Miracle-dz/UniFAR-FTUs huggingface dataset:
Cellular Interactions During Motor Nerve Regeneration

Vertebrate peripheral nerves can regenerate, enabling severed axons to reconnect with their original synaptic targets. The interactions between injured nerves with cells in their environment, as well as the functional significance of these interactions, have not been determined in vivo and in real time. Here we provide the first minute-by-minute account of cellular interactions between laser transected motor nerves, macrophages, and Schwann cells in live intact zebrafish using transgenic lines that label each cell type in vivo. We find that axon fragmentation triggers macrophage invasion into the nerve to engulf axonal debris, and that delaying nerve fragmentation in a Wlds model does not alter macrophage recruitment but induces a previously unknown `nerve scanning' behavior, suggesting that macrophage recruitment and subsequent nerve invasion are controlled by separate mechanisms, both independent of Schwann cells. A major challenge for regenerating peripheral axons is to identify their original trajectory; Schwann cells are known to provide regenerating axons with factors that stimulate outgrowth, and an adhesive substrate that axons preferentially extend along during regeneration, yet their role in guiding regenerating axons onto their original trajectory is less clear. We show in mutants lacking Schwann cells that axonal growth cones sprout and extend at rates comparable to wild type, but fail to identify their original path, and instead extend along aberrant trajectories. To determine whether Schwann cells function primarily as an adhesive substrate we tested whether a Schwann cell-less axonal scaffold is sufficient to direct axonal growth. These substrates failed to compensate for the absence of Schwann cells, providing evidence that Schwann cells direct regenerating axons towards their original trajectory. To identify signals that guide regenerating motor axons in vivo, we examined mutants lacking the guidance receptor DCC. We find that in DCC mutants a significant fraction of regenerating axons extend along aberrant trajectories. Collectively, this work details the dynamic activities of macrophages and Schwann cells during axon degeneration and early regeneration, while axons are regrowing and selecting their trajectory, and we propose that Schwann cells and DCC mediated guidance are critical early during regeneration, enabling growth cones to navigate towards their original axonal trajectories. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Michael Granato
Assessing the Natura 2000 network with a common breeding birds survey

Natura 2000 (N2000) is a network of European sites focused on the conservation of specific species and habitats. Despite the known importance of common biodiversity in ecosystem functioning, common species are currently not explicitly targeted by conservation initiatives in France. In this study, we investigated whether the N2000 network contributes to the protection of common breeding bird species. In particular, we focused on species abundance and species specialization, community specialization and community trophic levels. We also determined the effects of N2000 on temporal trends of specialist and generalist bird groups. We studied 100 species in 1461 plots monitored by the French Breeding Bird Survey (BBS) between 2001 and 2010. We found that species abundance increased for 54 species with the proportion of the plot covered by N2000 areas in the plot. The bird species with the abundances that were most influenced by proportion of the plot covered by N2000 areas were predominantly habitat specialists. Bird communities inside N2000 sites were more specialized and exhibited higher trophic indices than communities outside N2000 sites. We found no differences in the temporal trends of farmland and woodland birds inside and outside N2000 sites, but the temporal trend of generalist species was positive outside N2000 sites and stable inside. We concluded that N2000 sites showed greater abundance of a majority of common bird species but that the network was established too recently to assess its influence on population trends. The French BBS has proved to be an efficient tool in assessing protected area networks.
Physiological effects of TGFα‐PE40 expression in recombinant Escherichia coli JM109

Physiological effects of isopropyl‐thiogalactopyranoside (IPTG) induction were examined in Escherichia coli strain JM109 expressing a fusion protein composed of transforming growth factor alpha and a 40‐kD portion of Pseudomonas aeruginosa exotoxin A (TGFα‐PE40) under control of the tac promoter. Fermentations at the 15‐L scale in complex medium compared growth and metabolite profiles of the untransformed JM109 host strain, the strain transformed with the vector lacking the TGFα‐PE40 open reading frame (JM109[pKK2.7]), and the strain with the complete plasmid for TGFα‐PE40 expression (JM109[pTAC‐TGF57‐PE40]). Metabolite and growth profiles of JM109 (pTAC‐TGF57‐PE40) cultures changed significantly in IPTG‐induced versus uninduced cultures. Prior to induction, glucose was metabolized to acetate or completely oxidized to CO2. Following induction, pyruvate was also excreted in addition to acetate. In the absence of inducer, pyruvate was excreted by JM109 (pTAC‐TGF57‐PE40) only when dissolved oxygen levels fell to less than 10% of saturation (microaerobic rather than anaerobic conditions). The untransformed JM109 host strain or JM109 (pKK2.7) did not excrete pyruvate in the presence or absence of inducer, although JM109 (pKK2.7) exhibited a pattern of growth following addition of IPTG that closely resembled JM109 (pTAC‐TFG57‐PE40). Fermentations of JM109 (pTAC‐TFG57‐PE40) in a synthetic medium supported lower expression levels, but resulted in similar alterations in metabolite profiles. Induction in synthetic medium resulted in pyruvate excretion without further acetate accumulation. Taken together, these data suggest that one consequence of TGFα‐PE40 expression in JM109 is altered patterns of pyruvate oxidation. © 1992 John Wiley & Sons, Inc.
The Activin A‐Dependent Proliferation of PCC3/A/1 Embryonal Carcinoma Cells in Serum‐Free Medium

Examination of the growth requirements of murine embryonal carcinoma cells (EC cells) or embryonic stem cells (ES cells) in serum‐free medium revealed that PCC3 EC cells required activin A to grow and/or survive in such medium. In the absence of activin A, PCC3 cells began to disintegrate within 3 days under any serum‐free conditions examined. P19 and AT805 EC cells grew even in serum‐free medium without activin A but their growth rates were slightly facilitated by its addition. F9 EC cells also grew in the medium without activin A and its addition somewhat inhibited their growth rate. Three independently isolated ES cell lines and feeder‐dependent PSA‐1 EC cells also grew in serum‐free medium without activin A if leukemia inhibitory factor (LIF) was supplemented. The addition of activin A had little effect on their growth rates. These findings suggest that PCC3 EC cells are a sort of nutritional mutant requiring activin A, thus making them useful in stidies on the growth regulatory mechanisms of EC/ES cells and/or the action of activin on EC/ES cells.
Phenotypic evidence suggests a possible major-gene element to weevil resistance in Sitka spruce

The weevil resistance breeding program against the white pine weevil, Pissodes strobi Peck (Coleoptera: Curculionidae), particularly for Sitka spruce (Picea sitchensis (Bong.) Carr), is arguably one of the most successful pest resistance breeding programs for plantation forest species, and it has done a lot to rehabilitate this important western conifer. Nearly all planting stock currently comes from this breeding program and so far the resistance seems effective, durable, and stable. We have used this program to also study causes behind this resistance, including: various hindrance mechanisms including induced and constitutive resin cells, sclereid or stone cells, and terpene defenses. All of them appear factors in resistance, but none singly is strongly predictive to resistance - the strongest are sclereid cells. All of these factors are in their nature complex, multifaceted, and appear to offer some partial solution that is likely controlled by complex multigenic systems. We do note, however, that we have very strongly expressed and complete resistance in some individuals. This and some preliminary data investigation indicates that there may also be a major gene element in our observed resistance. Such elements are well described against rusts and other pathogens in forestry, but are also well described for insects and nematodes in crop breeding. Particularly interesting is the Hessian fly in wheat which has a similar life strategy to the weevil. We describe here the elements that suggest this conjecture and how we might go about proving this. Understanding the genetic elements behind this observed resistance has implications for the overall strength and durability to resistance against the white pine weevil.
Gametogenesis in Haematococcus pluvialis Flotow (Volvocales, Chlorophyta)

Abstract An effective method of inducing gametogenesis in Haematococcus pluvialis Flotow (Volvocales, Chlorophyta) is described. Cultures starved for at least one month and then supplied with fresh medium produced gametes the following day. Isolated gametocysts initiated subcultures without syngamy, suggesting parthenogenetic development. The gametes are illustrated by light and electron micrographs.
The Effects of Negative- and Positive- Charged Surfactants on In vitro DM Digestibility and the Growth of Ruminal Mixed Microorganisms

In order to investigate the effects of supplemental ionic surfactants in in vitro ruminal fermentation, N-Lauroylsarcosine sodium salt(N-LSS) and sodium dodecyl sulfate(SDS) for negative(－) ionic surfactant, and hexadecylpyridinium chloride monohydrate(HPCM) and hexadecyltrimethyl ammonium bromide(HTAB) for positive (+) ionic surfactant were supplemented by 0.05% and 0.1% into the Dehority’s artificial medium containing rice straw(1mm) as a substrate. In vitro DM digestibility, the growth of rumen mixed microbes, pH, cumulative gas production and SEM(Scanning Electron Microscopy) observation of microbial attachment on rice straw particle were investigated through the experiment composing 9 treatments (two supplemental levels of two positive ionic(+) surfactant, two supplemental levels of two negative(－) ionic surfactant) including the control. The sample collection was at 6, 12, 24, 48 and 72 h post fermentation with 3 replications per treatments. DM digestibility in treatments supplemented (+) or (－) surfactants almost stopped afterward 12 h fermentation, in vitro DM digestibility at 72 h post fermentation in the ionic surfactants was at half level of that of the control(P
Genetic Similarity Amongst Phenotypically Diverse Little Free-Tailed Bats, Chaerephon pumilus

The African molossid Chaerephon pumilus shows extensive variation in colour, size and echolocation across its wide distributional range with a light-winged form in north-eastern Africa and a dark form in southern Africa. There is also much variation in supposedly diagnostic characters (e.g., degree of palatial emargination) amongst the dark form of this species in southern Africa. These differences suggest that there may be cryptic species within C. pumilus. We used phylogenetic and phenetic analyses of sequence data from the mitochondrial cytochrome-b gene of a number of C. pumilus individuals to investigate the status of the light and dark-winged forms of this species and to evaluate the possibility of cryptic species within the dark-winged form of C. pumilus in southern Africa. We evaluated species status by comparing the level of sequence divergence amongst C. pumilus with the level of sequence divergence between known species in the genus. These included C. ansorgei, C. chapini, C. nigeriae and C. jobensis. Intrageneric sequence divergences among the Chaerephon spp. included here ranged from 6.51 to 11.18%, whereas the average sequence divergence between the light and dark forms was 0.9%. This suggests that these two forms are not distinct species. Individuals of the dark form of C. pumilus were genetically indistinguishable from each other having the same cytochrome b haplotype. We thus found no evidence of cryptic species in southern African C. pumilus.
MYCORRHIZAL FUNGI ASSOCIATED WITH THREE SPECIES OF TURFGRASS

Small plots of highly maintained turfs of creeping bentgrass (Agrostis palustris cv. Penncross) and velvet bentgrass (Agrostis canina cv. Kingstown) and a marginally maintained stand of annual bluegrass (Poa annua) were sampled intensively over a 15-month period to measure the populations of spores of arbuscular mycorrhizal fungi (AMF) associated with their root systems. Direct isolation of spores and trap cultures were used to assess the AMF communities. Spores of more than 18 species of AMF were isolated. The six dominant species (as measured by the abundance and frequency of occurrence of spores) were Acaulospora mellea, an undescribed species of Acaulospora, Scutellospora calospora, Glomus occultum, Glomus etunicatum, and Entrophospora infrequens. Spores of 17 species of AMF were recovered from the root zones of velvet bentgrass, 15 species from creeping bentgrass, and 14 from annual bluegrass. Soil fertility differed among the three sites, and it was not possible to ascribe differences in the AMF com.
Dispersal, evolution and range dynamics – a synthesis

A. Kubisch (alexander.kubisch@univ-montp2.fr), Inst. des Sciences de l’Evolution (UMR 5554), Univ. Montpellier II, CNRS, Place Eug e ne Bataillon, FR-34095 Montpellier cedex 5, France. – E. A. Fronhofer, Dept of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and TechnologUeber, y landstr133, CH-8600 Duebendorwitzf, S land. er
Fungi and Algae Co-Occur in Snow: An Issue of Shared Habitat or Algal Facilitation of Heterotrophs?

Abstract Late season alpine snows are often colonized by psychrophilic snow algae that may provide a source of nutrients for microbes. Such late season snows are a harsh environment, but support a diverse and complex fungal community. We used culture independent methods (Illumina MiSeq) to test if the presence of snow algae influences fungal communities. We compared algae-colonized snows to adjacent (3 m distant) noncolonized snows in a paired experimental design. Our data indicate that several fungi are locally enriched in algae colonized snows. Although many such fungi were basidiomycetous yeasts, our analyses identified a large number of snow-borne members of phylum Chytridiomycota. While the ecology and function of these Chytridiomycetes remain unclear, we hypothesize that their enrichment in the algal patches suggests that they depend on algae for nutrition. We propose that these chytrids are important components in snow ecosystems, highlighting the underestimation of their diversity and importance. Taken together, our data strongly indicate that fungal communities are heterogeneous in snow even among adjacent samples. Further, fungal and algal communities may be influenced by similar environmental drivers resulting in their co-occurrence in snow.
Complementary use of motion-activated cameras and unbaited wire snares for DNA sampling reveals diel and seasonal activity patterns of brown bears (Ursus arctos) foraging on adult sockeye salmon (Oncorhynchus nerka)

The seasonal and diel movements of predators to take advantage of shifts in prey availability are fundamental elements of their foraging ecology, and also have consequences for the prey populations. In this study, we used complementary noninvasive techniques (motion-activated cameras and hair snares) to investigate seasonal and diel activity of brown bears (Ursus arctos L., 1758) along six proximate streams supporting spawning populations of sockeye salmon (Oncorhynchus nerka (Walbaum in Artedi, 1792)) in southwestern Alaska. Camera records over 3 years showed a rapid increase in bear activity around the time salmon arrived in the streams, with differences among streams corresponding to differences in salmon phenology. Bears were active throughout the day and night, but there were clear crepuscular peaks when camera data were pooled. When wire snares (to collect hair samples) were paired with cameras, the data showed similar seasonal patterns, but each technique detected bears missed by the other. Roughly.
Referenzwerte blutchemischer Parameter bei Meerschweinchen bestimmt mit dem Vettest® 8008

Zusammenfassung Gegenstand: Die Studie präsentiert Referenzbereiche für ein praxisübliches Trockenchemiegerät (Vettest® 8008), die bei als Heimtiere gehaltenen Meerschweinchen ermittelt wurden. Material und Methoden: Bei den Probanden handelte es sich um 58 klinisch gesunde Meerschweinchen im Alter zwischen 8 Wochen und 5 Jahren (24 männlich, 34 weiblich). Die Plasmaproben wurden routinemäßig für die Untersuchung im Vettest® 8008 aufgearbeitet und auf 20 Parameter (s. u.) untersucht. Zur Ermittlung der Referenzwerte wurden mittels SPSS Statistics 17.0 (IBM®) die 2,5%- und 97,5%-Perzentile bestimmt. Ergebnisse: Folgende Referenzwerte wurden ermittelt: 1) Enzyme: alkalische Phosphatase: 50,80–328,10 U/l; Alaninaminotransferase: 41,45 bis 165,35 U/l; Amylase: 726,93–1831,55 U/l; Aspartataminotransferase: 25,25–349,23 U/l; Kreatinkinase: 66,13–1255,40 U/l, γ-Glutamyl- Transferase: 0,45–90,75 U/l; Laktatdehydrogenase: 5,61–1503,00 U/l, Lipase: keine messbare Aktivität. 2) Substrate: Albumin: 17,45 bis 31,65 g/l; Ammoniak: 4,80–225,30 mmol/l; Cholesterin: 0,0 bis 2,06 mmol/l; Kreatinin: 23,90–73,45 μmol/l; Gesamtbilirubin: 2,00 bis 17,60 μmol/l; Gesamteiweiß: 50,00–70,85 g/l; Glukose: 4,62 bis 19,55 mmol/l; Harnstoff-Stickstoff: 2,04–11,28 mmol/l; Triglyzeride: 0,46–4,23 mmol/l. Die Globuline wurden vom Gerät rechnerisch ermittelt: 30,43–42,00 g/l. 3) Elektrolyte: anorganisches Phosphat: 0,72 bis 2,12 mmol/l, Kalzium: 2,58–3,16 mmol/l; Magnesium: 0,72 bis 1,60 mmol/l. Schlussfolgerungen: Der Vergleich mit Angaben aus der Literatur zeigt Abweichungen der Studien untereinander und von der vorliegenden Arbeit. Daraus ist die Schlussfolgerung zu ziehen, dass Referenzwerte unterschiedlicher Untersuchungsverfahren nicht unkritisch für das tierärztliche Sofortlabor übernommen werden können und zur Interpretation von Blutbefunden eigene Referenzwerte für die einzelnen Gerätetypen notwendig sind. Mögliche Ursachen für die Abweichungen könnten in unentdeckten subklinischen Erkrankungen sowie chemischer oder statistischer Methodik liegen.
A xyloglucan-induced increase in lettuce germination and seedling elongation is not related to the degradation of the exogenous xyloglucan

Xyloglucans are the main hemicellulosic polysaccharides found in the primary cell walls of dicots and nongraminaceous monocots. Although xyloglucans are building blocks used in plant cell wall assembly, the function of these molecules in the structure and growth of the primary cell wall remains poorly understood. In this study, we demonstrate that treatment of lettuce seeds with a xyloglucan extracted from cotyledons of Hymenaea courbaril L. (Leguminosae (Fabaceae) – Caesalpinioideae) in the 0.1 to 10 nmol·L−1 range resulted in significantly increased germination percentage. In addition, lettuce seedlings grown in the presence of 500 nmol·L−1 xyloglucan presented a significantly larger length compared with seedlings grown in the absence of xyloglucan. Furthermore, the H. courbaril xyloglucan was not able to reverse a 2,4-dichlorophenoxy acetic acid induced inhibition of seedling elongation. High performance size exclusion chromatography (HPSEC) and high-performance liquid chromatography (HPLC) analyses in.
Mitochondrial phylogeography and cryptic divergence in the stickleback genus Pungitius

Stickleback fish exhibit considerable morphological variation within and between species, and similar armour phenotypes are often found in different taxonomic groups. Although several Pungitius species and subspecies have been recognized, their evolutionary history and relationships remain poorly known. We investigated the phylogenetic relationships and phenotypic divergence in this genus with a particular focus on P. pungitius and P. laevis.
Ontogeny of Asymmetry and Compensational Growth in Elm Ulmus glabra Leaves under Different Environmental Conditions

Levels of fluctuating asymmetry (random variation in size among sides) may be partly determined by compensational growth, and the efficiency of such compensation may be affected by stress. Here we provide the first test of this hypothesis by studying the effect of saline stress on the ontogeny of size and symmetry of leaf width in broad‐leaved elms Ulmus glabra. Leaves that developed on saline‐treated trees became more asymmetric with time but not significantly smaller than leaves on control trees. This saline effect resulted from an increase in the variance in ontogenetic trajectories. Serial autocorrelation in asymmetry between subsequent days was significantly more negative (i.e., indicating stronger compensational growth) in control than in saline‐treated trees. Leaves from saline‐treated trees took longer to develop than leaves on control trees. These findings indicate that ontogeny is disrupted by saline treatment, preventing or reducing compensational growth to constrain leaf asymmetry within the same boundary as in control trees.
Diversity and Distribution of Floral Resources Influence the Restoration of Plant–Pollinator Networks on a Reclaimed Strip Mine

Plant–pollinator mutualisms are one of the several functional relationships that must be reinstated to ensure the long‐term success of habitat restoration projects. These mutualisms are unlikely to reinstate themselves until all of the resource requirements of pollinators have been met. By meeting these requirements, projects can improve their long‐term success. We hypothesized that pollinator assemblage and structure and stability of plant–pollinator networks depend both on aspects of the surrounding landscape and of the restoration effort itself. We predicted that pollinator species diversity and network stability would be negatively associated with distance from remnant habitat, but that local floral diversity might rescue pollinator diversity and network stability in locations distant from the remnant. We created plots of native prairie on a reclaimed strip mine in central Ohio, U.S.A. that ranged in floral diversity and isolation from the remnant habitat. We found that the pollinator diversity declined with distance from the remnant habitat. Furthermore, reduced pollinator diversity in low floral diversity plots far from the remnant habitat was associated with loss of network stability. High floral diversity, however, compensated for losses in pollinator diversity in plots far from the remnant habitat through the attraction of generalist pollinators. Generalist pollinators increased network connectance and plant‐niche overlap. As a result, network robustness of high floral diversity plots was independent of isolation. We conclude that the aspects of the restoration effort itself, such as floral community composition, can be successfully tailored to incorporate the restoration of pollinators and improve success given a particular landscape context.