Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Random migration of induced pluripotent stem cell-derived human gastrulation-stage mesendoderm.

Gastrulation is the initial systematic deformation of the embryo to form germ layers, which is characterized by the placement of appropriate cells in their destined locations. Thus, gastrulation, which occurs at the beginning of the second month of pregnancy, is a critical stage in human body formation. Although histological analyses indicate that human gastrulation is similar to that of other amniotes (birds and mammals), much of human gastrulation dynamics remain unresolved due to ethical and technical limitations. We used human induced pluripotent stem cells (hiPSCs) to study the migration of mesendodermal cells through the primitive streak to form discoidal germ layers during gastrulation. Immunostaining results showed that hiPSCs differentiated into mesendodermal cells and that epithelial-mesenchymal transition occurred through the activation of the Activin/Nodal and Wnt/beta-catenin pathways. Single-cell time-lapse imaging of cells adhered to cover glass showed that mesendodermal differentiation resulted in the dissociation of cells and an increase in their migration speed, thus confirming the occurrence of epithelial-mesenchymal transition. These results suggest that mesendodermal cells derived from hiPSCs may be used as a model system for studying migration during human gastrulation in vitro. Using random walk analysis, we found that random migration occurred for both undifferentiated hiPSCs and differentiated mesendodermal cells. Two-dimensional random walk simulation showed that homogeneous dissociation of particles may form a discoidal layer, suggesting that random migration might be suitable to effectively disperse cells homogeneously from the primitive streak to form discoidal germ layers during human gastrulation

The Binding of Aripiprazole to Plasma Proteins in Chronic Renal Failure Patients

The binding of drugs to plasma protein is frequently altered in certain types of renal diseases. We recently reported on the effects of oxidation and uremic toxins on the binding of aripiprazole (ARP) to human serum albumin. In our continuing investigations, we examined the binding of ARP to plasma pooled from patients with chronic renal dysfunction. We examined the issue of the molecular basis for which factors affect the changes in drug binding that accompany renal failure. The study was based on the statistical relationships between ARP albumin binding and biochemical parameters such as the concentrations of oxidized albumin and uremic toxins. The binding of ARP to plasma from chronic renal patients was significantly lower than healthy volunteers. A rational relationship between the ARP binding rate and the concentration of toxins, including indoxyl sulphate (IS) and p-cresyl sulphate (PCS), was found, particularly for IS. Moreover, multiple regression analyses that involved taking other parameters such as PCS or oxidized albumin ratio to IS into account supports the above hypothesis. In conclusion, the limited data reported in this present study indicates that monitoring IS in the blood is a very important determinant in the dosage plan for the administration of site II drugs such as ARP, if the efficacy of the drug in renal disease is to be considered

Polythiol-containing, recombinant mannosylated-albumin is a superior CD68+/CD206+ Kupffer cell-targeted nano-antioxidant for the treatment of two acute hepatitis models

Since reactive oxygen species (ROS) derived from Kupffer cells (KC), especially CD68+ KC, play a key role in the induction of hepatic oxidative stress and injuries, we newly developed a polythiolated- and mannosylated-human serum albumin (SH-Man-HSA), a novel nano-antioxidant for delivering thiol to CD68+ KC. In vitro electron paramagnetic resonance (EPR) coupled with an in vivo pharmacokinetic and immunohistochemical study showed that SH-Man-HSA possessed powerful radical scavenging activity and was rapidly and selectively delivered thiols to the liver via mannose receptor (CD206) presented on the CD68+ cells surface. SH-Man-HSA significantly improved the survival rate of concanavalin-A (Con-A) treated mice. Moreover, SH-Man-HSA exhibited excellent hepato-protective action, not by influencing TNF or IFN-? production that closely associated with Con-A induced hepatitis, but by suppressing ROS production. Interestingly, such protective effect of SH-Man-HSA was superior to N-acetylcysteine (NAC). This could be due to the difference in the inhibition of hepatic oxidative stress between two antioxidant depending upon their potential of thiol delivery to liver. Similar results were also observed for acetaminophen (APAP)-induced hepatopathy models. Flow cytometric data further confirmed that an increase of F4/80+/ROS+ cells was dramatically decreased by SH-Man-HSA. The administration of SH-Man-HSA at 4 hours following a Con-A or APAP injection also exhibited profound hepato-protective action against two experimental hepatitis models, while this was not observed in the case of NAC. Therefore, SH-Man-HSA has a great potential for use as a rescue therapy for hepatopathy as a nano-antioxidant because of its efficient and rapid delivery of thiols to CD68+/CD206+ KC

Persistent release of IL-1s from skin is associated with systemic cardio-vascular disease, emaciation and systemic amyloidosis: the potential of anti-IL-1 therapy for systemic inflammatory diseases.

The skin is an immune organ that contains innate and acquired immune systems and thus is able to respond to exogenous stimuli producing large amount of proinflammatory cytokines including IL-1 and IL-1 family members. The role of the epidermal IL-1 is not limited to initiation of local inflammatory responses, but also to induction of systemic inflammation. However, association of persistent release of IL-1 family members from severe skin inflammatory diseases such as psoriasis, epidermolysis bullosa, atopic dermatitis, blistering diseases and desmoglein-1 deficiency syndrome with diseases in systemic organs have not been so far assessed. Here, we showed the occurrence of severe systemic cardiovascular diseases and metabolic abnormalities including aberrant vascular wall remodeling with aortic stenosis, cardiomegaly, impaired limb and tail circulation, fatty tissue loss and systemic amyloid deposition in multiple organs with liver and kidney dysfunction in mouse models with severe dermatitis caused by persistent release of IL-1s from the skin. These morbid conditions were ameliorated by simultaneous administration of anti-IL-1α and IL-1β antibodies. These findings may explain the morbid association of arteriosclerosis, heart involvement, amyloidosis and cachexia in severe systemic skin diseases and systemic autoinflammatory diseases, and support the value of anti-IL-1 therapy for systemic inflammatory diseases

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance

Soil microbial communities have great potential for bioremediation of recalcitrant aromatic compounds. However, it is unclear which taxa and genes in the communities, and how they contribute to the bioremediation in the polluted soils. To get clues about this fundamental question here, time-course (up to 24 weeks) metagenomic analysis of microbial community in a closed soil microcosm artificially polluted with four aromatic compounds, including phenanthrene, was conducted to investigate the changes in the community structures and gene pools. The pollution led to drastic changes in the community structures and the gene sets for pollutant degradation. Complete degradation of phenanthrene was strongly suggested to occur by the syntrophic metabolism by Mycobacterium and the most proliferating genus, Burkholderia. The community structure at Week 24 (-12 weeks after disappearance of the pollutants) returned to the structure similar to that before pollution. Our time-course metagenomic analysis of phage genes strongly suggested the involvement of the 'kill-the-winner' phenomenon (i.e. phage predation of Burkholderia cells) for the returning of the microbial community structure. The pollution resulted in a decrease in taxonomic diversity and a drastic increase in diversity of gene pools in the communities, showing the functional redundancy and robustness of the communities against chemical disturbance

KCASP1Tg and KIL-18Tg(+) mice developed amyloidosis in the liver, kidney and spleen.

<p><b>A</b>) Histological analyses showed loss of normal architecture: hepatocytes were replaced by dense deposits in the liver, the glomeruli and renal tubules were damaged in the kidney, and lymph-follicles were absent in the spleen. Dense amyloid deposition was detected in KCASP1Tg and KIL-18Tg(+) mice by Congo-red staining. <b>B</b>) KCASP1Tg mice showed mild liver and kidney dysfunction while renal function had significantly deteriorated in KIL-18Tg(+) mice (n = at least 7).</p

High serum amyloid A protein and organomegaly in KCASP1Tg and KIL-18Tg(+) mice.

<p><b>A</b>) Serum amyloid A protein (SAA) levels were significantly higher in KCASP1Tg mice than in normal control and 6-months old KIL-18Tg(−) mice. Eighteen-months old KIL-18Tg(+) mice also showed elevated SAA concentration (n = at least 7). <b>B</b>) <b>C</b>) The liver, kidney, and spleen of both KCASP1Tg and KIL-18Tg(+) mice were significantly enlarged compared to control and KIL-18Tg(−) mice.</p