Proteasome inhibition with bortezomib depletes plasma cells and autoantibodies in experimental autoimmune myasthenia gravis

Bortezomib, an inhibitor of proteasomes, has been reported to reduce autoantibody titers and to improve clinical condition in mice suffering from lupus-like disease. Bortezomib depletes both short- and long-lived plasma cells; the latter normally survive the standard immunosuppressant treatments targeting T and B cells. These findings encouraged us to test whether bortezomib is effective for alleviating the symptoms in the experimental autoimmune myasthenia gravis (EAMG) model for myasthenia gravis, a disease that is characterized by autoantibodies against the acetylcholine receptor (AChR) of skeletal muscle. Lewis rats were immunized with saline (control, n = 36) or Torpedo AChR (EAMG, n = 54) in CFA in the first week of an experimental period of 8 wk. After immunization, rats received twice a week s.c. injections of bortezomib (0.2 mg/kg in saline) or saline injections. Bortezomib induced apoptosis in bone marrow cells and reduced the amount of plasma cells in the bone marrow by up to 81%. In the EAMG animals, bortezomib efficiently reduced the rise of anti-AChR autoantibody titers, prevented ultrastructural damage of the postsynaptic membrane, improved neuromuscular transmission, and decreased myasthenic symptoms. This study thus underscores the potential of the therapeutic use of proteasome inhibitors to target plasma cells in Ab-mediated autoimmune diseases.     

Machine learning on normalized protein sequences

Background

Directed protein evolution has been used to modify protein activity and research has been carried out to enhance the production of high quality mutant libraries. Many theoretical approaches suggest that allowing a population to undergo neutral selection may be valuable in directed evolution experiments.

Findings

Here we report on an investigation into the value of neutral selection in a classical model system for directed evolution, the conversion of the E. coli β-glucuronidase to a β-galactosidase activity. We find that neutral selection, i.e. selection for retaining glucuronidase activity, can efficiently identify the majority of sites of mutation that have been identified as beneficial for galactosidase activity in previous experiments. Each variant demonstrating increased galactosidase activity identified by our neutral drift experiments contained a mutation at one of four sites, T509, S557, N566 or W529. All of these sites have previously been identified using direct selection for beta galactosidase activity.

Conclusions

Our results are consistent with others that show that a neutral selection approach can be effective in selecting improved variants. However, we interpret our results to show that neutral selection is, in this case, not a more efficient approach than conventional directed evolution approaches. However, the neutral approach is likely to be beneficial when the resulting library can be screened for a range of related activities. More detailed statistical studies to resolve the apparent differences between this system and others are likely to be a fruitful avenue for future research.     

Comparative cytogenetic mapping between the lima bean (Phaseolus lunatus L.) and the common bean (P. vulgaris L.)

The common bean (Phaseolus vulgaris) and lima bean (P. lunatus) are among the most important legumes in terms of direct human consumption. The present work establishes a comparative cytogenetic map of P. lunatus, using previously mapped markers from P. vulgaris, in association with analyses of heterochromatin distribution using the fluorochromes chromomycin A3 (CMA) and 4′,6-diamidino-2-phenylindole (DAPI) and localization of the 5S and 45S ribosomal DNA (rDNA) probes. Seven BACs selected from different common bean chromosomes demonstrated a repetitive pericentromeric pattern corresponding to the heterochromatic regions revealed by CMA/DAPI and could not be mapped. The subtelomeric repetitive pattern observed for BAC 63H6 in most of the chromosome ends of common bean was not detected in lima bean, indicating lack of conservation of this subtelomeric repeat. All chromosomes could be identified and 16 single-copy clones were mapped. These results showed a significant conservation of synteny between species, although change in centromere position suggested the occurrence of pericentric inversions on chromosomes 2, 9 and 10. The low number of structural rearrangements reflects the karyotypic stability of the genus.     

Distinguishing between turnover and nestedness in the quantification of biotic homogenization

Compositional changes through local extinction and colonization are inherent to natural communities, but human activities are increasingly influencing the rate and nature of the species being lost and gained. Biotic homogenization refers to the process by which the compositional similarity of communities increases over time through a non-random reshuffling of species. Despite the extensive conceptual development of the homogenization framework, approaches to quantify patterns of homogenization are scarcely developed. Most studies have used classical dissimilarity indices that actually quantify two components of compositional variation: turnover and nestedness. Here we demonstrate that a method that partitions those two components reveals patterns of homogenization that are otherwise obscured using traditional techniques. The forest understorey vegetation of an unmanaged reserve was recorded in permanent plots in 1979 and 2009. In only thirty years, the local species richness significantly decreased and the variation in the species composition from site to site shifted towards a structure with reduced true species turnover and increased dissimilarity due to nestedness. A classic analysis masked those patterns. In summary, we illustrated the need to move beyond the simple quantification of homogenization using classical indices and advocate integration of the multitude of ways to quantify community similarity into the homogenization framework.     

Homeodomain-interacting protein kinase regulates yorkie activity to promote tissue growth

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Highlights? Hipk induces tissues overgrowth and leads to activation of Yki target genes ? Hipk is required for activity of hyperactive Yki ? Hipk kinase function is essential to promote Yki target genes     

Rapid chromosomal evolution in the mesic four‐striped grass rat Rhabdomys dilectus (Rodentia,Muridae) revealed by mtDNA phylogeographic analysis

The mesic four‐striped grass rat Rhabdomys dilectus De Winton, 1897 is distributed in mesic regions of southern and eastern Africa. We carried out a molecular and chromosomal study of the northernmost populations of the species to provide insight into the subspecific boundaries identified within the species and to describe its genetic structure in Eastern Africa. Maximum likelihood, maximum parsimony and neighbour‐joining methods were used to construct phylogenetic relationships among all the haplotypes belonging to the large part of the species range. Times of divergences were estimated assuming a relaxed molecular clock with two calibration points. We identified three well‐supported clades within R. dilectus. One basal clade corresponding to Rhabdomys d. chakae (2n = 48) is found in South Africa. Two additional sister clades corresponding to R. d. dilectus (2n = 48 and 2n = 46) are allopatrically distributed in southern and northern parts of the species range. Genetic divergence among the three clades is relatively high (ranges 4.2–5.7%). A very divergent new karyotype 2n = 38, FNa = 60 was found in two high‐altitude populations on Mt. Meru and Mt. Kilimanjaro. The karyotype differences consist in three Robertsonian fusions and one whole‐arm reciprocal translocation. Interestingly, the mtDNA phylogeny does not match with the diploid numbers. In fact, the 2n = 38 specimens form a monophyletic group within a clade that includes specimens with the 2n = 46 karyotype that appears as paraphyletic. We estimated the new karyotype originated in peripatric condition during the last phases of the Pleistocene. This study confirms the importance of chromosomal analysis in detecting taxonomic units and cryptic diversity in rodents.     

On the use of weather data in ecological studies along altitudinal and latitudinal gradients

Global warming has created a need for studies along climatic gradients to assess the effects of temperature on ecological processes. Altitudinal and latitudinal gradients are often used as such, usually in combination with air temperature data from the closest weather station recorded at 1.5–2 m above the ground. However, many ecological processes occur in, at, or right above the soil surface. To evaluate how representative the commonly used weather station data are for the microclimate relevant for soil surface biota, we compared weather station temperatures for an altitudinal (500–900 m a.s.l.) and a latitudinal gradient (49–68°N) with data obtained by temperature sensors placed right below the soil surface at five sites along these gradients. The mean annual temperatures obtained from weather stations and adjusted using a lapse rate of ?5.5°C km^?1 were between 3.8°C lower and 1.6°C higher than those recorded by the temperature sensors at the soil surface, depending on the position along the gradients. The monthly mean temperatures were up to 10°C warmer or 5°C colder at the soil surface. The within‐site variation in accumulated temperature was as high as would be expected from a 300 m change in altitude or from a 4° change in latitude or a climate change scenario corresponding to warming of 1.6–3.8°C. Thus, these differences introduced by the decoupling are significant from a climate change perspective, and the results demonstrate the need for incorporating microclimatic variation when conducting studies along altitudinal or latitudinal gradients. We emphasize the need for using relevant temperature data in climate impact studies and further call for more studies describing the soil surface microclimate, which is crucial for much of the biota.     

Tree species traits cause divergence in soil acidification during four decades of postagricultural forest development

A change in land use from agriculture to forest generally increases soil acidity. However, it remains unclear to what extent plant traits can enhance or mitigate soil acidification caused by atmospheric deposition. Soil acidification is detrimental for the survival of many species. An in‐depth understanding of tree species‐specific effects on soil acidification is therefore crucial, particularly in view of the predicted global increases in acidifying nitrogen (N) deposition. Here, we report soil acidification rates in a chronosequence of broadleaved deciduous forests planted on former arable land in Belgium. This region receives one of the highest loads of potentially acidifying atmospheric deposition in Europe, which allowed us to study a ‘worst case scenario’. We show that less than four decades of forest development caused significant soil acidification. Atmospheric deposition undoubtedly and unequivocally drives postagricultural forests towards more acidic conditions, but the rate of soil acidification is also determined by the tree species‐specific leaf litter quality and litter decomposition rates. We propose that the intrinsic differences in leaf litter quality among tree species create fundamentally different nutrient cycles within the ecosystem, both directly through the chemical composition of the litter and indirectly through its effects on the size and composition of earthworm communities. Poor leaf litter quality contributes to the absence of a burrowing earthworm community, which retards leaf litter decomposition and, consequently, results in forest‐floor build‐up and soil acidification. Also nutrient uptake and N₂ fixation are causing soil acidification, but were found to be less important. Our results highlight the fact that tree species‐specific traits significantly influence the magnitude of human pollution‐induced soil acidification.     

Increased temperatures negatively affect Juniperus communis seeds: evidence from transplant experiments along a latitudinal gradient

With a distribution range that covers most of the Northern hemisphere, common juniper (Juniperus communis) has one of the largest ranges of all vascular plant species. In several regions in Europe, however, populations are decreasing in size and number due to failing recruitment. One of the main causes for this failure is low seed viability. Observational evidence suggests that this is partly induced by climate warming, but our mechanistic understanding of this effect remains incomplete. Here, we experimentally assess the influence of temperature on two key developmental phases during sexual reproduction, i.e. gametogenesis and fertilisation (seed phase two, SP2) and embryo development (seed phase three, SP3). Along a latitudinal gradient from southern France to central Sweden, we installed a transplant experiment with shrubs originating from Belgium, a region with unusually low juniper seed viability. Seeds of both seed phases were sampled during three consecutive years, and seed viability assessed. Warming temperatures negatively affected the seed viability of both SP2 and SP3 seeds along the latitudinal gradient. Interestingly, the effect on embryo development (SP3) only occurred in the third year, i.e. when the gametogenesis and fertilisation also took place in warmer conditions. We found strong indications that this negative influence mostly acts via disrupting growth of the pollen tube, the development of the female gametophyte and fertilisation (SP2). This, in turn, can lead to failing embryo development, for example, due to nutritional problems. Our results confirm that climate warming can negatively affect seed viability of juniper.