bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic maps of breast cancer subtypes
Authors: Tyanova Stefka , Albrechtsen Reidar , Kronqvist Pauliina , Cox Juergen , Mann Matthias , Geiger Tamar 
Published: January 2016

AbstractSystems-wide profiling of breast cancer has almost always entailed RNA and DNA analysis by microarray and sequencing techniques. Marked developments in proteomic technologies now enable very deep profiling of clinical samples, with high identification and quantification accuracy. We analysed 40 oestrogen receptor positive (luminal), Her2 positive and triple negative breast tumours and reached a quantitative depth of >10,000 proteins. These proteomic profiles identified functional differences between breast cancer subtypes, related to energy metabolism, cell growth, mRNA translation and cell–cell communication. Furthermore, we derived a signature of 19 proteins, which differ between the breast cancer subtypes, through support vector machine (SVM)-based classification and feature selection. Remarkably, only three proteins of the signature were associated with gene copy number variations and eleven were also reflected on the mRNA level. These breast cancer features revealed by our work provide novel insights that may ultimately translate to development of subtype-specific therapeutics.
A liquid-crystalline hexagonal columnar phase in highly-dilute suspensions of imogolite nanotubes
Authors: Paineau Erwan , Krapf Marie-Eve M. , Amara Mohamed-Salah , Matskova Natalia V. , Dozov Ivan , Rouzière Stéphan , Thill Antoine , Launois Pascale , Davidson Patrick 
Published: January 2016

AbstractLiquid crystals have found wide applications in many fields ranging from detergents to information displays and they are also increasingly being used in the ‘bottom-up’ self-assembly approach of material nano-structuration. Moreover, liquid-crystalline organizations are frequently observed by biologists. Here we show that one of the four major lyotropic liquid-crystal phases, the columnar one, is much more stable on dilution than reported so far in literature. Indeed, aqueous suspensions of imogolite nanotubes, at low ionic strength, display the columnar liquid-crystal phase at volume fractions as low as ∼0.2%. Consequently, due to its low visco-elasticity, this columnar phase is easily aligned in an alternating current electric field, in contrast with usual columnar liquid-crystal phases. These findings should have important implications for the statistical physics of the suspensions of charged rods and could also be exploited in materials science to prepare ordered nanocomposites and in biophysics to better understand solutions of rod-like biopolymers.
MYB96 shapes the circadian gating of ABA signaling in Arabidopsis
Authors: Lee Hong Gil , Mas Paloma , Seo Pil Joon 
Published: January 2016

AbstractCircadian clocks regulate the rhythms of biological activities with a period of approximately 24-hours and synchronize plant metabolism and physiology with the environmental cycles. The clock also gates responses to environmental stresses to maximize fitness advantages. Here we report that the MYB96 transcription factor is connected with the clock oscillator to shape the circadian gating of abscisic acid (ABA) responses. MYB96 directly binds to theTIMING OF CAB EXPRESSION 1(TOC1) promoter to positively regulate its expression. The use ofmyb96mutant plants shows that this regulation is essential for the gated induction ofTOC1by ABA. In turn,MYB96induction by ABA is also altered intoc1-3mutant plants. The increased tolerance to drought ofMYB96over-expressing plants is decreased in thetoc1-3mutant background, suggesting that MYB96 and TOC1 intersect the circadian clock and ABA signaling. The MYB96-TOC1 function might be also regulated by the clock component CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1), which binds to theMYB96promoter and alters its circadian expression. Thus, a complex circuitry of CCA1-MYB96-TOC1 regulatory interactions provides the mechanistic basis underlying the connection between circadian and stress signaling to optimize plant fitness to ambient stresses.
Talaromyces neofusisporus and T. qii, two new species of section Talaromyces isolated from plant leaves in Tibet, China
Authors: Wang Qi-Ming , Zhang Yong-Hong , Wang Bo , Wang Long 
Published: January 2016

AbstractTwo new species isolated from plant leaves belonging to Talaromyces section Talaromyces are reported, namely T. neofusisporus (ex-type AS3.15415 T = CBS 139516 T) and T. qii (ex-type AS3.15414 T = CBS 139515 T). Morphologically, T. neofusisporus is featured by forming synnemata on CYA and YES, bearing appressed biverticillate penicilli and smooth-walled fusiform conidia about 3.5–4.5 × 2–2.5 μm; and T. qii is characterized by velutinous colony texture, yellowish green conidia, yellow mycelium and ovoid to subglobose echinulate conidia measuring 3–3.5 μm. Phylogenetically, T. neofusisporus is such a unique species that no close relatives are found according to CaM, BenA and ITS1-5.8S-ITS2 as well as the combined three-gene sequences; and T. qii is related to T. thailandensis according to CaM, BenA and the combined sequence matrices, whereas ITS1-5.8S-ITS2 sequences do not support the close relationship between T. qii and T. thailandensis.
Off like a shot: scaling of ballistic tongue projection reveals extremely high performance in small chameleons
Authors: Anderson Christopher V. 
Published: January 2016

AbstractStretching elastic tissues and using their recoil to power movement allows organisms to release energy more rapidly than by muscle contraction directly, thus amplifying power output. Chameleons employ such a mechanism to ballistically project their tongue up to two body lengths, achieving power outputs nearly three times greater than those possibleviamuscle contraction. Additionally, small organisms tend to be capable of greater performance than larger species performing similar movements. To test the hypothesis that small chameleon species outperform larger species during ballistic tongue projection, performance was examined during feeding among 20 chameleon species in nine genera. This revealed that small species project their tongues proportionately further than large species, achieving projection distances of 2.5 body lengths. Furthermore, feedings with peak accelerations of 2,590 m s−2, or 264 gand peak power output values of 14,040 W kg−1are reported. These values represent the highest accelerations and power outputs reported for any amniote movement, highlighting the previously underestimated performance capability of the family. These findings show that examining movements in smaller animals may expose movements harbouring cryptic power amplification mechanisms and illustrate how varying metabolic demands may help drive morphological evolution.
3D macroporous electrode and high-performance in lithium-ion batteries using SnO2 coated on Cu foam
Authors: Um Ji Hyun , Choi Myounggeun , Park Hyeji , Cho Yong-Hun , Dunand David C. , Choe Heeman , Sung Yung-Eun 
Published: January 2016

AbstractA three-dimensional porous architecture makes an attractive electrode structure, as it has an intrinsic structural integrity and an ability to buffer stress in lithium-ion batteries caused by the large volume changes in high-capacity anode materials during cycling. Here we report the first demonstration of a SnO2-coated macroporous Cu foam anode by employing a facile and scalable combination of directional freeze-casting and sol-gel coating processes. The three-dimensional interconnected anode is composed of aligned microscale channels separated by SnO2-coated Cu walls and much finer micrometer pores, adding to surface area and providing space for volume expansion of SnO2 coating layer. With this anode, we achieve a high reversible capacity of 750 mAh g−1 at current rate of 0.5 C after 50 cycles and an excellent rate capability of 590 mAh g−1 at 2 C, which is close to the best performance of Sn-based nanoscale material so far.
Structural characterization of eRF1 mutants indicate a complex mechanism of stop codon recognition
Authors: Pillay Shubhadra , Li Yan , Wong Leo E , Pervushin Konstantin 
Published: January 2016

AbstractEukarya translation termination requires the stop codon recognizing protein eRF1. In contrast to the multiple proteins required for translation termination in Bacteria, eRF1 retains the ability to recognize all three of the stop codons. The details of the mechanism that eRF1 uses to recognize stop codons has remained elusive. This study describes the structural effects of mutations in the eRF1 N-domain that have previously been shown to alter stop codon recognition specificity. Here, we propose a model of eRF1 binding to the pre-translation termination ribosomal complex that is based in part on our solution NMR structures of the wild-type and mutant eRF1 N-domains. Since structural perturbations induced by these mutations were spread throughout the protein structure, residual dipolar coupling (RDC) data were recorded to establish the long-range effects of the specific mutations, E55Q, Y125F, Q122FM(Y)F126. RDCs were recorded on 15N-labeled eRF1 N-domain weakly aligned in either 5% w/v n-octyl-penta (ethylene glycol)/octanol (C8E5) or the filamentous phage Pf1. These data indicate that the mutations alter the conformation and dynamics of the GTS loop that is distant from the mutation sites. We propose that the GTS loop forms a switch that is key for the multiple codon recognition capability of eRF1.
Altered Phenylpropanoid Metabolism in the Maize Lc-Expressed Sweet Potato (Ipomoea batatas) Affects Storage Root Development
Authors: Wang Hongxia , Yang Jun , Zhang Min , Fan Weijuan , Firon Nurit , Pattanaik Sitakanta , Yuan Ling , Zhang Peng 
Published: January 2016

AbstractThere is no direct evidence of the effect of lignin metabolism on early storage root development in sweet potato. In this study, we found that heterologous expression of the maize leaf color (Lc) gene in sweet potato increased anthocyanin pigment accumulation in the whole plant and resulted in reduced size with an increased length/width ratio, low yield and less starch content in the early storage roots. RT-PCR analysis revealed dramatic up-regulation of the genes involved in the lignin biosynthesis pathway in developing storage roots, leading to greater lignin content in theLctransgenic lines, compared to the wild type. This was also evidenced by the enhanced lignification of vascular cells in the early storage roots. Furthermore, increased expression of the β-amylase gene in leaves and storage roots also accelerated starch degradation and increased the sugar use efficiency, providing more energy and carbohydrate sources for lignin biosynthesis in theLctransgenic sweet potato. Lesser starch accumulation was observed in the developing storage roots at the initiation stage in the Lc plants. Our study provides experimental evidence of the basic carbohydrate metabolism underlying the development of storage roots, which is the transformation of lignin biosynthesis to starch biosynthesis.
Characterization of vegetative inflorescence (mc-vin) mutant provides new insight into the role of MACROCALYX in regulating inflorescence development of tomato
Authors: Yuste-Lisbona Fernando J. , Quinet Muriel , Fernández-Lozano Antonia , Pineda Benito , Moreno Vicente , Angosto Trinidad , Lozano Rafael 
Published: January 2016

AbstractInflorescence development is a key factor of plant productivity, as it determines flower number. Therefore, understanding the mechanisms that regulate inflorescence architecture is critical for reproductive success and crop yield. In this study, a new mutant, vegetative inflorescence (mc-vin), was isolated from the screening of a tomato (Solanum lycopersicum L.) T-DNA mutant collection. The mc-vin mutant developed inflorescences that reverted to vegetative growth after forming two to three flowers, indicating that the mutated gene is essential for the maintenance of inflorescence meristem identity. The T-DNA was inserted into the promoter region of the MACROCALYX (MC) gene; this result together with complementation test and expression analyses proved that mc-vin is a new knock-out allele of MC. Double combinations between mc-vin and jointless (j) and single flower truss (sft) inflorescence mutants showed that MC has pleiotropic effects on the reproductive phase and that it interacts with SFT and J to control floral transition and inflorescence fate in tomato. In addition, MC expression was mis-regulated in j and sft mutants whereas J and SFT were significantly up-regulated in the mc-vin mutant. Together, these results provide new evidences about MC function as part of the genetic network regulating the development of tomato inflorescence meristem.
Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems
Authors: Grunert Oliver , Hernandez-Sanabria Emma , Vilchez-Vargas Ramiro , Jauregui Ruy , Pieper Dietmar H. , Perneel Maaike , Van Labeke Marie-Christine , Reheul Dirk , Boon Nico 
Published: January 2016

AbstractThe choice of soilless growing medium for plant nutrition, growth and support is crucial for improving the eco-sustainability of the production in horticultural systems. As our current understanding of the functional microbial communities inhabiting this ecosystem is still limited, we examined the microbial community development of the two most important growing media (organic and mineral) used in open soilless horticultural systems. We aimed to identify factors that influence community composition over time and to compare the distribution of individual taxa across growing media and their potential functionality. High throughput sequencing analysis revealed a distinctive and stable microbial community in the organic growing medium. Humidity, pH, nitrate-N, ammonium-N and conductivity were uncovered as the main factors associated with the resident bacterial communities. Ammonium-N was correlated with Rhizobiaceae abundance, while potential competitive interactions among both Methylophilaceae and Actinobacteridae with Rhizobiaceae were suggested. Our results revealed that soilless growing media are unique niches for diverse bacterial communities with temporal functional stability, which may possibly impact the resistance to external forces. These differences in communities can be used to develop strategies to move towards a sustainable horticulture with increased productivity and quality.
Cryptic effects of habitat declines: coral-associated fishes avoid coral-seaweed interactions due to visual and chemical cues
Authors: Brooker Rohan M. , Brandl Simon J. , Dixson Danielle L. 
Published: January 2016

AbstractSeaweed-dominated coral reefs are becoming increasingly common as environmental conditions shift away from those required by corals and toward those ideal for rampant seaweed growth. How coral-associated organisms respond to seaweed will not only impact their fate following environmental change but potentially also the trajectories of the coral communities on which they rely. However, behavioral responses by coral-associated organisms to seaweeds are poorly understood. This study examined interactions between a guild of obligate and opportunistic coral-feeding butterflyfishes (Chaetodontidae) and scleractinian corals to determine whether fishes continue to interact with corals in contact with seaweed or if they are avoided. Under natural conditions, all species interacted almost exclusively with seaweed-free corals. In a controlled patch reef experiment, fishes avoided corals in physical contact with seaweed, irrespective of dietary preferences. When visual seaweed cues were removed, butterflyfish continued to avoid corals that had been in contact with the allelopathic Galaxaura filamentosa, suggesting that chemical cues produced by coral-seaweed interactions are repellent. These findings suggest that, due to deleterious visual and chemical cues produced by coral-seaweed interactions, coral-associated organisms may struggle to locate resources as seaweed-free corals decline in abundance.
Potent Antibacterial Nanoparticles against Biofilm and Intracellular Bacteria
Authors: Mu Haibo , Tang Jiangjiang , Liu Qianjin , Sun Chunli , Wang Tingting , Duan Jinyou 
Published: January 2016

AbstractThe chronic infections related to biofilm and intracellular bacteria are always hard to be cured because of their inherent resistance to both antimicrobial agents and host defenses. Herein we develop a facile approach to overcome the above conundrum through phosphatidylcholine-decorated Au nanoparticles loaded with gentamicin (GPA NPs). The nanoparticles were characterized by scanning electron microscopy (SEM), dynamic light scattering (DLS) and ultraviolet−visible (UV−vis) absorption spectra which demonstrated that GPA NPs with a diameter of approximately 180 nm were uniform. The loading manner and release behaviors were also investigated. The generated GPA NPs maintained their antibiotic activities against planktonic bacteria, but more effective to damage established biofilms and inhibited biofilm formation of pathogens including Gram-positive and Gram-negative bacteria. In addition, GPA NPs were observed to be nontoxic to RAW 264.7 cells and readily engulfed by the macrophages, which facilitated the killing of intracellular bacteria in infected macrophages. These results suggested GPA NPs might be a promising antibacterial agent for effective treatment of chronic infections due to microbial biofilm and intracellular bacteria.
Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers
Authors: Wang Jun , Bonnesen Peter V. , Rangel E. , Vallejo E. , Sanchez-Castillo Ariadna , James Cleaves II H. , Baddorf Arthur P. , Sumpter Bobby G. , Pan Minghu , Maksymovych Petro , Fuentes-Cabrera Miguel 
Published: January 2016

AbstractSelf-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N9-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two or more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. These characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Further, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.
Connectomic markers of disease expression, genetic risk and resilience in bipolar disorder
Authors: Dima D , Roberts R E , Frangou S 
Published: January 2016

AbstractBipolar disorder (BD) is characterized by emotional dysregulation and cognitive deficits associated with abnormal connectivity between subcortical—primarily emotional processing regions—and prefrontal regulatory areas. Given the significant contribution of genetic factors to BD, studies in unaffected first-degree relatives can identify neural mechanisms of genetic risk but also resilience, thus paving the way for preventive interventions. Dynamic causal modeling (DCM) and random-effects Bayesian model selection were used to define and assess connectomic phenotypes linked to facial affect processing and working memory in a demographically matched sample of first-degree relatives carefully selected for resilience (n=25), euthymic patients with BD (n=41) and unrelated healthy controls (n=46). During facial affect processing, patients and relatives showed similarly increased frontolimbic connectivity; resilient relatives, however, evidenced additional adaptive hyperconnectivity within the ventral visual stream. During working memory processing, patients displayed widespread hypoconnectivity within the corresponding network. In contrast, working memory network connectivity in resilient relatives was comparable to that of controls. Our results indicate that frontolimbic dysfunction during affect processing could represent a marker of genetic risk to BD, and diffuse hypoconnectivity within the working memory network a marker of disease expression. The association of hyperconnectivity within the affect-processing network with resilience to BD suggests adaptive plasticity that allows for compensatory changes and encourages further investigation of this phenotype in genetic and early intervention studies.
Combination OX40 agonism/CTLA-4 blockade with HER2 vaccination reverses T-cell anergy and promotes survival in tumor-bearing mice
Authors: Linch Stefanie N. , Kasiewicz Melissa J. , McNamara Michael J. , Hilgart-Martiszus Ian F. , Farhad Mohammad , Redmond William L. 
Published: January 2016

SignificanceSeveral immunotherapies are approved for treating cancer patients, including aCTLA-4 (anti–cytotoxic T-lymphocyte–associated protein 4; ipilimumab) and anti–PD-1 (anti-programmed cell death protein 1; nivolumab; pembrolizumab), but the best clinical results are coming from combination immunotherapy. Our research demonstrates that aOX40 (anti-CD134)/aCTLA-4 immunotherapy can lead to a potentially tumor-promoting Th2-cytokine milieu (IL-4, IL-5, IL-13) when relying on endogenous antigen presentation. However, aOX40/aCTLA-4 treatment combined with a tumor antigen-specific vaccine, DEC-205 (anti–dendritic and epithelial cells, 205 kDa)–HER2 (human epidermal growth factor receptor 2), promoted robust tumor infiltration by effector CD8 T cells and restored Th1 polarization of CD4 T cells, leading to improved overall survival in a mammary carcinoma model. This study has direct relevance for the design of combination therapy trials in patients.
Scanning Electron Microscopic Features of Extubated Monoka Stents
Authors: Ali Mohammad Javed , Baig Farhana , Lakhsman Mekala , Naik Milind N. 
Published: January 2016

Purpose:
The aim of this study was to examine the presence of surface and intraluminal biofilms and physical deposits on the extubated Monoka stents.

Methods:
A prospective interventional study was performed on consecutive patients who underwent Monoka stents placement for varied indications. The patient samples were retrieved either at 6 weeks or 3 months after the surgery based on the indication for stent use. None of the patients had any clinical evidence of postoperative infection. The intraluminal portions studied include the distal cut ends as well as the entire intraluminal surface. The analysis was performed using the standard protocols of scanning electron microscopy. The external and internal surfaces were compared against sterile stents which acted as controls.

Results:
A total of 12 stents were studied. Ten were consecutive patient samples and 2 were sterile stents. The external surfaces, cut ends as well as intraluminal surfaces of all the patient stents demonstrated evidence of biofilm formation and physical deposits. The most preferential site of the deposits was the ampullary portion of the stent head. The biofilms and deposits were more extensive in stents retained for 3 months as compared with 6 weeks. Intraluminal surfaces, all through showed clumps of physical deposits and bacterial biofilms with intervening skip areas.

Conclusions:
All surfaces of Monoka stents harbor physical deposits and biofilms. Lumen-less Monoka stents may prevent the lumens from acting as additional biofilm nidus.