Next generation semiconductor based sequencing of the donkey (Equus asinus) genome provided comparative sequence data against the horse genome and a few millions of single nucleotide polymorphisms

Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be similar to 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources

CXCL12 Mediates CCR7-independent Homing of Central Memory Cells, But Not Naive T Cells, in Peripheral Lymph Nodes

Central memory CD8+ T cells (TCM) confer superior protective immunity against infections compared with other T cell subsets. TCM recirculate mainly through secondary lymphoid organs, including peripheral lymph nodes (PLNs). Here, we report that TCM, unlike naive T cells, can home to PLNs in both a CCR7-dependent and -independent manner. Homing experiments in paucity of lymph node T cells (plt/plt) mice, which do not express CCR7 ligands in secondary lymphoid organs, revealed that TCM migrate to PLNs at ∼20% of wild-type (WT) levels, whereas homing of naive T cells was reduced by 95%. Accordingly, a large fraction of endogenous CD8+ T cells in plt/plt PLNs displayed a TCM phenotype. Intravital microscopy of plt/plt subiliac lymph nodes showed that TCM rolled and firmly adhered (sticking) in high endothelial venules (HEVs), whereas naive T cells were incapable of sticking. Sticking of TCM in plt/plt HEVs was pertussis toxin sensitive and was blocked by anti-CXCL12 (SDF-1α). Anti-CXCL12 also reduced homing of TCM to PLNs in WT animals by 20%, indicating a nonredundant role for this chemokine in the presence of physiologic CCR7 agonists. Together, these data distinguish naive T cells from TCM, whereby only the latter display greater migratory flexibility by virtue of their increased responsiveness to both CCR7 ligands and CXCL12 during homing to PLN

Computer-assisted morphometry of the peripheral nervous system. A diagnostic tool.

A formal systematization of the set of procedures required in peripheral nerve morphometry has been implemented in a computer program, in an attempt to provide an easy-to-handle diagnostic tool in current neuropathological practice. The hardware is composed of an IBM-PC compatible computer and a graphic tablet. Programs are written in BASIC and run in computers compatible with the MS-DOS operating system. The flow of operative steps involved in the morphometric study is controlled by the software. Sequential measurements are also tested for congruence. Nerve fibre measurements are stored in pluri-dimensional matrices for subsequent statistical calculations, i.e. evaluation of size-frequency distribution of nerve fibres and correlation analysis between nerve fibre subcomponents. Stereological estimates of the parenchymal components are also derived. The increase in accuracy achieved using area instead of diameter measurements is stressed. Compared to "dedicated" machines such personal computer-assisted systems exhibit substantial advantages in terms of low cost and flexibility

Differenziazione cellulare e capacita' metastatica. Uno studio morfometrico sulle metastasi polmonari delle linee F1 ed F10 del melanoma B16 di topo

E' stato condotto uno studio morfometrico sulle linee cellulari F1 ed F10 del melanoma murino B16 che ha evidenziato interessanti correlazioni tra la differenziazione cellulare, valutata a livello ultrastrutturale, e la capacita' metastatic

A morphometric comparison of subcellular structures between primary breast tumors and their nodal metastases.

A morphometric study of subcellular structures in human primary breast tumors (of the ductal infiltrating type) and their synchronous lymph node metastases was carried out using planimetry and stereology. Each primary neoplasm was compared separately with its axillary metastatic growth in order to detect differences in the quantitative estimates of their subcellular components. A set of 24 morphometric parameters was used to quantitatively describe each neoplastic cell profile. Although some subcellular parameters showed significant differences between the cells of a primary tumor and its metastases, no parameter was found to be consistently altered in all cases. No consistent increase or decrease in the values of the affected parameters was observed in the metastases. More than being due to the expression of a biologically variant (more-or-less differentiated) metastatic phenotype, the differences in stereologic parameters detected in metastatic cells appear to reflect the existence of different functional states of the same cell type

Morphometric changes in sympathetic nerve fibres in diabetes.

A morphometric study was carried out on electron micrographs of lumbar sympathetic nerve fibres surgically removed from 12 patients with arteriosclerosis obliterans: 4 diabetics, 4 non-diabetics and 4 subjects with glucose intolerance. In patients with diabetes and glucose intolerance a significant decrease in the percent area fraction of unmyelinated axons and an increase in the percent area fraction of the endoneurial space were demonstrated