Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenotypic plasticity and plant adaptation

SUMMARY This paper focuses on phenotypic plasticity as a major mode of adaptation in plants. A methodological critique examines difficulties in studying plasticity, including the conceptually critical distinction between functionally adaptive and inevitable aspects of response. It is argued that plasticity studies depend critically upon the genotypic sample, the choice of environmental factors and factor states, and the definition of phenotypic traits. Examples are drawn from recent studies showing adaptive response by genotypes to physical aspects of the environment, as well as to biotic factors such as neighbour density and the presence of bacterial symbionts. Alterations of offspring traits by parental plants of Polygonum persicaria are discussed as a cross-generational aspect of plastic response to environment. Finally, individual plasticity and local ecotypes are examined as alternative bases of species ecological breadth, and methodological problems in distinguishing these alternatives are discussed.
Studies on the autecology and population biology of the weedy monocarpic perennial, Pastinaca sativa

(1) Wild parsnip (Pastinaca sativa L.) is a monocarpic perennial herb which grows as a weed in North America in grassy habitats that are usually mown in summer. Flowering occurs in May and June, and seeds are mature by early July. Seeds remain attached to the dead erect shoots until autumn, unless the plants are disturbed, as by mowing. (2) At maturity small numbers of seeds can germinate at summer temperatures. As the seeds after-ripen during summer their ability to germinate at high temperatures increases, but there is little increase in ability to germinate at autumn temperatures. Stratification (moist chilling) over winter lowers the temperature requirement for germination, and therefore the majority of seeds in the field germinate in early spring. (3) Seedling mortality is high; of 3980 seedlings marked in a natural population in Kentucky, only thirty-three (0.83%4) flowered before dying. Cohorts of seedlings marked in August, November, December, January and April had concave survivorship curves; cohorts marked in February and March initially had concave survivorship curves, but the curves subsequently became linear. (4) Plants produce rosettes and grow until the second, third, fourth or fifth growing season before producing flowers. Vernalization is required for flowering, and plants reach the flowering stage quicker under long than under short days. (5) An old-field population showed a wide range of individual plant sizes in late May: flowering plants had root-crown diameters (RCDs) of 5-39 mm, and non-flowering plants had RCDs of < 1 (first-year seedlings) to 10 mm. It is suggested that plants must reach a critical size before they can respond to the environmental stimuli of vernalization and photoperiod.
The effect of respiratory mode and oxygen concentration on the risk of aerial predation in fishes

Six bimodal and six water-breathing species of fish were exposed to predation by a green heron (Butorides striatus) in a laboratory experiment to examine the hypothesis that aerial predation selects against the evolution and use of air breathing. Tests were performed at 1.6 and 0.5 mg O2∙L−1 ( and 9 Torr, respectively; 1 Torr = 133.322 Pa). Most water breathers avoided the surface at 1.6 mg∙L−1 but not at 0.5 mg∙L−1, where they performed aquatic surface respiration. Most bimodal species breathed air at both oxygen concentrations. The risk of capture increased with proximity to the surface. The prey species responded to the predator by increasing mean depth, decreasing the rate of air breathing or aquatic surface respiration, and avoiding the vicinity of the predator when surfacing. Despite these and other antipredator characteristics, all species were vulnerable to capture in the test situation. Overall, the survivorship of water-breathing fishes was significantly higher than that of bimodal species at 1.
SHC and GRB-2 Are Constitutively Activated by an Epidermal Growth Factor Receptor with a Point Mutation in the Transmembrane Domain (*)

A single point mutation, Glu Val, equivalent to the activating mutation in the Neu oncogene, was inserted in the transmembrane domain of the human epidermal growth factor (EGF) receptor. Unlike the wild type, Glu-EGF receptor, transfected in NIH3T3 cells, gave rise to focal transformation and growth in agar even in the absence of EGF. Constitutive activity of mutant EGF receptor amounted to 20% of that of wild type receptor stimulated by EGF. In addition, the mutant receptor was more sensitive to EGF, reaching maximum transforming activity at 5 ng/ml EGF. NIH3T3 cells expressing Glu-EGF receptor showed a transformed phenotype and were not arrested in G0 upon serum deprivation. The mutant receptor was constitutively autophosphorylated, and several other cellular proteins were phosphorylated on tyrosine in absence of the ligand. Among these, the SHC adaptor protein was phosphorylated in absence of EGF, the other adaptor, GRB-2, was constitutively associated with the GluEGF receptor in vivo and in vitro, and mitogen-activated protein kinase was constitutively phosphorylated. In contrast, other EGF receptor substrates, like phospholipase C, were not phosphorylated in absence of EGF. The mutant receptor showed a higher sensitivity to cleavage by calpain both in absence and presence of EGF, appeared as a 170- and 150-kDa doublet in cell extracts, and a specific calpain inhibitor blocked the appearance of the 150-kDa form. Since the calpain cleavage site is located in the receptor cytoplasmic tail, this finding suggests that the Glu mutation induces a slightly different conformation in the EGF receptor intracellular domain. In conclusion, our data show that a point mutation in the EGF receptor transmembrane domain was able to constitutively activate the receptor and to induce transformation via constitutive activation of the Ras pathway.
State-of-the-artery: periadventitial adipose tissue (tunica adiposa)

Traditional view considers that the arterial wall is composed of three concentric tissue coats (tunicae): intima, media, and adventitia. However, large- and medium-sized arteries, where usually atherosclerosis develops, are consistently surrounded by periadventitial adipose tissue (PAAT). Here we update growing information about PAAT, and conceptualize it as the fourth coat of arterial wall, that is, tunica adiposa (in brief, adiposa, like intima, media, adventitia). Recent evidence has revealed that adipose tissue expresses not only metabolic, but also secretory (endo- and paracrine) phenotype, producing/releasing a large number of signaling proteins collectively termed adipokines. Through paracrine ("vasocrine") way, adiposa-derived mediators may contribute to various arterial functions such as contraction-relaxation, smooth muscle cell growth, inflammation, hemostasis, and innervation, hence to "outside-in" signaling pathway of atherogenesis. Biomedical Reviews 2009; 20: 41-44.
Impact of Thinning Ponderosa Pines (Pinus ponderosa) on Populations of Abert's Squirrels (Sciurus aberti)

Abstract We estimated the effect of thinning ponderosa pines (Pinus ponderosa) on populations of Abert's squirrels (Sciurus aberti). In 2008 and 2009, thinned and unthinned stands of ponderosa pines were sampled for evidence of over-winter feeding activity. Density of Abert's squirrels decreased from 2008 to 2009. In 2008, evidence of feeding was on 25 of 27 stands with no difference in density of Abert's squirrels between thinned and unthinned stands. Evidence of feeding was much lower in 2009, with 13 of 32 stands showing no evidence of feeding. Resumen Evaluamos los efectos del adelgazamiento de pinos ponderosa (Pinus ponderosa) en las poblaciones de ardillas de Abert (Sciurus aberti). En 2008 y 2009, las parcelas de pinos ponderosa raleadas y no raleadas fueron muestreadas para pruebas de actividad invernal de alimentación. La densidad de ardillas de Abert se redujo de 2008 a 2009. En 2008, la evidencia de la alimentación fue en 25 de 27 parcelas sin ninguna diferencia en la densidad de ardillas de Abert entre parcelas raleadas y no raleadas. La evidencia de la alimentación fue mucho más baja en 2009, con 13 de las 32 parcelas sin mostrar signos de alimentación.
DAMAGE AND ECONOMIC INJURY LEVELS OF THE MULLEIN BUG, CAMPYLOMMA VERBASCI (MEYER) (HETEROPTERA: MIRIDAE), ON APPLE IN THE OKANAGAN VALLEY

Abstract First-generation mullein bug, Campylomma verbasci (Meyer), nymphs damaged four major cultivars of apple in commercial and research orchards from 1982 to 1984. In commercial orchards, C. verbasci was ranked among the top three pests in 22 of 40 samples collected at harvest, and its damage exceeded the economic injury level of 1% culled apples in 17 of the samples. Injury was greatest in "Delicious" cultivars, for which a linear relationship was derived between population density and damage at harvest. Economic injury levels of one and four nymphs per tap are proposed for cvs. Golden and Red Delicious, respectively, in British Columbia. Résumé Des nymphes de la punaise de la molène, Campylomma verbasci (Meyer), de la première génération ont endommagé quatre grands cultivars de pommes dans des vergers commerciaux et expérimentaux de 1982 à 1984. Dans les vergers commerciaux, G. verbasci a été classé parmi les trois principaux ravageurs dans 22 des 40 échantillons recueillis à la récolte, et les dommages causés par cet insecte dépassaient le seuil économique d’endommagement qui est de 1% de pommes rejetées dans 17 échantillons. Les dommages étaient les plus importants chez les cultivars "Delicious", pour lesquels on a établi une relation linéaire entre la densité de la population et les dommages constatés à la récolte. On a proposé des seuils économiques d’endommagement d’une et de quatre nymphes par entaille pour les cultivars de Golden et de Red Delicious respectivement en Colombie-Britiannique
Cloning and characterization of a bursicon‐regulated gene Su(H) in the house fly Musca domestica

Abstract Bursicon is a neuropeptide that regulates cuticle sclerotization (hardening and tanning) in insect via a G‐protein coupled receptor. However, the signal transduction pathway downstream of the G‐protein coupled receptor is currently not well known. In our recent microarray analysis, we identified a panel of genes regulated by bursicon in Drosophila. One of the genes, Suppressor of Hairless, or Su(H), has drawn our attention because its product acts down‐stream of the bursicon receptor. In the present study, we cloned the Drosophila homolog, mdSu(H), from the house fly Musca domestica using 3′ and 5′ rapid amplification of complementary DNA ends. Real‐time polymerase chain reaction analysis revealed that the level of mdSu(H) transcript is up‐regulated by ∼3‐fold 1 h after recombinant bursicon injection, which correlates well with the cuticle sclerotization process observed in the recombinant bursicon‐injected flies. We infer that Su(H) is an essential gene involved in the insect cuticle sclerotization process.
TGFβ2 activation status during cardiac morphogenesis

Transforming growth factor beta (TGFβ) is secreted as a biologically inactive complex by many cell types in vitro, but little is known of TGFβ's activation status in vivo. This study examined the in vivo expression of active and total (active + acid‐activatable) TGFβ2 in embryonic chicken hearts during cardiac morphogenesis (Hamburger‐Hamilton stage 10–24). The concentration of TGFβ2 was measured by an enzyme‐linked immunoassay that recognized active TGFβ2. Whole heart homogenates were either left untreated to measure active TGFβ2 or treated with acid before assay to measure total (active + acid‐activatable) TGFβ2. Total TGFβ2 concentration increased more than 16‐fold between stage 10/11 and stage 24. Active TGFβ2 concentration was highest at stage 14/15, but overall remained relatively constant varying at most by 2.8‐fold. When expressed relative to total TGFβ2, the amount of active TGFβ2 progressively declined from 70% in stage 10/11 hearts to 7% in stage 24 hearts. The distribution of active and total TGFβ2 was examined by immunostaining with an antibody against active TGFβ2. Before immunostaining, sections were either treated with acid or left untreated to determine the distribution of total and active TGFβ2, respectively. Active TGFβ2 immunostaining was first detected in the endothelium, myocardium, and cardiac jelly of stage 14 hearts. Acid treatment had no effect on the distribution or intensity of immunostaining at this stage. Faint, active TGFβ2 immunostaining was restricted to the ventricular myocardium in stage 18 hearts. Acid treatment resulted in a marked increase in staining intensity in the ventricle, but no staining was observed in the atrium or outflow tract. In stage 24 hearts, faint active TGFβ2 staining was detected in the ventricle before acid treatment. After acid treatment, patches of intense punctate stain were found in all regions of the embryonic heart. Increases in TGFβ2 concentration and immunostaining intensity after acidification suggest that a significant amount of TGFβ2 is in the latent form. Stage‐dependent differences in activation status suggest that activation may be a developmentally regulated process in the chick heart and support the notion that activation is an important step in regulating TGFβ actions in vivo. © 2001 Wiley‐Liss, Inc.
Prevalence and characterization of pathogenic Yersinia enterocolitica in pig tonsils from different slaughterhouses

The prevalence of yadA-positive Yersinia enterocolitica was determined in 185 pig tonsils from nine slaughterhouses using both the PCR and culture method. The mean prevalence was 37%, varying from 13% to 45% when both PCR and culture-positive results were included. Of the 52 PCR-positive tonsil samples, 20 were culture-negative, while of the 48 culture-positive, 16 were PCR-negative. Using the culture method, Y. enterocolitica belonging to the bioserotype 4/O:3 was found in 61 tonsils, of which 48 were yadA-positive. Type 4/O:3 was the only pathogenic bioserotype found in this study. Most of the yadA-positive samples (85%) were recovered already after overnight enrichment. A total of 61 isolates, including 13 yadA-negative isolates from different samples, were characterized with PFGE. UsingNotI and XbaI, 20 and 17 PFGE patterns were obtained, respectively. Although the patterns were not identical, most of them played only minor deviations. A total of 26 pulsotypes, defined by combination of the various NotI andXbaI digestion profiles, were observed. Two to eight different pulsotypes were observed in each slaughterhouse, The most common pulsotypes, 1a and 4g, were found in 36% and 20% of the tonsils, respectively and these pulsotypes were widely distributed to most of the slaughterhouses. The pulsotype 1a was identified in eight out of nine slaughterhouses and the pulsotype 4g in seven slaughterhouses.
A Logistic Regression Model for Predicting the Upstream Extent of Fish Occurrence Based on Geographical Information Systems Data

Abstract Regulations governing human activities in streams and riparian zones frequently differ depending on whether or not a stream reach supports fish. Fish presence or absence is usually determined by sampling or by assuming the presence of fish if the stream exhibits certain physical characteristics. Field surveys of fish occurrence in streams are time consuming and expensive. Inference of fish presence from simple thresholds of physical attributes, such as gradient or channel width alone, is inaccurate. We attempted to improve the accuracy and efficiency of this determination by developing a geographical information systems (GIS)-based predictive model. A 10-m digital elevation model incorporated field data on fish distribution from 517 streams in western Washington State and GIS-derived representations of the physical characteristics of stream networks. A model predicting the upstream extent of fish occurrence was derived using logistic regression models coupled with a heuristic “stopping rule. ” Can.
Somatic embryogenesis for plant production of Abies lasiocarpa

Seeds of Abies lasiocarpa (Hook.) Nutt. (subalpine fir) were dissected, and the different parts were analyzed for elemental composition. The data were used to design a novel growth medium for initiation of somatic embryogenesis. Embryogenic cultures were initiated from immature zygotic embryos from six open-pollinated families of A. lasiocarpa on three different media. The frequency of initiation was the highest in early to mid-July when the zygotic embryo explants were ca. 0.8 mm long. Thereafter the response declined rapidly. The culture media did not significantly affect the initiation frequencies, but the subsequent growth and culture survival was dependent on the culture medium. On the Schenk Hildebrandt medium, many cultures ceased to grow and died. Several of the decaying cultures were rescued after transfer to one of the new media. Proliferating cultures could be stimulated to produce mature embryos. Of 2510 mature somatic embryos, 212 (8.4%) converted to plants, and 35 plants have grown over two .
Effect of monoglycerides on the thermal inactivation kinetics ofBacillus cereusF4165/75 spores

The combined effect of monoglycerides and heat on the inactivation of Bacillus cereusF4165/75 spores was investigated. Linear survivor curves were obtained for spores suspended in buffer with or without added monoglyceride, and were consistent with first-order inactivation kinetics. In the presence of 3.056 mmol l–1monoglyceride, the heat resistance of spores was affected differently depending upon the monoglyceride. Monolaurin and monolinolenin significantly lowered the spores' heat resistance, whereas monomyristin and monolinolein increased it but less dramatically. TheD91°Cvalues obtained increased in the following order: monolaurin (3.056 mmol l–1)< monolinolenin (3.056 mmol l–1)< phosphate buffer (pH 7)< monomyristin (3.056 mmol l–1)< monolinolein (3.056 mmol l–1). Monolaurin was the most effective monoglyceride, possibly because of its lipophilic nature and great emulsifying properties. Increasing its concentration from 1.058 to 5 mmol l–1significantly enhanced the heat inactivation rate ofB. cereusF4165/75 spores. The thermodynamic data were used to speculate on the mechanism of heat inactivation of the spores. These thermodynamic values were not significantly different in the presence or absence of monolaurin. This suggested that the enhancing effect due to increasing concentrations of monolaurin on the thermal inactivation of spores is essentially identical at any sterilization temperature, although it allows the heating temperature for sterilization to be reduced.
Dynamics of Human Reproduction: Biology Biometry, Demography

6 Dimension 3: Disciplinary Core Ideas Life Sciences | A The role of unifying principles in advancing modern life sciences is articulated in The Role of Theory in Advancing 21st-Century Biology and A New Biology for the 21st Century [2, 3]. In developing these core ideas, the committee also drew on the established K-12 science education literature, including National Science Education Standards and
How to assess the prediction accuracy of species presence–absence models without absence data?

It is very common that only presence data are available in ecological niche modeling. However, most existing methods for evaluating the accuracy of presence–absence (binary) predictions of species require presence–absence data. The aim of this study is to present a new method for accuracy assessment that does not rely on absence data. Two new statistics Fpb and Fcpb were derived based on presence–background data. With generated six virtual species, we used DOMAIN, generalized linear modeling (GLM), and maximum entropy (MAXENT) to produce different species presence–absence predictions. To investigate the effectiveness of the new statistics in accuracy assessment, we used Fpb, Fcpb, the traditional F-measure (F), kappa coefficient, true skill statistic (TSS), area under the receiver operating characteristic curve (AUC), and the contrast validation index (CVI) to evaluate the accuracy of predictions, and the behaviors of these accuracy measures were compared. The effectiveness of Fpb for threshold selection and estimation of species prevalence was also investigated. Experimental results show that Fcpb is an estimate of F. The Pearson's correlation coefficient (COR) between Fcpb and F is 0.9882, with a root-mean-square error (RMSE) of 0.0171. In general, Fpb, Fcpb, F, kappa coefficient, TSS, and CVI can sort models by the accuracy of binary prediction, but AUC is not appropriate to evaluate the accuracy of binary prediction. For DOMAIN, GLM, and MAXENT, finding the threshold by maximizing Fpb and by maximizing F result in similar accuracies. In addition, the estimation of species prevalence based on binary output with maximizing Fpb as the thresholding method is significantly more accurate than simply averaging the original continuous output. The best estimate of prevalence is provided by the binary output of MAXENT, with an RMSE of 0.0116. Finally, we conclude that the new method is promising in accuracy assessment, threshold selection, and estimation of species prevalence, all of which are important but challenging problems with presence-only data. Because it does not require absence data, the new method will have important applications in ecological niche modeling.