Articles

Protein-lipid interactions: correlation of a predictive algorithm for lipid-binding sites with three-dimensional structural data

Over the past decade our laboratory has focused on understanding how soluble cytoskeleton-associated proteins interact with membranes and other lipid aggregates. Many protein domains mediating specific cell me...

Authors: David L Scott, Gerold Diez and Wolfgang H Goldmann

The time-profile of cell growth in fission yeast: model selection criteria favoring bilinear models over exponential ones

There is considerable controversy concerning the exact growth profile of size parameters during the cell cycle. Linear, exponential and bilinear models are commonly considered, and the same model may not apply...

Authors: Peter Buchwald and Akos Sveiczer

Amino acid size, charge, hydropathy indices and matrices for protein structure analysis

Prediction of protein folding and specific interactions from only the sequence (ab initio) is a major challenge in bioinformatics. It is believed that such prediction will prove possible if Anfinsen's thermodynam...

Authors: JC Biro

Effect of transverse gap-junction channels on transverse propagation in an enlarged PSpice model of cardiac muscle

In previous PSpice modeling studies of simulated action potentials (APs) in parallel chains of cardiac muscle, it was found that transverse propagation could occur between adjacent chains in the absence of gap...

Authors: Lakshminarayanan Ramasamy and Nicholas Sperelakis

A method for the generation of standardized qualitative dynamical systems of regulatory networks

Modeling of molecular networks is necessary to understand their dynamical properties. While a wealth of information on molecular connectivity is available, there are still relatively few data regarding the pre...

Authors: Luis Mendoza and Ioannis Xenarios

A model for generating circadian rhythm by coupling ultradian oscillators

Organisms ranging from humans to cyanobacteria undergo circadian rhythm, that is, variations in behavior that cycle over a period about 24 hours in length. A fundamental property of circadian rhythm is that it...

Authors: Verner Paetkau, Roderick Edwards and Reinhard Illner

Number of active transcription factor binding sites is essential for the Hes7 oscillator

It is commonly accepted that embryonic segmentation of vertebrates is regulated by a segmentation clock, which is induced by the cycling genes Hes1 and Hes7. Their products form dimers that bind to the regulatory...

Authors: Stefan Zeiser, H Volkmar Liebscher, Hendrik Tiedemann, Isabel Rubio-Aliaga, Gerhard KH Przemeck, Martin Hrabé de Angelis and Gerhard Winkler

Distinguishing between linear and exponential cell growth during the division cycle: Single-cell studies, cell-culture studies, and the object of cell-cycle research

Two approaches to understanding growth during the cell cycle are single-cell studies, where growth during the cell cycle of a single cell is measured, and cell-culture studies, where growth during the cell cyc...

Authors: Stephen Cooper

Computer simulation analysis of normal and abnormal development of the mammalian diaphragm

Congenital diaphragmatic hernia (CDH) is a birth defect with significant morbidity and mortality. Knowledge of diaphragm morphogenesis and the aberrations leading to CDH is limited. Although classical embryolo...

Authors: Jason C Fisher and Lawrence Bodenstein

Sepsis progression and outcome: a dynamical model

Sepsis (bloodstream infection) is the leading cause of death in non-surgical intensive care units. It is diagnosed in 750,000 US patients per annum, and has high mortality. Current understanding of sepsis is p...

Authors: Sergey M Zuev, Stephen F Kingsmore and Damian DG Gessler

A multiscale mathematical model of cancer, and its use in analyzing irradiation therapies

Radiotherapy outcomes are usually predicted using the Linear Quadratic model. However, this model does not integrate complex features of tumor growth, in particular cell cycle regulation.

Authors: Benjamin Ribba, Thierry Colin and Santiago Schnell

An immune reaction may be necessary for cancer development

The hypothesis of immunosurveillance suggests that new neoplasms arise very frequently, but most are destroyed almost at their inception by an immune response. Its correctness has been debated for many years.

Authors: Richmond T Prehn

A stochastic model of oncogene expression and the relevance of this model to cancer therapy

Ablation of an oncogene or of the activity of the protein it encodes can result in apoptosis and/or inhibit tumor cell proliferation. Therefore, if the oncogene or set of oncogenes contributing maximally to a ...

Authors: Francis D Alfano

Identification of metabolic system parameters using global optimization methods

The problem of estimating the parameters of dynamic models of complex biological systems from time series data is becoming increasingly important.

Authors: Pradeep K Polisetty, Eberhard O Voit and Edward P Gatzke

Developing a realistic sexual network model of chlamydia transmission in Britain

A national chlamydia screening programme is currently being rolled out in the UK and other countries. However, much of the epidemiology remains poorly understood. In this paper we present a stochastic, individ...

Authors: Katherine ME Turner, Elisabeth J Adams, Nigel Gay, Azra C Ghani, Catherine Mercer and W John Edmunds

Memory in astrocytes: a hypothesis

Recent work has indicated an increasingly complex role for astrocytes in the central nervous system. Astrocytes are now known to exchange information with neurons at synaptic junctions and to alter the informa...

Authors: Robert M Caudle

Common angiotensin receptor blockers may directly modulate the immune system via VDR, PPAR and CCR2b

There have been indications that common Angiotensin Receptor Blockers (ARBs) may be exerting anti-inflammatory actions by directly modulating the immune system. We decided to use molecular modelling to rapidly...

Authors: Trevor G Marshall, Robert E Lee and Frances E Marshall

Neurogenetic interactions and aberrant behavioral co-morbidity of attention deficit hyperactivity disorder (ADHD): dispelling myths

Attention Deficit Hyperactivity Disorder, commonly referred to as ADHD, is a common, complex, predominately genetic but highly treatable disorder, which in its more severe form has such a profound effect on br...

Authors: David E Comings, Thomas JH Chen, Kenneth Blum, Julie F Mengucci, Seth H Blum and Brian Meshkin

A Global Workspace perspective on mental disorders

Recent developments in Global Workspace theory suggest that human consciousness can suffer interpenetrating dysfunctions of mutual and reciprocal interaction with embedding environments which will have early o...

Authors: Rodrick Wallace

Repolarization of the action potential enabled by Na⁺ channel deactivation in PSpice simulation of cardiac muscle propagation

In previous studies on propagation of simulated action potentials (APs) in cardiac muscle using PSpice modeling, we reported that a second black-box (BB) could not be inserted into the K⁺ leg of the basic membran...

Authors: Lakshminarayanan Ramasamy and Nicholas Sperelakis

Comment on and reply to "Analysis of variation of amplitudes in cell cycle gene expression" by Liu, Gaido and Wolfinger: On the analysis of gene expression during the normal, eukaryotic, cell cycle

The paper of Liu, Gaido and Wolfinger on gene expression during the division cycle of HeLa cells using the data of Whitfield et al. are discussed in order to see whether their analysis is related to gene expre...

Authors: Stephen Cooper

Analysis of variation of amplitudes in cell cycle gene expression

Variation in gene expression among cells in a population is often considered as noise produced from gene transcription and post-transcription processes and experimental artifacts. Most studies on noise in gene...

Authors: Delong Liu, Kevin W Gaido and Russ Wolfinger

Supply-demand balance in outward-directed networks and Kleiber's law

Recent theories have attempted to derive the value of the exponent α in the allometric formula for scaling of basal metabolic rate from the properties of distribution network models for arteries and capillarie...

Authors: Page R Painter

A mathematical model of the euglycemic hyperinsulinemic clamp

The Euglycemic Hyperinsulinemic Clamp (EHC) is the most widely used experimental procedure for the determination of insulin sensitivity, and in its usual form the patient is followed under insulinization for t...

Authors: Umberto Picchini, Andrea De Gaetano, Simona Panunzi, Susanne Ditlevsen and Geltrude Mingrone

Modeling the signaling endosome hypothesis: Why a drive to the nucleus is better than a (random) walk

Information transfer from the plasma membrane to the nucleus is a universal cell biological property. Such information is generally encoded in the form of post-translationally modified protein messengers. Text...

Authors: Charles L Howe

Hybrid dynamic/static method for large-scale simulation of metabolism

Many computer studies have employed either dynamic simulation or metabolic flux analysis (MFA) to predict the behaviour of biochemical pathways. Dynamic simulation determines the time evolution of pathway prop...

Authors: Katsuyuki Yugi, Yoichi Nakayama, Ayako Kinoshita and Masaru Tomita

Volume of the effect compartment in simulations of neuromuscular block

The study examines the role of the volume of the effect compartment in simulations of neuromuscular block (NMB) produced by nondepolarizing muscle relaxants.

Authors: Vladimir Nigrovic, Johannes H Proost, Anton Amann and Shashi B Bhatt

Uncertainty principle of genetic information in a living cell

Formal description of a cell's genetic information should provide the number of DNA molecules in that cell and their complete nucleotide sequences. We pose the formal problem: can the genome sequence forming t...

Authors: Pierluigi Strippoli, Silvia Canaider, Francesco Noferini, Pietro D'Addabbo, Lorenza Vitale, Federica Facchin, Luca Lenzi, Raffaella Casadei, Paolo Carinci, Maria Zannotti and Flavia Frabetti

Data from necropsy studies and in vitro tissue studies lead to a model for allometric scaling of basal metabolic rate

The basal metabolic rate (BMR) of a mammal of mass M is commonly described by the power function αM ^β where α and β are constants determined by linear regression of the logar...

Authors: Page R Painter

Targeting MDM2 by the small molecule RITA: towards the development of new multi-target drugs against cancer

The use of low-molecular-weight, non-peptidic molecules that disrupt the interaction between the p53 tumor suppressor and its negative regulator MDM2 has provided a promising alternative for the treatment of d...

Authors: L Michel Espinoza-Fonseca

A comparative study of a theoretical neural net model with MEG data from epileptic patients and normal individuals

The aim of this study was to compare a theoretical neural net model with MEG data from epileptic patients and normal individuals.

Authors: A Kotini, P Anninos, AN Anastasiadis and D Tamiolakis

Boundary effects influence velocity of transverse propagation of simulated cardiac action potentials

We previously demonstrated that transverse propagation of excitation (cardiac action potentials simulated with PSpice) could occur in the absence of low-resistance connections (gap – junction channels) between...

Authors: Nicholas Sperelakis, Bijoy Kalloor and Lakshminarayanan Ramasamy

Nucleic acid chaperons: a theory of an RNA-assisted protein folding

Proteins are assumed to contain all the information necessary for unambiguous folding (Anfinsen's principle). However, ab initio structure prediction is often not successful because the amino acid sequence its...

Authors: Jan C Biro

Review of "Systems Biology in Practice" by Edda Klipp, Ralf Hertwig, Axel Kowald, Christoph Wierling and Hans Lehrach

Authors: Paul S Agutter

Possible Cis-acting signal that could be involved in the localization of different mRNAs in neuronal axons

Messenger RNA (mRNA) comprises three major parts: a 5'-UTR (UnTranslated Region), a coding region, and a 3'-UTR. The 3'-UTR contains signal sequences involved in polyadenylation, degradation and localization/s...

Authors: Gonzalo E Aranda-Abreu, Ma Elena Hernández, Abraham Soto and Jorge Manzo

On the number of founding germ cells in humans

The number of founding germ cells (FGCs) in mammals is of fundamental significance to the fidelity of gene transmission between generations, but estimates from various methods vary widely. In this paper we obt...

Authors: Chang-Jiang Zheng, E Georg Luebeck, Breck Byers and Suresh H Moolgavkar

Allometric scaling of the maximum metabolic rate of mammals: oxygen transport from the lungs to the heart is a limiting step

The maximum metabolic rate (MMR) of mammals is approximately proportional to M ^0.9 , where M is the mammal's body weight. Therefore, MMR increases with body weight faster tha...

Authors: Page R Painter

The fractal geometry of nutrient exchange surfaces does not provide an explanation for 3/4-power metabolic scaling

A prominent theoretical explanation for 3/4-power allometric scaling of metabolism proposes that the nutrient exchange surface of capillaries has properties of a space-filling fractal. The theory assumes that ...

Authors: Page R Painter

Three subsets of sequence complexity and their relevance to biopolymeric information

Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instru...

Authors: David L Abel and Jack T Trevors

Modelling of oedemous limbs and venous ulcers using partial differential equations

Oedema, commonly known as tissue swelling, occurs mainly on the leg and the arm. The condition may be associated with a range of causes such as venous diseases, trauma, infection, joint disease and orthopaedic...

Authors: Hassan Ugail and Michael J Wilson

Statistical distribution of blood serotonin as a predictor of early autistic brain abnormalities

A wide range of abnormalities has been reported in autistic brains, but these abnormalities may be the result of an earlier underlying developmental alteration that may no longer be evident by the time autism ...

Authors: Skirmantas Janušonis

The complexity of anatomical systems

The conception of anatomical entities as a hierarchy of infinitely graduated forms and the increase in the number of observed anatomical sub-entities and structural variables has generated a growing complexity, t...

Authors: Fabio Grizzi and Maurizio Chiriva-Internati

Identification and isolation of embryonic stem cells in reproductive endocrinology: theoretical protocols for conservation of human embryos derived from in vitro fertilization

Embryonic stem cells (ESC) are pluripotent cells obtained from the inner cell mass (ICM) of blastocysts derived from in vitro culture associated with reproductive endocrinology therapy. Human ESCs are regarded as...

Authors: Eric Scott Sills, Takumi Takeuchi, Noriko Tanaka, Queenie V Neri and Gianpiero D Palermo

Vasculature deprivation – induced osteonecrosis of the rat femoral head as a model for therapeutic trials

The authors' experience with experimentally produced femoral capital osteonecrosis in rats is reviewed: incising the periosteum at the base of the neck of the femur and cutting the ligamentum teres leads to co...

Authors: Jacob Bejar, Eli Peled and Jochanan H Boss

Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach

The study of the network between transcription factors and their targets is important for understanding the complex regulatory mechanisms in a cell. Unfortunately, with standard microarray experiments it is no...

Authors: Anne-Laure Boulesteix and Korbinian Strimmer

The ups and downs of biological timers

The need to execute a sequence of events in an orderly and timely manner is central to many biological processes, including cell cycle progression and cell differentiation. For self-perpetuating systems, such ...

Authors: Noa Rappaport, Shay Winter and Naama Barkai

A new journal – "Theoretical Biology and Medical Modelling"

Biology has a conceptual basis that allows one to build models and theorize across many life sciences, including medicine and medically-related disciplines. A dearth of good venues for publication has been per...

Authors: Denys N Wheatley

Promoter addresses: revelations from oligonucleotide profiling applied to the Escherichia coli genome

Transcription is the first step in cellular information processing. It is regulated by cis-acting elements such as promoters and operators in the DNA, and trans-acting elements such as transcription factors and s...

Authors: Karthikeyan Sivaraman, Aswin Sai Narain Seshasayee, Krishnakumar Swaminathan, Geetha Muthukumaran and Gautam Pennathur

Quantification of the glycogen cascade system: the ultrasensitive responses of liver glycogen synthase and muscle phosphorylase are due to distinctive regulatory designs

Signaling pathways include intricate networks of reversible covalent modification cycles. Such multicyclic enzyme cascades amplify the input stimulus, cause integration of multiple signals and exhibit sensitiv...

Authors: Vivek K Mutalik and KV Venkatesh

Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition

Cell simulation, which aims to predict the complex and dynamic behavior of living cells, is becoming a valuable tool. In silico models of human red blood cell (RBC) metabolism have been developed by several la...

Authors: Yoichi Nakayama, Ayako Kinoshita and Masaru Tomita