Miracle-dz/UniFAR-FTUs huggingface dataset:
INDIVIDUAL IDENTIFICATION OF DECAPOD CRUSTACEANS II: NATURAL AND GENETIC MARKERS IN SNOW CRAB (CHIONOECETES OPILIO)

Abstract Methods for the identification of individual crustaceans are needed in many types of studies. Snow crab (Chionoecetes opilio) individuals have distinctive natural patterns of tubercles and spines on the carapace. The results of a double-marking experiment using these natural markers along with genetic (microsatellite) markers confirm that natural markings are a reliable means of recognizing individuals within groups of tens to hundreds of snow crabs. These natural markings are persistent through at least two molts. They have already demonstrated their usefulness in laboratory studies of molting and mating and could be applied to a wider spectrum of investigations. A cursory examination suggests that similar carapace features could be used to identify individuals in other crustacean species as well.
Degradabilidade in situ da matéria seca de três forrageiras tropicais nas formas in natura e ensilada

Dry matter (DM) ruminal degradability of corn (Zea mays L.), millet (Pennisetum glaucum (L. R. Br.) and sorghum (Sorghum bicolor L. Moench.) was evaluated using in situ technique with samples in green chopped and ensiled forms. Two crossbred fistulated (live weight of 480kg) dry cows participated. Samples of six grams in each forage were incubated in the rumen for 6, 24 and 96 hours. We estimated time zero (t0) washing the bags in water and it was used to calculate solubility. The experimental design followed a randomized block design with a split plot. We compared the average of DM through the SNK test at 5% probability. The results of disappearance (%) of dry matter forages of green chopped and ensiled forms in 0, 6, 24 and 96 hours were respectively: millet (10,07, 14,50, 20,36, 47,86; 11,64, 15,69, 21,60, 33,37), corn (12,64, 20,08, 31,77, 68,11; 13,31, 20,97, 35,31, 67,33) and sorghum (10,20, 21,55, 26,56, 58,95; 10,07, 15,10, 24,89, 44,52). The potential degradation (%) of silages was: millet (36,44), corn (81,18) and sorghum (51,30).
NOVEL INSIGHTS INTO PKG ACTIVATION AND cGMP SIGNALING IN RESPONSE TO NITRIC OXIDE AND ATRIAL NATRIURETIC PEPTIDE IN VASCULAR SMOOTH MUSCLE CELLS

Cyclic 3',5'-guanosine monophosphate (cGMP) is a key signaling molecule involved in a myriad of physiological processes, including vascular smooth muscle (VSM) tone, waterand electrolyte homeostasis, platelet aggregation, airway smooth muscle tone, smooth muscle proliferation and bone formation. Increased occurrence of vascular disorders including erectile dysfunction, hypertension, stroke and coronary artery disease, have made it increasingly important to study the dynamic interplay between cGMP synthesis and hydrolysis in VSM cells. This dissertation examines the spatial distribution of intracellular cGMP, [cGMP]i, in response to NO and atrial natriuretic peptide (ANP) in VSM cells. To investigate the spatial patterning of [cGMP]i, we have developed a new generation of non-FRET (fluorescence resonance energy transfer) cGMP biosensors that are suitable to monitor [cGMP]i in response to physiological (low-nanomolar) NO and ANP concentrations and that qualify for realtime, confocal imaging techniques. We have termed these indicators FlincGs, for green fluorescent indicators of cGMP. For the development of FlincGs, we made use of the specific cGMP binding characteristics of PKG. We utilized site-specific mutagenesis, kinetic cGMP binding, dissociation and kinase assays, as well as crystallography, in order to investigate PKG activation and cGMP binding dynamics in greater detail. Based on these studies, our novel, non-FRET cGMP biosensors were designed by attaching cGMP binding fragments of PKG to the N-terminus of circular permutated green fluorescent protein. We applied FlincGs in cultured VSM cells as well as in intact tissue to determine whether two spatially distinct populations of guanlylyl cyclase (cytosolic versus membrane bound) underlie the generation of spatiotemporally-specific patterns of [cGMP]i formation.
Engineered regenerated bacterial cellulose scaffolds for application in in vitro tissue regeneration

In this study, we sought to synthesize regenerated bacterial cellulose (rBC) scaffolds for application in in vitro tissue regeneration. Bacterial cellulose (BC) was dissolved in N-methyl morpholine-N-oxide (NMMO), and salt crystals were added as porogens, followed by casting in molds and incubation in water. The synthesized scaffolds were characterized using Fourier transform infrared (FT-IR) spectroscopy and field-emission scanning electron microscopy (FE-SEM). The FT-IR spectra exhibited bands characteristic for BC in rBC scaffolds, indicating no alteration in chemical structure, while FE-SEM revealed a porous structure of the rBC scaffold. The scaffolds exhibited very high swelling ratio, indicating enhanced water absorption and nutrient exchange capacity. The in vitro biocompatibility of the rBC scaffolds was tested based on the adhesion, growth, and proliferation of animal fibroblasts (NIH 3T3), and the osteogenesis of animal osteoblasts (MC3T3-E1). Results indicated good cell adhesion, penetration, and proliferation. Alkaline phosphatase (ALP) activity and Alizarin red staining (ARS) revealed osteogenic differentiation of animal osteoblasts on the scaffolds. These results demonstrate that the rBC scaffolds are potential candidates for future tissue engineering applications.
La identidad de Wissadula amplissima (Malvaceae)

Sida amplissima L. es el basiónimo de Wissadula amplissima (L.) RE Fr. Se basa en dos breves descripciones, una de Van Royen y la otra de Plumier. La falta de un espécimen van Royen enLeiden circunscribe las posibilidades de tipificación de la ilustración de Plumier, que fuera citada por Linneo y publicado posteriormente por Burman. La ilustración de Plumier es designada como lectotipo de Sida amplissima L. Se reproduce aquí, y se aporta una clave para distinguir esta especie de los asociados.
Molecular phylogeny and divergence time of the water penny genus Eubrianax (Coleoptera: Psephenidae) in Japan

The phylogenetic relationships among the Japanese members of the genus Eubrianax (Coleoptera: Psephenidae) were examined using the mitochondrial cytochrome oxidase subunit I (COI) gene and nuclear 28S rRNA gene sequences. Based on the molecular phylogeny as well as morphological features, the species status of Eubrianax brunneicornis Nakane, 1952 was proposed. The phylogenetic analyses recovered monophyly of the previously proposed pellucidus species group with four Japanese species, whereas a single Japanese species of the granicollis group was included in the lineage of the ramicornis group with five Japanese species. The divergence times of the species were estimated by dating the phylogenetic tree against the fossil record and a molecular clock based on the COI gene. The divergence of the Japanese species was inferred to have occurred during the Pliocene epoch.
Nutrient versus seed bank depletion approaches to controlling exotic annuals in threatened Box Gum woodlands

Control of exotic annuals is often a priority when restoring degraded grasslands or shrublands. This study evaluated combinations of nutrient-depleting (carbon addition) and seed bank-depleting approaches for controlling exotic annuals, and compared the seed bank depletion technique of spring burning with the more easily applied technique of pulse grazing. Treatments were applied in two Box Gum woodlands over 4 years. Consistent with earlier studies, carbon addition dramatically reduced exotic annuals and available nutrients in all 3 years at both sites. Exotic annual grass abundance was significantly reduced in burnt plots following the first year and in grazed plots following the second year of application. Spring burning or grazing did not reduce available nutrients or exotic annual broadleaf abundance at either site. The effect of carbon addition on exotic annuals and available nutrients was so powerful that no additional benefit of the combination treatments was found, although at one site burning and grazing slightly reduced the effectiveness of carbon addition in suppressing broadleaf exotic annuals. We conclude that nutrient-depleting approaches are most effective because they control both exotic annual grasses and broadleaf exotics annuals, but given their expense seed bank-depleting approaches may be more practical where exotic annual grasses dominate. In particular, pulse grazing is readily applied across large areas, offering a relatively simple tool that if appropriately implemented could enhance outcomes of restoration investments in vegetation communities invaded by exotic annual grasses.
Human serum resistance in Trypanosoma brucei

Trypanosoma brucei is the causative agent of both sleeping sickness in humans and the related veterinary disease, Nagana. Both diseases have a wide distribution across sub-Saharan Africa and affect some of the poorest areas of the world. T. brucei can be segregated into three morphologically identical sub-species based on host, geography and pathology. T. b. brucei is limited to domestic and wild animals throughout sub-Saharan Africa and is non-infective to humans due to trypanosome lytic factors found in human serum. T. b. gambiense and T. b. rhodesiense are human infective sub-species, named due to their relative geographic locations. T. b. gambiense is the dominant form of the disease, causing over 90% of reported cases. Study of T. b. gambiense is complicated in that there are two distinct groups. Group 1 is invariably resistant to lysis and by far the more prevalent group. Group 2 T. b. gambiense exhibit a variable resistance phenotype and are only found at a small number of Cote d’Ivoire disease foci. There are two trypanosome lytic factors in human serum (TLF-1 & 2), both containing the proteins Apolipoprotein L1 (ApoL1) and Haptogoblin-related protein (Hpr). It has been conclusively demonstrated that the lytic component of TLF is ApoL1, although Hpr is required for maximal lysis by facilitating uptake of TLF particles via the HpHbR cell surface receptor. This thesis has exposed several features of the human infectivity phenotype in both groups of T. b. gambiense, an area of research for which data has been lacking due to the difficulty of working with the organism. Fluorescence microscopy indicated that group 1 T. b. gambiense exhibit avoidance of TLF-1 particles by down-regulating HpHbR receptor expression and function. However, they are also able to resist the effects of recombinant ApoL1, suggesting an additional neutralisation or compensatory mechanism. Due to group 1 T. b. gambiense avoidance of TLF-1, TLF-2 is the more important lytic particle for this sub-species group and future research must take this into consideration. Unlike group 1, group 2 T. b. gambiense displays a variable human serum resistance phenotype that involves a neutralisation or compensatory mechanism for ApoL1, with no significant avoidance of lytic particles. Despite the high variability of the phenotype of group 2 T. b. gambiense, Quantitative Trait Analysis (QTL) using twenty-five F1 progeny from a T. b. brucei / group 2 T. b. gambiense cross indicated a strong heritable component to human serum resistance largely determined by a 30 gene locus on chromosome 8. Finally, a six multi-locus genotype population analysis of a Cote d’Ivoire T. b. gambiense focus was conducted, revealing little relationship between the two groups of T. b. gambiense in the field. The differences in the human serum resistance phenotypes and population genetics of both groups of T. b. gambiense revealed both prior and during this study make it appear likely that the two groups have evolved distinct human serum resistance strategies.
Glucose kinetics and substrate oxidation during exercise in the follicular and luteal phases

The purpose of this investigation was to determine whether plasma glucose kinetics and substrate oxidation during exercise are dependent on the phase of the menstrual cycle. Once during the follicular (F) and luteal (L) phases, moderately trained subjects [peak O(2) uptake (V(O(2))) = 48.2 +/- 1.1 ml. min(-1). kg(-1); n = 6] cycled for 25 min at approximately 70% of the V(O(2)) at their respective lactate threshold (70%LT), followed immediately by 25 min at 90%LT. Rates of plasma glucose appearance (R(a)) and disappearance (R(d)) were determined with a primed constant infusion of [6,6-(2)H]glucose, and total carbohydrate (CHO) and fat oxidation were determined with indirect calorimetry. At rest and during exercise at 70%LT, there were no differences in glucose R(a) or R(d) between phases. CHO and fat oxidation were not different between phases at 70%LT. At 90%LT, glucose R(a) (28.8 +/- 4.8 vs. 33.7 +/- 4.5 micromol. min(-1). kg(-1); P < 0.05) and R(d) (28.4 +/- 4.8 vs. 34.0 +/- 4.1 micromol. min(-1). kg(-1); P < 0.05) were lower during the L phase. In addition, at 90%LT, CHO oxidation was lower during the L compared with the F phase (82.0 +/- 12.3 vs. 93.8 +/- 9.7 micromol. min(-1) . kg(-1); P < 0.05). Conversely, total fat oxidation was greater during the L phase at 90%LT (7.46 +/- 1.01 vs. 6.05 +/- 0.89 micromol. min(-1). kg(-1); P < 0.05). Plasma lactate concentration was also lower during the L phase at 90%LT concentrations (2.48 +/- 0.41 vs. 3.08 +/- 0.39 mmol/l; P < 0.05). The lower CHO utilization during the L phase was associated with an elevated resting estradiol (P < 0.05). These results indicate that plasma glucose kinetics and CHO oxidation during moderate-intensity exercise are lower during the L compared with the F phase in women. These differences may have been due to differences in circulating estradiol.
Influence of soil properties on coastal sandplain grassland establishment on former agricultural fields

The decline in species‐rich grasslands across the United States has increased the importance of conservation and restoration efforts to preserve the biodiversity supported by these habitats. Abandoned agricultural fields often provide practical locations for the reestablishment of species‐rich grasslands. However, these fields often retain legacies of agriculture both in their soils, which may have higher pH and nitrogen (N) contents than soils that were never farmed, and in their plant communities, which are dominated by non‐native species and poor in native seed stock. We considered methods of reversing these legacies to create native‐species‐rich grassland on former agricultural land. We tested seeding and tilling combined with additions of sulfur (S), carbon (C), N or water to establish diverse sandplain grassland vegetation on an old field on Martha's Vineyard, Massachusetts. We measured soil pH, extractable nitrate and ammonium, and total and native species richness and native species cover for 5 years after treatment. S additions lowered pH to values typical of never‐tilled sandplain ecosystems and increased native species cover, but had no effect on species richness. C, N, and water additions had no significant effects on the soil or vegetation. Seeding and tilling were more effective at restoring native species richness than any soil amendments and indicated a greater importance of biotic factors compared with soil conditions in promoting sandplain vegetation establishment. S amendment accelerated establishment of native species cover for several years but the effect of S additions compared with seeding and tilling alone declined over time.
DEVELOPMENT OF THE COMPOUND EYE OF DROSOPHILA MELANOGASTER AND ITS BAR-EYED MUTANT

1. The cell groups, representing the primordia of the ommatidia of the compound eye of Drosophila melanogaster, have been found in the four-day larva.2. The fusion of the imaginal disks and the supra-esophageal ganglia take place on the third day of larval life.3. There is a correlation between the development of the nervous system and the dioptric apparatus, as shown by the reduction in the size of the optic tract in the bar-eyed mutant.
Tree water uptake in a tropical plantation varying in tree diversity: interspecific differences, seasonal shifts and complementarity

We studied tree water uptake patterns, tested for complementary water use among species and analysed controlling factors in a tropical tree diversity experiment. The water uptake depth of five species was investigated across seasons and diversity levels using the natural abundance of water isotopes (δ2H, δ18O) and modelling. Three distinct water acquisition strategies were found for trees growing in monocultures during the dry season: strong reliance (>70%) on soil water from the upper layer (0–30 cm) (Cedrela odorata), uptake from the upper and deeper layers (>30 cm) in equal proportions (Hura crepitans, Anacardium excelsum and Luehea seemannii) and water uptake predominately from deeper layers (Tabebuia rosea). Seasonal shifts in water uptake were most pronounced for T. rosea. The water uptake pattern of a given species was independent of the diversity level underlining the importance of species identity and species characteristics in spatial and temporal tree water use. Statistics did not show a significant effect of diversity on source water fractions, but we did see some evidence for complementary water resource utilization in mixed species plots, especially in the dry season. Our results also demonstrated that the depth of soil water uptake was related to leaf phenology and tree transpiration rates. A higher proportion of water obtained from deeper soil layers was associated with a high percentage foliage cover in the dry season, which explained the higher transpiration rates. Copyright © 2014 John Wiley & Sons, Ltd.
Prediction of carcase fat depth in live lambs: a comparison of techniques

The accuracy of condition scoring, the Scanogram and Scanoprobe for the prediction of carcase fat depth in live lambs was examined in 99 crossbred ewe lambs. The Scanogram was the most accurate predictor of fat depth at site C (12-13th rib junction, 40 mm from the dorsal midline), and soft tissue depth at site J110 (12-13th rib junction, 110 mm from the dorsal midline) in the carcase [residual standard deviations (RSD) of 1.1 67 and 2.166 mm, respectively]. The accuracy of the Scanogram in predicting carcase fat depth depended on variation in liveweight (P < 0.05). Condition scores were the next best predictors of measurements at sites C and J110 in the carcase (average RSD for three operators of 1.324 and 3.174 mm, respectively). The accuracy of condition scores by the best operator (i.e., the most repeatable and accurate) was largely independent of variation in liveweight. Condition scores were related (P < 0.05) to all carcase dimensions, although a general trend for the three operators was for condition scores to have the strongest relation with soft tissue depth at site J110 and then fat depth at site C, followed by the carcase classification fat score and lastly total tissue depth at site C. The Scanoprobe was the poorest predictor of C and J110 measurements in the carcase (RSD = 1.630 and 4.014 mm, respectively).
Development of a multiplex polymerase chain reaction assay for differentiation of field strain isolates and vaccine strains S19 and RB51 of Brucella in Iran

Summary Bovine brucellosis is a zoonotic disease distributed worldwide and characterized by abortion and reduced fertility in cows. Since brucellosis eradication programme in Iran uses vaccination, test, slaughter and quarantine as control measures, it is essential to distinguish vaccine strains from strains that cause infections among vaccinated cattle herds. We developed and evaluated a multiplex polymerase chain reaction (PCR) assay to identify and differentiate the vaccine strains from wild field isolates, including all Brucella types usually found in cattle in Iran. Two pair primers were used to amplify eri and wbo regions of DNA sequences those strain-specific targets for B. abortus S19 and RB51 vaccine strains. This multiplex PCR method evaluated with DNA from reference strains, two vaccine strains and 29 field strains of Brucella. The results showed that the multiplex PCR can differentiate Brucella isolates into three categories: strain 19 (S19), strain RB51 and field strains. This PCR assay was successfully used, compared with traditional method to differentiate of S19 and RB51 from field Brucella isolates.
Effect of Prior Heat Stress on the Early Growth of Carica papaya

The experiment was carried out to determine the effects of heat stress on some growth parameters like shoot height, leaf area, fresh weight, dry weight as well as the accumulation of chlorophylls in Carica papaya . Seedlings of C. papaya were exposed to prior heat stress at 40 °C. A group of plants was placed in a Gallenkamp oven for four hours; another group of plants was placed in the oven for eight hours while the third group of plants was placed in a dark cupboard for the period of eight hours. Sampling was carried out at weekly intervals starting from seven days after treatment. Plants were randomly picked from each of the three treatments. Three replicates were used for each parameter. The results obtained from the study showed that there was an increment in the shoot height, leaf area, fresh weight and dry weight from the beginning to the end of the experimental period. However, the accumulation of chlorophylls did not follow a particular pattern. The analysis of variance carried out on the data obtained showed that heat stress had a significant effect on the petiole length, shoot height, leaf length, leaf width, leaf area, fresh weight and dry weight. Heat stress, however, did not produce a significant effect on the accumulation of chlorophylls a and b and total chlorophyll.
Applications and data analysis of next-generation sequencing

Abstract: Over the past 6 years, next-generation sequencing (NGS) has been established as a valuable high-throughput method for research in molecular genetics and has successfully been employed in the identification of rare and common genetic variations. Although the high expectations regarding the discovery of new diagnostic targets and an overall reduction of cost have been achieved, technological challenges in instrument handling, robustness of the chemistry, and data analysis need to be overcome. Each workflow and sequencing platform have their particular problems and caveats, which need to be addressed. Regarding NGS, there is a variety of different enrichment methods, sequencing devices, or technologies as well as a multitude of analyzing software products available. In this manuscript, the authors focus on challenges in data analysis when employing different target enrichment methods and the best applications for each of them. Zusammenfassung: In den vergangenen 6 Jahren hat sich “next generation sequencing” (NGS) als wichtige Hochdurchsatz-Methode für die molekulargenetische Forschung etabliert und wurde erfolgreich zur Identifikation seltener und häufiger genetischer Varianten eingesetzt. Während die hohen Erwartungen hinsichtlich der Entdeckung neuer diagnostischer Zielstrukturen und einer Senkung der Kosten erreicht wurden, müssen etliche technologische Herausforderungen hinsichtlich Bedienung der Geräte, Robustheit der Chemie und Handhabung der Datenanalyse noch gemeistert werden. Jedes Anreicherungsverfahren und jede Sequenzierplattform haben ihre spezifischen Probleme und Herausforderungen, die man in Betracht ziehen muss. In Bezug auf „next generation sequencing“ gibt es neben einer Anzahl verschiedener Anreicherungsmethoden, Sequenziergeräten und –techniken auch eine Vielzahl von unterschiedlicher Auswertesoftware. In diesem Artikel richten die Autoren ihr Augenmerk vor allem auf die Schwierigkeiten in der Datenanalyse der verschiedenen Anreichungsverfahren und deren bestmögliche Verwendung.