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https://www.readbyqxmd.com/read/27914045/achievements-and-challenges-in-computational-protein-design
#1
Ilan Samish
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27909893/osteogain%C3%A2-loaded-onto-an-absorbable-collagen-sponge-induces-attachment-and-osteoblast-differentiation-of-st2-cells-in-vitro
#2
Richard J Miron, Masako Fujioka-Kobayashi, Yufeng Zhang, Anton Sculean, Benjamin Pippenger, Yoshinori Shirakata, Umadevi Kandalam, Maria Hernandez
OBJECTIVES: Dimensional changes of the alveolar bone following tooth extraction are a major challenge in daily dental practice. To limit bone loss, a variety of biomaterials including bone grafts, barrier membranes, and growth factors have been utilized either alone or in combination therapies to increase the speed and quality of new bone formation. The aim of the present in vitro study was to investigate the regenerative potential of Osteogain®, a new liquid carrier system of enamel matrix derivative (EMD) in combination with an absorbable collagen sponge (ACS) specifically designed for extraction socket healing...
December 1, 2016: Clinical Oral Investigations
https://www.readbyqxmd.com/read/27899895/developmental-origins-of-cardiometabolic-diseases-role-of-the-maternal-diet
#3
REVIEW
João H Costa-Silva, Aiany C Simões-Alves, Mariana P Fernandes
Developmental origins of cardiometabolic diseases have been related to maternal nutritional conditions. In this context, the rising incidence of arterial hypertension, diabetes type II, and dyslipidemia has been attributed to genetic programming. Besides, environmental conditions during perinatal development such as maternal undernutrition or overnutrition can program changes in the integration among physiological systems leading to cardiometabolic diseases. This phenomenon can be understood in the context of the phenotypic plasticity and refers to the adjustment of a phenotype in response to environmental input without genetic change, following a novel, or unusual input during development...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27899637/a-genome-wide-dosage-suppressor-network-reveals-genomic-robustness
#4
Biranchi Patra, Yoshiko Kon, Gitanjali Yadav, Anthony W Sevold, Jesse P Frumkin, Ravishankar R Vallabhajosyula, Arend Hintze, Bjørn Østman, Jory Schossau, Ashish Bhan, Bruz Marzolf, Jenna K Tamashiro, Amardeep Kaur, Nitin S Baliga, Elizabeth J Grayhack, Christoph Adami, David J Galas, Alpan Raval, Eric M Phizicky, Animesh Ray
Genomic robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of genomic robustness in budding yeast by genome wide dosage suppressor analysis of 53 conditional lethal mutations in cell division cycle and RNA synthesis related genes, revealing 660 suppressor interactions of which 642 are novel. This collection has several distinctive features, including high co-occurrence of mutant-suppressor pairs within protein modules, highly correlated functions between the pairs and higher diversity of functions among the co-suppressors than previously observed...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27894884/modulation-of-the-heat-shock-response-is-associated-with-acclimation-to-novel-temperatures-but-not-adaptation-to-climatic-variation-in-the-ants-aphaenogaster-picea-and-a-rudis
#5
Sara Helms Cahan, Andrew D Nguyen, John Stanton-Geddes, Clint A Penick, Yainna Hernáiz-Hernández, Bernice B DeMarco, Nicholas J Gotelli
Ecological diversification into thermally divergent habitats can push species toward their physiological limits, requiring them to accommodate temperature extremes through plastic or evolutionary changes that increase persistence under the local thermal regime. One way to withstand thermal stress is to increase production of heat shock proteins, either by maintaining higher baseline abundance within cells or by increasing the magnitude of induction in response to heat stress. We evaluated whether environmental variation was associated with expression of three heat shock protein genes in two closely-related species of woodland ant, Aphaenogaster picea and A...
November 25, 2016: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
https://www.readbyqxmd.com/read/27889579/protective-effects-of-high-tryptophan-diet-on-aging-induced-passive-avoidance-impairment-and-hippocampal-apoptosis
#6
Giuseppe Musumeci, Paola Castrogiovanni, Marta Anna Szychlinska, Rosa Imbesi, Carla Loreto, Sergio Castorina, Salvatore Giunta
In our previous work we have shown that L-Tryptophan (TrP) enriched diet prevents the age-induced decline of hippocampal Serotonin (5-HT) production. Considering that loss or reduction in 5-HT neurotransmission may contribute to age-related cognitive decline, here we have investigated the effect of such diet on passive avoidance (PA) behavior, cell death, pro- and anti- apoptotic molecules (BAX, Bcl-2 and Caspase-3) and an important transcription factor involved in synaptic plasticity and memory (CREB). The increase in 5-HT neurotransmission in the Hippocampus (Hp) of aged rats was induced by 1 month of high TrP administration...
November 23, 2016: Brain Research Bulletin
https://www.readbyqxmd.com/read/27885260/nitric-oxide-triggers-a-transient-metabolic-reprogramming-in-arabidopsis
#7
José León, Álvaro Costa, Mari-Cruz Castillo
Nitric oxide (NO) regulates plant growth and development as well as responses to stress that enhanced its endogenous production. Arabidopsis plants exposed to a pulse of exogenous NO gas were used for untargeted global metabolomic analyses thus allowing the identification of metabolic processes affected by NO. At early time points after treatment, NO scavenged superoxide anion and induced the nitration and the S-nitrosylation of proteins. These events preceded an extensive though transient metabolic reprogramming at 6 h after NO treatment, which included enhanced levels of polyamines, lipid catabolism and accumulation of phospholipids, chlorophyll breakdown, protein and nucleic acid turnover and increased content of sugars...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27881782/consolidation-of-goal-directed-action-depends-on-mapk-erk-signaling-in-rodent-prelimbic-cortex
#8
Genevra Hart, Bernard W Balleine
: The prelimbic prefrontal cortex (PL) has consistently been found to be necessary for the acquisition of goal-directed actions in rodents. Nevertheless, the specific cellular processes underlying this learning remain unknown. We assessed changes in learning-related expression of mitogen-activated protein kinase/extracellular signal-related kinase (MAPK/ERK1/2) phosphorylation (pERK) in layers 2-3 and 5-6 of the anterior and posterior PL and in the population of neurons projecting to posterior dorsomedial striatum (pDMS), also implicated in goal-directed learning...
November 23, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27881780/negative-allosteric-modulation-of-mglur5-partially-corrects-pathophysiology-in-a-mouse-model-of-rett-syndrome
#9
Jifang Tao, Hao Wu, Amanda A Coronado, Elizabeth de Laittre, Emily K Osterweil, Yi Zhang, Mark F Bear
: Rett syndrome (RTT) is caused by mutations in the gene encoding methyl-CpG binding protein 2 (MECP2), an epigenetic regulator of mRNA transcription. Here, we report a test of the hypothesis of shared pathophysiology of RTT and fragile X, another monogenic cause of autism and intellectual disability. In fragile X, the loss of the mRNA translational repressor FMRP leads to exaggerated protein synthesis downstream of metabotropic glutamate receptor 5 (mGluR5). We found that mGluR5- and protein-synthesis-dependent synaptic plasticity were similarly altered in area CA1 of Mecp2 KO mice...
November 23, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27876573/stem-cell-therapies-in-age-related-neurodegenerative-diseases-and-stroke
#10
REVIEW
Yuan Wang, Xunming Ji, Rehana K Leak, Fenghua Chen, Guodong Cao
Aging, a complex process associated with various structural, functional and metabolic changes in the brain, is an important risk factor for neurodegenerative diseases and stroke. These diseases share similar neuropathological changes, such as the formation of misfolded proteins, oxidative stress, loss of neurons and synapses, dysfunction of the neurovascular unit (NVU), reduction of self-repair capacity, and motor and/or cognitive deficiencies. In addition to gray matter dysfunction, the plasticity and repair capacity of white matter also decrease with aging and contribute to neurodegenerative diseases...
November 19, 2016: Ageing Research Reviews
https://www.readbyqxmd.com/read/27870021/temperature-dependence-of-predation-stress-and-the-nutritional-ecology-of-a-generalist-herbivore
#11
Oswald J Schmitz, Adam E Rosenblatt, Meredith Smylie
Prey at risk of predation may experience stress and respond physiologically by altering their metabolic rates. Theory predicts that such physiological changes should alter prey nutrient demands from N-rich to C-rich macronutrients and shift the balance between maintenance and growth/reproduction. Theory further suggests that for ectotherms, temperature stands to exacerbate this stress. Yet, the interactive effects of predation stress and temperature stress on diet, metabolism, and survival of ectotherms are not well known...
November 2016: Ecology
https://www.readbyqxmd.com/read/27866972/letrozole-regulates-actin-cytoskeleton-polymerization-dynamics-in-a-src-1-dependent-manner-in-the-hippocampus-of-mice
#12
Yangang Zhao, Yanlan Yu, Yuanyuan Zhang, Li He, Linli Qiu, Jikai Zhao, Mengying Liu, Jiqiang Zhang
In the hippocampus, local estrogens (E2) derived from testosterone that is catalyzed by aromatase play important roles in the regulation of hippocampal neural plasticity, but the underlying mechanisms remain unclear. The actin cytoskeleton contributes greatly to hippocampal synaptic plasticity; however, whether it is regulated by local E2 and the related mechanisms remain to be elucidated. In this study, we first examined the postnatal developmental profiles of hippocampal aromatase and specific proteins responsible for actin cytoskeleton dynamics...
November 17, 2016: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/27860379/behavior-associated-neuronal-activation-after-kainic-acid-induced-hippocampal-neurotoxicity-is-modulated-in-time
#13
Andrea Aguilar-Arredondo, Fernanda López-Hernández, Lizbeth García-Velázquez, Clorinda Arias, Angélica Zepeda
Kainic acid-induced (KA) hippocampal damage leads to neuronal death and further synaptic plasticity. Formation of aberrant as well as of functional connections after such procedure has been documented. However, the impact of such structural plasticity on cell activation along time after damage and in face of a behavioral demand has not been explored. We evaluated if the mRNA and protein levels of plasticity-related protein synaptophysin (Syp and SYP, respectively) and activity-regulated cytoskeleton-associated protein mRNA and protein levels (Arc and Arc, respectively) in the dentate gyrus were differentially modulated in time in response to a spatial-exploratory task after KA-induced hippocampal damage...
November 11, 2016: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/27857725/blood-micrornas-as-potential-diagnostic-and-prognostic-markers-in-cerebral-ischemic-injury
#14
REVIEW
Bridget Martinez, Philip V Peplow
MicroRNAs are a family of small, genome-encoded endogenous RNAs that are transcribed but are not translated into proteins. They serve essential roles in virtually every aspect of brain function, including neurogenesis, neural development, and cellular responses leading to changes in synaptic plasticity. They are also implicated in neurodegeneration and neurological disorders, in responses to hypoxia and ischemia, and in ischemic tolerance induced by ischemic preconditioning. In recent developments, miRNA expression profiling has been examined in stroke, and these studies indicate that miRNAs have emerged as key mediators in ischemic stroke biology...
September 2016: Neural Regeneration Research
https://www.readbyqxmd.com/read/27856287/the-inhibition-of-spinal-synaptic-plasticity-mediated-by-activation-of-amp-activated-protein-kinase-signaling-alleviates-the-acute-pain-induced-by-oxaliplatin
#15
Yun-Zhi Ling, Zhen-Yu Li, Han-Dong Ou-Yang, Chao Ma, Shao-Ling Wu, Jia-You Wei, Huan-Huan Ding, Xiao-Long Zhang, Meng Liu, Cui-Cui Liu, Zhen-Zhen Huang, Wen-Jun Xin
Our recent findings demonstrated that oxaliplatin entering CNS may directly induce spinal central sensitization, and contribute to the rapid development of CNS-related side effects including acute pain during chemotherapy. However, the mechanism is largely unclear. In the current study, we found that the amplitude of C-fiber-evoked field potentials was significantly increased and the expression of phosphorylated mammalian AMP-activated protein kinase α (AMPKα) was markedly decreased following high frequency stimulation (HFS) or single intraperitoneal injection of oxaliplatin (4mg/kg)...
November 14, 2016: Experimental Neurology
https://www.readbyqxmd.com/read/27852964/spinal-astrocytic-activation-contributes-to-mechanical-allodynia-in-a-rat-model-of-cyclophosphamide-induced-cystitis
#16
Bolong Liu, Minzhi Su, ShaoJun Tang, Xiangfu Zhou, Hailun Zhan, Fei Yang, Wenbiao Li, Tengcheng Li, Juncong Xie
BACKGROUND: Previous studies have demonstrated that glial cells play an important role in the generation and maintenance of neuropathic pain. Activated glial cells produce numerous mediators such as proinflammatory cytokines that facilitate neuronal activity and synaptic plasticity. Similarly, bladder pain syndrome/interstitial cystitis shares many characteristics of neuropathic pain. However, related report on the involvement of spinal glia in bladder pain syndrome/interstitial cystitis-associated pathological pain and the underlying mechanisms are still lacking...
2016: Molecular Pain
https://www.readbyqxmd.com/read/27845056/antidepressant-like-effects-of-yl-ipa08-a-potent-ligand-for-the-translocator-protein-18%C3%A2-kda-in-chronically-stressed-rats
#17
Li-Ming Zhang, Yu-Lu Wang, Yan-Qin Liu, Rui Xue, You-Zhi Zhang, Ri-Fang Yang, Yun-Feng Li
The present study aimed to examine the molecular and cellular mechanisms underlying the antidepressant-like effect of YL-IPA08, a novel TSPO ligand designed and synthesized at our institute. We firstly used the chronic unpredictable stress (CUS) procedure of rats, a well validated stress-related animal model of depression, to further determine the antidepressant-like of YL-IPA08. And we found that YL-IPA08 caused significant suppression of inhibiting of locomotor activity, reducing the sucrose preference and increasing the latency to eat induced by CUS...
November 11, 2016: Neuropharmacology
https://www.readbyqxmd.com/read/27825385/neurogenomics-and-the-role-of-a-large-mutational-target-on-rapid-behavioral-change
#18
Craig E Stanley, Rob J Kulathinal
BACKGROUND: Behavior, while complex and dynamic, is among the most diverse, derived, and rapidly evolving traits in animals. The highly labile nature of heritable behavioral change is observed in such evolutionary phenomena as the emergence of converged behaviors in domesticated animals, the rapid evolution of preferences, and the routine development of ethological isolation between diverging populations and species. In fact, it is believed that nervous system development and its potential to evolve a seemingly infinite array of behavioral innovations played a major role in the successful diversification of metazoans, including our own human lineage...
November 8, 2016: Biology Direct
https://www.readbyqxmd.com/read/27818352/exercise-combined-with-low-level-gabaa-receptor-inhibition-up-regulates-the-expression-of-neurotrophins-in-the-motor-cortex
#19
Kazuma Takahashi, Hiroshi Maejima, Gaku Ikuta, Hiroki Mani, Tadayoshi Asaka
Neurotrophins play a crucial role in neuroplasticity, neurogenesis, and neuroprotection in the central nervous system. Aerobic exercise is known to increase the expression of BDNF in the cerebral cortex. Several animal studies have evaluated the tonic inhibition of GABAergic synapses to enhance hippocampal plasticity as well as learning and memory, whereas the effects of GABAergic inhibition on plasticity in the cerebral cortex related to motor learning are not well characterized. The objective of the present study was to examine the interactive effect of low-level GABAA receptor inhibition and exercise on the expression of neurotrophins including BDNF in the murine motor cortex...
November 4, 2016: Neuroscience Letters
https://www.readbyqxmd.com/read/27815219/existence-of-muscarinic-acetylcholine-receptor-machr-and-fibroblast-growth-factor-receptor-fgfr-heteroreceptor-complexes-and-their-enhancement-of-neurite-outgrowth-in-neural-hippocampal-cultures
#20
V Di Liberto, D O Borroto-Escuela, M Frinchi, V Verdi, K Fuxe, N Belluardo, G Mudò
BACKGROUND: Recently, it was demonstrated that G-protein-coupled receptors (GPCRs) can transactivate tyrosine kinase receptors in absence of their ligands. In this work, driven by the observation that mAChRs and fibroblast growth factor receptors (FGFRs) share signalling pathways and regulation of brain functions, it was decided to explore whether mAChRs activation may transactivate FGFRs and, if so, to characterize the related trophic effects in cultured hippocampal neurons. METHODS: Oxotremorine-M transactivation of FGFRs and related trophic effects were tested in primary hippocampal neurons...
November 1, 2016: Biochimica et Biophysica Acta
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