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| Registros recuperados: 2.284 | |
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| Satya N. V. Arjunan; Masaru Tomita. |
| Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization... |
| Tipo: Manuscript |
Palavras-chave: Developmental Biology; Microbiology; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3845/version/1 |
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| Mahesh Satwekar; Abhijeet Satwekar. |
| Acute and chronic progression of injury to the kidney leads to the failure of the renal system and has become an increasingly important cause of morbidity and mortality. Present diagnosis detects the condition only after irreversible loss of 70 percent of kidney function. Current research is focused only on the clinical manifestations after the kidney injuries and not towards the exact cause of the condition. Here we propose a new outlook- that there is an involvement of a pathogen in the pathogenesis of kidney injuries. Basis for our proposal is given by the similarity of the pathogenesis events occurring between a classical example of hepatitis and kidney injuries. Furthermore, literature regarding the role of early kidney injury biomarkers in innate... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Immunology; Microbiology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7021/version/1 |
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| Jian-She Yang; Bo-Zhang Yu; Wen-Xin Li. |
| Radiotherapy plays a very important role in cancer treatment. Radiosensitizers have been widely used to enhance the radiosensitivity of cancer cells at given radiations. Here we fabricate multi-walled carbon nanotubes with ammonium persulfate, and get very short samples with 30-50 nanometer length. Cell viability assay show that f-WCNTs induce cell death significantly. We hypothesize that free radicals originated from hydroxyl and carbonyl groups on the surface of f-WCNTs lead cell damage. |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Cancer; Chemistry. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1421/version/1 |
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| Xi-Nian Zuo. |
| In statistics, signal processing and mathematical finance, a time series is a sequence of data points, measured typically at successive times spaced at uniform time intervals. Here, I only focus on the discrete time series. The motivation of writing this methodology note is to clarify the relationship between the measures to quantify activity of an observed timeseries. Particularly, focus one several measures used in recently emerged field of resting-state fMRI studies. Although all these measures have been extensively developed in EEG or other timeseries studies, many researchers focusing on various applications in or new comers to this new field need to know existed measures and the relationships among these measures. |
| Tipo: Manuscript |
Palavras-chave: Neuroscience; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4379/version/1 |
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| Niccolo Caldararo. |
| The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective. |
| Tipo: Manuscript |
Palavras-chave: Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5360/version/1 |
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| Niccolo Caldararo; Michael Guthrie. |
| The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective. |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5360/version/3 |
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| Niccolo Caldararo; Michael Guthrie. |
| The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective. |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Evolutionary Biology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/5360/version/4 |
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| Niccolo Caldararo; Michael Guthrie. |
| The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective. |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5360/version/2 |
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| Rainer Kiefmann; Paula Keller; Oliver Tritt; Kai Heckel; Sascha Tank; Martina Kiefmann; Leoni Schulte-Uentrop; Alwin Goetz. |
| Pulmonary perfusion disorders provoke atelectasis in order to minimize ventilation/perfusion mismatch. However, the underlying mechanisms remain unknown. Because intraalveolar CO2 concentration ([CO2]iA) declines as a consequence of poor pulmonary perfusion we postulated the existence a novel alveolar CO2-sensing mechanism which adapts the ventilation to perfusion. Real-time fluorescence imaging of rat lungs revealed that low [CO2]iA decreased cytosolic and increased mitochondrial Ca2+ in alveolar epithelial cells (AEC), leading to reduction of surfactant secretion and alveolar ventilation. Mitochondrial inhibition by ruthenium red or rotenone blocked the hypocapnia-induced responses. In cultured Type 2 AEC hypocapnia decreased cytosolic Ca2+ independently... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6185/version/1 |
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| Samuel Dolzani; Donald C. Cooper. |
| Innovative molecular tools allow neuroscientists to study neural circuitry associated with specific behaviors. Consequently, behavioral methods must be developed to interface with these new molecular tools in order for neuroscientists to identify the causal elements underlying behavior and decision-making processes. Here we present an apparatus and protocol for a novel Go/No-Go behavioral paradigm to study the brain attention and motivation/reward circuitry in awake, head-restrained rodents. This experimental setup allows: (1) Painless and stable restraint of the head and body; (2) Rapid acquisition to simple or complex operant tasks; (3) Repeated electrophysiological single and multiple unit recordings during ongoing behavior; (4) Pharmacological and... |
| Tipo: Manuscript |
Palavras-chave: Neuroscience; Pharmacology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7152/version/1 |
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| Tongjun Gu; James Q. Yin; Yanwei Xu; ZhengHua Dai; Zhengge Qiu; Shenzhong Feng; Xiang Yi; Ling Jiang; Hongjie Zhang. |
| Until now it is still not clear how many types and amounts of small RNAs (sRNAs) exist in humans. Here we report the identification of 1258 distinct sRNAs derived from intronic regions of protein-coding genes in human with a new approach. These endogenous short hairpin RNAs (shRNAs) appear to be similar to exogenous shRNAs in structure, have a broad distribution in the stem length, and function as microRNAs (miRNAs), small interfering RNAs (siRNA) and/or piwi-interacting RNAs (piRNAs). Except for a few shRNAs, the majority of shRNAs are not phylogenetically conserved. They are differentially expressed in different cells and at diverse developmental stages. Overall, their expression levels are lower than miRNAs', but can be detected by quantitative... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1531/version/1 |
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| Priyanka Singh; Farhan Mohammad*; Abhay Sharma. |
| A _Drosophila_ behavioral and transcriptomic model of locomotor plasticity induced by chronic pentylenetetrazole (PTZ) has recently been developed. In this model, two of the five antiepileptic drugs (AEDs) tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic PTZ induced locomotor alteration. Transcriptomic effect of the AEDs and PTZ in fly head has been described. Here, we analyze microarray expression profile of heads of flies treated with the convulsants tetraethylammonium chloride (TEA) and pilocarpine hydrochloride (PILO). Strikingly, microarray clustering placed TEA, not PILO, with LEV and NaVP in one group that was distinct from the other one... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Neuroscience; Pharmacology; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3418/version/1 |
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| Farhan Mohammad; Priyanka Singh; Abhay Sharma. |
| In a newly described _Drosophila_ model, two of the five antiepileptic drugs (AEDs) tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic pentylenetetrazole (PTZ) induced locomotor alteration. To further characterize the model, we analyze here the microarray expression profile of heads of flies treated with depolarizing compound potassium chloride (KCl). Surprisingly, microarray clustering showed unexpected similarity among KCl, LEV and NaVP. Further, like the two effective AEDs in the fly model, KCl regulated genes overrepresented ribosomal pathway. Interestingly, KCl also ameliorated development of locomotor deficit in the chronic PTZ model. Both... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Neuroscience; Pharmacology; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3429/version/1 |
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| Arunava Goswami; Pabitra Pal Choudhury; Rajneesh Singh; Sk. Sarif Hassan. |
| Darwinian evolution hypothesizes that a short stretch of DNA was first constructed and then it expanded to give rise to a long strand. This long strand then produced a mix of exons, introns and repetitive DNA sequence. The order of production of above three kinds of DNA sequence is unknown. Reshuffling of stretches of DNA like above within organisms has given rise to different chromosomes. Till date it is not known how this process is governed. In this paper we show that starting with a sixteen base-pair human olfactory DNA sequence one can form a highly conserved protein domain. Once this domain is formed repetitive DNA sequences of a particular kind starts generating which signifies that this particular conserved protein domain will be unique in nature.... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4850/version/1 |
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| Małgorzata Dudkiewicz; Anna Lenart; Krzysztof Pawłowski. |
| Protein kinases are essential effectors of cellular signaling. Surprisingly, using bioinformatics tools, we predicted protein kinase structure and function for proteins of unknown function (FAM69 family) coded by five related human genes and their Metazoan homologues. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases in four of human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. The FAM69 genes, FAM69A, FAM69B, FAM69C, C3ORF58 and CXORF36, are by large uncharacterized molecularly, yet linked to several neurological disorders in genetics studies. An EF-hand Ca2+-binding domain in FAM69A and FAM69B proteins, inserted within the structure of the kinase... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7015/version/1 |
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| Bo Young Ahn; Diane Trinh; Laura Zajchowski; Sung-Woo Kim. |
| The p53 tumor suppressor protein induces apoptosis in response to genotoxic and environmental stress. Recent studies have revealed the existence of a transcription-independent mitochondrial p53 apoptosis pathway, however the mechanism regulating p53 translocation to mitochondria and subsequent initiation of apoptosis was not known. Here, we show that Tid1, also known as mtHsp40 or Dnaja3, interacts with p53 and directs its translocation to mitochondria in cells exposed to hypoxia. Overexpression of Tid1 in tumor cells promoted mitochondrial localization of both wildtype and mutant forms of p53 and was able to restore the pro-apoptotic activity of mutant p53 proteins that were otherwise unable to induce apoptosis. Tid1's mitochondrial signal... |
| Tipo: Manuscript |
Palavras-chave: Cancer; Molecular Cell Biology. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1892/version/1 |
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| Dr Sudarsan Prasad. |
| A method based on the Concentration Derivative Product (CDP) is proposed to analyze the thermodynamics of Drug-Receptor interactions. CDP is defined as the product of the fractional inhibition f and it’s concentration derivative. Assuming Michaelis-Menten kinetics, it is shown that for a number of drug-receptor systems (HIV protease, ACE, HMG-CoA, Opioid receptor inhibitors, etc.) f max = 0.333, irrespective of the nature of bonding interactions and Ki. The CDP max = [4 / ( 27 Ki ) ], and gives a measure of the drug potency directly. CDP also gives thermodynamic information about the ratio of the gradients of the inhibitor chemical potential in the free and bound states. |
| Tipo: Manuscript |
Palavras-chave: Pharmacology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6006/version/1 |
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| Registros recuperados: 2.284 | |
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