Science,medicine, and the future. Non-insulin dependent diabetes mellitus: the gathering storm.

A massive increase in the global prevalence of non-insulin dependent diabetes is likely to occur as "Westernisation" of dietary habits and patterns of physical activity becomes more widespread. Advances in molecular and cellular science may provide some useful insights and therapeutic tools to assist in the fight against the severe consequences of this epidemic. These will include the better identification of specific aetiological subtypes of the disease; the identification of new drugs through the better understanding of the biology of insulin secretion and action; and the targeting of therapies to specific subtypes of the disease. In addition, knowledge of the precise mode of action and antidiabetes drugs may facilitate the design of more effective non-pharmacological manipulations; the genetic identification of "high risk" asymptomatic people may allow us to target screening and preventive strategies more effectively; and investigations into the mechanisms that underlie the link between low birth weight and later diabetes should provide new routes towards treatment and prevention. Barriers to the implementation of the global measures required to stem the predicted flood of non-insulin dependent diabetes may prove insuperable, but if we are to have any success, then close collaboration between clinicians, epidemiologists, public health physicians, and laboratory scientists will be essential.     

Impact of image segmentation on high-content screening data quality for SK-BR-3 cells

Background  

High content screening (HCS) is a powerful method for the exploration of cellular signalling and morphology that is rapidly being adopted in cancer research. HCS uses automated microscopy to collect images of cultured cells. The images are subjected to segmentation algorithms to identify cellular structures and quantitate their morphology, for hundreds to millions of individual cells. However, image analysis may be imperfect, especially for "HCS-unfriendly" cell lines whose morphology is not well handled by current image segmentation algorithms. We asked if segmentation errors were common for a clinically relevant cell line, if such errors had measurable effects on the data, and if HCS data could be improved by automated identification of well-segmented cells.     

Variations in alphoid DNA sequences escape detection of aneuploidy at interphase by FISH technique.

The advent of a new staining technique, termed fluorescence in situ hybridization (FISH), allows the rapid identification of the genomic constitution of an individual with aneuploidy even in interphase nuclei through the use of a series of chromosome-specific DNA probes, an approach termed "interphase cytogenetics." However, alphoid DNA sequences of every centromere are polymorphic (heteromorphic), and the number of targeted sequences may be below the detection level of a specific DNA probe, thus escaping detection and resulting in the imprecise identification of the chromosomal constitution at interphase. The limitations associated with the FISH technique have dire consequences which are emphasized here with an example in which the presence of an additional chromosome 21 in two siblings born consecutively with trisomy 21 (Down syndrome) was not detected by "interphase cytogenetics." The copy number of alphoid DNA sequences of one of the paternal chromosomes 21 was low and resulted in discordance between domain numbers at interphase and actual chromosome numbers at metaphase in both children. This is an isolated incident that could have led to a misdiagnosis if FISH were the only test employed. Although the advantages of this technology are undeniably enormous, the present finding has made it apparent that precise standards and reliability of the procedure must be established prior to its routine application.     

Applicability of the coefficient of variation method for analyzing synaptic plasticity.

The classical coefficient of variation method for "quantal" analysis of synaptic responses allows unambiguous identification of pre- and postsynaptic loci underlying synaptic plasticity only when extensive simplifying restrictions are made. They include invariance of quantal parameters and the assumption that a single afferent produces the evoked potentials or currents. More general theoretical formulations and simulations demonstrate that the standard criteria do not always provide useful guidelines because when the other sources of physiological variance are included, putative pre- and postsynaptic domains may overlap. For example, data typically interpreted as indicating modifications at both sites can be due to a mechanism localized to only one of the two, if parameter variances are taken into consideration in the case of a single input cell, or if there are multiple inputs and the stimulus does not activate all of them reliably. With this perspective, other physiologically realistic hypotheses relevant to the expression of synaptic plasticity, such as that during long-term potentiation, can be envisioned.     

Testing for Associations of Opposite Directionality in a Heterogeneous Population

In gene networks, it is possible that the patterns of gene co-expression may exist only in a subset of the sample. In studies of relationships between genotypes and expressions of genes over multiple tissues, there may be associations in some tissues but not in the others. Despite the importance of the problem in genomic applications, it is challenging to identify relationships between two variables when the correlation may only exist in a subset of the sample. The situation becomes even less tractable when there exist two subsets in which correlations are in opposite directions. By ranking subset relationships according to Kendall’s tau, a tau-path can be derived to facilitate the identification of correlated subsets, if such subsets exist. However, the current tau-path methodology only considers the situation in which there is association in a subsample; the more complex scenario depicting the existence of two subsets with opposite directionality of associations was not addressed. Further, existing algorithms for finding tau-paths may be suboptimal given their greedy nature. In this paper, we extend the tau-path methodology to accommodate the situation in which the sample may be drawn from a heterogeneous population composed of subpopulations portraying positive and negative associations. We also propose the use of a cross entropy Monte Carlo procedure to obtain an optimal tau-path, CEMC\(_{tp}\). The algorithm not only can provide simultaneous detection of positive and negative correlations in the same sample, but also can lead to the identification of subsamples that provide evidence for the detected associations. An extensive simulation study shows the aptness of CEMC\(_{tp}\) for detecting associations under various scenarios. Compared with two standard tests for detecting associations, CEMC\(_{tp}\) is seen to be more powerful when there are indeed complex subset associations with well-controlled type-I error rates. We applied CEMC\(_{tp}\) to the NCI-60 gene expression data to illustrate its utility for uncovering network relationships that were missed with standard methods.     

Forensic applications of DNA fingerprinting

In many ways, DNA profiling technology is very similar to the conventional techniques used for forensic identification. As with, for example, blood grouping techniques, the molecular characteristics of the scene of crime sample may be determined and compared with those of the scene of reference samples from suspects and victim. If the molecular characteristics of the crime sample and the suspect are different, then they cannot be from the same person, whereas if they match, then the possibility remains that they may be from a single source. Similar material, such as blood or semen stains, may be used for both biochemical and genetic tests, and the main applications of identification and relationship testing are shared by both techniques. At this point, the similarity ends; DNA profiling has the following characteristics:

1. It is more sensitive, being able to generate sound data from only a tiny amount of even partially degraded biological material.
2. It is capable of resolving mixtures of semen or tissue from up to several individuals.
3. It has a far greater power of discrimination between individuals—sometimes up to 1 millionfold higher than conventional techniques.
4. It provides considerably more information on the nature of relationships, particularly in cases of incest.

As such, the technique represents a quantum leap in forensic identification and relationship testing.     

Genotyping faeces links individuals to their diet

The detection of individual variation in foraging behaviour within wild mammal populations requires large sample sizes and relies on the multifold re-sampling of individuals. However, limits for observational studies are posed by the rarity and nocturnal or otherwise elusive habits of many mammals. We propose that the detection of foraging variation within populations of mammals may be facilitated if conventional diet analysis from faeces is combined with DNA-based individual identification methods using "genetic fingerprinting" from faeces. We applied our approach to a coyote ( Canis latrans ) population, and showed how individuals may vary from one another in their diet profiles. Two main groups of coyotes were distinguished on the basis of their relative use of small mammals and "other vertebrates" as primary food sources, and these two groups were further subdivided on the basis of their relative use of "other vertebrates" and fruit as secondary food sources. We show that, unless a faecal sampling scheme is used that maximizes the number of different individuals included in a survey, individual foraging variation that is left unaccounted for may result in downwardly biased faecal diet diversity estimates. Our approach allows the re-sampling of individuals over time and space, and thus may be generally useful for the testing of optimal foraging theory hypotheses in mammals and also has conservation applications.     

Polycystic renal diseases: morphology and genetic counseling

The designation "polycystic kidneys" is vague and causes considerable confusion. This term comprises a number of affections, characterized by the presence of renal cysts. Cystic kidneys may be hereditary or sporadic. The defect may be isolated or occur as part of a syndrome. The identification of the exact nature of the lesion is therefore of paramount importance, not only for the prognosis of the propositus, but especially for the correct genetic counselling of the family. In this context, the perinatal autopsy represents an irreplaceable method of investigation. Since the pathogenesis of many, if not all, types of polycystic kidneys remains unknown, a practical classification must be based on gross and microscopic pathologic study, clinical features, and family history. Osathanondh and Potter (1964) distinguished four varieties, based on morphological findings, revealed by microdissection. Unfortunately, not all types of cystic kidneys are included in this classification. Moreover, their type III cystic kidney collects a number of clearly different entities. Nevertheless, once one is familiar with its deficiencies, the Osathanondh and Potter classification is still very useful.     

Statistical basis for positive identification in forensic anthropology

Forensic scientists are often expected to present the likelihood of DNA identifications in US courts based on comparative population data, yet forensic anthropologists tend not to quantify the strength of an osteological identification. Because forensic anthropologists are trained first and foremost as physical anthropologists, they emphasize estimation problems at the expense of evidentiary problems, but this approach must be reexamined. In this paper, the statistical bases for presenting osteological and dental evidence are outlined, using a forensic case as a motivating example. A brief overview of Bayesian statistics is provided, and methods to calculate likelihood ratios for five aspects of the biological profile are demonstrated. This paper emphasizes the definition of appropriate reference samples and of the "population at large," and points out the conceptual differences between them. Several databases are introduced for both reference information and to characterize the "population at large," and new data are compiled to calculate the frequency of specific characters, such as age or fractures, within the "population at large." Despite small individual likelihood ratios for age, sex, and stature in the case example, the power of this approach is that, assuming each likelihood ratio is independent, the product rule can be applied. In this particular example, it is over three million times more likely to obtain the observed osteological and dental data if the identification is correct than if the identification is incorrect. This likelihood ratio is a convincing statistic that can support the forensic anthropologist's opinion on personal identity in court.     

Patents in combi-space: patent challenges in combinatorial chemistry

Patent protection of inventions relating to combinatorial chemistry is attended by special challenges. The "breakthrough" nature of the field together with the always complex and often arcane chemical manipulations, apparatus, and strategies which suffuse this field make it difficult to describe the inventions adequately. It can be a challenge to communicate effectively with official authorities charged with patent examination. Extraordinary effort is called for in clarifying such inventions such that their patentability can be appreciated. The utility of some types of inventions in this field may be open to question; clear statements of at least one acceptable utility-even if only a minor utility-is beneficial. Because a principal product of many aspects of combinatorial chemistry is information, e.g., the identification of a lead compound, offshore "piracy" is a risk. Domestic claim tie-ins may improve the ability to abate such piracy. Copyright 1998 John Wiley & Sons, Inc.     

Cross entropy minimization in uninvadable states of complex populations

Selection is often. viewed as a process that maximizes the average fitness of a population. However, there are often constraints even on the phenotypic level which may prevent fitness optimization. Consequently, in evolutionary game theory, models of frequency dependent selection are investigated, which focus on equilibrium states that are characterized by stability (or uninvadability) rather than by optimality. The aim of this article is to show that nevertheless there is a biologically meaningful quantity, namely cross (fitness) entropy, which is optimized during the course of evolution: a dynamical model adapted to evolutionary games is presented which has the property that relative entropy decreases monotonically, if the state of a (complex) population is close to an uninvadable state. This result may be interpreted as if evolution has an order stabilizing effect.     

Evolution of major histocompatibility complex by “en bloc” duplication before mammalian radiation

Duplications are an important mechanism for the emergence of genetic novelties. Reports on duplicated genes are numerous, and mechanisms for polyploidization or local gene duplication are beginning to be understood. When a local duplication is studied, searches are usually done gene-by-gene, and the size of duplicated segments is not often investigated. Therefore, we do not know if the gene in question has duplicated alone or with other genes, implying that "en bloc" duplications are poorly studied. We propose a method for identification of "en bloc" duplication using mapping, phylogenetic and statistical analyses. We show that two segments present in the major histocompatibility complex (MHC) region of human chromosome 6 have resulted from an "en bloc" duplication that took place between divergence of amniotes and methaterian/eutherian separation. These segments contain members of the same multigenic families, namely olfactory receptors genes, genes encoding proteins containing B30.2 domain, genes encoding proteins containing immunoglobulin V domain and MHC class I genes. We will discuss the fact that olfactory receptors and MHC genes have undergone positive selection, which could have helped in fixation of the surrounding genes.     

Linking phenotype,genotype and environment to unravel genetic components underlying cold hardiness in coastal Douglas-fir (<Emphasis Type="Italic">Pseudotsuga menziesii</Emphasis> var. <Emphasis Type="Italic">menziesii</Emphasis>)

Global climate change may detrimentally affect future generations of numerous forest tree species, hampering their long-term sustainability if appropriate evolutionary responses remain lacking. To face these novel threats, conservation biologists are in need of a thorough understanding and identification of adaptive variation in key fitness traits. We here provide an elaborate synthesis of pre-existing and novel analyses of an association mapping, genecological and landscape genomic study integrating genotypic, environmental and phenotypic data to gain insights into the genetic basis of cold-hardiness adaptation in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii). Data were collected across part of the natural range for a total of 643 individuals. A landscape genomic approach revealed 28 putative non-neutral genes, although a variance partitioning analysis indicated only moderate power of this gene set in explaining cold-hardiness-related phenotypic variation, and suggests many important genes await discovery. Integrating these results within the entire phenotype-genotype-environment spectrum allowed us to delineate the six most promising candidate genes under selection. By combining genomic, phenotypic and environmental data, this study attempts to gain insights in the genetic basis of key adaptations, which may ultimately aid forestry managers to establish resilient ecosystems in face of future climate change.     

Envelope capture by retroviruses

Retroelement transposition is a major source of diversity in genome evolution. Among the retrotransposable elements, the retroviruses are distinct in that their "transposition" extends from their initial host cells to neighboring cells and organisms. A determining step in the conversion of a retrotransposable element into an infectious retrovirus is the acquisition of an envelope glycoprotein, designated Env. Here, we review some examples of envelope "capture" by mammal retroviruses and provide evidence for such a mechanism by HTLV. This phenomenon may explain the notable conservation of env genes observed between phylogenetically distant retroviruses. Elucidation of these recombination processes should help to clarify retroviral phylogeny, better understand retroviral pathogenesis, and may lead to the identification of new retroelements.     

Birth and population prevalence of Duchenne muscular dystrophy in the Netherlands

Summary Mutations causing Duchenne muscular dystrophy (DMD) have a short survival. Therefore, birth and population prevalence are maintained by new mutations. The present inventory was made to estimate the birth and population prevalence rates of DMD in the Netherlands. Seven methods of case identification were used. Data on 496 definite, probable or possible DMD patients born since 1961, or alive on January 1, 1983, were obtained. Several methods gave an estimated ascertainment of more than 95%. The prevalence rate at birth of DMD was estimated at 23.7×10^–5 (14215) male live births (MLB) yearly. The prevalence rate in the male population on January 1, 1983 was 5.4×10^–5 (118496). About 1% of the males in this study may have autosomal recessive Duchenne-like muscular dystrophy. Until now there has been no convincing evidence for geographic differences in DMD prevalence at birth. A list of frequency studies of Duchenne muscular dystrophy is included. The DMD mutation rate calculated by the indirect method is 7.9×10^–5 genes per generation. However, this may well be an over-estimate, as this method does not account for germline mosaicism. Using a modified sex ratio method the proportion of sporadic DMD among all cases was estimated to be 0.106 (range 0–0.332). High frequency of germline mosaicism in DMD is a likely cause for the apparent lack of sporadic cases as found in previous studies, if mutation rates in male and female gametes are equal. Therefore, methods for estimating the proportion of new mutants in DMD should take germline mosaicism into account. The modified sex ratio method allows incorporation of data on germline mosaicism if available.     

Implications of absence of measurement invariance for detecting sex limitation and genotype by environment interaction.

Using univariate sum scores in genetic studies of twin data is common practice. This practice precludes an investigation of the measurement model relating the individual items to an underlying factor. Absence of measurement invariance across a grouping variable such as gender or environmental exposure refers to group differences with respect to the measurement model. It is shown that a decomposition of a sum score into genetic and environmental variance components leads to path coefficients of the additive genetic factor that are biased differentially across groups if individual items are non-invariant. The arising group differences in path coefficients are identical to what is known as "scalar sex limitation" when gender is the grouping variable, or as "gene by environment interaction" when environmental exposure is the grouping variable. In both cases the interpretation would be in terms of a group-specific effect size of the genetic factor. This interpretation may be incorrect if individual items are non-invariant.     

Timing of Antimicrobial Therapy after Identification of Ventilator-Associated Condition Is Not Associated with Mortality in Patients with Ventilator-Associated Pneumonia: A Cohort Study

Purpose

Delays in antimicrobial therapy increase mortality in ventilator-associated pneumonia (VAP). The more objective ventilator-associated complications (VAC) are increasingly used for quality reporting. It is unknown if delays in antimicrobial administration, after patients meet VAC criteria, leads to worse outcomes.

Materials and Methods

Cohort of 81 episodes of antimicrobial treatment for VAP. We compared mortality, superinfections and treatment failures conditional on the timing of identification of VAC.

Results

60% of patients with VAC had an identifiable episode at least 48 before the initiation of antimicrobials. Antimicrobial administration after the identification of VAC was not associated with intensive care unit (ICU) mortality (OR 0.71, 95% CI 0.11–4.48, p = 0.701) compared to immediate antimicrobial administration. Similarly, the risk of treatment failure or superinfection was not affected by the timing of administration of antimicrobials in VAC (HR 0.95, 95% CI 0.42–2.19, p = 0.914).

Conclusions

We observed no signal of harm associated with the timing to initiate antimicrobials after the identification of a VAC. The identification of VAC should not lead clinicians to start antimicrobials before a diagnosis of VAP can be established.     

Identification of jellyfish from Continuous Plankton Recorder samples

Previous analysis of the Continuous Plankton Recorder (CPR) long-term data set for the presence of ‘coelenterate’ tissue revealed changes in the frequency of jellyfish occurrence in the North Atlantic Ocean and North Sea; however, the identities of the jellyfish were unknown, causing uncertainty in interpreting these findings. To improve the utility of the ‘coelenterate’ data from the CPR, 62 CPR samples were selected for re-analysis from an area where the widespread occurrence of the holoplanktonic scyphomedusan, Pelagia noctiluca (Forsskål, 1775), was previously documented from net tows to test if the CPR sampled P. noctiluca. Examination of the samples revealed smears (<1 mm) of golden gelatinous tissue on the sampling mesh. Subsequent microscopic examination and measurement of nematocysts identified most of the smears as P. noctiluca. Indeed, P. noctiluca was identified on 53% of the CPR samples from the area that best coincided with the documented bloom area. Although hydrozoans were also identified in the samples, the characteristic golden colour of P. noctiluca and its distinct suite of nematocysts allowed identification to species level. The identification of other jellyfish may be more complicated due to the labour-intensive examination of samples and unclear delineation of nematocyst types when multiple similar species are present. Nevertheless, re-analysis of CPR samples holds great promise for identifying the underlying reason for increases in jellyfish occurrence in the CPR records.     

Recent Taxonomic Developments with <Emphasis Type="Italic">Candida</Emphasis> and Other Opportunistic Yeasts

Increases in susceptible patient populations and advances in identification methods have resulted in the continued recognition of novel yeasts as agents of human infection. Most of these agents are members of the well-recognized genera Candida, Cryptococcus, Trichosporon, and Rhodotorula. Some of these agents are “cryptic species,” members of species complexes, and may not be detectable using classical carbohydrate assimilation-based methods of yeast identification. Such species require DNA- or MALDI-based methods for correct identification, although sporadic isolates may not routinely require delineation to the individual species level. The coming end of the fungal taxonomy rules requiring separate names for sexual and asexual forms of the same fungus will hopefully allow greater clarity, as names for medically important yeast can now be based on the needs of the medical mycology community and the common goal of better communication between laboratory and clinician.