Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactive effects of CO2 and nitrogen supply on growth and physiological traits of millet cultivars under drought stress

ABSTRACT An experiment was conducted to evaluate the effects of irrigation regimes (irrigation after 40 and 75% depletion of available soil water) and nitrogen levels (0 and 85 mg N kg−1 soil) on millet cultivars (Bastan and Pishahang) under two atmospheric CO2 concentrations (390 ± 50 and 700 ± 50 µmol mol−1). Evaluation of different biochemical traits at 50% flowering stage and measurement of dry matter weight at milk stage revealed that water shortage reduced shoot dry weight as the consequence of decreasing chlorophyll and carotenoid contents, leaf area, membrane stability index, and root dry weight but it increased not only the production of H2O2 but also MDA and antioxidant enzyme activities. Drought conditions with elevated levels of CO2 and nitrogen supply, however, partly relaxed limitations observed under water shortage conditions so that H2O2 and MDA production decreased but chlorophyll content and leaf area increased, leading to reduced loss of shoot dry weight. Increased CO2 had a greater effect on the reduction of ascorbate peroxidase and catalase in Bastan, while in Pishahang it had more effect on the reduction of malondialdehyde. Results showed that elevated CO2 and nitrogen supply depended for their effects on both irrigation regime and the genotype grown.
The Function of Autophagy in Lace Plant Programmed Cell Death

The lace plant (Aponogeton madagascariensis) is an aquatic monocot that utilizes programmed cell death (PCD) to form perforations throughout its mature leaves as part of normal development. The lace plant is an emerging model system representing a unique form of developmental PCD. The role of autophagy in lace plant PCD was investigated using live cell imaging, transmission electron microscopy (TEM), immunolocalization, and in vivo pharmacological experimentation. ATG8 immunostaining and acridine orange staining revealed that autophagy occurs in both healthy and dying cells. Autophagosome-like vesicles were also found in healthy and dying cells through ultrastructural analysis with TEM. Following autophagy modulation, there was a noticeable increase in vesicles and vacuolar aggregates. A novel cell death assay utilizing lace plant leaves revealed that autophagy enhancement with rapamycin significantly decreased cell death rates compared to the control, whereas inhibition of autophagosome formation with wortmannin or blocking the degradation of cargoes with concanamycin A had an opposite effect. Although autophagy modulation significantly affected cell death rates in cells that are destined to die, neither the promotion nor inhibition of autophagy in whole plants had a significant effect on the number of perforations formed in lace plant leaves. Our data indicate that autophagy predominantly contributes to cell survival, and we found no clear evidence for its direct involvement in the induction of developmental PCD during perforation formation in lace plant leaves.
Effect of Preharvest Abiotic Stresses on the Accumulation of Bioactive Compounds in Horticultural Produce

The quality of horticultural products is the result of the interaction of different factors, including grower’s crop management ability, genotype, and environment. Sub-optimal environmental conditions during plant growth can induce abiotic stresses and reduce the crop performance with yield reduction and quality losses. However, abiotic stresses can induce several physiological, biochemical, and molecular responses in plants, aiming to cope with the stressful conditions. It is well known that these abiotic stresses are also elicitors of the biosynthesis of many metabolites in plants, including a wide range of bioactive compounds, which firstly serve as functional molecules for crop adaptation, but they have also a great interest for their beneficial effects on human health. Nowadays, the consumer is oriented to low-energy foods with low fat content, but at the same time, growing attention is paid to the presence of bioactive molecules, which are recognized as health-related compounds and concur to the nutraceutical value of plant-derived foods. In this context, fruit and vegetables play an important role as sources of bioactive ingredients in the diet. At the cultivation level, the understanding of crop responses to abiotic stresses and how they act in the biosynthesis/accumulation of these bioactive compounds is crucial. In fact, controlled abiotic stresses can be used as tools for improving the nutraceutical value of fruit and vegetables. This review focuses on the quality of vegetables and fruits as affected by preharvest abiotic stressors, with particular attention to the effect on the nutraceutical aspects.
Helios: A Scalable 3D Plant and Environmental Biophysical Modeling Framework

This article presents an overview of Helios, a new three-dimensional (3D) plant and environmental modeling framework. Helios is a model coupling framework designed to provide maximum flexibility in integrating and running arbitrary 3D environmental system models. Users interact with Helios through a well-documented open-source C++ API. Version 1.0 comes with model plug-ins for radiation transport, the surface energy balance, stomatal conductance, photosynthesis, solar position, and procedural tree generation. Additional plug-ins are also available for visualizing model geometry and data and for processing and integrating LiDAR scanning data. Many of the plug-ins perform calculations on the graphics processing unit, which allows for efficient simulation of very large domains with high detail. An example modeling study is presented in which leaf-level heterogeneity in water usage and photosynthesis of an orchard is examined to understand how this leaf-scale variability contributes to whole-tree and -canopy fluxes.
Temporal dynamics of taxonomic homogenization in the fish communities of the Laurentian Great Lakes

As a result of the loss of native species and the spread of non‐native species, fish communities are becoming increasingly homogenous globally. In the Laurentian Great Lakes, 21 native fish species have been extirpated from one or more lakes as a result of habitat alteration and destruction, overexploitation and invasive species since the 1800s. Over the same time period, 30 non‐native species became established in at least one lake as a result of authorized and unauthorized introductions. This study examines temporal changes in taxonomic dissimilarity over 15 time periods spanning the last 150 years.
The history of the Atlantic Salmon in Lake Ontario

The history of the Atlantic Salmon (Salmo salar), also referred to as Salmon below, in Lake Ontario is an accumulation of authentic published accounts, which were almost completed by J. R. Dymond before his death. H. H. MacKay completed the work on Dymond’s behalf (Dymond and MacKay, unpublished, 1966), but it remained largely unknown. The present authors (MEB, EH, PWB) have sought to present an updated subset of Dymond and MacKay’s work as the history of Lake Ontario Salmon is a crucial story in the history of the Great Lakes and its fisheries. The information provided should add materially to the knowledge of the causes that led to the decline and ultimate extirpation of a fascinating and valuable fish, notwithstanding all the efforts that were made to restore it by artificial means.
Ethanol versus swabs: what is a better tool to preserve faecal samples for non-invasive genetic analyses?

Acknowledgements We are particular grateful to E. Bottero (University of Sassari), D. Passilongo (University of Sassari), S. Luccarini (University of Sassari), F. Morimando (Univeristy of Siena), D. Berzi (Ischetus), M. Canestrini (Wolf Apennine Center) and all the students, apprentices and volunteers, for sample collection, and to N. Mucci (ISPRA), E. Randi (University of Bologna), M. Apollonio (University of Sassari), M. Scandura (University of Sassari), A. Canu (University of Sassari), W. Reggioni (Wolf Apennine Center), F. Moretti (Wolf Apennine Center) and P. Ciucci (Univeristy of Rome La Sapienza), for their useful suggestions on the manuscript. We are indebted with the Editor in Chief, the Associate Editor and two anonymous referees for their constructive comments and insightful ideas that deeply improved the manuscript.
Temperature response of wheat affects final height and the timing of stem elongation under field conditions

In wheat, temperature affects the timing and intensity of stem elongation (SE). Genetic variation for this process is therefore important for adaptation. This study investigates the genetic response to temperature fluctuations during SE and its relationship to phenology and height. Canopy height of 315 wheat genotypes (GABI wheat panel) was scanned twice weekly in the field phenotyping platform (FIP) of ETH Zurich using a LIDAR. Temperature response was modelled using linear regressions between SE and mean temperature in each measurement interval. This led to a temperature–responsive (slope) and a temperature-irresponsive (intercept) component. The temperature response was highly heritable (H2 = 0.81) and positively related to a later start and end of SE as well as final height. Genome-wide association mapping revealed three temperature-responsive and four temperature-irresponsive quantitative trait loci (QTL). Furthermore, putative candidate genes for temperature-response QTL were frequently related to the flowering pathway in A. thaliana, whereas temperature-irresponsive QTLs corresponded with growth and reduced height genes. In combination with Rht and Ppd alleles, these loci, together with the loci for the timing of SE accounted for 71% of the variability in height. This demonstrates how high-throughput field phenotyping combined with environmental covariates can contribute to a smarter selection of climate-resilient crops. Highlight We measured ambient temperature response of stem elongation in wheat grown under field conditions. The results indicate that temperature response is highly heritable and linked to the flowering pathway.
The mitochondrial genome of Vulgichneumon sp. (Hymenoptera: Ichneumonidae)

Abstract The Vulgichneumon sp. belongs to the subfamily Ichneumoninae of Ichneumonidae. The mitogenome (GenBank accession number: MN178162) of Vulgichneumon sp. was sequenced, the first representative of the mitogenome of the subfamily. The nearly complete mitogenome is 15,306 bp totally, consisting of 13 protein-coding genes, 2 rRNAs and 22 transfer RNAs. The nucleotide composition biases toward A and T, which together made up 83.6% of the entirety. Bayesian inference analysis supported the monophyly of Evanioidea, Chalcidoidea, Platygastroidea, Proctotrupoidea, Ceraphronoidea, and Ichneumonoidea. This result also suggested that the clade that contains other six superfamilies was the sister group to the clade that consist of Trigonaloidea, Megalyroidea and Ichneumonoidea.
Mismatches between the resources for adult herbivores and their offspring suggest invasive Spartina alterniflora is an ecological trap

Plant invasions can alter the behaviour and performance of native herbivorous insects because the insects are evolutionarily naïve to the novel plants. An ecological trap results when native insects prefer invasive plants over their native hosts but suffer reduced fitness on the invaders. Although such traps are predicted to occur frequently, given the prevalence of invasive plants, empirical support for ecological traps and their underlying mechanisms remains sparse. We examined the potential for the invasive plant Spartina alterniflora to act as an ecological trap for the native moth Laelia coenosa, which previously fed mainly on the indigenous plant Phragmites australis in a Chinese saltmarsh. We surveyed Laelia egg densities on Spartina and Phragmites in the field, and determined adult oviposition preference and offspring development on the two plant species. To investigate the causes of adult preference and offspring performance patterns, we compared resource abundance in the field, plant‐odour attractiveness and leaf nutritional and defensive traits between Spartina and Phragmites. We found that Laelia egg density and female preference for ovipositing were higher on Spartina than Phragmites. However, performance of offspring was poorer on Spartina than Phragmites. Spartina dominated a larger area and had greater leaf biomass than Phragmites in the field, and volatile odours released by Spartina were more attractive to Laelia females than those released by Phragmites. Although leaf C, C:P ratio and terpenoid content did not differ significantly between the two plant species, Spartina leaves were tougher and more waxy, had lower N and had higher concentrations of alkaloids and phenolics than Phragmites leaves. Synthesis. Our data suggest that invasive Spartina can create an ecological trap for the native insect Laelia. This trap appears to result from environmental cues (resource availability and leaf odours) that attract the herbivore to the plant, but do not reliably predict the dietary qualities (nutrition and defences) that negatively affect herbivore offspring performance. These findings reveal an important negative effect of plant invasions on resident herbivores and highlight the roles of resource availability and plant traits at different life stages of the insect.
An addition of a Trichodinid parasite (Ciliophora: Trichodinidae) from cultured Nile Tilapia ( Oreochromis niloticus ) (Linnaeus, 1758) in Bangladesh

Trichodina compacta Van As & Basson, 1989 is reported from the gills of Oreochromis niloticus (Linnaeus, 1758) taken from a large culture pond named Boro Dighi in Chittagong, Bangladesh. This represents a new geographical region for this species. The species is redescribed according to current biometric characteristics based on silver impregnated adhesive disc. Comparisons are made with the original description.
Matrix methods for stochastic dynamic programming in ecology and evolutionary biology

Organisms are constantly making tradeoffs. These tradeoffs may be behavioural (e.g. whether to focus on foraging or predator avoidance) or physiological (e.g. whether to allocate energy to reproduction or growth). Similarly, wildlife and fishery managers must make tradeoffs while striving for conservation or economic goals (e.g. costs vs. rewards). Stochastic dynamic programming (SDP) provides a powerful and flexible framework within which to explore these tradeoffs. A rich body of mathematical results on SDP exist but have received little attention in ecology and evolution. Using directed graphs – an intuitive visual model representation – we reformulated SDP models into matrix form. We synthesized relevant existing theoretical results which we then applied to two canonical SDP models in ecology and evolution. We applied these matrix methods to a simple illustrative patch choice example and an existing SDP model of parasitoid wasp behaviour. The proposed analytical matrix methods provide the same results as standard numerical methods as well as additional insights into the nature and quantity of other, nearly optimal, strategies, which we may also expect to observe in nature. The mathematical results highlighted in this work also explain qualitative aspects of model convergence. An added benefit of the proposed matrix notation is the resulting ease of implementation of Markov chain analysis (an exact solution for the realized states of an individual) rather than Monte Carlo simulations (the standard, approximate method). It also provides an independent validation method for other numerical methods, even in applications focused on short‐term, non‐stationary dynamics. These methods are useful for obtaining, interpreting, and further analysing model convergence to the optimal time‐independent (i.e. stationary) decisions predicted by an SDP model. SDP is a powerful tool both for theoretical and applied ecology, and an understanding of the mathematical structure underlying SDP models can increase our ability to apply and interpret these models.
Developing Functional and Antioxidant-Rich Table Grape Cultivars by Crossing Alicante Bouschet x Alphonse Lavallee

Son zamanlarda kirmizi ve siyah renkli uzum cesitleri, tanelerinin kabuk ve etindeki antosiyaninler nedeniyle ki bunlar tenturiye uzumler diye bilinir, gittikce populer olmaktadir. Antosiyaninler fenolik maddelerin bir grubu olup oksidasyon zararini engelleyerek veya geciktirerek bircok hastaligi onleyebilir. Turkiye’de Alicante Bouschet gibi bazi tenturiye saraplik uzum cesitleri olmasina karsin tenturiye sofralik bir uzum cesidi yoktur. Bu calismanin ana amaci Alphonse Lavallee ve Alicante Bouschet uzum cesitlerinin melezlenmesi yoluyla tenturiye gnotipler elde etmek ve tenturiye cesit adaylarinin erken seleksiyonu icin kotiledon ve gercek yapraklarin antosiyanin renklenmesini karsilastirmaktir. Antosiyaninler kotiledon yapraklarinda gorsel olarak gozlenmistir. Gercek yapraklarda antosiyanin miktari spektrofotomerik olarak disk yontemiyle saptanmistir. Cogu genotipin kotiledon ve gercek yapraklari yesil renktedir ve her iki yaprak arasinda paralellik vardir. Gercek yapraklardaki antosiyanin miktari yesil renkli yapraklarda 50.21 mg/kg, koyu renkli yapraklarda ise 131.51 mg/kg olarak saptanmistir.
Visual looming and receding networks in awake marmosets investigated with fMRI

An object that is looming toward a subject or receding away contains important information for determining if this object is dangerous, beneficial or harmless to them. This information (motion, direction, identity, time-to-collision, size, velocity) is analyzed by the brain in order to execute the appropriate behavioral responses depending on the context: fleeing, freezing, grasping, eating, exploring. In the current study, we performed ultra-high-field functional MRI (fMRI) in awake marmosets to explore the patterns of brain activation elicited by visual stimuli looming toward or receding away from the monkey. We found that looming and receding visual stimuli both activate a large cortical network in frontal, parietal, temporal and occipital cortex in areas involved in the analysis of motion, shape, identity and features of the objects. Looming stimuli strongly activated a network composed of the pulvinar, superior colliculus, prefrontal cortex and temporal cortical areas. This may underlie the existence of an alert network that processes the visual stimuli looming toward their peripersonal space by extracting the crucial information brought by the stimulus and evaluating its potential consequences to the observer. We hypothesize that this network is involved in the planning of protective behaviors (e.g. fleeing or freezing) and in emotional reaction (e.g. anxiety, fear). These findings support the view that this network is preserved through evolution and that the marmoset is a viable model to study visual and multisensory processes by using fMRI to guide further invasive recordings and/or pharmacological manipulations. Significant statement An object that is looming toward a subject or receding away contains important information for determining if this object is dangerous, beneficial or harmless to them. Here, we identified the functional network in non-human primates that was activated by visual stimuli looming toward or away from the animals using ultra-high-field functional magnetic resonance imaging. Our findings show that large cortical activations are elicited by both looming and receding visual conditions. However, some activations were specific to the looming condition, suggesting that the integration of cues in the looming direction rely on strong connections between cortical and subcortical areas, which allows primates to react properly for protecting themselves against a potential threat.
EFEITO DA QUALIDADE DE LUZ NO DESENVOLVIMENTO DA MORINGA SOB TELADOS DE DIFERENTES CORES

A moringa originária da Ásia é conhecida por suas utilidades, sendo uma planta de crescimento rápido e alta adaptabilidade a diversos climas. O trabalho objetivou-se em avaliar o desenvolvimento da moringa, sob uso de telados de diferentes cores. O experimento foi realizado no Instituto Federal de Educação, Ciência e tecnologia (IFCE), em Limoeiro do Norte-CE. O delineamento experimental foi inteiramente casualizado, constituído por cinco tratamentos com oito repetições, (TI-Telado cinza, TII-telado vermelho, TIII-telado verde, TIV-telado preto, TV-sem telado). Foi avaliado o IVE (índice de velocidade de emergência), altura (m), diâmetro do caule (cm), massa seca (%), açucares solúveis totais (%) e Proteína Bruta (%). No IVE, massa seca da parte radicular e proteína bruta, não houve diferença estatística significativa entre os tratamentos. Na altura das plantas, os tratamentos com telados obtiveram as melhores medias ficando acima dos valores obtidos pela testemunha, exceto na terceira avaliação que o TIII se sobressaiu dos outros tratamentos. No diâmetro do caule, o TV obteve resultado diferente dos demais tratamentos, apresentando valores inferiores. Na massa seca da parte aérea, o tratamento TV obteve o melhor resultado com 18,09%. Na concentração de açúcares soluveis totais, o tratamento TV apresentou o valor maior com uma média de 19,3%. Os telados promoveram apenas o alongamento celular, porém não ocorreu a incorporação de matéria seca.
PHYSIOLOGICAL ASPECTS OF COMPLETE MIXED DIET DIGESTION IN COMPLEX STOMACH OF RUMINANTS ON THE EXAMPLE OF CATTLE (Bos taurus taurus)

Modern systems of normalized cattle feeding are based on the position that different feed- ing technologies do not affect the processes of digestion and absorption of nutrients of the same diet. In our studies, data were obtained for the first time, indicating changes in the parameters of the ration digestion process in the complex stomach of cattle, depending on the method of feeding: separate delivery of separate feeds and simultaneous delivery by the form of the Total Mixed Ration (TMR). To determine mechanisms of increasing feed dry matter intake in cattle when they were switched to Total Mixed Ration feeding, daily flux rates of chyme, its chemical composition and digestibility of main nutrient groups in the compound stomach of young cattle were studied. A Latin square design experiment was carried out using two diets differing in the forage fodder the same type of diet, can reduce fiber digestibility due to accelerated outflow of rumen’s content with small particles, whereas with the other type of diet, on the contrary, can increase digestion due to improvement of fermentation conditions.