N‐glycan processing selects ERAD‐resistant misfolded proteins for ER‐to‐lysosome‐associated degradation

Efficient degradation of by‐products of protein biogenesis maintains cellular fitness. Strikingly, the major biosynthetic compartment in eukaryotic cells, the endoplasmic reticulum (ER), lacks degradative machineries. Misfolded proteins in the ER are translocated to the cytosol for proteasomal degradation via ER‐associated degradation (ERAD). Alternatively, they are segregated in ER subdomains that are shed from the biosynthetic compartment and are delivered to endolysosomes under control of ER‐phagy receptors for ER‐to‐lysosome‐associated degradation (ERLAD). Demannosylation of N‐linked oligosaccharides targets terminally misfolded proteins for ERAD. How misfolded proteins are eventually marked for ERLAD is not known. Here, we show for ATZ and mutant Pro‐collagen that cycles of de‐/re‐glucosylation of selected N‐glycans and persistent association with Calnexin (CNX) are required and sufficient to mark ERAD‐resistant misfolded proteins for FAM134B‐driven lysosomal delivery. In summary, we show that mannose and glucose processing of N‐glycans are triggering events that target misfolded proteins in the ER to proteasomal (ERAD) and lysosomal (ERLAD) clearance, respectively, regulating protein quality control in eukaryotic cells.     

Integrating ecosystem engineering and food webs

Ecosystem engineering, the physical modification of the environment by organisms, is a common and often influential process whose significance to food web structure and dynamics is largely unknown. In the light of recent calls to expand food web studies to include non‐trophic interactions, we explore how we might best integrate ecosystem engineering and food webs. We provide rationales justifying their integration and present a provisional framework identifying how ecosystem engineering can affect the nodes and links of food webs and overall organization; how trophic interactions with the engineer can affect the engineering; and how feedbacks between engineering and trophic interactions can affect food web structure and dynamics. We use a simple integrative food chain model to illustrate how feedbacks between the engineer and the food web can alter 1) engineering effects on food web dynamics, and 2) food web responses to extrinsic environmental perturbations. We identify four general challenges to integration that we argue can readily be met, and call for studies that can achieve this integration and help pave the way to a more general understanding of interaction webs in nature. Synthesis All species are affected by their physical environment. Because ecosystem engineering species modify the physical environment and belong to food webs, such species are potentially one of the most important bridges between the trophic and non‐trophic. We examine how to integrate the so far, largely independent research areas of ecosystem engineering and food webs. We present a conceptual framework for understanding how engineering can affect food webs and vice versa, and how feedbacks between the two alter ecosystem dynamics. With appropriate empirical studies and models, integration is achievable, paving the way to a more general understanding of interaction webs in nature.     

Effect of the replacement of tropical forests with tree plantations on soil organic carbon levels in the Jomoro district,Ghana

Background and aims

In the Jomoro district in Ghana, tree plantations were the first cause of deforestation in the past, drastically reducing the area occupied by primary forests. The aim of this study was to quantify soil organic carbon (SOC) losses due to a change in land use from primary forest to tree plantations (cocoa, coconut, rubber, oil palm) on the different substrates of the district. Secondary forests and mixed plantations were also included in the study.

Methods

Soils were sampled at different depths up to 100 cm along a series of chronosequences in each of the three substrates (Granite, Lower Birrimian and Tertiary Sands) present in the area.

Results

The highest SOC losses in the 0–30 cm layer were caused by the conversion of primary forests to tree plantations: cocoa ?61 % of the original SOC stock, coconut ?55 %, rubber ?35 % and oil palm 28 %, while mixed plantations and secondary forests showed a loss of 23 % and 21 % of the original SOC stock, respectively. C losses were less apparent from the entire profile (to a depth of 100 cm).

Conclusions

All conversions to tree plantations caused substantial SOC losses, comparable to the conversion of forests to agricultural systems. Secondary forests and mixed plantations were the only sustainable land uses that restricted SOC losses considerably.     

Virulence variation among epidemic and non-epidemic strains of Saint Louis encephalitis virus circulating in Argentina

Saint Louis encephalitis virus caused an outbreak of febrile illness and encephalitis cases in Córdoba, Argentina, in 2005. During this outbreak, the strain CbaAr-4005 was isolated from Culex quinquefasciatus mosquitoes. We hypothesised that this epidemic variant would be more virulent in a mouse model than two other non-epidemic strains (78V-6507 and CorAn-9275) isolated under different epidemiological conditions. To test this hypothesis, we performed a biological characterisation in a murine model, including mortality, morbidity and infection percentages and lethal infection indices using the three strains. Mice were separated into age groups (7, 10 and 21-day-old mice) and analysed after infection. The strain CbaAr-4005 was the most infective and lethal of the three variants, whereas the other two strains exhibited a decreasing mortality percentage with increasing animal age. The strain CbaAr-4005 produced the highest morbidity percentages and no significant differences among age groups were observed. The epidemic strain caused signs of illness in all inoculated animals and showed narrower ranges from the onset of symptoms than the other strains. CbaAr-4005 was the most virulent for Swiss albino mice. Our results highlight the importance of performing biological characterisations of arbovirus strains likely to be responsible for emerging or reemerging human diseases.     

Sperm ubiquitination in epididymal feline semen

Ubiquitin is a 8.5-kDa peptide that tags other proteins for proteasomal degradation. It has been proposed that ubiquitination might be responsible for the elimination of defective spermatozoa during transit through the epididymis in humans and cattle, but its exact biological function in seminal plasma has not yet been clarified. In the domestic cat (Felis catus), the percentage of immature, unviable, and abnormal spermatozoa decreases during the epididymal transit, indicating the existence of a mechanism that removes defective spermatozoa. Magnetic cell separation techniques, based on the use of magnetic beads coated with anti-ubiquitin antibodies, may allow the selective capture of ubiquitinated spermatozoa from semen, thus contributing to the identification of a potential correlation between semen quality and ubiquitination process. Moreover, the selective identification of all the ubiquitinated proteins in different epididymal regions could give a better understanding of the ubiquitin role in feline sperm maturation. The aims of this study were as follows: (1) to verify the possibility of separating ubiquitinated spermatozoa with magnetic ubiquitin beads and identify the morphological and acrosomal differences between whole sample and unbound gametes, (2) to characterize all the ubiquitinated proteins in spermatozoa retrieved in the three epididymal regions by a proteomic approach. The data indicated the presence of ubiquitinated proteins in cat epididymal semen. However, a correlation between abnormal and ubiquitinated spermatozoa has not been found, and ubiquitin cannot be considered as a biomarker of quality of epididymal feline spermatozoa. To the author's knowledge, this is the first identification of all the ubiquitinated proteins of cat spermatozoa collected from different epididymal regions. The proteomic pattern allows a further characterization of cat epididymal semen and represents a contribute to a better understanding of the ubiquitin role in feline sperm maturation.     

Moderate Warming in Microcosm Experiment Does Not Affect Microbial Communities in Temperate Vineyard Soils

Changes in the soil microbial community structure can lead to dramatic changes in the soil ecosystem. Temperature, which is projected to increase with climate change, is commonly assumed to affect microbial communities, but its effects on agricultural soils are not fully understood. We collected soil samples from six vineyards characterised by a difference of about 2 °C in daily soil temperature over the year and simulated in a microcosm experiment different temperature regimes over a period of 1 year: seasonal fluctuations in soil temperature based on the average daily soil temperature measured in the field; soil temperature warming (2 °C above the normal seasonal temperatures); and constant temperatures normally registered in these temperate soils in winter (3 °C) and in summer (20 °C). Changes in the soil bacterial and fungal community structures were analysed by automated ribosomal intergenic spacer analysis (ARISA). We did not find any effect of warming on soil bacterial and fungal communities, while stable temperatures affected the fungal more than the bacterial communities, although this effect was soil dependent. The soil bacterial community exhibited soil-dependent seasonal fluctuations, while the fungal community was mainly stable. Each soil harbours different microbial communities that respond differently to seasonal temperature fluctuations; therefore, any generalization regarding the effect of climate change on soil communities should be made carefully.     

Effects of arboriculture stands on European hare <Emphasis Type="Italic">Lepus europaeus</Emphasis> spring habitat use in an agricultural area of northern Italy

Habitat changes due to agricultural intensification is widely considered a main cause of European hare (Lepus europaeus Pallas, 1778) decline. We investigated the potential of arboriculture stands to enhance landscape diversity and increase farmland suitability for European hares in an intensive agricultural area of northern Italy. In spring 2005, we recorded hare habitat use during feeding activity and resting time by nocturnal censuses and searching for daytime resting sites, respectively. Hare presence/absence, based on faecal pellets, was assessed in 150 1-m radius plots. Hares positively selected edges and avoided woods and stubble during both feeding activity and resting time, which highlights the key role of permanent linear cover in providing the variety of vegetation types required by hares for shelter and feed. Forms were typically located in covered places, surrounded by denser vegetation than sample plots, in order to gain protection from avian and terrestrial predators. Arboriculture stands seem to be able to satisfy a part of hare habitat requirement, thanks to ground flora that provide tasty food, and tree cover that offers refuge against predators and bad weather conditions. However, more focused studies are necessary to improve knowledge of the long-term effects of these crops on farmland biodiversity.     

Clinical neurophysiology in ALS

Amyotrophic lateral sclerosis (ALS) belongs to a group of disorders known as motor neuron diseases. Despite being one of the most devastating diseases known, there is little evidence for diagnosing and managing patients with ALS. Clinical neurophysiologic tests are essential, when no biological marker exists to aid early diagnosis, not only in relation to diagnosis, but also in the development of disease progression, and perhaps, in the future, in measuring patients' response to therapy. The electrophysiological features used in the diagnosis of ALS are based on Awaji-shima consensus recommendations for the application of electrophysiological tests, as applied to the revised El Escorial Criteria. Measurements of axonal excitability through nerve conduction study (ENG) is useful to evaluate axonal degeneration. Electromyography (EMG) recordings with needle examination are essential for confirming lower motor neuron involvement in the initial diagnosis of ALS. EMG abnormalities are frequent and these include fibrillation potentials or positive sharp wave potentials, or both, with fasciculation potentials in resting muscle, and an incomplete interference pattern, with abnormal motor unit potentials. Collateral or terminal nerve sprouting is common in ALS and is frequent large macro-motor unit potentials (MUPs). Motor unit number estimation (MUNE) may be useful in measuring loss of functioning motor units and is an attractive endpoint measure in clinical drug trials in ALS because it directly assesses loss of lower motor neurons and is sensitive to disease progression. Transcortical magnetic stimulation protocols, and cortical excitability may be useful to assess the involvement of upper motor neuron system. In this chapter the advantages, limitations and promise of these various methods are discussed, in order to indicate the direction for further neurophysiological studies in this disorder.     

The handling of the mechanistic probe 5-fluorouridine by the pseudouridine synthase TruA and its consistency with the handling of the same probe by the pseudouridine synthases TruB and RluA

RNA containing 5-fluorouridine (F(5)U) had previously been used to examine the mechanism of the pseudouridine synthase TruA, formerly known as pseudouridine synthase I [Gu et al. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 14270-14275]. From that work, it was reasonably concluded that the pseudouridine synthases proceed via a mechanism involving a Michael addition by an active site aspartic acid residue to the pyrimidine ring of uridine or F(5)U. Those conclusions rested on the assumption that the hydrate of F(5)U was obtained after digestion of the product RNA and that hydration resulted from hydrolysis of the ester intermediate between the aspartic acid residue and F(5)U. As reported here, (18)O labeling definitively demonstrates that ester hydrolysis does not give rise to the observed hydrated product and that digestion generates not the expected mononucleoside product but rather a dinucleotide between a hydrated isomer of F(5)U and the following nucleoside in RNA. The discovery that digestion products are dinucleotides accounts for the previously puzzling differences in the isolated products obtained following the action of the pseudouridine synthases TruB and RluA on F(5)U in RNA.