LIMK1 and CLIP-115: linking cytoskeletal defects to Williams syndrome

Williams Syndrome is a developmental disorder that is characterized by cardiovascular problems, particular facial features and several typical behavioral and neurological abnormalities. In Williams Syndrome patients, a heterozygous deletion is present of a region on chromosome 7q11.23 (the Williams Syndrome critical region), which spans approximately 20 genes. Two of these genes encode proteins that regulate dynamic aspects of the cytoskeleton of the cell, either via the actin filament system (LIM kinase 1, or LIMK1), or through the microtubule network (cytoplasmic linker protein of 115 kDa, or CLIP-115). The recent findings that knockout mice lacking LIMK1 or CLIP-115 have distinct neurological and behavioural phenotypes, indicates that cytoskeletal defects might play a role in the development of neurological symptoms in Williams Syndrome patients. In this review, we discuss the properties of LIMK and CLIP family proteins, their function in the regulation of the actin and microtubule cytoskeletal systems, respectively, and the relationship with neurodevelopmental aspects of Williams Syndrome.     

Different methods for extracting bacteria from freshwater sediment and a simple method to measure bacterial production in sediment samples

The efficiency of different treatments was tested to extract bacterial cells from freshwater sediment samples. The influence of sonication, density gradient centrifugation, fixation by formalin and centrifugation speed on bacterial recovery was investigated. The method developed by Smith and Azam [Mar. Microb. Food Webs 6 (1992) 107] to measure microbial activity on bacterioplankton (3H-leucine incorporation), was also evaluated in sediment samples. After 1 min of sonication bacterial abundance was reduced by about 47% in diluted sediments with tetrasodium pyrophosphate. With the addition of Percoll after sonication, bacterial counts were not significantly different (P<0.05). Fixation by formalin increased bacterial counts using sonication. However, higher bacterial abundance was estimated in non-sonicated samples. Bacterial abundance in samples centrifuged at 7000xg with and without Percoll was not significantly different (P<0.05). Highest bacterial abundance was obtained after centrifugation at low speed (750xg). Bacterial abundance decreased with higher centrifugation speed (750, 1500 and 3000xg), the difference, however, was not significant. Bacterial production ranged from 0.10 microg C cm(-3) d(-1) in autoclaved sediment to 0. 27 microg C cm(-3) d(-1) in untreated sediment. The radioactivity measured in controls of both untreated and autoclaved sediment was high (70 and 91%, respectively), indicating a high level of leucine adsorption in sediment particles. In contrast, radioactivity in control samples previously centrifuged was markedly lower (6%). Despite the high values of radioactivity in the controls, bacterial production in untreated sediment was significantly higher than in centrifuged sediment (P<0.05).     

Plant and nutrient controls on microbial functional characteristics in a tropical Oxisol

Aims

Extracellular enzymes mediate the decomposition of organic matter and the release of plant-available nutrients. Current theory predicts that enzyme production by soil microbes is regulated by the stoichiometric demands of microbial biomass and the complexity of environmental resources, but most experiments ignore the potential effect of alleviated carbon limitation in the rhizosphere. Our objective was to investigate linkages between enzyme activities, soil nutrient availability and plant roots in a tropical Oxisol.

Methods

We conducted a greenhouse experiment using soils from the Luquillo Experimental Forest and seedlings of Tabebuia heterophylla. Planted and unplanted pots were fertilized with different combinations of phosphorus and either mineral nitrogen (ammonia chloride) or a nitrogen-rich organic compound (casein). We measured changes in plant and soil nutrients and five extracellular enzyme activities.

Results

Phosphatase activity declined by 28% in the P and 40% in the complex nitrogen treatment, while N-acetyl glucosaminidase increased 162% in the complex nitrogen treatment. Beta-glucosidase, beta-xylosidase, cellobiohydrolase and N-acetyl glucosaminidase all increased significantly over time in the simple nitrogen treatment (P?<?0.05).

Conclusions

Enzymatic responses support microbial resource allocation theory, that is, the concept that soil microbes regulate enzyme production based on scarcity of resources. However, we did not observe any additional effect of roots on extracellular enzyme activities. Enzymatic C:N, C:P and N:P ratios further support the notion that shifts in microbial stoichiometric demand drive responses to nutrients.     

Effects of open-top passive warming chambers on soil respiration in the semi-arid steppe to taiga forest transition zone in Northern Mongolia

The response of soil respiration to warming has been poorly studied in regions at higher latitude with low precipitation. We manipulated air temperature, soil temperature and soil moisture using passive, open-top chambers (OTCs) in three different ecosystem settings in close proximity (boreal forest, riparian area, and semi-arid steppe) to investigate how environmental factors would affect soil respiration in these different ecosystems, anticipating that soil respiration would increase in response to the chamber treatment. The results indicated that OTCs significantly increased air and soil temperature in areas with open canopy and short-statured vegetation (i.e., steppe areas) but not in forest. OTCs also affected soil moisture, but the direction of change depended on the ecosystem, and the magnitude of change was highly variable. Generally, OTCs did not affect soil respiration in steppe and riparian areas. Although soil respiration was slightly greater in OTCs placed in the forest, the difference was not statistically significant. Analyses of relationships between soil respiration and environmental variables suggested that different factors controlled soil respiration in the different ecosystems. Competing effects analysis using a model selection approach and regression analyses (e.g., Q₁₀) demonstrated that soil respiration in the forest was more sensitive to warming, while soil respiration in the steppe was more sensitive to soil moisture. The differing responses and controlling factors among these neighboring forest, riparian and steppe ecosystems in Northern Mongolia highlight the importance of taking into account potential biome shifts in C cycling modeling to generate more accurate predictions of landscape-scale responses to anticipated climate change.     

Assessing the Effect of Litter Species on the Dynamic of Bacterial and Fungal Communities during Leaf Decomposition in Microcosm by Molecular Techniques

Although bacteria and fungi are well-known to be decomposers of leaf litter, few studies have examined their compositions and diversities during the decomposition process in tropical stream water. Xishuangbanna is a tropical region preserving one of the highest floristic diversity areas in China. In this study, leaf litter of four dominant plant species in Xishuangbanna was incubated in stream water for 42 days during which samples were taken regularly. Following DNA extraction, PCR-DGGE (denaturing gradient gel electrophoresis) and clone-sequencing analyses were performed using bacterial and fungal specific primers. Leaf species have slightly influences on bacterial community rather than fungal community. The richness and diversity of bacteria was higher than that of fungi, which increased towards the end of the 42-day-incubation. The bacterial community was initially more specific upon the type of leaves and gradually became similar at the later stage of decomposition with alpha-proteobacteria as major component. Sequences affiliated to methanotrophs were obtained that indicates potentially occurrence of methane oxidation and methanogenesis. For the fungal community, sequences affiliated to Aspergillus were predominant at the beginning and then shifted to Pleosporales. Our results suggest that the microorganisms colonizing leaf biofilm in tropical stream water were mostly generalists that could exploit the resources of leaves of various species equally well.     

Cell-permeating alpha-ketoglutarate derivatives alleviate pseudohypoxia in succinate dehydrogenase-deficient cells

Succinate dehydrogenase (SDH) and fumarate hydratase (FH) are components of the tricarboxylic acid (TCA) cycle and tumor suppressors. Loss of SDH or FH induces pseudohypoxia, a major tumor-supporting event, which is the activation of hypoxia-inducible factor (HIF) under normoxia. In SDH- or FH-deficient cells, HIF activation is due to HIF1alpha stabilization by succinate or fumarate, respectively, either of which, when in excess, inhibits HIFalpha prolyl hydroxylase (PHD). To reactivate PHD, we focused on its substrate, alpha-ketoglutarate. We designed and synthesized cell-permeating alpha-ketoglutarate derivatives, which build up rapidly and preferentially in cells with a dysfunctional TCA cycle. This study shows that succinate- or fumarate-mediated inhibition of PHD is competitive and is reversed by pharmacologically elevating intracellular alpha-ketoglutarate. Introduction of alpha-ketoglutarate derivatives restores normal PHD activity and HIF1alpha levels to SDH-suppressed cells, indicating new therapy possibilities for the cancers associated with TCA cycle dysfunction.     

Apoplastic Venom Allergen-like Proteins of Cyst Nematodes Modulate the Activation of Basal Plant Innate Immunity by Cell Surface Receptors

Despite causing considerable damage to host tissue during the onset of parasitism, nematodes establish remarkably persistent infections in both animals and plants. It is thought that an elaborate repertoire of effector proteins in nematode secretions suppresses damage-triggered immune responses of the host. However, the nature and mode of action of most immunomodulatory compounds in nematode secretions are not well understood. Here, we show that venom allergen-like proteins of plant-parasitic nematodes selectively suppress host immunity mediated by surface-localized immune receptors. Venom allergen-like proteins are uniquely conserved in secretions of all animal- and plant-parasitic nematodes studied to date, but their role during the onset of parasitism has thus far remained elusive. Knocking-down the expression of the venom allergen-like protein Gr-VAP1 severely hampered the infectivity of the potato cyst nematode Globodera rostochiensis. By contrast, heterologous expression of Gr-VAP1 and two other venom allergen-like proteins from the beet cyst nematode Heterodera schachtii in plants resulted in the loss of basal immunity to multiple unrelated pathogens. The modulation of basal immunity by ectopic venom allergen-like proteins in Arabidopsis thaliana involved extracellular protease-based host defenses and non-photochemical quenching in chloroplasts. Non-photochemical quenching regulates the initiation of the defense-related programmed cell death, the onset of which was commonly suppressed by venom allergen-like proteins from G. rostochiensis, H. schachtii, and the root-knot nematode Meloidogyne incognita. Surprisingly, these venom allergen-like proteins only affected the programmed cell death mediated by surface-localized immune receptors. Furthermore, the delivery of venom allergen-like proteins into host tissue coincides with the enzymatic breakdown of plant cell walls by migratory nematodes. We, therefore, conclude that parasitic nematodes most likely utilize venom allergen-like proteins to suppress the activation of defenses by immunogenic breakdown products in damaged host tissue.     

The FTLD risk factor TMEM106B and MAP6 control dendritic trafficking of lysosomes

TMEM106B is a major risk factor for frontotemporal lobar degeneration with TDP‐43 pathology. TMEM106B localizes to lysosomes, but its function remains unclear. We show that TMEM106B knockdown in primary neurons affects lysosomal trafficking and blunts dendritic arborization. We identify microtubule‐associated protein 6 (MAP6) as novel interacting protein for TMEM106B. MAP6 over‐expression inhibits dendritic branching similar to TMEM106B knockdown. MAP6 knockdown fully rescues the dendritic phenotype of TMEM106B knockdown, supporting a functional interaction between TMEM106B and MAP6. Live imaging reveals that TMEM106B knockdown and MAP6 overexpression strongly increase retrograde transport of lysosomes in dendrites. Downregulation of MAP6 in TMEM106B knockdown neurons restores the balance of anterograde and retrograde lysosomal transport and thereby prevents loss of dendrites. To strengthen the link, we enhanced anterograde lysosomal transport by expressing dominant‐negative Rab7‐interacting lysosomal protein (RILP), which also rescues the dendrite loss in TMEM106B knockdown neurons. Thus, TMEM106B/MAP6 interaction is crucial for controlling dendritic trafficking of lysosomes, presumably by acting as a molecular brake for retrograde transport. Lysosomal misrouting may promote neurodegeneration in patients with TMEM106B risk variants.     

Climate change and grazing interact to alter flowering patterns in the Mongolian steppe

Socio-economic changes threaten nomadic pastoralism across the world, changing traditional grazing patterns. Such land-use changes will co-occur with climate change, and while both are potentially important determinants of future ecosystem functioning, interactions between them remain poorly understood. We investigated the effects of grazing by large herbivores and climate manipulation using open-top chambers (OTCs) on flower number and flowering species richness in mountain steppe of northern Mongolia. In this region, sedentary pastoralism is replacing nomadic pastoralism, and temperature is predicted to increase. Grazing and OTCs interacted to affect forb flowering richness, which was reduced following grazing removal, and reduced by OTCs in grazed plots only. This interaction was directly linked to the soil moisture and temperature environments created by the experimental treatments: most species flowered when both soil moisture and temperature levels were high (i.e. in grazed plots without OTCs), while fewer species flowered when either temperature, or moisture, or both, were low. Removal of grazing increased the average number of graminoid flowers produced at peak flowering in Year 1, but otherwise grazing removal and OTCs did not affect community-level flower composition. Of four abundant graminoid species examined individually, three showed increased flower number with grazing removal, while one showed the reverse. Four abundant forb species showed no significant response to either treatment. Our results highlight how climate change effects on mountain steppe could be contingent on land-use, and that studies designed to understand ecosystem response to climate change should incorporate co-occurring drivers of change, such as altered grazing regimes.