Are There Rearrangement Hotspots in the Human Genome?

In a landmark paper, Nadeau and Taylor [18] formulated the random breakage model (RBM) of chromosome evolution that postulates that there are no rearrangement hotspots in the human genome. In the next two decades, numerous studies with progressively increasing levels of resolution made RBM the de facto theory of chromosome evolution. Despite the fact that RBM had prophetic prediction power, it was recently refuted by Pevzner and Tesler [4], who introduced the fragile breakage model (FBM), postulating that the human genome is a mosaic of solid regions (with low propensity for rearrangements) and fragile regions (rearrangement hotspots). However, the rebuttal of RBM caused a controversy and led to a split among researchers studying genome evolution. In particular, it remains unclear whether some complex rearrangements (e.g., transpositions) can create an appearance of rearrangement hotspots. We contribute to the ongoing debate by analyzing multi-break rearrangements that break a genome into multiple fragments and further glue them together in a new order. In particular, we demonstrate that (1) even if transpositions were a dominant force in mammalian evolution, the arguments in favor of FBM still stand, and (2) the "gene deletion" argument against FBM is flawed.     

Whose Turn? Chromosome Research and the Study of the Human Genome

A common account sees the human genome sequencing project of the 1990s as a “natural outgrowth” of the deciphering of the double helical structure of DNA in the 1950s. The essay aims to complicate this neat narrative by putting the spotlight on the field of human chromosome research that flourished at the same time as molecular biology. It suggests that we need to consider both endeavors – the human cytogeneticists who collected samples and looked down the microscope and the molecular biologists who probed the molecular mechanisms of gene function – to understand the rise of the human genome sequencing project and the current genomic practices. In particular, it proposes that what has often been described as the “molecularization” of cytogenetics could equally well be viewed as the turn of molecular biologists to human and medical genetics – a field long occupied by cytogeneticists. These considerations also have implications for the archives that are constructed for future historians and policy makers.     

Are Human and Mouse Satellite Cells Really the Same?

Satellite cells are quiescent cells located under the basal lamina of skeletal muscle fibers that contribute to muscle growth, maintenance, repair, and regeneration. Mouse satellite cells have been shown to be muscle stem cells that are able to regenerate muscle fibers and self-renew. As human skeletal muscle is also able to regenerate following injury, we assume that the human satellite cell is, like its murine equivalent, a muscle stem cell. In this review, we compare human and mouse satellite cells and highlight their similarities and differences. We discuss gaps in our knowledge of human satellite cells, compared with that of mouse satellite cells, and suggest ways in which we may advance studies on human satellite cells, particularly by finding new markers and attempting to re-create the human satellite cell niche in vitro. (J Histochem Cytochem 58:941–955, 2010)     

Tuberculosis and Poverty: Why Are the Poor at Greater Risk in India?

Background

Although poverty is widely recognized as an important risk factor for tuberculosis (TB) disease, the specific proximal risk factors that mediate this association are less clear. The objective of our study was to investigate the mechanisms by which poverty increases the risk of TB.

Methods

Using individual level data from 198,754 people from the 2006 Demographic Health Survey (DHS) for India, we assessed self-reported TB status, TB determinants and household socioeconomic status. We used these data to calculate the population attributable fractions (PAF) for each key TB risk factor based on the prevalence of determinants and estimates of the effect of these risk factors derived from published sources. We conducted a mediation analysis using principal components analysis (PCA) and regression to demonstrate how the association between poverty and TB prevalence is mediated.

Results

The prevalence of self-reported TB in the 2006 DHS for India was 545 per 100,000 and ranged from 201 in the highest quintile to 1100 in the lowest quintile. Among those in the poorest population, the PAFs for low body mass index (BMI) and indoor air pollution were 34.2% and 28.5% respectively. The PCA analysis also showed that low BMI had the strongest mediating effect on the association between poverty and prevalent TB (12%, p = 0.019).

Conclusion

TB control strategies should be targeted to the poorest populations that are most at risk, and should address the most important determinants of disease—specifically low BMI and indoor air pollution.     

Why Do Unrelated Insertion Sequences Occur Together in the Genome of Escherichia Coli?

Natural isolates of Escherichia coli are polymorphic for the presence or absence of insertion sequences. Among the ECOR reference collection of 71 natural isolates studied for the number of copies of the insertion sequences IS1, IS2, IS3, IS4, IS5 and IS30, the number of strains containing no copies of the insertion sequences were 11, 28, 23, 43, 46 and 36, respectively. Significant correlations occur in the ECOR strains in the presence or absence of unrelated insertion sequences in the chromosome and plasmid complements. Strains containing any insertion sequence are more likely to contain additional, unrelated insertion sequences than would be expected by chance. We suggest that the positive correlations result from horizontal transfer mediated by plasmids. A branching-process model for the plasmid-mediated transmission of insertion sequences among hosts yields such a correlation, even in the absence of interactions affecting transposition or fitness. The predictions of the model are quantitatively in agreement with the observed correlations among insertion sequences.     

Are Free Radicals Involved in the Pathobiology of Human Essential Hypertension?

Possible involvement of reactive oxygen species and nitric oxide in the pathogenesis of human essential hypertension was investigated. It was observed that both superoxide anion and hydrogen peroxide production by polymorphonuclear leukocytes and the plasma levels of lipid peroxides are higher in uncontrolled essential hypertension compared with normal controls. Nitric oxide levels measured as its stable metabolite nitrite, as an index of nitric oxide synthesis, revealed its levels to be low in hypertensive patients. Superoxide anion, hydrogen peroxide, lipid peroxides and nitric oxide levels reverted to normal values after the control of hypertension by drugs. The concentrations of anti-oxidants such as vitamin E and superoxide dismutase were found to be decreased in patients with uncontrolled hypertension. Several anti-hypertensive drugs inhibited lipid peroxidation in vitro. Angiotensin-II, a potent vasoconstrictor, stimulated free radical generation in normal leukocytes which could be blocked by calmodulin antagonists. These results suggest that an increase in free radical generation and a simultaneous decrease in the production of nitric oxide and anti-oxidants such as SOD and vitamin E occurs in essential hypertension. This increase in free radical generation can inactivate prostacyclin and nitric oxide and decrease their half life which can lead to an increase in peripheral vascular resistance and hypertension.     

Pervasive Natural Selection in the Drosophila Genome?

Over the past four decades, the predominant view of molecular evolution saw little connection between natural selection and genome evolution, assuming that the functionally constrained fraction of the genome is relatively small and that adaptation is sufficiently infrequent to play little role in shaping patterns of variation within and even between species. Recent evidence from Drosophila, reviewed here, suggests that this view may be invalid. Analyses of genetic variation within and between species reveal that much of the Drosophila genome is under purifying selection, and thus of functional importance, and that a large fraction of coding and noncoding differences between species are adaptive. The findings further indicate that, in Drosophila, adaptations may be both common and strong enough that the fate of neutral mutations depends on their chance linkage to adaptive mutations as much as on the vagaries of genetic drift. The emerging evidence has implications for a wide variety of fields, from conservation genetics to bioinformatics, and presents challenges to modelers and experimentalists alike.     

Why Do Child-Directed Interactions Support Imitative Learning in Young Children?

Child-directed cues support imitation of novel actions at 18 months, but not at two years of age. The current studies explore the mechanisms that underlie the propensity that children have to copy others at 18 months, and how the value of child-directed communication changes over development. We ask if attentional allocation accounts for children''s failure to imitate observed actions at 18 months, and their success at two years of age, and we explore the informational value child-directed contexts may provide across ontogeny. Eighteen-month-old (Study 1) and two-year-old (Study 2) children viewed causally non-obvious actions performed by child-directed (Study 1 & 2), observed (Study 1 & 2), or non-interactive (Study 2) actors, and their visual attention and imitative behaviors were assessed. Results demonstrated that child-directed contexts supported imitative learning for 18-month-old children, independent of their effects on proximal attention. However, by two years of age, neither directness nor communication between social partners was a necessary condition for supporting social imitation. These findings suggest that developmental changes in children''s propensity to extract information from observation cannot be accounted for by changes in children''s interpretation of what counts as child-directed information, and are likely not due to changes in how children allocate attention to observed events.     

Why the ISMNI and the Utah paradigm? Their role in skeletal and extraskeletal disorders

Besides bringing problems, aging can let the mind's eye see more clearly than before, and it can let us express ourselves better. As age, experience and common sense examine today's skeletal medicine and surgery two questions keep popping up: A) How did we fail?; B) How to make it better? The Utah paradigm of skeletal physiology and the seminal ISMNI offer some answers, but exploiting them faces problems. Problem #1: By 1960 all clinicians and physiologists 'knew' (as the ancients 'knew' this world is flat) that effector cells controlled solely by nonmechanical agents explain all skeletal physiology and disorders ('effector cells' include osteoblasts, osteoclasts, chondroblasts and fibro-blasts). Or, nonmechanical agents -->cell level -->organ and intact subject. Adding later-discovered information to that 1960 view led to the Utah paradigm, which reveals the formerly hidden tissue-level 'dimension' of skeletal physiology. It builds on this idea: (mechanical + nonmechanical agents) -->(tissue level + cell level) --> organ and intact subject. The paradigm assigns great influence of neuromuscular physiology and physical activities on skeletal architecture, strength and mechanical competence. It also exposes flaws in many older views so controversies arise. Problem #2: The Utah paradigm and Wegner's concept of plate tectonics in geology seem alike in that each is valid but came before its time, so others fought it. They differ in this: The fight about Wegner's idea is over, but for the Utah paradigm and the ISMNI it just began. Hence more controversies. Nevertheless: A growing minority realizes that paradigm provides a far better base to build on than its antecedents, and since it keeps evolving as more evidence comes in it could endure for some decades. Yet very few realize this: It and the ISMNI have important implications for fields besides biomechanics and orthopaedics. Examples include anatomy, cardiovascular disease, dentistry, endocrinology, family medicine, gastroenterology, general surgery, genetics, gerontology, gynecology, maxillofacial surgery, neurology, neurosurgery, nutrition, ophthalmology, pathology, pediatrics, physical medicine and rehabilitation, plastic surgery, radiology, rheumatology, space and sports medicine, and urology. Quite a list! For the italicized questions above this article offers answers, of which its conclusion distills an essence.     

What's in a name? Are MSG and umami the same?

The Japanese word `umami' has a long past. It was already inuse during the Edo period (Tokugawa Shogunate) of Japanese history,which ended in 1868 (Mason, 1993). In Japanese, `umami' oftenconnotes a cognitive category (Yamaguchi and Ninomiya, 1998) oftaste, or perhaps flavor, with definitions that include deliciousness, flavor,relish,     

Living the Good Life? Mortality and Hospital Utilization Patterns in the Old Order Amish

Lifespan increases observed in the United States and elsewhere throughout the developed world, have been attributed in part to improvements in medical care access and technology and to healthier lifestyles. To differentiate the relative contributions of these two factors, we have compared lifespan in the Old Order Amish (OOA), a population with historically low use of medical care, with that of Caucasian participants from the Framingham Heart Study (FHS), focusing on individuals who have reached at least age 30 years.Analyses were based on 2,108 OOA individuals from the Lancaster County, PA community born between 1890 and 1921 and 5,079 FHS participants born approximately the same time. Vital status was ascertained on 96.9% of the OOA cohort through 2011 and through systematic follow-up of the FHS cohort. The lifespan part of the study included an enlargement of the Anabaptist Genealogy Database to 539,822 individuals, which will be of use in other studies of the Amish. Mortality comparisons revealed that OOA men experienced better longevity (p<0.001) and OOA women comparable longevity than their FHS counterparts.We further documented all OOA hospital discharges in Lancaster County, PA during 2002–2004 and compared OOA discharge rates to Caucasian national rates obtained from the National Hospital Discharge Survey for the same time period. Both OOA men and women experienced markedly lower rates of hospital discharges than their non-Amish counterparts, despite the increased lifespan.We speculate that lifestyle factors may predispose the OOA to greater longevity and perhaps to lesser hospital use. Identifying these factors, which might include behaviors such as lesser tobacco use, greater physical activity, and/or enhanced community assimilation, and assessing their transferability to non-Amish communities may produce significant gains to the public health.     

Why Are Autism Spectrum Conditions More Prevalent in Males?

Autism Spectrum Conditions (ASC) are much more common in males, a bias that may offer clues to the etiology of this condition. Although the cause of this bias remains a mystery, we argue that it occurs because ASC is an extreme manifestation of the male brain. The extreme male brain (EMB) theory, first proposed in 1997, is an extension of the Empathizing-Systemizing (E-S) theory of typical sex differences that proposes that females on average have a stronger drive to empathize while males on average have a stronger drive to systemize. In this first major update since 2005, we describe some of the evidence relating to the EMB theory of ASC and consider how typical sex differences in brain structure may be relevant to ASC. One possible biological mechanism to account for the male bias is the effect of fetal testosterone (fT). We also consider alternative biological theories, the X and Y chromosome theories, and the reduced autosomal penetrance theory. None of these theories has yet been fully confirmed or refuted, though the weight of evidence in favor of the fT theory is growing from converging sources (longitudinal amniocentesis studies from pregnancy to age 10 years old, current hormone studies, and genetic association studies of SNPs in the sex steroid pathways). Ultimately, as these theories are not mutually exclusive and ASC is multi-factorial, they may help explain the male prevalence of ASC.     

Why Are Computational Neuroscience and Systems Biology So Separate?

Despite similar computational approaches, there is surprisingly little interaction between the computational neuroscience and the systems biology research communities. In this review I reconstruct the history of the two disciplines and show that this may explain why they grew up apart. The separation is a pity, as both fields can learn quite a bit from each other. Several examples are given, covering sociological, software technical, and methodological aspects. Systems biology is a better organized community which is very effective at sharing resources, while computational neuroscience has more experience in multiscale modeling and the analysis of information processing by biological systems. Finally, I speculate about how the relationship between the two fields may evolve in the near future.