Habitat amount hypothesis and passive sampling explain mammal species composition in Amazonian river islands

Nested structures of species assemblages have been frequently associated with patch size and isolation, leading to the conclusion that colonization–extinction dynamics drives nestedness. The ‘passive sampling’ model states that the regional abundance of species randomly determines their occurrence in patches. The ‘habitat amount hypothesis’ also challenges patch size and isolation effects, arguing that they occur because of a ‘sample area effect’. Here, we (a) ask whether the structure of the mammal assemblages of fluvial islands shows a nested pattern, (b) test whether species’ regional abundance predicts species’ occurrence on islands, and (c) ask whether habitat amount in the landscape and matrix resistance to biological flow predict the islands’ species composition. We quantified nestedness and tested its significance using null models. We used a regression model to analyze whether a species’ relative regional abundance predicts its incidence on islands. We accessed islands’ species composition by an NMDS ordination and used multiple regression to evaluate how species composition responds to habitat amount and matrix resistance. The degree of nestedness did not differ from that expected by the passive sampling hypothesis. Likewise, species’ regional abundance predicted its occurrence on islands. Habitat amount successfully predicted the species composition on islands, whereas matrix resistance did not. We suggest the application of habitat amount hypothesis for predicting species composition in other patchy systems. Although the island biogeography perspective has dominated the literature, we suggest that the passive sampling perspective is more appropriate for explaining the assemblages’ structure in this and other non‐equilibrium patch systems. Abstract in Portuguese is available with online material.     

Lattice population dynamics for plants with dispersing seeds and Vegetative propagation

The population dynamics of plants in a lattice structured habitat are studied theoretically. Plants are assumed to propagate both by producing seeds that scatter over the population and by vegetative reproduction by extending runners, rhizomes, or roots, to neighboring vacant sites. In addtion, the seed production rate may be dependent on the local density in the neighborhood, indicating beneficial or harmful crowding effects. Two sets of population dynamical equation(s) are derived: one based onmean-field approximation and the other based onpair approximation (tracing both global and local densities simultaneously). We examine the accuracy of these approximate dynamics by comparing them with direct computer simulation of the stochastic lattice model. Pair approximation is much more accurate than mean-field approximation. Mean-field approximation overestimates the parameter range for persistence if crowding effects on seed production are harmful or weakly beneficial, but underestimates it if crowding effects are highly beneficial. Dynamics may show bistability (both population persistence and extinction) if the effect of crowding is strongly beneficial. If there is a linear trade-off between seed production and vegetative reproduction, the equilibrium abundance of the population may be maximised by a mixture of seed production and vegetative reproduction, rather than by pure seed production or by pure vegetative reproduction. This result is correctly predicted by pair approximation but not by mean-field approximation.     

科尔沁沙地景观格局特征分析

用修改分维数,分维数和景观多样性指数方法,对科尔沁沙地没沙漠化土地景观空间格局２进行了研究。结果表明,在所划分的人工固沙区,围封保护区和流动沙丘区三种沙地景观类型中,人工固沙区景观空间格局最复杂,修改分维数Ｄｍ为１．５４７６;其次为围封保护区Ｄｍ为１．４９７５;流动沙丘景观格局最简单Ｄｍ为１．４２０５。     

Methylerythritol phosphate pathway to isoprenoids: Kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum

The methylerythritol phosphate (MEP) pathway of Plasmodium falciparum (P. falciparum) has become an attractive target for anti-malarial drug discovery. This study describes a kinetic model of this pathway, its use in validating 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) as drug target from the systemic perspective, and additional target identification, using metabolic control analysis and in silico inhibition studies. In addition to DXR, 1-deoxy-d-xylulose 5-phosphate synthase (DXS) can be targeted because it is the first enzyme of the pathway and has the highest flux control coefficient followed by that of DXR. In silico inhibition of both enzymes caused large decrement in the pathway flux. An added advantage of targeting DXS is its influence on vitamin B1 and B6 biosynthesis. Two more potential targets, 2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase and 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, were also identified. Their inhibition caused large accumulation of their substrates causing instability of the system.     

Using Head Patch Pattern as a Reliable Biometric Character for Noninvasive Individual Recognition of an Endangered Pitviper Protobothrops mangshanensis

Mangshan pitviper, Protobothrops mangshanensis(formerly Zhaoermia mangshanensis) is endemic to China. Unfortunately, due to the decreasing size of its wild populations, this snake has been listed as critically endangered. Research carried out on the Mangshan pitviper's population ecology and captive reproduction has revealed that the unique head patch patterns of different individuals may potentially be used as a noninvasive recognition biometric character. We collected head patch pattern images of 40 individuals of P. mangshanensis between 1994 and 2011. By comparing each pitviper's head patch pattern, we found that the head patch pattern of individual snakes was different and unique. Additionally, we observed and recorded the head patch pattern characters of four adults and five juveniles before and after ecdysis. Our findings confirmed that head patch patterns of Mangshan pitvipers are unique and stable, remaining unchanged after ecdysis. Thus, individuals can be quickly identified by examining the head patch pattern within a specific recognition area on the head. This method may be useful for noninvasive individual recognition in many other species that display color patch pattern variations, especially in studies of endangered species where the use of invasive marking techniques is undesirable.     

An In-vitro Preparation of Isolated Enteric Neurons and Glia from the Myenteric Plexus of the Adult Mouse

The enteric nervous system is a vast network of neurons and glia running the length of the gastrointestinal tract that functionally controls gastrointestinal motility. A procedure for the isolation and culture of a mixed population of neurons and glia from the myenteric plexus is described. The primary cultures can be maintained for over 7 days, with connections developing among the neurons and glia. The longitudinal muscle strip with the attached myenteric plexus is stripped from the underlying circular muscle of the mouse ileum or colon and subjected to enzymatic digestion. In sterile conditions, the isolated neuronal and glia population are preserved within the pellet following centrifugation and plated on coverslips. Within 24-48 hr, neurite outgrowth occurs and neurons can be identified by pan-neuronal markers. After two days in culture, isolated neurons fire action potentials as observed by patch clamp studies. Furthermore, enteric glia can also be identified by GFAP staining. A network of neurons and glia in close apposition forms within 5 - 7 days. Enteric neurons can be individually and directly studied using methods such as immunohistochemistry, electrophysiology, calcium imaging, and single-cell PCR. Furthermore, this procedure can be performed in genetically modified animals. This methodology is simple to perform and inexpensive. Overall, this protocol exposes the components of the enteric nervous system in an easily manipulated manner so that we may better discover the functionality of the ENS in normal and disease states.     

Conformational analysis of protein and nucleic acid fragments with the new grid search algorithm FOUND

The new computer algorithm FOUND, which is implemented as an integrated module of the DYANA structure calculation program, is capable of performing systematic local conformation analyses by exhaustive grid searches for arbitrary contiguous fragments of proteins and nucleic acids. It uses torsion angles as the only degrees of freedom to identify all conformations that fulfill the steric and NMR-derived conformational restraints within a contiguous molecular fragment, as defined either by limits on the maximal restraint violations or by the fragment-based DYANA target function value. Sets of mutually dependent torsion angles, for example in ribose rings, are treated as a single degree of freedom. The results of the local conformation analysis include allowed torsion angle ranges and stereospecific assignments for diastereotopic substituents, which are then included in the input of a subsequent structure calculation. FOUND can be used for grid searches comprising up to 13 torsion angles, such as the backbone of a complete -helical turn or dinucleotide fragments in nucleic acids, and yields a significantly higher number of stereospecific assignments than the precursor grid search algorithm HABAS.     

Estimating product and energy substitution benefits in national‐scale mitigation analyses for Canada

The potential of forests and the forest sector to mitigate greenhouse gas (GHG) emissions is widely recognized, but challenging to quantify at a national scale. Mitigation benefits through the use of forest products are affected by product life cycles, which determine the duration of carbon storage in wood products and substitution benefits where emissions are avoided using wood products instead of other emissions‐intensive building products and energy fuels. Here we determined displacement factors for wood substitution in the built environment and bioenergy at the national level in Canada. For solid wood products, we compiled a basket of end‐use products and determined the reduction in emissions for two functionally equivalent products: a more wood‐intensive product vs. a less wood‐intensive one. Avoided emissions for end‐use products basket were weighted by Canadian consumption statistics to reflect national wood uses, and avoided emissions were further partitioned into displacement factors for sawnwood and panels. We also examined two bioenergy feedstock scenarios (constant supply and constrained supply) to estimate displacement factors for bioenergy using an optimized selection of bioenergy facilities which maximized avoided emissions from fossil fuels. Results demonstrated that the average displacement factors were found to be similar: product displacement factors were 0.54 tC displaced per tC of used for sawnwood and 0.45 tC tC^?1 for panels; energy displacement factors for the two feedstock scenarios were 0.47 tC tC^?1 for the constant supply and 0.89 tC tC^?1 for the constrained supply. However, there was a wide range of substitution impacts. The greatest avoided emissions occurred when wood was substituted for steel and concrete in buildings, and when bioenergy from heat facilities and/or combined heat and power facilities was substituted for energy from high‐emissions fossil fuels. We conclude that (1) national‐level substitution benefits need to be considered within a systems perspective on climate change mitigation to avoid the development of policies that deliver no net benefits to the atmosphere, (2) the use of long‐lived wood products in buildings to displace steel and concrete reduces GHG emissions, (3) the greatest bioenergy substitution benefits are achieved using a mix of facility types and capacities to displace emissions‐intensive fossil fuels.     

Polyploidy: a missing link in the conversation about seed transfer of a commonly seeded native grass in western North America

The use of local, native plant materials is now common in restoration but testing for polyploidy in seed sources is not. Diversity in cytotypes across a landscape can pose special seed transfer challenges, because the methods used to determine genetically appropriate materials for seed transfer do not account for cytotypic variation. This lack of consideration may result in mixing cytotypes through revegetation, which could reduce long‐term population viability. We surveyed nine populations of a native bunchgrass, Pseudoroegneria spicata, in three EPA Level III Ecoregions in the western United States to determine the frequency of polyploidy, whether there are differences in traits (phenotype, fecundity, and mortality) among plants of different cytotypes, and whether cytotype frequency varies among ecoregions. We assessed trait variation over 2 years in a common garden and determined ploidy using flow cytometry. Polyploidy and mixed cytotype populations were common, and polyploids occurred in all ecoregions. Four of the nine populations were diploid. The other five had tetraploids present: three had only tetraploid individuals whereas two had mixed diploid/tetraploid cytotypes. There was significant variation in traits among cytotypes: plants from tetraploid populations were larger than diploid or mixed populations. The frequency and distribution of cytotypes make it likely that seed transfer in the study area will inadvertently mix diploid and polyploid cytotypes in this species. The increasing availability of flow cytometry may allow ploidy to be incorporated into native plant materials sourcing and seed transfer.