Universidad Autónoma de la Ciudad de México

The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed "fragment recruitment," addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed "extreme assembly," made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

During angiogenesis, new vessels emerge from existing endothelial lined vessels to promote the degradation of the vascular basement membrane and remodel the extracellular matrix (ECM), followed by endothelial cell migration, and proliferation and the new generation of matrix components. Matrix metalloproteinases (MMPs) participate in the disruption, tumor neovascularization, and subsequent metastasis while tissue inhibitors of metalloproteinases (TIMPs) downregulate the activity of these MMPs. Then, the angiogenic response can be directly or indirectly mediated by MMPs through the modulation of the balance between pro- and anti-angiogenic factors. This review analyzes recent knowledge on MMPs and their participation in angiogenesis.

Phase transitions and structural and magnetic properties of rapidly solidified Ni50Mn38Sn12 alloy ribbons have been studied. Ribbon samples crystallize as a single-phase, ten-layered modulated (10M) monoclinic martensite with a columnar-grain microstructure and a magnetic transition temperature of 308 K. By decreasing the temperature, martensite undergoes an intermartensitic phase transition around 195 K. Above room temperature, the high temperature martensite transforms into austenite. Below 100 K, magnetization hysteresis loops shift along the negative H-axis direction, confirming the occurrence of an exchange bias effect. On heating, the thermal dependence of the coercive field HC shows a continuous increase, reaching a maximum value of 1017 Oe around 50 K. Above this temperature, HC declines to zero around 195 K. But above this temperature, it increases again up to 20 Oe falling to zero close to 308 K. The coercivity values measured in both temperature intervals suggest a significant difference in the magnetocrystalline anisotropy of the two martensite phases.

In November 2004, a regional climate change workshop was held in Guatemala with the goal of analyzing how climate extremes had changed in the region. Scientists from Central America and northern South America brought long‐term daily temperature and precipitation time series from meteorological stations in their countries to the workshop. After undergoing careful quality control procedures and a homogeneity assessment, the data were used to calculate a suite of climate change indices over the 1961–2003 period. Analysis of these indices reveals a general warming trend in the region. The occurrence of extreme warm maximum and minimum temperatures has increased while extremely cold temperature events have decreased. Precipitation indices, despite the large and expected spatial variability, indicate that although no significant increases in the total amount are found, rainfall events are intensifying and the contribution of wet and very wet days are enlarging. Temperature and precipitation indices were correlated with northern and equatorial Atlantic and Pacific Ocean sea surface temperatures. However, those indices having the largest significant trends (percentage of warm days, precipitation intensity, and contribution from very wet days) have low correlations to El Niño–Southern Oscillation. Additionally, precipitation indices show a higher correlation with tropical Atlantic sea surface temperatures.

The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement) from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry) among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region.

Large volcanic eruptions on Earth commonly occur with a collapse of the roof of a crustal magma reservoir, forming a caldera. Only a few such collapses occur per century, and the lack of detailed observations has obscured insight into the mechanical interplay between collapse and eruption. We use multiparameter geophysical and geochemical data to show that the 110-square-kilometer and 65-meter-deep collapse of Bárdarbunga caldera in 2014-2015 was initiated through withdrawal of magma, and lateral migration through a 48-kilometers-long dike, from a 12-kilometers deep reservoir. Interaction between the pressure exerted by the subsiding reservoir roof and the physical properties of the subsurface flow path explain the gradual, near-exponential decline of both collapse rate and the intensity of the 180-day-long eruption.

During carcinogenesis, advanced tumors are surrounded by both stromal and immune cells, which support tumor development. In addition, inflammation and angiogenesis are processes that play important roles in the development of cancer, from the initiation of carcinogenesis, tumor in situ and advanced stages of cancer. During acute inflammation, vascular hyperpermeability allows inflammatory mediators and immune response cells, including leukocytes and monocytes/macrophages, to infiltrate the site of damage. As a factor that regulates vascular permeability, vascular endothelial growth factor (VEGF) also plays a vital role as a multifunctional molecule and growth factor. Furthermore, stromal and immune cells secrete soluble factors that activate endothelial cells and favor their transmigration to eliminate the aggressive agent. In this review, we present a comprehensive view of both the relationship between chronic inflammation and angiogenesis during carcinogenesis and the participation of endothelial cells in the inflammatory process. In addition, the regulatory mechanisms that contribute to the endothelium returning to its basal permeability state after acute inflammation are discussed. Moreover, the manner in which immune cells participate in pathological angiogenesis release pro-angiogenic factors that contribute to early tumor vascularization, even before the angiogenic switch occurs, is also examined. Also, we discuss the role of hypoxia as a mechanism that drives the acquisition of tumor hallmarks that make certain cancers more aggressive. Finally, some combinations of therapies that inhibit the angiogenesis process and that may be a successful strategy for cancer patients are indicated.

Genetic variation is fundamental to population fitness and adaptation to environmental change. Human activities are driving declines in many wild populations and could have similar effects on genetic variation. Despite the importance of estimating such declines, no global estimate of the magnitude of ongoing genetic variation loss has been conducted across species. By combining studies that quantified recent changes in genetic variation across a mean of 27 generations for 91 species, we conservatively estimate a 5.4%-6.5% decline in within-population genetic diversity of wild organisms since the industrial revolution. This loss has been most severe for island species, which show a 27.6% average decline. We identified taxonomic and geographical gaps in temporal studies that must be urgently addressed. Our results are consistent with single time-point meta-analyses, which indicated that genetic variation is likely declining. However, our results represent the first confirmation of a global decline and provide an estimate of the magnitude of the genetic variation lost from wild populations.

ABSTRACT Despite their critical role as freshwater resources and their vulnerability to anthropogenic pressures, our knowledge of the ecohydrology of tropical montane cloud forests remains limited. Here, we use a dual stable isotope approach (δ 2 H and δ 18 O) to trace water inputs, fluxes, and pools through a seasonally dry tropical montane cloud forest in central Veracruz, Mexico. We found strong seasonal variation in the isotope composition of precipitation inputs (δ 2 H ~130‰ and δ 18 O ~18‰), with significantly more depleted wet‐season values as compared with dry‐season values. These seasonal differences are subject to inter‐annual variation, as reflected by shifts in the local meteoric water line. Even at the peak of the dry season, stable isotope values of plant xylem water from six different deciduous and evergreen species occurring in the understory and canopy of mature and secondary forests were all consistent with the use of shallow soil water (20–60 cm). Alternative limiting factors, such as nutrient distribution along the soil profile, may be strongly contributing to plant rooting patterns. Stable isotope values of soil water were evaporatively enriched compared with precipitation inputs, whereas stream values plotted with precipitation on the local meteoric water line. In contrast to current hydrologic models, this indicates the presence of two distinct soil water pools, one highly mobile pool of precipitation that contributes to streams and a second less mobile pool of soil water that contributes to plant fluxes. This comprehensive perspective can provide the basis for generating process‐based models of ecohydrology in the future. Copyright © 2011 John Wiley & Sons, Ltd.

Archaeological research in the Gulf Coast of Tabasco reveals the earliest record of maize cultivation in Mexico. The first farmers settled along beach ridges and lagoons of the Grijalva River delta. Pollen from cultivated Zea appears with evidence of forest clearing about 5100 calendar years B.C. (yr B.C.) [6200 (14)C years before the present (yr B.P.)]. Large Zea sp. pollen, typical of domesticated maize (Zea mays), appears about 5000 calendar yr B.C. (6000 yr B.P.). A Manihot sp. pollen grain dated to 4600 calendar yr B.C. (5800 yr B.P.) may be from domesticated manioc. About 2500 calendar yr B.C. (4000 yr B.P.), domesticated sunflower seeds and cotton pollen appear as farming expanded.

Colorectal cancer (CCR) is the third most common cancer worldwide in men and women, the second largest cause of death related to cancer, and the main cause of death in gastrointestinal cancer. The risk of developing this cancer is related to bad alimentary habits, smoking, intestinal inflammatory disease, polyps, genetic factors, and aging. Of the patients that are diagnosed with colorectal cancer 90% are older than 50, with a median age of 64 years; however, the disease is more aggressive in patients that are diagnosed at younger ages. According to the American Cancer Association, it was accounted for more than 49,700 deaths in 2015. The goal is to reduce the mortality rate with early diagnosis and treatment. Currently, the survival rate is used to predict a patient’s prognosis. The patient is considered to have a positive familial history if a first-degree relative has been diagnosed with colorectal cancer or colonic polyps before the age of 60, or also if two or more first-degree relatives have been diagnosed with cancer or polyps at any age. There are several methods for detecting colorectal cancer, such as the guaiac test, immunochemical test of stool, DNA stool test, sigmoidoscopy, colonoscopy, and barium enema. The stage in which the cancer is detected determines the prognosis, survival, and treatment of the patient. Provide a review about generalities, genetic basis, risk factors, protective factors, clinical course, diagnostic methods, therapy and survival in colorectal cancer. Conducted research from different databases such as PubMed, Medline, MedScape, on the definition, genetic factors, classification, risk factors, protective factors, diagnostic methods, epidemiology, survival and treatment of colorectal cancer. Articles from 2000 to 2017 were included using the following keywords.

Pathway analysis is a set of widely used tools for research in life sciences intended to give meaning to high-throughput biological data. The methodology of these tools settles in the gathering and usage of knowledge that comprise biomolecular functioning, coupled with statistical testing and other algorithms. Despite their wide employment, pathway analysis foundations and overall background may not be fully understood, leading to misinterpretation of analysis results. This review attempts to comprise the fundamental knowledge to take into consideration when using pathway analysis as a hypothesis generation tool. We discuss the key elements that are part of these methodologies, their capabilities and current deficiencies. We also present an overview of current and all-time popular methods, highlighting different classes across them. In doing so, we show the exploding diversity of methods that pathway analysis encompasses, point out commonly overlooked caveats, and direct attention to a potential new class of methods that attempt to zoom the analysis scope to the sample scale.

ABSTRACT The liver is the most common site of metastasis in patients with colorectal cancer due to its anatomical situation regarding its portal circulation. About 14 to 18% of patients with colorectal cancer present metastasis at the first medical consultation, and 10 to 25% at the time of the resection of the primary colorectal cancer. The incidence is higher (35%) when a computed tomography (CT) scan is used. In the last decades, a significant increase in the life expectancy of patients with colorectal cancer has been achieved with different diagnostic and treatment programs. Despite these improvements, the presence of metastasis, disease recurrence, and advanced local tumors continue to remain poor prognostic factors. Median survival without treatment is <8 months from the moment of its presentation, and a survival rate at 5 years of 11% is the best prognosis for those who present with local metastasis. Even in patients with limited metastatic disease, 5-year survival is exceptional. Patients with hepatic metastasis of colorectal cancer have a median survival of 5 to 20 months with no treatment. Approximately 20 to 30% of patients with colorectal metastasis have disease confined to the liver, and this can be managed with surgery. Modern surgical strategies at the main hepatobiliary centers have proved that hepatectomy of 70% of the liver can be performed, with a mortality rate of <5%. It is very important to have knowledge of predisposing factors, diagnostic methods, and treatment of hepatic metastasis. However, the establishment of newer, efficient, preventive screening programs for early diagnosis and adequate treatment is vital. How to cite this article Valderrama-Treviño AI, Barrera-Mera B, Ceballos-Villalva JC, Montalvo-Javé EE. Hepatic Metastasis from Colorectal Cancer. Euroasian J Hepato-Gastroenterol 2017;7(2):166-175.

Glucose-6-phosphate dehydrogenase (G6PD) is a key regulatory enzyme in the pentose phosphate pathway which produces nicotinamide adenine dinucleotide phosphate (NADPH) to maintain an adequate reducing environment in the cells and is especially important in red blood cells (RBC). Given its central role in the regulation of redox state, it is understandable that mutations in the gene encoding G6PD can cause deficiency of the protein activity leading to clinical manifestations such as neonatal jaundice and acute hemolytic anemia. Recently, an extensive review has been published about variants in the g6pd gene; recognizing 186 mutations. In this work, we review the state of the art in G6PD deficiency, describing 217 mutations in the g6pd gene; we also compile information about 31 new mutations, 16 that were not recognized and 15 more that have recently been reported. In order to get a better picture of the effects of new described mutations in g6pd gene, we locate the point mutations in the solved three-dimensional structure of the human G6PD protein. We found that class I mutations have the most deleterious effects on the structure and stability of the protein.

Norm enforcement may be important for resolving conflicts and promoting cooperation. However, little is known about how preferred responses to norm violations vary across cultures and across domains. In a preregistered study of 57 countries (using convenience samples of 22,863 students and non-students), we measured perceptions of the appropriateness of various responses to a violation of a cooperative norm and to atypical social behaviors. Our findings highlight both cultural universals and cultural variation. We find a universal negative relation between appropriateness ratings of norm violations and appropriateness ratings of responses in the form of confrontation, social ostracism and gossip. Moreover, we find the country variation in the appropriateness of sanctions to be consistent across different norm violations but not across different sanctions. Specifically, in those countries where use of physical confrontation and social ostracism is rated as less appropriate, gossip is rated as more appropriate.

Epigenetic mechanisms control gene expression during normal development and their aberrant regulation may lead to human diseases including cancer. Natural phytochemicals can largely modulate mammalian epigenome through regulation of mechanisms and proteins responsible for chromatin remodeling. Phytochemicals are mainly contained in fruits, seeds, and vegetables as well as in foods supplements. These compounds act as powerful cellular antioxidants and anti-carcinogens agents. Several dietary compounds such as catechins, curcumin, genistein, quercetin and resveratrol, among others, exhibit potent anti-tumor activities through the reversion of epigenetic alterations associated to oncogenes activation and inactivation of tumor suppressor genes. In this review, we summarized the actual knowledge about the role of dietary phytochemicals in the restoration of aberrant epigenetic alterations found in cancer cells with a particular focus on DNA methylation and histone modifications. Furthermore, we discussed the mechanisms by which these natural compounds modulate gene expression at epigenetic level and described their molecular targets in diverse types of cancer. Modulation of epigenetic activities by phytochemicals will allow the discovery of novel biomarkers for cancer prevention, and highlights its potential as an alternative therapeutic approach in cancer.

Subduction zone magmatism produces calc‐alkaline andesite melts that combine the high SiO 2 , Na 2 O, and K 2 O abundances of the differentiated continental crust with low FeO, FeO/MgO, and TiO 2 typical of melts from depleted mantle. Ni‐rich olivines in basaltic andesites and andesites of the central Mexican Volcanic Belt suggest that this dichotomy reflects a particular mechanism of mantle processing in the subduction environment. Hydrous slab components rich in Si, Na, and fluid mobile large‐ion lithophile elements (LILE) transform mantle olivine to “reaction orthopyroxene.” Along the ascent paths, and embedded into surrounding peridotite, secondary pyroxenite lithologies are created that are composed of “reaction orthopyroxene” next to mantle clinopyroxene and orthopyroxene. Partial melts from peridotite and pyroxenite then mix to produce primary calc‐alkaline basaltic andesites and andesites that are rich in Na and LILE. The steady slab flux maintains high levels of Na and LILE in the mantle source but also induces repetitive melting that steadily depletes the subarc mantle in FeO, TiO 2 , and other high field strength elements. If mantle processing thus creates primary basaltic andesite and andesite melts with the fractionated major element signature of the continental crust, the high magnesium number (Mg # (=Mg/Mg + Fe 2+ )) ∼60–70 of these melts still requires additional differentiation to arrive at the lower Mg # ∼55 of average continental crust.

Abstract We performed a genome-wide association study of 6447 bipolar disorder (BD) cases and 12 639 controls from the International Cohort Collection for Bipolar Disorder (ICCBD). Meta-analysis was performed with prior results from the Psychiatric Genomics Consortium Bipolar Disorder Working Group for a combined sample of 13 902 cases and 19 279 controls. We identified eight genome-wide significant, associated regions, including a novel associated region on chromosome 10 (rs10884920; P =3.28 × 10 −8 ) that includes the brain-enriched cytoskeleton protein adducin 3 ( ADD3), a non-coding RNA, and a neuropeptide-specific aminopeptidase P ( XPNPEP1) . Our large sample size allowed us to test the heritability and genetic correlation of BD subtypes and investigate their genetic overlap with schizophrenia and major depressive disorder. We found a significant difference in heritability of the two most common forms of BD (BD I SNP- h 2 =0.35; BD II SNP- h 2 =0.25; P =0.02). The genetic correlation between BD I and BD II was 0.78, whereas the genetic correlation was 0.97 when BD cohorts containing both types were compared. In addition, we demonstrated a significantly greater load of polygenic risk alleles for schizophrenia and BD in patients with BD I compared with patients with BD II, and a greater load of schizophrenia risk alleles in patients with the bipolar type of schizoaffective disorder compared with patients with either BD I or BD II. These results point to a partial difference in the genetic architecture of BD subtypes as currently defined.

Abstract Many of the world's vertebrates have experienced large population and geographic range declines due to anthropogenic threats that put them at risk of extinction. The largest vertebrates, defined as megafauna, are especially vulnerable. We analyzed how human activities are impacting the conservation status of megafauna within six classes: mammals, ray‐finned fish, cartilaginous fish, amphibians, birds, and reptiles. We identified a total of 362 extant megafauna species. We found that 70% of megafauna species with sufficient information are decreasing and 59% are threatened with extinction. Surprisingly, direct harvesting of megafauna for human consumption of meat or body parts is the largest individual threat to each of the classes examined, and a threat for 98% (159/162) of threatened species with threat data available. Therefore, minimizing the direct killing of the world's largest vertebrates is a priority conservation strategy that might save many of these iconic species and the functions and services they provide.