Nuclear and mitochondrial genetic variation in the Yanomamö: a test case for ancient DNA studies of prehistoric populations

Ancient DNA provides a potentially revolutionary way to study biological relationships in prehistoric populations, but genetic patterns are complex and require careful interpretation based on robust, well-tested models. In this study, nuclear and mitochondrial markers were compared in the Yanomam?, to assess how well each data set could differentiate among closely related groups. The villages selected for the study share a recent fission history and are closely related to each other, as would likely be the case among prehistoric peoples living in the same valley or region. The Yanomam? generally practice village-level endogamy, but some migration and gene flow are known to occur between villages. Nuclear and mitochondrial DNA data were compared using F-statistics and genetic distance analyses. The nuclear data performed as expected, males and females from the same village were similar, and the villages were genetically distinct, with the magnitude of genetic differences correlated with historical relationship. However, mtDNA analyses did not yield the expected results. The genetic distances between villages did not correlate with historical relationship, and the sexes were significantly different from each other in two villages. Both the Lane and Sublett and the Spence methods, used to test for archaeological residence patterns, were consistent with endogamy. Hence, ancient DNA can, in principle, provide us with a unique opportunity to study genetic structure and gene flow in archaeological populations. However, interpretations, particularly those based on single loci such as mitochondrial DNA, should be cautious because sex-specific migration and sampling issues may have dramatic effects.     

Host dispersal as the driver of parasite genetic structure: a paradigm lost?

Understanding traits influencing the distribution of genetic diversity has major ecological and evolutionary implications for host–parasite interactions. The genetic structure of parasites is expected to conform to that of their hosts, because host dispersal is generally assumed to drive parasite dispersal. Here, we used a meta‐analysis to test this paradigm and determine whether traits related to host dispersal correctly predict the spatial co‐distribution of host and parasite genetic variation. We compiled data from empirical work on local adaptation and host–parasite population genetic structure from a wide range of taxonomic groups. We found that genetic differentiation was significantly lower in parasites than in hosts, suggesting that dispersal may often be higher for parasites. A significant correlation in the pairwise genetic differentiation of hosts and parasites was evident, but surprisingly weak. These results were largely explained by parasite reproductive mode, the proportion of free‐living stages in the parasite life cycle and the geographical extent of the study; variables related to host dispersal were poor predictors of genetic patterns. Our results do not dispel the paradigm that parasite population genetic structure depends on host dispersal. Rather, we highlight that alternative factors are also important in driving the co‐distribution of host and parasite genetic variation.     

Assumption validity in human optimal foraging: The Barí hunters of Venezuela as a test case

Optimal foraging theory is being used increasingly as a means of understanding human foraging behavior. One of the central assumptions of optimal foraging theory is that prey items or patches are encountered sequentially and as a Poisson process. Using empirical data gathered on the Barí hunters of Venezuela, we assess the validity of this central assumption. We compare our observed distribution of encounter frequencies with an expected Poisson distribution, utilizing chisquare tests and graphic representations. The results are strikingly consonant with the expected Poisson distribution and lend support to the applicability of optimal foraging models to human hunting behavior.     

Early detection of genetic hemochromatosis: should all young adults be offered the genetic test?

Genetic hemochromatosis (GH) is a late-onset, autosomal recessive disorder. The majority of those at risk from iron overload and its clinical consequences may be detected by a simple genetic test. Furthermore, treatment by phlebotomy, if instituted early, removes excess iron and prevents the complications of iron overload which include arthralgia, diabetes, and cirrhosis of the liver. GH seems to be an obvious candidate for inclusion in national screening programs. However, important questions remain concerning the proportion of individuals with the high-risk genotype who eventually show clinical manifestations of iron overload and the significance of heterozygosity for haemochromatosis in terms of morbidity. Until these questions are resolved, the introduction of widespread genetic screening cannot be justified.     

Tuberculosis masquerading as malignancy: a multimodality approach to the correct diagnosis – a case report

BACKGROUND: Extrapulmonary tuberculosis is one of the great mimickers of medicine, and often masquerades as malignancy. As a result, patients may be referred to oncologists and surgeons for further evaluation and management, delaying the institution of appropriate anti-tuberculous drug therapy. CASE PRESENTATION: We present the case of a 21 year old man with tuberculous osteomyelitis, who was referred to the Bone and Soft Tissue Sarcoma Service at our institution with a provisional diagnosis of malignancy. Further investigation revealed extensive retroperitoneal abdominal and pelvic lymphadenopathy. The recognition of certain patterns on imaging, and finally the isolation of Mycobacterium tuberculosis from tissue samples obtained under image guidance, enabled the correct diagnosis to be made. CONCLUSION: This case highlights the importance of remaining cognisant of the protean manifestations of extrapulmonary tuberculosis, and illustrates the advantage of a clinically directed multi-modality imaging approach to diagnosis.     

A nature reserve as a repository of genetic richness – The case of European larch from the Gorce Mountains

Conservation of valuable populations must be based on a thorough understanding of their genetic variation, especially for species negatively affected by human activities. We investigated the population of larch from the nature reserve in the Gorce Mountains, which was established to preserve a unique stand of Larix decidua subsp. polonica, a remnant of one of the largest native complexes of this species. The chloroplast marker ll-TaqI was used to investigate whether the gene pool of the analysed population was contaminated with the alien larch species. We used eleven nuclear DNA microsatellite markers (nSSRs) to examine this population’s genetic diversity and verify the hypothesis about historical use of the larch from the reserve as a source of reproductive material for the Tatra Mountains. The link between the reserve population and the European larch’s ancestral groups was also verified. No contamination of the studied pool of individuals by alien species was found. The study showed high genetic variability in larch from the Gorce Mountains (H_E = 0.689, H_O = 0.671). The differentiation between the Gorce and Tatra National Park populations was F_ST = 0.038 (p < 0.001). Trees from the reserve and the national park formed two distinct genetic groups. We rejected the hypothesis that the nature reserve was the source of the regeneration material used in the Tatra Mountains. The study proved the uniqueness of the reserve population, and confirmed the appropriateness of the protection measures taken.     

“Out-of-India” dispersal for Adina (tribe Naucleeae; family Rubiaceae): evidence from the early Eocene fossil record from India

This study reports the oldest fossil record of the genus Adina, A. vastanenesis n. sp., from the early Eocene of Vastan lignite mine (Cambay Shale Formation), Surat district, Gujarat. This fossil wood is characterized by diffuse porous wood, predominantly solitary tylosed vessels, simple perforations, scanty paratracheal to diffuse to sometimes diffuse in aggregate axial parenchyma, predominantly uniseriate to occasionally biseriate rays, and non septate fibres with bordered pits and shows its best resemblance with the modern species, Adina multifolia Haviland, belonging to the tribe Naucleeae (subfamily Cinchonoideae) of the family Rubiaceae. The present discovery becomes the first fossil record of the wood of Adina, which provides an insight about the Gondwanan origin either for the genus Adina or the tribe Naucleeae and its further dispersal to Southeast Asia.     

“The Skunk and the Smallpox:” Mythology and Historical Reality

Abstract

Rare is the myth which provides an understanding of the historic circumstances which brought about its creation, but a narrative collected among the Wyandot Indians of Oklahoma does lend itself to historical analysis. The myth is both etiological and medicinal in its relation of the cause and cure for smallpox. Unique features of the myth’s content relative to cause and cure can be logically and historically related to the Wyandot situation in the second decade of the 19thcentury-in’ close proximity to the white settlement at Sandusky, Ohio. Sandusky Wyandots not only observed white treatment of smallpox, but heard tales told of white exploits in the Great Northwest Trading Company. It is contended here that the Wyandots selected as the etiology of smallpox the explanation offered by whites as a result of experiences of traders on the Columbia river; and that they selected as a cure for smallpox a form based on observation of white treatment at Sandusky. The myth, therefore, had its origin about 1815, when the Wyandot were at Sandusky, Ohio.     

Leaf dry matter content as a predictor of grassland litter decomposition: a test of the ��mass ratio hypothesis��

The mass ratio hypothesis provides the key link between plant functional traits (PFTs) and ecosystem processes. Despite its centrality to the field it has had few direct tests. A litter decomposition study using grassland species, singly and in mixtures, was set up to see whether simple leaf traits could be used to predict the decomposition of leaf mixtures. Leaf Dry Matter Content (LDMC) was the trait that performed best. Mass loss in single species bags was best predicted using an exponential model. LDMC explained 48% of the variance in mixture mass loss. There was no significant impact of mixture species richness on mass loss. This study generally confirmed the predictions of the mass ratio hypothesis, but adds some support to other studies that indicate it needs broadening to take into account non-linear and threshold relationships between PFTs and ecosystem processes.     

Ammonium nutrition in the halophyte Spartina alterniflora under salt stress: evidence for a priming effect of ammonium?

Background and aims

The effects of salt stress on the salt marsh halophyte Spartina alterniflora have been well documented. However, plant responses to combined salinity and ammonium toxicity and the underlying mechanisms are relatively unknown. The aim of the present investigation was to study the effects of both salinity (0, 200 and 500 mM NaCl) and nitrogen form (NO₃ ^?, NH₄ ⁺ or NH₄NO₃) on S. alterniflora.

Methods

Plants were cultivated in sandy soil under greenhouse conditions for 3 months. At harvest, growth parameters were measured and leaf samples were analysed for oxidative stress parameters (malondialdehyde, MDA; electrolyte leakage, EL; and hydrogen peroxide, H₂O₂ concentration) and the activity of antioxidant enzymes (glutathione reductase, GR; superoxide dismutase, SOD; catalase, CAT; ascorbate peroxidase, APX and Guaiacol peroxidase, GPX).

Results

In the absence of NaCl, plant growth rate was the highest in the medium containing both nitrogen forms, and the lowest in the medium containing only nitrate. Irrespective of the nitrogen form, plant growth was generally higher at 200 mM NaCl than without salinity. Ammonium-fed plants showed better growth than nitrate-fed plants under high salinity. In the absence of salinity, ammonium-fed plants showed higher SOD, APX, GR, CAT, and GPX activities than nitrate-fed ones. The antioxidant enzymes exhibited higher activity in saline-treated plants. The considerable advantage of NH₄ ⁺ nutrition to S. alterniflora under saline conditions was associated with high antioxidant enzyme activities, together with low MDA content, EL, and H₂O₂ concentration.

Conclusion

These data clearly demonstrate that NH₄ ⁺ is more favourable for the growth of S. alterniflora under high salinity than NO₃ ^?. It is suggested that NH₄ ⁺ nutrition improves the plant’s capacity to limit oxidative damage by stimulating the activities of the major antioxidant enzymes.     

How to remain nonfolded and pliable: the linkers in modular α-amylases as a case study

The primary structure of linkers in a new class of modular α-amylases constitutes a paradigm of the structural basis that allows a polypeptide to remain nonfolded, extended and pliable. Unfolding is mediated through a depletion of hydrophobic residues and an enrichment of hydrophilic residues, amongst which Ser and Thr are over-represented. An extended and flexible conformation is promoted by the sequential arrangement of Pro and Gly, which are the most abundant residues in these linkers. This is complemented by charge repulsion, charge clustering and disulfide-bridged loops. Molecular dynamics simulations suggest the existence of conformational transitions resulting from a transient and localized hydrophobic collapse, arising from the peculiar composition of the linkers. Accordingly, these linkers should not be regarded as fully disordered, but rather as possessing various discrete structural patterns allowing them to fulfill their biological function as a free energy reservoir for concerted motions between structured domains.     

Origin of genetic variation: regulation of genetic recombination in the higher organisms — a theory

Summary Recent studies in the fungi, particularly Neurospora and Schizophyllum, have revealed a number of genetic features which, viewed in conjunction with earlier observations on other organisms, form a pattern, or model, which appears to be basic to the control of recombination in all eukaryotes, including higher organisms. It is assumed that the control is exercised on mechanisms that produce new alleles through recombination, as understood in broad terms and including such a likely phenomenon as gene conversion, which may or may not involve crossing-over, as well as equal and unequal crossing-over. The recombination may thus occur between alleles in either the homozygous or heterozygous condition. In the model, regulatory genes and breeding behaviour are integrated into one self-regulatory system controlling the production of new genetic variation.The model is based on the following five general features, largely substantiated by the results in Neurospora and Schizophyllum: 1) The frequency of recombination in a particular chromosomal region is controlled by specific regulatory genes (rec). 2) There may be a number of such specific, regulatory genes responsible for recombination in a given region. 3) A rec. locus may influence recombination in more than one region. 4) The regulatory genes have no specific physical relationship with the region(s) they control, and are usually located at random in the genome. 5) Of the allelic forms of the regulatory genes it is always the dominant gene which suppresses recombination and the recessive gene which increases recombination. The rec system is epistatic to other genetic elements jointly involved in the overall control of recombination in a specific region. It is suggested that usually the control of recombination in a given region is exercised, cumulatively, by the balance of the dominant and recessive genes of the specific rec loci in the organism. Outbreeding, with the associated high heterozygosity of the regulatory rec loci, virtually switches off recombination, producing few new variations. Inbreeding produces homozygosity of these loci, resulting in certain individuals which will have a considerable number of their regulatory loci in the homozygous recessive condition and in which recombination will be switched on, producing new variation at a high frequency. Inbreeding is thus an integrated, evolutionary system of considerable importance, and is not a degenerate dead end, as many investigators have previously thought.The model has another compensatory function in evolution. In major loci, or in an operon, where there are structural genes and closely linked operator genes, as exemplified by the S locus, there are indications that the present model is concerned with the regulation of both structural and operator genes. The consequences of the model in the two classes of genes, however, are in direct contrast to each other: High heterozygosity which is instrumental in switching off recombination, and which is therefore helpful in maintaining stability in the structural gene, is conducive to functional variation of the operator gene; and high homozygosity, which is instrumental in switching on recombination, and which is therefore helpful in producing variation in the structural gene, is conducive to the stability of the operator gene.This model of the control of genetic variation in a specific chromosomal region is significant in development as well as in evolution, and throws light on a number of hitherto intractable problems peculiar to the higher organisms. For example, the model is helpful in explaining: 1) the origin of new self-incompatibility alleles in the flowering plants; 2) the impressive speciation in the waif flora (and fauna) of the oceanic islands; 3) the presence of high genetic variability in inbreeding species of plants; 4) environmentally-induced heritable variation in certain plants; and 5) the genetic mechanism of antibody diversity in animals.     

PPAR-γ as a therapeutic target in cardiovascular disease: evidence and uncertainty

Peroxisome proliferator-activated receptor γ (PPAR-γ) is a key regulator of fatty acid metabolism, promoting its storage in adipose tissue and reducing circulating concentrations of free fatty acids. Activation of PPAR-γ has favorable effects on measures of adipocyte function, insulin sensitivity, lipoprotein metabolism, and vascular structure and function. Despite these effects, clinical trials of thiazolidinedione PPAR-γ activators have not provided conclusive evidence that they reduce cardiovascular morbidity and mortality. The apparent disparity between effects on laboratory measurements and clinical outcomes may be related to limitations of clinical trials, adverse effects of PPAR-γ activation, or off-target effects of thiazolidinedione agents. This review addresses these issues from a clinician's perspective and highlights several ongoing clinical trials that may help to clarify the therapeutic role of PPAR-γ activators in cardiovascular disease.     

Anhydrobiosis: the model worm as a model?

New work now shows that the dauer larvae of Caenorhabditis elegans can survive anhydrobiotically. The genetic tractability of this model organism may be useful in studying how organisms survive when losing most or all of their water.     

Effects of temperature on the nitric oxide-dependent modulation of the Frank–Starling mechanism: the fish heart as a case study

The Frank–Starling law is a fundamental property of the vertebrate myocardium which allows, when the end-diastolic volume increases, that the consequent stretch of the myocardial fibers generates a more forceful contraction. It has been shown that in the eel (Anguilla anguilla) heart, nitric oxide (NO) exerts a direct myocardial relaxant effect, increasing the sensitivity of the Frank–Starling response (Garofalo et al., 2009). With the use of isolated working heart preparations, this study investigated the relationship between NO modulation of Frank–Starling response and temperature challenges in the eel. The results showed that while, in long-term acclimated fish (spring animals perfused at 20 °C and winter animals perfused at 10 °C) the inhibition of NO production by L-N5 (1-iminoethyl)ornithine (L-NIO) significantly reduced the Frank–Starling response, under thermal shock conditions (spring animals perfused at 10 or 15 °C and winter animals perfused at 15 or 20 °C) L-NIO treatment resulted without effect. Western blotting analysis revealed a decrease of peNOS and pAkt expressions in samples subjected to thermal shock. Moreover, an increase in Hsp90 protein levels was observed under heat thermal stress. Together, these data suggest that the NO synthase/NO-dependent modulation of the Frank–Starling mechanism in fish is sensitive to thermal stress.