Fusing spatial resource heterogeneity with a competition–colonization trade-off in model communities

Two commonly cited mechanisms of multispecies coexistence in patchy environments are spatial heterogeneity in competitive abilities caused by variation in resources and a competition–colonization trade-off. In this paper, a model that fuses these mechanisms together is presented and analyzed. The model suggests that spatial variation in resource ratios can lead to multispecies coexistence, but this mechanism by itself is weak when the number of resources for which species compete is small. However, spatial resource heterogeneity is a powerful mechanism for multispecies coexistence when it acts synergistically with a competition–colonization trade-off. The model also shows how resource supply can control the competitive balance between species that are weak competitors but superior colonizers and strong competitors/inferior colonizers. This provides additional theoretical support for a possible explanation of empirically observed hump-shaped relationships between species diversity and ecological productivity.     

An introduction to the mathematical structure of the Wright–Fisher model of population genetics

In this paper, we develop the mathematical structure of the Wright–Fisher model for evolution of the relative frequencies of two alleles at a diploid locus under random genetic drift in a population of fixed size in its simplest form, that is, without mutation or selection. We establish a new concept of a global solution for the diffusion approximation (Fokker–Planck equation), prove its existence and uniqueness and then show how one can easily derive all the essential properties of this random genetic drift process from our solution. Thus, our solution turns out to be superior to the local solution constructed by Kimura.     

Analyzing the spatial dynamics of a prey–predator lattice model with social behavior

A lattice prey–predator model is studied. Transition rules applied sequentially describe processes such as reproduction, predation, and death of predators. The movement of predators is governed by a local particle swarm optimization algorithm, which causes the formation of swarms of predators that propagate through the lattice. Starting with a single predator in a lattice fully covered by preys, we observe a wavefront of predators invading the zones dominated by preys; subsequent fronts arise during the transient phase, where a monotonic approach to a fixed point is present. After the transient phase the system enters an oscillatory regime, where the amplitude of oscillations appears to be bounded but is difficult to predict. We observe qualitative similar behavior even for larger lattices. An empirical approach is used to determine the effects of the movement of predators on the temporal dynamics of the system. Our results show that the algorithm used to model the movement of predators increases the proficiency of predators.     

The forest resources input–output model: An application in China

Understanding the state of forest resource utilization in China and correctly evaluating the role and function of forest resources in national economic development are essential for realizing balanced development of forests, the environment, and the economy. This is especially true given the present situation of increasingly scarce forest resources. Using data from Chinese forest industry statistical yearbooks, forestry development reports, and other documents, this paper examines the current state of forest resource utilization in China from the angle of combining quantities and values based on input–output tables. We show that demand for and input use of forest resources varies greatly across industrial sectors; the paper products and furniture manufacturing industries have the greatest direct consumption coefficient for timber use. When considering direct and indirect demand, it is clear that forest resources restrict different industrial sectors in diverse ways. These results provide an important set of reference values regarding the utilization of forest resources and coordinated industrial development in China.     

Detection,isolation, and characterization of chikungunya viruses associated with the Pakistan outbreak of 2016–2017

The chikungunya virus(CHIKV) is a mosquito-transmitted alphavirus, which has infected millions of people in Africa, Asia, Americas, and Europe since it reemerged in India and Indian Ocean regions in 2005–2006. Starting in the middle of November 2016, CHIKV has been widely spread, and more than 4,000 cases of infections in humans were confirmed in Pakistan. Here, we report the first isolation and characterization of CHIKV from the Pakistan outbreak. Eight CHIKV strains were newly isolated from human serum samples using a cell culture procedure. A full-length genome sequence and eight complete envelope(E1) sequences of CHIKV from Pakistan were obtained in this study. Alignment of the CHIKV E1 sequences revealed that the eight new CHIKV isolates were highly homogeneous, with only two nonsynonymous substitutions found at generally conserved sites(E99 and Q235). Based on the comparison of 342 E1 sequences, the two nonsynonymous mutations were located in well-recognized domains associated with viral functions such as the cell fusion and vector specificity, suggesting their potential functional importance. Phylogenetic analysis indicated that the CHIKV strains from Pakistan originated from CHIKV circulating in the Indian region. This study helps elucidate the epidemics of CHIKV in Pakistan and also provides a foundation for studies of evolution and expansion of CHIKV in South Asia.     

An almost periodic Ross–Macdonald model with structured vector population in a patchy environment

Journal of Mathematical Biology - An almost periodic Ross–Macdonald model with age structure for the vector population in a patchy environment is considered. The basic reproduction ratio...     

A reaction–diffusion malaria model with incubation period in the vector population

Malaria is one of the most important parasitic infections in humans and more than two billion people are at risk every year. To understand how the spatial heterogeneity and extrinsic incubation period (EIP) of the parasite within the mosquito affect the dynamics of malaria epidemiology, we propose a nonlocal and time-delayed reaction–diffusion model. We then define the basic reproduction ratio R₀{\mathcal{R}_0} and show that R₀{\mathcal{R}_0} serves as a threshold parameter that predicts whether malaria will spread. Furthermore, a sufficient condition is obtained to guarantee that the disease will stabilize at a positive steady state eventually in the case where all the parameters are spatially independent. Numerically, we show that the use of the spatially averaged system may highly underestimate the malaria risk. The spatially heterogeneous framework in this paper can be used to design the spatial allocation of control resources.     

An olfactory receptor pseudogene whose function emerged in humans: a case study in the evolution of structure–function in GPCRs

Human olfactory receptor, hOR17-210, is identified as a pseudogene in the human genome. Experimental data has shown however, that the gene product of frame-shifted, cloned hOR17-210 cDNA was able to bind an odorant-binding protein and is narrowly tuned for excitation by cyclic ketones. Supported by experimental results, we used the bioinformatics methods of sequence analysis (genome-wide and pair-wise), computational protein modeling and docking, to show that functionality in this receptor is retained due to sequence-structure features not previously observed in mammalian ORs. This receptor does not possess the first two transmembrane helical domains (of seven typically seen in GPCRs). It however, possesses an additional TM that has not been observed in other human olfactory receptors. By incorporating these novel structural features, we created two putative models for this receptor. We also docked odor ligands that were experimentally shown to bind hOR17-210. We show how and why structural modifications of OR17-210 do not hinder this receptor's functionality. Our studies reveal that novel gene rearrangements that result in sequence and structural diversity may have a bearing on OR and GPCR function and evolution.     

Seroepidemiological study of herpes simplex virus type 2 in patients with the acquired immunodeficiency syndrome in the city of Niterói, Rio de Janeiro, Brazil

This study was designed to determine the seroprevalence of herpes simplex virus type 2 (HSV-2) and to evaluate its association with age, sex as well as other demographic and behavioural factors in 150 human immunodeficiency virus (HIV) positive adults patients attending the general medical outpatient ward for routine care of Niterói, state of Rio de Janeiro, Brazil. Serum samples were screened for HSV-2 antibodies using an indirect ELISA. Eighty-three patients were men (mean age: 38.8) and 67 were women (mean age: 35.4). The estimated prevalence of HSV-2 was 52% (95% CI: 44-60%) and it was higher among men (53%) than among women (50.7%). Overall, the age of first sexual intercourse and past history of genital herpes were associated with HSV-2 seropositivity. Analysis by gender disclosed significant association of number of lifetime sex partners only among men. Although HSV-2 antibodies were frequent in the study group, genital herpes was reported by 21.8% of the HSV-2 positive subjects, indicating low awareness of the HSV-2 infection. These results may have public health importance for Brazil as the high rate of HSV-2 infection may act as a cofactor of HIV transmission.     

Modeling the spatial–temporal dynamics of water use efficiency in Yangtze River Basin using IBIS model

Climate change alters regional water and carbon cycling, which has been a hot study point in the filed of climatology and ecology. As a traditionally “water-rich” region of China, Yangtze River Basin plays an important role in regional economic development and ecosystem productivity. However, the mechanism of the influence of climate change on water and carbon cycling has been received little attention. As a coupling indicator for carbon and water, the water use efficiency (WUE) is widely used, which indicates the water consumption for carbon sequestration in watershed and regional scale. A lot of studies showed that climate change has significantly affected the water resource and production of the ecosystems in Yangtze River Basin during the period of 1956–2006, when great climate variations were occurred. To better understand the alternation pattern for the relationship between water and carbon cycling under climate change at regional scale, the WUE and the spatiotemporal variations patterns were simulated in the study area from 1956 to 2006 by using the Integrated Biosphere Simulator (IBIS). The results showed that the WUE spatial pattern had the annual and seasonal variations. In general, the average annual WUE value per square meter was about 0.58 g C/kg H₂O in Yangtze River Basin. The high WUE levels were mainly distributed in the eastern area of Sichuan, western area of Jiangxi and Hunan, and the highest value reached 0.88 g C/kg H₂O. The lowest WUE’s were mainly located in the western area of Sichuan and Qinghai with the lowest values reaching to 0.36 g C/kg H₂O. The WUE in other regions mostly ranged from 0.5 to 0.6 g C/kg H₂O. For the whole study area, the annual WUE slowly increased from 1956 to 2006. The WUE in the upper reaches of Yangtze River increased based on the simulated temporal trends, which mainly located in the western area of the Sichuan Basin; the WUE of the middle reaches of Yangtze River had increased slightly from 1987 to 1996, and then decreased from 1996 to 2006; the lower reaches of Yangtze River always had smaller WUE’s than the average from 1956 to 2006. The spatiotemporal variability of the WUE in the vegetation types was obvious in the Yangtze River Basin, and it was depended on the climate and soil conditions, and as well the disturbance in its distribution areas. The temporal variations of WUE among different vegetation types had similar trends but different in values. The forest type had higher WUE than any other vegetation types ranging from 0.65 to 0.8 g C/kg H₂O. The WUE of shrubland ranged from 0.45 to 0.6 g C/kg H₂O. The WUE of tundra was the lowest, indicating the differences in plant physiology. The consistence of the spatial pattern of WUE with the NPP indicated that the regional production of Yangtze River Basin increased based on the water resources prompted and vegetation restoration. We found the drought climate was one of critical factor that impacts the alteration of WUE in Yangtze River Basin in the simulation.     

Modeling the spatial–temporal dynamics of water use efficiency in Yangtze River Basin using IBIS model

Climate change alters regional water and carbon cycling, which has been a hot study point in the filed of climatology and ecology. As a traditionally “water-rich” region of China, Yangtze River Basin plays an important role in regional economic development and ecosystem productivity. However, the mechanism of the influence of climate change on water and carbon cycling has been received little attention. As a coupling indicator for carbon and water, the water use efficiency (WUE) is widely used, which indicates the water consumption for carbon sequestration in watershed and regional scale. A lot of studies showed that climate change has significantly affected the water resource and production of the ecosystems in Yangtze River Basin during the period of 1956–2006, when great climate variations were occurred. To better understand the alternation pattern for the relationship between water and carbon cycling under climate change at regional scale, the WUE and the spatiotemporal variations patterns were simulated in the study area from 1956 to 2006 by using the Integrated Biosphere Simulator (IBIS). The results showed that the WUE spatial pattern had the annual and seasonal variations. In general, the average annual WUE value per square meter was about 0.58 g C/kg H₂O in Yangtze River Basin. The high WUE levels were mainly distributed in the eastern area of Sichuan, western area of Jiangxi and Hunan, and the highest value reached 0.88 g C/kg H₂O. The lowest WUE’s were mainly located in the western area of Sichuan and Qinghai with the lowest values reaching to 0.36 g C/kg H₂O. The WUE in other regions mostly ranged from 0.5 to 0.6 g C/kg H₂O. For the whole study area, the annual WUE slowly increased from 1956 to 2006. The WUE in the upper reaches of Yangtze River increased based on the simulated temporal trends, which mainly located in the western area of the Sichuan Basin; the WUE of the middle reaches of Yangtze River had increased slightly from 1987 to 1996, and then decreased from 1996 to 2006; the lower reaches of Yangtze River always had smaller WUE’s than the average from 1956 to 2006. The spatiotemporal variability of the WUE in the vegetation types was obvious in the Yangtze River Basin, and it was depended on the climate and soil conditions, and as well the disturbance in its distribution areas. The temporal variations of WUE among different vegetation types had similar trends but different in values. The forest type had higher WUE than any other vegetation types ranging from 0.65 to 0.8 g C/kg H₂O. The WUE of shrubland ranged from 0.45 to 0.6 g C/kg H₂O. The WUE of tundra was the lowest, indicating the differences in plant physiology. The consistence of the spatial pattern of WUE with the NPP indicated that the regional production of Yangtze River Basin increased based on the water resources prompted and vegetation restoration. We found the drought climate was one of critical factor that impacts the alteration of WUE in Yangtze River Basin in the simulation.     

An ant–plant mutualism induces shifts in the protist community structure of a tank-bromeliad

Although ants may induce community-wide effects via changes in physical habitats in terrestrial environments, their influence on aquatic communities living in plant-held waters remains largely underexplored. The neotropical tank-bromeliad Aechmea mertensii (Bromeliaceae) occurs along forest edges in ant-gardens initiated by Camponotus femoratus or by Pachycondyla goeldii. Its leaves form wells that hold rainwater and provide suitable habitats for many aquatic organisms. We postulated that these ant–plant mutualisms indirectly affect the microbial community structure via changes in the environmental conditions experienced by the plants. To test this hypothesis, we analyzed the protist communities from 63 tank-bromeliads associated with either C. femoratus or P. goeldii (hereafter Cf-Aechmea and Pg-Aechmea) along a forest edge in French Guiana. For each plant, a large number of environmental variables (including habitat structure, food resources, incident radiation and the presence of aquatic invertebrates) were quantified to determine their relative importance in driving any observed differences across ant-associated plants. Pg-Aechmea are located in sun-exposed areas and hold low volumes of water and low amounts of detritus, whereas Cf-Aechmea are located in partially shaded areas and accumulate higher amounts of water and detritus. Protists (i.e., protozoa and algae) inhabiting Cf-Aechmea exhibit greater richness and abundances than those in Pg-Aechmea. Variations in detritus content, number of leaves, incident radiation, and the epiphyte richness of the ant-garden were the main factors explaining the variation in protist richness. A shift in the functional group composition of protists between bromeliads tended by different ant species suggested that mutualistic ants indirectly mediate changes in the microbial food web.     

An in vitro model quantifying the effect of calcification on the tissue–stent interaction in a stenosed aortic root

Transcatheter Aortic Valves rely on the tissue-stent interaction to ensure that the valve is secured within the aortic root. Aortic stenosis presents with heavily calcified leaflets and it has been proposed that this calcification also acts to secure the valve, but this has never been quantified. In this study, we developed an in vitro calcified aortic root model to quantify the role of calcification on the tissue-stent interaction. The in vitro model incorporated artificial calcifications affixed to the leaflets of porcine aortic heart valves. A self-expanding nitinol braided stent was deployed into non-calcified and artificially calcified porcine aortic roots and imaged by micro computed tomography. Mechanical tests were then conducted to dislodge the stent from the aortic root and it was found that, in the presence of calcification, there was a significant increase in pullout force (8.59 ± 3.68 N vs. 2.84 ± 1.55 N p = 0.045), stent eccentricity (0.05 ± 0.01 vs. 0.02 ± 0.01, p = 0.049), and coefficient of friction between the stent and aortic root (0.36 ± 0.12 vs. 0.09 ± 0.05, p = 0.018), when compared to non-calcified roots. This study quantifies for the first time the impact of calcification on the friction between the aortic tissue and transcatheter aortic valve stent, showing the role of calcification in anchoring the valve stent in the aortic root.     

In vitro structure–activity relationships of aplysinopsin analogs and their in vivo evaluation in the chick anxiety–depression model

Aplysinopsins are tryptophan-derived natural products that have been isolated from a variety of marine organisms and have been shown to possess a range of biological activities. In vitro receptor binding assays showed that of the 12 serotonin receptor subtypes, analogues showed a high affinity for the 5-HT_2B and 5-HT_2C receptor subtypes, with selectivity for 5-HT_2B over 5-HT_2C. While no conclusions could be drawn about the number and position of N-methylations, bromination at C-4 and C-5 of the indole ring resulted in greater binding affinities, with K_i’s as low as 35 nM. This data, combined with previous knowledge of the CNS activity of aplysinopsin analogs, suggested that these compounds may have potential as leads for antidepressant drugs. Compounds 3c, 3u, and 3x were evaluated in the chick anxiety–depression model to assess their in vivo efficacy. Compound 3c showed a modest antidepressant effect at a dose of 30 nM/kg in the animal model.     

A numerical model of cellular blebbing: A volume-conserving,fluid–structure interaction model of the entire cell

In animal cells, blebs are smooth, quasi-hemispherical protrusions of the plasma membrane that form when a section of the membrane detaches from the underlying actin cytoskeleton and is inflated by flowing cytosol. The mechanics behind this common cellular activity are not yet clear. As a first step in the development of a full computational framework, we present a numerical model of overall cell behavior based upon the interaction between a background Newtonian-fluid cytosol and elastic structures modeling the membrane and filaments. The detailed micromechanics of the cytoskeletal network are the subject of future work. Here, the myosin-driven contraction of the actin network is modeled through stressed elastic filaments. Quantitative models of cytoskeletal micromechanics and biochemistry require accurate estimates of local stress and flow conditions. The main contribution of this paper is the development of a computationally efficient fluid–structure interaction model based on operator splitting, to furnish this data. Cytosol volume conservation (as supported by experimental evidence) is enforced through an intermediate energy minimization step. Realistic bleb formation and retraction is observed from this model, offering an alternative formulation to positing complex continuum behavior of the cytoplasm (e.g. poroelastic model of Charras et al., 2008).     

Excitation energy transfer in the LHC-II trimer: a model based on the new 2.72 Å structure

Energy transfer of the light harvesting complex LHC-II trimer, extracted from spinach, was studied in the Q(y) region at room temperature by femtosecond transient absorption spectroscopy. Configuration interaction exciton method [Linnanto et al. (1999) J Phys Chem B 103: 8739-8750] and 2.72 A structural information reported by Liu et al. was used to calculate spectroscopic properties and excitation energy transfer rates of the complex. Site energies of the pigments and coupling constants of pigment pairs in close contact were calculated by using a quantum chemical configuration interaction method. Gaussian random variation of the diagonal and off-diagonal exciton matrix elements was used to account for inhomogeneous broadening. Rate calculations included only the excitonic states initially excited and probed in the experiments. A kinetic model was used to simulate time and wavelength dependent absorption changes after excitation on the blue side of the Q(y) transition and compared to experimentally recorded rates. Analysis of excitonic wavefunctions allowed identification of pigments initially excited and probed into later. It was shown that excitation of the blue side of the Q(y) band of a single LHC-II complex results in energy transfer from chlorophyll b's of the lumenal side to chlorophyll a's located primarly on one of the monomers of the stromal side.     

Anticooperativity in diffusion-controlled reactions with pairs of anisotropic domains: a model for the antigen–antibody encounter

The encounter between anisotropic agents in diffusion-controlled reactions is a topic of very general relevance in chemistry and biology. Here we introduce a simplified model of encounter of an isotropic molecule with a pair of partially reacting agents and apply it to the encounter reaction between an antibody and its antigen. We reduce the problem to the solution of dual series relations, which can be solved iteratively, yielding the exact solution for the encounter rate constant at any desired order of accuracy. We quantify the encounter effectiveness by means of a simple indicator and show that the two binding centers systematically behave in an anti-cooperative fashion. However, we demonstrate that a reduction of the binding active sites allows the composite molecule to recover binding effectiveness, in spite of the overall reduction of the rate constant. In addition, we provide a simple formula that enables one to calculate the anti-cooperativity as a function of the size of the binding site for any values of the separation between the two active lobes and of the antigen size. Finally, some biological implications of our results are discussed.     

Fine-scale spatial genetic structure in predominantly selfing plants with limited seed dispersal:a rule or exception?

Gene flow at a fine scale is still poorly understood despite its recognized importance for plant population demographic and genetic processes.We tested the hypothesis that intensity of gene flow will be lower and strength of spatial genetic structure(SGS) will be higher in more peripheral populations because of lower population density.The study was performed on the predominantly selfing Avena sterilis and included:(1) direct measurement of dispersal in a controlled environment;and(2) analyses of SGS in three natural populations,sampled in linear transects at fixed increasing inter-plant distances.We found that in A.sterilis major seed dispersal is by gravity in close(less than 2 m) vicinity of the mother plant,with a minor additional effect of wind.Analysis of SGS with six nuclear SSRs revealed a significant autocorrelation for the distance class of 1 m only in the most peripheral desert population,while in the two core populations with Mediterranean conditions,no genetic structure was found.Our results support the hypothesis that intensity of SGS increases from the species core to periphery as a result of decreased within-population gene flow related to low plant density.Our findings also show that predominant self-pollination and highly localized seed dispersal lead to SGS at a very fine scale,but only if plant density is not too high.     

Fine-scale spatial genetic structure in predominantly selfing plants with limited seed dispersal: a rule or exception?

Gene flow at a fine scale is still poorly understood despite its recognized importance for plant population demographic and genetic processes. We tested the hypothesis that intensity of gene flow will be lower and strength of spatial genetic structure (SGS) will be higher in more peripheral populations because of lower population density. The study was performed on the predominantly selfing Avena sterilis and included: (1) direct measurement of dispersal in a controlled environment; and (2) analyses of SGS in three natural populations, sampled in linear transects at fixed increasing inter plant distances. We found that in A.sterilis major seed dispersal is by gravity in close (less than 2m) vicinity of the mother plant, with a minor additional effect of wind. Analysis of SGS with six nuclear SSRs revealed a significant autocorrelation for the distance class of 1m only in the most peripheral desert population, while in the two core populations with Mediterranean conditions, no genetic structure was found. Our results support the hypothesis that intensity of SGS increases from the species core to periphery as a result of decreased within population gene flow related to low plant density. Our findings also show that predominant self pollination and highly localized seed dispersal lead to SGS at a very fine scale, but only if plant density is not too high.     

‘Big science’ in the field: experimenting with badgers and bovine TB, 1995–2015

History and Philosophy of the Life Sciences - Since wild badgers were first connected with outbreaks of bovine TB (bTB) in UK cattle herds in the early 1970s, the question of whether to cull them...