen composite scaffold. With the aid of MHMs, the water-insoluble simvastatin was homogenously incorporated into the hydrophilic collagen matrix and presented a sustained release profile. In vivo experiments showed that the S-MHMs/collagen scaffolds enhanced the bone regeneration and neovascularization simultaneously. These results demonstrated that the water-insoluble simvastatin could be incorporated into the MHMs and maintained its biological activities, more importantly, the S-MHMs/collagen scaffolds fabricated in this study are of immense potential in bone defect repair by enhancing osteogenesis and angiogenesis simultaneously.
Radiation-associated circulatory disease mortality in a pooled analysis of 77,275 patients from the Massachusetts and Canadian tuberculosis fluoroscopy cohorts
Authors: Tran Van , Zablotska Lydia B. , Brenner Alina V. , Little Mark P.
Published: March 2017

High-dose ionising radiation is associated with circulatory disease. Risks associated with lower-dose (<0.5 Gy) exposures remain unclear, with little information on risk modification by age at exposure, years since exposure or dose-rate. Tuberculosis patients in Canada and Massachusetts received multiple diagnostic x-ray fluoroscopic exposures, over a wide range of ages, many at doses <0.5 Gy. We evaluated risks of circulatory-disease mortality associated with <0.5 Gy radiation exposure in a pooled cohort of 63,707 patients in Canada and 13,568 patients in Massachusetts. Under 0.5 Gy there are increasing trends for all circulatory disease (n = 10,209; excess relative risk/Gy = 0.246; 95% CI 0.036, 0.469; p = 0.021) and for ischaemic heart disease (n = 6410; excess relative risk/Gy = 0.267; 95% CI 0.003, 0.552; p = 0.048). All circulatory-disease and ischaemic-heart-disease risk reduces with increasing time since exposure (p < 0.005). Over the entire dose range, there are negative mortality dose trends for all circulatory disease (p = 0.014) and ischaemic heart disease (p = 0.003), possibly due to competing causes of death over this dose interval.These results confirm and extend earlier findings and strengthen the evidence for circulatory-disease mortality radiation risk at doses <0.5 Gy. The limited information on well-known lifestyle/medical risk factors for circulatory disease implies that confounding of the dose trend cannot be entirely excluded.
Endogenous TNFα orchestrates the trafficking of neutrophils into and within lymphatic vessels during acute inflammation
Authors: Arokiasamy Samantha , Zakian Christian , Dilliway Jessica , Wang Wen , Nourshargh Sussan , Voisin Mathieu-Benoit
Published: March 2017

Neutrophils are recognised to play a pivotal role at the interface between innate and acquired immunities following their recruitment to inflamed tissues and lymphoid organs. While neutrophil trafficking through blood vessels has been extensively studied, the molecular mechanisms regulating their migration into the lymphatic system are still poorly understood. Here, we have analysed neutrophil-lymphatic vessel interactions in real time and in vivo using intravital confocal microscopy applied to inflamed cremaster muscles. We show that antigen sensitisation of the tissues induces a rapid but transient entry of tissue-infiltrated neutrophils into lymphatic vessels and subsequent crawling along the luminal side of the lymphatic endothelium. Interestingly, using mice deficient in both TNF receptors p55 and p75, chimeric animals and anti-TNFα antibody blockade we demonstrate that tissue-release of TNFα governs both neutrophil migration through the lymphatic endothelium and luminal crawling. Mechanistically, we show that TNFα primes directly the neutrophils to enter the lymphatic vessels in a strictly CCR7-dependent manner; and induces ICAM-1 up-regulation on lymphatic vessels, allowing neutrophils to crawl along the lumen of the lymphatic endothelium in an ICAM-1/MAC-1-dependent manner. Collectively, our findings demonstrate a new role for TNFα as a key regulator of neutrophil trafficking into and within lymphatic system in vivo.
A High-Concentrate Diet Induced Milk Fat Decline via Glucagon-Mediated Activation of AMP-Activated Protein Kinase in Dairy Cows
Authors: Li Lin , Cao Yang , Xie Zhenglu , Zhang Yuanshu
Published: March 2017

Dairy cows are often fed a high-concentrate (HC) diet to meet lactation demands; however, long-term concentrate feeding is unhealthy and decreases milk fat. Therefore, we investigated the effects of liver lipid metabolism on milk fat synthesis. Ten lactating Holstein cows were assigned randomly into HC and LC (low-concentrate) diet groups. After 20 weeks of feeding, milk fat declined, and lipopolysaccharide levels in the jugular, portal, and hepatic veins increased in the HC group. Liver consumption and release of nonesterified fatty acid (NEFA) into the bloodstream also decreased. AMP-activated protein kinase alpha (AMPKα) was up-regulated significantly in the livers of the HC-fed cows. The HC diet also up-regulated the expression of the transcription factor peroxisome proliferator-activated receptor α (PPARα) and its downstream targets involved in fatty acid oxidation, including carnitine palmitoyltransferase-1,2 (CPT-1, CPT-2), liver-fatty acid-binding protein (L-FABP), and acyl-CoA oxidase (ACO). The HC diet increased blood glucagon (GC) levels, and liver glucagon receptor (GCGR) expression was elevated. Cumulatively, a long-term HC diet decreased plasma concentrations of NEFA via the GC/GCGR-AMPK-PPARα signalling pathway and reduced their synthesis in the liver. The decreased NEFA concentration in the blood during HC feeding may explain the decline in the milk fat of lactating cows.
A unified nonlinear stochastic time series analysis for climate science
Authors: Moon Woosok , Wettlaufer John S.
Published: March 2017

Earth’s orbit and axial tilt imprint a strong seasonal cycle on climatological data. Climate variability is typically viewed in terms of fluctuations in the seasonal cycle induced by higher frequency processes. We can interpret this as a competition between the orbitally enforced monthly stability and the fluctuations/noise induced by weather. Here we introduce a new time-series method that determines these contributions from monthly-averaged data. We find that the spatio-temporal distribution of the monthly stability and the magnitude of the noise reveal key fingerprints of several important climate phenomena, including the evolution of the Arctic sea ice cover, the El Ni"Equation missing"o Southern Oscillation (ENSO), the Atlantic Ni"Equation missing"o and the Indian Dipole Mode. In analogy with the classical destabilising influence of the ice-albedo feedback on summertime sea ice, we find that during some time interval of the season a destabilising process operates in all of these climate phenomena. The interaction between the destabilisation and the accumulation of noise, which we term the memory effect, underlies phase locking to the seasonal cycle and the statistical nature of seasonal predictability.
Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue
Authors: Morrow Jarrett D. , Zhou Xiaobo , Lao Taotao , Jiang Zhiqiang , DeMeo Dawn L. , Cho Michael H. , Qiu Weiliang , Cloonan Suzanne , Pinto-Plata Victor , Celli Bartholome , Marchetti Nathaniel , Criner Gerard J. , Bueno Raphael , Washko George R. , Glass Kimberly , Quackenbush John , Choi Augustine M. K. , Silverman Edwin K. , Hersh Craig P.
Published: March 2017

In comparison to genome-wide association studies (GWAS), there has been poor replication of gene expression studies in chronic obstructive pulmonary disease (COPD). We performed microarray gene expression profiling on a large sample of resected lung tissues from subjects with severe COPD. Comparing 111 COPD cases and 40 control smokers, 204 genes were differentially expressed; none were at significant GWAS loci. The top differentially expressed gene was HMGB1, which interacts with AGER, a known COPD GWAS gene. Differentially expressed genes showed enrichment for putative interactors of the first three identified COPD GWAS genes IREB2, HHIP, and FAM13A, based on gene sets derived from protein and RNA binding studies, RNA-interference, a murine smoking model, and expression quantitative trait locus analyses. The gene module most highly associated for COPD in Weighted Gene Co-Expression Network Analysis (WGCNA) was enriched for B cell pathways, and shared seventeen genes with a mouse smoking model and twenty genes with previous emphysema studies. As in other common diseases, genes at COPD GWAS loci were not differentially expressed; however, using a combination of network methods, experimental studies and careful phenotype definition, we found differential expression of putative interactors of these genes, and we replicated previous human and mouse microarray results.
PET Cell Tracking Using 18F-FLT is Not Limited by Local Reuptake of Free Radiotracer
Authors: MacAskill Mark G. , Tavares Adriana S. , Wu Junxi , Lucatelli Christophe , Mountford Joanne C. , Baker Andrew H. , Newby David E. , Hadoke Patrick W. F.
Published: March 2017

Assessing the retention of cell therapies following implantation is vital and often achieved by labelling cells with 2′-[18F]-fluoro-2′-deoxy-D-glucose (18F-FDG). However, this approach is limited by local retention of cell-effluxed radiotracer. Here, in a preclinical model of critical limb ischemia, we assessed a novel method of cell tracking using 3′-deoxy-3′-L-[18F]-fluorothymidine (18F-FLT); a clinically available radiotracer which we hypothesise will result in minimal local radiotracer reuptake and allow a more accurate estimation of cell retention. Human endothelial cells (HUVECs) were incubated with 18F-FDG or 18F-FLT and cell characteristics were evaluated. Dynamic positron emission tomography (PET) images were acquired post-injection of free 18F-FDG/18F-FLT or 18F-FDG/18F-FLT-labelled HUVECs, following the surgical induction of mouse hind-limb ischemia. In vitro, radiotracer incorporation and efflux was similar with no effect on cell viability, function or proliferation under optimised conditions (5 MBq/mL, 60 min). Injection of free radiotracer demonstrated a faster clearance of 18F-FLT from the injection site vs. 18F-FDG (p ≤ 0.001), indicating local cellular uptake. Using 18F-FLT-labelling, estimation of HUVEC retention within the engraftment site 4 hr post-administration was 24.5 ± 3.2%. PET cell tracking using 18F-FLT labelling is an improved approach vs. 18F-FDG as it is not susceptible to local host cell reuptake, resulting in a more accurate estimation of cell retention.
Biofunctionalized 3-D Carbon Nano-Network Platform for Enhanced Fibroblast Cell Adhesion
Authors: Chowdhury A. K. M. Rezaul Haque , Tavangar Amirhossein , Tan Bo , Venkatakrishnan Krishnan
Published: March 2017

Carbon nanomaterials have been investigated for various biomedical applications. In most cases, however, these nanomaterials must be functionalized biologically or chemically due to their biological inertness or possible cytotoxicity. Here, we report the development of a new carbon nanomaterial with a bioactive phase that significantly promotes cell adhesion. We synthesize the bioactive phase by introducing self-assembled nanotopography and altered nano-chemistry to graphite substrates using ultrafast laser. To the best of our knowledge, this is the first time that such a cytophilic bio-carbon is developed in a single step without requiring subsequent biological/chemical treatments. By controlling the nano-network concentration and chemistry, we develop platforms with different degrees of cell cytophilicity. We study quantitatively and qualitatively the cell response to nano-network platforms with NIH-3T3 fibroblasts. The findings from thein vitrostudy indicate that the platforms possess excellent biocompatibility and promote cell adhesion considerably. The study of the cell morphology shows a healthy attachment of cells with a well-spread shape, overextended actin filaments, and morphological symmetry, which is indicative of a high cellular interaction with the nano-network. The developed nanomaterial possesses great biocompatibility and considerably stimulates cell adhesion and subsequent cell proliferation, thus offering a promising path toward engineering various biomedical devices.
Formation of novel transition metal hydride complexes with ninefold hydrogen coordination
Authors: Takagi Shigeyuki , Iijima Yuki , Sato Toyoto , Saitoh Hiroyuki , Ikeda Kazutaka , Otomo Toshiya , Miwa Kazutoshi , Ikeshoji Tamio , Orimo Shin-ichi
Published: March 2017

Ninefold coordination of hydrogen is very rare, and has been observed in two different hydride complexes comprising rhenium and technetium. Herein, based on a theoretical/experimental approach, we present evidence for the formation of ninefold H- coordination hydride complexes of molybdenum ([MoH9]3−), tungsten ([WH9]3−), niobium ([NbH9]4−) and tantalum ([TaH9]4−) in novel complex transition-metal hydrides, Li5MoH11, Li5WH11, Li6NbH11 and Li6TaH11, respectively. All of the synthesized materials are insulated with band gaps of approximately 4 eV, but contain a sufficient amount of hydrogen to cause the H 1s-derived states to reach the Fermi level. Such hydrogen-rich materials might be of interest for high-critical-temperature superconductivity if the gaps close under compression. Furthermore, the hydride complexes exhibit significant rotational motions associated with anharmonic librations at room temperature, which are often discussed in relation to the translational diffusion of cations in alkali-metal dodecahydro-closo-dodecaborates and strongly point to the emergence of a fast lithium conduction even at room temperature.
Spatial confluence of psychological and anatomical network constructs in the human brain revealed by a mass meta-analysis of fMRI activation
Authors: Thompson William Hedley , Fransson Peter
Published: March 2017

It is well-known that the brain’s activity is organized into networks but it is unclear how many networks exist. Additionally, there is also a risk of ambiguity since different names for the same network are frequently reported in the literature. In this study, we employed a mass meta-analysis of fMRI data associated with network constructs originating from both psychology and neuroscience. Based on the results from the meta-analysis, we derived a spatial similarity map between all construct terms, showing that the brain’s networks cluster hierarchically into several levels. The results presented are useful as a first step in developing a unified terminology for large-scale brain network and a platform for a queryable network atlas.
Single Molecule Investigation of Kinesin-1 Motility Using Engineered Microtubule Defects
Authors: Gramlich Michael W. , Conway Leslie , Liang Winnie H. , Labastide Joelle A. , King Stephen J. , Xu Jing , Ross Jennifer L.
Published: March 2017

The structure of the microtubule is tightly regulated in cells via a number of microtubule associated proteins and enzymes. Microtubules accumulate structural defects during polymerization, and defect size can further increase under mechanical stresses. Intriguingly, microtubule defects have been shown to be targeted for removal via severing enzymes or self-repair. The cell’s control in defect removal suggests that defects can impact microtubule-based processes, including molecular motor-based intracellular transport. We previously demonstrated that microtubule defects influence cargo transport by multiple kinesin motors. However, mechanistic investigations of the observed effects remained challenging, since defects occur randomly during polymerization and are not directly observable in current motility assays. To overcome this challenge, we used end-to-end annealing to generate defects that are directly observable using standard epi-fluorescence microscopy. We demonstrate that the annealed sites recapitulate the effects of polymerization-derived defects on multiple-motor transport, and thus represent a simple and appropriate model for naturally-occurring defects. We found that single kinesins undergo premature dissociation, but not preferential pausing, at the annealed sites. Our findings provide the first mechanistic insight to how defects impact kinesin-based transport. Preferential dissociation on the single-molecule level has the potential to impair cargo delivery at locations of microtubule defect sites in vivo.
Heterogeneity assessment of functional T cell avidity
Authors: Ioannidou Kalliopi , Baumgaertner Petra , Gannon Philippe O. , Speiser Michel F. , Allard Mathilde , Hebeisen Michael , Rufer Nathalie , Speiser Daniel E.
Published: March 2017

The potency of cellular immune responses strongly depends on T cell avidity to antigen. Yet, functional avidity measurements are rarely performed in patients, mainly due to the technical challenges of characterizing heterogeneous T cells. The mean functional T cell avidity can be determined by the IFN-γ Elispot assay, with titrated amounts of peptide. Using this assay, we developed a method revealing the heterogeneity of functional avidity, represented by the steepness/hillslope of the peptide titration curve, documented by proof of principle experiments and mathematical modeling. Our data show that not only natural polyclonal CD8 T cell populations from cancer patients, but also monoclonal T cells differ strongly in their heterogeneity of functional avidity. Interestingly, clones and polyclonal cells displayed comparable ranges of heterogeneity. We conclude that besides the mean functional avidity, it is feasible and useful to determine its heterogeneity (hillslope) for characterizing T cell responses in basic research and patient investigation.
Fabrication of graded index single crystal in glass
Authors: Veenhuizen Keith , McAnany Sean , Nolan Daniel , Aitken Bruce , Dierolf Volkmar , Jain Himanshu
Published: March 2017

Lithium niobate crystals were grown in 3D through localized heating by femtosecond laser irradiation deep inside 35Li2O-35Nb2O5-30SiO2 glass. Laser scanning speed and power density were systematically varied to control the crystal growth process and determine the optimal conditions for the formation of single crystal lines. EBSD measurements showed that, in principle, single crystals can be grown to unlimited lengths using optimal parameters. We successfully tuned the parameters to a growth mode where nucleation and growth occur upon heating and ahead of the scanning laser focus. This growth mode eliminates the problem reported in previous works of non-uniform polycrystallinity because of a separate growth mode where crystallization occurs during cooling behind the scanning laser focus. To our knowledge, this is the first report of such a growth mode using a fs laser. The crystal cross-sections possessed a symmetric, smooth lattice misorientation with respect to the c-axis orientation in the center of the crystal. Calculations indicate the observed misorientation leads to a decrease in the refractive index of the crystal line from the center moving outwards, opening the possibility to produce within glass a graded refractive index single crystal (GRISC) optically active waveguide.
Synergistic Degradation of a Hyperuricemia-Causing Metabolite Using One-Pot Enzyme-Nanozyme Cascade Reactions
Authors: Jung Secheon , Kwon Inchan
Published: March 2017

Multi-enzyme cascade reactions are frequently found in living organisms, in particular when an intermediate should be eliminated. Recently, enzyme-mimic nanomaterials (nanozymes) received much attention for various applications, because they are usually more stable and cost-effective than enzymes. However, enzyme-nanozyme cascade reations have not been yet extensively exploited. Therefore, in this study, we investigated one-pot enzyme-nanozyme cascade reactions using urate oxidase (UOX) and catalase-mimic gold nanoparticle nanozyme (AuNP) with the ultimate goal of treatment of hyperuricemia. UOX degrades hyperuricemia-causing uric acid, but also generates hydrogen peroxide raising several health concerns. We successfully demonstrated that one-pot UOX-AuNP cascade systems degrade uric acid more than five times faster than UOX alone, by eliminating potentially cytotoxic hydrogen peroxide, similar to enzyme-enzyme reactions.
Quality of seminal fluids varies with type of stimulus at ejaculation
Authors: Jeannerat E. , Janett F. , Sieme H. , Wedekind C. , Burger D.
Published: March 2017

The theory of ejaculate economics was mainly built around different sperm competition scenarios but also predicts that investments into ejaculates depend on female fecundity. Previous tests of this prediction focused on invertebrates and lower vertebrate, and on species with high female reproductive potential. It remains unclear whether the prediction also holds for polygynous mammals with low female reproductive potential (due to low litter size and long inter-birth intervals). We used horses (Equus caballus) to experimentally test whether semen characteristics are adjusted to the oestrous cycle of the mare a stallion is exposed to during few moments before ejaculation. We analysed 122 weekly semen samples collected from 16 stallions during exposure to either an oestrous or a dioestrous mare. Semen volume and the rate of motile sperm were higher when stallions were exposed to an oestrous than to a diestrous mare, while total sperm counts and sperm velocity remained unchanged. Sperm collected after exposure to an oestrous mare also showed reduced oxidative degeneration of cell membranes over a period of 48 hours. We conclude that stallions invest more into their seminal fluids when the chance of fertilization is elevated, and that this adjustment of ejaculate quality can happen very quickly.
Asymmetry of short-term control of spatio-temporal gait parameters during treadmill walking
Authors: Kozlowska Klaudia , Latka Miroslaw , West Bruce J.
Published: March 2017

Optimization of energy cost determines average values of spatio-temporal gait parameters such as step duration, step length or step speed. However, during walking, humans need to adapt these parameters at every step to respond to exogenous and/or endogenic perturbations. While some neurological mechanisms that trigger these responses are known, our understanding of the fundamental principles governing step-by-step adaptation remains elusive. We determined the gait parameters of 20 healthy subjects with right-foot preference during treadmill walking at speeds of 1.1, 1.4 and 1.7 m/s. We found that when the value of the gait parameter was conspicuously greater (smaller) than the mean value, it was either followed immediately by a smaller (greater) value of the contralateral leg (interleg control), or the deviation from the mean value decreased during the next movement of ipsilateral leg (intraleg control). The selection of step duration and the selection of step length during such transient control events were performed in unique ways. We quantified the symmetry of short-term control of gait parameters and observed the significant dominance of the right leg in short-term control of all three parameters at higher speeds (1.4 and 1.7 m/s).
Taishan Pinus massoniana pollen polysaccharide inhibits subgroup J avian leucosis virus infection by directly blocking virus infection and improving immunity
Authors: Yu Cuilian , Wei Kai , Liu Liping , Yang Shifa , Hu Liping , Zhao Peng , Meng Xiuyan , Shao Mingxu , Wang Chuanwen , Zhu Lijun , Zhang Hao , Li Yang , Zhu Ruiliang
Published: March 2017

Subgroup J avian leucosis virus (ALV-J) generally causes neoplastic diseases, immunosuppression and subsequently increases susceptibility to secondary infection in birds. The spread of ALV-J mainly depends on congenital infection and horizontal contact. Although ALV-J infection causes enormous losses yearly in the poultry industry worldwide, effective measures to control ALV-J remain lacking. In this study, we demonstrated that Taishan Pinus massoniana pollen polysaccharide (TPPPS), a natural polysaccharide extracted from Taishan Pinus massoniana pollen, can significantly inhibit ALV-J replication in vitro by blocking viral adsorption to host cells. Electron microscopy and blocking ELISA tests revealed that TPPPS possibly blocks viral adsorption to host cells by interacting with the glycoprotein 85 protein of ALV-J. Furthermore, we artificially established a congenitally ALV-J-infected chicken model to examine the anti-viral effects of TPPPS in vivo. TPPPS significantly inhibited viral shedding and viral loads in immune organs and largely eliminated the immunosuppression caused by congenital ALV-J infection. Additionally, pre-administration of TPPPS obviously reduced the size and delayed the occurrence of tumors induced by acute oncogenic ALV-J infection. This study revealed the prominent effects and feasible mechanisms of TPPPS in inhibiting ALV-J infection, thereby providing a novel prospect to control ALV-J spread.
A significant net sink for CO2 in Tokyo Bay
Authors: Kubo Atsushi , Maeda Yosaku , Kanda Jota
Published: March 2017

Most estuaries and inland waters are significant source for atmospheric CO2 because of input of terrestrial inorganic carbon and mineralization of terrestrially supplied organic carbon. In contrast to most coastal waters, some estuaries with small freshwater discharge are weak source or sometimes sink for CO2. Extensive surveys of pCO2 in Tokyo Bay showed that the overall bay acts as a strong net sink for atmospheric CO2. Although small area was a consistent source for CO2, active photosynthesis driven by nutrient loading from the land overwhelmed the CO2 budget in the bay. Here we show a comprehensive scheme with a border where air-sea CO2 flux was ±0 between nearshore waters emitting CO2 and offshore waters absorbing CO2. The border in Tokyo Bay was extremely shifted toward the land-side. The shift is characteristic of highly urbanized coastal waters with an extensive sewage treatment system in the catchment area. Because highly urbanized coastal areas worldwide are expected to quadruple by 2050, coastal waters such as Tokyo Bay are expected to increase as well. Through extrapolation of Tokyo Bay data, CO2 emission from global estuaries would be expected to decrease roughly from the current 0.074 PgC year−1 to 0.014 PgC year−1 in 2050.
Immunofluorescence identifies distinct subsets of endothelial cells in the human liver
Authors: Strauss Otto , Phillips Anthony , Ruggiero Katya , Bartlett Adam , Dunbar P. Rod
Published: March 2017

As well as systemic vascular endothelial cells, the liver has specialised sinusoidal endothelial cells (LSEC). LSEC dysfunction has been documented in many diseased states yet their phenotype in normal human liver has not been comprehensively assessed. Our aim was to improve characterisation of subsets of endothelial cells and associated pericytes in the human liver. Immunofluorescence microscopy was performed on normal human liver tissue samples to assess endothelial and structural proteins in a minimum of three donors. LSEC are distributed in an acinar pattern and universally express CD36, but two distinctive subsets of LSEC can be identified in different acinar zones. Type 1 LSEC are CD36hiCD32−CD14−LYVE-1−and are located in acinar zone 1 of the lobule, while Type 2 LSEC are LYVE-1+CD32hiCD14+CD54+CD36mid-loand are located in acinar zones 2 and 3 of the lobule. Portal tracts and central veins can be identified using markers for systemic vascular endothelia and pericytes, none of which are expressed by LSEC. In areas of low hydrostatic pressure LSEC are lined by stellate cells that express the pericyte marker CD146. Our findings identify distinctive populations of LSEC and distinguish these cells from adjacent stellate cells, systemic vasculature and pericytes in different zones of the liver acinus.
Bystander cells enhance NK cytotoxic efficiency by reducing search time
Authors: Zhou Xiao , Zhao Renping , Schwarz Karsten , Mangeat Matthieu , Schwarz Eva C. , Hamed Mohamed , Bogeski Ivan , Helms Volkhard , Rieger Heiko , Qu Bin
Published: March 2017

Natural killer (NK) cells play a central role during innate immune responses by eliminating pathogen-infected or tumorigenic cells. In the microenvironment, NK cells encounter not only target cells but also other cell types including non-target bystander cells. The impact of bystander cells on NK killing efficiency is, however, still elusive. In this study we show that the presence of bystander cells, such as P815, monocytes or HUVEC, enhances NK killing efficiency. With bystander cells present, the velocity and persistence of NK cells were increased, whereas the degranulation of lytic granules remained unchanged. Bystander cell-derived H2O2was found to mediate the acceleration of NK cell migration. Using mathematical diffusion models, we confirm that local acceleration of NK cells in the vicinity of bystander cells reduces their search time to locate target cells. In addition, we found that integrin β chains (β1, β2 and β7) on NK cells are required for bystander-enhanced NK migration persistence. In conclusion, we show that acceleration of NK cell migration in the vicinity of H2O2-producing bystander cells reduces target cell search time and enhances NK killing efficiency.
DNA-conjugated gold nanoparticles based colorimetric assay to assess helicase activity: a novel route to screen potential helicase inhibitors
Authors: Deka Jashmini , Mojumdar Aditya , Parisse Pietro , Onesti Silvia , Casalis Loredana
Published: March 2017

Helicase are essential enzymes which are widespread in all life-forms. Due to their central role in nucleic acid metabolism, they are emerging as important targets for anti-viral, antibacterial and anti-cancer drugs. The development of easy, cheap, fast and robust biochemical assays to measure helicase activity, overcoming the limitations of the current methods, is a pre-requisite for the discovery of helicase inhibitors through high-throughput screenings. We have developed a method which exploits the optical properties of DNA-conjugated gold nanoparticles (AuNP) and meets the required criteria. The method was tested with the catalytic domain of the human RecQ4 helicase and compared with a conventional FRET-based assay. The AuNP-based assay produced similar results but is simpler, more robust and cheaper than FRET. Therefore, our nanotechnology-based platform shows the potential to provide a useful alternative to the existing conventional methods for following helicase activity and to screen small-molecule libraries as potential helicase inhibitors.
Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar
Authors: Jaiswal Amit K. , Elad Yigal , Paudel Indira , Graber Ellen R. , Cytryn Eddie , Frenkel Omer
Published: March 2017

Biochar, in addition to sequestering carbon, ameliorating soil, and improving plant performance, can impact foliar and soilborne plant diseases. Nevertheless, the mechanisms associated with suppression of soilborne diseases and improved plant performances are not well understood. This study is designed to establish the relationships between biochar-induced changes in rhizosphere microbial community structure, taxonomic and functional diversity, and activity with soilborne disease suppression and enhanced plant performance in a comprehensive fashion. Biochar suppressed Fusarium crown and root-rot of tomato and simultaneously improved tomato plant growth and physiological parameters. Furthermore, biochar reduced Fusarium root colonization and survival in soil, and increased the culturable counts of several biocontrol and plant growth promoting microorganisms. Illumina sequencing analyses of 16S rRNA gene revealed substantial differences in rhizosphere bacterial taxonomical composition between biochar-amended and non-amended treatments. Moreover, biochar amendment caused a significant increase in microbial taxonomic and functional diversity, microbial activities and an overall shift in carbon-source utilization. High microbial taxonomic and functional diversity and activity in the rhizosphere has been previously associated with suppression of diseases caused by soilborne pathogens and with plant growth promotion, and may collectively explain the significant reduction of disease and improvement in plant performance observed in the presence of biochar.
Small Molecule-Induced Domain Swapping as a Mechanism for Controlling Protein Function and Assembly
Authors: Karchin Joshua M. , Ha Jeung-Hoi , Namitz Kevin E. , Cosgrove Michael S. , Loh Stewart N.
Published: March 2017

Domain swapping is the process by which identical proteins exchange reciprocal segments to generate dimers. Here we introduce induced domain swapping (INDOS) as a mechanism for regulating protein function. INDOS employs a modular design consisting of the fusion of two proteins: a recognition protein that binds a triggering molecule, and a target protein that undergoes a domain swap in response to binding of the triggering ligand. The recognition protein (FK506 binding protein) is inserted into functionally-inactivated point mutants of two target proteins (staphylococcal nuclease and ribose binding protein). Binding of FK506 to the FKBP domain causes the target domain to first unfold, then refold via domain swap. The inactivating mutations become ‘swapped out’ in the dimer, increasing nuclease and ribose binding activities by 100-fold and 15-fold, respectively, restoring them to near wild-type values. INDOS is intended to convert an arbitrary protein into a functional switch, and is the first example of rational design in which a small molecule is used to trigger protein domain swapping and subsequent activation of biological function.
Batrachochytrium salamandrivorans is the predominant chytrid fungus in Vietnamese salamanders
Authors: Laking Alexandra E. , Ngo Hai Ngoc , Pasmans Frank , Martel An , Nguyen Tao Thien
Published: March 2017

The amphibian chytrid fungi, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), pose a major threat to amphibian biodiversity. Recent evidence suggests Southeast Asia as a potential cradle for both fungi, which likely resulted in widespread host-pathogen co-existence. We sampled 583 salamanders from 8 species across Vietnam in 55 locations for Bsal and Bd, determined scaled mass index as a proxy for fitness and collected environmental data. Bsal was found within 14 of the 55 habitats (2 of which it was detected in 2013), in 5 salamandrid species, with a prevalence of 2.92%. The globalized pandemic lineage of Bd was found within one pond on one species with a prevalence of 0.69%. Combined with a complete lack of correlation between infection and individual body condition and absence of indication of associated disease, this suggests low level pathogen endemism and Bsal and Bd co-existence with Vietnamese salamandrid populations. Bsal was more widespread than Bd, and occurs at temperatures higher than tolerated by the type strain, suggesting a wider thermal niche than currently known. Therefore, this study provides support for the hypothesis that these chytrid fungi may be endemic to Asia and that species within this region may act as a disease reservoir.
Effects of Cdh23 single nucleotide substitutions on age-related hearing loss in C57BL/6 and 129S1/Sv mice and comparisons with congenic strains
Authors: Johnson Kenneth R. , Tian Cong , Gagnon Leona H. , Jiang Haiyan , Ding Dalian , Salvi Richard
Published: March 2017

A single nucleotide variant (SNV) of the cadherin 23 gene (Cdh23c.753A), common to many inbred mouse strains, accelerates age-related hearing loss (AHL) and can worsen auditory phenotypes of other mutations. We used homologous recombination in C57BL/6 NJ (B6N) and 129S1/SvImJ (129S1) embryonic stem cells to engineer mouse strains with reciprocal single base pair substitutions (B6-Cdh23c.753A>G and 129S1-Cdh23c.753G>A). We compared ABR thresholds and cochlear pathologies of these SNV mice with those of congenic (B6.129S1-Cdh23Ahl+ and 129S1.B6-Cdh23ahl) and parental (B6N and 129S1) strain mice. Results verified the protective effect of the Cdh23c.753G allele, which prevented high frequency hearing loss in B6 mice to at least 18 months of age, and the AHL-inducing effect of the Cdh23c.753A allele, which worsened hearing loss in 129S1 mice. ABR thresholds differed between 129S-Cdh23c.753A SNV and 129S1.B6-Cdh23ahl congenic mice, and a linkage backcross involving these strains localized a Chr 10 QTL contributing to the difference. These results illustrate the large effects that strain background and congenic regions have on the hearing loss associated with Cdh23c.753alleles. Importantly, the B6-Cdh23c.753Gstrain can be used to eliminate the confounding influence of the Cdh23c.753Avariant in hearing studies of B6 mice and mutant mice on the B6 background.