Stochastic models for cell motion and taxis

Certain biological experiments investigating cell motion result in time lapse video microscopy data which may be modeled using stochastic differential equations. These models suggest statistics for quantifying experimental results and testing relevant hypotheses, and carry implications for the qualitative behavior of cells and for underlying biophysical mechanisms. Directional cell motion in response to a stimulus, termed taxis, has previously been modeled at a phenomenological level using the Keller-Segel diffusion equation. The Keller-Segel model cannot distinguish certain modes of taxis, and this motivates the introduction of a richer class of models which is nevertheless still amenable to statistical analysis. A state space model formulation is used to link models proposed for cell velocity to observed data. Sequential Monte Carlo methods enable parameter estimation via maximum likelihood for a range of applicable models. One particular experimental situation, involving the effect of an electric field on cell behavior, is considered in detail. In this case, an Ornstein- Uhlenbeck model for cell velocity is found to compare favorably with a nonlinear diffusion model.     

An epigenetically altered tumor cell vaccine

Functional inactivation of genes critical to immunity may occur by mutation and/or by repression, the latter being potentially reversible with agents that modify chromatin. This study was constructed to determine whether reversal of gene silencing, by altering the acetylation status of chromatin, might lead to an effective tumor vaccine. We show that the expression of selected genes important to tumor immunity, including MHC class II, CD40, and B7-1/2 are altered by treating tumor cells in vitro with a histone deacetylase inhibitor, trichostatin A (TSA). Tumor cells treated in vitro with TSA showed delayed onset and rate of tumor growth in 70% of the J558 plasmacytoma and 100% of the B16 melanoma injected animals. Long-term tumor specific immunity was elicited to rechallenge with wild-type cells in approximately 30% in both tumor models. Splenic T cells from immune mice lysed untreated tumor cells, and SCID mice did not manifest immunity, suggesting that T cells may be involved in immunity. We hypothesize that repression of immune genes is involved in the evasion of immunity by tumors and suggest that epigenetically altered cancer cells should be further explored as a strategy for the induction of tumor immunity.Abbreviations APCs antigen-presenting cells - CIITA MHC class II transactivator - CTLs cytotoxic T lymphocytes - HDACs histone deacetylases - LPAM L-phenylalanine mustard - TSA trichostatin AThis work was supported by grant HD 17013 from the National Institutes of Health, and utilized core facilities supported in part by RPCIs NCI Cancer Support Grant CA16056.     

The control of copy number of IS6110 in Mycobacterium tuberculosis

Insertion sequence (IS) elements are bacterial genes that are able to transpose to different locations in the genome. These elements are often used in molecular epidemiology as genetic markers that track the spread of pathogens. Transposable elements have frequently been described as "selfish DNA" because they facilitate their own transposition, causing damage when they insert into coding regions, while contributing little if anything to the bacterial host. According to this hypothesis, the expansion of copy number of insertion sequences is opposed by negative selection against high copy numbers. From an alternative point of view, we might expect IS elements to intrinsically regulate transposition within cells, thereby limiting damage to their bacterial host. Here, we report evidence that the copy number of IS6110 in Mycobacterium tuberculosis is controlled by selection against the element. We first construct 12 different models of marker change resulting from a combination of possible transposition functions and selective regimes. We then compute the Akaike Information Criterion for each model to identify the models that best explain data consisting of serial isolates of M. tuberculosis genotyped with IS6110. We find that the best performing models all include selection against the accumulation of copies. Specifically, our analysis points to the interaction of separate copies of the element causing lethal effects. We discuss the implications of these findings for genome evolution and molecular epidemiology.     

Phase-synchronization of daily motor activities can reveal differential circadian patterns

The aim of the study was to determine any alteration of the 24 h motor activity pattern of a bipolar patient in different mood states. Actigraphic records were collected on an outpatient basis for a total of 387 days. The daily actograms were synchronized in phase to the time of morning awakening before averaging, which significantly enhanced the structure of the averaged traces. The actograms were divided into three groups based on total daily count. The daily motor activity patterns of the low- and high-activity days have a different circadian pattern. We propose it may have a relevance to the different mood states. The phase-synchronization of the 24 h actograms to the patient's sleep-wake cycle, specifically to the time of awaking from the nighttime sleep, may help reveal differences in the daily temporal patterns of motor activity.     

Speculations on the role of the microtubule network in glucocorticoid receptor signaling

The glucocorticoid receptor (GR) is an important player in the life of a cell. This is underlined by a cohort of protein and nucleic acid structures interacting with the GR. Among many issues surrounding GR activity that are under active investigation, the role of microtubules (MTs) is still unclear. This article aims to evaluate the ayes and noes in favor of microtubule importance and then form a hypothesis on their function in GR activity.     

Sap flow measurements with some thermodynamic methods,flow integration within trees and scaling up from sample trees to entire forest stands

Sap flow measurement techniques and evaluation of data are reviewed. Particular attention is paid to the trunk segment heat balance (THB) and heat field deformation (HFD) methods based on 30 years experience. Further elaboration of sap flow data is discussed in terms of integrating flow for whole stems from individual measuring points, considering variation of radial patterns in sapwood and variation around stems. Scaling up of data from sets of sample trees to entire forest stands based on widely available biometric data (partially on remote sensing images) is described and evaluated with a discussion of the magnitude of errors, the routine procedure applicable in any forest stand and practical examples.     

Cloning and developmental expression of MARK/Par-1/MELK-related protein kinase xMAK-V in<Emphasis Type="Italic"> Xenopus laevis</Emphasis>

MAK-V/Hunk is a recently identified MARK/Par-1-related mammalian protein kinase. Although the precise function of this protein kinase is yet to be established, available data suggest its involvement in animals development and in the physiology of the nervous system. Here we report characterization of a cDNA encoding Xenopus laevis orthologue of MAK-V/Hunk protein kinase, xMAK-V. The in silico analysis also revealed MAK-V/Hunk orthologues in the fish Fugu rubripes and primitive chordate Ciona intestinalis but not in invertebrate species such as Drosophila melanogaster and Caenorhabditis elegans, suggesting that MAK-V/Hunk is a chordate-specific protein kinase. The expression of xmak-v in X. laevis embryos was analyzed using whole-mount in situ hybridization. Expression of xmak-v has been detected in all developmental stages studied including maternal expression in unfertilized eggs. The xmak-v mRNA has a predominant occurrence on the animal hemisphere of the egg, and this pattern of expression is sustained throughout cleavage and blastula stages. At the gastrula stage xmak-v expression is restricted to the ectoderm. In the later stage embryos xmak-v is expressed over the entire embryonic surface including the open neural plate at stage 15 and also in neural tube at stage 22. At tadpole stage xmak-v expression is strong in embryonic epidermis, nervous system and sensory organs, and is also obvious in perisomitic mesoderm and brachial arches.Edited by N. Satoh     

The microbiology of a pharmaceutical effluent and its public health implications

The effluent of a pharmaceutical company was examined microbiologically. Its bacterial count was 2.15 × 10⁵ c.f.u./ml and there was evidence of faecal contamination with MPN of > 1800. The organisms encountered included Staphylococcus aureus, Escherichia coli, Proteus vulgaris, Serratia marcescens and Pseudomonas aeruginosa. The resistances of the 25 bacterial strains isolated from the effluent to the commonly used antibiotics were studied. About 80% of the isolates were resistant to Amoxycillin, 76% to Nitrofurantoin, 64% to Cotrimoxazole and Augmentin, 60% were resistant to Nalidixic acid, 52% were resistant to Tetracycline and Ofloxacin, while resistance of 12% was obtained for Gentamicin. Among the eight antibiotics tested, seven patterns of drug resistance were obtained and all of them were multiple-drug resistance with the number of antibiotics ranging from 2–8. All the strains of E. coli and S. aureus had high MIC values for Cloxacillin and Amoxycillin. In all, 13 strains of the bacterial isolates had evidence for the production of -lactamases. The potential of the effluent in spreading drug resistance and the public health implications are discussed.     

Role of benzylsuccinate in the induction of the tutE tutFDGH gene complex of T. aromatica strain T1

Expression of the tutE tutFDGH gene cluster of Thauera aromatica strain T1 was examined by Northern and Western analysis in a wild-type strain and chromosomally deleted strains with or without in-frame deletion plasmids. While expression was observed when the wild-type strain was induced with toluene, various chromosomally deleted strains exhibited little or no expression of the tut genes. In contrast, both wild-type and chromosomally deleted strains expressed the tut genes when induced with benzylsuccinate. We conclude that benzylsuccinate is required for the full induction of the tutE tutFDGH gene cluster of T. aromatica strain T1.