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

Tallo: A global tree allometry and crown architecture database

Tommaso Jucker Jörg Fischer Jerome Chave David Coomes John Caspersen Arshad Ali Grace Jopaul Loubota Panzou Ted R. Feldpausch Daniel Falster Vladimir Andreevich Usoltsev Stephen Adu-Bredu Luciana Alves Mohammad Aminpour Bhely ANGOBOY Ilondea Niels Anten Cécile Antin yousef askari Rodrigo Muñoz Ayyappan Narayanan Patricia Balvanera Lindsay Banin Nicolas Barbier John J. Battles Hans Beeckman Yannick Enock Bocko Benjamin Bond_Lamberty Frans Bongers Samuel Bowers THOMAS BRADE Michiel van Breugel ARTHUR CHANTRAIN Rajeev Chaudhary JINGYU DAI Michele Dalponte Kangbéni Dimobe jean-christophe domec Jean-Louis Doucet Remko Duursma Moisés Enriquez KARIN Y. VAN EWIJK WILLIAM FARFAN_RIOS Adeline FAYOLLE ERIC FORNI David Forrester Hammad Gilani John Godlee Sylvie Gourlet-Fleury Matthias Haeni Jefferson Hall Jie He Andreas Hemp JOSE LUIS HERNANDEZ STEFANONI Steven Higgins ROBERT J. HOLDAWAY Kiramat Hussain Lindsay Hutley Tomoaki Ichie Yoshiko Iida Hai Jiang Puspa Raj Joshi Seyed Hasan Kaboli Maryam Kazempour Larsary Tanaka Kenzo Brian Kloeppel Takashi Kohyama Suwash Kunwar Shem Kuyah Jakub Kvasnica Siliang Lin Emily Lines Hongyan Liu CRAIG LORIMER Joel Loumeto Yadvinder Malhi Peter Marshall Eskil Mattsson Radim Matula Jorge Arturo Meave del Castillo Sylvanus Mensah XIANGCHENG MI Stephane MOMO Takoudjou Glenn Moncrieff Francisco Mora Sarath Nissanka Kevin O'Hara steven pearce Raphaël Pélissier Pablo Luis Peri Pierre Ploton Lourens Poorter mohsen javanmiri pour Hassan pourbabaei JUAN MANUEL DUPUY RADA Sabina Ribeiro Ryan Casey ANVAR SANAEI Jennifer Sanger Michael Schlund Giacomo Sellan Alexander Shenkin Bonaventure Sonké Frank Sterck Martin Svatek Kentaro Takagi Anna Trugman Farman Ullah Matthew Vadeboncoeur Ahmad Valipour Mark Vanderwel Alejandra Vovides Weiwei WANG Li Qiu Christian Wirth MURRAY WOODS Wenhua Xiang Fabiano de Aquino Ximenes Yaozhan Xu TOSHIHIRO YAMADA Miguel A. Zavala (2022, [Artículo])

Data capturing multiple axes of tree size and shape, such as a tree's stem diameter, height and crown size, underpin a wide range of ecological research—from developing and testing theory on forest structure and dynamics, to estimating forest carbon stocks and their uncertainties, and integrating remote sensing imagery into forest monitoring programmes. However, these data can be surprisingly hard to come by, particularly for certain regions of the world and for specific taxonomic groups, posing a real barrier to progress in these fields. To overcome this challenge, we developed the Tallo database, a collection of 498,838 georeferenced and taxonomically standardized records of individual trees for which stem diameter, height and/or crown radius have been measured. These data were collected at 61,856 globally distributed sites, spanning all major forested and non-forested biomes. The majority of trees in the database are identified to species (88%), and collectively Tallo includes data for 5163 species distributed across 1453 genera and 187 plant families. The database is publicly archived under a CC-BY 4.0 licence and can be access from: https://doi.org/10.5281/zenodo.6637599. To demonstrate its value, here we present three case studies that highlight how the Tallo database can be used to address a range of theoretical and applied questions in ecology—from testing the predictions of metabolic scaling theory, to exploring the limits of tree allometric plasticity along environmental gradients and modelling global variation in maximum attainable tree height. In doing so, we provide a key resource for field ecologists, remote sensing researchers and the modelling community working together to better understand the role that trees play in regulating the terrestrial carbon cycle. © 2022 The Authors. Global Change Biology published by John Wiley & Sons Ltd.

ALLOMETRIC SCALING CROWN RADIUS FOREST BIOMASS STOCKS FOREST ECOLOGY REMOTE SENSING STEM DIAMETER TREE HEIGHT BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) ECOLOGÍA VEGETAL ECOLOGÍA VEGETAL

UNA ESPECIE NUEVA DE ESCOBEDIA (OROBANCHACEAE), DEL ESTADO DE MICHOACÁN, MÉXICO

ELEAZAR CARRANZA GONZALEZ MARIA DEL CONSUELO MEDINA GARCIA (2008, [Artículo])

Se describe como nueva a Escobedia michoacana (Orobanchaceae), encontrada en Michoacán, México. También se presenta una ilustración de la misma, una pequeña discusión de las posibles relaciones que guarda con otras especies del género y una clave para determinar los componentes de Escobedia que se reconocen para México. Se trata de una planta aparentemente escasa y restringida a la porción noroccidental del estado, aunque probablemente se encuentre también en Jalisco. Difiere de las demás especies mexicanas del género, por presentar cinco (no diez) nervaduras principales que corren a manera de costillas a lo largo del cáliz.

BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) BOTÁNICA GENERAL BOTÁNICA GENERAL

Plants of the Popol vuh, the sacred book of the Maya

Plantas del Popol Vuh, el libro sagrado de los Mayas

CANDELARIA ISABEL PEREZ MARTIN SIGFREDO EDMUNDO ESCALANTE REBOLLEDO SILVIA VERGARA YOISURA FRANCISCO ALFONSO LARQUE SAAVEDRA (2022, [Artículo])

A compilation of the plants mentioned in the sacred book of the Mayans Popol Vuh, recognized as the framework of their cosmogony that was written in the K’iche’ area in Guatemala around the year 1550 was made. Thirty-two different species were identified, from 21 plant families, all native to Mesoamerica. The largest number of species was in Fabaceae with four species, Moraceae and Solanaceae with three species each, in addition to Bromeliaceae, Cucurbitaceae, Malvaceae and Poaceae with two species each. The five most important and frequently named species are maize (Zea mays), jícaro (Crescentia cujete), copal (Protium copal), rubber (Castilla elastica) and cocoa (Theobroma cacao). Eleven species were identified, such as pito wood (Erythrina berteroana) and zibak (Cyperus canus), considered of cosmogonic significance and food plants that are integrated into five groups: fruit trees [zapote (Manilkara zapota), nance (Byrsonima crassifolia), jocote (Spondias mombin), anona (Annona reticulata), matasano (Casimiroa edulis)], grains and seeds [maize, beans (Phaseolus lunatus), cocoa, pataxte (Theobroma bicolor)], vegetables [squash (Cucurbita moschata), tomato (Solanum lycopersicum), chilacayote (Cucurbita ficifolia)], flavourings [chili (Capsicum annuum)], and beverages [maguey (Agave americana)]. Seven species were domesticated: maize, squash, chilacayote, tobacco (Nicotiana tabacum), beans, tomato and cocoa and others for medicinal purposes, fuel and instruments. The description of the creation of man asserts the close relationship of the Mayan culture with plant biodiversity; moreover, the famous milpa, a multi-species Mesoamerican agroecosystem is mentioned that was practiced by their gods © 2022. Revista Fitotecnia Mexicana.All Rights Reserved.

COSMOGONY MILPA PLANT FAMILIES POPOL VUH SACRED BOOK SPECIES BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) PALEOBOTÁNICA PALEOBOTÁNICA

Érase una vez un jardín

BLANCA MARINA VERA KU WENDY MARISOL TORRES AVILEZ (2022, [Artículo])

En la ciudad, existen “refugios de plantas y fauna”, también conocidos como “montes o terrenos baldíos”. Podría pensarse que se trata de un lugar desagradable y sucio, pero no es así. El monte no es más que un jardín luchando por restaurar el esplendor que tenía antes de ser degradado por los cambios de uso (asentamientos humanos o fenómenos naturales). Hace muchos años, un terreno baldío tuvo la suerte de encontrarse con un grupo de ecólogos que fueron capaces de apreciar su importancia. El jardín pudo sentir el aprecio de sus cuidadores y los recompensó dándoles la frescura de su sombra, sus aromas perfumados, el aire fresco lleno de oxígeno y sus frutos. Además, el jardín empezó a ser refugio de aves y ayuda para las nubes al soltar la lluvia que alivia el calor.

CIRCUITO ETNOBIOLOGICO JARDIN MEDICINAL PRESERVACION DE LA VIDA RESTAURACION DE LA BIODIVERSIDAD BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) ECOLOGÍA VEGETAL ECOLOGÍA VEGETAL

Bunchosia swartziana (sip ché), un arbusto de importancia ceremonial maya en las comunidades del norte de Campeche, México

LUIS ALBERTO CARRILLO CAN William Rolando Cetzal Ix CRHISTIAN LAYNES MAGAÑA (2022, [Artículo])

Cuando se trata de ceremonias y rituales mayas, en lo primero que pensamos es en los yuntziles (Dioses) y los aluxes (guardianes del monte), personajes místicos que representan lo sagrado y mágico de nuestra cultura maya. Otro personaje importante por su papel de intermediario entre las deidades y los humanos son los sacerdotes o jméen, tradicionalmente se recurre para pedir por la salud, bendición y protección a través de la santiguada o “limpias”. Para conocer cómo se desarrolla el uso ceremonial de “limpias” con la planta Bunchosia swartziana Griseb. (Malpighiaceae) en el norte de Campeche, se entrevistaron a sacerdotes mayas, los cuales, a través de plegarias, música, danzas y ofrendas realizan “limpias” para pedir por salud y buena cosecha, siendo un equilibrio entre lo místico y lo natural.

LIMPIAS MALPIGHIACEAE RITUALES SACERDOTES MAYAS SIP CHE BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) ECOLOGÍA VEGETAL ECOLOGÍA VEGETAL

Comportamiento agronómico de la variedad Chichén Itzá: maíz de alta calidad proteica desarrollada en Yucatán

MONICA GUADALUPE LOZANO CONTRERAS GENOVEVO RAMIREZ JARAMILLO (2022, [Artículo])

El maíz es un alimento muy completo, que contiene muchas vitaminas y minerales que favorecen nuestro metabolismo. Sin embargo, la proteína del grano de maíz es deficiente en la proporción de lisina y triptofano, aminoácidos esenciales para el ser humano. Lo que podría conllevar a una desnutrición, de manera especial en niños, madres, lactantes y ancianos. Como alternativa a la escasa calidad y baja producción del maíz, en los últimos años y en diversos países se ha trabajado con los llamados “maíces de calidad proteínica” (o QPM, del inglés quality protein maize). Si se lograra aumentar el consumo de los maíces de calidad proteínica en la población, especialmente la rural, se podría mejorar el nivel nutricional en México.

CALIDAD PROTEICA MAIZ AMARILLO NUTRICION POACEAE ZEA MAYS L BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) AGRICULTURA, SILVICULTURA, PESCA AGRICULTURA, SILVICULTURA, PESCA

Técnicas antiguas para resolver problemas nuevos: el caso de las cícadas

Andrew Vovides Sonia Galicia (2022, [Artículo])

En apoyo de las técnicas modernas de genética y la filogenia molecular, la anatomía vegetal puede aportar caracteres útiles de la amplia gama de tejidos vegetales que tienen las plantas que estudiamos. Se presenta algunos casos concretos de las cícadas (Ceratozamia y Zamia) mexicanas donde la anatomía ha sido de gran ayuda para dilucidar los límites estre especies.

ANATOMIA CERATOZAMIA MEXICO ZAMIA ZAMIACEAE BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) ECOLOGÍA VEGETAL ECOLOGÍA VEGETAL

Chronic toxicity of shrimp feed added with silver nanoparticles (Argovit-4®) in Litopenaeus vannamei and immune response to white spot syndrome virus infection

Carlos Rosendo Romo Quiñonez Píndaro Álvarez Ruiz CLAUDIO HUMBERTO MEJIA RUIZ NINA BOGDANCHIKOVA Alexey Pestryakov CARINA GAMEZ JIMENEZ WENCESLAO VALENZUELA QUIÑONEZ Magnolia Montoya Mejía EUSEBIO NAVA PEREZ (2022, [Artículo])

"In recent years, the application of silver nanoparticles (AgNPs) as antibacterial compounds has been widely used in human and veterinary medicine. In this work, we investigated the effects of AgNPs (Argovit-4 R ) as feed additives (feed-AgNPs) on shrimp (Litopenaeus vannamei) using three different methods: 1) chronic toxicity after 28 days of feeding, 2) Effects against white spot syndrome virus (WSSV) challenged by oral route, and 3) transcriptional responses of immune-related genes (PAP, ProPO, CTL-3, Crustin, PEN3, and PEN4) following WSSV infection. The results showed that the feed-AgNPs did not interfere with the growth and survival of shrimp. Also, mild lesions in the hepatopancreas were recorded, proportional to the frequency of the feed-AgNP supply. Challenge test versus WSSV showed that feeding every 7 days with feed-AgNPs reduced mortality, reaching a survival rate of 53%, compared to the survival rates observed in groups fed every 4 days, daily and control groups of feed-AgNPs for the 30%, 10%, and 7% groups, respectively. Feed-AgNPs negatively regulated the expression of PAP, ProPO, and Crustin genes after 28 days of treatment and altered the transcriptional responses of PAP, ProPO, CTL-3, and Crustin after WSSV exposure. The results showed that weekly feeding-AgNPs could partially prevent WSSV infection in shrimp culture. However, whether or not transcriptional responses against pathogens are advantageous remains to be elucidated."

Silver nanoparticles, Shrimp, Aquaculture, Chronic toxicity, WSSV, AgNP, Argovit, Litopenaeus vannamei , Silver fed, White spot syndrome virus BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA INMUNOLOGÍA INMUNIZACIÓN INMUNIZACIÓN

Dynamic simulation of diploid vs. triploid Pacific oyster (Crassostrea gigas) productive performance in northwestern Mexico

ROBERTO ASCENCIO MICHEL Ana María Ibarra Humphries MARCELO EDUARDO ARANEDA PADILLA GERMAN PONCE DIAZ FRANCISCO JAVIER VERGARA SOLANA (2022, [Artículo])

"The Pacific oyster Crassostrea gigas was introduced in northwestern Mexico for aquaculture purposes. Although its cultivation has been successful, this species has shown high mortalities during summer. To mitigate this problem, producers have resorted to biotechnology (triploidy), whose performance -regarding diploid seedling- depends on site conditions and stocking time. Hence, uncertainty exists on its benefits under real production conditions. This research evaluates triploidy performance by implementing a Dynamic simulation model considering environmental effects (temperature and chlorophyll) on culture production. The dynamic simulation was based on systems theory, dividing the productive system into two sub-models (environmental and biological), including temperature and chlorophyll effects, growth, mortality, and condition index parameterized in the function of the environmental parameters. The dynamic simulation results suggest that implementing triploid culture is advantageous in zones under high stress associated with high temperatura and low productivity; likewise, triploid spat tends to show better performance independently of the site. Nevertheless, performance by ploidy varies depending on the environmental conditions of the sites."

BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) FISIOLOGÍA ANIMAL FISIOLOGÍA ANIMAL