Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE)

BACKGROUND: Serial Analysis of Gene Expression (SAGE) is a functional genomic technique that quantitatively analyzes the cellular transcriptome. The analysis of SAGE libraries relies on the identification of ditags from sequencing files; however, the software used to examine SAGE libraries cannot distinguish between authentic versus false ditags ("quasi-ditags"). RESULTS: We provide examples of quasi-ditags that originate from cloning and sequencing artifacts (i.e. genomic contamination or random combinations of nucleotides) that are included in SAGE libraries. We have employed a mathematical model to predict the frequency of quasi-ditags in random nucleotide sequences, and our data show that clones containing less than or equal to 2 ditags (which include chromosomal cloning artifacts) should be excluded from the analysis of SAGE catalogs. CONCLUSIONS: Cloning and sequencing artifacts contaminating SAGE libraries could be eliminated using simple pre-screening procedure to increase the reliability of the data

Interfacial Properties of Fluids Exhibiting Liquid Polyamorphism and Water-Like Anomalies

It has been hypothesized that liquid polyamorphism, the existence of multiple amorphous states in a single component substance, may be caused by molecular or supramolecular interconversion. A simple microscopic model [Caupin and Anisimov, Phys. Rev. Lett., 127, 185701, (2021)] introduces interconversion in a compressible binary lattice to generate various thermodynamic scenarios for fluids that exhibit liquid polyamorphism and/or water-like anomalies. Using this model, we demonstrate the dramatic effects of interconversion on the interfacial properties. In particular, we find that the liquid-vapor surface tension exhibits either an inflection point or two extrema in its temperature dependence. Correspondingly, we observe anomalous behavior of the interfacial thickness and a significant shift in the location of the concentration profile with respect to the location of the density profile.Comment: This manuscript has been submitted to the Journal of Physical Chemistry B, as a part of the special issue, "Pablo G. Debenedetti Festschrift.

Growth Factors and Feeder Cells Promote Differentiation of Human Embryonic Stem Cells into Dopaminergic Neurons: A Novel Role for Fibroblast Growth Factor-20

Human embryonic stem cells (hESCs) are a potential source of dopaminergic neurons for treatment of patients with Parkinson's disease (PD). Dopaminergic neurons can be derived from hESCs and display a characteristic midbrain phenotype. Once transplanted, they can induce partial behavioral recovery in animal models of PD. However, the potential research field faces several challenges that need to be overcome before clinical application of hESCs in a transplantation therapy in PD can be considered. These include low survival of the hESC-derived, grafted dopaminergic neurons after transplantation; unclear functional integration of the grafted neurons in the host brain; and, the risk of teratoma/tumor formation from the transplanted cells. This review is focused on our recent efforts to improve the survival of hESC-dervied dopaminergic neurons. In a recent study, we examined the effect of fibroblast growth factor (FGF)-20 in the differentiation of hESCs into dopaminergic neurons. We supplemented cultures of hESCs with FGF-20 during differentiation on PA6 mouse stromal cells for 3 weeks. When we added FGF-20 the yield of neurons expressing tyrosine hydroxylase increased. We demonstrated that at least part of the effect is contributed by enhanced cell differentiation towards the dopaminergic phenotype as well as reduced cell death. We compare our results with those obtained in other published protocols using different sets of growth factors. Taken together, our data indicate that FGF-20 has potent effects to generate large number of dopaminergic neurons derived from hESCs, which may be useful for hESC-based therapy in PD

Pressure-induced magnetic transitions with change of the orbital configuration in dimerised systems

We suggest a possible scenario for magnetic transition under pressure in dimerised systems where electrons are localised on molecular orbitals. The mechanism of transition is not related with competition between kinetic energy and on-site Coulomb repulsion as in Mott-Hubbard systems, or between crystal-field splitting and intra-atomic exchange as in classical atomic spin-state transitions. Instead, it is driven by the change of bonding-antibonding splitting on part of the molecular orbitals. In the magnetic systems with few half-filled molecular orbitals external pressure may result in increase of the bonding-antibonding splitting and localise all electrons on low-lying molecular orbitals suppressing net magnetic moment of the system. We give examples of the systems, where this or inverse transition may occur and by means of ab initio band structure calculations predict that it can be observed in α−MoCl(4) at pressure P ~ 11 GPa

Single-Walled Carbon Nanotube Network Field Effect Transistor as a Humidity Sensor

Single-walled carbon nanotube network field effect transistors were fabricated and studied as humidity sensors. Sensing responses were altered by changing the gate voltage. At the open channel state (negative gate voltage), humidity pulse resulted in the decrease of the source-drain current, and, vice versa, the increase in the source-drain current was observed at the positive gate voltage. This effect was explained by the electron-donating nature of water molecules. The operation speed and signal intensity was found to be dependent on the gate voltage polarity. The positive or negative change in current with humidity pulse at zero-gate voltage was found to depend on the previous state of the gate electrode (positive or negative voltage, respectively). Those characteristics were explained by the charge traps in the gate dielectric altering the effective gate voltage, which influenced the operation of field effect transistor.Peer reviewe

π

We report on measurements of neutral pion production in the inclusive reactions d + C → π0 + x and d + Cu → π0 + x at an incident momentum of 4.5 GeV/c per nucleon. The experiments were performed on the LHE 90-channel lead glass γ-spectrometer. The cross sections were measured over the kinematical region specified by the inequalities θπ ≤ 16° and Eπ ≥ 2 GeV (in the laboratory frame). The cumulative number and transverse momentum dependencies of the exponent n in the invariant cross section parameterization Ed3 σ / d3 p ~ Atn are investigated by comparing of the observed cross sections for π0 production on carbon and copper targets in the intervals 0.6 ≤ X ≤ 1.8 and 0.04 ≤ pT2 ≤ 0.40 (GeV/c)2. The double differential cross section for the reaction d + C → π0 + x is measured using statistics of about 4.5 · 104π0 mesons. On the basis of these data we verified the so-called cluster mechanism of π0 production. We have compared our data for the reaction d + C → π0 + x, extrapolated to θπ = 0°, with the data from another experiments on π− production: d + C → π−(0°) + x (P = 1.75 and 2.88 GeV/c per nucleon) [1]; p + d → π−(180°) + x and p + d → π+(180°) + x (P = 8.9 GeV/c per nucleon) [2]; d + p → π−(0°) + x (P = 8.9 GeV/c per nucleon) [3]. The invariant cross sections were approximated by an exponential function Ed3 σ / d3 p ~ exp(−X / X0). The slope parameter X0 at different kinetic energies of the projectiles in the range of 1.05÷8.0 GeV per nucleon is determined

Insight into Microevolution of Yersinia pestis by Clustered Regularly Interspaced Short Palindromic Repeats

BACKGROUND: Yersinia pestis, the pathogen of plague, has greatly influenced human history on a global scale. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR), an element participating in immunity against phages' invasion, is composed of short repeated sequences separated by unique spacers and provides the basis of the spoligotyping technology. In the present research, three CRISPR loci were analyzed in 125 strains of Y. pestis from 26 natural plague foci of China, the former Soviet Union and Mongolia were analyzed, for validating CRISPR-based genotyping method and better understanding adaptive microevolution of Y. pestis. METHODOLOGY/PRINCIPAL FINDINGS: Using PCR amplification, sequencing and online data processing, a high degree of genetic diversity was revealed in all three CRISPR elements. The distribution of spacers and their arrays in Y. pestis strains is strongly region and focus-specific, allowing the construction of a hypothetic evolutionary model of Y. pestis. This model suggests transmission route of microtus strains that encircled Takla Makan Desert and ZhunGer Basin. Starting from Tadjikistan, one branch passed through the Kunlun Mountains, and moved to the Qinghai-Tibet Plateau. Another branch went north via the Pamirs Plateau, the Tianshan Mountains, the Altai Mountains and the Inner Mongolian Plateau. Other Y. pestis lineages might be originated from certain areas along those routes. CONCLUSIONS/SIGNIFICANCE: CRISPR can provide important information for genotyping and evolutionary research of bacteria, which will help to trace the source of outbreaks. The resulting data will make possible the development of very low cost and high-resolution assays for the systematic typing of any new isolate

The Adult Human Brain Harbors Multipotent Perivascular Mesenchymal Stem Cells

Blood vessels and adjacent cells form perivascular stem cell niches in adult tissues. In this perivascular niche, a stem cell with mesenchymal characteristics was recently identified in some adult somatic tissues. These cells are pericytes that line the microvasculature, express mesenchymal markers and differentiate into mesodermal lineages but might even have the capacity to generate tissue-specific cell types. Here, we isolated, purified and characterized a previously unrecognized progenitor population from two different regions in the adult human brain, the ventricular wall and the neocortex. We show that these cells co-express markers for mesenchymal stem cells and pericytes in vivo and in vitro, but do not express glial, neuronal progenitor, hematopoietic, endothelial or microglial markers in their native state. Furthermore, we demonstrate at a clonal level that these progenitors have true multilineage potential towards both, the mesodermal and neuroectodermal phenotype. They can be epigenetically induced in vitro into adipocytes, chondroblasts and osteoblasts but also into glial cells and immature neurons. This progenitor population exhibits long-term proliferation, karyotype stability and retention of phenotype and multipotency following extensive propagation. Thus, we provide evidence that the vascular niche in the adult human brain harbors a novel progenitor with multilineage capacity that appears to represent mesenchymal stem cells and is different from any previously described human neural stem cell. Future studies will elucidate whether these cells may play a role for disease or may represent a reservoir that can be exploited in efforts to repair the diseased human brain