Patterns of richness and endemism of the Mexican herpetofauna,a matter of spatial scale?

The goal of this study was to compare the richness and endemism patterns of Mexican species of amphibians and reptiles at different spatial scales. We used the best available dataset of distributional ranges generated from ecological niche models and employed geographically weighted regressions (GWRs) to test whether richness and endemism were related. Patterns were found to vary with the scale used for richness and endemism, and these patterns were not coincident. The results showed that: (1) only relatively coarse spatial scales can address latitudinal patterns in amphibians and reptiles, and, in fine scales, they are related to topographic formations; (2) areas of greatest endemism for amphibians and reptiles are located in the highlands of the central or southern part of the country, although not necessarily in the same specific highlands for both groups; (3) there is a strong average correlation between richness and endemism for both groups, indicating that the same factors contribute to both patterns, but these factors act differentially in terms of regions among amphibians and reptiles; and (4) the scale at which the analysis is conducted is important, and we believe that careful consideration of spatial scale must be undertaken to avoid false conclusions. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 305–316.     

Can tree species richness attenuate the effect of drought on organic matter decomposition and stabilization in young plantation forests?

Changes in precipitation due to climate change are likely to influence soil organic matter (SOM) decomposition and stabilization. In forests, increased tree species diversity could modulate the effects of drought on SOM decomposition and stabilization. We addressed this issue by a decomposition study under simulated drought (through precipitation reduction at Zedelgem, Belgium) and natural drought (ORPHEE, southern France) in young experimental plantations (tree species richness 1 to 5). In Zedelgem, the study focused on tree species richness around oak and beech trees. Two tea bag indices (TBI) – decomposition rate (k) and stabilization factor (S) – were calculated by measuring the decay of green and rooibos tea in soils. Overall, TBI's were higher in Zedelgem than at ORPHEE. In Zedelgem, k increased with tree species richness under drought around oak, indicating that tree species richness modulated the effects of drought on decomposition. Under beech, k decreased with drought while no effect of tree species richness was detected. S increased with drought under both oak and beech, without any effect of tree species richness. In ORPHEE, we did not detect any tree species richness effect on both TBIs. S decreased significantly, while k was marginally reduced under drought. The higher S under drought in Zedelgem and under control in OPRHEE suggests that the carbon sequestration potential under climate change would be dependent on the environmental context. Further, in young plantations, high species richness may modulate the drought effect on SOM decomposition, but not on stabilization.     

Trade-offs and the evolution of virulence of microparasites: do details matter?

Models of the within-host dynamics of parasites have been used to consider the evolution of microparasites causing acute infections in vertebrate hosts. In this paper, we use these models to examine how the level of virulence to which a parasite evolves, depends on factors such as the relationship between parasite density and its rate of transmission from infected hosts, and the mechanism of parasite-induced pathogenesis. We show that changes in the terms describing transmissibility and pathogenesis may lead to dramatic differences in the level of virulence to which a parasite evolves. This suggests that no single factor is likely to be responsible for the differences in virulence of different parasites, and that understanding of the evolution of virulence of parasites will require a detailed quantitative understanding of the interaction between the parasite and its host.     

Comparison of the efficiency of polygalacturonase and β-glucosidase enzyme preparations in stabilization of cherry plum wine material

Pektofoetidin and Pectinex, enzyme preparations with the highest polygalacturonase and β-glucosidase activities, were covalently immobilized on DEAE cellulose and Aminosilochromes 10 and 30. After treatment of cherry plum wine material with the soluble and immobilized enzyme preparations, the content of phenolics increased by 26 and 40%, respectively. The increase was accompanied by a decrease in the protein content (by up to 37%), carbohydrate content (by 17% on the average), and antioxidant activity (5–37%). The most efficient treatment involved Pektofoetidin immobilized on Aminosilochrome 10. It increased the clarity of the wine material and its antioxidant activity by 100 and 10%, respectively.     

Immobilization and stabilization of α-galactosidase on Sepabeads EC-EA and EC-HA

α-Galactosidase from tomato has been immobilized on Sepabead EC-EA and Sepabead EC-HA, which were activated with ethylendiamino and hexamethylenediamino groups, respectively. Two strategy was used for the covalent immobilization of α-galactosidase on the aminated Sepabeads: covalent immobilization of enzyme on glutaraldehyde activated support and cross-linking of the adsorbed enzymes on to the support with glutaraldehyde. By using these two methods, all the immobilized enzymes retained very high activity and the stability of the enzyme was also improved. The obtained results showed that, the most stable immobilized α-galactosidase was obtained with the second strategy. The immobilized enzymes were characterized with respect to free counterpart. Some parameters effecting to the enzyme activity and stability were also analyzed. The optimum temperature and pH were found as 60 °C and pH 5.5 for all immobilized enzymes, respectively. All the immobilized α-galactosidases were more thermostable than the free enzyme at 50 °C. The stabilities of the Sepabead EC-EA and EC-HA adsorbed enzymes treated with glutaraldehyde compared to the stability of the free enzyme were a factor of 6 for Sepabead EC-EA and 5.3 for Sepabead EC-HA. Both the free and immobilized enzymes were very stable between pH 3.0 and 6.0 and more than 85% of the initial activities were recovered. Under the identical storage conditions the free enzyme lost its initial activity more quickly than the immobilized enzymes at the same period of time. The immobilized α-galactosidase seems to fulfill the requirements for different industrial applications.     

Decomposition and stabilization of root litter in top- and subsoil horizons: what is the difference?

Mechanisms leading to high mean residence times of organic matter in subsoil horizons are poorly understood. In lower parts of the soil profile root material contributes greatly to soil organic matter (SOM). The objective of this study was to elucidate the decomposition dynamics of root-derived C and N in different soil depths during a 3 year field experiment and to examine the importance of different protection mechanisms as well as abiotic factors for the decomposition dynamics. Additionally, we assessed the effect of root litter addition on native SOM. Our conceptual approach included the exposure of litterbags with ¹³C and ¹⁵N labeled wheat root material mixed to loamy agricultural soil at three different soil depths (30, 60 and 90 cm). During the incubation period, we monitored soil temperature, humidity and the incorporation of root derived C and N into the soil microbial biomass and physical SOM fractions. Our results showed that abiotic decay conditions were better in subsurface horizons compared to the topsoil. Root litter addition significantly increased the size of microbial biomass in all three soil horizons. In the topsoil, root-derived C decomposition was significantly higher in the first 6 months of incubation compared to subsoil horizons. In 60 and 90 cm depths, a lag phase with development of soil microbial biomass seemed to be prevailing before decomposition was activated. For root-derived N, similar decomposition kinetics could be observed in top- and subsoil horizons. Despite of higher SOM contents, better soil structure and higher microbial activity in the topsoil horizon compared to subsoil horizons, the amounts of root-derived C and N remaining after 3 years were similar for all three depths. Most of the root-derived C and N was present as organo-mineral complexes or occluded in soil aggregates (oPOM), illustrating similar importance of these two protection mechanisms in all three soil depths. Addition of fresh root litter caused small losses of native soil C whereas native N was retained. We conclude that despite of similar SOM protection mechanisms, there are distinct differences in decomposition dynamics of root litter between top- and subsoil horizons. In the long run, the better abiotic decay conditions prevailing in subsoil horizons may compensate for their poorer physico-chemical characteristics.     

Review of the fauna of Rotatoria,Cladocera, and Copepoda of the basin of the Anadyr’ River

The zooplankton composition is studied in the thermokarst, glacial and meteorite lakes, channels, former riverbeds, and hollows in the basin of Anadyr’. We found 174 taxa: 78, Rotatoria, 55, Cladocera, and 41, Copepoda. The most diverse is the lake fauna: 51 taxa of Rotatoria, 48, Cladocera, and 37, Copepoda. The thermokarst Lake Maiorskoe hosts 68 taxa: 31, Rotatoria, 14, Cladocera, and 23, Copepoda, wheras the cold ultraoligotrophic Lake El’gygytgyn features only one species of Cyclop of the group scutifer Cyclops neymanae Strel., and Rotatoria and Cladocera are present as allochtonous forms. The Copepoda illustrate the relations of the Anadyr’ fauna with those of Europe, North America, and Japan.     

Living matter—nexus of physics and biology in the 21st century

Cells are made up of complex assemblies of cytoskeletal proteins that facilitate force transmission from the molecular to cellular scale to regulate cell shape and force generation. The “living matter” formed by the cytoskeleton facilitates versatile and robust behaviors of cells, including their migration, adhesion, division, and morphology, that ultimately determine tissue architecture and mechanics. Elucidating the underlying physical principles of such living matter provides great opportunities in both biology and physics. For physicists, the cytoskeleton provides an exceptional toolbox to study materials far from equilibrium. For biologists, these studies will provide new understanding of how molecular-scale processes determine cell morphological changes.The distinction between being “alive” or “not alive” has been a long-standing question for those interested in our natural world. In many ancient cultures, the difference between living organisms and inorganic matter was thought to be due to innate differences arising from a “vital force,” such that biology operated with different fundamental properties than the physical world. The ability to disprove such theories came about over the course of the 17th to the 19th centuries, as scientists developed theories of atoms and were able to synthesize organic matter from inorganic constituents. Over the past 100 years, developments in molecular biology and biochemistry have provided a wealth of information on the structure and function of biological molecules, much of which was acquired in collaborations between physical and biological scientists. Application of X-ray–scattering techniques first developed to study metals enabled discovery of the structure of complicated biological molecules ranging from DNA to ion channels. Use of laser trapping techniques first developed to trap and cool atoms enabled precise force spectroscopy measurements of single molecular motors. We now know that biological molecules, while more complicated than their inorganic counterparts, must obey the rules of physics and chemistry.This wealth of molecular-scale information does not directly inform the behaviors of living cells. The organelles within cells are made up of complex and dynamic assemblies of proteins, lipids, and nucleic acids, all immersed within an aqueous environment. These assemblies are somehow able to build materials that can robustly facilitate the plethora of morphological and physical behaviors of cells at the subcellular (intracellular transport), cellular (division, adhesion, migration), and multicellular (tissue morphogenesis, wound healing) length scales. The dynamic cytoskeleton transmits information and forces from the molecular to the cellular length scales. But what is it about the behaviors of biological molecules that endow cells with the ability to respirate, move, and replicate themselves robustly—all qualities we consider essential to “life”? For these questions, understanding of the physics and chemistry of systems of biological molecules is needed. Interactions that occur within ensembles of molecules lead to emergent properties and behaviors that cannot be predicted at the single-molecule level. These emergent chemical and physical properties of living matter are likely fundamentally different from inorganic or “dead” materials. Discovering the underlying principles of living matter provides fantastic opportunities to learn new physics and biology.The fields of condensed matter physics and materials science study the physical properties that emerge when objects (e.g., atoms, molecules, grains of sand, or soap bubbles) are placed in sufficiently close proximity, such that interactions between them cannot be ignored. Interatomic or intermolecular interactions give rise to emergent properties that are not seen in isolated species. Familiar examples involve electron transport across a material or a material''s response to externally applied magnetic fields or mechanical forces. These emergent properties, such as conductivity, elasticity, and viscosity, enable us to predict the behavior of a collection of objects in these condensed phases. In this paper, I will focus on my perspective of how approaches to understanding the mechanical properties of physical materials can inform understanding of the mechanical properties of living matter found within cells.In a crystal of metal, precisely organized atoms are located nanometers apart, and the energies of their interactions are on the scale of an electron volt (40-fold larger than thermal energy or twice the energy released on the hydrolysis of a single ATP molecule). These give rise to an energy density, or elastic modulus, on the order of gigapascals, which underlies the rigidity of metals. For small deformations, the restoring force between atoms means that this metal behaves like an elastic spring: after a force is applied, the metal returns to its original shape. Understanding force transmission through crystalline metals was facilitated by the development of elasticity theory in the 16th and 17th centuries. Fluids, such as water, lack crystalline order, but predictive understanding of fluid flows and forces was captured through development of theories of fluid dynamics. Now think of another material, Silly Putty, which behaves elastically at short timescales (it bounces like a rubber ball) but then oozes and flows at long timescales, acting like a viscous fluid. Silly Putty is made of long polymers that are trapped by one another at short timescales, but thermal energy is sufficient to allow them to diffuse and translocate at long timescales. Silly Putty is also a “soft material,” in that the polymer''s interaction energies are at the thermal energy level, and its length scale is at the micrometer level. Materials like Silly Putty were thought to be too complicated for analytical theory. It was only in the middle of the 20th century that the theoretical framework to understand these “messy” and “disorganized” polymer-based materials was developed.The most powerful theories for understanding these vastly different forms of physical matter were developed in the absence of even the simplest of computers. The theories relied on developing physical properties or parameters to describe the material with a “mean field,” a type of coarse-graining that identifies the essential properties of individual constituents and interactions but ignores many other details. These mean fields give us new intuitions concerning the origin of material properties and give rise to definitions of physical parameters, such as elasticity and viscosity. However, these theories also require materials that do not jostle around a lot and remain close to equilibrium. In fact, understanding materials “far from equilibrium” has been identified as a major challenge in physics for the next century (National Research Council, 2007) .Materials formed by dynamic protein assemblies in the cytoskeleton are disorganized, heterogeneous, and driven far from equilibrium. Motor proteins generate local stresses, and their activity is spatially modulated. The polymerization and depolymerization of cytoskeletal polymers is controlled by a myriad of regulatory proteins. All these dynamic molecular processes endow the cytoskeletal assemblies with unique behaviors that enable them to support complex physiological tasks. It is likely these dynamics also provide underlying robustness of the cells in response to fluctuating and changing environments. These properties make living cells exquisite materials that cannot be captured by existing frameworks of physical matter. I suspect that we have not yet identified the important parameters needed to characterize their properties. The rich dynamics created by active biological matter present a formidable challenge in the area of materials science.How do we hope to understand the properties of these complex cytoskeletal assemblies and materials? It may seem as though understanding cytoskeletal machinery is an insurmountable feat, the approaches that have been successful for physical materials will not work, and we must rely on complex simulations that require modeling of all individual components. This may be true. However, I think that this is a pessimistic view. Just consider how complicated physical materials would be if we did not have the appropriate parameters to describe the macroscopic responses and had instead became obsessed about knowing the details of all the interactions between underlying atoms and molecules? In the same vein, I believe that predictive insights into biological matter will emerge through development of new physical theories that use mean-field approaches to understanding materials that contain active components and are driven far from equilibrium. The burgeoning field of active-matter physics is currently considering these questions (Ramaswamy, 2010) . However, these theoretical approaches require physical measurements of cells and cellular proteins that may not be clearly linked to a physiological process or have a clear biological context. Materials built from cytoskeletal proteins in vitro should also provide an excellent source of experimental measurements, but closer collaboration with theorists working in this field and collaboration between biochemists and experimental physical scientists is needed to develop control over such materials. Developing predictive physical theories of the cytoskeleton will elucidate principles of why “the whole is more than the sum of its parts” that will provide greater control and design over living matter, in the same way that engineering has provided great advances in applications of materials from the physical world.What do biologists gain from theories of living matter? These theories will provide a crucial link between molecular and cellular length scale behaviors and will provide insight into the mechanisms of why specific molecular perturbations alter cell behavior. Moreover, they should provide us with general design principles of living matter. What are the basic aspects of a machine needed to separate chromosomes, establish polarity, or generate contractile forces that is utilized across different cell types? Can knowing these aspects provide insight into the evolution of cellular machines and the robustness of cell behavior? Thus, study of cellular materials both provides new opportunities for physicists and will provide crucial predictive understanding of cell physiology.Open in a separate windowMargaret L. Gardel     

The continuity of living matter and the discontinuities of its constituents: do plankton and benthos really exist?

Plankton and benthos are popular concepts identifying two ways of life of aquatic organisms. Their spatial separation led to the development of different sampling techniques and to separate conceptualizations of the principles governing these subsets of the aquatic environment. Reciprocal connections between plankton and benthos, however, are very strong both from a functional (energy fluxes) and a structural (life cycle dynamics) point of view. A full appreciation of such links is forcing marine ecology towards a more integrated approach.     

Effects of a plume front on the distribution of inorganic and organic matter off the Rhône River

Hydrological and chemical structures off the Rhône River estuary resulting from the introduction of the river flow into the Mediterranean Sea are described. The effect of the fresh-water/sea-water interface on the distribution of inorganic and organic matter off the Rhône river is investigated. Strong vertical gradients of inorganic and dissolved organic matter such as lipids characterized the first few meters in this area (from 83.7 to 0.6 N-NO₃ µgat l^–1, from 6.39 to 0.92 N-NH₄ µgat l^–1 and from 299 to 73 µg l^–1 of total dissolved lipids). At the interface, substantial increases of particulate organic (PON: from 45 µg l^–1 at surface to 118 µg l^–1 at the interface, POC: from 462 to 876 µg l^–1, total particulate lipids: from 33 to 648 µg l^–1) and suspended matter in general (from 18 to 22.2 mg l^–1) were observed. High phytoplanktonic production may account for some of this enrichment, although passive accumulation might also be involved.     

Who is where in the Plastisphere,and why does it matter?

To fully understand how plastic is affecting the ocean, we need to understand how marine life interacts directly with it. Besides their ecological relevance, microbes can affect the distribution, degradation and transfer of plastics to the rest of the marine food web. From amplicon sequencing and scanning electron microscopy, we know that a diverse array of microorganisms rapidly associate with plastic marine debris in the form of biofouling and biofilms, also known as the “Plastisphere.” However, observation of multiple microbial interactions in situ, at small spatial scales in the Plastisphere, has been a challenge. In this issue of Molecular Ecology Resources, Schlundt et al. apply the combination labelling and spectral imaging – fluorescence in situ hybridization to study microbial communities on plastic marine debris. The images demonstrate the colocalization of abundant bacterial groups on plastic marine debris at a relatively high taxonomic and spatial resolution while also visualizing biofouling of eukaryotes, such as diatoms and bryozoans. This modern imaging technology provides new possibilities to address questions regarding the ecology of marine microbes on plastic marine debris and describe more specific impacts of plastic pollution in the marine food webs.     

Getting to the guts of the matter: The status and potential of ‘omics’ research of parasitic protists of the human gastrointestinal system

Parasitic protists are a major cause of diarrhoeal illnesses in humans globally. Collectively, enteric pathogens exceed all other forms of infectious disease, in terms of their estimated global prevalence and socioeconomic impact. They have a disproportionately high impact on children in impoverished communities, leading to acute (diarrhoea, vomiting, dehydration and death) and chronic disease (malabsorption, malnutrition, physical and cognitive stunting and predisposition to chronic, non-communicable disease) consequences. However, historically, investment in research and disease control measures has been disproportionately poor, leading to their current classification as neglected pathogens. A sound understanding of their biology is essential in underpinning detection, treatment and control efforts. One major tool in rapidly improving our knowledge of these parasites is the use of biological systems, including ‘omic’ technologies. In recent years, these tools have shown significant success when applied to enteric protists. This review summarises much of this knowledge and highlights the significant remaining knowledge gaps. A major focus of the present review was to provide a perspective on a way forward to address these gaps using advanced biotechnologies.     

The course of diabetes in children,adolescents and young adults: does the autoimmunity status matter?

Background

Initial classification of diabetes of young may require revision to improve diagnostic accuracy of different forms of diabetes.The aim of our study was to examine markers of beta-cell autoimmunity in a cohort of young (0–25 years) patients with type 1 diabetes and compare the presentation and course of the disease according to the presence of pancreatic antibodies.

Methods

Cross-sectional population-based study was performed covering 100% of pediatric (n?=?860) and 70% of 18–25 years old adult patients (n?=?349) with type 1 diabetes in Lithuania.

Results

No antibodies (GAD65, IA-2, IAA and ICA) were found in 87 (7.5%) cases. Familial history of diabetes was more frequent in those with antibodies-negative diabetes (24.1 vs. 9.4%, p?<?0.001). Gestational age, birth weight and age at diagnosis was similar in both groups. Ketosis at presentation was more frequent in patients with autoimmune diabetes (88.1 vs. 73.5%, p?<?0.05). HbA1c at the moment of investigation was 8.6 (3) vs. 8.7 (2.2)% in antibodies-negative and antibodies-positive diabetes groups, respectively, p?>?0.05. In the whole cohort, neuropathy was found in 8.8% and nephropathy - in 8.1% of cases, not depending on autoimmunity status. Adjusted for age at onset, disease duration and HbA1c, retinopathy was more frequent in antibodies-negative subjects (13.8 vs. 7.8%, p?<?0.05).

Conclusion

Antibodies-negative pediatric and young adult patients with type 1 diabetes in this study had higher incidence of family history of diabetes, higher frequency of retinopathy, less frequent ketosis at presentation, but similar age at onset, HbA1c, incidence of nephropathy and neuropathy compared to antibodies-positive patients.