Bile: miRNA pattern and protein-based biomarkers may predict acute cellular rejection after liver transplantation

Context: Bile rather than blood depicts the local inflammation in the liver and may improve prediction and diagnosis of acute cellular rejection (ACR) after liver transplantation (OLT).

Methods: Secretome and miRNAs were analyzed during the first two weeks and on clinical suspicion of ACR in the bile of 45 OLT recipients.

Results: Levels of CD44, CXCL9, miR-122, miR-133a, miR-148a and miR-194 were significantly higher in bile of patients who developed ACR within the first 6 months after OLT and during ACR.

Conclusion: Analysis of secretome and miRNA in bile could improve our understanding of the local inflammatory process during rejection.     

Choline transporter‐like1 (CHER1) is crucial for plasmodesmata maturation in Arabidopsis thaliana

Plasmodesmata (PD) are microscopic pores connecting plant cells and enable cell‐to‐cell transport. Currently, little information is known about the molecular mechanisms regulating PD formation and development. To uncover components of PD development we made use of the 17 kDa movement protein (MP17) encoded by the Potato leafroll virus (PLRV). The protein is required for cell‐to‐cell movement of the virus and localises to complex PD. Forward genetic screening for Arabidopsis mutants with altered PD binding of MP17 revealed several mutant lines, while molecular genetics, biochemical and microscopic studies allowed further characterisation. Map‐based cloning of one mutant revealed a point mutation in the choline transporter‐like 1 (CHER1) protein, changing glycine²⁴⁷ into glutamate. Mutation in CHER1 resulted in a starch excess phenotype and stunted growth. Ultrastructure analysis of shoot apical meristems, developing and fully developed leaves showed reduced PD numbers and the absence of complex PD in fully developed leaves. This indicates that cher1 mutants are impaired in PD formation and development. Global lipid profiling revealed only slight modifications in the overall lipid composition, however, altered composition of PD‐associated lipids cannot be ruled out. Thus, cher1 is devoid of complex PD in developed leaves and provides insights into the formation of complex PD at the molecular level.     

Gerbil: a fast and memory-efficient <Emphasis Type="Italic">k</Emphasis>-mer counter with GPU-support

Background

A basic task in bioinformatics is the counting of k-mers in genome sequences. Existing k-mer counting tools are most often optimized for small k < 32 and suffer from excessive memory resource consumption or degrading performance for large k. However, given the technology trend towards long reads of next-generation sequencers, support for large k becomes increasingly important.

Results

We present the open source k-mer counting software Gerbil that has been designed for the efficient counting of k-mers for k ≥ 32. Our software is the result of an intensive process of algorithm engineering. It implements a two-step approach. In the first step, genome reads are loaded from disk and redistributed to temporary files. In a second step, the k-mers of each temporary file are counted via a hash table approach. In addition to its basic functionality, Gerbil can optionally use GPUs to accelerate the counting step. In a set of experiments with real-world genome data sets, we show that Gerbil is able to efficiently support both small and large k.

Conclusions

While Gerbil’s performance is comparable to existing state-of-the-art open source k-mer counting tools for small k < 32, it vastly outperforms its competitors for large k, thereby enabling new applications which require large values of k.

     

Modulation of substrate adhesion dynamics via microtubule targeting requires kinesin-1.

Recent studies have shown that the targeting of substrate adhesions by microtubules promotes adhesion site disassembly (Kaverina, I., O. Krylyshkina, and J.V. Small. 1999. J. Cell Biol. 146:1033-1043). It was accordingly suggested that microtubules serve to convey a signal to adhesion sites to modulate their turnover. Because microtubule motors would be the most likely candidates for effecting signal transmission, we have investigated the consequence of blocking microtubule motor activity on adhesion site dynamics. Using a function-blocking antibody as well as dynamitin overexpression, we found that a block in dynein-cargo interaction induced no change in adhesion site dynamics in Xenopus fibroblasts. In comparison, a block of kinesin-1 activity, either via microinjection of the SUK-4 antibody or of a kinesin-1 heavy chain construct mutated in the motor domain, induced a dramatic increase in the size and reduction in number of substrate adhesions, mimicking the effect observed after microtubule disruption by nocodazole. Blockage of kinesin activity had no influence on either the ability of microtubules to target substrate adhesions or on microtubule polymerisation dynamics. We conclude that conventional kinesin is not required for the guidance of microtubules into substrate adhesions, but is required for the focal delivery of a component(s) that retards their growth or promotes their disassembly.     

Mid to Late Holocene palaeoenvironment of Lake Eastern Juyanze (north-western China) based on ostracods and stable isotopes

An exposed section of nearly 13 m thick was investigated in the ancient depression of Lake Eastern Juyanze, north-eastern China. The succession of lacustrine and aeolian deposits covers a period from about 5400 to 2700 cal. a BP as indicated by four radiocarbon ages of macro-plant debris. Fifteen ostracod taxa were identified of which Limnocythere inopinata and Darwinula stevensoni are by far the most abundant species. Stable isotope (O, C) data of ostracod calcite as well as ostracod species abundances and X-ray diffraction results of bulk sediment samples were used to reconstruct the history of Lake Eastern Juyanze. Highest lake levels (water depth ∼10 m) occurred between 5100 and 4100 cal. a BP and were succeeded by intermediate and low levels until about 3150 cal. a BP. Three short-term events of complete desiccation were recorded between 3150 and 2900 cal. a BP. The lake experienced relatively high levels again for some decades at about 3000 cal. a BP and for at least two centuries after 2900 cal. a BP. According to the ostracod and gastropod record and the high abundance of a large diatom (Campylodiscus clypeus) in the lake sediments oligohaline to slightly mesohaline conditions were reconstructed for most of the lake periods (4-6 g/l). Geochemical and palaeontological records of Lake Eastern Juyanze reveal the retreat of the Asian monsoon after China’s Hypsithermal culminating in climate instability at about 3000 cal. a BP.     

About some aporrhaid and strombid gastropods from the Late Cretaceous

Sixteen species of the Stromboidea (Gastropoda) from the Late Cretaceous are described in this study. One species belongs to the Strombidae, the others to eight genera and subgenera of the Aporrhaidae. Eight species are new. They have been found in the Cenomanian of Kassenberg in western Germany, the Coniacian of the Mungo River in Cameroon, the Santonian of the Eastern Cape Province of South Africa, the Santonian/Campanian of the Ariyalur area in southern India, the Campanian of northern Spain, and the Maastrichtian of the Western Desert in Egypt. Two species ofDrepanocheilus from South Africa are considered stem-group representatives of the aporrhaids which inhabited the Weddellian Province in the early Tertiary. One new species of the strombid genusHippocrenes is regarded as an early species of the evolutionary lineage leading to the Seraphsidae. The new species areLatiala? ponsi, Drepanocheilus herberti, Drepanocheilus triliratus, Drepanocheilus (Tulochilus) jouberti, Graciliala quaasi, Kaunhowenia catalanica, Kaunhowenia punctata andHippocrenes kussi.     

Structure and floristic composition of community forests and their compatibility with villagers' traditional needs for forest products

A persisting problem in protected area management in Nepal is whether resources from buffer zones can replace villagers' extraction of resources from protected areas. Community forestry is assigned a major role in supplying these substitutes, and natural regeneration and rehabilitation of degraded forests are thought to be means to establish forests with a high compatibility with villagers' demand. This study investigates the structure and floristic composition of six community forests established through natural regeneration of degraded sal (Shorea robusta) forests and of former riverine forest areas which have been cleared and overgrazed. The inventories are compared to an in-depth survey of the extraction of forest products from Royal Chitwan National Park (RCNP) for 12 consecutive months by nine households. The results show that natural regeneration creates a multi-layered forest structure and that early succession stages of mixed forests, which floristically resemble former primary forests, emerged in only a few years when protected from grazing. The presence of timber and fuelwood species in the community forest matched to some extent the species traditionally extracted by people from the Park. With regard to non-timber forest products (NTFP), the natural regenerated community forests were much less compatible with the villagers' traditional dependency on and extraction from the Park, which points to the limitations of community forestry in relieving anthropogenic pressure on the RCNP.     

A land cover map of South America

A digital land cover map of South America has been produced using remotely sensed satellite data acquired between 1995 and the year 2000. The mapping scale is defined by the 1 km spatial resolution of the map grid‐cell. In order to realize the product, different sources of satellite data were used, each source providing either a particular parameter of land cover characteristic required by the legend, or mapping a particular land cover class. The map legend is designed both to fit requirements for regional climate modelling and for studies on land cover change. The legend is also compatible with a wider, global, land cover mapping exercise, which seeks to characterize the world's land surface for the year 2000. As a first step, the humid forest domain has been validated using a sample of high‐resolution satellite images. The map demonstrates both the major incursions of agriculture into the remaining forest domains and the extensive areas of agriculture, which now dominate South America's grasslands.     

Structure of the Bacillus subtilis Peptide Antibiotic Subtilosin A Determined by 1H-NMR and Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Subtilosin A produced by Bacillus subtilis is a macrocyclic peptide antibiotic which comprises 35 amino acids. Its molecular mass (3399.7 Da), determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and chemical properties gave experimental support for unusual intramolecular linkages. The three-dimensional fold of native subtilosin in dimethylsulfoxide was determined from two-dimensional ¹H-NMR spectra recorded at 600 MHz. Based on the backbone conformation, a structure for subtilosin A is presented which is characterized by three inter-residue bridges where two cysteines are linked with two phenylalanine residues, respectively, and a third cysteine is bound to a threonine residue.