Contributors: William W. Macfarlane, Joseph M. Wheaton, Nicolaas Bouwes, Martha L. Jensen, Jordan T. Gilbert, Nate Hough-Snee, John A. Shivik
... The construction of beaver dams facilitates a suite of hydrologic, hydraulic, geomorphic, and ecological feedbacks that increase stream complexity and channel–floodplain connectivity that benefit aquatic and terrestrial biota. Depending on where beaver build dams within a drainage network, they impact lateral and longitudinal connectivity by introducing roughness elements that fundamentally change the timing, delivery, and storage of water, sediment, nutrients, and organic matter. While the local effects of beaver dams on streams are well understood, broader coverage network models that predict where beaver dams can be built and highlight their impacts on connectivity across diverse drainage networks are lacking. Here we present a capacity model to assess the limits of riverscapes to support dam-building activities by beaver across physiographically diverse landscapes. We estimated dam capacity with freely and nationally-available inputs to evaluate seven lines of evidence: (1) reliable water source, (2) riparian vegetation conducive to foraging and dam building, (3) vegetation within 100m of edge of stream to support expansion of dam complexes and maintain large colonies, (4) likelihood that channel-spanning dams could be built during low flows, (5) the likelihood that a beaver dam is likely to withstand typical floods, (6) a suitable stream gradient that is neither too low to limit dam density nor too high to preclude the building or persistence of dams, and (7) a suitable river that is not too large to restrict dam building or persistence. Fuzzy inference systems were used to combine these controlling factors in a framework that explicitly also accounts for model uncertainty. The model was run for 40,561km of streams in Utah, USA, and portions of surrounding states, predicting an overall network capacity of 356,294 dams at an average capacity of 8.8dams/km. We validated model performance using 2852 observed dams across 1947km of streams. The model showed excellent agreement with observed dam densities where beaver dams were present. Model performance was spatially coherent and logical, with electivity indices that effectively segregated capacity categories. That is, beaver dams were not found where the model predicted no dams could be supported, beaver avoided segments that were predicted to support rare or occasional densities, and beaver preferentially occupied and built dams in areas predicted to have pervasive dam densities. The resulting spatially explicit reach-scale (250m long reaches) data identifies where dam-building activity is sustainable, and at what densities dams can occur across a landscape. As such, model outputs can be used to determine where channel–floodplain and wetland connectivity are likely to persist or expand by promoting increases in beaver dam densities.
Contributors: Heiko Groenitz
... The diagonal method (DM) is an innovative technique to obtain trustworthy survey data on an arbitrary categorical sensitive characteristic Y∗ (e.g., income classes, number of tax evasions). The estimation of the unconditional distribution of Y∗ from DM data has already been shown. Now, a covariate extension of the DM, that is, methods to investigate the dependence of Y∗ on nonsensitive covariates, is sought. For instance, the dependence of income on gender and profession may be under study. The covariate extensions of privacy-protecting survey designs are broadened by the covariate DM, especially because existing methods focus on binary Y∗. LR-DM estimation and stratum-wise estimation are described, where the former is based on a logistic regression model, leads to a generalized linear model, and requires computer-intensive methods. The existence of a certain regression estimate is investigated. Moreover, the connection between efficiency of the LR-DM estimation and the degree of privacy protection is studied and appropriate model parameters of the DM are searched. This problem of finding suitable model parameters is rarely addressed for privacy-protecting survey methods for multicategorical Y∗. Finally, the LR-DM estimation is compared with the stratum-wise estimation. MATLAB programs that conduct the presented estimations are provided as supplemental material.
Contributors: Krista C. Drechsler, Maria J. Ferrua
... Solid food disintegration within the stomach has a major role on the rate and final bioavailability of nutrients within the body. Understanding the link between food material properties and their behaviour during gastric digestion is key to the design of novel structures with enhanced functionalities. However, despite extensive research, the establishment of proper relationships has proved difficult. This work builds on the hypothesis that to bridge this knowledge gap a better understanding of the underlying mechanisms of food disintegration during digestion is needed. The purpose of this study is to propose a new protocol that, by uncoupling the physicochemical processes occurring during gastric digestion, allows for a more rigorous understanding of these mechanisms. Using steamed potatoes as a product model, this study aims to develop a viable methodology to characterize the role of gastric juice and compressive forces on the breakdown mechanics of solid foods during digestion. From a general viewpoint, this work not only reveals the importance of the parameter used to describe the size distribution of food particles on the interpretation of their breakdown behaviour, but also provides a new framework to characterize the mechanisms involved. Results also illustrate that food breakdown during gastric digestion might well not follow a unimodal behaviour, highlighting the need to characterize their performance based on parameters describing broad aspects of their particle size distribution rather than single point values. Arguably simplistic on its approach, this study illustrates how an improved understanding of the role of chemical and physical processes on the breakdown mechanics of solid foods can facilitate valid inferences with respect to their in-vivo performance during digestion. In particular, it shows that while the contraction forces occurring in the stomach can easily disintegrate the potato matrix at the molecular level, the continuous exposure to gastric juices will promote their disintegration into progressively smaller debris. A discussion on the challenges and future directions for the implementation of a more general and standardized protocol is provided. Not intended to reproduce the breakdown behaviour of foods during gastric digestion, but rather to characterize the mechanisms involved, the proposed protocol would open new opportunities to identify the material properties governing the performance of different foods upon ingestion.
Contributors: Samuel M. Gross, Robert Tibshirani
... A model is presented for the supervised learning problem where the observations come from a fixed number of pre-specified groups, and the regression coefficients may vary sparsely between groups. The model spans the continuum between individual models for each group and one model for all groups. The resulting algorithm is designed with a high dimensional framework in mind. The approach is applied to a sentiment analysis dataset to show its efficacy and interpretability. One particularly useful application is for finding sub-populations in a randomized trial for which an intervention (treatment) is beneficial, often called the uplift problem. Some new concepts are introduced that are useful for uplift analysis. The value is demonstrated in an application to a real world credit card promotion dataset. In this example, although sending the promotion has a very small average effect, by targeting a particular subgroup with the promotion one can obtain a 15% increase in the proportion of people who purchase the new credit card.
Evaluating long-term monitoring of temperate reef fishes: A simulation testing framework to compare methods
Contributors: Denham Parker, Henning Winker, Anthony Bernard, Albrecht Götz
... A simulation testing framework was developed to evaluate the efficacy of detecting population trends of two sampling methods used to monitor inshore fish populations: angling and baited remote underwater stereo-video systems (stereo-BRUVs). The study is based on data collected as part of a long-term monitoring program in the Tsitsikamma National Park marine protected area, South Africa. As a test scenario, declining population trajectories of the most abundant species, Chrysoblephus laticeps, were simulated by introducing consecutive years of reduced recruitment over periods of 10 and 20 years applying an age-structured operating model. The operating model was designed to generate method-specific relative abundance indices and length–frequency data, using parameters derived from existing data collected in the long-term monitoring program. These were then fitted with an age-structured estimation model. Estimated spawner-biomass depletion was compared to the ‘true’ simulated population to quantify method-specific accuracy and bias using root-mean-squared error. Due to higher data variability and inherent size selectivity of angling, stereo-BRUVs provided more accurate spawner-biomass trends when describing a distinct population decline over 10 and 20 years. Additionally, spawner-biomass was found to be a more accurate population estimate than relative abundance indices due to the inclusion of population size structure information. The study demonstrates the potential of using simulation testing to evaluate sampling methods, given that the process generates the ‘true’ population with a known abundance and size structure.
Research article - ZmNAC55, a maize stress-responsive NAC transcription factor, confers drought resistance in transgenic Arabidopsis
Contributors: Hude Mao, Lijuan Yu, Ran Han, Zhanjie Li, Hui Liu
... Abiotic stress has been shown to significantly limit the growth and productivity of crops. NAC transcription factors play essential roles in response to various abiotic stresses. However, only little information regarding stress-related NAC genes is available in maize. Here, we cloned a maize NAC transcription factor ZmNAC55 and identified its function in drought stress. Transient expression and transactivation assay demonstrated that ZmNAC55 was localized in the nucleus and had transactivation activity. Expression analysis of ZmNAC55 in maize showed that this gene was induced by drought, high salinity and cold stresses and by abscisic acid (ABA). Promoter analysis demonstrated that multiple stress-related cis-acting elements exist in promoter region of ZmNAC55. Overexpression of ZmNAC55 in Arabidopsis led to hypersensitivity to ABA at the germination stage, but enhanced drought resistence compared to wild-type seedlings. Transcriptome analysis identified a number of differentially expressed genes between 35S::ZmNAC55 transgenic and wild-type plants, and many of which are involved in stress response, including twelve qRT–PCR confirmed well-known drought-responsive genes. These results highlight the important role of ZmNAC55 in positive regulates of drought resistence, and may have potential applications in transgenic breeding of drought-tolerant crops.
Research article - Overexpression of sucrose transporter gene PbSUT2 from Pyrus bretschneideri, enhances sucrose content in Solanum lycopersicum fruit
Contributors: Li-Fen Wang, Xiao-Xiao Qi, Xiao-San Huang, Lin-Lin Xu, Cong Jin, Jun Wu, Shao-Ling Zhang
... Sucrose transporters (SUTs) belong to the major facilitator superfamily. The function of SUTs has been intensively investigated in some higher plants, whereas that in pear fruit is unknown. In this study, the cloning and functional characterization of a sucrose transporter, PbSUT2, in pear (Pyrus bretschneideri Rehd. cv. ‘Yali’) fruits are reported. PbSUT2 encoded a protein of 498 amino acid residues, and was localized in the plasma membrane of transformed onion epidermal cells and Arabidopsis protoplasts. Phylogenetic analysis revealed that PbSUT2 belonged to the SUT4 clade. The phenotype of overexpression of PbSUT2 tomato plants included early flowering, higher fruit quantity and lower plant height. Overexpression of PbSUT2 in transgenic tomato plants led to increases in the net photosynthetic rate in leaves and sucrose content in mature fruit compared with wild-type tomato plants, and a decrease in the contents of glucose, fructose and total soluble sugars in mature fruits. These results suggested that PbSUT2 affected sucrose content in sinks and the flowering phase during tomato plant growth and development.
Clupeiformes’ Egg Envelope Proteins characterization: The case of Engraulis encrasicolus as a proxy for stock assessment through a novel molecular tool
Contributors: Andrea Miccoli, Iole Leonori, Andone Estonba, Andrea De Felice, Chiara Carla Piccinetti, Oliana Carnevali
... Zona radiata proteins are essential for ensuring bactericidal resistance, oocyte nutrients uptake and functional buoyancy, sperm binding and guidance to the micropyle, and protection to the growing oocyte or embryo from the physical environment.
Contributors: Yihong Zheng, Ming Tao, Ze Li, Zhangli Hu
... Thioredoxin reductase (TR) as a selenoprotein is involved in many cellular processes and mainly serves as a key member of the thioredoxin system, which is a crucial antioxidant system in defense against oxidative stress. We investigated selenoproteins in the important commercial microalgae Haematococcus pluvialis. HpTR1 was identified and its molecular properties were analyzed. The full-length cDNA of HpTR1 consists of 2506 base pairs encoding a putative 535-amino acid product. The conformation of HpTR1 has been characterized via sequence analysis and protein structure modelling. A comprehensive phylogenetic tree of TR1 in animals and algae was constructed, which provided an evolution history of selenoprotein from aquatic to terrestrial environment. The expression pattern of TR1 mRNA and TR activity assay indicate that Selenium is an important regulator of HpTR1 and plays different roles in a dosage dependent manner.
Contributors: N.R. Bennett, J.M. Brenan, Y. Fei
... We have performed experiments to investigate the solubility and metal–silicate partitioning of gold as a function of metal sulphur content (XS), silicate melt polymerization (NBO/T) and pressure (P). These experiments show that Au becomes less siderophile both with increasing pressure and as the metal phase becomes more sulphur-rich. For the studied range of compositions, melt polymerization has no effect on the solubility of Au. The reduction in the siderophile tendency of gold with increasing metal sulphur content is greater than expected on the basis of activity–composition relationships in the metal phase. This suggests a significant role for complexing between Au and S in the silicate melt. Our new experimental results are combined with literature data to yield a parameterisation for the exchange coefficient of Au (KdAuMet/Sil) as a function of P, T and XS:logKdAuMet/Sil=-1.10(0.04)+1.11(0.01)104T(K)-67.8(10.9)P(GPa)T(K)+5.81(0.24)log(1-XS)