SwissSidechain: a molecular and structural database of non-natural sidechains.

Amino acids form the building blocks of all proteins. Naturally occurring amino acids are restricted to a few tens of sidechains, even when considering post-translational modifications and rare amino acids such as selenocysteine and pyrrolysine. However, the potential chemical diversity of amino acid sidechains is nearly infinite. Exploiting this diversity by using non-natural sidechains to expand the building blocks of proteins and peptides has recently found widespread applications in biochemistry, protein engineering and drug design. Despite these applications, there is currently no unified online bioinformatics resource for non-natural sidechains. With the SwissSidechain database (http://www.swisssidechain.ch), we offer a central and curated platform about non-natural sidechains for researchers in biochemistry, medicinal chemistry, protein engineering and molecular modeling. SwissSidechain provides biophysical, structural and molecular data for hundreds of commercially available non-natural amino acid sidechains, both in l- and d-configurations. The database can be easily browsed by sidechain names, families or physico-chemical properties. We also provide plugins to seamlessly insert non-natural sidechains into peptides and proteins using molecular visualization software, as well as topologies and parameters compatible with molecular mechanics software.

The category 'natural' in the discourse of couples who used medically assisted procreation

As a constantly evolving set of complex biotechnologies, medically assisted procreation (MAP) jeopardises a category that seems to be taken for granted: that of 'natural'. What is 'natural' or not when MAP is used to procreate? What are the boundaries between a 'natural' and a 'non-natural' fertilisation? Drawing upon a dialogical approach to language and cognition, our study examined the semantic field of the category 'natural' as expressed in interviews between a psychiatrist and seven couples who resorted to MAP and had to decide whether to keep their frozen pre-embryonic cells (zygotes) for further procreation or to allow them be destroyed. We examined how these couples evoked the category 'natural' and showed that in their argumentation, the category 'natural' encompassed a wide variety of phenomena, which shifted the boundaries between the 'natural' and 'non-natural'. In so doing, the couples 'renaturalised' MAP, normalized it, moved the boundaries between what is legitimate or not, and showed their accountability. Hence, reference to the category 'natural' seemed to act both as an argumentative and a psychological resource in the elaboration of the person's experience in resorting to MAP.

Seasonal flight and resource collection patterns of colonies of the stingless bee Melipona bicolor schencki Gribodo (Apidae, Meliponini) in an Araucaria forest area in southern Brazil

Melipona bicolor schencki occurs in southern Brazil and at high elevations in southeastern Brazil. It has potential for use in meliponiculture but this stingless bee species is vulnerable to extinction and we have little knowledge about its ecology. In order to gather essential information for species conservation and management, we made a study of seasonal flight activities in its natural environment. We sampled bees entering the nests with pollen, nectar/water and resin/mud, in five colonies during each season. In parallel, we analyzed the influence of hour of the day and meteorological factors on flight activity. Flights were most intense during spring and summer, with daily mean estimates of 2,100 and 2,333 flights respectively, while in fall and winter the daily flight estimate was reduced to 612 and 1,104 flights, respectively. Nectar and water were the most frequently-collected resources, followed by pollen and building materials. This preference occurred in all seasons, but with variations in intensity. During spring, daily flight activity lasted over 14 hours; this period was reduced in the other seasons, reaching eight hours in winter. Meteorological factors were associated with 40.2% of the variation in flight and resource collection activity. Apparently, other factors that we did not measure, such as colony needs and availability of floral resources, also strongly influence the intensity of resource collection.

Fossil resource depletion and climate change emissions: the role of physical constrictions

[spa] En lo que concierne al cambio climático, los pronósticos de cercanos picos de combustible fósiles parecen buenas noticias pues la mayoría de las emisiones proceden de la quema de combustibles fósiles. Sin embargo, esto podría resultar engañoso de confirmarse las enormes estimaciones de reservas de carbón pues puede divisarse un intercambio de combustible fósiles con baja concentración de carbono (petróleo y gas) por otros de mayor (carbón). Ciñéndonos a esta hipótesis desarrollamos escenarios donde tan pronto el petróleo y el gas natural alcanzan su cénit la extracción de carbón crece lo necesario para compensar el descenso de los primeros. Estimamos las emisiones que se deriva de tales supuestos y las comparamos con el peor escenario del IPCC. Si bien dicho escenario parece improbable concluimos que los picos de petróleo y gas no son suficientes para evitar peligrosas sendas de gases de efecto invernadero. Las concentraciones de CO2 halladas superan con creces las 450 ppm sin signos de remisión.

Fossil resource depletion and climate change emissions: the role of physical constrictions

[spa] En lo que concierne al cambio climático, los pronósticos de cercanos picos de combustible fósiles parecen buenas noticias pues la mayoría de las emisiones proceden de la quema de combustibles fósiles. Sin embargo, esto podría resultar engañoso de confirmarse las enormes estimaciones de reservas de carbón pues puede divisarse un intercambio de combustible fósiles con baja concentración de carbono (petróleo y gas) por otros de mayor (carbón). Ciñéndonos a esta hipótesis desarrollamos escenarios donde tan pronto el petróleo y el gas natural alcanzan su cénit la extracción de carbón crece lo necesario para compensar el descenso de los primeros. Estimamos las emisiones que se deriva de tales supuestos y las comparamos con el peor escenario del IPCC. Si bien dicho escenario parece improbable concluimos que los picos de petróleo y gas no son suficientes para evitar peligrosas sendas de gases de efecto invernadero. Las concentraciones de CO2 halladas superan con creces las 450 ppm sin signos de remisión.

Natural malaria infection reduces starvation resistance of nutritionally stressed mosquitoes.

In disease ecology, there is growing evidence that environmental quality interacts with parasite and host to determine host susceptibility to an infection. Most studies of malaria parasites have focused on the infection costs incurred by the hosts, and few have investigated the costs on mosquito vectors. The interplay between the environment, the vector and the parasite has therefore mostly been ignored and often relied on unnatural or allopatric Plasmodium/vector associations. Here, we investigated the effects of natural avian malaria infection on both fecundity and survival of field-caught female Culex pipiens mosquitoes, individually maintained in laboratory conditions. We manipulated environmental quality by providing mosquitoes with different concentrations of glucose-feeding solution prior to submitting them to a starvation challenge. We used molecular-based methods to assess mosquitoes' infection status. We found that mosquitoes infected with Plasmodium had lower starvation resistance than uninfected ones only under low nutritional conditions. The effect of nutritional stress varied with time, with the difference of starvation resistance between optimally and suboptimally fed mosquitoes increasing from spring to summer, as shown by a significant interaction between diet treatment and months of capture. Infected and uninfected mosquitoes had similar clutch size, indicating no effect of infection on fecundity. Overall, this study suggests that avian malaria vectors may suffer Plasmodium infection costs in their natural habitat, under certain environmental conditions. This may have major implications for disease transmission in the wild.

Iowa Department of Naturals Resource Performance Report, FY 2013-2014, January 2014

This report provides insight on accomplishments we have achieved in Fiscal Year 2015 as well as some challenges we face in the not so distant future. The DNR, in partnership with the Iowa Department of Agriculture and Land Stewardship and Iowa State University,

Iowa Department of Naturals Resource Agency Performance Plan, FY2015, July 1, 2014

This report provides insight on accomplishments the department of Natural Resources have achieved in Fiscal Year 2015 as well as some challenges face in the not so distant future.

Dynamic Modelling of Material Flows and Sustainable Resource Use: Case Studies in Regional Metabolism and Space Life Support Systems

Sustainable resource use is one of the most important environmental issues of our times. It is closely related to discussions on the 'peaking' of various natural resources serving as energy sources, agricultural nutrients, or metals indispensable in high-technology applications. Although the peaking theory remains controversial, it is commonly recognized that a more sustainable use of resources would alleviate negative environmental impacts related to resource use. In this thesis, sustainable resource use is analysed from a practical standpoint, through several different case studies. Four of these case studies relate to resource metabolism in the Canton of Geneva in Switzerland: the aim was to model the evolution of chosen resource stocks and flows in the coming decades. The studied resources were copper (a bulk metal), phosphorus (a vital agricultural nutrient), and wood (a renewable resource). In addition, the case of lithium (a critical metal) was analysed briefly in a qualitative manner and in an electric mobility perspective. In addition to the Geneva case studies, this thesis includes a case study on the sustainability of space life support systems. Space life support systems are systems whose aim is to provide the crew of a spacecraft with the necessary metabolic consumables over the course of a mission. Sustainability was again analysed from a resource use perspective. In this case study, the functioning of two different types of life support systems, ARES and BIORAT, were evaluated and compared; these systems represent, respectively, physico-chemical and biological life support systems. Space life support systems could in fact be used as a kind of 'laboratory of sustainability' given that they represent closed and relatively simple systems compared to complex and open terrestrial systems such as the Canton of Geneva. The chosen analysis method used in the Geneva case studies was dynamic material flow analysis: dynamic material flow models were constructed for the resources copper, phosphorus, and wood. Besides a baseline scenario, various alternative scenarios (notably involving increased recycling) were also examined. In the case of space life support systems, the methodology of material flow analysis was also employed, but as the data available on the dynamic behaviour of the systems was insufficient, only static simulations could be performed. The results of the case studies in the Canton of Geneva show the following: were resource use to follow population growth, resource consumption would be multiplied by nearly 1.2 by 2030 and by 1.5 by 2080. A complete transition to electric mobility would be expected to only slightly (+5%) increase the copper consumption per capita while the lithium demand in cars would increase 350 fold. For example, phosphorus imports could be decreased by recycling sewage sludge or human urine; however, the health and environmental impacts of these options have yet to be studied. Increasing the wood production in the Canton would not significantly decrease the dependence on wood imports as the Canton's production represents only 5% of total consumption. In the comparison of space life support systems ARES and BIORAT, BIORAT outperforms ARES in resource use but not in energy use. However, as the systems are dimensioned very differently, it remains questionable whether they can be compared outright. In conclusion, the use of dynamic material flow analysis can provide useful information for policy makers and strategic decision-making; however, uncertainty in reference data greatly influences the precision of the results. Space life support systems constitute an extreme case of resource-using systems; nevertheless, it is not clear how their example could be of immediate use to terrestrial systems.

Combined Heat and Power Resource Guide, December 2015

Combined Heat and Power (CHP) refers to the onsite production of electricity and thermal energy from the same fuel source. Integrating power and thermal energy production is more efficient than separate generating systems and used in the right situation can yield several benefits.

Water resource availability : executive summary, 1978

The information presented in this summary document has been based on the comprehensive, "Task Force Report on Water Resource Availability", prepared by the Iowa Geological Survey and filed with the Iowa Natural Resources Council. The reader should refer to the task force document for more detailed information.

PRDM1 is a tumor suppressor gene in natural killer cell malignancies.

Natural killer cell lymphoma (NKCL) constitutes a rare and aggressive form of non-Hodgkin lymphoma, and there is little insight into its pathogenesis. Here we show that PRDM1 is a tumor suppressor gene in NKCLs that is inactivated by a combination of monoallelic deletion and promoter CpG island hypermethylation. We observed monoallelic deletion of PRDM1 loci in 8 of 18 (44%) NKCL cases. The other allele showed significant promoter methylation in 12 of 17 (71%) cases. In support of its role as a tumor suppressor gene, the reconstitution of PRDM1 in PRDM1-null NK cell lines led to G2/M cell cycle arrest, increased apoptosis, and a strong negative selection pressure with progressive elimination of PRDM1-expressing cells, which was enhanced when IL-2 concentration is limiting. We observed a progressive increase in PRDM1 expression-in particular, PRDM1α-in normal NK cells in response to IL-2 and in normal NK cells activated with an engineered NK cell target, K562-Cl9-mb21, suggesting its role in NK cell homeostasis. In support of this role, knockdown of PRDM1 by shRNA in normal NK cells resulted in the positive selection of these cells. We identified MYC and 4-1BBL as targets of PRDM1 in NK cells. Disruption of homeostatic control by PRDM1 may be an important pathogenetic mechanism for NKCL.

Drosophila rely on learning while foraging under semi-natural conditions

Learning is predicted to affect manifold ecological and evolutionary processes, but the extent to which animals rely on learning in nature remains poorly known, especially for short-lived non-social invertebrates. This is in particular the case for Drosophila, a favourite laboratory system to study molecular mechanisms of learning. Here we tested whether Drosophila melanogaster use learned information to choose food while free-flying in a large greenhouse emulating the natural environment. In a series of experiments flies were first given an opportunity to learn which of two food odours was associated with good versus unpalatable taste; subsequently, their preference for the two odours was assessed with olfactory traps set up in the greenhouse. Flies that had experienced palatable apple-flavoured food and unpalatable orange-flavoured food were more likely to be attracted to the odour of apple than flies with the opposite experience. This was true both when the flies first learned in the laboratory and were then released and recaptured in the greenhouse, and when the learning occurred under free-flying conditions in the greenhouse. Furthermore, flies retained the memory of their experience while exploring the greenhouse overnight in the absence of focal odours, pointing to the involvement of consolidated memory. These results support the notion that even small, short lived insects which are not central-place foragers make use of learned cues in their natural environments.

Psychotherapy for Personality Disorders in a Natural Setting: A Pilot Study over Two Years of Treatment.

Long-term assessment of the effects of psychotherapy for personality disorders (PDs) in a natural environment is an important task. Such research contributes to enlarge the practice-based evidence, embedded in broad collaborations between clinicians and researchers in psychotherapy for PDs. The present pilot study used rigorous assessment procedures and incorporated feedback loops of outcome information to the therapists in demonstrating the effects of psychotherapy for PD in a natural setting. The number of Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV), criteria for any PD was the primary outcome (along with psychological distress, depression, impulsiveness, and quality of life as secondary measures), assessed at intake, 6, 12, 18, and 24 months of psychotherapy for N = 13 patients with PD. Data were analyzed using hierarchical linear modeling. Results demonstrated a large pre-post effect (d = 2.22) for the observer-rated measure (primary outcome), and small to medium effects for the secondary outcomes; these results were corroborated by a steady decrease of symptoms over all five time points, which was significant for several outcomes. These results add a piece to the literature by demonstrating the effects of long-term psychotherapy for PDs in increasingly diverse contexts and suggest that practice-oriented research can be carried out in a collaborative and systematic manner.

Adaptive Dynamics of Resource Specialization

Ecological specialization in resource utilization has various facades ranging from nutritional resources via host use of parasites or phytophagous insects to local adaptation in different habitats. Therefore, the evolution of specialization affects the evolution of most other traits, which makes it one of the core issues in the theory of evolution. Hence, the evolution of specialization has gained enormous amounts of research interest, starting already from Darwin’s Origin of species in 1859. Vast majority of the theoretical studies has, however, focused on the mathematically most simple case with well-mixed populations and equilibrium dynamics. This thesis explores the possibilities to extend the evolutionary analysis of resource usage to spatially heterogeneous metapopulation models and to models with non-equilibrium dynamics. These extensions are enabled by the recent advances in the field of adaptive dynamics, which allows for a mechanistic derivation of the invasion-fitness function based on the ecological dynamics. In the evolutionary analyses, special focus is set to the case with two substitutable renewable resources. In this case, the most striking questions are, whether a generalist species is able to coexist with the two specialist species, and can such trimorphic coexistence be attained through natural selection starting from a monomorphic population. This is shown possible both due to spatial heterogeneity and due to non-equilibrium dynamics. In addition, it is shown that chaotic dynamics may sometimes inflict evolutionary suicide or cyclic evolutionary dynamics. Moreover, the relations between various ecological parameters and evolutionary dynamics are investigated. Especially, the relation between specialization and dispersal propensity turns out to be counter-intuitively non-monotonous. This observation served as inspiration to the analysis of joint evolution of dispersal and specialization, which may provide the most natural explanation to the observed coexistence of specialist and generalist species.