The influence of sampling design on tree-ring-based quantification of forest growth

Tree-rings offer one of the few possibilities to empirically quantify and reconstruct forest growth dynamics over years to millennia. Contemporaneously with the growing scientific community employing tree-ring parameters, recent research has suggested that commonly applied sampling designs (i.e. how and which trees are selected for dendrochronological sampling) may introduce considerable biases in quantifications of forest responses to environmental change. To date, a systematic assessment of the consequences of sampling design on dendroecological and-climatological conclusions has not yet been performed. Here, we investigate potential biases by sampling a large population of trees and replicating diverse sampling designs. This is achieved by retroactively subsetting the population and specifically testing for biases emerging for climate reconstruction, growth response to climate variability, long-term growth trends, and quantification of forest productivity. We find that commonly applied sampling designs can impart systematic biases of varying magnitude to any type of tree-ring-based investigations, independent of the total number of samples considered. Quantifications of forest growth and productivity are particularly susceptible to biases, whereas growth responses to short-term climate variability are less affected by the choice of sampling design. The world's most frequently applied sampling design, focusing on dominant trees only, can bias absolute growth rates by up to 459% and trends in excess of 200%. Our findings challenge paradigms, where a subset of samples is typically considered to be representative for the entire population. The only two sampling strategies meeting the requirements for all types of investigations are the (i) sampling of all individuals within a fixed area; and (ii) fully randomized selection of trees. This result advertises the consistent implementation of a widely applicable sampling design to simultaneously reduce uncertainties in tree-ring-based quantifications of forest growth and increase the comparability of datasets beyond individual studies, investigators, laboratories, and geographical boundaries.

Growth in Virologically Suppressed HIV Positive Children on Antiretroviral Therapy: Individual and Population-Level References

BACKGROUND Combination antiretroviral therapy (ART) suppresses viral replication in HIV-infected children. The growth of virologically suppressed children on ART has not been well documented. We aimed to develop dynamic reference curves for weight-for-age z scores (WAZ) and height-for-age z scores (HAZ). RESULTS A total of 4,876 children were followed for 7,407 person-years. Analyses were stratified by baseline z-scores and age, which were the most important predictors of growth response. The youngest children showed the most pronounced increase in weight and height initially but catch-up growth stagnated after 1-2 years. Three years after starting ART, WAZ ranged from -2.2 (95% Prediction interval -5.6 to 0.8) in children with baseline age "5 years and z-score "-3 to 0.0 (-2.7 to 2.4) in children with baseline age "2 years and WAZ "-1. For HAZ the corresponding range was -2.3 (-4.9 to 0.3) in children with baseline age"5 years and z-score "-3 to 0.3 (-3.1 to 3.4) in children with baseline age 2-5 years and HAZ "-1. CONCLUSIONS We have developed an online tool to calculate reference trajectories in fully suppressed children. The web application could help to define 'optimal' growth response and identify children with treatment failure.

Relationship of Turfgrass Growth and Quality to Soil Nitrate Desorbed from Anion Exchange Membranes

Anion exchange membranes (AEMs) are a potential method for determining the plant available N status of soils; however, their capacity for use with turfgrass has not been researched extensively. The main objective of this experiment was to determine the relationship between soil nitrate desorbed from AEMs and growth response and quality of turfgrass managed as a residential lawn. Two field experiments were conducted with a bluegrass-ryegrass-fescue mixture receiving four rates of N fertilizer (0, 98, 196, and 392 kg N ha(-1) yr(-1)) with clippings returned or removed. The soils at the two sites were a Paxton fine sandy loam (coarse-loamy, mixed, active, mesic Oxyaquic Dystrudepts) and a variant of a Hinckley gravelly sandy loam (sandy-skeletal, mixed, mesic Typic Udorthents). Anion exchange membranes were inserted into plots and exchanged weekly during the growing seasons of 1998 and 1999. Nitrate-N was desorbed from AEMs and quantified. As N fertilization rates increased, desorbed NO3-N increased. The relationship of desorbed NO3-N from AEMs to clipping yield and turfgrass quality was characterized using quadratic response plateau (QRP) and Cate-Nelson models (C-Ns). Critical levels of desorbed NO3-N ranged from 0.86 to 8.0 microgram cm(-2) d(-1) for relative dry matter yield (DMY) and from 2.3 to 12 microgram cm(-2) d(-1) for turfgrass quality depending upon experimental treatment. Anion exchange membranes show promise of indicating the critical levels of soil NO3-N desorbed from AEMs necessary to achieve maximum turfgrass quality and yield without overapplication of N.

THE BACON CHOW STUDY: THE RELATIONSHIP BETWEEN INFECTIOUS ILLNESS AND GROWTH OF INFANTS

Multiple dietary deficiencies and high rates of infectious illness are major health problems leading to malnutrition and limitation of growth of children in developing countries. Longitudinal studies which provide information on illness incidence and growth velocity are needed in order to untangle the complex interrelationship between nutrition, illness and growth. From 1967 to 1973, researchers led by Dr. Bacon Chow of the Johns Hopkins University School of Hygiene undertook a quasi-experimental prospective study in Suilin Township, Taiwan to determine the effects of a nutritional supplement to the diets of pregnant and lactating women on the growth, development and resistance to disease of their offspring. This dissertation presents results from the analysis of infant morbidity and postnatal growth.^ Maternal nutritional supplementation has no apparent effect on the postnatal growth or morbidity of infants. Significant sex differences exist in growth response to illness and in illness susceptibility. Male infants have more diarrhea and upper respiratory illness. Respiratory illness is positively associated with growth rate in weight in the first semester of life. Diarrhea is significantly negatively associated with growth in length in the second semester. Small-for-date infants are more susceptible to illness in general and have a different pattern of growth response than large-for-date infants.^ Principal components analysis of illness data is shown to be an effective technique for making more precise use of ambiguous morbidity data. Multiple regression with component scores is an accurate method for estimating variance in growth rate predicted by indepenent illness variables. A model is advanced in which initial postnatal growth rate determines subsequent susceptibility to nutritional stress and infection. Initial growth rate is a function of prenatal nutrition, but is not significantly affected by maternal supplementation during gestation or lactation. Critical evaluation is made of nutritional supplementation programs which do not afford disease control.^

Elevated pCO2 from late summer coastal upwellings in the western Baltic Sea enhances vegetative growth in the brown algae Fucus serratus: a laboratory assessment

The brown algae Fucus serratus is one of the major meadow forming algae of the Western Baltic Sea nearshore ecosystem. At the end of summer, those meadows are exposed to local upwelling suddenly increasing the pCO2 and DIC up to 2500 µatm and 2250 µmol/kg resp., for period of days to weeks. This study investigates the growth response of summer's vegetative Fucus serratus to elevated pCO2 (1350 and 4080 µatm) during a 40 days laboratory incubation. After 10 days, increases of growth rates of 20 % and 47 % of the control were observed in the 1350 and 4080 µatm pCO2 treatments respectively. Beyond 20 days, the growth rates collapsed in all treatments due to nutrients shortage, as demonstrated by high C:N ratios (95:1) and low N tissue content (0.04 % of dry weight). The collapse occurs faster at higher pCO2. On day 30, growth rates were reduced by 40 % and 100 % relative to the control at 1350 and 4080 µatm respectively. These results are consistent with a fertilizing effect of elevated pCO2 on Fucus serratus presumably linked to the transition from active HCO3- to passive CO2(aq) uptake. This positive effect is limited by nutrients resources, low seawater dissolved inorganic N and P and shortage of the nutrients reserves accumulated over the previous autumn and winter.

Insulin-like growth factor I is a growth-promoting factor for Leishmania promastigotes and amastigotes

Leishmaniases are diseases caused by protozoa of the genus Leishmania that affect more than 20 million people in the world. The initial phase of the infection is fundamental for either the progression or control of the disease. The Leishmania parasites are injected in the skin as promastigotes and then, after been phagocytized by the host macrophages, rapidly transform into amastigotes. In this phase different nonspecific cellular and humoral elements participate. We have shown previously that insulin-like growth factor (IGF)-I that is constitutively present in the skin induces growth of Leishmania promastigotes. In the present paper we show further evidence for the importance of this factor: (i) IGF-I also can induce a growth response in Leishmania (Leishmania) mexicana amastigotes; (ii) IGF-I binds specifically to a putative single-site receptor on both promastigotes and amastigotes; (iii) IGF-I induces a rapid tyrosine phosphorylation of parasite proteins with different molecular mass in promastigotes and amastigotes of L. (L.) mexicana; and, finally, (iv) the cutaneous lesion in the mice when challenged by IGF-I-preactivated Leishmania (Viannia) panamensis is increased significantly because of inflammatory process and growth of parasites. We thus suggest that IGF-I is another important host factor participating in the Leishmania–host interplay in the early stage during the establishment of the infection and presumably also in the later stages.

Evidence That Auxin-Induced Growth of Tobacco Leaf Tissues Does Not Involve Cell Wall Acidification1

Interveinal strips (10 × 1.5 mm) excised from growing tobacco (Nicotiana tabacum L. cv Xanthi) leaves have an auxin-specific, epinastic growth response that is developmentally regulated and is not the result of ethylene induction (C.P. Keller, E. Van Volkenburgh [1997] Plant Physiol 113: 603–610). We report here that auxin (10 μm naphthalene acetic acid) treatment of strips does not result in plasma membrane hyperpolarization or detectable proton efflux. This result is in contrast to the expected responses elicited by 1 μm fusicoccin (FC) treatment, which in other systems mimics auxin growth promotion through stimulation of the plasma membrane H+-ATPase and resultant acid wall loosening; FC produced both hyperpolarization and proton efflux in leaf strips. FC-induced growth was much more inhibited by a strong neutral buffer than was auxin-induced growth. Measurements of the osmotic concentration of strips suggested that osmotic adjustment plays no role in the auxin-induced growth response. Although cell wall loosening of some form appears to be involved, taken together, our results suggest that auxin-induced growth stimulation of tobacco leaf strips results primarily from a mechanism not involving acid growth.

Transcription factor EGR-1 suppresses the growth and transformation of human HT-1080 fibrosarcoma cells by induction of transforming growth factor beta 1.

The early growth response 1 (EGR-1) gene product is a transcription factor with role in differentiation and growth. We have previously shown that expression of exogenous EGR-1 in various human tumor cells unexpectedly and markedly reduces growth and tumorigenicity and, conversely, that suppression of endogenous Egr-1 expression by antisense RNA eliminates protein expression, enhances growth, and promotes phenotypic transformation. However, the mechanism of these effects remained unknown. The promoter of human transforming growth factor beta 1 (TGF-beta 1) contains two GC-rich EGR-1 binding sites. We show that expression of EGR-1 in human HT-1080 fibrosarcoma cells uses increased secretion of biologically active TGF-beta 1 in direct proportion (rPearson = 0.96) to the amount of EGR-1 expressed and addition of recombinant human TGF-beta 1 is strongly growth-suppressive for these cells. Addition of monoclonal anti-TGF-beta 1 antibodies to EGR-1-expressing HT-1080 cells completely reverses the growth inhibitory effects of EGR-1. Reporter constructs bearing the EGR-1 binding segment of the TGF-beta 1 promoter was activated 4- to 6-fold relative to a control reporter in either HT-1080 cells that stably expressed or parental cells cotransfected with an EGR-1 expression vector. Expression of delta EGR-1, a mutant that cannot interact with the corepressors, nerve growth factor-activated factor binding proteins NAB1 and NAB2, due to deletion of the repressor domain, exhibited enhanced transactivation of 2- to 3.5-fold over that of wild-type EGR-1 showing that the reporter construct reflected the appropriate in vivo regulatory context. The EGR-1-stimulated transactivation was inhibited by expression of the Wilms tumor suppressor, a known specific DNA-binding competitor. These results indicate that EGR-1 suppresses growth of human HT-1080 fibrosarcoma cells by induction of TGF-beta 1.

Effect of root zone temperature on oilseed rape (Brassica napus) response to boron

Oilseed rape (Brassica napus) is sensitive to low boron (B) supply, and its growth response to B may be influenced by soil temperature. To test the relationship between B and temperature, oilseed rape (cv. Hyola 42) seedlings were grown at 10 degrees C (low) root zone temperature (RZT) with B supply from deficient to adequate B levels until growth of low B plants just began to slow down. Half of the pots were then transferred to 20 degrees C (warm) RZT for 11 days before they were moved back to 10 degrees C RZT for the final 4 days. Both plant dry mass and B uptake increased after plants were exposed to warm RZT. However, plant B deficiency was exacerbated by warm RZT in low B plants because of increased relative growth rate and shoot-root ratio without a commensurate increase in B uptake rate. It is concluded that RZT above the critical threshold for chilling injury in oilseed rape can nevertheless affect the incidence of B deficiency by altering shoot-root ratio and hence the balance between shoot B demand and B uptake.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Data compilation of ciliates growth rate, grazing rate and gross gowth efficiency from field and labratory experiments

The present data compilation includes ciliates growth rate, grazing rate and gross growth efficiency determined either in the field or in laboratory experiments. From the existing literature, we synthesized all data that we could find on cilliate. Some sources might be missing but none were purposefully ignored. Field data on microzooplankton grazing are mostly comprised of grazing rate using the dilution technique with a 24h incubation period. Laboratory grazing and growth data are focused on pelagic ciliates and heterotrophic dinoflagellates. The experiment measured grazing or growth as a function of prey concentration or at saturating prey concentration (maximal grazing rate). When considering every single data point available (each measured rate for a defined predator-prey pair and a certain prey concentration) there is a total of 1485 data points for the ciliates, counting experiments that measured growth and grazing simultaneously as 1 data point.

Effects of vermicomposted spent mushroom compost on growing medium characteristics, plant growth, yield and abiotic stress tolerance

Treatment of agricultural biodegradable wastes and by-products can be carried out using composting or vermicomposting, or a combination of both treatment methods, to create a growing medium amendment suitable for horticultural use. When compared to traditional compost-maturation, vermicompost-maturation resulted in a more mature growing medium amendment i.e. lower C/N and pH, with increased nutrient content and improved plant growth response, increasing lettuce shoot fresh and dry weight by an average of 15% and 14%, respectively. Vermicomposted horse manure compost was used as a growing medium amendment for lettuce and was found to significantly increase lettuce shoot and root growth, and chlorophyll content. When used as a growing medium amendment for tomato fruit production, vermicomposted spent mushroom compost increased shoot growth and marketable yield, and reduced blossom end rot in two independent studies. Vermicompost addition to peat-based growing media increased marketable yield by an average of 21%. Vermicompost also improved tomato fruit quality parameters such as acidity and sweetness. Fruit sweetness, as measured using Brix value, was significantly increased in fruits grown with 10% or 20% vermicompost addition by 0.2 in truss one and 0.3 in truss two. Fruit acidity (% citric acid) was significantly increased in plants grown with vermicompost by an average of 0.65% in truss one and 0.68% in truss two. These changes in fruit chemical parameters resulted in a higher tomato fruit overall acceptability rating as determined by a consumer acceptance panel. When incorporated into soil, vermicomposted spent mushroom compost increased plant growth and reduced plant stress under conditions of cold stress, but not salinity or heat stress. The addition of 20% vermicompost to cold-stressed plants increased plant growth by an average of 30% and increased chlorophyll fluorescence by an average of 21%. Compared to peat-based growing medium, vermicompost had consistently higher nutrient content, pH, electrical conductivity and bulk density, and when added to a peat-based growing medium, vermicomposted spent mushroom compost altered the microbial community. Vermicompost amendment increased the microbial activity of the growing medium when incorporated initially, and this increased microbial activity was observed for up to four months after incorporation when plants were grown in it. Vermicomposting was shown to be a suitable treatment method for agricultural biodegradable wastes and by-products, with the resulting vermicompost having suitable physical, chemical and biological properties, and resulting in increased plant growth, marketable yield and yield quality, when used as an amendment in peat-based growing medium.

Salicaceae Endophytes: Growth Promotion Potential in Rice (Oryza sativa L.) and Maize (Zea mays L.) and Bio-Control of Plant Pathogen

Thesis (Ph.D.)--University of Washington, 2016-08

Essential regulatory elements for NHE3 gene transcription in renal proximal tubule cells

The objectives of the present study were to identify the cis-elements of the promoter absolutely required for the efficient rat NHE3 gene transcription and to locate positive and negative regulatory elements in the 5’-flanking sequence (5’FS), which might modulate the gene expression in proximal tubules, and to compare this result to those reported for intestinal cell lines. We analyzed the promoter activity of different 5’FS segments of the rat NHE3 gene, in the OKP renal proximal tubule cell line by measuring the activity of the reporter gene luciferase. Because the segment spanning the first 157 bp of 5’FS was the most active it was studied in more detail by sequential deletions, point mutations, and gel shift assays. The essential elements for gene transcription are in the region -85 to -33, where we can identify consensual binding sites for Sp1 and EGR-1, which are relevant to NHE3 gene basal transcription. Although a low level of transcription is still possible when the first 25 bp of the 5’FS are used as promoter, efficient transcription only occurs with 44 bp of 5’FS. There are negative regulatory elements in the segments spanning -1196 to -889 and -467 to -152, and positive enhancers between -889 and -479 bp of 5’FS. Transcription factors in the OKP cell nuclear extract efficiently bound to DNA elements of rat NHE3 promoter as demonstrated by gel shift assays, suggesting a high level of similarity between transcription factors of both species, including Sp1 and EGR-1.

Numerical modeling of ductile crack extension in high pressure pipelines with longitudinal flaws

This study examines the applicability of a micromechanics approach based upon the computational cell methodology incorporating the Gurson-Tvergaard (GT) model and the CTOA criterion to describe ductile crack extension of longitudinal crack-like defects in high pressure pipeline steels. A central focus is to gain additional insight into the effectiveness and limitations of both approaches to describe crack growth response and to predict the burst pressure for the tested cracked pipes. A verification study conducted on burst testing of large-diameter, precracked pipe specimens with varying crack depth to thickness ratio (a/t) shows the potential predictive capability of the cell approach even though both the CT model and the CTOA criterion appear to depend on defect geometry. Overall, the results presented here lend additional support for further developments in the cell methodology as a valid engineering tool for integrity assessments of pipelines with axial defects. (C) 2011 Elsevier Ltd. All rights reserved,