Apoptotic cells are cleared by directional migration and elmo1- dependent macrophage engulfment

Apoptotic cell death is essential for development and tissue homeostasis. Failure to clear apoptotic cells can ultimately cause inflammation and autoimmunity. Apoptosis has primarily been studied by staining of fixed tissue sections, and a clear understanding of the behavior of apoptotic cells in living tissue has been elusive. Here, we use a newly developed technique to track apoptotic cells in real time as they emerge and are cleared from the zebrafish brain. We find that apoptotic cells are remarkably motile, frequently migrating several cell diameters to the periphery of living tissues. F-actin remodeling occurs in surrounding cells, but also within the apoptotic cells themselves, suggesting a cell-autonomous component of motility. During the first 2 days of development, engulfment is rare, and most apoptotic cells lyse at the brain periphery. By 3 days postfertilization, most cell corpses are rapidly engulfed by macrophages. This engulfment requires the guanine nucleotide exchange factor elmo1. In elmo1-deficient macrophages, engulfment is rare and may occur through macropinocytosis rather than directed engulfment. These findings suggest that clearance of apoptotic cells in living vertebrates is accomplished by the combined actions of apoptotic cell migration and elmo1-dependent macrophage engulfment.     

A stereo-controlled synthesis of 2,4-dimethyl-4-hydroxy-16-phenylhexadecanoic acid 1,4-lactone and its PPAR activities

A novel class of natural PPAR agonists, 2,4-dimethyl-4-hydroxy-16-phenylhexadecanoic acid 1,4-lactone (1), were discovered in marine natural product libraries. The synthesis of 1 was accomplished starting from vinylmethyl ketone. Ring formation of the α,γ dialkyl γ-lactone was achieved via the stereo-controlled reaction of a ketyl radical anion with a chiral methacrylate. In the PPAR agonistic assay, the most potent of the four stereoisomers had EC₅₀ values of 12 μM for mPPARα, 9 μM for mPPARδ and >100 μM for mPPARγ.     

Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data

Inference of protein functions is one of the most important aims of modernbiology. To fully exploit the large volumes of genomic data typically producedin modern-day genomic experiments, automated computational methods for proteinfunction prediction are urgently needed. Established methods use sequence orstructure similarity to infer functions but those types of data do not sufficeto determine the biological context in which proteins act. Currenthigh-throughput biological experiments produce large amounts of data on theinteractions between proteins. Such data can be used to infer interactionnetworks and to predict the biological process that the protein is involved in.Here, we develop a probabilistic approach for protein function prediction usingnetwork data, such as protein-protein interaction measurements. We take aBayesian approach to an existing Markov Random Field method by performingsimultaneous estimation of the model parameters and prediction of proteinfunctions. We use an adaptive Markov Chain Monte Carlo algorithm that leads tomore accurate parameter estimates and consequently to improved predictionperformance compared to the standard Markov Random Fields method. We tested ourmethod using a high quality S.cereviciae validation networkwith 1622 proteins against 90 Gene Ontology terms of different levels ofabstraction. Compared to three other protein function prediction methods, ourapproach shows very good prediction performance. Our method can be directlyapplied to protein-protein interaction or coexpression networks, but also can beextended to use multiple data sources. We apply our method to physical proteininteraction data from S. cerevisiae and provide novelpredictions, using 340 Gene Ontology terms, for 1170 unannotated proteins and weevaluate the predictions using the available literature.     

Phagocytosis of degenerating myelin in transected feline optic nerve: an immunohistochemical study

The phagocytic activity of neuroglial cells in adult feline degenerating optic nerve was investigated by immunocytochemistry at both light and electron microscopy levels. Degeneration was initiated by unilateral eye enucleation and the segment distal to the transection showing true Wallerian degeneration was examined. Following enucleation, twelve adult domestic cats were examined over a period of seven to 215 days. All cases showed slow clearance of myelin debris and absence of proliferating monocytes throughout the post-enucleation period. All phagocytic cells present were neuroglial cells, and many of these cells expressed oligodendroglial antigens. These findings demonstrate the persistence of an active population of oligodendrocytes that might play an additional functional role during Wallerian degeneration of feline optic nerve.     

Pollen morphology of Trigonostemon and its relatives (Euphorbiaceae)

The pollen of Trigonostemon and the related genera Dimorphocalyx, Ostodes, Tritaxis and Jatropha (outgroup) has been studied with light microscopy, and scanning and transmission electron microscopy. The two major pollen types within Trigonostemon correlate well with macromorphological characters. Species belonging to the Trigonostemon reidioides type have pollen with ‘croton pattern’ ornamentation, a pistil with deeply divided stigmas (to at least half the length of the stigma arm) and stamens with a protruding appendage on the connective, while species of the Trigonostemon verrucosus type have verrucate (to almost gemmate) pollen, stigmas that are shortly cleft and stamens without an appendage on the connective. Dimorphocalyx, Ostodes, Tritaxis and Jatropha (outgroup) have similar pollen morphology, while Trigonostemon deviates from these genera in the absence of the ‘vertically’ striate ornamentation on the subunits. Therefore, when compared with an existing phylogeny of the Euphorbiaceae, the pollen characters of Trigonostemon appear to be derived. Moreover, because the ‘croton pattern’ ornamentation itself is widely shared by the ‘inaperturate crotonoids’, the loss of that structure in the Trigonostemon verrucosus type pollen is considered a further apomorphy.     

Elevated CO22 and Leaf Longevity in the C44 Grassland-Dominant Andropogon gerardii

In central U.S. grasslands, plant and ecosystem responses to elevated CO2 are most pronounced when water availability is limited. In a northeast Kansas grassland, responses to elevated CO2 in leaf area, number, development, and longevity were quantified for the tallgrass prairie dominant, Andropogon gerardii. Plants were grown in open-top chambers (OTCs) modified to limit water availability and to maximize responses to elevated CO2. In OTCs with elevated (x2 ambient) levels of CO2, aboveground biomass production and leaf water potentials were increased significantly compared with those of plants in OTCs with ambient CO2. There were no differences in leaf area or leaf number per tiller in A. gerardii in elevated compared with ambient OTCs. However, leaf area in adjacent unchambered plots with greater water availability was significantly higher than in the OTCs. The time required for developing leaves to achieve maximum leaf area was reduced by 29%, and the period of time until leaves senesced was increased by 20% for plants exposed to elevated compared with ambient CO2. Thus, leaves of this C4 grass species expanded more rapidly (6 d) and remained green longer (9 d) when exposed to elevated CO2. Such CO2-mediated increases in leaf longevity in the dominant species may allow this grassland to respond more opportunistically to temporally variable rainfall patterns in high-CO2 environments. These responses should be included in leaf-based simulation models that attempt to mechanistically link physiological alterations to predicted canopy responses to increased CO2.     

Novel polymorphisms in <Emphasis Type="Italic">HLA-DOA</Emphasis> and <Emphasis Type="Italic">HLA-DOB</Emphasis> in B-cell malignancies

In B cells, HLA-DO controls HLA-DM-mediated peptide loading on MHC class II molecules. We analyzed whether HLA-DO mutations are associated with autoimmune diseases characterized by an autoantibody component and with a linkage to HLA-DR or HLA-DQ. These diseases include systemic lupus erythematosus, rheumatoid arthritis, celiac disease, and Graves' disease. In addition, several B-cell leukemias were screened for mutations in HLA-DO. A limited number of polymorphisms in DOA and DOB were found, most of which are non-coding changes or result in a conserved amino acid change. A novel non-conserved Arg to Cys mutation in DOA was found in a patient suffering from chronic lymphocytic leukemia. Further analysis did not reveal any effect on the function of HLA-DO. We conclude that HLA-DO variants are not critically involved in the autoimmune diseases and B-cell leukemias studied here.     

C. elegans Model Identifies Genetic Modifiers of α-Synuclein Inclusion Formation During Aging

Inclusions in the brain containing α-synuclein are the pathological hallmark of Parkinson's disease, but how these inclusions are formed and how this links to disease is poorly understood. We have developed a C. elegans model that makes it possible to monitor, in living animals, the formation of α-synuclein inclusions. In worms of old age, inclusions contain aggregated α- synuclein, resembling a critical pathological feature. We used genome-wide RNA interference to identify processes involved in inclusion formation, and identified 80 genes that, when knocked down, resulted in a premature increase in the number of inclusions. Quality control and vesicle-trafficking genes expressed in the ER/Golgi complex and vesicular compartments were overrepresented, indicating a specific role for these processes in α-synuclein inclusion formation. Suppressors include aging-associated genes, such as sir-2.1/SIRT1 and lagr-1/LASS2. Altogether, our data suggest a link between α-synuclein inclusion formation and cellular aging, likely through an endomembrane-related mechanism. The processes and genes identified here present a framework for further study of the disease mechanism and provide candidate susceptibility genes and drug targets for Parkinson's disease and other α-synuclein related disorders.