bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computing protein dynamics from protein structure with elastic network models
Authors: Bastolla Ugo 
Published: April 2014

Elastic network models ENMs allow to analytically predict the equilibrium dynamics of proteins without the need of lengthy simulations and force fields, and they depend on a small number of parameters and choices. Despite they are valid only for small fluctuations from the mean native structure, it was observed that large functional conformation changes are well described by a small number of low frequency normal modes. This observation has greatly stimulated the application of ENMs for studying the functional dynamics of proteins, and it is prompting the question whether this functional dynamics is a target of natural selection. From a physical point of view, the agreement between low frequency normal modes and large conformation changes is stimulating the study of anharmonicity in protein dynamics, probably one of the most interesting direction of development in ENMs. ENMs have many applications, of which we will review four general types: (1) the efficient sampling of native conformation space, with applications to molecular replacement in X‐ray spectroscopy, cryo electro‐miscroscopy, docking and homology modeling; (2) the prediction of paths of conformation change between two known end states; (3) the comparison of the dynamics of evolutionarily related proteins; (4) the prediction of dynamical couplings that allow the allosteric regulation of the active site from a distant control regions, with possible applications in the development of allosteric drugs. These goals have important biotechnological applications that are driving more and more attention on the analytical study of protein dynamics through ENMs. WIREs Comput Mol Sci 2014, 4:488–503.This article is categorized under:

Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Two‐year cyclicity in recruitment of a fish population is driven by an inter‐stage effect
Authors: Marjomäki Timo J. , Urpanen Olli , Karjalainen Juha 
Published: April 2014

AbstractA 25‐year time series for a vendace (Coregonus albula (L.)) population was analysed with mathematical models to reveal the factors that regulate its recruitment. The fitted recruitment model was an age‐structured model incorporating the compensatory effects of the spawning population and the abundance of the previous year class. Wind forcing index was also added as an example of an external source of recruitment variability. The auto‐correlation analysis revealed a tendency for 2‐year generation cyclicity in recruitment. The compensatory effects of both spawning biomass and previous year class abundance on recruitment had to be incorporated into the model to remove cyclicity from residuals. Wind forcing during the larval and early juvenile periods negatively affected recruitment. Re‐estimating the parameters of the Cushing recruitment function and the effect of previous year‐class from simulated data revealed that the time series structure and measurement errors induce strong biases in parameters exaggerating the density independent population growth rate parameter and the amount of compensation. The negative effect of previous year class was also exaggerated but less severely. Simulations with the artificially perturbed deterministic model skeleton revealed a tendency for cyclicity in recruitment. The model typically generated dampening oscillations, but the dynamics appeared as limit cycles when assuming high mortality, a low level of compensation by spawning biomass and a considerable negative effect of the previous year‐class. No single ultimate mechanism for inter‐stage effects causing cyclicity can be presently designated despite the rather extensive studies on vendace population dynamics. Several of the suggested mechanisms may be operating in concert.
Covariation between mean vole density and variability drives the numerical response of storks to vole prey
Authors: Barraquand Frédéric , Hušek Jan 
Published: April 2014

AbstractHušek et al. (Popul Ecol 55:363–375, 2013) showed that the numerical response of storks to vole prey was stronger in regions where variability in vole density was higher. This finding is, at first sight, in contradiction with the predictions of life‐history theory in stochastic environments. Since the stork productivity‐vole density relationship is concave, theory predicts a negative association between the temporal variability in vole density and stork productivity. Here, we illustrate this negative effect of vole variability on stork productivity with a simple mathematical model relating expected stork productivity to vole dynamics. When comparing model simulations to the observed mean density and variability of thirteen Czech and Polish vole populations, we find that the observed positive effect of vole variability on stork numerical response is most likely due to an unusual positive correlation between mean and variability of vole density.
Does darkness limit the use of tree cavities for nesting by birds?
Authors: Maziarz Marta , Wesołowski Tomasz 
Published: April 2014

AbstractTree cavities are usually superabundant, and offer the safest nest sites. However, not all bird species utilize them. One of the reasons could be insufficient illumination in such places. As no visual system can operate in complete darkness, some nest cavities may be too dark to be usable even by cavity nesters, and some species may not have sufficient visual sensitivity to make use of dark cavities. So, presumably, light conditions could constrain both the evolution of the cavity-nesting habit and the selection of the nest site by the cavity-nesting birds. However, due to a paucity of data on light conditions in cavities, these suggestions have not been investigated to date. To provide more information on illumination inside tree cavities, we took measurements inside the nest cavities of Collared FlycatchersFicedula albicollisbreeding in a primeval forest (Białowieża National Park, Poland). Illuminance inside cavities was recorded at daybreak, just after the parents commenced feeding nestlings. We found that only ca. 4 % of incoming light reached the nest level, and birds could adjust light conditions inside cavities by placing their nests closer to smaller entrances. Illuminance at nests (median = 0.05 lx) fell within the mesopic–scotopic range of vertebrate eyes. Measurements performed on a sunny, cloudless midday in a model cavity showed that illuminance strongly decreased with distance from the entrance. Our results indicate cavities are always dark places where colour vision is usually impaired or absent and the “lighting” requirements of cavity nesters can affect their use of tree cavities. We discuss the implications of the findings for understanding the adaptations of cavity nesting in birds.
Characterization of miRNomes in Acute and Chronic Myeloid Leukemia Cell Lines
Authors: Xiong Qian , Yang Yadong , Wang Hai , Li Jie , Wang Shaobin , Li Yanming , Yang Yaran , Cai Kan , Ruan Xiuyan , Yan Jiangwei , Hu Songnian , Fang Xiangdong 
Published: April 2014

Abstract
Myeloid leukemias are highly diverse diseases and have been shown to be associated with microRNA (miRNA) expression aberrations. The present study involved an in-depth miRNome analysis of two human acute myeloid leukemia (AML) cell lines, HL-60 and THP-1, and one human chronic myeloid leukemia (CML) cell line, K562, via massively parallel signature sequencing. mRNA expression profiles of these cell lines that were established previously in our lab facilitated an integrative analysis of miRNA and mRNA expression patterns. miRNA expression profiling followed by differential expression analysis and target prediction suggested numerous miRNA signatures in AML and CML cell lines. Some miRNAs may act as either tumor suppressors or oncomiRs in AML and CML by targeting key genes in AML and CML pathways. Expression patterns of cell type-specific miRNAs could partially reflect the characteristics of K562, HL-60 and THP-1 cell lines, such as actin filament-based processes, responsiveness to stimulus and phagocytic activity. miRNAs may also regulate myeloid differentiation, since they usually suppress differentiation regulators. Our study provides a resource to further investigate the employment of miRNAs in human leukemia subtyping, leukemogenesis and myeloid development. In addition, the distinctive miRNA signatures may be potential candidates for the clinical diagnosis, prognosis and treatment of myeloid leukemias.
Interventions for Attention Problems After Pediatric Traumatic Brain Injury: What Is the Evidence?
Authors: Backeljauw Barynia , Kurowski Brad G. 
Published: April 2014

ObjectiveTo gain an understanding of the current state of the evidence for management of attention problems after traumatic brain injury (TBI) in children, determine gaps in the literature, and make recommendations for future research.TypeFocused systematic review.Literature SurveyPubMed/Medline and PsychINFO databases were searched for relevant articles published in English during the last 20 years. Keywords included “attention” “attention deficit and disruptive behavior disorders,” and “brain injuries.” Studies were limited to children.MethodologyTitles were examined first and eliminated based on lack of relevancy to attention problems after brain injury in children. This was followed by an abstract and full text review. Article quality was determined based on the US Preventative Services Task Force recommendations for evidence grading.SynthesisFour pharmacologic and 10 cognitive therapy intervention studies were identified. These studies varied in level of evidence quality but were primarily nonrandomized or cohort studies.ConclusionsThere are studies that demonstrate benefits of varying pharmacologic and cognitive therapies for the management of attention problems after TBI. However, there is a paucity of evidence available to definitively guide management of attention problems after pediatric TBI. Larger randomized, controlled trials and multicenter studies are needed to elucidate optimal treatment strategies in this population.
Cortical control of adaptation and sensory relay mode in the thalamus
Authors: Mease Rebecca A. , Krieger Patrik , Groh Alexander 
Published: April 2014

Significance
Given the mismatch between the nervous system's limited computational capability and the immense information content of the sensory environment, the brain must selectively focus attention on relevant stimulus aspects. “Sensory gating” describes the filtering of relevant sensory cues from irrelevant or redundant stimuli. One such filter may involve cortical control of sensory relay through the thalamus. Using optogenetics to turn on specific cortical input to the thalamus, we investigated how the brain actively controls and gates the information that reaches higher stages of processing in the cortex. We found that this pathway, conserved across most mammalian sensory systems, serves as an effective top-down controller of thalamic gating of dynamic patterns of sensory input.
Long-range repulsion of colloids driven by ion exchange and diffusiophoresis
Authors: Florea Daniel , Musa Sami , Huyghe Jacques M. R. , Wyss Hans M. 
Published: April 2014

Significance
The ability to displace particles or solutes relative to a background liquid is of central importance to technologies such as filtration/separation, chromatography, and water purification. Such behavior is observed in so-called exclusion zone formation, an effect where particles are pushed away from a surface over long distances of up to hundreds of micrometers. However, it is still unclear which physical mechanisms are responsible. Our work provides a detailed understanding of this exclusion zone formation, enabling a precise control of the behavior. This could be exploited, for instance, for sorting in microfluidic devices, in advanced antifouling coatings, or for elucidating biological processes where it is likely to play an important, yet unexplored role.
Stoichiometry and specific assembly of Best ion channels
Authors: Bharill Shashank , Fu Zhu , Palty Raz , Isacoff Ehud Y. 
Published: April 2014

Significance
Human Bestrophin (hBest) proteins represent a four-member family of calcium-activated chloride channels that regulate neuronal excitability, synaptic activity and retinal homeostasis. The number of subunits in a hBest channel and the ability to form heteromeric channels have been matters of debate. Using single molecule subunit analysis, we find that each of the hBest channels forms a homotetrameric channel. Despite considerable conservation among hBests, the members have little or no tendency to hetero-assemble. We identify the domain responsible for homo-assembly specificity.
CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference
Authors: Hochstrasser Megan L. , Taylor David W. , Bhat Prashant , Guegler Chantal K. , Sternberg Samuel H. , Nogales Eva , Doudna Jennifer A. 
Published: April 2014

Significance
Bacteria use clustered regularly interspaced short palindromic repeats (CRISPRs) together with CRISPR-associated (Cas) proteins to defend themselves against viral infection. The CRISPR locus contains short segments acquired from viral genomes, and RNAs derived from these segments assemble with Cas proteins into programmable DNA-binding complexes that target DNA molecules complementary to the guide RNA for cleavage. In type I CRISPR-Cas systems, the CRISPR-associated complex for antiviral defense (Cascade) binds to target DNA sequences and then recruits the Cas3 enzyme to repeatedly cleave the bound DNA. In this study, we show how Cascade positions both the DNA and Cas3 to ensure DNA cleavage.
The ARC1 E3 Ligase Promotes Two Different Self-Pollen Avoidance Traits inArabidopsis
Authors: Indriolo Emily , Safavian Darya , Goring Daphne R. 
Published: April 2014

AbstractFlowering plants have evolved various strategies for avoiding self-pollen to drive genetic diversity. These strategies include spatially separated sexual organs (herkogamy), timing differences between male pollen release and female pistil receptivity (dichogamy), and self-pollen rejection. Within the Brassicaceae, these outcrossing systems are the evolutionary default state, and many species display these traits, including Arabidopsis lyrata. In contrast to A. lyrata, closely related Arabidopsis thaliana has lost these self-pollen traits and thus represents an excellent system to test genes for reconstructing these evolutionary traits. We previously demonstrated that the ARC1 E3 ligase is required for self-incompatibility in two diverse Brassicaceae species, Brassica napus and A. lyrata, and is frequently deleted in self-compatible species, including A. thaliana. In this study, we examined ARC1's requirement for reconstituting self-incompatibility in A. thaliana and uncovered an important role for ARC1 in promoting a strong and stable pollen rejection response when expressed with two other A. lyrata self-incompatibility factors. Furthermore, we discovered that ARC1 promoted an approach herkogamous phenotype in A. thaliana flowers. Thus, ARC1's expression resulted in two different A. lyrata traits for self-pollen avoidance and highlights the key role that ARC1 plays in the evolution and retention of outcrossing systems.
The Enzyme-Like Domain of Arabidopsis Nuclear β-Amylases Is Critical for DNA Sequence Recognition and Transcriptional Activation
Authors: Soyk Sebastian , Šimková Klára , Zürcher Evelyne , Luginbühl Leonie , Brand Luise H. , Vaughan Cara K. , Wanke Dierk , Zeeman Samuel C. 
Published: April 2014

Abstract
Plant BZR1-BAM transcription factors contain a β-amylase (BAM)–like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains appear to be noncatalytic, but they determine the function of the two Arabidopsis thaliana BZR1-BAM isoforms (BAM7 and BAM8) during transcriptional initiation. Removal or swapping of the BAM domains demonstrates that the BAM7 BAM domain restricts DNA binding and transcriptional activation, while the BAM8 BAM domain allows both activities. Furthermore, we demonstrate that BAM7 and BAM8 interact on the protein level and cooperate during transcriptional regulation. Site-directed mutagenesis of residues in the BAM domain of BAM8 shows that its function as a transcriptional activator is independent of catalysis but requires an intact substrate binding site, suggesting it may bind a ligand. Microarray experiments with plants overexpressing truncated versions lacking the BAM domain indicate that the pseudo-enzymatic domain increases selectivity for the preferred cis-regulatory element BBRE (BZR1-BAM Responsive Element). Side specificity toward the G-box may allow crosstalk to other signaling networks. This work highlights the importance of the enzyme-derived domain of BZR1-BAMs, supporting their potential role as metabolic sensors.
The Cyanobacterial Photoactive Orange Carotenoid Protein Is an Excellent Singlet Oxygen Quencher
Authors: Sedoud Arezki , López-Igual Rocío , ur Rehman Ateeq , Wilson Adjélé , Perreau François , Boulay Clémence , Vass Imre , Krieger-Liszkay Anja , Kirilovsky Diana 
Published: April 2014

Abstract
Cyanobacteria have developed a photoprotective mechanism that decreases the energy arriving at the photosynthetic reaction centers under high-light conditions. The photoactive orange carotenoid protein (OCP) is essential in this mechanism as a light sensor and energy quencher. When OCP is photoactivated by strong blue-green light, it is able to dissipate excess energy as heat by interacting with phycobilisomes. As a consequence, charge separation and recombination leading to the formation of singlet oxygen diminishes. Here, we demonstrate that OCP has another essential role. We observed that OCP also protects Synechocystis cells from strong orange-red light, a condition in which OCP is not photoactivated. We first showed that this photoprotection is related to a decrease of singlet oxygen concentration due to OCP action. Then, we demonstrated that, in vitro, OCP is a very good singlet oxygen quencher. By contrast, another carotenoid protein having a high similarity with the N-terminal domain of OCP is not more efficient as a singlet oxygen quencher than a protein without carotenoid. Although OCP is a soluble protein, it is able to quench the singlet oxygen generated in the thylakoid membranes. Thus, OCP has dual and complementary photoprotective functions as an energy quencher and a singlet oxygen quencher.
Calcitriol inhibits keratinocyte proliferation by upregulating leukocyte elastase inhibitor (serpin B1)
Authors: Hui Li , Yongxia Zheng , Zhili Guo , Jun Gu 
Published: April 2014

AbstractCalcitriol had been proved to be effective for treatment of psoriasis vulgaris. However, the molecular events leading to the normalization of keratinocyte differentiation had not been fully explored. The aim of the study was to evaluate the role of calcitriol and serpin B1 in human keratinocyte cell line (HaCaT) proliferation. Proteins extracted from calcitriol‐treated and untreated HaCaT were separated by 2‐D differential gel electrophoresis (2DE). Then, the 2DE profiles were analyzed to screen for differentially expressed proteins, which were identified by matrix‐assisted laser desorption/ionization time of flight mass spectrometry. The upregulation of serpin B1 was confirmed by quantitative reverse transcription polymerase chain reaction (qRT–PCR) and western blot analysis. The effect of serpin B1 on HaCaT proliferation was analyzed by RNA interference experiments, methylthiazoletetrazolium assay and flow cytometry. Reproducible 2‐DE profiles of HaCaT were established. The result that serpin B1 was upregulated in the calcitriol‐treated group was confirmed by qRT–PCR and western blot analysis. Calcitriol could inhibit proliferation of HaCaT at the concentration of 10−9–10−6 mol/L. HaCaT proliferation was promoted when serpin B1 was interfered. The inhibition effect of calcitriol was stopped after serpin B1 was interfered. Serpin B1 was overexpressed in calcitriol‐treated HaCaT cells and may play an important role in inhibiting HaCaT proliferation by calcitriol.
Entero‐Behçet's disease coexisting with long‐term epilepsy and schizophrenia‐like symptoms
Authors: Ohtsuka Tsutomu 
Published: April 2014

AbstractEntero‐Behçet's disease coexisting with long‐term epilepsy and schizophrenia‐like symptoms is presented. A 43‐year‐old woman presented with repeatedly occurring aphthous stomatitis for several years. She had been treated for absence seizures, epilepsy and schizophrenia since she was 9 years old. She presented with multiple aphthous stomatitis on her gingiva, erythema nodosum‐like symptoms on the right lateral aspect of her leg and genital ulcers on her perianal area. She also showed polyarthritis. Laboratory examinations revealed elevated C‐reactive protein, elevated neutrophil counts, decreased serum Fe and elevated serum Cu. Histological examination showed perivascular neutrophil and mononuclear cell infiltrates and eosinophilic change of the vessel wall in the lobules of subcutaneous fat tissue. Six weeks after the oral prednisolone therapy, she showed resolution of aphthous stomatitis, folliculitis‐like eruption and genital ulcer. She experienced severe abdominal pain after the start of treatment of Behçet's disease. Plain computed tomography revealed edematous change in the appendix, and ascending and transverse colon. These results led to the diagnosis of entero‐Behçet's disease acute exaggeration. Treatment with infliximab (300 mg/once) was started. Eight weeks after the start of infliximab, her abdominal pain disappeared and C‐reactive protein decreased, followed by the successful change to adalimumab infusion therapy.
Mouse bone marrow‐derived dendritic cells can phagocytize the Sporothrix schenckii, and mature and activate the immune response by secreting interleukin‐12 and presenting antigens to T lymphocytes
Authors: Kusuhara Masahiro , Qian Hua , Li Xiaoguang , Tsuruta Daisuke , Tsuchisaka Atsunari , Ishii Norito , Ohata Chika , Furumura Minao , Hashimoto Takashi 
Published: April 2014

AbstractIn sporotrichosis, dermal dendritic cells were considered to participate in induction of the immune responses against Sporothrix schenckii infection. However, it is still unclear whether and how dermal dendritic cells were involved in the progress. To clarify the pathogenic role of dermal dendritic cells (DC) in sporotrichosis, we examined the phagocytosis, maturation stages, cytokine production and antigen‐presenting ability of mouse bone marrow‐derived DC after stimulation with S. schenckii. By analysis of flow cytometry, electron microscope and confocal microscope, mouse bone marrow‐derived DC were proved to be able to phagocytize the S. schenckii. The increased expression of CD40, CD80 and CD86 on the surface of S. schenckii‐pulsed mouse bone marrow‐derived DC was detected by flow cytometer, indicating that the S. schenckii‐pulsed mouse bone marrow‐derived DC underwent the maturation program. The secretory enhancement of interleukin (IL)‐12, but not IL‐4, was found in S. schenckii‐pulsed mouse bone marrow‐derived DC, suggesting the possible activation of T‐helper 1 prone immune responses. Furthermore, S. schenckii‐pulsed mouse bone marrow‐derived DC were demonstrated to be capable of inducing the proliferation of T lymphocytes from BALB/c mice that were pre‐sensitized with S. schenckii. Together, all the results implied that dermal DC may participate in the induction of immune responses against S. schenckii infection in sporotrichosis.