Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine-scale ecological dynamics of closely related marine microbes

Microbial dynamics in the environment are major drivers of global biogeochemical cycles; hence there is great interest in characterizing their rates and causes. While dynamics are affected by processes across many spatiotemporal scales, and even closely related microbes are known to vary in their ecological distributions, most work has characterized dynamics at bulk scales and with low genetic resolution. Thus, little is known about the effects of finer structure. In this thesis, I show that characterizing the dynamics of environmental microbes with finer spatiotemporal and genetic resolution reveals otherwise concealed dynamics. I use the Vibrionaceae, an ecologically diverse family of marine heterotrophs, as a model system. First, I review past studies on environmental associations of the Vibrionaceae, showing that few abiotic parameters have consistent predictive value, and that observed patterns vary based on taxonomic resolution. Biotic associations, however, may represent more specific predictors for fine-scale Vibrionaceae taxa, reflecting their diverse lifestyles. I then characterize Vibrionaceae dynamics within a high-resolution environmental time-series, with three months of daily sampling across four habitat partitions, population-level resolution, and large datasets of potential biological correlates. These data reveal diverse and spatially structured population dynamics. Individual populations varied from consistently abundant generalists to rare populations that occasionally displayed brief but intense peaks of abundance. Free-living and particle-attached habitat partitions were distinct in terms of diversity, turnover, and biotic interactors. These results emphasize the ecological differentiation of the Vibrionaceae populations, and the extent to which spatial partitions can function as distinct ecological regimes. Finally, I use
Thermoregulatory Behavior of Anaxyrus americanus in Response to Infection with Batrachochytrium dendrobatidis

Fever is an evolutionarily conserved and effective organismal response used to reduce infection burden. Although ectotherms are unable to induce a fever endogenously because they only produce negligible heat from their metabolism, they can increase their body temperature in response to infection by selecting warm microclimates (“behavioral fever”). For amphibians, behavioral fever is hypothesized to be critical in their defense against pathogens because many amphibian immune parameters are more effective at warm temperatures. We explored this topic using the pathogenic amphibian chytrid fungus (Batrachochytrium dendrobatidis; “Bd”), a fungal pathogen implicated in the worldwide amphibian declines. Behavioral fever in amphibians should be an effective defense against Bd because fungal growth is temperature dependent and does not survive above 30°C. We conducted a laboratory experiment in which we allowed Bd-infected and sham inoculated metamorphic American toads (Anaxyrus americanus) to behaviorally thermoregulate. During the experiment, we recorded the body temperature of each toad and also determined their Bd infection intensity. Bd-infected toads behaviorally increased their body temperatures through the course of an infection compared to sham inoculated toads, which did not change their body temperatures. In addition, toads with higher initial Bd infection intensities (measured prior to the start of the thermoregulation experiment) had higher average body temperatures compared to the body temperature of toads with lower infection intensities. Collectively, these findings build upon our understanding of the relationship between temperature and disease in the amphibian-Bd system and offer hope that amphibians might be able to induce behavioral fevers to clear their Bd infections in nature.
Genetic Variability of Bovine Viral Diarrhea Virus Persistently Infected Cattle in Central Java, Indonesia

Fifte en bovine viral diarrhea virus (BVDV) positive samples collected from persistently infected (PI) dairy cattle in Central Java, Indonesia detect the genetic characterization of BVDV based on the 5' Region (5'UTR) of the viral geno me. Through phylogenetic and nucleotide sequence analysis of the 5'UTR regions of the samples investigated, it was determined that all the 15 IP -BVDV field positive samples genotype. No evidence of BVDV-2 genotype was found in our recent collected blood samples. The presence of the genetic variability among the BVDV -1 circulating in the dairy cattle population in Central Java, Indonesia was not proven. As a conclusion, further research involving higher number of BVDV -1 positive samples fr om different region of Indonesia is urgently needed.
Moving forward: insights and applications of moving‐habitat models for climate change ecology

Predicting and managing species’ responses to climate change is one of the most significant challenges of our time. Tools are needed to address problems associated with novel climatic conditions, biotic interactions and greater climate velocities. We present a spatially explicit moving‐habitat model (MHM) and demonstrate its versatility in tackling critical questions in climate change research, including dispersal in multiple spatial dimensions, population stage structure, interspecific interactions, asymmetric range shifts, Allee effects and the presence of infectious diseases. The model utilizes integrodifference equations to track changes in population density over time in a habitat that is moving. The model is quite flexible and can accommodate variation in demography, dispersal patterns, biotic interaction and stochasticity in the velocity of climate change. The methods provide a general mechanistic understanding of the underlying ecological processes that drive a system. Field data can be readily incorporated into the model to give insight into specific populations of interest and inform management decisions. Synthesis. Moving‐habitat models unite ecological theory, data‐centred modelling and conservation decision support under a single framework. Their ability to generate testable hypotheses, incorporate data and inform best management practices proves that these models provide a valuable framework for climate change biologists.
Searching for a lost frog (Rhinoderma rufum): identification of the most promising areas for future surveys and possible reasons of its enigmatic decline

Currently amphibians are more threatened than birds and mammals with more than one-third of all amphibians facing extinction. In Chile, Darwin's frog (Rhinoderma rufum) is classified as Critically Endangered by IUCN, and no individuals have been found since the 80's. Herein, a species distribution model (SDM) was generated to identify the most likely areas were remaining R. rufum populations might be detected as a first step to help to rediscover this lost frog. The SDM was based on bioclimatic and land cover information with a comprehensive collection of 19 species records compiled from literature, museum records and personal communications. The SDM suggests a potential distribution of R. rufum, which differs slightly from the one previously proposed. However, it shows an overlap with cultivation and artificial areas in Chile. Therefore, it seems likely that the major factor leading to R. rufum declines and possible extinction was anthropogenic habitat destruction.
Comparative Growth-rates of Upland and Swamp Rice Varieties

The growth of swamp rice (Dima) and upland rice (Kindinga) was studied under tropical glass-house conditions in Trinidad. Kindinga ultimately attained greater dry weight and height than Dima but the total number of leaves and tillers per plant were greater in Dima than in Kindinga. Kindinga had a greater number of leaves, on the main shoot, than Dima. Growth curve of leaf-lamina area per plant was similar to that of leaf-lamina dry weight in both varieties but leaf area per unit dry weight of lamina and per plant were usually greater in Kindinga than in Dima. Over the whole period, the mean relative growth rate, leaf weight ratio were greater in Kindinga than in Dima but net assimilation rate was greater in Dima than in Kindinga. Total nitrogen content was greater in Dima than in Kindinga during the tillering period but later the reverse was the case. The rate of nitrogen absorption was high in both varieties during the tillering and reproductive phases. Split applications of nitrogenous fertilizer are therefore suggested. The rate of nitrogen absorption was, however, greater in Dima than in Kindinga during the tillering period and latter half of the reproductive phase.
Genetic variability of drought tolerance of trees of agronomic interest : the role of vulnerability to xylem cavitation

In a context of climatic changes, drought stress and water management are regarded as one of the most important constraints for agricultural sector. Thus the selection for drought tolerance became a main objective for many breeding programs. Vulnerability to cavitation is considered a trait of interest for the selection for extreme drought stress, especially for woody species. However, the extent of its variability and its relation to drought tolerance are poorly documented on intraspecific level, particularly for cultivated species. In this study the genetic variability of vulnerability to cavitation was studied on three different experimental devices with three trees of agronomic interest that are threatened by the risk of drought: walnut, rubber and apple trees. Low or no variation in xylem vulnerability to cavitation was found in the studied species and between two species of walnuts despite differences previously reported features. These results suggested a canalization of cavitation resistance on critical organs (branches and stems). In apple tree, the rootstock was suspected to cause the narrow resistance to cavitation on the scion. On the contrary, differences on other traits in response to drought stress such as stomatal regulation, leaf shedding or vulnerability to cavitation on petiole were found. Therefore, vulnerability to cavitation of critical organs was not a relevant parameter for the selection of drought tolerance and breeding programs on the species studied did not appear to affect this parameter.
The Role of Claudins in Bone Metabolism

48 Introduction . 49 Materials and Methods . 51 Animals . 51 Experimental Design . 51 Measurement of Gastric pH . 52 Total Calcium Serum Measurement . 52 Bone Densitometry . 52 Micro-CT Analysis . 53 Dynamic Calcein Labeling and Histomorphometry . 53 Cell Culture . 54 RNA Extraction and Gene Expression Analysis . 54 Statistical Analysis . 54 Results . 55 Cldn-18 Deficiency Affects Gastric pH . 55 The Effect of Dietary Calcium on Serum Calcium levels in 10 Week Old Cldn-18 KO and Heterozygous Control Mice . 55 The Effect of Dietary Calcium on Bone Mineral Density (BMD) of Cldn-18 and Heterozygous Control Mice at Different Skeletal Sites . 57 The Effect of Dietary Calcium on Lumber Vertebrae5 Bone Mass Parameters of 10 Week Old Cldn-18 KO and Heterozygous Control Mice . 62 The Effect of Dietary Calcium on Lumber Vertebrae5 Bone Size Parameters of 10 Week Old Cldn-18 KO and Heterozygous Control Mice . 62 The Effect of Dietary Calcium on Histomorphometric Parameters of Lumber Vertebrae 5 of 10 Week Old Cldn-18 KO and Heterozygous Control Mice . 64
A genomic analysis of the insect pest populations of cowpea in West Africa

Insect pests often develop resistance to insecticides, and such resistance represents a serious management problem. Devising methods that concurrently delay resistance and minimize injury by insects to field crops and stored grain has long been a goal of integrated pest management (IPM). A centerpiece of IPM has been the combined use of biological control agents and prudent application of chemical insecticides. Unfortunately, successful application of IPM has remained a challenge. This chapter describes the use of emerging genomic technologies that may lead to a “systems” perspective of IPM for the control of pests of cowpea and other crops. This emerging field, which we refer to as “IPM-omics”, builds upon recent advances in genome sequencing technologies and detection of large-scale gene polymorphisms, which are becoming economically feasible for pest insect systems. IPM-omics will also need to involve the use of information and communications technologies both to collect critical information on pest populations and to deploy practical IPM solutions. The information obtained on the temporal fluctuations, spatial distribution, and ecological diversification within target, non-target, and natural enemy populations can be overlaid on a geographic information systems (GIS) map to 1 This chapter has been published as Agunbiade et al. 2012. IPM-omics: From genomics to extension for integrated pest management of cowpea. In Boukar O, Coulibaly O, Fatokun C, Lopez K, Tamò M (Eds.), Improving livelihoods in the cowpea value chain through advancements in science. Proceedings of the 5th World Cowpea Research Conference, pp. 231 – 248. It is reprinted with the permission of the copyright owner. I acknowledge the contribution of coauthors to the publication.
Molecular mechanisms of resveratrol-induced apoptosis in human pancreatic cancer cells

Resveratrol is a polyphenolic phytoalexin found at high concentrations in grapes, nuts, fruits and red wine with reported anti-carcinogenic effects. In this study, the molecular mechanism of resveratrol-induced apoptosis in human pancreatic cancer (Panc 2.03) cells is investigated. Resveratrol treatment of Panc 2.03 cells results in dose-dependent inhibition of cell growth and cells accumulated at the S phase transition of the cell cycle. The anti-proliferative effect of resveratrol is due to apoptosis as seen by the appearance of chromatin condensation, nuclear fragmentation, DNA ladder formation and increased annexin V-stained cells. The apoptotic process is induced by decreased Bcl-2 expression concomitant with increased Bax expression, leading to an increase in the Bax/Bcl-2 ratio and subsequent activation of caspase-9 and caspase-3. In addition, resveratrol treatment also decreases the survivin level and increases the apoptosis-inducing factor level in a dose-dependent manner. These results suggest that resveratrol induces apoptosis of Panc 2.03 cells, at least in part through a mitochondrial-associated intrinsic pathway in both caspase- dependent and independent manners. The present findings suggest that resveratrol has potential as a chemopreventive agent, and possibly as a therapeutic one against pancreatic cancer.
Soil enzyme activity changes in different-aged spruce forests of the eastern Qinghai-Tibetan plateau

Activities of selected soil enzymes (invertase, acid phosphatase, proteinase, catalase, peroxidase and polyphenoloxidase) were determined under different spruce forests with restoration histories of 5, 13, 18, 23, 27 years and an old growth forest over 400 years old in the eastern Qinghai-Tibetan Plateau, China, and their possible use as indicators of ecosystems health were analyzed. Plots 10 x 10 m with 4 replications were established to investigate three hypotheses: soil enzyme activities a) would increase with the restoration process; b) would be greater in surface soils than at lower depths; and c) would be correlated to selected physicochemical properties. Results showed that as the forests developed after restoration, invertase and peroxidase activities usually increased up to the 23 year point. Also soil enzyme activities were associated with surface soils and decreased with depths, suggesting that in earlier restoration stages surface addition of organic fertilizer to soils might be more effective than additions at depth. In the 0-20 cm soil, there were significant correlations (P < 0.01 or < 0.05) between some soil enzyme activities and some selected chemical properties. Therefore, temporal changes in enzyme activities should be included as an indicator when evaluating sustainable forest management practices.
Species pools and environmental sorting control different aspects of plant diversity and functional trait composition in recovering grasslands

Succession theory argues that the taxonomic and functional structure of assembling communities is regulated by the interplay of local environmental conditions and regional factors such as available species pools or landscape configurations that moderate dispersal. Yet, the relative importance of these factors and whether they control different aspects of community structure, for example species diversity or the composition of plant traits, is not well understood. This limits predictions of spatial variation in successional outcomes. We explored patterns of species diversity and traits in recovering calcareous grasslands that varied in environmental conditions, age, past and present spatial landscape configuration, as well as in the propagule pressure they receive from historical grasslands that have large and functionally distinct species pools. Mixed‐effects modelling and multimodel inference were used to dissect the leading drivers of species diversity and functional composition. Propagule pressure from the regional species pools of old grasslands during early stages of grassland re‐assembly was an important determinant of community structure, with significant effects not only on species diversity but also on the composition of traits related to resource economics. Such species pool effects exceeded positive influences of environmental heterogeneity on species richness and confounded well‐known diversity–environment and trait–environment relationships. As an orthogonal axis of community assembly, environmental sorting occurred along a gradient of soil texture that discriminated species according to their canopy height and – to a smaller extent – phenology. Additionally, high grassland perimeter–area ratios favoured specialist species richness and increased the proportion of species with predicted poor epizoochorous and wind dispersal. Synthesis. We provide empirical evidence that both species pool effects and local environmental sorting operate during community assembly of recovering calcareous grasslands, but that they influence different aspects of plant community structure. Further, we show that geographic variation in propagule pressure from large and functionally distinct source species pools can confound diversity–environment and trait–environment relationships. Therefore, besides accounting for environmental factors, considering the location of source species pools, as well as their compositional and functional characteristics, is a prerequisite for robust predictions of contingencies in taxonomic and functional community structure of successional habitats.
Persistence in the seed bank: The effects of fungi and invertebrates on seeds of native and exotic plants

Abstract Fungal pathogens and invertebrate seed predators both may limit the establishment of persistent seed banks. Exotic plants may be less subject to attack by these natural enemies than are native species; if so, this may provide exotics with an important advantage by reducing seed mortality and enhancing the persistence of colonizing populations. We investigated this idea with a field experiment in which we used fungicides and screening to protect seeds of 39 native and exotic old field plants. The recovery of germinable seeds was improved by fungicide additions, but not by the exclusion of macroinvertebrates. The effects of fungicide varied among species and sampling dates, but the recovery of natives was not consistently improved more than the recovery of exotics. These results suggest that soil fungi have important impacts on the seed banks of many species, but that exotics are not consistently more resistant than natives to attacks by either fungal pathogens or invertebrates. Consequently, it is unlikely that the majority of invaders benefit from reduced pest loads at the seed bank stage.
BOREAL SWAMP FORESTS : BIODIVERSITY HOTSPOTS IN AN IMPOVERISHED FOREST LANDSCAPE

wamp forests in the boreal part of Sweden are dominated by Norway spruce (Picea abies). These forests typically grow on peat deposits with a water table that is often situated well below the ground surface (Figure 1). At present, only a few small stands of old-growth swamp forests are still found in remote areas because of extensive logging over the past two centuries. The primeval appearance of these forests, the wet conditions, the lack of charred stumps, and the absence of fire scars on trees have led to the
ARE BODY RESERVES IMPORTANT FOR REPRODUCTION IN MALE DARK GREEN SNAKES (COLUBRIDAE: COLUBER VIRIDIFLAVUS)?

Data on 128 adult male dark green snakes (Coluber viridiflavus) were gathered in the wild in western central France. We describe the reproductive cycle of the males, which serves as basis for examining changes in body condition and plasma levels of testosterone. Males emerged from hibernation in late March to early April; indications of mating (obtained on females) were found in May and June, and snakes returned to hibernation in late October-November. Blood samples (n = 69) were taken by cardiac puncture, and plasma testosterone values were measured by radioimmunoassay. There was a peak in plasma testosterone levels before and during the mating season. This suggests that the sexual behavior could depend on plasma testosterone levels. We dissected 49 males, killed accidentally, to investigate the relationship between body condition index (BCI) and the mass of different organs (fat bodies, liver, muscles, skin, testes, and viscera). In males of C. viridiflavus, BCI was an indicator of the mass of the fat bodies and muscles while body length correlated strongly with the mass of the other organs studied. BCI did not correlate with the mass of the liver or with the mass of the viscera or testes. As the BCI is a good estimator of body reserves in wild-caught individuals, we compared means of BCI between months. The mean BCI was very high in April and decreased strongly in May and June (the mating period). This study provides the first empirical results suggesting that in male snakes, most of the body reserves are invested in reproduction.