Ubiquitin‐specific protease‐like 1 (USPL1) is a SUMO isopeptidase with essential,non‐catalytic functions

Isopeptidases are essential regulators of protein ubiquitination and sumoylation. However, only two families of SUMO isopeptidases are at present known. Here, we report an activity‐based search with the suicide inhibitor haemagglutinin (HA)‐SUMO‐vinylmethylester that led to the identification of a surprising new SUMO protease, ubiquitin‐specific protease‐like 1 (USPL1). Indeed, USPL1 neither binds nor cleaves ubiquitin, but is a potent SUMO isopeptidase both in vitro and in cells. C13orf22l—an essential but distant zebrafish homologue of USPL1—also acts on SUMO, indicating functional conservation. We have identified invariant USPL1 residues required for SUMO binding and cleavage. USPL1 is a low‐abundance protein that colocalizes with coilin in Cajal bodies. Its depletion does not affect global sumoylation, but causes striking coilin mislocalization and impairs cell proliferation, functions that are not dependent on USPL1 catalytic activity. Thus, USPL1 represents a third type of SUMO protease, with essential functions in Cajal body biology.     

A sequential expression system for high-throughput functional genomic analysis

A method employing sequential rounds of cell-free protein synthesis (CFPS) was developed to identify gene products influencing the complex metabolic systems that result in protein accumulation and folding in vitro. The first round of CFPS creates an array of cell extracts individually enriched with a single gene product expressed in-parallel from linear DNA expression templates (ETs). The cell extract is engineered to enhance template stability and to provide reaction conditions conducive for general protein activation. Following first-round expression, linear templates are selectively degraded and a plasmid template for a reporter enzyme is added to initiate a subsequent round of protein expression. Reporter concentration and activity identify first-round gene products that affect amino acid and nucleic acid stability, energy supply, protein expression, stability, and activation. This sequential CFPS system provides a unique format for the functional genomic identification of broadly diverse metabolic activities.     

Structural understanding of stabilization patterns in engineered bispecific Ig‐like antibody molecules

Bispecific immunoglobulin‐like antibodies capable of engaging multiple antigens represent a promising new class of therapeutic agents. Engineering of these molecules requires optimization of the molecular properties of one of the domain components. Here, we present a detailed crystallographic and computational characterization of the stabilization patterns in the lymphotoxin‐beta receptor (LTβR) binding Fv domain of an anti‐LTβR/anti‐TNF‐related apoptosis inducing ligand receptor‐2 (TRAIL‐R2) bispecific immunoglobulin‐like antibody. We further describe a new hierarchical structure‐guided approach toward engineering of antibody‐like molecules to enhance their thermal and chemical stability. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Quantifying the evidence for ecological synergies

There is increasing concern that multiple drivers of ecological change will interact synergistically to accelerate biodiversity loss. However, the prevalence and magnitude of these interactions remain one of the largest uncertainties in projections of future ecological change. We address this uncertainty by performing a meta-analysis of 112 published factorial experiments that evaluated the impacts of multiple stressors on animal mortality in freshwater, marine and terrestrial communities. We found that, on average, mortalities from the combined action of two stressors were not synergistic and this result was consistent across studies investigating different stressors, study organisms and life-history stages. Furthermore, only one-third of relevant experiments displayed truly synergistic effects, which does not support the prevailing ecological paradigm that synergies are rampant. However, in more than three-quarters of relevant experiments, the outcome of multiple stressor interactions was non-additive (i.e. synergies or antagonisms), suggesting that ecological surprises may be more common than simple additive effects.     

Biochemical and strain properties of CJD prions: complexity versus simplicity

Prions, the agents responsible for transmissible spongiform encephalopathies, are infectious proteins consisting primarily of scrapie prion protein (PrP(Sc)), a misfolded, β-sheet enriched and aggregated form of the host-encoded cellular prion protein (PrP(C)). Their propagation is based on an autocatalytic PrP conversion process. Despite the lack of a nucleic acid genome, different prion strains have been isolated from animal diseases. Increasing evidence supports the view that strain-specific properties may be enciphered within conformational variations of PrP(Sc). In humans, sporadic Creutzfeldt-Jakob disease (sCJD) is the most frequent form of prion diseases and has demonstrated a wide phenotypic and molecular spectrum. In contrast, variant Creutzfeldt-Jakob disease (vCJD), which results from oral exposure to the agent of bovine spongiform encephalopathy, is a highly stereotyped disease, that, until now, has only occurred in patients who are methionine homozygous at codon 129 of the PrP gene. Recent research has provided consistent evidence of strain diversity in sCJD and also, unexpectedly enough, in vCJD. Here, we discuss the puzzling biochemical/pathological diversity of human prion disorders and the relationship of that diversity to the biological properties of the agent as demonstrated by strain typing in experimental models.     

Flexible Solar Thermal Fuel Devices: Composites of Fabric and a Photoliquefiable Azobenzene Derivative

Controllable storage and release of solar energy has always been a highlighted scientific issue for its benefit of mankind. Solar thermal fuels (STFs) supply a closed cycle and renewable energy‐storage strategy by transforming solar energy into chemical energy stored in the conformation of molecular isomers, such as cis/trans‐azobenzene, and releasing it as heat under various stimuli. Although the potential high energy density of the STFs which are based on the hybrids of azobenzene derivatives and carbon nanomaterials has been reported the solvent‐assistant charging hinders their practicability. In this study, a solid‐state STF device is designed and fabricated by compositing one photoliquefiable azobenzene (PLAZ) derivative with a flexible fabric template. The photoinduced phase transition of the PLAZ derivative enables the charging of the flexible STFs to be totally solvent‐free. Interestingly, the energy‐storage capacity (energy density ≈201 J g^?1) of flexible PLAZ STFs has been improved by the soft fabric template. The exothermic situation is monitored with one infrared camera, which shows 4 °C temperature difference between charged and discharged samples under blue light stimulus. The flexible STFs are may be used in practice as heating equipment.     

Variability in factors causing light attenuation in Lake Victoria

1. The major optical components controlling the attenuation of photosynthetic available radiation in nearshore areas of Lake Victoria (Uganda and Kenya) were examined and their impact compared. It was found that chromophoric dissolved organic matter and tripton play a dominating role in many nearshore areas, indicating that the coastal areas of Lake Victoria cannot be considered as Case I waters.
2. Concentrations of chromophoric dissolved organic matter declined with distance from the coast in an exponential manner indicating dilution and degradation of terrestrial sources of organic matter rather than in situ production. The importance of tripton was found to follow a similar pattern, while the relative importance of phytoplankton biomass in overall attenuation of photosynthetic available radiation was found to increase with distance from the coast. A specific attenuation coefficient for phytoplankton biomass was determined (0.019 m² mg Chl a ⁻¹).
3. Using a light limitation approach based on carrying capacity, it was possible to map areas that are closer to being light limited. Light limitation appears to occur throughout most bays and some coastal areas receiving catchment waters. This spatial information, geographically referenced to bathymetric and catchment conditions, was utilized to understand the importance of environmental conditions in limiting phytoplankton biomass.     

Distribution of ichthyoplankton in the eastern Peter the Great Bay,Sea of Japan,in June and July of 2007

Comparison of the results of ichthyoplankton surveys conducted at 97 stations in the eastern part of the Peter the Great Bay of the Sea of Japan, in June–July 2007 with the similar research data of the 1950s shows that at present, as was the case 50 years ago, flatfish eggs belonging mainly to the yellowfin sole Limanda aspera and brown sole Pleuronectes herzensteini prevail in the local ichthyoplankton (up to 86%). The highest concentrations of these species’ eggs were recorded in the Vostok Bay and Strelok Bay. The spawning activity of flatfish in 2007 is found to be lower than in the mid 1900s, but the significance of the eastern part of the Peter the Great Bay for flatfish reproduction remains large. The importance of long-term monitoring in this area, which is being subjected to steadily growing anthropogenic impacts, is also proven.