Miracle-dz/UniFAR-FTUs huggingface dataset:
Épocas de semeadura afetando índices morfofisiológicos de cultivares de arroz de terras altas

The expression of the full yield potential of crops depends on genetic factors, favorable environmental conditions and management. This study aimed to determine the effects of sowing dates on the solar radiation use efficiency (RUE), on morphophysiological indices, and on the grain yield of contrasting upland rice cultivars. The field experiment was conducted in the central region of Brazil in soils in Cerrado areas. The experiment had a 3 x 5 factorial randomized design with eight replications. The treatments consisted of combinations of three cultivars (BRS Primavera, BRSMG Curinga, and Douradao) with five sowing dates (11/09/2012, 22/10/2012, 11/28/2012, 21/12/2012, and 27/2/2013). All cultivars required less accumulated degree-days to reach the reproductive phase as the sowing was delayed. The lower biomass accumulation and leaf area index (LAI) of the three cultivars occurred on the earlier sowing date, which may have been a result of lower RUE. The assimilate partitioning to leaves and stems was similar among cultivars, but the translocation rate of carbohydrates to the panicle was higher in the cultivars BRSMG Curinga and Douradao. The cultivars differed in the total number of grains per area, with the highest values found in Douradao and the lowest in BRS Primavera. The highest grain yields were obtained in sowing dates covering the traditional period of sowing upland rice, which is October to December.
A molecular network of the aging brain implicates INPPL1 and PLXNB1 in Alzheimer’s disease

The fact that only symptomatic therapies of small effect are available for Alzheimer’s disease (AD) today highlights the need for new therapeutic targets with which to prevent a major contributor to aging-related cognitive decline. Here, we report the construction and validation of a molecular network of the aging human frontal cortex. Using RNA sequence data from 478 individuals, we first identify the role of modules of coexpressed genes, and then confirm them in independent AD datasets. Then, we prioritize influential genes in AD-related modules and test our predictions in human model systems. We functionally validate two putative regulator genes in human astrocytes: INPPL1 and PLXNB1, whose activity in AD may be related to semaphorin signalling and type II diabetes, which have both been implicated in AD. This arc of network identification followed by statistical and experimental validation provides specific new targets for therapeutic development and illustrates a network approach to a complex disease. One sentence summary Molecular network analysis of RNA sequencing data from the aging human cortex identifies new Alzheimer’s and cognitive decline genes.
Soil‐mediated filtering organizes tree assemblages in regenerating tropical forests

Secondary forests are increasingly dominant in human‐modified tropical landscapes, but the drivers of forest recovery remain poorly understood. Soil conditions influence plant community composition, and are expected to change over a gradient of succession. However, the role of soil conditions as an environmental filter driving community assembly during forest succession has rarely been explicitly assessed. We evaluated the role of stand basal area and soil conditions on community assembly and its consequences for community functional properties along a chronosequence of Atlantic forest regeneration following sugar cane cultivation. Specifically, we tested whether community functional properties are related to stand basal area, soil fertility and soil moisture. Our expectations were that edaphic environmental filters play an increasingly important role along secondary succession by increasing functional trait convergence towards more conservative attributes. We sampled soil and woody vegetation features across 15 second‐growth (3–30 years) and 11 old‐growth forest plots (300 m2 each). We recorded tree functional traits related to resource‐use strategies (specific leaf area, SLA; leaf dry matter content, LDMC; leaf area, LA; leaf thickness, LT; and leaf succulence, LS) and calculated community functional properties using the community‐weighted mean (CWM) of each trait and the functional dispersion (FDis) of each trait separately and all traits together. With exception of LA, all leaf traits were strongly associated with stand basal area; LDMC and SLA increased, while LT and LS decreased with forest development. Such changes in LDMC, LT and LS were also related to the decrease in soil nutrient availability and pH along succession, while soil moisture was weakly related to community functional properties. Considering all traits, as well as leaf thickness and succulence separately, FDis strongly decreased with increasing basal area and decreasing soil fertility along forest succession, presenting the lowest values in old‐growth forests. Synthesis. Our findings suggest that tropical forest regeneration may be a deterministic process shaped by soil conditions. Soil fertility operates as a key filter causing functional convergence towards more conservative resource‐use strategies, such as leaves with higher leaf dry matter content.
An integrated approach to understanding the metabolic rewiring of cancer cells

Cancer remains a leading worldwide health problem, and in the U.S., 1 in 3 women and 1 in 2 men are expected to develop it during their lifetimes. The last several decades have provided tremendous understanding of the genetic mutations and signaling pathways that give rise to oncogenic transformation. However, the field of oncology has only relatively recently begun to appreciate the extent of metabolic rewiring required to sustain the uncontrolled growth of tumors. Cancer metabolism is now an active area of research, and efforts are underway to expand the range of oncology diagnostics and therapeutics through targeting metabolism. Despite this progress, there remains much unknown about the extent of metabolic remodeling in cancer cells, including the influence of proliferation, oncogene activation, tumor suppressor loss, tissue of origin, metastatic potential, environmental cues, and many other factors. Further, metabolism comprises a large and complex network of interconnected reactions and transport processes that interface with many other components of cell physiology. However, in the field of metabolic engineering, there is precedence for using systems-wide approaches to studying metabolism, and these can be applied to cancer cells to unravel the contribution of such factors the metabolic phenotype. In this thesis, we describe an integrated approach, spanning multiple computational and empirical techniques based on metabolic engineering, to understand contributors to cancer metabolism. We specifically focused on the influence of growth for our analysis. We first review how some of the techniques of metabolic engineering, most notably stable isotope tracers, can be used to study metabolism in cancer cells. Next, using a published account of hybridoma composition, we analyzed the metabolic requirements of proliferation through reducing mammalian cell biomass needs to a small number of precursors and cofactors. We then incorporated this information into a stoichiometric network to understand how metabolic flux became redistributed following either shifts in metabolic objective or the introduction of constraints to simulate respiratory impairment. These investigations revealed the high biosynthetic burdens of amino acids, ATP, and NADPH, but also demonstrated the flexibility through which metabolism can adapt to fulfill these needs. Finally, we established a cell line system to study the differential metabolic effects of proliferation and expression of an oncogenic mutant of KRAS that drives growth factor-independent division. We found that, in the growthtitratable control cell line, proliferation was accompanied by a dramatic switch of branched-chain amino acid catabolism for TCA cycle flux to proteinogenesis. Additionally, we saw that cells undergoing oncogenic KRAS-driven growth possessed lower consumption rates of the major carbon metabolic substrates, glucose and glutamine, than the growth factor-sensitive control line growing at comparable rates.
Intraflagellar transport proteins undergo nonaxonemal staged hindrance between the recruiting distal appendages and the cilium

Primary cilia play a vital role in cellular sensing and signaling [1]. An essential component of ciliogenesis is intraflagellar transport (IFT), which first requires IFT-protein recruitment, IFT-protein–motor-protein assembly, axonemal engagement of IFT-protein complexes, and transition zone (TZ) gating [2–9]. The mechanistic understanding of these processes at the ciliary base was largely missing, because it is exceedingly challenging to observe the motion of IFT proteins in this crowded region using conventional microscopy. Here, we report short trajectory tracking of IFT proteins at the base of mammalian primary cilia by optimizing single-particle tracking photoactivated localization microscopy (sptPALM) [10, 11], balancing the imaging requirements of tracking speed, tracking duration, and localization precision for IFT88-mEOS4b in live human retinal pigment epithelial (hTERT-RPE-1) cells. Intriguingly, we found that mobile IFT proteins “switched gears” multiple times from the distal appendages (DAPs) to the ciliary compartment (CC), moving slowly in the DAPs, relatively fast in the proximal TZ, slowly again in the distal TZ, and then much faster in the CC. They could travel through the space between the DAPs and the axoneme without following DAP structures, and reached the space enveloped by the ciliary pocket in the proximal TZ. Together, our live-cell superresolution imaging revealed region-dependent slowdown of IFT proteins at the ciliary base, shedding light on staged control of ciliogenesis homeostasis.
Impact of exogenous nitrogen on cyanobacterial abundance and community in oil-contaminated sediment mesocosms

High concentrations of crude oil are toxic to cyanobacteria but can facilitate the emergence of cyanobacterial aggregation at an appropriate concentration range; however, the exact inducing factor has never been clearly elucidated. We hypothesized that increasing exposure to elevated concentrations of nitrogen would inhibit the accumulation of cyanobacteria in oil-contaminated sediments. To test this hypothesis, we simulated an oil spill in estuarine sediment microcosms with and without the removal of nitrogen limitation by supplementation of exogenous nitrogen. An integrated MiSeq sequencing of 16S rRNA gene analysis along with metatranscriptome sequence was performed to achieve a comprehensive study of cyanobacterial blooms. The number of cyanobacterial sequences increased over time in both oil-contaminated and non-oil-contaminated sediments at different time points after 42 days of incubation. And, supplementation with a nitrogen resource could accelerate cyanobacterial blooms under uncontaminated microcosms but delay the bloom phenomenon and reduce the cyanobacterial abundance to a great degree when exposed to oil. Our results clearly illustrated that nitrogen limitation was a vital driver of the increased abundance of cyanobacteria in oil-contaminated mesocosms. In addition, the abundance and compositions of blooming cyanobacteria varied significantly among the different treatment groups, and Oscillatoria may play a potential and non-negligible role in oil-contaminated mesocosms.
Effect of tillage, subsidiary crops and fertilisation on plant‐parasitic nematodes in a range of agro‐environmental conditions within Europe

The overall goal in nematode management is to develop sustainable systems where nematode populations are kept under the economic damage threshold. Conservation tillage and subsidiary crops, applied as cover crops and living mulches, generally improve soil health by increasing soil organic matter content and stimulating soil microbial activity. However, more permanent crop and weed cover associated with subsidiary crops and noninversion tillage, respectively, may benefit plant-parasitic nematodes with broad host spectra such as Meloidogyne and Pratylenchus. These genera are major constraints to many field crops throughout Europe and there is a need to identify effective and reliable management options that can be applied to avoid excessive infestations. The dynamics of the indigenous fauna of plant-parasitic nematodes were studied in eight coordinated multi-environment field experiments (MEEs) under four agro-environmental conditions in Europe (Continental, Nemoral, Atlantic North and Mediterranean North). The MEEs consisted of a 2-year sequence of wheat combined with a living mulch or subsequent cover crops and second main crops maize, potatoes or tomatoes depending on site. Additionally, the effects of inversion tillage using the plough were compared with various forms of conservation tillage (no-tillage, shallow and deep noninversion tillage). Overall, Helicotylenchus, Paratylenchus, Pratylenchus and Tylenchorhynchus were the most frequent genera across sites while Meloidogyne occurred only in Germany at very low densities. During the wheat–maize sequences in Switzerland, the populations of Pratylenchus increased from 63 to 146 nematodes per 100 mL soil and Helicotylenchus from 233 to 632 nematodes per 100 mL soil. The effects of tillage on plant-parasitic nematodes were generally minor, although no tillage in Italy supported higher densities of Pratylenchus (184 nematodes per 100 mL soil) than inversion tillage (59 nematodes per 100 mL soil). Furthermore, Pratylenchus densities were 160 nematodes per 100 mL soil when leguminous subsidiary crops were grown, 122 nematodes per 100 mL soil in the green fallow and 84 nematodes per 100 mL soil after growing black oat (Avena strigosa) or oilseed radish (Raphanus sativus). The differences were greatest in Italy, in a sandy soil with low organic matter. Application of compost or nitrogen fertiliser had no consistent effects on plant-parasitic nematodes. We conclude that crop rotations including specific subsidiary crops are prominent factors affecting the indigenous nematode community, while tillage and fertiliser are of lower importance.
Functional groups of Sahelian trees in a semiarid agroforestry system of Senegal

Aims Addressing plant responses to water stress is critical to understand the structure of plant communities in water‐limited environments and to forecast their resilience to future changes in climate. In a semiarid agroforestry system in the Sahelian savannah of Leona (Senegal), we selected nine common tree species and explored their stress‐resistance mechanisms. These species represent a variety of life forms and are of high regional socio‐economic importance. We hypothesized that different species would show different suites of traits to cope with water stress and expected to identify functional groups differing in strategies to withstand water shortage. Methods Along a dry and a wet season, we monitored four traits reflecting above‐ and below‐ground strategies of resource acquisition such as predawn leaf water potential (&psgr;pd), specific leaf area (SLA), leaf thickness and leaf area index (LAI). We also measured two morphological traits: trunk diameter and tree height. LAI and &psgr;pd were measured six times during the dry and rainy seasons, and the other traits were measured once. Important Findings We identified two functional classes subdivided into two functional groups of each class. The first class included deciduous and semi‐deciduous species that generally had large SLA, low leaf thickness and small‐to‐intermediate inter‐seasonal variations in &psgr;pd. The second class included evergreen species of two functional groups that differ in SLA, leaf thickness and the magnitude of inter‐seasonal variations of &psgr;pd throughout the year. The four functional groups identified in this study represent plant strategies differing in their response to changing environmental conditions.
The α2‐Subunit of AMP‐activated Protein Kinase Is a Potent Modulator of Myocardial Diastolic Calcium Homeostasis

The heterotrimeric enzyme 5′‐adenosine monophosphate‐activated protein kinase (AMPK) is known to have cardioprotective effects which may be partly due to a participation in the control of intracellular calcium concentration. Recently, we described in vascular smooth muscle a dilator role for AMPK which is due to sarcoplasmic reticulum Ca2+‐ATPase (SERCA)‐dependent calcium decrease. The present study elucidates a possible role of AMPK for myocardial diastolic calcium decrease.
IN VITRO DIGESTIBILITY OF RICE STRAW-BASED RATIONS OF DAIRY COWS CONTAINING FERMENTED CONCENTRATE BY Saccharomyces cerevisiae AND Effective Microorganisms-4 (EM-4)

Concentrate was used to improve rice straw-based rations of dairy cows. Rejected foods can be used to formulate concentrate but it can contain unwanted materials. This research aimed to know the best of fermentation time and rations formulation . Research phase 1 was to observe nutrient and energy contents of concentrate fermented by Saccharomyces cerevisiae and EM-4 at 0, 3, and 6 days. Phase 2 was to evaluate the use of the best fermented concentrate of the phase 1 to be used in the ration on i n v itro rumen degradability using treatments as follows: 1) 50% rice straws + 50% concentrate, 2) 50% rice straws + 25 concentrate + 25% fermented concentrate, 3) 50% rice straws + 50% fermented concentrate . This study used c ompletely randomized design and the collected data were analyzed by Contrast Orthogonal test . The results showed that crude protein (CP) increased but crude fiber (CF) and bruto energy decreased due to concentrate fermentation. A 3 day fermentation resulted in the highest (P<0.05) CP (14.48%) and the lowest CF (17.01%). The use of fermented concentrate at 50% in the ration resulted in the highest (P<0.05) digestibility of dry matter (63.68%) and organic matter ( 58.70% ) . It can be concluded that concentrate fermentation at 3 days by Saccharomyces cerevisiae and Effective Microorganisms-4 (EM-4) was the best treatments. I ts use in rice straws-based rations of dairy cows at 50% and result in the highest digestibility of dry matter and organic matter .
Disentangling the Relative Strength of Niche Competition from Grazing-Induced Phytoplankton Mortality

The dilution method is the principal tool used to infer in situ microzooplankton grazing rates. However, grazing is the only mortality process considered in the theoretical model underlying the interpretation of dilution method experiments. Here we evaluate the robustness of mortality estimates inferred from dilution experiments when there is concurrent niche competition amongst phytoplankton. Using a combination of mathematical analysis and numerical simulations, we find that grazing rates may be overestimated – the degree of overestimation is related to the importance of niche competition relative to microzooplankton grazing. In response, we propose a conceptual method to disentangle the effects of niche competition and grazing by diluting out microzooplankton, but not phytoplankton. Our theoretical results suggest this revised “Z-dilution” method can robustly infer grazing mortality, regardless of the dominant phytoplankton mortality driver in our system. Further, we show it is possible to independently estimate both grazing mortality and niche competition if the classical and Z-dilution methods can be used in tandem. We discuss the significance of these results for quantifying phytoplankton mortality rates; and the feasibility of using the Z-dilution method in practice.
Spatial mismatch in morphological, ecological and phylogenetic diversity, in historical and contemporary European freshwater fish faunas

Biodiversity encompasses multiple facets, among which taxonomic, functional and phylogenetic aspects are the most often considered. Understanding how those diversity facets are distributed and what are their determinants has become a central concern in the current context of biodiversity crisis, but such multi‐faceted measures over large geographical areas are still pending. Here, we measured the congruence between the biogeographical patterns of freshwater fish morphological, ecological and phylogenetic diversity across Europe and identified the natural and anthropogenic drivers shaping those patterns. Based on freshwater fish occurrence records in 290 European river catchments, we computed richness and evenness for morphological, ecological and phylogenetic diversity using standardized effect sizes for each diversity index. We then used linear models including climatic, geo‐morphological, biotic and human‐related factors to determine the key drivers shaping freshwater fish biodiversity patterns across Europe. We found a weak spatial congruence between facets of diversity. Patterns of diversity were mainly driven by elevation range, climatic seasonality and species richness while other factors played a minor role. Finally, we found that non‐native species introductions significantly affected diversity patterns and influenced the effects of some environmental drivers. Morphological, ecological and phylogenetic diversity constitute complementary facets of fish diversity rather than surrogates, testifying that they deserve to be considered altogether to properly assess biodiversity. Although the same environmental and anthropogenic factors overall explained those diversity facets, their relative influence varied. In the current context of global change, non‐native species introductions may also lead to important reshuffling of assemblages resulting in profound changes of diversity patterns.
Inducing genetic variation in growth related characteristics of poplar germplasm, by producing inter-specific hybrids between P. alba and P. euphratica

Abstract Crosses were made between two Populus species to create two hybrid groups, P. alba ♀ * P. euphratica ♂ and P. euphratica ♀ * P. alba ♂. Aseptic immature hybrid seeds were first grown on MS medium. Hybrid seedlings were then acclimatized and grown in greenhouse conditions and transplanted to an experimental field. Growth related characteristics were recorded on 307 three years-old seedlings of new inter-specific hybrids of six half-sib families, in order to assess possible potentials of the two hybrid groups. Double nested analysis of variance revealed significant differences between the hybrid groups and siblings based on majority of the studied characters. The hybrid groups formed two distinct groups for some of the studied characteristics which implied maternal effects of inheritance on the traits. The first hybrid group had more but shorter and closer branches than the second group. Adaxial stomata number for the two hybrid groups varied between 4.7 to 123. Whereas, there were no such strong differences between vegetative characteristics of the two groups. The second hybrid group had a very condense layer of white fuzz on its abaxial leaf surface, inherited from its female parents. This may lead to suggest some kinds of photosynthesis and respiration functions such as leaf sub-stomatal chambers’ functions for the mentioned fuzzy trichomes of the second hybrid group and their female parental species, P. alba. In essence, 307 new divergent poplar hybrid genotypes were produced by which ecological zone of poplar species could be extended in the country as well as high yielding genotypes would be promising.