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: 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: Luca Grosset, Bruno Viscolani
... In this paper we search for conditions on age-structured differential games to make their analysis more tractable. We focus on a class of age-structured differential games which show the features of ordinary linear-state differential games, and we prove that their open-loop Nash equilibria are sub-game perfect. By means of a simple age-structured advertising problem, we provide an application of the theoretical results presented in the paper, and we show how to determine an open-loop Nash equilibrium.
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 - 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.
Original research article - Long-distance seed dispersal by straw-coloured fruit bats varies by season and landscape
Contributors: Michael Abedi-Lartey, Dina K.N. Dechmann, Martin Wikelski, Anne K. Scharf, Jakob Fahr
... On-going fragmentation of tropical forest ecosystems and associated depletion of seed dispersers threatens the long-term survival of animal-dispersed plants. These threats do not only affect biodiversity and species abundance, but ultimately ecosystem functions and services. Thus, seed dispersers such as the straw-coloured fruit bat, E. helvum, which traverse long distances across fragmented landscapes, are particularly important for maintaining genetic connectivity and colonizing new sites for plant species. Using high-resolution GPS-tracking of movements, field observations and gut retention experiments, we quantify dispersal distances for small- and large-seeded fruits foraged by E. helvum during periods of colony population low (wet season) and high (dry season) in an urban and a rural landscape in the forest zone of Ghana. Gut passage time averaged 116 min (range 4–1143 min), comparable to other fruit bats. Movements were generally longer in the urban than in the rural landscape and also longer in the dry than in the wet season. As the majority of seeds are dispersed only to feeding roosts, median dispersal distances were similar for both large (42–67 m) and small (42–65 m) seeds. However, small seeds were potentially dispersed up to 75.4 km, four times further than the previous maximum distance estimated for a similar-sized frugivore. Maximum seed dispersal distances for small seeds were almost twice as long in the rural (49.7 km) compare to the urban (31.2 km) landscape. Within the urban landscape, estimated maximum dispersal distances for small seeds were three times longer during the dry season (75.4 km) compared to the wet season (22.8 km); in contrast, distances in the rural landscape were three times longer in the wet season (67 km) compared to the dry season (24.4). Dispersal distances for large seeds during the dry season (551 m) in the rural landscape were almost twice that in the wet season (319 m). We found no influence of food phenology on dispersal distances. The maximum likelihood for seed dispersal beyond feeding roosts (mean distance from food tree 263 m) was 4.7%. Small seeds were dispersed over even longer distances, >500 and >1000 m, with a likelihood of 3.0 % and 2.3 % respectively. Our data show that E. helvum retains ingested seeds for very long periods and may traverse large distances, probably making it an important long distance seed disperser in tropical Africa. We suggest E. helvumis important for ecosystem functioning and urge its conservation.
Short communication - When immigration mask threats: The rescue effect of a Scopoli's shearwater colony in the Western Mediterranean as a case study
Contributors: Ana Sanz-Aguilar, José Manuel Igual, Giacomo Tavecchia, Meritxell Genovart, Daniel Oro
... Populations of long-lived species are highly sensitive to increases in mortality, but a loss of breeders can be compensated for by recruitment of local individuals or immigrants. Populations maintained through immigration can be sinks, jeopardizing the viability of the metapopulation in the long term when additive mortality from anthropogenic impacts occurs. Thus, the correct identification of whether a breeding population is maintained by local recruitment or by immigration is of special importance for conservation purposes. We developed robust population models to disentangle the importance of local recruitment and immigration in the dynamics of a Western Mediterranean population of Scopoli's shearwater Calonectris diomedea showing low adult survival but stable breeding numbers. Our results show that the shearwater population is not self-maintained but rescued by immigration: yearly immigrants recruiting in the population represents ~10–12% of total population size. We believe that this situation may be common to other Western Mediterranean populations, currently acting as sinks. We recommend urgent demographic studies at large core colonies to evaluate the global conservation status of the species.
Research paper - Investigation of vital pathogenic target orotate phosphoribosyltransferases (OPRTase) from Thermus thermophilus HB8: Phylogenetic and molecular modeling approach
Contributors: Kanagarajan Surekha, Damodharan Prabhu, Mariadasse Richard, Mutharasappan Nachiappan, Jayashree Biswal, Jeyaraman Jeyakanthan
... Biosynthesis pathways of pyrimidine and purine are shown to play an important role in regular cellular activities. The biosynthesis can occur either through de novo or salvage pathways based on the requirement of the cell. The pyrimidine biosynthesis pathway has been linked to several disorders and various autoimmune diseases. Orotate phosphoribosyl transferase (OPRTase) is an important enzyme which catalyzes the conversion of orotate to orotate monophosphate in the fifth step of pyrimidine biosynthesis. Phylogenetic analysis of 228 OPRTase sequences shows the distribution of proteins across different living forms of life. High structural similarities between Thermus thermophilus and other organisms kindled us to concentrate on OPRTase as an anti-pathogenic target. In this study, a homology model of OPRTase was constructed using 2P1Z as a template. About 100ns molecular dynamics simulation was performed to investigate the conformational stability and dynamic patterns of the protein. The amino acid residues (Met1, Asp2, Glu43, Ala44, Glu47, Lys51, Ala157 and Leu158) lining in the binding site were predicted using SiteMap. Further, structure based virtual screening was performed on the predicted binding site using ChemBridge, Asinex, Binding, NCI, TosLab and Zinc databases. Compounds retrieved from the screening collections were manually clustered. The resultant protein–ligand complexes were subjected to molecular dynamics simulations, which further validates the binding modes of the hits. The study may provide better insight for designing potent anti-pathogenic agent.
Abiotic and biotic interactions determine whether increased colonization is beneficial or detrimental to metapopulation management
Contributors: Darren M. Southwell, Jonathan R. Rhodes, Eve McDonald-Madden, Sam Nicol, Kate J. Helmstedt, Michael A. McCarthy
... Increasing the colonization rate of metapopulations can improve persistence, but can also increase exposure to threats. To make good decisions, managers must understand whether increased colonization is beneficial or detrimental to metapopulation persistence. While a number of studies have examined interactions between metapopulations, colonization, and threats, they have assumed that threat dynamics respond linearly to changes in colonization. Here, we determined when to increase colonization while explicitly accounting for non-linear dependencies between a metapopulation and its threats. We developed patch occupancy metapopulation models for species susceptible to abiotic, generalist, and specialist threats and modeled the total derivative of the equilibrium proportion of patches occupied by each metapopulation with respect to the colonization rate. By using the total derivative, we developed a rule for determining when to increase metapopulation colonization. This rule was applied to a simulated metapopulation where the dynamics of each threat responded to increased colonization following a power function. Before modifying colonization, we show that managers must understand: (1) whether a metapopulation is susceptible to a threat; (2) the type of threat acting on a metapopulation; (3) which component of threat dynamics might depend on colonization, and; (4) the likely response of a threat-dependent variable to changes in colonization. The sensitivity of management decisions to these interactions increases uncertainty in conservation planning decisions.
Genome-wide analysis of the SPL family transcription factors and their responses to abiotic stresses in maize
Contributors: Hu-De Mao, Li-Juan Yu, Zhan-Jie Li, Yan Yan, Ran Han, Hui Liu, Meng Ma
... SQUAMOSA promoter binding protein-like (SPL) transcription factors (TFs) are plant-specific and play vital regulatory roles in plant growth and development. Even though they are one of the unique groups of TFs in plants, their characteristics, evolutionary relationships and expression patterns are largely unknown in maize, an important food crop worldwide. In this study, we identified 31 SPL genes (ZmSPLs) in the maize B73 genome. A phylogenetic analysis showed that these genes were divided into six groups (Groups 1–6) and members within the same group shared conserved exon/intron distributions and motif compositions, implying their functional redundancy. The 31 ZmSPL genes were distributed unevenly on 9 of the 10 chromosomes, with 10 segmental duplication events, suggesting that the expansion of the ZmSPL genes occurred due to segmental duplication. Analysis of the Ka/Ks ratios showed that the duplicated ZmSPL genes had primarily undergone strong purifying selection. In addition, 19 of the 31 ZmSPLs, belonging to Groups 1, 2 and 3, were targets of microRNA miR156, indicating of the miR156-mediated posttranscriptional regulation of these ZmSPL genes. Expression analysis of the ZmSPLs in various tissues at different development stages revealed distinct spatiotemporal patterns. Moreover, quantitative real-time PCR analysis identified several ZmSPL genes that were potentially involved in response to abiotic stresses. Our results present a comprehensive overview of the maize SPL gene family and provide an important foundation for further uncovering the biological functions of ZmSPLs in the growth and development of maize.