Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern.

An organism's entire protein modification repertoire has yet to be comprehensively mapped. N-myristoylation (MYR) is a crucial eukaryotic N-terminal protein modification. Here we mapped complete Homo sapiens and Arabidopsis thaliana myristoylomes.

How the Warburg effect supports aggressiveness and drug resistance of cancer cells?

Cancer cells employ both conventional oxidative metabolism and glycolytic anaerobic metabolism. However, their proliferation is marked by a shift towards increasing glycolytic metabolism even in the presence of O (Warburg effect). HIF1, a major hypoxia induced transcription factor, promotes a dissociation between glycolysis and the tricarboxylic acid cycle, a process limiting the efficient production of ATP and citrate which otherwise would arrest glycolysis.

Mechanical stress increases brain amyloid β, tau, and α-synuclein concentrations in wild-type mice.

Introduction: Exposure to traumatic brain injury is a core risk factor that predisposes an individual to sporadic neurodegenerative diseases. We provide evidence that mechanical stress increases brain levels of hallmark proteins associated with neurodegeneration.

Methods: Wild-type mice were exposed to multiple regimens of repetitive mild traumatic brain injury, generating a range of combinations of impact energies, frequencies, and durations of exposure.

The Redox Status of Cancer Cells Supports Mechanisms behind the Warburg Effect.

To better understand the energetic status of proliferating cells, we have measured the intracellular pH (pHi) and concentrations of key metabolites, such as adenosine triphosphate (ATP), nicotinamide adenine dinucleotide (NAD), and nicotinamide adenine dinucleotide phosphate (NADP) in normal and cancer cells, extracted from fresh human colon tissues. Cells were sorted by elutriation and segregated in different phases of the cell cycle (G0/G1/S/G2/M) in order to study their redox (NAD, NADP) and bioenergetic (ATP, pHi) status. Our results show that the average ATP concentration over the cell cycle is higher and the pHi is globally more acidic in normal proliferating cells.

Necessary and sufficient conditions for protocell growth.

We consider a generic protocell model consisting of any conservative chemical reaction network embedded within a membrane. The membrane results from the self-assembly of a membrane precursor and is semi-permeable to some nutrients. Nutrients are metabolized into all other species including the membrane precursor, and the membrane grows in area and the protocell in volume.

Mechanical stress models of Alzheimer's disease pathology.

Introduction: Extracellular accumulation of amyloid-β protein and intracellular accumulation of tau in brain tissues have been described in animal models of Alzheimer's disease (AD) and mechanical stress-based diseases of different mechanisms, such as traumatic brain injury (TBI), arterial hypertension (HTN), and normal pressure hydrocephalus (NPH).

Methods: We provide a brief overview of experimental models of TBI, HTN, and NPH showing features of tau-amyloid pathology, neuroinflammation, and neuronal loss.

Results: "Alzheimer-like" hallmarks found in these mechanical stress-based models were compared with AD features found in transgenic models.

Filamentation as primitive growth mode?

Osmotic pressure influences cellular shape. In a growing cell, chemical reactions and dilution induce changes in osmolarity, which in turn influence the cellular shape. Using a protocell model relying upon random conservative chemical reaction networks with arbitrary stoichiometry, we find that when the membrane is so flexible that its shape adjusts itself quasi-instantaneously to balance the osmotic pressure, the protocell either grows filamentous or fails to grow.

Mechanical Stress as the Common Denominator between Chronic Inflammation, Cancer, and Alzheimer's Disease.

The pathogenesis of common diseases, such as Alzheimer's disease (AD) and cancer, are currently poorly understood. Inflammation is a common risk factor for cancer and AD. Recent data, provided by our group and from others, demonstrate that increased pressure and inflammation are synonymous.

MELD Score Kinetics in Decompensated HIV+/HCV+ Patients: A Useful Prognostic Tool (ANRS HC EP 25 PRETHEVIC Cohort Study).

To assess prognostic factors for survival and describe Model for End-Stage liver disease (MELD) dynamics in human immunodeficiency virus+/hepatitis C virus+ (HIV+/HCV+) patients after an initial episode of hepatic decompensation.An HIV+/HCV+ cohort of patients experiencing an initial decompensation episode within the year preceding enrollment were followed prospectively. Clinical and biological data were collected every 3 months.

Chemical Schemes for Maintaining Different Compositions Across a Semi-permeable Membrane with Application to Proto-cells.

Osmotic pressure arising from a higher total chemical concentration inside proto-cells is thought to have played a role in the emergence and selection of self-replicating proto-cells. We present two chemical schemes through which different equilibrium compositions can coexist on each side of a semi-permeable membrane. The first scheme relies upon the concept of moieties and associated number of degrees of freedom.

Mechanical stress related to brain atrophy in Alzheimer's disease.

Introduction: The effects related to endogenous mechanical energy in Alzheimer's disease (AD) pathology have been widely overlooked. With the support of available data from literature and mathematical arguments, we hypothesize that brain atrophy in AD could be co-driven by the cumulative impact of the pressure within brain tissues.

Methods: Brain volumetric and physical data in AD and normal aging (NA) were extracted from the literature.

Cell cycle progression is regulated by intertwined redox oscillators.

The different phases of the eukaryotic cell cycle are exceptionally well-preserved phenomena. DNA decompaction, RNA and protein synthesis (in late G1 phase) followed by DNA replication (in S phase) and lipid synthesis (in G2 phase) occur after resting cells (in G0) are committed to proliferate. The G1 phase of the cell cycle is characterized by an increase in the glycolytic metabolism, sustained by high NAD+/NADH ratio.

Minimal conditions for protocell stationary growth.

We show that self-replication of a chemical system encapsulated within a membrane growing from within is possible without any explicit feature such as autocatalysis or metabolic closure, and without the need for their emergence through complexity. We use a protocell model relying upon random conservative chemical reaction networks with arbitrary stoichiometry, and we investigate the protocell's capability for self-replication, for various numbers of reactions in the network. We elucidate the underlying mechanisms in terms of simple minimal conditions pertaining only to the topology of the embedded chemical reaction network.

The metabolic cooperation between cells in solid cancer tumors.

Cancer cells cooperate with stromal cells and use their environment to promote tumor growth. Energy production depends on nutrient availability and O₂ concentration. Well-oxygenated cells are highly proliferative and reorient the glucose metabolism towards biosynthesis, whereas glutamine oxidation replenishes the TCA cycle coupled with OXPHOS-ATP production.

Metabolic treatment of cancer: intermediate results of a prospective case series.

Background: The combination of hydroxycitrate and lipoic acid has been demonstrated by several laboratories to be effective in reducing murine cancer growth.

Patients And Methods: All patients had failed standard chemotherapy and were offered only palliative care by their referring oncologist. Karnofsky status was between 50 and 80.

Supersecondary structure prediction of transmembrane beta-barrel proteins.

We introduce a graph-theoretic model for predicting the supersecondary structure of transmembrane β-barrel proteins--a particular class of proteins that performs diverse important functions but it is difficult to determine their structure with experimental methods. This ab initio model resolves the protein folding problem based on pseudo-energy minimization with the aid of a simple probabilistic filter. It also allows for determining structures whose barrel follows a given permutation on the arrangement of β-strands, and allows for rapidly discriminating the transmembrane β-barrels from other kinds of proteins.

Tumor regression with a combination of drugs interfering with the tumor metabolism: efficacy of hydroxycitrate, lipoic acid and capsaicin.

Cellular metabolic alterations are now well described as implicated in cancer and some strategies are currently developed to target these different pathways. In previous papers, we demonstrated that a combination of molecules (namely alpha-lipoic acid and hydroxycitrate, i.e.

A graph-theoretic approach for classification and structure prediction of transmembrane β-barrel proteins.

Background: Transmembrane β-barrel proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of transmembrane β-barrel proteins with known structures is very small. Over the years, a number of learning-based methods have been introduced for recognition and structure prediction of transmembrane β-barrel proteins.

Normal human melanocytes exposed to chronic insulin and glucose supplementation undergo oncogenic changes and methyl group metabolism cellular redistribution.

Recent epidemiological studies have suggested a link between cancer and pathophysiological conditions associated with hyperinsulinemia. In this report, we address the possible role of insulin exposure in melanocyte transformation. To this aim, normal melanocytes were exposed to chronic insulin and glucose supplementation (twice the standard medium concentration) for at least 3 wk.

Expected distance between terminal nucleotides of RNA secondary structures.

In "The ends of a large RNA molecule are necessarily close", Yoffe et al. (Nucleic Acids Res 39(1):292-299, 2011) used the programs RNAfold [resp. RNAsubopt] from Vienna RNA Package to calculate the distance between 5' and 3' ends of the minimum free energy secondary structure [resp.

Counting RNA pseudoknotted structures.

In 2004, Condon and coauthors gave a hierarchical classification of exact RNA structure prediction algorithms according to the generality of structure classes that they handle. We complete this classification by adding two recent prediction algorithms. More importantly, we precisely quantify the hierarchy by giving closed or asymptotic formulas for the theoretical number of structures of given size n in all the classes but one.

A model of phospholipid biosynthesis in tumor in response to an anticancer agent in vivo.

We study, in this paper, a model for the core of the system of the Glycerophospholipid metabolism in the murine cells. It comprises the simple and enzymatic reactions of PhosphatidylEthanolamine and the PhosphatidylCholine. The model's general structure is taken from a number of books and articles.

A combination of alpha lipoic acid and calcium hydroxycitrate is efficient against mouse cancer models: preliminary results.

The impact of metabolic dysregulation on tumor development has long been established. We have targeted two enzymes that are altered during carcinogenesis: pyruvate dehydrogenase (PDH), which is down-regulated, and ATP citrate lyase, which is overexpressed in cancer cells. Alpha lipoic acid is a cofactor of PDH, while hydroxycitrate is a known inhibitor of ATP citrate lyase.

Alignment of minisatellite maps based on run-length encoding scheme.

Subsequent duplication events are responsible for the evolution of the minisatellite maps. Alignment of two minisatellite maps should therefore take these duplication events into account, in addition to the well-known edit operations. All algorithms for computing an optimal alignment of two maps, including the one presented here, first deduce the costs of optimal duplication scenarios for all substrings of the given maps.