Contrasting spatial patterns in active-fire and fire-suppressed mediterranean climate old-growth mixed conifer forests

Danny L. Fry  (2014, [Artículo])

In Mediterranean environments in western North America, historic fire regimes in frequent-fire conifer forests are highly variable both temporally and spatially. This complexity influenced forest structure and spatial patterns, but some of this diversity has been lost due to anthropogenic disruption of ecosystem processes, including fire. Information from reference forest sites can help management efforts to restore forests conditions that may be more resilient to future changes in disturbance regimes and climate. In this study, we characterize tree spatial patterns using four-ha stem maps from four old-growth, Jeffrey pine-mixed conifer forests, two with active-fire regimes in northwestern Mexico and two that experienced fire exclusion in the southern Sierra Nevada. Most of the trees were in patches, averaging six to 11 trees per patch at 0.007 to 0.014 ha-1, and occupied 27-46% of the study areas. Average canopy gap sizes (0.04 ha) covering 11-20% of the area were not significantly different among sites. The putative main effects of fire exclusion were higher densities of single trees in smaller size classes, larger proportion of trees (≥56%) in large patches (≥10 trees), and decreases in spatial complexity. While a homogenization of forest structure has been a typical result from fire exclusion, some similarities in patch, single tree, and gap attributes were maintained at these sites. These within-stand descriptions provide spatially relevant benchmarks from which to manage for structural heterogeneity in frequent-fire forest types.

article, climate, controlled study, ecosystem fire history, forest structure, geographic distribution, geographic mapping, land use, mathematical computing, mathematical model, Mexico, spatial analysis, taiga, United States, comparative study, conife CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

GWAS identifies genetic loci underlying nitrogen responsiveness in the climate resilient C4 model Setaria italica (L.)

Tirthankar Bandyopadhyay Stéphanie M. Swarbreck Vandana Jaiswal Rajeev Gupta Alison Bentley Manoj Prasad (2022, [Artículo])

C4 Model Crop Climate Resilience CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CLIMATE RESILIENCE FOOD SECURITY GENE EXPRESSION NITROGEN

Nitrogen use efficiency and genotype-by-environment interaction in durum wheat genotypes under varying nitrogen supply

Tesfaye Geleta Aga Bekele Abeyo (2024, [Artículo])

Straw Nitrogen Uptake Nitrogen Harvest Index CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA NITROGEN-USE EFFICIENCY STRAW GENOTYPE ENVIRONMENT INTERACTION HARD WHEAT

Enhancing maize's nitrogen-fixing potential through ZmSBT3, a gene suppressing mucilage secretion

jiafa chen XUECAI ZHANG Jianyu Wu (2023, [Artículo])

Aerial Roots ZmSBT3 Diazotroph CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA MAIZE ADVENTITIOUS ROOTS MUCILAGES NITROGEN FIXATION GENOME-WIDE ASSOCIATION STUDIES GENE CLONING NITROGEN FIXING BACTERIA

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

The input reduction principle of agroecology is wrong when it comes to mineral fertilizer use in sub-Saharan Africa

Gatien Falconnier Marc Corbeels Frédéric Baudron Antoine Couëdel leonard rusinamhodzi bernard vanlauwe Ken Giller (2023, [Artículo])

Can farmers in sub-Saharan Africa (SSA) boost crop yields and improve food availability without using more mineral fertilizer? This question has been at the center of lively debates among the civil society, policy-makers, and in academic editorials. Proponents of the “yes” answer have put forward the “input reduction” principle of agroecology, i.e. by relying on agrobiodiversity, recycling and better efficiency, agroecological practices such as the use of legumes and manure can increase crop productivity without the need for more mineral fertilizer. We reviewed decades of scientific literature on nutrient balances in SSA, biological nitrogen fixation of tropical legumes, manure production and use in smallholder farming systems, and the environmental impact of mineral fertilizer. Our analyses show that more mineral fertilizer is needed in SSA for five reasons: (i) the starting point in SSA is that agricultural production is “agroecological” by default, that is, very low mineral fertilizer use, widespread mixed crop-livestock systems and large crop diversity including legumes, but leading to poor soil fertility as a result of widespread soil nutrient mining, (ii) the nitrogen needs of crops cannot be adequately met solely through biological nitrogen fixation by legumes and recycling of animal manure, (iii) other nutrients like phosphorus and potassium need to be replaced continuously, (iv) mineral fertilizers, if used appropriately, cause little harm to the environment, and (v) reducing the use of mineral fertilizers would hamper productivity gains and contribute indirectly to agricultural expansion and to deforestation. Yet, the agroecological principles directly related to soil fertility—recycling, efficiency, diversity—remain key in improving soil health and nutrient-use efficiency, and are critical to sustaining crop productivity in the long run. We argue for a nuanced position that acknowledges the critical need for more mineral fertilizers in SSA, in combination with the use of agroecological practices and adequate policy support.

Manure Crop Yields Smallholder Farming Systems Environmental Hazards CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA BIOLOGICAL NITROGEN FIXATION LEGUMES NUTRIENT BALANCE SOIL FERTILITY AGROECOLOGY YIELD INCREASES LITERATURE REVIEWS

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

Evaluación morfológica, bioquímica y diversidad genética del germoplasma silvestre de Jojoba (Simmondsia chinensis) y Jatropha (Jatropha curcas) del Noroeste de México

NIDIA ARAIZA LIZARDE (2016, [Tesis de doctorado])

Jojoba (Simmondsia chinensis) and jatropha (Jatropha curcas) are potential sources to obtaining oil for industrial purposes and production of biodiesel (Masayuki, 1976; Masayuki and Takeshi, 1980). The objectives of this study were to analyze the morphological characteristics of seeds, oil content, physicochemical parameters of lipid, fatty acids composition and genetic variability of ecotypes of jojoba and jatropha in the Northwest of Mexico. Three ecotypes of jojoba named Indígena la Huerta, Sonoyta, and Todos Santos were evaluated. Sonoyta seeds ecotype has the highest weight, length and thickness (0.82g, 15.98 mm and 9.28 mm). Significant differences in color and seed moisture were observed. The number of seeds per kilogram was higher in the ecotype Indígena la Huerta (1217). The oil content was between 43, 44 and 49% in the 3 ecotypes. Viscosity, density, index of acidity, peroxide, yodine and refraction showed no significant differences. The most abundant fatty acids were the Eicosanoic (52 to 62.43%), oleic (13.80 to 27.36%) and Palmitic (6.43-9.70%). ISSR analysis on the accessions of S. chinensis showed a 54% polymorphic. On the other hand 3 ecotypes of Jatropha curcas Estación Dimas, El Quelite and La Campana were analyzed. No significant differences in weight, length, thickness, humidity and number of seeds per kg. The color of the seeds was 60.80 to 65.64 °Hue. The oil content of the germ of J. curcas was 52 to 56%. Viscosity, density, index of acidity, peroxide, iodine and refraction showed no significant differences in the seeds collected in the three ecotypes in study. The most abundant saturated fatty acids were oleic (44 to 46%), linoleic (42 to 44%) and palmitic (4-6%). SSR analysis of J. curcas accessions showed expected heterozygosity (He) of 0.7524, 0.7092 and 0.7956 in ecotypes of La Campana, Estación Dimas and El Quelite respectively. The wild germplasm of jatropha and jojoba is an alternative in the cosmetics and energy industry and represents a potential for activating the economy in arid and semi-arid regions of México.

Jojoba (Simmondsia chinensis) y jatropha (Jatropha curcas) son fuentes potenciales para la obtención de aceite con fines industriales y para la producción de biodiesel (Masayuki, 1976; Masayuki y Takeshi, 1980). Los objetivos de este trabajo fueron analizar las características morfológicas de las semillas, el contenido de aceite, los parámetros fisicoquímicos de los lípidos, la composición de ácidos grasos y la diversidad genética de ecotipos de jojoba y jatropha en el Noroeste de México. Se evaluaron tres ecotipos de jojoba denominados Indígena la Huerta, Sonoyta y Todos Santos. Las semillas del ecotipo de Sonoyta presentaron el mayor peso, longitud y grosor (0.82 g, 15.98 mm y 9.28 mm). Se observaron diferencias significativas en el color y la humedad de la semilla. El número de semillas por kilogramo fue mayor en el ecotipo de Indígena la Huerta (1217 semillas). El contenido de aceite fue de 43 a 49% en los 3 ecotipos. La viscosidad, densidad específica, índice de acidez, peróxido, yodo y refracción no mostraron diferencias significativas. Los ácidos grasos más abundantes fueron el eicosanoico (52 a 62.43%), oleico (13.80 a 27.36%), y palmítico (6.43 a 9.70%). El análisis ISSR mostró un porcentaje polimórfico de 54 %. Por otro lado, se analizaron 3 ecotipos de Jatropha curcas denominados Estación Dimas, El Quelite y La Campana. No se observaron diferencias significativas en el peso, longitud, grosor, humedad y número de semillas por kilogramo. El color de las semillas fue de 60.80 a 65.64 °Hue. El contenido de aceite del germen de J. curcas fue de 52 a 56%. La viscosidad, densidad específica, índice de acidez, peróxido, yodo y refracción del aceite no mostraron diferencias significativas entre los ecotipos estudiados. Los ácidos grasos más abundantes fueron el oleico (44 a 46%), linoleico (42 a 44%) y palmítico (4 a 6%). El análisis SSR de accesiones de J. curcas mostró la heterocigosidad esperada (He) de 0.7524, 0.7092 y 0.7956 en los ecotipos de La Campana, Estación Dimas y El Quelite, respectivamente. El germoplasma silvestre de jojoba y jatropha es una alternativa en la industria cosmética y energética, representan un potencial para activar la economía en las regiones áridas y semiáridas de México.

ácidos grasos, semillas, ISSR, lípidos, jatropha, jojoba, SSR INGENIERÍA Y TECNOLOGÍA CIENCIAS TECNOLÓGICAS TECNOLOGÍA BIOQUÍMICA ACEITES Y GRASAS VEGETALES ACEITES Y GRASAS VEGETALES

Waterhole detection using a vegetation index in desert bighorn sheep (Ovis canadensis cremnobates) habitat

Jonathan Gabriel Escobar Flores (2019, [Artículo])

In arid ecosystems, desert bighorn sheep are dependent on natural waterholes, particularly in summer when forage is scarce and environmental temperatures are high. To detect waterholes in Sierra Santa Isabel, which is the largest area of desert bighorn sheep habitat in the state of Baja California, Mexico, we used the normalized difference vegetation index (NDVI) and normalized difference water index (NDWI) from Sentinel-2 satellite images. Waterhole detection was based on the premise that sites with greater water availability, where NDVI was higher, can be identified by their density of vegetation greenness. For the detected waterholes, we estimated the escape terrain (presence of cliffs or steep, rocky slopes) around each by the vector ruggedness measure to determine their potential use by desert bighorn sheep based on the animals’ presence as documented by camera traps. We detected 14 waterholes with the NDVI of which 11 were known by land owners and 3 were unrecorded. Desert bighorn were not detected in waterholes with high values of escape terrain, i.e., flat areas. Waterhole detection by NDVI is a simple method, and with the assistance and knowledge of the inhabitants of the Sierra, it was possible to confirm the presence each waterhole in the field. © 2019 Escobar-Flores 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.

Article, bighorn sheep, environmental aspects and related phenomena, environmental parameters, habitat, Mexico, nonhuman, normalized difference vegetation index, normalized difference water index, water availability, waterhole, animal, bighorn sheep, CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGRARIAS CIENCIA FORESTAL CIENCIA FORESTAL

Screening of xylose utilizing and high lipid producing yeast strains as a potential candidate for industrial application

Linnea Qvirist RICARDO VAZQUEZ JUAREZ Thomas Andlid (2022, [Artículo])

"Background: Sustainable production of oil for food, feed, fuels and other lipid-based chemicals is essential to meet the demand of the increasing human population. Consequently, novel and sustainable resources such as lignocel- lulosic hydrolysates and processes involving these must be explored. In this paper we screened for naturally-occurring xylose utilizing oleaginous yeasts as cell factories for lipid production, since pentose sugar catabolism plays a major role in efcient utilization of lignocellulosic feedstocks. Glycerol utilization, which is also benefcial in yeast-based oil production as glycerol is a common by-product of biodiesel production, was investigated as well. Natural yeast isolates were studied for lipid accumulation on a variety of substrates, and the highest lipid accumulating strains were further investigated in shake fask cultivations and fermenter studies on xylose and hydrolysate. Results: By collecting leaves from exotic plants in greenhouses and selective cultivation on xylose, a high frequency of oleaginous yeasts was obtained (>40%). Diferent cultivation conditions lead to diferences in fatty acid contents and compositions, resulting in a set of strains that can be used to select candidate production strains for diferent purposes. In this study, the most prominent strains were identifed as Pseudozyma hubeiensis BOT-O and Rhodosporidium toruloides BOT-A2. The fatty acid levels per cell dry weight after cultivation in a nitrogen limited medium with either glucose, xylose or glycerol as carbon source, respectively, were 46.8, 43.2 and 38.9% for P. hubeiensis BOT-O, and 40.4, 27.3 and 42.1% for BOT-A2. Furthermore, BOT-A2 accumulated 45.1% fatty acids per cell dry weight in a natural plant hydrolysate, and P. hubeiensis BOT-O showed simultaneous glucose and xylose consumption with similar growth rates on both carbon sources. The fatty acid analysis demonstrated both long chain and poly-unsaturated fatty acids, depending on strain and medium. Conclusions: We found various natural yeast isolates with high lipid production capabilities and the ability to grow not only on glucose, but also xylose, glycerol and natural plant hydrolysate. R. toruloides BOT-A2 and P. hubeiensis BOT-O specifcally showed great potential as production strains with high levels of storage lipids and comparable growth to that on glucose on various other substrates, especially compared to currently used lipid production strains..."

Microbial lipids, Oleaginous yeast, Lignocellulose, Pseudozyma hubeiensis, Rhodosporidium toruloides BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA MICROBIOLOGÍA MICROBIOLOGÍA MICROBIOLOGÍA