Defective Autophagy and mTORC1 Signaling in Myotubularin Null Mice

Autophagy is a vesicular trafficking pathway that regulates the degradation of aggregated proteins and damaged organelles. Initiation of autophagy requires several multiprotein signaling complexes, such as the ULK1 kinase complex and the Vps34 lipid kinase complex, which generates phosphatidylinositol 3-phosphate [PtdIns(3)P] on the forming autophagosomal membrane. Alterations in autophagy have been reported for various diseases, including myopathies. Here we show that skeletal muscle autophagy is compromised in mice deficient in the X-linked myotubular myopathy (XLMTM)-associated PtdIns(3)P phosphatase myotubularin (MTM1). Mtm1-deficient muscle displays several cellular abnormalities, including a profound increase in ubiquitin aggregates and abnormal mitochondria. Further, we show that Mtm1 deficiency is accompanied by activation of mTORC1 signaling, which persists even following starvation. In vivo pharmacological inhibition of mTOR is sufficient to normalize aberrant autophagy and improve muscle phenotypes in Mtm1 null mice. These results suggest that aberrant mTORC1 signaling and impaired autophagy are consequences of the loss of Mtm1 and may play a primary role in disease pathogenesis.     

Exopeptidase activity in eggs of Trichostrongylus colubriformis (Nematoda)

Summary

A supernatant from eggs of the ruminant nematode Trichostrongylus colubriformis contained an enzyme that was similar to leucine aminopeptidase (LAP), based on hydrolysis of the substrate L-leucine β-naphthylamide to β-naphthylamine. A Michaelis-Menten constant (K _m) of 0.155 mM was obtained. Rate of hydrolysis of 16 substrates revealed that L-phenylalanine and L-tyrosine β-naphthylamides were hydrolyzed most readily while seven additional substrates were hydrolyzed at lesser rates. The optimum pH for enzymatic activity was 6.75–7.5. Enzymatic activity was lost by heating the egg supernatant to 60°C for 5 min or freezing at 0°C for 28 days. Addition of millimolar concentrations of the chlorides of zinc, manganese and magnesium to the egg supernatant had no stimulatory effect on enzyme activity while 10 and 100 mM concentrations significantly reduced activity. Ethylenediamine tetraacetic acid at 10^?4 M had no effect on enzymatic activity. Activity was inhibited by 10^?4 M 1,10-phenanthroline, but the inhibition was reversed by zinc chloride at 10^?3 M. Di-isopropylphosphofluoridate at 10^?3 M reduced enzymatic activity moderately. Enzyme activity in egg supernatant increased 2.2-fold from 21 days to 60–90 days of a primary infection in the host while a 3.3-fold increase was found in primary versus secondary infections.     

Birds to watch: a Red Data List for East Africa

Bennun, L.A., Njoroge, P. & Pomeroy, D. 2000. Birds to watch: a Red Data List for East Africa. Ostrich 71 (1 & 2): 310–314.

The value of Red Data books and lists is well established; there has been much recent work on improving the criteria for listing species of conservation concern. So far these have been applied mainly at the global level. Regional lists can be useful, however, in improving the resolution of conservation priorities and setting an agenda for research, monitoring and conservation, especially where data are collected by amateur naturalists. A Red Data list for East African birds has been drawn up following an eight-month process that involved wide consultation within the region, defined as Uganda, Rwanda, Tanzania, Kenya and Burundi. The criteria for listing were based on those defined by IUCN, and summarised in a single, simple table that could be used for screening large numbers of species. A criterion based on geographic range eliminated from consideration vagrant species or those on the extreme edge of their range. A separate Near Threatened category (Lower Risk but very close to Vulnerable) proved useful. An additional category of Regional Responsibility captured species that are entirely or mainly confiied to East Africa, or to three habitats where the region has special responsibility: coastal forests, Albertine Rift forests, and papyrus swamps. A total of 107 species (about 8% of the regional avifauna) were listed as regionally threatened. This includes four Critical, 18 Endangered and 85 Vulnerable species, proportions very close to those expected from the theoretical probabilities of extinction in each case. One hundred and four species were listed as Near-threatened and 153 as Regional Responsibility, 87 of which are not under threat. Placing a species in a particular category of threat, for explicit reasons, poses an hypothesis about its status that can be tested with additional data. This process is now under way with the compilation of a more detailed, annotated list.     

Greater phosphorus uptake in forested headwater streams modified by clearfell forestry

Clearfell, burn and sow (CBS) forestry can potentially alter stream environments by increasing available light and the input of woody debris. However, little is known about how CBS forestry affects in-stream processes such as nutrient uptake. We evaluate whether short-term (2–7 years) environmental changes (e.g. light availability and woody debris) associated with CBS forestry lead to differences in nutrient uptake metrics. To do this, we measured in-stream uptake of soluble reactive phosphorus (SRP) and ammonium (NH₄) in three old growth (OG) and four CBS-affected headwater stream reaches. The abundance of fine woody debris and light availability were significantly greater in CBS-affected than in OG reaches. Uptake velocities varied from 0.0880 to 0.951 mm min^?1 for NH₄ and from 0.0383 to 1.06 mm min^?1 for SRP across all sites. The mean uptake of SRP, but not NH₄, was significantly greater (i.e. higher uptake velocities and lower uptake lengths) in CBS-affected than in OG reaches. These results suggest that CBS forestry altered the stream environment enabling greater SRP uptake relative to OG reaches. Our findings highlight the tight linkage between headwater streams and their surrounding terrestrial environment, which has direct implications for catchment-scale biogeochemical processes.     

Functional,structural and phylogenetic analysis of domains underlying the Al sensitivity of the aluminum‐activated malate/anion transporter,TaALMT1

Triticum aestivum aluminum‐activated malate transporter (TaALMT1) is the founding member of a unique gene family of anion transporters (ALMTs) that mediate the efflux of organic acids. A small sub‐group of root‐localized ALMTs, including TaALMT1, is physiologically associated with in planta aluminum (Al) resistance. TaALMT1 exhibits significant enhancement of transport activity in response to extracellular Al. In this study, we integrated structure–function analyses of structurally altered TaALMT1 proteins expressed in Xenopus oocytes with phylogenic analyses of the ALMT family. Our aim is to re‐examine the role of protein domains in terms of their potential involvement in the Al‐dependent enhancement (i.e. Al‐responsiveness) of TaALMT1 transport activity, as well as the roles of all its 43 negatively charged amino acid residues. Our results indicate that the N‐domain, which is predicted to form the conductive pathway, mediates ion transport even in the absence of the C‐domain. However, segments in both domains are involved in Al³⁺ sensing. We identified two regions, one at the N‐terminus and a hydrophobic region at the C‐terminus, that jointly contribute to the Al‐response phenotype. Interestingly, the characteristic motif at the N‐terminus appears to be specific for Al‐responsive ALMTs. Our study highlights the need to include a comprehensive phylogenetic analysis when drawing inferences from structure–function analyses, as a significant proportion of the functional changes observed for TaALMT1 are most likely the result of alterations in the overall structural integrity of ALMT family proteins rather than modifications of specific sites involved in Al³⁺ sensing.     

Impacts of inundation and drought on eukaryote biodiversity in semi‐arid floodplain soils

Floodplain ecosystems are characterized by alternating wet and dry phases and periodic inundation defines their ecological character. Climate change, river regulation and the construction of levees have substantially altered natural flooding and drying regimes worldwide with uncertain effects on key biotic groups. In southern Australia, we hypothesized that soil eukaryotic communities in climate change affected areas of a semi‐arid floodplain would transition towards comprising mainly dry‐soil specialist species with increasing drought severity. Here, we used 18S rRNA amplicon pyrosequencing to measure the eukaryote community composition in soils that had been depleted of water to varying degrees to confirm that reproducible transitional changes occur in eukaryotic biodiversity on this floodplain. Interflood community structures (3 years post‐flood) were dominated by persistent rather than either aquatic or dry‐specialist organisms. Only 2% of taxa were unique to dry locations by 8 years post‐flood, and 10% were restricted to wet locations (inundated a year to 2 weeks post‐flood). Almost half (48%) of the total soil biota were detected in both these environments. The discovery of a large suite of organisms able to survive nearly a decade of drought, and up to a year submerged supports the concept of inherent resilience of Australian semi‐arid floodplain soil communities under increasing pressure from climatic induced changes in water availability.     

Social encounter networks: characterizing Great Britain

A major goal of infectious disease epidemiology is to understand and predict the spread of infections within human populations, with the intention of better informing decisions regarding control and intervention. However, the development of fully mechanistic models of transmission requires a quantitative understanding of social interactions and collective properties of social networks. We performed a cross-sectional study of the social contacts on given days for more than 5000 respondents in England, Scotland and Wales, through postal and online survey methods. The survey was designed to elicit detailed and previously unreported measures of the immediate social network of participants relevant to infection spread. Here, we describe individual-level contact patterns, focusing on the range of heterogeneity observed and discuss the correlations between contact patterns and other socio-demographic factors. We find that the distribution of the number of contacts approximates a power-law distribution, but postulate that total contact time (which has a shorter-tailed distribution) is more epidemiologically relevant. We observe that children, public-sector and healthcare workers have the highest number of total contact hours and are therefore most likely to catch and transmit infectious disease. Our study also quantifies the transitive connections made between an individual''s contacts (or clustering); this is a key structural characteristic of social networks with important implications for disease transmission and control efficacy. Respondents'' networks exhibit high levels of clustering, which varies across social settings and increases with duration, frequency of contact and distance from home. Finally, we discuss the implications of these findings for the transmission and control of pathogens spread through close contact.     

Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates

The efficient production of biofuels from cellulosic feedstocks will require the efficient fermentation of the sugars in hydrolyzed plant material. Unfortunately, plant hydrolysates also contain many compounds that inhibit microbial growth and fermentation. We used DNA‐barcoded mutant libraries to identify genes that are important for hydrolysate tolerance in both Zymomonas mobilis (44 genes) and Saccharomyces cerevisiae (99 genes). Overexpression of a Z. mobilis tolerance gene of unknown function (ZMO1875) improved its specific ethanol productivity 2.4‐fold in the presence of miscanthus hydrolysate. However, a mixture of 37 hydrolysate‐derived inhibitors was not sufficient to explain the fitness profile of plant hydrolysate. To deconstruct the fitness profile of hydrolysate, we profiled the 37 inhibitors against a library of Z. mobilis mutants and we modeled fitness in hydrolysate as a mixture of fitness in its components. By examining outliers in this model, we identified methylglyoxal as a previously unknown component of hydrolysate. Our work provides a general strategy to dissect how microbes respond to a complex chemical stress and should enable further engineering of hydrolysate tolerance.     

Activating and Relaxing Music Entrains the Speed of Beat Synchronized Walking

Inspired by a theory of embodied music cognition, we investigate whether music can entrain the speed of beat synchronized walking. If human walking is in synchrony with the beat and all musical stimuli have the same duration and the same tempo, then differences in walking speed can only be the result of music-induced differences in stride length, thus reflecting the vigor or physical strength of the movement. Participants walked in an open field in synchrony with the beat of 52 different musical stimuli all having a tempo of 130 beats per minute and a meter of 4 beats. The walking speed was measured as the walked distance during a time interval of 30 seconds. The results reveal that some music is ‘activating’ in the sense that it increases the speed, and some music is ‘relaxing’ in the sense that it decreases the speed, compared to the spontaneous walked speed in response to metronome stimuli. Participants are consistent in their observation of qualitative differences between the relaxing and activating musical stimuli. Using regression analysis, it was possible to set up a predictive model using only four sonic features that explain 60% of the variance. The sonic features capture variation in loudness and pitch patterns at periods of three, four and six beats, suggesting that expressive patterns in music are responsible for the effect. The mechanism may be attributed to an attentional shift, a subliminal audio-motor entrainment mechanism, or an arousal effect, but further study is needed to figure this out. Overall, the study supports the hypothesis that recurrent patterns of fluctuation affecting the binary meter strength of the music may entrain the vigor of the movement. The study opens up new perspectives for understanding the relationship between entrainment and expressiveness, with the possibility to develop applications that can be used in domains such as sports and physical rehabilitation.     

Distinct molecular features of colorectal cancer in Ghana

Objectives: While colorectal cancer (CRC) is common, its incidence significantly varies around the globe. The incidence of CRC in West Africa is relatively low, but it has a distinctive clinical pattern and its molecular characteristics have not been studied. This study is one of the first attempts to analyze molecular, genetic, and pathological characteristics of colorectal cancer in Ghana. Methods: DNA was extracted from microdissected tumor and adjacent normal tissue of 90 paraffin blocks of CRC cases (1997–2007) collected at the University of Ghana. Microsatellite instability (MSI) was determined using fragment analysis of ten microsatellite markers. We analyzed expression of mismatch repair (MMR) proteins by immunohistochemistry and sequenced exons 2 and 3 of KRAS and exon 15 of BRAF. Results: MSI analysis showed 41% (29/70) MSI-High, 20% (14/70) MSI-Low, and 39% (27/70) microsatellite-stable (MSS) tumors. Sequencing of KRAS exons 2 and 3 identified activating mutations in 32% (24/75) of tumors, and sequencing of BRAF exon 15, the location of the common activating mutation (V600), did not show mutations at codons 599 and 600 in 88 tumors. Conclusions: Our study found a high frequency of MSI-High colorectal tumors (41%) in Ghana. While the frequency of KRAS mutations is comparable with other populations, absence of BRAF mutations is intriguing and would require further analysis of the molecular epidemiology of CRC in West Africa.