A new method of estimating the pollen dispersal curve independently of effective density

We introduce a novel indirect method of estimating the pollen dispersal curve from mother-offspring genotypic data. Unlike an earlier indirect approach (TwoGener), this method is based on a normalized measure of correlated paternity between female pairs whose expectation does not explicitly depend on the unknown effective male population density (d(e)). We investigate the statistical properties of the new method, by comparison with those of TwoGener, considering the sensitivity to reductions of d(e), relative to census density, resulting from unequal male fecundity and asynchronous flowering. Our main results are: (i) it is possible to obtain reliable estimates of the average distance of pollen dispersal, delta, from indirect methods, even under nonuniform male fecundity and variable flowering phenology; (ii) the new method yields more accurate and more precise delta-estimates than TwoGener under a wide range of sampling and flowering scenarios; and (iii) TwoGener can be used to obtain approximate d(e) estimates, if needed for other purposes. Our results also show that accurately estimating the shape of the tail of the pollen dispersal function by means of indirect methods remains a very difficult challenge.     

A theory for the estimation of DNA synthesis rates by flow cytometry

A method is presented for estimating the rate of DNA synthesis of a cell population by examining the DNA histogram generated by flow cytometry (FCM). The model is based on the use renewal equations to estimate the steady-state fraction of cells in each DNA compartment. The fraction of cells in each compartment is shown to be related to the Laplace transform of the transit time through that compartment. Two methods are introduced for estimating the rate of DNA synthesis utilizing different transit time distributions. One method is shown to be a simplification of the method of Dean and Anderson. The other method allows for variability in the DNA synthesis rate. The effects of quiescent cells are considered and attention is paid to the various assumptions underlying the estimation.     

Elevated Levels of Thymidylate Synthase Linked to Neoplastic Transformation of Mammalian Cells

Thymidylate synthase (TS), an enzyme that is essential for DNA synthesis and repair has been identified as an important biomarker for colorectal and other human cancers. The elevated steady-state levels of TS found in many common human malignancies have been thought to represent a secondary event in tumor formation. However, it has recently been demonstrated that the deregulated levels of ectopic TS may also have a causal effect on tumorgenesis since overexpression of human TS transforms immortalized mammalian cells to a malignant phenotype. Since the levels of TS are regulated by E2F-1 and thus are linked to the cell cycle pathway, regulating TS activity may be an important factor for the control of cell cycle progression and for the development of therapeutic strategies and cancer prevention.     

Human dihydrofolate reductase and thymidylate synthase form a complex in vitro and co-localize in normal and cancer cells

Enzymes involved in thymidylate biosynthesis, thymidylate synthase (TS), and dihydrofolate reductase (DHFR) are well-known targets in cancer chemotherapy. In this study, we demonstrated for the first time, that human TS and DHFR form a strong complex in vitro and co-localize in human normal and colon cancer cell cytoplasm and nucleus. Treatment of cancer cells with methotrexate or 5-fluorouracil did not affect the distribution of either enzyme within the cells. However, 5-FU, but not MTX, lowered the presence of DHFR-TS complex in the nucleus by 2.5-fold. The results may suggest the sequestering of TS by FdUMP in the cytoplasm and thereby affecting the translocation of DHFR-TS complex to the nucleus. Providing a strong likelihood of DHFR-TS complex formation in vivo, the latter complex is a potential new drug target in cancer therapy. In this paper, known 3D structures of human TS and human DHFR, and some protozoan bifunctional DHFR-TS structures as templates, are used to build an in silico model of human DHFR–TS complex structure, consisting of one TS dimer and two DHFR monomers. This complex structure may serve as an initial 3D drug target model for prospective inhibitors targeting interfaces between the DHFR and TS enzymes.     

A Parvancorina-like arthropod from the Cambrian of South China

Constraining the origin of animal groups is allowed, to some extent, by discoveries of Cambrian Lagerstätten that preserve both mineralizing and nonmineralizing organisms. A new species is reported here of the Cambrian arthropod Skania, which bears an exoskeleton that shares homologies with the Neoproterozoic (Ediacaran) organism Parvancorina and firmly establishes a Precambrian root for arthropods. A new monophyletic group, Parvancorinomorpha, is proposed as the first clade within the arthropod crown group demonstrably ranging across the Neoproterozoic–Paleozoic transition. The Parvancorinomorpha is interpreted to be the sister group of the Arachnomorpha. Incipient cephalization in Skania and related genera represents a step in the progression toward division of a cephalon from a large posterior trunk as shown in Cambrian arachnomorphs such as naraoiids and the addition of a pygidium and thoracic tergites as shown in the arachnomorph clade basal to trilobites. This evidence can serve as a new calibration point for estimating the divergence time for the last common ancestor of arthropods and priapulids based on molecular clock methods.     

A trojan horse approach for silencing thymidylate synthase

In this paper we present a new and possibly more effective way of inhibiting thymidylate synthase (TS) in cells than through the use of substrate analogue inhibitors. An inactive double mutant of TS (DM), Arg(126)Glu/Cys(146)Trp, is shown to progressively impair the reactivation of native Escherichia coli TS when the two are denatured together in vitro. The individual single mutant proteins Arg(126)Glu and Cys(146)Trp showed little or no inhibition. When the DM is introduced into E. coli and induced from an expression plasmid, the mutant subunits act as a decoy in deceiving newly formed native TS subunits to fold with them to yield inactive heterodimers. As a consequence of the depletion of TS, the cells die a "thymineless" death when grown in medium devoid of thymine. Addition of thymine to the medium enables the cells to grow normally, although only very low levels of TS activity could be detected in those cells containing induced DM. The individual single-site mutations of the DM, Arg(126)Glu and Cys(146)Trp, did not inhibit growth, as might be expected from the in vitro studies. However, when a nontoxic level of 5-fluoro-2'-deoxyuridine 5'-monophosphate (FdUMP) is added to growing DM-transformed cells, the combination is lethal to the cells. These experiments suggest that a similar dominant-negative response to the DM of TS could be affected in tumor cells, for which preliminary evidence is presented. This technique, either alone or combined with other modalities, suggest a new approach to targeting cells for chemotherapy.     

A new method of estimating gauge length for porcine aortic valve test specimens

Porcine aortic valve (PAV) cusps are folded and wrinkled in the in vitro state. In the tensile testing of PAV specimens, estimating gauge length (the length at which a specimen starts to offer measurable resistance to load) is often difficult and subjective. We have therefore developed a new method for estimating the gauge length of such tissues. The method is based on the observation that the specimen's gauge length can be associated with a stationary point on the slope of its load-length curve if loaded from a wrinkled state, or a state of slight compression. We represented the load-length response of test specimens in the low-load, high-compliance region by a cubic function and determined the stationary point on the slope of the function using elementary calculus. The cubic function representation is fine-tuned by reducing or expanding an originally selected "test region" until the correlation coefficient of the cubic fit is maximized. The new method was applied to data obtained from the tensile testing of strips of heart valve tissue and was found to be objective, repeatable and robust.     

A Fast Method to Estimate Kinetic Constants for Enzyme Inhibitors

We present a method to determine the reaction type and kinetic constants for enzyme inhibitors that decreases the number of experimental assays by at least a factor of five. It is based on a new theoretical formalism in terms of concentrations that dismisses the requirement of estimating initial velocities. Expressions for the time evolution of the concentrations of all the reactants are also given.     

Suppression of defective RAS1 and RAS2 functions in yeast by an adenylate cyclase activated by a single amino acid change.

We have constructed the yeast strain TS1, with the RAS2 gene replaced by mutant allele encoding a partially defective gene product, and with an inactive RAS1 gene. TS1 cells accumulate as unbudded cells upon temperature shift from 30 to 37 degrees C, thus showing that the RAS1 and RAS2 gene functions are important for progression through the G1 phase of the cell cycle. After the isolation of revertants able to grow at the nonpermissive temperature, we have found that a chromosomal point mutation can bypass the G1 arrest of TS1 and cdc25 cells, and the lethality of ras1 ras2 mutants. The mutation predicts the replacement of threonine by isoleucine at position 1651 of yeast adenylate cyclase. The RAS-independent, as well as the RAS-dependent adenylate cyclase activity, is increased by the mutation. Like the wild-type enzyme, the RAS-dependent activity of the mutant adenylate cyclase is turned on by the GTP-bound form of the RAS2 protein. The amino acid sequence surrounding the threonine 1651 shows similarity with protein kinase substrates. Possible implications for the function of adenylate cyclase are discussed.     

New method for estimation of adult skeletal age at death from the morphology of the auricular surface of the ilium

A new method for estimating skeletal age at death from the morphology of the auricular surface of the ilium is presented. It uses a multiple regression analysis with dummy variables, and is based on the examination of 700 modern Japanese skeletal remains with age records. The observer using this method needs only to check for the presence or absence of nine (for a male) or seven (for a female) features on the auricular surface and to select the parameter estimates of each feature, calculated by multiple regression analysis with dummy variables. The observer can obtain an estimated age from the sum of parameter estimates. It is shown that a fine granular texture of the auricular surface is typical of younger individuals, whereas a heavily porous texture is characteristic of older individuals, and that both of these features are very useful for estimating age. Our method is shown here to be more accurate than other methods, especially in the older age ranges. Since the auricular surface allows more expedient observations than other parts of the skeleton, this new method can be expected to improve the overall accuracy of estimating skeletal age at death.     

A theory for analysis of cell populations with non-cycling S phase cells

Analyses of cell populations that have been labeled in vivo with analogs of thymidine that are incorporated by cells synthesizing DNA and then monitored over time by bivariate flow cytometry sometimes detect populations of cells that have S phase DNA content but that have not acquired label. Two alternative explanations for the lack of labeling are that either the cells were not exposed to the label or that the cells stopped DNA synthesis and ceased progression through S phase. To help determine which scenario is the more likely, a model has been devised for studying a population of cells that includes the possibility that cells in S phase will cease DNA synthesis. In this model, the initial fraction of unlabeled cells in S phase depends on two rates: the growth rate of the total population and the number of cells that cease progression through S phase per unit time. The model is used to analyze the changing quantities which can be measured by monitoring the population of cells over time and is used to estimate the two rates required to compute the initial fraction of unlabeled S phase cells. Thus, the initial fraction of unlabeled cells can be compared with that predicted by the population dynamics to determine whether one explanation for the failure of some cells to be labeled is preferable to the other, which in turn might offer information about tumor microvascular or cytologic properties.     

Alloantigen-activated lymphocytes from mice bearing a spontaneous "nonimmunogenic" adenocarcinoma inhibit its growth in vivo by recruiting host immunoreactivity

Nylon wool columns eluting lymphocytes from the spleen of mice bearing a clinically evident spontaneous, nonimmunogenic adenocarcinoma of recent origin (TS/A) do not display cytotoxic response, release of lymphokines, and proliferation in vitro against TS/A cells, nor do they inhibit TS/A tumor growth in a Winn-type neutralization assay in vivo. After 5-day co-culture with allogeneic spleen cells from mice differing at multiple minor histocompatibility antigens only, these lymphocytes are still noncytolytic against TS/A cells, whereas they release interferon-gamma, mediate delayed-type hypersensitivity (DTH) reactions, and inhibit TS/A tumor growth in the Winn assay. In the Winn test, alloactivated lymphocytes from TS/A tumor-bearing mice are more effective than those from normal mice on a per cell basis. The induction of this TS/A tumor inhibition ability depends on the presence in the cultures of Thy-1+ lymphocytes. The presence of Lyt-2+ lymphocytes is also important, whereas that of asialo GM1+ is not. The TS/A inhibition in vivo by alloactivated lymphocytes mostly depends on Thy-1+, Lyt-2- and asialo GM- lymphocytes, even though a few Thy- cells are also very efficient tumor inhibitors. The alloactivated lymphocytes inhibit TS/A tumor growth by recruiting the radiosensitive effector mechanisms of the recipient mice required for ultimate tumor rejection. TS/A tumor rejection leaves a specific DTH and an immunologic memory resulting in rejection of a second lethal TS/A challenge in a significant number of mice.     

Computing multiple cell kinetic properties from a single time point

New developments in experimental procedures have made it necessary to extend the theory for describing the movement of a population of cells and estimating the kinetic properties of the population. The new procedures are based on the use of fluorescent monoclonal antibodies to halogenated analogues of thymidine, which are incorporated as a label into cells during DNA synthesis. These populations may be examined by dual-parameter flow cytometry to discriminate between the labelled and unlabelled populations of cells and define their position within the DNA reproductive cycle. A particular need exists for a theory that can be used for measurements of tumors in which many cells are not actively cycling and only a single time point can be obtained. In order to develop a useful theory for evaluating the kinetic properties of the cells observed by these techniques, the standard methods of theoretical cell kinetics have been recast in a form that is amenable to the type of analysis demanded by these constraints and a novel method for the rapid analysis of the kinetic properties of the cell population is presented. The method is shown to yield a direct measurement for the population doubling time from a single time point as well as estimates for the transit times through each phase of the cell cycle. The method which is approximately linear is shown to be robust to the effects of different assumptions about the distribution of transit times as well as being insensitive to the effects of variation in the transit times of the cells. The methodology developed in this paper may also be used to examine other theoretical methods of computing kinetic properties.     

Wet-dry-wet drug screen leads to the synthesis of TS1, a novel compound reversing lung fibrosis through inhibition of myofibroblast differentiation

Therapies halting the progression of fibrosis are ineffective and limited. Activated myofibroblasts are emerging as important targets in the progression of fibrotic diseases. Previously, we performed a high-throughput screen on lung fibroblasts and subsequently demonstrated that the inhibition of myofibroblast activation is able to prevent lung fibrosis in bleomycin-treated mice. High-throughput screens are an ideal method of repurposing drugs, yet they contain an intrinsic limitation, which is the size of the library itself. Here, we exploited the data from our “wet” screen and used “dry” machine learning analysis to virtually screen millions of compounds, identifying novel anti-fibrotic hits which target myofibroblast differentiation, many of which were structurally related to dopamine. We synthesized and validated several compounds ex vivo (“wet”) and confirmed that both dopamine and its derivative TS1 are powerful inhibitors of myofibroblast activation. We further used RNAi-mediated knock-down and demonstrated that both molecules act through the dopamine receptor 3 and exert their anti-fibrotic effect by inhibiting the canonical transforming growth factor β pathway. Furthermore, molecular modelling confirmed the capability of TS1 to bind both human and mouse dopamine receptor 3. The anti-fibrotic effect on human cells was confirmed using primary fibroblasts from idiopathic pulmonary fibrosis patients. Finally, TS1 prevented and reversed disease progression in a murine model of lung fibrosis. Both our interdisciplinary approach and our novel compound TS1 are promising tools for understanding and combating lung fibrosis.Subject terms: Drug discovery, Respiratory tract diseases     

Heterogeneity of muscle activation in relation to force direction: A multi-channel surface electromyography study on the triceps surae muscle

Several skeletal muscles can be divided into sub-modules, called neuromuscular compartments (NMCs), which are thought to be controlled independently and to have distinct biomechanical functions. We looked for distinct muscle activation patterns in the triceps surae muscle (TS) using surface electromyography (EMG) during voluntary contraction. Nine subjects performed isometric and isotonic plantar flexions combined with forces along pre-defined directions. Besides the forces under the ball of the foot, multi-channel surface EMG was measured with electrodes homogeneously distributed over the entire TS. Using principal component analysis, common (global) components were omitted from the EMG signals, thereby estimating muscle activity sufficiently accurate to track fine fluctuations of force during an isotonic contraction (r = 0.80 ± 0.09). A subsequent cluster analysis showed a topographical organization of co-activated parts of the muscle that was different between subjects. Low and negative correlations between the EMG activity within clusters were found, indicating a substantial heterogeneity of TS activation. The correlations between cluster time series and forces at the foot in specific directions differed substantially between clusters, showing that the differentially activated parts of the TS had specific biomechanical functions.     

Measuring cell proliferation by relative movement. I. Introduction and in vitro studies

This paper presents two new ways of analysing data which may be obtained from pulse labelling a population of cells with bromodeoxyuridine and analysing that population as a function of time with bivariate flow cytometry. The progression of cells is measured by the change in position in the cell cycle, as shown by a change in the mean DNA content of the labelled and unlabelled cells. The particular measures of the mean DNA content used are extensions of the relative movement of the labelled undivided cells, RMlu(t), which was introduced by Begg and co-workers to measure the DNA synthesis time, TS. In general, the relative movement is defined as the mean DNA fluorescence of a population of cells less the DNA fluorescence of the cells in G1 and divided by the difference in DNA fluorescence of the cells in G2 + M and G1. In this paper we examine the relative movements of all the labelled cells and all of the unlabelled cells, denoted RML(t) and RMU(t) respectively. It is found that RML(t) and RMU(t) exhibit clear cyclic behaviour and distinguishable characteristics which depend directly on the transit times (T) of the cell cycle phases, i.e. TG1, TS and TG2 + M. Furthermore, the peak heights of the RMU(t) curve are shown to depend strongly on the growth fraction of the population under consideration. A theoretical treatment of the curves so obtained is presented, and is shown to yield values in close agreement with those from other methods for measuring these transit times and a lower limit to values for the growth fraction of Chinese hamster ovary cells grown in vitro.     

Inferring somatic mutation rates using the stop-enhanced green fluorescent protein mouse

A new method is developed for estimating rates of somatic mutation in vivo. The stop-enhanced green fluorescent protein (EGFP) transgenic mouse carries multiple copies of an EGFP gene with a premature stop codon. The gene can revert to a functional form via point mutations. Mice treated with a potent mutagen, N-ethyl-N-nitrosourea (ENU), and mice treated with a vehicle alone are assayed for mutations in liver cells. A stochastic model is developed to model the mutation and gene expression processes and maximum-likelihood estimators of the model parameters are derived. A likelihood-ratio test (LRT) is developed for detecting mutagenicity. Parametric bootstrap simulations are used to obtain confidence intervals of the parameter estimates and to estimate the significance of the LRT. The LRT is highly significant (alpha < 0.01) and the 95% confidence interval for the relative effect of the mutagen (the ratio of the rate of mutation during the interval of mutagen exposure to the rate of background mutation) ranges from a minimum 200-fold effect of the mutagen to a maximum 2000-fold effect.