Gene Promoter Evolution Targets the Center of the Human Protein Interaction Network

Assessing the contribution of promoters and coding sequences to gene evolution is an important step toward discovering the major genetic determinants of human evolution. Many specific examples have revealed the evolutionary importance of cis-regulatory regions. However, the relative contribution of regulatory and coding regions to the evolutionary process and whether systemic factors differentially influence their evolution remains unclear. To address these questions, we carried out an analysis at the genome scale to identify signatures of positive selection in human proximal promoters. Next, we examined whether genes with positively selected promoters (Prom+ genes) show systemic differences with respect to a set of genes with positively selected protein-coding regions (Cod+ genes). We found that the number of genes in each set was not significantly different (8.1% and 8.5%, respectively). Furthermore, a functional analysis showed that, in both cases, positive selection affects almost all biological processes and only a few genes of each group are located in enriched categories, indicating that promoters and coding regions are not evolutionarily specialized with respect to gene function. On the other hand, we show that the topology of the human protein network has a different influence on the molecular evolution of proximal promoters and coding regions. Notably, Prom+ genes have an unexpectedly high centrality when compared with a reference distribution (P = 0.008, for Eigenvalue centrality). Moreover, the frequency of Prom+ genes increases from the periphery to the center of the protein network (P = 0.02, for the logistic regression coefficient). This means that gene centrality does not constrain the evolution of proximal promoters, unlike the case with coding regions, and further indicates that the evolution of proximal promoters is more efficient in the center of the protein network than in the periphery. These results show that proximal promoters have had a systemic contribution to human evolution by increasing the participation of central genes in the evolutionary process.

The Caribbean-North America-Cocos Triple Junction and the dynamics of the Polochic-Motagua fault systems: Pull-up and zipper models

The Polochic-Motagua fault systems (PMFS) are part of the sinistral transform boundary between the North American and Caribbean plates. To the west, these systems interact with the subduction zone of the Cocos plate, forming a subduction-subduction-transform triple junction. The North American plate moves westward relative to the Caribbean plate. This movement does not affect the geometry of the subducted Cocos plate, which implies that deformation is accommodated entirely in the two overriding plates. Structural data, fault kinematic analysis, and geomorphic observations provide new elements that help to understand the late Cenozoic evolution of this triple junction. In the Miocene, extension and shortening occurred south and north of the Motagua fault, respectively. This strain regime migrated northward to the Polochic fault after the late Miocene. This shift is interpreted as a ``pull-up'' of North American blocks into the Caribbean realm. To the west, the PMFS interact with a trench-parallel fault zone that links the Tonala fault to the Jalpatagua fault. These faults bound a fore-arc sliver that is shared by the two overriding plates. We propose that the dextral Jalpatagua fault merges with the sinistral PMFS, leaving behind a suturing structure, the Tonala fault. This tectonic ``zipper'' allows the migration of the triple junction. As a result, the fore-arc sliver comes into contact with the North American plate and helps to maintain a linear subduction zone along the trailing edge of the Caribbean plate. All these processes currently make the triple junction increasingly diffuse as it propagates eastward and inland within both overriding plates.

Chromosomal evolution and zoogeographic origin of southeast Asian shrews (genus Crocidura).

To the origins and evolution of Indomalayan shrews, we investigated the chromosomal variations of 14 species of Crocidura from SE Asia. Intraspecific polymorphism was mainly due to variation in the number of short chromosomal arms but C. lepidura and C. hutanis showed a polymorphism due to a centric fusion. The undifferentially stained karyotypes were similar in 9 species, all possessing 2n = 38 and FN = 54-56 (68); C. fuliginosa had 2n = 40 and FN = 54-58. These karyotypes are close to the presumed ancestral state for the genus Crocidura. Four species from Sulawesi had a reduced diploid number (2n = 30-34), a trend not observed among other SE Asian species but present in few Palaearctic taxa. Compared to the apparent stasis of karyotypic evolution observed among other SE Asian species, the high degree of interspecific differences reported among Sulawesian shrews is unusual and needs further investigation. Stasis and reduction in diploid number found in both Indomalayan and Palaeractic species suggest that these two groups share a common ancestry. This is in sharp contrast to most Afrotropical species which evolved towards higher diploid and fundamental numbers. The zoogeographical implications of these results are discussed.

Loss of egg yolk genes in mammals and the origin of lactation and placentation

Embryonic development in nonmammalian vertebrates depends entirely on nutritional reserves that are predominantly derived from vitellogenin proteins and stored in egg yolk. Mammals have evolved new resources, such as lactation and placentation, to nourish their developing and early offspring. However, the evolutionary timing and molecular events associated with this major phenotypic transition are not known. By means of sensitive comparative genomics analyses and evolutionary simulations, we here show that the three ancestral vitellogenin-encoding genes were progressively lost during mammalian evolution (until around 30-70 million years ago, Mya) in all but the egg-laying monotremes, which have retained a functional vitellogenin gene. Our analyses also provide evidence that the major milk resource genes, caseins, which have similar functional properties as vitellogenins, appeared in the common mammalian ancestor approximately 200-310 Mya. Together, our data are compatible with the hypothesis that the emergence of lactation in the common mammalian ancestor and the development of placentation in eutherian and marsupial mammals allowed for the gradual loss of yolk-dependent nourishment during mammalian evolution

Cigarette, cigar, and pipe smoking and the risk of head and neck cancers: pooled analysis in the International Head and Neck Cancer Epidemiology Consortium.

Cigar and pipe smoking are considered risk factors for head and neck cancers, but the magnitude of effect estimates for these products has been imprecisely estimated. By using pooled data from the International Head and Neck Cancer Epidemiology (INHANCE) Consortium (comprising 13,935 cases and 18,691 controls in 19 studies from 1981 to 2007), we applied hierarchical logistic regression to more precisely estimate odds ratios and 95% confidence intervals for cigarette, cigar, and pipe smoking separately, compared with reference groups of those who had never smoked each single product. Odds ratios for cigar and pipe smoking were stratified by ever cigarette smoking. We also considered effect estimates of smoking a single product exclusively versus never having smoked any product (reference group). Among never cigarette smokers, the odds ratio for ever cigar smoking was 2.54 (95% confidence interval (CI): 1.93, 3.34), and the odds ratio for ever pipe smoking was 2.08 (95% CI: 1.55, 2.81). These odds ratios increased with increasing frequency and duration of smoking (Ptrend ≤ 0.0001). Odds ratios for cigar and pipe smoking were not elevated among ever cigarette smokers. Head and neck cancer risk was elevated for those who reported exclusive cigar smoking (odds ratio = 3.49, 95% CI: 2.58, 4.73) or exclusive pipe smoking (odds ratio = 3.71, 95% CI: 2.59, 5.33). These results suggest that cigar and pipe smoking are independently associated with increased risk of head and neck cancers.

Evolution and cellular function of monothiol glutaredoxins: involvement in iron-sulphur cluster assembly

A number of bacterial species, mostly proteobacteria, possess monothiol glutaredoxins homologous to the Saccharomyces cerevisiae mitochondrial protein Grx5, which is involved in iron–sulphur cluster synthesis. Phylogenetic profiling is used to predict that bacterial monothiol glutaredoxins also participate in the iron–sulphur cluster (ISC) assembly machinery, because their phylogenetic profiles are similar to the profiles of the bacterial homologues of yeast ISC proteins. High evolutionary cooccurrence is observed between the Grx5 homologues and the homologues of the Yah1 ferredoxin, the scaffold proteins Isa1 and Isa2, the frataxin protein Yfh1 and the Nfu1 protein. This suggests that a specific functional interaction exists between these ISC machinery proteins. Physical interaction analyses using low-definition protein docking predict the formation of strong and specific complexes between Grx5 and several components of the yeast ISC machinery. Two-hybrid analysis has confirmed the in vivo interaction between Grx5 and Isa1. Sequence comparison techniques and cladistics indicate that the other two monothiol glutaredoxins of S. cerevisiae, Grx3 and Grx4, have evolved from the fusion of a thioredoxin gene with a monothiol glutaredoxin gene early in the eukaryotic lineage, leading to differential functional specialization. While bacteria do not contain these chimaeric glutaredoxins, in many eukaryotic species Grx5 and Grx3/4-type monothiol glutaredoxins coexist in the cell.

Natural vitamin C intake and the risk of head and neck cancer : a pooled analysis in the International Head and Neck Cancer Epidemiology Consortium

Evidence of associations between single nutrients and head and neck cancer (HNC) is still more limited and less consistent than that for fruit and vegetables. However, clarification of the protective mechanisms of fruit and vegetables is important to our understanding of HNC etiology. We investigated the association between vitamin C intake from natural sources and cancer of the oral cavity/pharynx and larynx using individual-level pooled data from ten case-control studies (5,959 cases and 12,248 controls) participating in the International Head and Neck Cancer Epidemiology (INHANCE) consortium. After harmonization of study-specific exposure information via the residual method, adjusted odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were estimated using unconditional multiple logistic regression models on quintile categories of 'non-alcohol energy-adjusted' vitamin C intake. In the presence of heterogeneity of the estimated ORs among studies, we derived those estimates from generalized linear mixed models. Higher intakes of vitamin C were inversely related to oral and pharyngeal (OR = 0.54, 95% CI: 0.45-0.65, for the fifth quintile category versus the first one, p for trend<0.001) and laryngeal cancers (OR = 0.52, 95% CI: 0.40-0.68, p for trend = 0.006), although in the presence of heterogeneity among studies for both sites. Inverse associations were consistently observed for the anatomical subsites of oral and pharyngeal cancer, and across strata of age, sex, education, body mass index, tobacco, and alcohol, for both cancer sites. The inverse association of vitamin C intake from foods with HNC may reflect a protective effect on these cancers; however, we cannot rule out other explanations.

Comparative genomics of Hedgehog loci in chordates and the origin of Shh regulatory novelties

The origin and evolution of the complex regulatory landscapes of some vertebrate developmental genes, often spanning hundreds of Kbp and including neighboring genes, remain poorly understood. The Sonic Hedgehog (Shh) genomic regulatory block (GRB) is one of the best functionally characterized examples, with several discrete enhancers reported within its introns, vast upstream gene-free region and neighboring genes (Lmbr1 and Rnf32). To investigate the origin and evolution of this GRB, we sequenced and characterized the Hedgehog (Hh) loci from three invertebrate chordate amphioxus species, which share several early expression domains with Shh. Using phylogenetic footprinting within and between chordate lineages, and reporter assays in zebrafish probing >30 Kbp of amphioxus Hh, we report large sequence and functional divergence between both groups. In addition, we show that the linkage of Shh to Lmbr1 and Rnf32, necessary for the unique gnatostomate-specific Shh limb expression, is a vertebrate novelty occurred between the two whole-genome duplications.

Early Modern Persian, Urdu, and English Historiography and the Imagination of Islamic India under British Rule

This paper analyses the early modern transformations of South Asian literary cultures through the production of historiography in Persian, English, and Urdu. In the 18th-19th centuries, South Asian communities experienced and participated in a major restructuring of the languages of the subcontinent. Urdu and English were institutionalized as governmental languages and utilized in new literary productions as Persian was gradually marginalized from the centre of literary and governmental polities. Three interrelated colonial policies reshaped the historical consciousness of South Asia and Britain: the production of new Persian histories commissioned under British patronage, the initiation of Urdu historiography through the translation of Persian and English histories, and the construction of the British history of India written in English. This article explores the historical and social dynamics of these events and situates the origins and evolution of the colonial historiographical project. Major works discussed are the Tārīkh-i Bangālah of Salīm Allāh Munshī (fl. 1763), James Mill's (1773-1836) The History of British India first published in 1817, Mīr Sher ʿAlī Afsos' the Ārāʾish-i mahfil, as well as the production of original Urdu histories such as Muḥammad Zakāʾ-Allāh's (1832-1910) the Tārīkh-i Hindustān.

Evolution and Stellar Content of AGN Host Galaxies

In this dissertation, Active Galactic Nuclei (AGN) and their host galaxies are discussed. Together with transitional events, such as supernovae and gamma-ray bursts, AGN are the most energetic phenomena in the Universe. The dominant fraction of their luminosity originates from the center of a galaxy, where accreting gas falls into a supermassive black hole, converting gravitational energy to radiation. AGN have a wide range of observed properties: e.g. in their emission lines, radio emission, and variability. Most likely, these properties depend significantly on their orientation to our line-of-sight, and to unify AGN into physical classes it is crucial to observe their orientation-independent properties, such as the host galaxies. Furthermore, host galaxy studies are essential to understand the formation and co-evolution of galactic bulges and supermassive black holes. In this thesis, the main focus is on observationally characterizing AGN host galaxies using optical and near-infrared imaging and spectroscopy. BL Lac objects are a class of AGN characterized by rapidly variable and polarized continuum emission across the electromagnetic spectrum, and coredominated radio emission. The near-infrared properties of intermediate redshift BL Lac host galaxies are studied in Paper I. They are found to be large elliptical galaxies that are more luminous than their low redshift counterparts suggesting a strong luminosity evolution, and a contribution from a recent star formation episode. To analyze the stellar content of galaxies in more detail multicolor data, especially observations at blue wavelengths, are essential. In Paper III, optical - near-infrared colors and color gradients are derived for low redshift BL Lac host galaxies. They show bluer colors and steeper color gradients than inactive ellipticals which, most likely, are caused by a relatively young stellar population indicating a different evolutionary stage between AGN hosts and inactive ellipticals. In Paper II, near-infrared imaging of intermediate redshift radio-quiet quasar hosts is used to study their luminosity evolution. The hosts are large elliptical galaxies, but they are systematically fainter than the hosts of radio-loud quasars at similar redshifts, suggesting a link between the luminosity of the host galaxies and the radio properties of AGN. In Paper IV, the characteristics of near-infrared stellar absorption features of low redshift radio galaxies are compared with those of inactive early-type galaxies. The comparison suggests that early-type galaxies with AGN are in a different evolutionary stage than their inactive counterparts. Moreover, radio galaxies are found to contain stellar populations containing both old and intermediate age components.

Evolution in the profile of thyroid cancer cases treated in an oncology reference service: what changed in the last 20 years

Objective: To evaluate the characteristics of thyroid carcinoma cases treated at a reference hospital for cancer between 2008 and 2010.Methods: we studied 807 cases and analyzed the following clinicopathologic variables: symptoms, risk factors, diagnostic tests, staging, histological type, treatment performed and complications.Results: Females were more affected, with 660 cases (82%). The average age at diagnosis was 44.5 years. Prior exposure to ionizing radiation was reported by 22 (3%) patients, a family history of thyroid cancer by 89 (11%), and 289 (36%) individuals reported other types of cancer in the family. The fine needle aspiration biopsy was the main parameter for surgical indication and was suggestive of carcinoma in 463 patients (57%). Papillary carcinoma was the most common histological type, with 780 cases (96.6%). There were 728 (90%) total thyroidectomies, 43 (5.3%) reoperations or partial thyroidectomies followed by totalization, 23 (2.8%) extended thyroidectomies and only 13 (1.6%) partial thyroidectomies (lobectomy with isthmectomy). Neck dissection associated with thyroidectomy was done in 158 patients (19.5%). We observed a predominance of tumors classified as T1 in 602 (74.6%) patients. Transient hypocalcemia was the most frequent complication.Conclusion: The results show that the worldwide increase in the incidence of thyroid cancer has changed the profile of patients seen at a referral service. In addition, there were changes in the type of surgical treatment used, with increased use of total thyroidectomy in relation to partial and subtotal ones, and decreased use of elective neck dissections.

Effect of L-arginine, dimercaptosuccinic acid (DMSA) and the association of L-arginine and DMSA on tissue lead mobilization and blood pressure level in plumbism

Lead (Pb)-induced hypertension is characterized by an increase in reactive oxygen species (ROS) and a decrease in nitric oxide (NO). In the present study we evaluated the effect of L-arginine (NO precursor), dimercaptosuccinic acid (DMSA, a chelating agent and ROS scavenger), and the association of L-arginine/DMSA on tissue Pb mobilization and blood pressure levels in plumbism. Tissue Pb levels and blood pressure evolution were evaluated in rats exposed to: 1) Pb (750 ppm, in drinking water, for 70 days), 2) Pb plus water for 30 more days, 3) Pb plus DMSA (50 mg kg-1 day-1, po), L-arginine (0.6%, in drinking water), and the combination of L-arginine/DMSA for 30 more days, and 4) their respective matching controls. Pb exposure increased Pb levels in the blood, liver, femur, kidney and aorta. Pb levels in tissues decreased after cessation of Pb administration, except in the aorta. These levels did not reach those observed in nonintoxicated rats. All treatments mobilized Pb from the kidney, femur and liver. Pb mobilization from the aorta was only effective with the L-arginine/DMSA treatment. Blood Pb concentrations in Pb-treated groups were not different from those of the Pb/water group. Pb increased blood pressure starting from the 5th week. L-arginine and DMSA treatments (4th week) and the combination of L-arginine/DMSA (3rd and 4th weeks) decreased blood pressure levels of intoxicated rats. These levels did not reach those of nonintoxicated rats. Treatment with L-arginine/DMSA was more effective than the isolated treatments in mobilizing Pb from tissues and in reducing the blood pressure of intoxicated rats.