Miracle-dz/UniFAR-FTUs huggingface dataset:
AFTER THE ICE AGE : THE RETURN OF LIFE TO GLACIATED NORTH AMERICA

Review by James M. Peek, Ph.D. Professor of Wildlife Resources, University of Idaho, Moscow, ID 83844, USA. TEL: 208-885-7120. Pielou, E.C. AFTER THE ICE AGE : THE RETURN OF LIFE TO GLACIATED NORTH AMERICA. Chicago: University of Chicago Press, 1991, 1992 paperback ed. 366 pp. US$13.95 paperback ISBN: 0-226-66812-6. E.C. Pielou's descriptions of events on earth following the last maximum glacial advances of 20,000 years ago should dispel the notion that we live in a static world. It should cause the reader to ponder whether our contemporary society is structured to adapt as we inexorably advance towards the next ice age. As our lake shores change and our climate changes, are we short-sighted humans ready to adjust our lives to accommodate the future? And those of us who concern ourselves with conservation of natural resources: where do our activities, which are often centered on the short-term, fit into the long-term picture? In AFTER THE ICE AGE : THE RETURN OF LIFE TO GLACIATED NORTH AMERICA, such thought-provoking issues are raised as Pielou guides us through the geological evidence, using examples from little-known and seemingly inconsequential species, extinct and extant. We learn of the Malankovich Cycle describing the earth's orbit around the sun, the climatic warming of 10,000 years ago, and the Little Ice Age of 1600 A.D. The Glacial Lakes Agassiz and McConnell are delineated on a map, and their influences on current landform and vegetation pattern, are narrated eloquently. Also, we discover how species like the northern pike are distributed in North America across many major drainages because of their ability to migrate when lakes at headwaters ebbed and flowed, causing them to drain in different directions. We marvel at the careful observation of such seemingly insignificant species as the foraminifera, floating single-celled organisms which have shells that become fossilized and sink into the lake sediments. Forams with right-coiled shells live in warm waters while the left-coiled varieties live in cold waters. Abrupt changes in the presence of these different forams in sea sediments signals changes in climate. The events surrounding the evolution of Glacial Lake Missoula, and the catastrophic floods that modified so much of the terrain in eastern Washington when the ice dams failed, are also covered. The volcanic eruptions and the huge deposits of ash, the major extinction of the large mammals and birds, and how aboriginal man must have occupied the land as it changed through long time spans, are all discussed in sufficient detail to enhance our understanding. Each chapter of AFTER THE ICE AGE. is documented and a section on footnotes is included in the back. This book is highly recommended for those who are interested in the natural world and who wish to acquire a bit of humility and a unique perspective on how forces beyond our control will ultimately dictate the condition of our environment and our future.
Prediction of bacterial growth on xenobiotics

The utilisation of a given substrate leads to bacterial growth and the associated yield is normally determined experimentally. Different yield estimation methods exist based on knowledge of the Gibbs energy of reaction and the energy needed for synthesis of new biomass [1-4]. Estimating yield from thermodynamic considerations of stoichiometrically balanced reactions is typically done in biotechnology and wastewater treatment [5], an approach recently adopted by Helbling et al. [6]. More recent methods specifically incorporate detailed knowledge of the degradation pathway and bacterial metabolism to attain predictions closer to the experimentally observed yields [3]. However, this knowledge is seldom known for xenobiotics in the environment but is needed to assess the turnover leading to biomass production, i.e. for sludge production or biogenic residues. The objectives of the present study were thus to (i) formulate and use a simple quantitative structure-activity relationship to estimate a minimum growth yield under aerobic conditions and (ii) compare the estimations with experimental results from literature . We based our estimation method on the approach suggested by Diekert [2], requiring as input just the Gibbs energy of formation of the reactants and products and a limited amount of structural data (e.g., the number of carbon atoms in the substrate). To estimate the yield, the Gibbs energy of reaction was quantified from balanced mineralisation reactions as the difference between the Gibbs energy of formation of the products and reactants. The Gibbs energy of the mineralisation reaction can be regarded as the maximum energy released and partly captured by the biomass. The carbon present in the substrate is used for synthesis and oxidised to CO 2 to yield energy for anabolism. We accounted for this by specifying how much of the energy can be used as a function of the chemical structure based on general rules of microbial turnover. Thus, we obtain a minimum yield from use of the substrate as a sole source of energy and carbon. In order to test the applicability of our estimation method, we evaluated
Genome-wide expression analysis and regulation of microRNAs and cis natural antisense transcripts in Arabidopsis thaliana

GENOME-WIDE EXPRESSION ANALYSIS AND REGULATION OF MICRORNAS AND CIS NATURAL ANTISENSE TRANSCRIPTS IN ARABIDOPSIS THALIANA Shuhua Zhan Advisor: University of Guelph, 2011 Dr. Lewis Lukens Small RNAs (sRNAs), circa 21-26nt RNA molecules, are a novel class of regulatory molecules that influence many aspects of plant biology. The first objective of this thesis was to utilize computational approaches both to investigate how microRNAs (miRNAs), a type of sRNA, as a class affect their target transcripts’ accumulation and to identify novel miRNAs in Arabidopsis thaliana. The second objective of this thesis was to examine the regulation of protein coding (PC) cis natural antisense transcripts (cis-NATs), which have the potential to make double stranded RNA. Computational analysis of the expression of miRNA-regulated genes demonstrated that the transcriptomes of the inflorescences of plants defective in miRNA biogenesis were similar to normal leaf tissues and dissimilar to normal pollen and seed. Thus, miRNAs cause the plant transcriptome to shift from a vegetative to reproductive state. Known miRNA targets fail to explain miRNA-defective mutant transcriptome patterns. Novel computational approaches were used to discover five new mature miRNAs. Interestingly, two miRNAs have different functions but are encoded by perfect complements of the same precursor molecule. Genome-wide analysis of cis-NAT abundances revealed that protein coding (PC) cisNATs tend to be co-expressed, broadly expressed, and highly expressed across diverse abiotic stress conditions. These expression patterns were negatively associated with sRNAs because sRNAs were under-represented within PC cis-NATs compared to PC non-cis-NATs. sRNAs also mapped to cis-NATs and non-cis-NATs at similar frequencies in mutants defective in natsiRNA biogenesis relative to other genotypes. We suggest a common euchromatin environment and possibly antisense RNA stabilization of mRNA transcripts may contribute to the high level, breadth, and co-expression of cis-NATs. However, cis-NATs are correlated less frequently than expected, and cis-NAT transcript abundances often differ more than expected. In addition, sRNAs matched PC cis-NATs relative to PC non-cis-NATs more frequently in abiotic stress conditions than in control conditions. Thus, although sRNAs do not have a widespread role in regulating cis-NATs, sRNAs may have a focused role in regulating cis-NAT transcript abundances.
Response of Day 8 Equine Embryos to Saccharide Solutions at Various Temperatures

Response of Day Eight Equine Embryos to Saccharide Solutions at Various Temperatures Brittany A Foster Advisor: University of Guelph, 2012 Dr. Tracey Chenier The response of Day Eight equine embryos to saccharide solutions was investigated as a first step in their potential use as non-permeating cryoprotective agents. Embryos were exposured to seven increasing concentrations of either sucrose or galactose at a temperature of 22°, 30° or 37°C. Each embryo was then rehydrated by exposing it to the same solutions in reverse. Embryos underwent osmotic dehydration, independent of treatment group, but embryo size had a significant effect on the response pattern. Embryos < 500! m dehydrated osmotically to 20% of their original volume. Those > 500! m exhibited a delayed response and only dehydrated to 40% of their original volume. When placed into decreasing concentrations, embryos partially rehydrated. Preand post-treatment embryo quality was compared and embryos were stained to determine the amount of apoptosis, with no difference in embryo survival between treatments. Results indicate that saccharides show promise for use in equine embryos < 500! m.
ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy

Chromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors, and DNA. This technique in combination with RNA-sequencing (RNA-seq) is a powerful tool to better understand biological processes in eukaryotes. We developed a combined ChIP-seq and RNA-seq protocol for tree buds (Prunus avium L., Prunus persica L Batch, Malus x domestica Borkh.) that has also been successfully tested on Arabidopsis thaliana and Saccharomyces cerevisiae. Tree buds contain phenolic compounds that negatively interfere with ChIP and RNA extraction. In addition to solving this problem, our protocol is optimised to work on small amounts of material. Furthermore, one of the advantages of this protocol is that samples for ChIP-seq are cross-linked after flash freezing, making it possible to work on trees growing in the field and to perform ChIP-seq and RNA-seq on the same starting material. Focusing on dormant buds in sweet cherry, we explored the link between expression level and H3K4me3 enrichment for all genes, including a strong correlation between H3K4me3 enrichment at the DORMANCY-ASSOCIATED MADS-box 5 (PavDAM5) loci and its expression pattern. This protocol will allow analysis of chromatin and transcriptomic dynamics in tree buds, notably during its development and response to the environment.
Body mass estimation for †Cyonasua (Procyonidae, Carnivora) and related taxa based on postcranial skeleton

Abstract Procyonidae were the first northern placental carnivorans that reached the Neotropics. They are represented by two extinct genera: †Cyonasua and †Chapalmalania (late Miocene – early Pleistocene). Postcranial elements are only known for †Cyonasua and related taxa (†Parahyaenodon argentinus and †Tetraprothomo argentinus). To obtain highly reliable allometric equations for body mass estimations of fossil procyonids, we performed least squares regressions (multiple and bivariate lineal models) using 51 postcranial linear measurements. The extant sample included 124 taxa corresponding to nine families of Carnivora, with body mass data from the literature. We obtained about 63 equations from diverse combinations of postcranial measurements; 14 of them were selected using several reliability indexes as criteria. Our results show that body masses calculated for †Cyonasua range between 12.63 and 28.45 kg, †P. argentinus was estimated at 14.41 kg, while †T. argentinus at 25.31 kg. Thus, the body mass of †Cyonasua would have been at least twice as high as the mean of the extant procyonid Procyon cancrivorus. †Cyonasua was probably able to fend off predators and quite capable of climbing slowly on thick-enough branches. Other palaeoecological and palaeobiological inferences are discussed.
The role of GRAS-domain proteins in arbuscular mycorrhizal symbiosis

A major limitation to plant growth is the restricted access to nutrients in the soil. To improve nutrient acquisition, the majority of land plants enter a beneficial symbiosis with arbuscular mycorrhizal (AM) fungi. The accommodation of fungal hyphae in roots requires the extensive transcriptional reprogramming of host cells. Several GRASdomain proteins, including NSP1 (NODULATION SIGNALLING PATHWAY 1), NSP2, and RAM1 (REQUIRED FOR ARBUSCULAR MYCORRHIZATION 1), have emerged as important transcriptional regulators during mycorrhization. Interaction studies suggest that these proteins form multicomponent complexes, raising the question whether they regulate similar or different mycorrhizal processes. Here, the functions of NSP1, NSP2 and RAM1 during AM development were investigated by detailed phenotypic and transcriptional analyses of the corresponding loss‐of‐function mutants. Global gene expression profiling of nsp1‐1 revealed that NSP1 is required for the expression of a large number of genes involved in strigolactone and gibberellin biosynthesis at the pre‐contact stage of AM development. Strigolactones are known to attract the fungus to the root. In line with this, the quantification of mycorrhizal structures showed a delay in mycorrhization in nsp1‐1. Transcriptional profiling confirmed that the expression of the majority of mycorrhizal‐induced genes was delayed, but not abolished in nsp1‐1, suggesting that NSP1 only has a minor role in the transcriptional regulation once the contact between the fungus and the roots has been established. Unlike NSP1, RAM1 plays a critical role in the transcriptional regulation at later stages of AM symbiosis. Mycorrhization was strongly impaired in ram1‐1, and transcriptional profiling revealed that RAM1 is essential for the expression of several genes involved in arbuscule development and the nutrient exchange between the symbionts. Meanwhile, the exact function of NSP2 remains unclear, as no effect on mycorrhization was observed in nsp2‐2 under the conditions tested here. These findings suggest that NSP1, NSP2 and RAM1 play largely different roles in the transcriptional regulation during AM development.
Minor food sources can play a major role in secondary production in detritus‐based ecosystems

In many ecosystems, detritus is the dominant source of energy and the driver of ecosystem functioning. In particular, in forested headwater streams, allochthonous detritus (e.g. leaf litter, dead wood) constitute the main energy source for detritivores and living primary producers contribute marginally to ecosystem metabolism and energy flows. We hypothesised that a low consumption of benthic diatoms, a high-quality resource, could be of major importance for the growth of detritivores. In particular, these resources might represent an essential source of polyunsaturated fatty acids (PUFAs). In a microcosm experiment, three food resources were manipulated: alder (Alnus glutinosa: Betulaceae) leaf litter, fungal mycelium and a common benthic diatom. They were offered to juveniles of Gammarus fossarum (Crustacea: Amphipoda) as food resources, either alone or in combination, with each resource type being enclosed in agarose pellets. Juveniles were fed for 5 weeks in controlled conditions. Survival, feeding and growth rates were monitored. The fatty acids content of food resources and gammarids were also quantified. Our results showed that detritus alone permits survival, but not the significant growth of detritivores. The presence of diatoms in food resources was necessary to ensure a significantly positive mass growth of detritivores over the 5-week experiment. More importantly, detritivores that did not receive algae in their food were generally unable to maintain their PUFA levels when compared to juveniles collected in the field. Gut-content analysis of field-collected G. fossarum showed that low amounts of benthic algae were always visible, indicating that most individuals fed at least for a small part on benthic algae. These minor, but high quality, food sources might therefore be essential for ensuring the growth and survival of detritivores. Our results clearly highlight the need to consider the functional importance of such minor food sources.
Effect of Cell Lysis (CLs) Products on Acidophilic Chemolithotrophic Microorganisms and the Role of Acidocella Species

ABSTRACT Acidophilic chemolithotrophic microorganisms (CMs) are widely used for bioleaching of mineral resources. However, the growth of bacteria and their leaching activity are often inhibited (restricted) by organic components, e.g. lysates and exudates. The aims of this study were to examine the extent of cell lysis (CLs) inhibition on acidophilic microorganisms and to identify microorganisms that can utilize CLs products and eliminate their inhibition effect on acidophilic microorganisms. Specifically, it was revealed that Acidithiobacillus caldus was severely inhibited at 5% CLs products, whereas A. ferrooxidans and Leptospirillum ferriphilum are severely inhibited at 20%. It has been found that strains RBA and RBB of heterotrophic bacteria, isolated from anaerobic sludge, can biodegrade CLs products and when co-cultured with A. ferrooxidans, they can alleviate the toxic effect of CLs products under low pH (2–3). It has been shown that besides CLs, isolated strains can grow on glucose, glycerol, yeast extract, citric acid, and tryptone soya broth with an optimum temperature of 35°C and a pH of 3. The strains showed the ability to reduce ferric ions to ferrous ions when glycerol was used as a substrate after 2 days under both aerobic and anaerobic conditions. On the basis of morphophysiological and molecular biological studies, the isolated strains RBA and RBB were identified as Acidocella spp.
Life-History Traits and Temperature-Dependent Performance of Tranosema rostrale (Hym.: Ichneumonidae), a Parasitoid of Low-Density Spruce Budworm (Lep.: Tortricidae) Populations

The eastern spruce budworm Choristoneura fumiferana (Clemens) (Lepidoptera: Tortricidae) is one of the most important outbreaking defoliator in conifer forests of eastern North America. In low-density populations, the larval endoparasitoid Tranosema rostrale (Brischke) (Hymenoptera: Ichneumonidae) is known as an important mortality factor, but relatively little information is available about the factors influencing its ability to keep spruce budworm populations low. A series of studies were conducted to investigate T. rostrale’s: 1) reproductive biology and behaviour; 2) seasonal pattern of parasitism and host instar preference; 3) developmental, survival, and reproductive response to temperature; 4) ability to abrogate spruce budworm’s immune response at high temperatures; and 5) spatiotemporal biology in response to changing temperature. Three traits of the parasitoid’s reproductive biology contribute to its successful parasitism: its lack of a pre-mating and preoviposition period, the rapid maturity of its eggs soon after emergence despite being synovigenic, and its efficacy in host searching and oviposition behaviour. As T. rostrale does not prefer to attack any one particular host instar, its seasonal pattern of parasitism is likely influenced by its phenology or competition with the ectoparasitoid Elachertus cacoeciae (Howard)
17-(Allylamino)-17demethoxygeldanamycin reduces Endoplasmic Reticulum (ER) stress-induced mitochondrial dysfunction in C2C12 myotubes

In patients with myositis, persistent skeletal muscle weakness in the absence of significant inflammatory cell infiltrates is a well-recognised, but poorly understood, cause of morbidity. This has led researchers to investigate cellular mechanisms independent of immune cells, which may contribute to this underlying muscle weakness. Chronic ER stress pathway activation is evident in the muscle of myositis patients, and is now a potential mediator of muscle weakness in the absence of inflammation. Abnormal ER stress pathway activation is associated with mitochondrial dysfunction, resulting in bioenergetic deficits and reactive oxygen species (ROS) generation, which in this context may potentially damage muscle proteins and thus impair contractile performance. This study examined whether treatment with the HSP90 inhibitor 17-N-allylamino-17-demethoxygeldanamycin (17AAG) could mitigate these ER stress-induced changes. C2C12 myotubes were treated with the ER stress-inducing compound Tunicamycin, in the presence or absence of 17AAG. Myotubes were examined for changes relating to ER stress pathway activation, mitochondrial function, markers of oxidative damage and in myotubular dimensions. ER stress pathway activation caused mitochondrial dysfunction, as evidenced by reduced oxygen consumption and ATP generation and by increased gene expression levels of the bio-energetic regulator, uncoupling protein 3 (UCP-3), the latter indicative of electron transport chain uncoupling. ER stress pathway activation also caused increased gene expression of superoxide dismutase (SOD) 2 and peroxiredoxin (PRDX) 3, elevated H2O2 levels, and reduced total thiol pool levels and a significant diminution of myotubular dimensions. Exposure to 17AAG ameliorated these ER stress-induced changes. These findings, which suggest that 17AAG can reduce ER stress-induced mitochondrial dysfunction, oxidative damage and myotubular atrophy, have potential implications in the context of human myositis.
Planting date and row spacing effects on the agronomic potential of sesame in the southeastern USA

ABSTRACT Sesame (Sesamum indicum L.) is being considered for commercial production in the southeastern USA, but very little is known about its potential and the appropriate management practices required to achieve sustainable yield potential in the area. This study thus aims to determine the optimal planting date and row spacing for several sesame cultivars. Traits examined were yield, plant height, number of nodes on the main stem, number of branches, height to first capsule on the main stem, and number of plants per meter. A first trial investigated three planting dates in Citra, FL (May, June, and July); whereas a second one examined several row spacings at two locations: 19 and 38.1 cm in Citra; and 19, 38.1, and 76.2 cm in Live Oak, FL. The May planting date showed higher yields, number of nodes, and taller plants than the other dates. Accumulated air and soil growing degree days (GDDs), rainfall, and solar radiation values were calculated for each planting date in both years. Soil GDDs provided similar results to air GDDs; thus, either model would seem appropriate for predicting crop development in this region. Plant height, number of nodes with capsules, and number of branches were increased at wider row spacings in the Live Oak trials as compared with narrow rows. These two trials illustrated the potential of sesame for attaining economically sustainable yields in the southeastern USA, but further exploration and modeling of agronomic traits will be needed to reach the crop’s full yield potential in these regions.
New England Range Extension of American Brook Lamprey (Lethenteron appendix), as Confirmed by Genetic Analysis

Abstract Genetic analysis (i.e., DNA sequence data from the mitochondrial cytochrome b and cytochrome oxidase subunit I genes) confirms the presence of Lethenteron appendix (American Brook Lamprey) in Shorey's Brook, a small stream located in the towns of Eliot and South Berwick, ME. This study documents the easternmost record of this species in New England, and the first known occurrence of the American Brook Lamprey in Maine.