Functional characterization and cellular dynamics of the CDC-42 - RAC - CDC-24 module in neurospora crassa

CYNTHIA LIZZETH ARAUJO PALOMARES (2011, [Artículo])

Rho-type GTPases are key regulators that control eukaryotic cell polarity, but their role in fungal morphogenesis is only beginning to emerge. In this study, we investigate the role of the CDC-42 - RAC - CDC-24 module in Neurospora crassa. rac and cdc-42 deletion mutants are viable, but generate highly compact colonies with severe morphological defects. Double mutants carrying conditional and loss of function alleles of rac and cdc-42 are lethal, indicating that both GTPases share at least one common essential function. The defects of the GTPase mutants are phenocopied by deletion and conditional alleles of the guanine exchange factor (GEF) cdc-24, and in vitro GDP-GTP exchange assays identify CDC-24 as specific GEF for both CDC-42 and RAC. In vivo confocal microscopy shows that this module is organized as membrane-associated cap that covers the hyphal apex. However, the specific localization patterns of the three proteins are distinct, indicating different functions of RAC and CDC-42 within the hyphal tip. CDC-42 localized as confined apical membrane-associated crescent, while RAC labeled a membrane-associated ring excluding the region labeled by CDC42. The GEF CDC-24 occupied a strategic position, localizing as broad apical membrane-associated crescent and in the apical cytosol excluding the Spitzenkörper. RAC and CDC-42 also display distinct localization patterns during branch initiation and germ tube formation, with CDC-42 accumulating at the plasma membrane before RAC. Together with the distinct cellular defects of rac and cdc-42 mutants, these localizations suggest that CDC-42 is more important for polarity establishment, while the primary function of RAC may be maintaining polarity. In summary, this study identifies CDC-24 as essential regulator for RAC and CDC-42 that have common and distinct functions during polarity establishment and maintenance of cell polarity in N. crassa. © 2011 Araujo-Palomares 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.

CDC24 protein, guanine nucleotide exchange factor, protein Cdc42, Rac protein, unclassified drug, cell cycle protein, fungal protein, membrane protein, multiprotein complex, protein Cdc42, Rac protein, allele, apical membrane, article, assay, cell me BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA MICROBIOLOGÍA MICROBIOLOGÍA

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

Rapid effects of marine reserves via larval dispersal

Richard Cudney Bueno (2009, [Artículo])

Marine reserves have been advocated worldwide as conservation and fishery management tools. It is argued that they can protect ecosystems and also benefit fisheries via density-dependent spillover of adults and enhanced larval dispersal into fishing areas. However, while evidence has shown that marine reserves can meet conservation targets, their effects on fisheries are less understood. In particular, the basic question of if and over what temporal and spatial scales reserves can benefit fished populations via larval dispersal remains unanswered. We tested predictions of a larval transport model for a marine reserve network in the Gulf of California, Mexico, via field oceanography and repeated density counts of recently settled juvenile commercial mollusks before and after reserve establishment. We show that local retention of larvae within a reserve network can take place with enhanced, but spatially-explicit, recruitment to local fisheries. Enhancement occurred rapidly (2 yrs), with up to a three-fold increase in density of juveniles found in fished areas at the downstream edge of the reserve network, but other fishing areas within the network were unaffected. These findings were consistent with our model predictions. Our findings underscore the potential benefits of protecting larval sources and show that enhancement in recruitment can be manifested rapidly. However, benefits can be markedly variable within a local seascape. Hence, effects of marine reserve networks, positive or negative, may be overlooked when only focusing on overall responses and not considering finer spatially-explicit responses within a reserve network and its adjacent fishing grounds. Our results therefore call for future research on marine reserves that addresses this variability in order to help frame appropriate scenarios for the spatial management scales of interest. © 2009 Cudney-Bueno et al.

article, environmental monitoring, fishery, larva, marine environment, marine species, Mexico, mollusc, nonhuman, oceanography, prediction, animal, biology, environmental protection, food industry, geography, growth, development and aging, larva, met CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

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

Hacia el desarrollo de un nuevo antiparasitario basado en células en suspensión de Carica papaya

CYNTHIA ALEJANDRA GUZMÁN MEDINA (2023, [Tesis de doctorado])

Las enfermedades parasitarias son un problema de salud pública que afectan a más de la

quinta parte de la población a nivel mundial. Además de la morbilidad que generan, sino

son tratadas y controladas de manera adecuada pueden llegar a causar la muerte.

En el mercado existen diferentes antiparasitarios comerciales, que si bien son efectivos,

presentan diferentes efectos adversos tanto para el individuo parasitado (i.e. destrucción

de la microbiota intestinal) como para el medio ambiente. Este panorama señala la

relevancia de desarrollar tratamientos antiparasitarios más amigables con el ambiente y con

menores efectos adversos que estén disponibles actualmente en el mercado. Productos

obtenidos a partir de plantas con propiedades anti-parasitarias, cultivadas in vitro en

condiciones controladas, podrían representar una alternativa realista. Entre ellas figura la

planta Carica papaya, especie de zonas tropicales y subtropicales del planeta a cuyos frutos

se les adjudica actividades antiparasitarias. Estas propiedades se atribuyen a algunos de

sus compuestos concentrados en el latex y en las semillas como la papaina, la

quimiopapaína, la lisozima, la glicil-endopeptidasa, la proteasa de cisteína y el benzil-

isotiocinato.

El objetivo del presente trabajo fue evaluar la actividad antiparasitaria in vitro e in vivo de

un conjunto de callos y líneas de células de papaya de Carica papaya contra cisticercos de

Taenia crassiceps (cestodo) y contra trofozoitos de Entamoeba histolytica (protozoario). Los

extractos acuosos obtenidos a partir de callos y células cultivados en placa o en suspensión,

respectivamente, de las diferentes líneas de papaya revelaron alta capacidad cisticida

(>98% de mortalidad) in vitro contra cisticercos de Taenia crassiceps. En la evaluación in

vivo la línea no transformada obtuvo mayor efecto cisticida a 10mg/mL reduciendo el

número de cisticercos gemantes y aumentando los cisticercos calcificados en niveles

similares a los obtenidos utilizando antiparasitarios comerciales (albendazol y niclosamida).

Las líneas transformadas y sin transformar de papaya evaluadas indujeron una alta

capacidad amebicida (97% de mortalidad) in vitro contra trofozoitos de Entamoeba

histolytica. Las diferentes líneas transformadas y sin transformar de papaya redujeron

significativamente el número de abscesos amebianos y previnieron la hepatomegalia de

manera no significativamente diferente que el anti-parasitario comercial (metronidazol).

Los resultados generados en el presente estudio señalan al extracto acuoso obtenido a

partir de cultivos en suspensión de células de papaya transformada y no transformada

indujeron alto nivel de protección in vitro e in vivo por lo tanto; este es un producto efectivo

para el tratamiento de la cisticercosis y la amebiasis.

Parasitic diseases are a public health problem that affect more than a fifth of the population

worldwide. Additionally, and along with the morbidity the produce, they can cause death if

they are not treated and controlled adequately.

There are different commercial antiparasitic on the market which, although effective,

present different adverse effects both for the individual (i.e., destruction of the intestinal

microbiota) and for the environment alike. This panorama points out the relevance of

developing more environmentally friendly antiparasitic treatments with fewer adverse effects

than the ones currently available on the market. Products obtained from plants with anti-

parasitic properties, grown in vitro under controlled conditions, could represent a realistic

alternative. Among them is the Carica papaya, a species from tropical and subtropical areas

of the planet whose fruits are believed to have antiparasitic activities. These properties are attributed to some of its compounds concentrated in the latex and seeds such as papain,

chymopapain, lysozyme, glycyl-endopeptidase, cysteine-proteinase and benzyl-

isothiocyanate.

The objective of the present work is to evaluate the in vitro and in vivo antiparasitic activity

of a set of papaya callus and cell lines from Carica papaya against cysticerci of Taenia

crassiceps (cestode) and against trophozoites of Entamoeba histolytica (protozoan). The

aqueous extracts obtained from callus and cells cultured in plates or in suspension,

respectively, of the different papaya lines revealed high cysticidal capacity (>98% mortality)

in vitro against Taenia crassiceps cysticerci. Meanwhile, in the in vivo evaluation, the non-

transformed line obtained a greater cysticidal effect at 10 mg/mL, reducing the number of

budding cysticerci and increasing calcified cysticerci at levels like those obtained using

commercial antiparasitic (albendazole and niclosamide). The papaya lines evaluated

induced a high amoebicidal capacity (97% mortality) in vitro against Entamoeba histolytica

trophozoites. The different papaya lines significantly reduced the number of amoebic

abscesses and prevented hepatomegaly in a non-significantly different manner than the

commercial anti-parasitic (metronidazole).

The results produced in this thesis indicate that the aqueous extract obtained from

suspension cultures of transformed and non-transformed papaya cells induced a high level

of protection in vitro and in vivo. Therefore, this may represent an effective product for the

treatment of cysticercosis and amoebiasis.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGRARIAS Carica papaya, antiparasitario, células en suspensión, T. crassiceps, E. histolytica. Carica papaya, antiparasitic, in-suspension cells, T. crassiceps, E. histolytica.

Solanum tuberosum Microtuber Development under Darkness Unveiled through RNAseq Transcriptomic Analysis

ELIANA VALENCIA LOZANO LISSET HERRERA ISIDRON Osiel Salvador Recoder-Meléndez Aarón Barraza Celis JOSE LUIS CABRERA PONCE (2022, [Artículo])

"Potato microtuber (MT) development through in vitro techniques are ideal propagules for producing high quality potato plants. MT formation is influenced by several factors, i.e., photoperiod, sucrose, hormones, and osmotic stress. We have previously developed a protocol of MT induction in medium with sucrose (8% w/v), gelrite (6g/L), and 2iP as cytokinin under darkness. To understand the molecular mechanisms involved, we performed a transcriptome-wide analysis. Here we show that 1715 up- and 1624 down-regulated genes were involved in this biological process. Through the protein–protein interaction (PPI) network analyses performed in the STRING database (v11.5), we found 299 genes tightly associated in 14 clusters. Two major clusters of up-regulated proteins fundamental for life growth and development were found: 29 ribosomal proteins (RPs) interacting with 6 PEBP family members and 117 cell cycle (CC) proteins. The PPI network of up-regulated transcription factors (TFs) revealed that at least six TFs–MYB43, TSF, bZIP27, bZIP43, HAT4 and WOX9–may be involved during MTs development. The PPI network of down-regulated genes revealed a cluster of 83 proteins involved in light and photosynthesis, 110 in response to hormone, 74 in hormone mediate signaling pathway and 22 related to aging."

transcriptome-wide analysis, microtubers, potato, Solanum tuberosum, darkness, cell cycle, ribosomal proteins, PEBP family genes, cytokinin BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA MOLECULAR DE PLANTAS GENÉTICA MOLECULAR DE PLANTAS

Diluted density. Urban planning in the Monterrey Metropolitan Area

Sheila Ferniza Quiroz Jesús Manuel Fitch Osuna (2021, [Artículo, Artículo])

The Monterrey Metropolitan Area (mma) in Northern Mexico has had an expansive and dispersed growth in recent decades. In 35 years, the city doubled its population and grew 8 times in territory (Secretariat for Sustainable Development, 2020). As a mitigation measure and with the objective of repopulating the areas within the city, urban regulations have been promoted that allow higher density and building potentials in some municipalities; however, the efforts are isolated and without metropolitan coordination. What are the urban regulation guidelines in the municipalities of the mma? How dense are its municipalities? Where are located the densest areas of the city? The objective of this research is to establish the current state of local regulation regarding urban development and to map the housing density to identify the locations with the lowest and highest density at the mma. The gross density at the Ageb scale is mapped for the 18 municipalities of the mma through the QGis software; data from the Inegi 2020 National Population and Housing Census is used. It is found that the peripheral municipalities of recent incorporation to the mma, unlike those of greater urbanization, lack urban development plans, and that most of the municipalities do not have updated regulations based on the current laws. The areas with the highest density are located in the peripheral municipalities, associated with the construction of low-income mass housing, and those with the lowest density in interior municipalities in areas of higher socioeconomic status, diluting the small efforts of densification in the city.

density urban sprawl urban planning densidad expansión urbana planeación urbana HUMANIDADES Y CIENCIAS DE LA CONDUCTA HUMANIDADES Y CIENCIAS DE LA CONDUCTA

Funcionamiento del proceso de digestión en rumiantes

Abel Jaime Leal González (2021, [Libro])

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA RUMIANTE DIGESTIÓN RUMINAL NUTRIENTES CARBOHIDRATOS ABOMASO ABSORCIÓN DIGESTIVA GANADO BOVINO PASTOREO RUMINANTS RUMEN DIGESTION NUTRIENTS CARBOHYDRATES ABOMASUM DIGESTIVE ABSORPTION CATTLE GRAZING

Modeling spatiotemporal patterns of land use/land cover change in Central Malawi using a neural network model

Leah Mungai Joseph Messina Leo Zulu Jiaguo Qi Sieglinde Snapp (2022, [Artículo])

Multilayer Perceptrons CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA AGRICULTURE LAND USE POPULATION SATELLITE IMAGERY TEXTURE LAND COVER NEURAL NETWORKS REMOTE SENSING

Agroecology can promote climate change adaptation outcomes without compromising yield in smallholder systems

Sieglinde Snapp Yodit Kebede Eva Wollenberg (2023, [Artículo])

A critical question is whether agroecology can promote climate change mitigation and adaptation outcomes without compromising food security. We assessed the outcomes of smallholder agricultural systems and practices in low- and middle-income countries (LMICs) against 35 mitigation, adaptation, and yield indicators by reviewing 50 articles with 77 cases of agroecological treatments relative to a baseline of conventional practices. Crop yields were higher for 63% of cases reporting yields. Crop diversity, income diversity, net income, reduced income variability, nutrient regulation, and reduced pest infestation, indicators of adaptative capacity, were associated with 70% or more of cases. Limited information on climate change mitigation, such as greenhouse gas emissions and carbon sequestration impacts, was available. Overall, the evidence indicates that use of organic nutrient sources, diversifying systems with legumes and integrated pest management lead to climate change adaptation in multiple contexts. Landscape mosaics, biological control (e.g., enhancement of beneficial organisms) and field sanitation measures do not yet have sufficient evidence based on this review. Widespread adoption of agroecological practices and system transformations shows promise to contribute to climate change services and food security in LMICs. Gaps in adaptation and mitigation strategies and areas for policy and research interventions are finally discussed.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CLIMATE CHANGE CROPS FOOD SUPPLY GAS EMISSIONS GREENHOUSE GASES FARMING SYSTEMS AGROECOLOGY FOOD SECURITY LESS FAVOURED AREAS SMALLHOLDERS YIELDS NUTRIENTS BIOLOGICAL PEST CONTROL CARBON SEQUESTRATION LEGUMES