Miracle-dz/UniFAR-FTUs huggingface dataset:
Life history and eco-evolutionary dynamics in light of the gut microbiota

The recent emergence of powerful genomic tools, such as high-throughput genomics, transcriptomics and metabolomics, combined with the study of gnotobiotic animals, have revealed overwhelming impacts of gut microbiota on the host phenotype. In addition to provide their host with metabolic functions that are not encoded in its own genome, evidence is accumulating that gut symbionts affect host traits previously thought to be solely under host genetic control, such as development and behavior. Metagenomics and metatranscriptomics studies further revealed that gut microbial communities can rapidly respond to changes in host diet or environmental conditions through changes in their structural and functional profiles, thus representing an important source of metabolic flexibility and phenotypic plasticity for the host. Hence, gut microbes appear to be an important factor affecting host ecology and evolution which is, however, not accounted for in life-history theory, or in classic population genetics, ecological and eco-evolutionary models. In this forum, we shed new light on life history and eco-evolutionary dynamics by viewing these processes through the lens of host-microbiota interactions. We follow a three-level approach. First, current knowledge on the role of gut microbiota in host physiology and behavior points out that gut symbionts can be a crucial medium of life history strategies. Second, the particularity of the microbiota is based on its multilayered structure, composed of both a core microbiota, under host genetic and immune control, and a flexible pool of microbes modulated by the environment, which differ in constraints on their maintenance and in their contribution to host adaptation. Finally, gut symbionts can drive the ecological and evolutionary dynamics of their host through effects on individual, population, community and ecosystem levels. In conclusion, we highlight some future perspectives for integrative studies to test hypotheses on life history and eco-evolutionary dynamics in light of the gut microbiota. This article is protected by copyright. All rights reserved.
Inflammation du tissu adipeux au cours de l'obésité humaine : implication des lymphocytes Th17

Une serie d’etudes recentes chez l’homme et dans les modeles murins a conduit a la mise en evidence d’une reponse immune, qui met en jeu des cellules de l’immunite innee et de l’immunite adaptative dans le tissu adipeux (TA) obese. Nous avons mis en evidence un dialogue pro-inflammatoire entre les macrophages et les LT CD4+ dans le TA humain obese mettant en jeu l’IL-1β, l’IL-17 et l’IL-22. Le pourcentage de Th17 est positivement correle au % d’HbA1c. De plus, la secretion des cytokines impliquees dans cette boucle pro-inflammatoire diminuent apres une perte de poids induite par la chirurgie bariatrique. Par la suite, nous avons montre que l’IL-1β et l’IL-17 induisent des programmes transcriptionnels pro-inflammatoires concordant dans trois types de cellules non-immunitaires du TA, les pre-adipocytes, les cellules endotheliales et les adipocytes, et diminuent les genes du metabolisme dans les adipocytes. Les effets d’IL-1β sont nettement plus prononces que ceux de l’IL-17. Le milieu conditionne de cellules immunitaires CD45+ reproduit les reponses pro-inflammatoire et catabolique induites par les cytokines recombinantes dans les adipocytes, et ces reponses sont inhibees apres la neutralisation de l’IL-17 et l’IL-1β. Ces resultats demontrent une implication pathologique de l'IL-1β et de l'IL-17 dans les alterations du TA induites par l'obesite.
Systématique évolutive et biogéographie de Angraecum (Orchidaceae, Angraecinae) à Madagascar

Madagascar is one of the 34 World biodiversity hotspots. Islands like Madagascar are often used to study diversification processes because of their high endemism and isolation. Angraecum is the largest genus of subtribe Angraecinae (Orchidaceae) with about 221 species. Madagascar is the center of the diversity for the genus with ca. 142 species, of which 90% are endemic. The great morphological diversity associated with species diversification in the genus on the island of Madagascar offers valuable insights for macroevolutionary studies. Phylogenies of the Angraecinae have been published but lack of sampling and the limited taxonomic resolution limit their uses for macroevolutionary studies. We present a new phylogeny of Angraecum based on chloroplast sequence data (matk, rps16, trnL), nuclear ribosomal (ITS2) and 39 morphological characters from 194 Angraecinae specimens of which 69 were newly collected, including 98 Angraecum species and five outgroups from subtribes Aeridinae and Polystachyinae. Using this phylogeny, we evaluated the monophyly of the sections of Angraecum as defined by Garay and investigated the patterns of species diversification within the genus. We used maximum parsimony and bayesian analyses to generate phylogenetic trees and dated divergence times of the phylogeny. We analyzed diversification patterns within Angraecinae and Angraecum with an emphasis on four floral traits (flower color, flower size, labellum position, spur length) using macroevolutionary models to evaluate which traits or character states are associated to speciation rates, and inferred ancestral states of these characters. The phylogenetic analysis showed the polyphyly of Angraecum sensu lato and of all Angraecum sections except sect. Hadrangis, and that morphology is consistent with the phylogeny. The uppermost and lowermost position of the labellum was the main character helping to delimit clades within a monophyletic Angraecum sensu stricto. This character appeared also to be associated with speciation rates in
Temporal trophic shifts and feeding diversity in two sympatric, neotropical, omnivorous fishes : Astyanax bimaculatus and Pimelodus maculatus in Rio Tibagi (Paraná, Southern Brazil)

In this study, we explored whether the two dominant, morphologically divergent, omnivores, Astyanax bimaculatus (Characidae) and Pimelodus maculatus (Pimelodidae) in the high diversity (>100 species) fish assemblage of the Neotropical Rio Tibagi (southern Brazil) exhibited full overlap in the use of feeding resources similar to those reported for closely related species in Rio Amazonas. Monthly feeding patterns were assessed in two years of contrasting hydrological conditions and were compared with those reported for other, allopatric populations within their distributional range. Astyanax and Pimelodus fed at all trophic levels and exhibited an acute ability to shift prey as a response to environmental variations or food shortage. Although aquatic and terrestrial insects and seeds of native and introduced plants were the major food items, spatial separation across the water column and ecomorphological constrains seem to prevent a simultaneous use of the same food items by the two species. Except when cultivated seeds (i.e. maize) were most abundant after harvest, overlap in the use of feeding resources was negligible, if any. We suggest that the assessment of trophic relationships in Neotropical fish assemblages require more detailed studies than those actually available.
Growth patterns of three bivalve species targeted by the Ocean Cockle Fishery, southern New South Wales: Eucrassatella kingicola (Lamarck, 1805); Glycymeris grayana (Dunker, 1857); and Callista (Notocallista) kingii (Gray, 1827)

ABSTRACT The Ocean Cockle Fishery is a small fishery in southern New South Wales targeting three bivalve species: Eucrassatella kingicola; Glycymeris grayana; and Callista (Notocallista) kingii. The fishery currently consists of a single licensed fisher harvesting a defined patch of seabed but has been identified as potentially able to support expansion. All target species have unknown population dynamics and life histories, and the degree to which expansion can be supported is therefore also unknown. We used internal growth marks in cross sections of shell to determine ages from the commercial catch. The assumption that the alternating bands represent seasonal variations in growth rate was validated by laser ablation induction-coupled plasma mass spectrometry (LA-ICPMS), a small tag-recapture program and preliminary marginal increment analysis. Mean length-at-age was modelled using the von Bertalanffy growth equation. Callista kingii (L∞ = 43.8, K = 0.43) grew substantially faster to a smaller maximum size than E. kingicola (L∞ = 70.0, K = 0.18) and G. grayana (L∞ = 54.3, K = 0.20). These growth characteristics may explain anecdotal observations that C. kingii has increased in relative abundance in recent catches and is relatively rare in unfished areas while E. kingicola in particular has declined in mean size and abundance.
Fine-scale Structure Design for 3D Printing

Modern additive fabrication technologies can manufacture shapes whose geometric complexities far exceed what existing computational design tools can analyze or optimize. At the same time, falling costs have placed these fabrication technologies within the average consumer’s reach. Especially for inexpert designers, new software tools are needed to take full advantage of 3D printing technology. This thesis develops such tools and demonstrates the exciting possibilities enabled by fine-tuning objects at the small scales achievable by 3D printing. The thesis applies two high-level ideas to invent these tools: two-scale design and worst-case analysis. The two-scale design approach addresses the problem that accurately simulating—let alone optimizing—the full-resolution geometry sent to the printer requires orders of magnitude more computational power than currently available. However, we can decompose the design problem into a small-scale problem (designing tileable structures achieving a particular deformation behavior) and a macro-scale problem (deciding where to place these structures in the larger object). This separation is particularly effective, since structures for every useful behavior can be designed once, stored in a database, then reused for many different macroscale problems. Worst-case analysis refers to determining how likely an object is to fracture by studying the worst possible scenario: the forces most efficiently breaking it. This analysis is needed when the designer has insufficient knowledge or experience to predict what forces an object will undergo, or when the design is intended for use in many different scenarios unknown a priori. The thesis begins by summarizing the physics and mathematics necessary to rigorously approach these design and analysis problems. Specifically, the second chapter introduces linear elasticity and periodic homogenization.
Breeding Trials during the Planktonic and Benthic Stages of Sea Cucumbers (Holothuria nobilis and H. scabra)

We obtained 3,521,600 and 1,760,000 fertilized eggs of Holothuria nobilis and H. scabra, respectively, bred them by the density of 0.08-0.50 individual/ml, and observed the growth of fertilized eggs, larvae, and juveniles. We distinguished the planktonic stages breeding, of which the doliolaria stage and later stages accounted for 50% of all stages, from the benthic stage breeding after that. We fed Cheatoceros gracilis during the planktonic stages breeding, and benthic diatom cultures during benthic stage breeding. The planktonic periods of H. nobilis and H. scabra were 44-51 days and 18-25 days, respectively. We acquired 10,392 juveniles (about 20 mm) of H. nobilis and 7,118 juveniles (about 20 mm) of H. scabra after 92-187 days of juvenile breeding.
Risk to genetic effective population size should be an important consideration in fish stock-enhancement programs

Conservation of single-locus and quantitative genetic variation in managed populations requires maintenance of sufficiently large (genetic) effective population sizes, but the reductive effect exerted by large-scale fish-stocking programs on the effective sizes of natural populations has been largely ignored in conventional stocking guidelines. Using a model described by Ryman and Laikre (1991), we evaluate the effects of stocking on the effective sizes of fish populations and the accompanying genetic risks. We examine the parameters of the model as they relate specifically to the supplementation of fish populations. Then employing the model we present case studies of two species, red drum (Sciaenops ocellatus) and Gulf sturgeon (Acipenser oxyrinchus desotoi), which differ greatly in biology and demography and are both currently subjects of proposed or ongoing aquaculture programs designed for supplementation of wild stocks. The red drum is a pelagic, marine species comprising few, extremely large, randomly mating populations. Under typical stocking conditions, the red drum population we examined is unlikely to experience significant loss of single-locus or quantitative (polygenic) variability. The diadromous Gulf sturgeon (a threatened species) is divided into several discrete populations, each of very limited abundance. The stocking program proposed for Gulf sturgeon could reduce their effective population sizes well below suggested threshold values; this reduction could result in the rapid loss of rare alleles and in other drift-associated alterations in frequencies of selectively neutral alleles, as well as in greatly reduced polygenic variability. These case studies illustrate the need to weigh the long-term risks to genetic variation, both single-locus and quantitative, in natural fish populations against the immediate benefits of artificially increasing their abundance.
A MONOGRAPH OF THE GENUS ROSA IN

The study of Rosa setigera Michx. (a diploid species in the section Synstylae) is discussed under the disciplines of gross- and micro-morphology, phy- togeography, ecology (transplant experiments), cytology, and taxonomy. Walter (1788) added to his description of R. carolina L. 1762 (= R. palustris Marsh.): "varietates, calycis laciniis brevibus integris; et longis laciniatis. " This is a clear reference to R. setigera as named and described by Michaux (1803) from material collected in lower Caro- lina and Georgia. Several striking characters in his description include stems with paired prickles, glabrous leaves, each 3 to 5 foliolate, and leaflet veins, petioles and sepals, hispid. Michaux also cited a variety of R. setigera with taller stems and scattered prickles having leaflets pubescent near the veins below and sepals with fewer bristles. Persoon (1806) called this variation with "leaflets pubescent toward the veins" var. elatior. Aiton f. (1811) described R. rubifolia based upon a form with pubescent leaflets which had been introduced into the gardens of England. Lindley (1820) felt he could distinguish between R. seti- gera Michx. and R. rubifolia Ait. f. apart from the presence or absence of pubescence on the leaflets and established R. rubifolia var. fenes- tralis as a glabrous leafed form of R. rubifolia. This variety is synony- mous with the typical IR. setigera. In 1820, Refinesque duplicated the work of Persoon (1806) and described R. setigera var. pubescens, a form with pubescent leaflet veins, but otherwise glabrous. He further described three species, R. kentukensis, R. cursor, and R. trifoliata, the former two descriptions approaching R. rubifolia while R. trifoliata is R. setigera. The division of this complex at the specific level into individuals with leaflets glabrous below or with leaflet veins pubescent (R. seti- gera) and into individuals with leaflets puberulent, pubescent, or to- 1 All techniques and methods used in this study are similar to those described for the monographic treatment of Rosa acicularis Lindl. (Lewis 1959b).
ANTIBACTERIAL INVESTIGATED OF PHOSPHOLIPASE A2FROM THE SPINES VENOM OF CROWN OF THORNS STARFISH ACANTHASTER PLANCI

Phospholipase A2 isolated from venoms is a potential new antibacterial source. Antibacterial activity tests of phospholipase A2 were performed against Staphylococcus aureus and Bacillus subtilis. Phospholipase A2 which was isolated from spines venom of Acanthaster planci by using fractionated 20% saturated ammonium sulfate precipitation and its antibacterial assay was done by using disc diffusion method whereas 40 µl isolate at a concentration of 6.29 µg/µl was applied onto 7 mm paper disc. The assay exhibited inhibition zone around the phospholipase A2disc against Staphylococcus aureus while no inhibition zone against Bacillus subtilis. As a result, phospholipase A2 posses an antibacterial activity against Staphylococcus aureus. KEYWORD: Phospholipase A2, venom, Acanthaster planci, antibacterial activity
Plant and insect microbial symbionts alter the outcome of plant–herbivore–parasitoid interactions: implications for invaded, agricultural and natural systems

Understanding how soil microbial communities influence plant interactions with other organisms, and how this varies with characteristics of the interacting organisms, is important for multiple systems. Solanum spp. are a suitable model for trophic interactions in studies of agricultural and natural systems and can also provide useful corollaries in invaded systems. This study examined the influence of soil mutualist arbuscular mycorrhizal (AM) fungi on growth of different Solanum types fed on by the potato aphid, Macrosiphum euphorbiae, in relation to the presence of the aphid facultative endosymbiont Hamiltonella defensa. Four Solanum types comprising two wild species, S. berthaultii and S. polyadenum, and two accessions of S. tuberosum, were grown with or without AM fungi and infested with one of four clonal lines of a single M. euphorbiae genotype (two with and two without H. defensa). Two experiments were conducted to (i) characterize plant responses to AM fungi and aphids and (ii) assess whether soil AM fungi could influence the success of the parasitoid wasp Aphidius ervi when attacking aphids reared on each Solanum type. In both experiments, similar patterns of plant biomass were observed in relation to AM fungal and aphid treatments. Solanum biomass depended on plant type and aphid infection with H. defensa. Plants exposed to aphids harbouring H. defensa had smaller root biomass, and therefore total plant biomass, compared to plants infested with H. defensa‐free aphids. M. euphorbiae performance varied with aphid clonal line, Solanum type and the presence of AM fungi. Parasitoid success, measured as the proportion of aphids from which a wasp emerged, was highest from aphids that had fed on plants colonized by AM fungi, although this result also varied with Solanum type and aphid clonal line. Synthesis. The presence of soil AM fungi, combined with within‐species plant and insect variation in key traits, can have subtle – but significant – effects on plant fitness and insect success. This study highlights the importance of exploring genotypic variation in plant and pest responses to soil microbiota to identify suitable biocontrol options.
Gender in European forest ownership and management: reflections on women as “New forest owners”

ABSTRACT The group of female forest owners is growing across Europe and currently estimated to be about 30% of all private owners. This new category of forest owner merits a closer look. By introducing a gender perspective across three different research frameworks, this paper substantiates that gender matters in forest ownership, management, operations, and the understandings of these three aspects. Where gender-disaggregated data is available, and gender is assessed as an empirical variable, we find the differences in numbers between male and female forest owners in most countries. By adding the concept of gender as a relational and structuralizing category, we demonstrate that gender structures affect, for example, actual behavior of female and male forest owners and the self-evaluation of forestry competence. Further, when considering gender as a meaning category we explore how meaning produces behavior and behavior produces meanings, and how both shape institutions and natural and artificial matter. Here forestry competence is the applied example. To further increase the knowledge on new forest owners, we recommend (i) fellow researchers in the field to assume that gender matters and design their empirical studies accordingly and (ii) policy-makers to guarantee access to gender-disaggregated data in official registers and statistics.
Effects of Early Spring Burning on Yields of Native Vegetation.

LOBB, W. R. AND R. L. BENNETTS. 1957. Improvement of tussock grassland in Canterbury. New Zeal. Jour. Agr. 96: 537-549. MARTIN, W. E. 1958. Sulfur deficiency widespread. Calif. Agric. 12 (11) : 10-12. MCKELL, C. M. AND A. M. WILSON. 1963. Effects of temperature on S35 uptake and translocation by rose and subterranean clovers. Agron. Jour. 55: 134-137. MCKELL, C. M. AND W. A. WILLIAMS. 1960. A lysimeter study of sulfur fertilization of an annual-range soil. Jour. Range Mangt. 13: 113117. STARKEY, R. L. 1950. Relations of microorganisms to transformations
Spatial and temporal variations in soil respiration hot spots in a lowland tropical rain forest, Peninsular Malaysia

Many studies have reported the presence of soil respiration hot spots, which are areas of extremely high soil respiration, but little is known about their causes. Because previous studies implied that they were caused by macrofauna, we conducted a field survey in a Malaysian lowland rainforest to examine whether increased soil respiration was induced by the activities of macrofauna such as termites, ants and earthworms. Soil respiration was measured in a grid system of 10 m intervals in a 1 ha plot. We measured soil respiration again three or four days after the first measurement to examine the spatiotemporal change in hot spots. After the second measurement, we excavated soil to a depth of 20 cm at the five points showing the highest soil respiration rates (hot spots) and their neighboring points as controls and visually searched for macrofauna. The average soil respiration for two measurements did not differ significantly (8.21 and 7.93 μmol CO2 m s, respectively). Four hot spots were revealed in each of the two measurements, but only one appeared in both measurements. Several ants (100-500 individuals, Lophomyrmex sp.) were observed in soil under soil respiration chamber areas at one hot spot and one control point, respectively. This suggests that the hot spots in the study site were not located near active nests or intensively active areas of macrofauna, and it is possible that the hot spots may represent the points of mass CO2flux transport events.
REGULATION OF GEOTROPISM, GROWTH, AND ETHYLENE PRODUCTION BY INHIBITORS OF AUXIN

The inhibitors of auxin transport-NPA (N-1-naphthylphthalamic acid), DPX1840 (3,3a-dihydro -2- (p-methoxyphenyl)-8H-pyrazolo[5, 1-a]isoindol-8-one), and TIBA (2,3,5-triiodobenzoic acid)-inhibited geotropism in roots of intact Pisum sativum L. seedlings. NPA and DPX1840 also caused cellular swelling in the roots. The swelling was due to a greater inhibition of elongation than increase in weight and looked identical to the one caused by ethylene. However, ethylene did not act as an intermediate in the action of auxin transport inhibitors because all three failed to stimulate ethylene production and some of their growthinhibiting effect was retained in the presence of saturating levels of ethylene. In the presence of 10 jLM indoleacetic
Brevipalpus oncidii, a new record for Australia, is not a vector of Orchid fleck virus

ABSTRACT Brevipalpus oncidii Baker was detected for the first time in Australia naturally present as a pest on Brassia verrucosa Bateman ex Lindl. orchids. Although the majority of Brevipalpus species are believed to be predominantly thelytokous, males in the population described in this study were observed to be sexually functional. In repeated transmission studies, this B. oncidii population failed to successfully acquire an isolate of Orchid fleck virus (OFV) and transmit to cymbidium hosts. Mites fed on OFV-infected cymbidium leaves initially tested positive for OFV, but this was lost within 48 hours in absence of the OFV host suggesting failure to internalize the virus within the mite. http://www.zoobank.org/urn:lsid:zoobank.org:pub:1A8E42C2-9A9E-4066-94DC-E9E9683D8C68