Miracle-dz/UniFAR-FTUs huggingface dataset:
The comparative study of range-wide genetic structure across related, co-distributed rainforest trees reveals contrasting evolutionary histories

Australia’s rainforests exhibit high taxonomic diversity and endemism, yet relatively little is known about patterns of genetic diversity across the flora. Habitat contractions caused by the aridification of the continent and the recent glacial cycles have left discrete genetic signatures on modern-day populations, with the nature of between-population differentiation likely to be influenced by a range of ecological and environmental factors. We used microsatellites to examine range-wide population genetic structure in two congeneric rainforest trees, Elaeocarpus angustifolius and E. largiflorens (Elaeocarpaceae), with similar habitat preference and dispersal potential. The aim was to investigate the relationships between genetic structure, geographic disjunction and morphological differentiation and attempt to clarify the likely evolutionary processes responsible for the observed patterns. We found substantial differences in the amount and type of genetic differentiation within the two co-distributed species. While Elaeocarpus largiflorens revealed an abrupt genetic disjunction front between two subspecies separated by a recognised biogeographic barrier (the Black Mountain Corridor), E. angustifolius showed lower genetic differentiation across a much wider geographic area. Our findings suggest that biogeographic features have different impacts on related species, and that generalisations on evolutionary patterns can be untenable without considering a range of factors. Also, on the basis of the available molecular data, a likely hypothesis is of pre-Pleistocene differentiation followed by reinforcement of differentiation patterns during recent glacial cycles (further studies are needed to conclusively date divergence).
Introduced reed canary grass attracts and supports a common native amphibian

The control of introduced plants is frequently a demanding and expensive activity for wildlife managers. It can be difficult to suppress some well-established species, and control measures may harm native organisms. Reed canary grass (Phalaris arundinacea) is a common wetland invader that can dominate and greatly alter wetlands. To examine the relationship between this plant and native amphibians, we analyzed field survey data and quantified amphibian-plant relationships in constructed replicated experimental ponds. Surveys showed positive associations between reed canary grass and the abundance of 3 native amphibians in 62 natural and constructed urban and suburban ponds in Portland, Oregon. Experiments elucidated mechanisms whereby 2 native and 2 introduced plants influenced breeding habitat use and larval performance of the common native Pacific chorus frog (Pseudacris regilla). Males preferred to call from reed canary grass, and there was a strong trend for females to lay eggs on the invasive grass compared to other plants offered. Tadpoles had 7 times higher survival in reed canary grass. These patterns were likely due to the morphology of reed canary grass: it provides support for calling males, its leaves and shoots are of ideal size for oviposition, and its branching may provide effective refuges from predators. This study demonstrates that some introduced plants may be beneficial for some native amphibians. Improved understanding of the relationships between introduced plants and native wildlife can help guide management actions by recognizing that the control of introduced plants may not be a priority in all systems. © 2015 The Wildlife Society.
Discovery of the Male of Parabuthus muelleri, and Implications for the Phylogeny of Parabuthus (Scorpiones: Buthidae)

Abstract The male of Parabuthus muelleri Prendini, 2000 is described, based on a specimen discovered in the Alexis Harington Scorpion Collection (recently acquired by the American Museum of Natural History). This is only the third known specimen of P. muelleri. The holotype and paratype are both female. The male presents several character states, including the lobate condition of the pectinal proximal median lamella and pedipalp chelae that are not incrassate, that are uncommon in male Parabuthus Pocock, 1890. These character states, previously scored with missing entries in a cladistic character matrix for Parabuthus species, are now added and a reanalysis of Parabuthus phylogeny, resulting in new insights about the phylogenetic position of P. muelleri, is presented. Lectotypes are designated for four northeastern African species of Parabuthus.
Crystal Structures of [Met5] and [(4-Bromo)Phe4, Met5]: Formation of a Dimeric Antiparallel β-Structure

: The crystal structure of [(4-bromo)Phe4,Met5]enkephalin (Tyr-Gly-Gly-(4-bromo)-Phe-Met) shows two independent molecular conformations. The molecules are arranged in parallel in a head-to-tail fashion and form an antiparallel beta-sheet structure involving intermolecular hydrogen bonds. This dimeric beta-structure is also observed in the [Met5]enkephalin crystal, in spite of their different crystal packing environments, which shows the energetic stability of this molecular conformation. The three-dimensional similarity between the dimeric beta-structure and the beta-turn form is discussed in the relation to the opioid delta and mu receptors.
Pseudocharaciopsis Texensis Gen. et sp. nov., a new member of the Eustigmatophyceae

A new genus of the Eustigmatophyceae and its type species, Pseudocharaciopsis texensis, are described. The actively growing vegetative cells have a short stalk and an attaching disc. The pyrenoid is spherical and is attached to the typically single, parietal chloroplast. There may be 1–4 or sometimes more pyrenoids and chloroplasts in older cells. Zoospore ultrastructure is similar to that of Ellipsoidion acuminatum Pascher. However, the zoospore of P. texensis is characterised by the presence of two large, conspicuously membrane-bounded osmiophilic vesicles and by the fan-shaped (in transverse section) flagellar swelling instead of the T-shaped one of Ellipsoidion acuminatum.
Qualidade higiênico sanitária de alfaces (Lactuca sativa) comercializadas em feiras livres na cidade de Uberlândia, MG, Brasil = Hygienic-sanitary quality of the lettuce (Lactuca sativa) commercialized in free fairs in Uberlandia city, MG, Brazil

No Brasil, as parasitoses intestinais estao entre os problemas mais comumente diagnosticados em saude publica. Essas doencas sao amplamente difundidas em virtude da precariedade das condicoes sanitarias, e as hortalicas servem como um dos principais veiculos de sua transmissao. A contaminacao dos vegetais pode ocorrer no campo, no periodo de producao, durante o processo de colheita ou ate mesmo na saida do produto em direcao a mesa do consumidor, pois os microrganismos podem se multiplicar nos alimentos de acordo com a umidade e temperatura. O objetivo deste trabalho foi avaliar a qualidade de alfaces provenientes de feiras livres do municipio de Uberlândia, em relacao a contaminacao microbiologica e parasitologica. De junho a setembro/2009 foram coletadas aleatoriamente 96 amostras de alfaces, da variedade crespa, em 12 bancas de diferentes produtores. Tais amostras foram submetidas ao metodo de sedimentacao espontânea por 24 horas para analise parasitologica. Os resultados obtidos indicaram 100% de contaminacao parasitaria nas amostras avaliadas, destacando-se Balantidium coli, Entamoeba histolytica/dispar, Giardia lamblia e Cryptosporidium spp. Considerando a elevada frequencia de contaminacao parasitaria e o potencial risco de doencas veiculadas pelas hortalicas, sugere-se uma vigilância sanitaria mais atuante na fiscalizacao de alimentos oferecidos a populacao, como tambem um programa de educacao sanitaria para os produtores e consumidores.
Relação solo/vegetação em ambiente de cerrado sobre influência do grupo Urucuia

The Brazilian Cerrado vegetation comprises a mosaic of natural types, from open fields to savannas and forests. It is believed that the presence of different vegetation types in a region can be explained in part by the direct relationship with the attributes present in the same soil. The present study investigated the relationship between soil and vegetation in an area of Cerrado biome with influence of Urucuia Group. To do so, we conducted a survey of soils and vegetation in 1:50,000 scale in an area of ​​approximately 32,000 hectares located in the tri-border region of Minas Gerais, Goias and Bahia states, with the sandstone substrate of Urucuia Group. The analytical results of soil classes were related to the present data of the physiognomies through common statistical analysis and through the determination of the main components. The soils of the region reflected well the source material, with high percentages of sand, with a predominance of Oxisol Hapludox and Oxisol dystrophic, present in over 35% of the entire study area. The most common vegetation type was Cerrado sense, restrict and typical. The principal component analysis indicated that the fine sand, clay and aluminum accounted for 93.7% of the variability of the relationship between soils and vegetation type
Acute adaptive responses of central sensorimotor neurons after spinal cord injury

Spinal cord injury (SCI) can be a lifelong, devastating condition for both the patient and the caregiver, with a daunting incidence rate. Still, there are only limited available therapies and the effectiveness of precise regeneration within the central nervous system is minimal throughout postnatal life. Recently, improved regeneration after SCI was seen by manipulating a pathway in sensorimotor neocortices that is involved in phosphorylation of an RNA binding protein (RBP) required for mRNA translation, the Eukaryotic translation initiation factor 4E (eIF4E). Our data identifies rapid molecular alterations of eIF4E in the sensorimotor neocortices 1 and 3 days after a lateral hemisection SCI, used as a model for Brown-Séquard syndrome. The function of an RBP depends on both its distribution sites within the cell and its phosphorylation states. Indeed, we found both to be affected after SCI. There was a distinct subcellular redistribution of eIF4E and phosphorylated-eIF4E was reduced, indicating that the eIF4E’s translation was disrupted. Upon identification and analysis of the mRNA cargo of eIF4E in uninjured sensorimotor neocortices, we found that eIF4E binds both Importin-13 (Ipo13) and Parvalbumin (Pv) mRNAs, indicating a role in their translation. Remarkably, eIF4E’s interaction with both Ipo13 and Pv mRNAs was disrupted 1 and 3 days after SCI, despite preservation of total Ipo13 and Pv mRNA levels. Finally, we detected a selective loss of expression of both IPO13 and PV proteins in projection neurons of sensorimotor neocortices, as well as their disrupted dendritic polarity. Since IPO13 is predominantly expressed in neocortical projection neurons and PV in a subset of neocortical interneurons, these data suggest a strong acute effect of SCI on neocortical microcircuitry. Taken together, these data indicate that neocortical eIF4E and a subset of mRNAs may be rapidly recruited to translational machinery after SCI to promote adaptive regeneration response of sensorimotor neurons.
The 2005 KwaZulu-Natal sardine run survey sheds new light on the ecology of small pelagic fish off the east coast of South Africa

Despite much public awareness surrounding the annual migration of sardine Sardinops sagax northward along the east coast of South Africa in winter each year, relatively little research effort has been expended to improve understanding of the ‘sardine run’. For this reason, a dedicated multidisciplinary survey, timed to coincide with the annual sardine run, was conducted off the East Coast in June and July of 2005. The major objective of the survey was to estimate the biomass of sardine off the East Coast during the run, and to compare this with biomass estimates collected during previous surveys conducted in this area during the late 1980s when the South African sardine population was at a considerably smaller size. We also collected data on the distribution of sardine and other small pelagic fish species and their eggs, the biological characteristics of sardine during the run, and data on the hydrography (temperature and currents) and lower trophic levels (phytoplankton and zooplankton) of the region. Results suggest that the biomass of sardine off the East Coast in winter remains relatively small and consistent, regardless of overall sardine population size. The narrow continental shelf to the east of Port Alfred, which is dominated offshore by the fast-flowing warm Agulhas Current, constrains the amount of suitable habitat for sardine and other clupeoids such as anchovy Engraulis encrasicolus, West Coast round herring Etrumeus whiteheadi and East Coast round herring Etrumeus teres, and hence precludes these species from attaining a high biomass in this region. Additionally, primary and secondary productivity levels are much lower than elsewhere on the western and eastern Agulhas Bank off the south coast of South Africa, suggesting that the sardine run is not a feeding migration. A previous hypothesis that the run is mainly a result of an expansion of the distributional range of these fish as conditions become favourable in winter due to sporadic cooling off the East Coast is also not entirely supported by results from the survey. It is suggested that a migration for the purposes of spawning off this coast when conditions become favourable is a more likely incentive for sardine to undertake this arduous journey, despite increased predation and poor feeding conditions.
Request for a consensus on the definition of putative embryonic stem cells

Embryonic stem cells (ES cells) are totipotent cell lines, obtained from the inner cell mass of blastocysts, able to colonize the germ line in mosaics. Only mouse ES cells lines responding to this definition have been obtained. In order to avoid long lasting rumors and an increasing flow of papers on putative non-murine embryonic stem cells (ES cells), I suggest that prior to designation as ES-like or putative ES cells, candidate cell lines, or short term embryonic cultured cells, cell type characterization similar to that used in a recent study (Van Stekelenburg-Hamers et al., 1994) should be required. The assumption is that the ES cells of other mammalian species should exhibit similar markers as murine ES cells, EC cells and inner cell mass cells. For a rapid and universally agreed test, it is possible to use just a few cell markers. I suggest at least one positive cell surface marker such as SSEAl or its equivalent TECOl (Draber et al., 1984) and/or alkaline phosphatase, a negative nuclear marker (Jamin MC), and a negative cytoplasmic marker (cytokeratins 8 + 18) (Galli et al., 1994). The criteria retained may have a broader value, in application to other stem cells: haemapoietic cells may lack both lamins A/C and intermediate filaments (Paulin-Levasseur et al., 1989). These criteria may also apply to male and female gonia (Moens et al., 1994) which are, after all, the stem cells of gametes. It would also be interesting to confirm if murine EG cells express these markers similarly. Cultured cells from a blastocyst which respond to these criteria may not necessarily be ES cells, but could be embryonic ectoderm cells, as commitment of embryonic cells may occur before expression of lamin A/C (Rober
STUDIES ON SLIME ACCUMULATIONS IN PULP AND PAPER MILLS: VI. ISOLATION OF THERMOPHILIC AND THERMOTOLERANT FUNGI FROM PAPER MILLS

Thermotolerant fungi have been found in slimes at temperatures of 38 to 52 °C in paper mills in Eastern Canada. The growth of some of these isolates on malt agar plates maintained at temperatures of 10 to 65 °C has been examined. Optimum temperatures varied between 30 and 50 °C, depending upon the species. Thiamine deficiency was noted in Trichosporon capitatum and Mycelium sterilium. The requirement of T. capitatum for this vitamin could be met by incorporating the thiazole and pyrimidine moieties together in the medium.
ANATOMY, HISTOCHEMISTRY AND CYTOLOGY OF DORMANT AND STRATIFIED APPLE EMBRYOS

SUMMARY Changes in the anatomy and cytology of apple embryos isolated from seeds during after-ripening (3-month stratification at +4°C)were investigated. Structural changes differed in cotyledons and embryo axes. In cotyledons they were limited to stepwise differentiation of the vascular tissue, whereas the structural alterations in axes were related to starch accumulation. A general increase of starch up to the end of after-ripening was noted after a temporary decrease during the first 10 days of stratification. Accumulation of starch during the third month of after-ripening was restricted to the limit zone between the radicle and hypocotyl. Starch accumulation (followed by degradation) was localized in a zone corresponding to that in which cell elongation begins. The structural changes were correlated with the metabolic changes known to occur during the after-ripening of apple seed.
Harvest dates, fertilizer and varietal effects on yield, concentration and molecular distribution of fructan in Jerusalem artichoke (Helianthus tuberosus L.)

In a pot experiment two varieties of Jerusalem artichoke (Helianths tuberosus L., cv. Topianka and cv. Violet de Rennes) were exposed to different supplies of N, P and K. Nitrogen supply increased tuber yield more than the productivity of aerial parts. Violet de Rennes responded better to N than Topianka. Nutrient regimes without P or K addition but including N to some extent depressed the yields of tubers only (by 8–23 %). Carbohydrate concentrations (78–81 % of d.m.) and molecular fructan distributions were neither influenced by fertilizer regimes nor by mineral concentrations in the tubers. Genotypic differences were significant for yield, for concentrations of N, P, Ca, S and Cu, and for fructan concentration in the tubers. At harvest time the fructose/glucose ratio in tubers of Violet de Rennes was about 10 % higher than in Topianka and remained on a higher level during storage. Harvest time had the greatest influence on carbohydrate composition. Depolymerization of fructan proceeded at a high rate in November and slowed down during subsequent storage, accompanied by a decline in polydispersity. Simultaneously osmolanty increased, resulting in a freezing point depression of < 0.5 °C.
Ultrastructure of human in vitro-matured (IVM) oocytes

Breeding of agriculturally important species may take advantage of the technique of in vitro maturation (IVM) of the oocytes. In assisted reproduction technology, IVM may be an alternative treatment to avoid the problems of standard ovarian stimulation. Even if IVM of human oocytes can generate live births, this technique is still controversial and not yet optimized [1,2]. We studied the ultrastructure of human IVM oocytes in order to evaluate if they might present cytoplasmic fine morphological markers eventually related to a maturation failure. We obtained in vivo-matured oocytes (controls, n=10); and immature oocytes that reached the metaphase II stage in vitro after 24-hour culture (IVM oocytes, n=10). Female age was 24-34 years. Microscopy samples were prepared and evaluated according to protocols previously described [3,4]. IVM oocytes showed shape, ooplasm morphology as well as organelle dimension and distribution comparable to those of in vivo-matured oocytes. Mitochondria-smooth endoplasmic reticulum aggregates were more numerous in controls, whereas mitochondria-vesicle complexes increased in IVM oocytes. Cortical granule distribution was slightly compromised in IVM oocytes. The above changes of IVM oocytes are signs of a maturation impairment and are likely in relation with the culture period and/or medium conditions.
LIGULE: An evaluation of indigenous perennial grasses for dryland salinity management in south-eastern Australia. 1. A base germplasm collection

This paper reports on the collection phase of a research program which aimed to identify Australian native grasses that may be useful for pastoral purposes and for controlling land degradation on hill-lands in the high (>500 mm) rainfall zone of south-eastern Australia. Live plants of 37 target species were collected along a number of transects, and at specific locations, in New South Wales and Victoria. The collection sites were generally along public roads, and were chosen for their vegetation diversity. Each collection site was marked on a 1: 250000 topographic map, and detailed notes were taken of the native vegetation, geology, soil types, land use, and other features. Surface (00—10 cm) soil samples were collected at most sites and analysed for phosphorus, pH CaCl 2 , electrical conductivity, and particle size distribution. A total of 807 accessions were collected from 210 locations. At most collection sites, soils were acidic (median pH 5.6); soil phosphorus (Olsen) was in the low range (<8.5 mg/kg); and the target genera occurred with a low frequency (half of the sites yielded 3 accessions or less). Although genera collected in the study could be ranked on the basis of the mean pH of their collection sites, they all tolerated a considerable soil pH range (of about 2mp;mdash;5 pH units). Allowing root and shoot growth to recommence by growing collected plants for a short period in coarse sand considerably improved establishment success. Accessions collected in this study will be further evaluated.
Single-molecule DNA sensors and cages for transcription factors in vitro and in vivo

Gene regulation is vital to the success of all living organisms. Understanding this complex process is crucial to our knowledge of how cells function and how in some cases they can lead to debilitating or even fatal disease. In this thesis I focus on a set of DNA-binding proteins known as transcription factors (TFs), proteins fundamental to the process of gene regulation at the level of transcription. I develop assays and techniques for the detection and quantitation of TFs in vitro and in vivo as well as a method for TF encapsulation and release. The advantages of the TF detection assays in this thesis are made possible through the use of single-molecule (sm) fluorescence. This methodology enables detection of individually labeled molecules allowing discrimination of sample heterogeneities inaccessible with ensemble techniques. Here I present two different TF assays based on two sm observables: relative probe stoichiometry and Forster resonance energy transfer (FRET). The first assay design, based on stoichiometry, detects TFs using TF-dependent coincidence of two distinctly labelled DNA ‘half-sites’. I demonstrate sensitive detection (~ pM) in solution and on surfaces, multiplexed detection of multiple TFs, and detection in cell lysates. A kinetic model of the system is also developed, verified experimentally and used to quantify TF concentrations without the need for a calibration curve. The second assay design, based on FRET, is a novel approach to TF detection using TFmediated DNA bending. TFs are detected by bending the sensor and monitored with FRET at the single-molecule or ensemble level. I demonstrate TF detection in purifed form and expressed in cell lysates. As this sensor was designed for use in vivo, methods to hinder nuclease degradation are explored. For TF detection in vivo, I describe a successful strategy to internalise fluorescently labeled molecules into live E.coli. Viability and internalisation efficiency are characterised and ensemble measurements with FRET standards are demonstrated. Importantly, sm FRET measurements in vivo are achieved opening many exciting possibilities. The FRET based TF sensor is then internalised as a step towards real-time in vivo monitoring of TF concentrations. Finally a system based on DNA nanotechnology is presented for the non-covalent encapsulation and release of TFs. Such a system could be delivered into a cell to alter levels of gene expression using external stimuli as inputs. We believe these tools will generate valuable information in the study of prokaryotic gene expression as well as providing a potential commercial avenue towards diagnostics.