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https://www.readbyqxmd.com/read/27936329/chemomechanical-coupling-in-hexameric-protein-protein-interfaces-harness-energy-within-v-type-atpases
#1
Abhishek Singharoy, Christophe Chipot, Mahmoud Moradi, Klaus Schulten
ATP synthase is the most prominent bioenergetic macromolecular motor in all life-forms, utilizing the proton gradient across the cell membrane to fuel the synthesis of ATP. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, the precise molecular mechanism whereby vacuolar (V-type) ATP synthase fulfills its biological function remains largely fragmentary. Recently, crystallographers provided the first high-resolution view of ATP activity in Enterococcus hirae V1-ATPase...
December 9, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27934224/heterogeneity-during-plasticization-of-poly-vinylpyrrolidone-insights-from-reorientational-mobility-of-single-fluorescent-probes
#2
Sukanya Bhattacharya, Dharmendar Kumar Sharma, Suman De, Jaladhar Mahato, Arindam Chowdhury
While dynamics of single-molecule (SM) fluorescent probes have been used to investigate the structure and relaxation processes in polymers near the glass transition temperature (Tg), it is difficult to perform SM imaging at elevated temperatures which restricts such studies to a limited number of polymers for which Tg is close to room temperature (RT). Plasticization, solvent (or additive) induced lowering of Tg, offers an alternate avenue to access various effective temperatures in the glassy and rubbery phases of polymers under ambient conditions...
December 8, 2016: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/27933791/mechanistic-insights-from-the-crystal-structure-of-bacillus-subtilis-o-succinylbenzoyl-coa-synthetase-complexed-with-the-adenylate-intermediate
#3
Yaozong Chen, Yiping Jiang, Zhihong Guo
o-Succinylbenzoyl-CoA (OSB-CoA) synthetase, or MenE, catalyzes an essential step in vitamin K biosynthesis and is a valuable drug target. Like many other adenylating enzymes, it changes its structure to accommodate substrate binding, catalysis, and product release along the path of a domain alternation catalytic mechanism. We have determined the crystal structure of its complex with the adenylation product, o-succinylbenzoyl-adenosine monophosphate (OSB-AMP), and captured a new postadenylation state. This structure presents unique features such as a strained conformation for the bound adenylate intermediate to indicate that it represents the enzyme state after completion of the adenylation reaction but before release of the C domain in its transition to the thioesterification conformation...
December 6, 2016: Biochemistry
https://www.readbyqxmd.com/read/27932399/novel-hybrid-phenotype-revealed-in-small-cell-lung-cancer-by-a-transcription-factor-network-model-that-can-explain-tumor-heterogeneity
#4
Akshata R Udyavar, David J Wooten, Megan D Hoeksema, Mukesh Bansal, Andrea Califano, Lourdes Estrada, Santiago Schnell, Jonathan M Irish, Pierre P Massion, Vito Quaranta
Small cell lung cancer (SCLC) is a devastating disease due to its propensity for early invasion and refractory relapse after initial treatment response. Although these aggressive traits have been associated with phenotypic heterogeneity, our understanding of this association remains incomplete. To fill this knowledge gap, we inferred a set of 33 transcription factors (TF) associated with gene signatures of the known neuroendocrine/epithelial (NE) and non-neuroendocrine/mesenchymal-like (ML) SCLC phenotypes...
December 8, 2016: Cancer Research
https://www.readbyqxmd.com/read/27929005/a-persistent-and-dynamic-east-greenland-ice-sheet-over-the-past-7-5-million-years
#5
Paul R Bierman, Jeremy D Shakun, Lee B Corbett, Susan R Zimmerman, Dylan H Rood
Climate models show that ice-sheet melt will dominate sea-level rise over the coming centuries, but our understanding of ice-sheet variations before the last interglacial 125,000 years ago remains fragmentary. This is because terrestrial deposits of ancient glacial and interglacial periods are overrun and eroded by more recent glacial advances, and are therefore usually rare, isolated and poorly dated. In contrast, material shed almost continuously from continents is preserved as marine sediment that can be analysed to infer the time-varying state of major ice sheets...
December 7, 2016: Nature
https://www.readbyqxmd.com/read/27928633/rna-processing-body-p-body-dynamics-in-mesophyll-protoplasts-re-initiating-cell-division
#6
Dilbag S Bhullar, Michael B Sheahan, Ray J Rose
The ability of plants to regenerate lies in the capacity of differentiated cells to reprogram and re-enter the cell cycle. Reprogramming of cells requires changes in chromatin organisation and gene expression. However, there has been less focus on changes at the post transcription level. We have investigated P-bodies, sites of post transcriptional gene regulation, in plant cell reprogramming in cultured mesophyll protoplasts; by using a YFP-VARICOSE (YFP-VCSc) translational fusion. We showed an early increase in P-body number and volume, followed by a decline, then a subsequent continued increase in P-body number and volume as cell division was initiated and cell proliferation continued...
December 7, 2016: Protoplasma
https://www.readbyqxmd.com/read/27928070/novel-response-patterns-during-repeated-presentation-of-affective-and-neutral-stimuli
#7
Ajay B Satpute, Lydia Hanington, Lisa F Barrett
Repeated stimulus presentations are commonly used in social and affective neuroimaging tasks, but much remains to be known about how the brain processes such repetitions. Using functional magnetic resonance imaging, we found three groups of brain regions with distinct response patterns during repeated presentations of natural scene images. One group consisted of several limbic, paralimbic, frontoparietal and medial prefrontal areas and showed a habituation-like response across pleasant, unpleasant, and neutral image categories...
December 2016: Social Cognitive and Affective Neuroscience
https://www.readbyqxmd.com/read/27924812/interstitial-oxygen-as-a-source-of-p-type-conductivity-in-hexagonal-manganites
#8
Sandra H Skjærvø, Espen T Wefring, Silje K Nesdal, Nikolai H Gaukås, Gerhard H Olsen, Julia Glaum, Thomas Tybell, Sverre M Selbach
Hexagonal manganites, h-RMnO3 (R=Sc, Y, Ho-Lu), have been intensively studied for their multiferroic properties, magnetoelectric coupling, topological defects and electrically conducting domain walls. Although point defects strongly affect the conductivity of transition metal oxides, the defect chemistry of h-RMnO3 has received little attention. We use a combination of experiments and first principles electronic structure calculations to elucidate the effect of interstitial oxygen anions, Oi, on the electrical and structural properties of h-YMnO3...
December 7, 2016: Nature Communications
https://www.readbyqxmd.com/read/27923652/mir-211-inhibits-invasion-and-epithelial-to-mesenchymal-transition-emt-of-cervical-cancer-cells-via-targeting-muc4
#9
Dongkui Xu, Shikai Liu, Liang Zhang, Lili Song
The dysregulated molecules and their involvement in lymph node metastases of cervical cancer are far from been fully revealed. In this study, by reviewing MUC4 expression in The Human Protein Atlas and retrieving gene microarray data in GEO dataset (No. GDS4664), we found that MUC4 upregulation is associated with lymph node metastasis in cervical cancer. Knockdown of MUC4 in Hela and SiHa cells significantly reduced their invasion and also reduced the mesenchymal properties. By performing bioinformatics analysis, we observed that miR-211 is a potential suppressor of MUC4, which has a predicted highly conserved binding site in the 3'UTR of MUC among mammals...
December 3, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27923525/using-clinical-information-to-make-individualized-prognostic-predictions-in-people-at-ultra-high-risk-for-psychosis
#10
Andrea Mechelli, Ashleigh Lin, Stephen Wood, Patrick McGorry, Paul Amminger, Stefania Tognin, Philip McGuire, Jonathan Young, Barnaby Nelson, Alison Yung
Recent studies have reported an association between psychopathology and subsequent clinical and functional outcomes in people at ultra-high risk (UHR) for psychosis. This has led to the suggestion that psychopathological information could be used to make prognostic predictions in this population. However, because the current literature is based on inferences at group level, the translational value of the findings for everyday clinical practice is unclear. Here we examined whether psychopathological information could be used to make individualized predictions about clinical and functional outcomes in people at UHR...
December 3, 2016: Schizophrenia Research
https://www.readbyqxmd.com/read/27913265/hearing-preservation-during-anterior-petrosectomy-the-cochlear-safety-line
#11
Xiaoming Guo, Halima Tabani, Dylan Griswold, Ali Tayebi Meybodi, Jose Juan Gonzalez Sanchez, Michael T Lawton, Arnau Benet
BACKGROUND: Identification and protection of the cochlea during anterior petrosectomy is key to prevent hearing loss. Currently, there is no optimal method to infer the position of the cochlea in relation to the Kawase quadrangle, therefore damage to the cochlea during anterior petrosectomy remains a substantial risk. OBJECTIVES: To identify and define landmarks available during anterior petrosectomy to locate the cochlea and prevent its damage. METHODS: Kawase approach was simulated in eleven specimens...
November 29, 2016: World Neurosurgery
https://www.readbyqxmd.com/read/27893946/predicting-animal-home-range-structure-and-transitions-using-a-multistate-ornstein-uhlenbeck-biased-random-walk
#12
Greg A Breed, Emily A Golson, M Tim Tinker
The home-range concept is central in animal ecology and behavior, and numerous mechanistic models have been developed to understand home range formation and maintenance. These mechanistic models usually assume a single, contiguous home range. Here we describe and implement a simple home-range model that can accommodate multiple home-range centers, form complex shapes, allow discontinuities in use patterns, and infer how external and internal variables affect movement and use patterns. The model assumes individuals associate with two or more home-range centers and move among them with some estimable probability...
October 6, 2016: Ecology
https://www.readbyqxmd.com/read/27890449/independent-evolution-of-genomic-characters-during-major-metazoan-transitions
#13
REVIEW
Oleg Simakov, Takeshi Kawashima
Metazoan evolution encompasses a vast evolutionary time scale spanning over 600 million years. Our ability to infer ancestral metazoan characters, both morphological and functional, is limited by our understanding of the nature and evolutionary dynamics of the underlying regulatory networks. Increasing coverage of metazoan genomes enables us to identify the evolutionary changes of the relevant genomic characters such as the loss or gain of coding sequences, gene duplications, micro- and macro-synteny, and non-coding element evolution in different lineages...
November 25, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27889550/to-infinity-and-beyond-children-generalize-the-successor-function-to-all-possible-numbers-years-after-learning-to-count
#14
Pierina Cheung, Miriam Rubenson, David Barner
Recent accounts of number word learning posit that when children learn to accurately count sets (i.e., become "cardinal principle" or "CP" knowers), they have a conceptual insight about how the count list implements the successor function - i.e., that every natural number n has a successor defined as n+1 (Carey, 2004, 2009; Sarnecka & Carey, 2008). However, recent studies suggest that knowledge of the successor function emerges sometime after children learn to accurately count, though it remains unknown when this occurs, and what causes this developmental transition...
November 24, 2016: Cognitive Psychology
https://www.readbyqxmd.com/read/27886023/quantifying-the-dynamic-of-osa-brain-using-multifractal-formalism-a-novel-measure-for-sleep-fragmentation
#15
Somayeh Raiesdana
It is thought that the critical brain dynamics in sleep is modulated during frequent periods of wakefulness. This paper utilizes the capacity of EEG based scaling analysis to quantify sleep fragmentation in patients with obstructive sleep apnea. The scale-free (fractal) behavior refers to a state where no characteristic scale dominates the dynamics of the underlying process which is evident as long range correlations in a time series. Here, Multiscaling (multifractal) spectrum is utilized to quantify the disturbed dynamic of an OSA brain with fragmented sleep...
November 18, 2016: Technology and Health Care: Official Journal of the European Society for Engineering and Medicine
https://www.readbyqxmd.com/read/27883889/inferring-cell-state-transition-dynamics-from-lineage-trees-and-endpoint-single-cell-measurements
#16
Sahand Hormoz, Zakary S Singer, James M Linton, Yaron E Antebi, Boris I Shraiman, Michael B Elowitz
As they proliferate, living cells undergo transitions between specific molecularly and developmentally distinct states. Despite the functional centrality of these transitions in multicellular organisms, it has remained challenging to determine which transitions occur and at what rates without perturbations and cell engineering. Here, we introduce kin correlation analysis (KCA) and show that quantitative cell-state transition dynamics can be inferred, without direct observation, from the clustering of cell states on pedigrees (lineage trees)...
November 23, 2016: Cell Systems
https://www.readbyqxmd.com/read/27883031/transition-from-glass-to-gel-like-states-in-clay-at-a-liquid-interface
#17
A Gholamipour-Shirazi, M S Carvalho, M F G Huila, K Araki, P Dommersnes, J O Fossum
Colloidal clay in water suspensions are known to exhibit a multitude of bulk phases depending on initial colloidal concentration and ionic strength, and examples of this include repulsive Wigner colloidal glasses at low ionic strength and attractive gels at higher ionic strength due to screened electrostatic forces by the electrolyte. From confocal Raman microscopy combined with elasticity measurements, we infer that clay trapped at quasi two-dimensional interfaces between oil and water also exhibit confined glass-like or gel-like states...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27872245/the-transcription-factor-athb5-affects-ga-mediated-plasticity-in-hypocotyl-cell-growth-during-seed-germination
#18
Petra Stamm, Alexander T Topham, Nur K Mukhtar, Matthew Jackson, Daniel Tome, Jim L Beynon, George W Bassel
The seed to seedling transition is driven exclusively by cell shape changes within the axis of the plant embryo. Using digital single cell analysis of 3D cellular growth, here we identify the presence of two spatially and temporally distinct cell expansion modules within subdomains of the growing embryo. The second growth module is within the hypocotyl and drives the final phase of the completion of germination under optimal conditions. Using network inference, we identified the transcription factor ATHB5 as a genetic factor specifically induced and localized to the hypocotyl prior to its expansion...
November 21, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27870840/single-nanotube-tracking-reveals-the-nanoscale-organization-of-the-extracellular-space-in-the-live-brain
#19
Antoine G Godin, Juan A Varela, Zhenghong Gao, Noémie Danné, Julien P Dupuis, Brahim Lounis, Laurent Groc, Laurent Cognet
The brain is a dynamic structure with the extracellular space (ECS) taking up almost a quarter of its volume. Signalling molecules, neurotransmitters and nutrients transit via the ECS, which constitutes a key microenvironment for cellular communication and the clearance of toxic metabolites. The spatial organization of the ECS varies during sleep, development and aging and is probably altered in neuropsychiatric and degenerative diseases, as inferred from electron microscopy and macroscopic biophysical investigations...
November 21, 2016: Nature Nanotechnology
https://www.readbyqxmd.com/read/27869456/evaluation-of-relational-reasoning-by-a-transitive-inference-task-in-attention-deficit-hyperactivity-disorder
#20
Emiliano Brunamonti, Floriana Costanzo, Anna Mammì, Cristina Rufini, Diletta Veneziani, Pierpaolo Pani, Stefano Vicari, Stefano Ferraina, Deny Menghini
Objective: Here we explored whether children with ADHD have a deficit in relational reasoning, a skill subtending the acquisition of many cognitive abilities and social rules. Method: We analyzed the performance of a group of children with ADHD during a transitive inference task, a task requiring first to learn the reciprocal relationship between adjacent items of a rank ordered series (e.g., A>B; B>C; C>D; D>E; E>F), and second, to deduct the relationship between novel pairs of items never matched during the learning (e...
November 21, 2016: Neuropsychology
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