Maize ZmBES1/BZR1-3 and-9 transcription factors negatively regulate drought tolerance in transgenic arabidopsis

Fuai Sun XUECAI ZHANG Haoqiang Yu (2022, [Artículo])

BZR1s CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA ARABIDOPSIS DNA BINDING PROTEINS PLANT PROTEIN TRANSCRIPTION FACTORS DROUGHT GENE EXPRESSION REGULATION GENETICS MAIZE METABOLISM TRANSGENIC PLANTS ABIOTIC STRESS

Explorando microbiomas extremófilos para descubrir enzimas inéditas que transforman almidón

Víctor Manuel Carballo Uicab XITLALLI MONTSERRAT ROMERO JIMENEZ JORGE IVAN ARANDA CARABALLO SARA GUILLERMINA CENTENO LEIJA (2022, [Artículo])

Las cicloglucanotransferasas (CGTasas) transforman el polímero almidón en nanomoléculas anfipáticas de interés biotecnológico llamadas ciclodextrinas. Aunque las CGTasas termófilas son ideales para procesos industriales, el 75 % de las CGTasas caracterizadas pertenecen a bacterias mesófilas de la sobreexplorada clase Bacilli. Recientemente la minería de datos (meta)genómicos ha permitido detectar nuevas CGTasas presentes en nichos ecológicos inexplorados. El estudio de éstas CGTasas inéditas, ofrece pistas sobre su papel fisiológico en microbiomas extremófilos y su caracterización abre la oportunidad de ampliar el conocimiento sobre su estructura, mecanismos funcionales y proponer modificaciones racionales que incrementen su eficiencia para obtener productos de valor agregado.

CICLODEXTRINAS CICLOGLUCANOTRANSFERASAS METABOLISMO DE CARBOHIDRATOS MINERIA DE (META)GENOMAS TERMOENZIMAS BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) ECOLOGÍA VEGETAL ECOLOGÍA VEGETAL

¿Desvinculación o decrecimiento? Un marco analítico para abordar la transición socioecológica desde los estudios urbanos

Jerónimo Aurelio Díaz Marielle (2023, [Artículo])

Artículo número 1 de la Sección Articulos de Investigación.

La transición socioecológica se perfila como un nuevo paradigma científico centrado en las interacciones sociedad-naturaleza y es, al mismo tiempo, la punta de lanza de una nueva agenda urbana y ambiental que no está exenta de contradicciones y dilemas. Con un pie en la divulgación de los conceptos y las metodologías que conforman este paradigma, y con otro en el análisis sociológico de los nuevos ecologismos, el artículo ofrece una revisión de dos corrientes de ecología política que buscan orientar el sentido de la transición: la desvinculación ecológica y el decrecimiento. La primera coloca sus expectativas en el desarrollo tecnológico y el mercado, es favorable al modelo de la ciudad compacta y promueve las llamadas soluciones basadas en la naturaleza. La segunda reconoce el valor de los saberes urbanos vernáculos, pero apela a la descentralización de las urbes y pugna por una reducción equitativa y democrática de los estándares de vida de la población. El artículo concluye que los estudios urbanos (en particular la sociología urbana y la planeación territorial) pueden contribuir a comprender el funcionamiento de los metabolismos urbanos y aportar soluciones a las dificultades que impiden el tránsito hacia una sociedad sustentable, esto es, una sociedad que sea capaz de autolimitarse, ajustando su metabolismo a los ciclos y a los tiempos que requiere la naturaleza para regenerarse.

The socio-ecological transition is emerging as a new scientific paradigm focused on the interactions between society and nature, and at the same time, it is the spearhead of a new urban and environmental agenda. With one foot in the dissemination of the concepts and methodologies that make up this paradigm, and with the other in the sociological analysis of the new environmental movements, the article offers a review of two political ecology forces that seek to guide the direction of the transition: ecological decoupling and degrowth. The former places its expectations on technological development and the market, is favorable to the compact city model and promotes so-called nature-based solutions. The latter recognizes the value of vernacular urban knowledge, but calls for the decentralization of cities and advocates for an equitable and democratic reduction of the population standards of living. The article concludes that urban studies (particularly urban sociology and territorial planning) can contribute to understanding the functioning of urban metabolisms and providing ways to address social inertia regarding climate change.

Cambio climático, metabolismo urbano, planeación territorial. Climate change, urban metabolism, territorial planning. HUMANIDADES Y CIENCIAS DE LA CONDUCTA CIENCIAS DE LAS ARTES Y LAS LETRAS ARQUITECTURA URBANISMO

A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations

David Israel Flores Granados (2014, [Artículo])

The automatic identification of catalytic residues still remains an important challenge in structural bioinformatics. Sequence-based methods are good alternatives when the query shares a high percentage of identity with a well-annotated enzyme. However, when the homology is not apparent, which occurs with many structures from the structural genome initiative, structural information should be exploited. A local structural comparison is preferred to a global structural comparison when predicting functional residues. CMASA is a recently proposed method for predicting catalytic residues based on a local structure comparison. The method achieves high accuracy and a high value for the Matthews correlation coefficient. However, point substitutions or a lack of relevant data strongly affect the performance of the method. In the present study, we propose a simple extension to the CMASA method to overcome this difficulty. Extensive computational experiments are shown as proof of concept instances, as well as for a few real cases. The results show that the extension performs well when the catalytic site contains mutated residues or when some residues are missing. The proposed modification could correctly predict the catalytic residues of a mutant thymidylate synthase, 1EVF. It also successfully predicted the catalytic residues for 3HRC despite the lack of information for a relevant side chain atom in the PDB file. © 2014 Flores et al.

1UU9 protein, 3HRC protein, protein, thymidylate synthase, unclassified drug, protein kinase, thymidylate synthase, accuracy, algorithm, Article, CMASA, CMASA Substitution Matrix, Contact Matrix Average Deviation, controlled study, correlation coeffi CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA MATEMÁTICAS ANÁLISIS NUMÉRICO ANÁLISIS NUMÉRICO

Suppression of breast tumor growth and metastasis by an engineered transcription factor

Adriana Beltran Lopez (2011, [Artículo])

Maspin is a tumor and metastasis suppressor playing an essential role as gatekeeper of tumor progression. It is highly expressed in epithelial cells but is silenced in the onset of metastatic disease by epigenetic mechanisms. Reprogramming of Maspin epigenetic silencing offers a therapeutic potential to lock metastatic progression. Herein we have investigated the ability of the Artificial Transcription Factor 126 (ATF-126) designed to upregulate the Maspin promoter to inhibit tumor progression in pre-established breast tumors in immunodeficient mice. ATF-126 was transduced in the aggressive, mesenchymal-like and triple negative breast cancer line, MDA-MB-231. Induction of ATF expression in vivo by Doxycycline resulted in 50% reduction in tumor growth and totally abolished tumor cell colonization. Genome-wide transcriptional profiles of ATF-induced cells revealed a gene signature that was found over-represented in estrogen receptor positive (ER+) "Normal-like" intrinsic subtype of breast cancer and in poorly aggressive, ER+ luminal A breast cancer cell lines. The comparison transcriptional profiles of ATF-126 and Maspin cDNA defined an overlapping 19-gene signature, comprising novel targets downstream the Maspin signaling cascade. Our data suggest that Maspin up-regulates downstream tumor and metastasis suppressor genes that are silenced in breast cancers, and are normally expressed in the neural system, including CARNS1, SLC8A2 and DACT3. In addition, ATF-126 and Maspin cDNA induction led to the re-activation of tumor suppressive miRNAs also expressed in neural cells, such as miR-1 and miR-34, and to the down-regulation of potential oncogenic miRNAs, such as miR-10b, miR-124, and miR-363. As expected from its over-representation in ER+ tumors, the ATF-126-gene signature predicted favorable prognosis for breast cancer patients. Our results describe for the first time an ATF able to reduce tumor growth and metastatic colonization by epigenetic reactivation of a dormant, normal-like, and more differentiated gene program. © 2011 Beltran et al.

artificial transcription factor 126, complementary DNA, doxycycline, estrogen receptor, maspin, microRNA, retrovirus vector, transcription factor, unclassified drug, estrogen receptor, serine proteinase inhibitor, SERPIN B5, SERPIN-B5, transcription BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) BIOLOGÍA ANIMAL (ZOOLOGÍA)

Effect of antimicrobial nanocomposites on Vibrio cholerae lifestyles: Pellicle biofilm, planktonic and surface-attached biofilm

ANAID MEZA VILLEZCAS (2019, [Artículo])

Vibrio cholerae is an important human pathogen causing intestinal disease with a high incidence in developing countries. V. cholerae can switch between planktonic and biofilm lifestyles. Biofilm formation is determinant for transmission, virulence and antibiotic resistance. Due to the enhanced antibiotic resistance observed by bacterial pathogens, antimicrobial nanomaterials have been used to combat infections by stopping bacterial growth and preventing biofilm formation. In this study, the effect of the nanocomposites zeolite-embedded silver (Ag), copper (Cu), or zinc (Zn) nanoparticles (NPs) was evaluated in V. cholerae planktonic cells, and in two biofilm states: pellicle biofilm (PB), formed between air-liquid interphase, and surface-attached biofilm (SB), formed at solid-liquid interfaces. Each nanocomposite type had a distinctive antimicrobial effect altering each V. cholerae lifestyles differently. The ZEO-AgNPs nanocomposite inhibited PB formation at 4 μg/ml, and prevented SB formation and eliminated planktonic cells at 8 μg/ml. In contrast, the nanocomposites ZEO-CuNPs and ZEO-ZnNPs affect V. cholerae viability but did not completely avoid bacterial growth. At transcriptional level, depending on the nanoparticles and biofilm type, nanocomposites modified the relative expression of the vpsL, rbmA and bap1, genes involved in biofilm formation. Furthermore, the relative abundance of the outer membrane proteins OmpT, OmpU, OmpA and OmpW also differs among treatments in PB and SB. This work provides a basis for further study of the nanomaterials effect at structural, genetic and proteomic levels to understand the response mechanisms of V. cholerae against metallic nanoparticles. © 2019 Meza-Villezcas et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

bacterial protein, copper nanoparticle, nanocomposite, OmpT protein, OmpU protein, OmpW protein, outer membrane protein A, silver nanoparticle, unclassified drug, zeolite, zinc nanoparticle, antiinfective agent, copper, metal nanoparticle, nanocompos BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA MICROBIOLOGÍA MICROBIOLOGÍA

Trophic ecology of Mexican Pacific harbor seal colonies using carbon and nitrogen stable isotopes

MARICELA JUAREZ RODRIGUEZ (2020, [Artículo])

There is limited information that provides a comprehensive understanding of the trophic ecology of Mexican Pacific harbor seal (Phoca vitulina richardii) colonies. While scat analysis has been used to determine the diet of some colonies, the integrative characterization of its feeding habits on broader temporal and spatial scales remains limited. We examined potential feeding grounds, trophic niche width, and overlap, and inferred the degree of dietary specialization using stable carbon and nitrogen isotope ratios (δ13C and δ15N) in this subspecies. We analyzed δ13C and δ15N on fur samples from pups collected at five sites along the western coast of the Baja California Peninsula, Mexico. Fur of natal coat of Pacific harbor seal pups begins to grow during the seventh month in utero until the last stage of gestation. Therefore pup fur is a good proxy for the mother's feeding habits in winter (∼December to March), based on the timing of gestation for the subspecies in this region. Our results indicated that the δ13C and δ15N values differed significantly among sampling sites, with the highest mean δ15N value occurring at the southernmost site, reflecting a well-characterized north to south latitudinal 15N-enrichment in the food web. The tendency identified in δ13C values, in which the northern colonies showed the most enriched values, suggests nearshore and benthic-demersal feeding habits. A low variance in δ13C and δ15N values for each colony (<1‰) and relatively small standard ellipse areas suggest a specialized foraging behavior in adult female Pacific harbor seals in Mexican waters. © 2020 Juárez-Rodríguez et al.

carbon, delta carbon 13, delta nitrogen 15, isotope, nitrogen, unclassified drug, carbon, nitrogen, Article, correlational study, feeding behavior, latitude, Mexico, nonhuman, organism colony, Pinnipedia, population abundance, species richness, troph BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) BIOLOGÍA ANIMAL (ZOOLOGÍA)

Comparative live-cell imaging analyses of SPA-2, BUD-6 and BNI-1 in Neurospora crassa reveal novel features of the filamentous fungal polarisome

Alexander Lichius (2012, [Artículo])

A key multiprotein complex involved in regulating the actin cytoskeleton and secretory machinery required for polarized growth in fungi, is the polarisome. Recognized core constituents in budding yeast are the proteins Spa2, Pea2, Aip3/Bud6, and the key effector Bni1. Multicellular fungi display a more complex polarized morphogenesis than yeasts, suggesting that the filamentous fungal polarisome might fulfill additional functions. In this study, we compared the subcellular organization and dynamics of the putative polarisome components BUD-6 and BNI-1 with those of the bona fide polarisome marker SPA-2 at various developmental stages of Neurospora crassa. All three proteins exhibited a yeast-like polarisome configuration during polarized germ tube growth, cell fusion, septal pore plugging and tip repolarization. However, the localization patterns of all three proteins showed spatiotemporally distinct characteristics during the establishment of new polar axes, septum formation and cytokinesis, and maintained hyphal tip growth. Most notably, in vegetative hyphal tips BUD-6 accumulated as a subapical cloud excluded from the Spitzenkörper (Spk), whereas BNI-1 and SPA-2 partially colocalized with the Spk and the tip apex. Novel roles during septal plugging and cytokinesis, connected to the reinitiation of tip growth upon physical injury and conidial maturation, were identified for BUD-6 and BNI-1, respectively. Phenotypic analyses of gene deletion mutants revealed additional functions for BUD-6 and BNI-1 in cell fusion regulation, and the maintenance of Spk integrity. Considered together, our findings reveal novel polarisome-independent functions of BUD-6 and BNI-1 in Neurospora, but also suggest that all three proteins cooperate at plugged septal pores, and their complex arrangement within the apical dome of mature hypha might represent a novel aspect of filamentous fungal polarisome architecture. © 2012 Lichius et al.

fungal protein, protein BNI 1, protein BUD 6, protein SPA 2, protein Spk, unclassified drug, actin binding protein, cytoskeleton protein, fungal protein, article, cell fusion, cellular distribution, comparative study, conidium, controlled study, cyto BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA MICROBIOLOGÍA MICROBIOLOGÍA

The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences

ARLETTE MARIMAR PACHECO SANDOVAL (2019, [Artículo])

Diet is a primary driver of the composition of gut microbiota and is considered one of the main routes of microbial colonization. Prey identification is fundamental for correlating the diet with the presence of particular microbial groups. The present study examined how diet influenced the composition and function of the gut microbiota of the Pacific harbor seal (Phoca vitulina richardii) in order to better understand the role of prey consumption in shaping its microbiota. This species is a good indicator of the quality of the local environment due to both its foraging and haul-out site fidelity. DNA was extracted from 20 fecal samples collected from five harbor seal colonies located in Baja California, Mexico. The V4 region of 16S rRNA gene was amplified and sequenced using the Illumina technology. Results showed that the gut microbiota of the harbor seals was dominated by the phyla Firmicutes (37%), Bacteroidetes (26%) and Fusobacteria (26%) and revealed significant differences in its composition among the colonies. Funtional analysis using the PICRUSt software suggests a high number of pathways involved in the basal metabolism, such as those for carbohydrates (22%) and amino acids (20%), and those related to the degradation of persistent environmental pollutants. In addition, a DNA metabarcoding analysis of the same samples, via the amplification and sequencing of the mtRNA 16S and rRNA 18S genes, was used to identify the prey consumed by harbor seals revealing the consumption of prey with mainly demersal habits. Functional redundancy in the seal gut microbiota was observed, irrespective of diet or location. Our results indicate that the frequency of occurrence of specific prey in the harbor seal diet plays an important role in shaping the composition of the gut microbiota of harbor seals by influencing the relative abundance of specific groups of gut microorganisms. A significant relationship was found among diet, gut microbiota composition and OTUs assigned to a particular metabolic pathway. © 2019 Pacheco-Sandoval et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

RNA 16S, RNA 18S, amino acid analysis, animal food, Article, bacterium colony, Bacteroidetes, basal metabolic rate, biodegradation, controlled study, DNA barcoding, feces analysis, Firmicutes, Fusobacteria, intestine flora, metabolism, Mexico, microb BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) BIOLOGÍA ANIMAL (ZOOLOGÍA)

Coronin is a component of the endocytic collar of hyphae of neurospora crassa and is necessary for normal growth and morphogenesis

RAMON OSVALDO ECHAURI ESPINOSA (2012, [Artículo])

Coronin plays a major role in the organization and dynamics of actin in yeast. To investigate the role of coronin in a filamentous fungus (Neurospora crassa), we examined its subcellular localization using fluorescent proteins and the phenotypic consequences of coronin gene (crn-1) deletion in hyphal morphogenesis, Spitzenkörper behavior and endocytosis. Coronin-GFP was localized in patches, forming a subapical collar near the hyphal apex; significantly, it was absent from the apex. The subapical patches of coronin colocalized with fimbrin, Arp2/3 complex, and actin, altogether comprising the endocytic collar. Deletion of crn-1 resulted in reduced hyphal growth rates, distorted hyphal morphology, uneven wall thickness, and delayed establishment of polarity during germination; it also affected growth directionality and increased branching. The Spitzenkörper of Δcrn-1 mutant was unstable; it appeared and disappeared intermittently giving rise to periods of hyphoid-like and isotropic growth respectively. Uptake of FM4-64 in Δcrn-1 mutant indicated a partial disruption in endocytosis. These observations underscore coronin as an important component of F-actin remodeling in N. crassa. Although coronin is not essential in this fungus, its deletion influenced negatively the operation of the actin cytoskeleton involved in the orderly deployment of the apical growth apparatus, thus preventing normal hyphal growth and morphogenesis. © 2012 Echauri-Espinosa et al.

actin related protein 2-3 complex, F actin, fimbrin protein, fluorescent dye, fungal protein, fungal protein coronin, green fluorescent protein, unclassified drug, actin binding protein, coronin proteins, fungal protein, article, cell polarity, contr BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA MICROBIOLOGÍA MICROBIOLOGÍA