A Chemically Well-Defined, Self-Assembling 3D Substrate for Long-Term Culture of Human Pluripotent Stem Cells.

Clinical applications of human pluripotent stem cells (PSCs) are limited by the lack of chemically well-defined scaffolds for cell expansion, differentiation, and implantation. In this study, we systematically screened various self-assembling hexapeptides to identify the best matrix for long-term 3D PSC culture. Lysine-containing Ac-ILVAGK-NH2 hydrogels maintained best the pluripotency of human embryonic and induced PSCs even after 30 passages. This peptide matrix is also compatible with the use of xeno-free and defined differentiation media. By exploiting its stimuli-responsive sol-gel transition, arrays of encapsulated PSCs can be bioprinted for large-scale cell expansion and derivation of miniaturized organoid cultures for high-throughput screening.

Observation of the Self-Modulation Instability via Time-Resolved Measurements.

Self-modulation of an electron beam in a plasma has been observed. The propagation of a long (several plasma wavelengths) electron bunch in an overdense plasma resulted in the production of multiple bunches via the self-modulation instability. Using a combination of a radio-frequency deflector and a dipole spectrometer, the time and energy structure of the self-modulated beam was measured. The longitudinal phase space measurement showed the modulation of a long electron bunch into three bunches with an approximately 200 keV/c amplitude momentum modulation. Demonstrating this effect is a breakthrough for proton-driven plasma accelerator schemes aiming to utilize the same physical effect.

Annual variation of (7)Be soil inventory in a semiarid region of central Argentina.

Reliable information on environmental radionuclides atmospheric entrance, and their distribution along the soil profile, is a necessary condition for using these soil and sediment tracers to investigate key environmental processes. To address this need, (7)Be content in rainwater and the wet deposition in a semiarid region at San Luis Province, Argentina, were studied. Following these researches, in the same region, we have assessed the (7)Be content along a soil profile, during 2.5 years from September 2009 to January 2012. As expected, the specific activity values in soil samples in the wet period (November-April) were higher than in the dry period (May-October). During the investigated period (2009 - beginning 2012) and for all sampled points, the maximum value of the (7)Be specific activity (Bq kg(-1)) was measured at the surface level. A typical decreasing exponential function of (7)Be areal activity (Bq m(-2)) with soil mass depth (kg m(-2)) was found and the key distribution parameters were determined for each month. The minimum value of areal activity was 51 Bq m(-2) in August, and the maximum was 438 Bq m(-2) in February. The relaxation mass depth ranges from 2.9 kg m(-2) in March to 1.3 kg m(-2) in August. (7)Be wet deposition can explain in a very significant proportion the (7)Be inventory in soil. During the period of winds in the region (September and October), the (7)Be content in soil was greater than the expected contribution from wet deposition, situation that is compatible with a higher relative contribution of dry deposition at this period of the year.

Assessment of 7Be content in precipitation in a South American semi-arid environment.

There are two naturally occurring radiogenic isotopes of beryllium, 7Be and ¹°Be. These are produced when cosmic radiation interacts with oxygen and nitrogen in the atmosphere. After production, these radionuclides are input to ecosystems through wet and dry deposition. In recent years 7Be and ¹°Be have proved to be powerful tools for studying dynamic processes that occur on the surface of the earth. We measured the 7Be content in precipitation at a semiarid location in central Argentina. From November 2006 to March 2009, 68 precipitation events were collected. Measured 7Be content ranged from 0.7±0.4 Bq L⁻¹ to 3.2±0.7 Bq L⁻¹, with a mean of 1.7 Bq L⁻¹ ±0.6 Bq L⁻¹. Beryllium-7 content of rainfall did not show clear relationships with amount of rainfall (mm), mean intensity (mm h⁻¹) or duration (h⁻¹), or elapsed time between events (day). The general results indicate that for the typical range of precipitation there was no atmospheric washout and that the reload of the atmosphere is not a relevant factor, but when the amount of precipitation is very high washout may occur. On the other hand, when the 7Be content was measured during single rain events, a high content of this radionuclide was found to be associated with very low rainfall intensity (≈3 mm h⁻¹), this suggests that rain intensity could affect the 7Be content. Using all data, a good linear relationship between 7Be deposition and rain magnitude was obtained (r²=0.82, p<0.0001). Because of this, the slope of this linear regression equation may be applied as a tool for tracing environmental processes that affect the surface of the earth. We can do this by directly estimating erosion/sedimentation processes using 7Be or by estimating the input of ¹°Be in the environment with the aim to evaluate land degradation phenomena.

Development of a Tandem-Electrostatic-Quadrupole facility for Accelerator-Based Boron Neutron Capture Therapy.

We describe the present status of an ongoing project to develop a Tandem-ElectroStatic-Quadrupole (TESQ) accelerator facility for Accelerator-Based (AB)-BNCT. The project final goal is a machine capable of delivering 30 mA of 2.4 MeV protons to be used in conjunction with a neutron production target based on the (7)Li(p,n)(7)Be reaction. The machine currently being constructed is a folded TESQ with a high-voltage terminal at 0.6 MV. We report here on the progress achieved in a number of different areas.

Development of high intensity ion sources for a Tandem-Electrostatic-Quadrupole facility for Accelerator-Based Boron Neutron Capture Therapy.

Several ion sources have been developed and an ion source test stand has been mounted for the first stage of a Tandem-Electrostatic-Quadrupole facility For Accelerator-Based Boron Neutron Capture Therapy. A first source, designed, fabricated and tested is a dual chamber, filament driven and magnetically compressed volume plasma proton ion source. A 4 mA beam has been accelerated and transported into the suppressed Faraday cup. Extensive simulations of the sources have been performed using both 2D and 3D self-consistent codes.

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species.

Mammalian preimplantation embryonic development (PED) is thought to be governed by highly conserved processes. While it had been suggested that some plasticity of conserved signaling networks exists among different mammalian species, it was not known to what extent modulation of the genomes and the regulatory proteins could "rewire" the gene regulatory networks (GRN) that control PED. We therefore generated global transcriptional profiles from three mammalian species (human, mouse, and bovine) at representative stages of PED, including: zygote, two-cell, four-cell, eight-cell, 16-cell, morula and blastocyst. Coexpression network analysis suggested that 40.2% orthologous gene triplets exhibited different expression patterns among these species. Combining the expression data with genomic sequences and the ChIP-seq data of 16 transcription regulators, we observed two classes of genomic changes that contributed to interspecies expression difference, including single nucleotide mutations leading to turnover of transcription factor binding sites, and insertion of cis-regulatory modules (CRMs) by transposons. About 10% of transposons are estimated to carry CRMs, which may drive species-specific gene expression. The two classes of genomic changes act in concert to drive mouse-specific expression of MTF2, which links POU5F1/NANOG to NOTCH signaling. We reconstructed the transition of the GRN structures as a function of time during PED. A comparison of the GRN transition processes among the three species suggested that in the bovine system, POU5F1's interacting partner SOX2 may be replaced by HMGB1 (a TF sharing the same DNA binding domain with SOX2), resulting in rewiring of GRN by a trans change.

Dissecting early differentially expressed genes in a mixture of differentiating embryonic stem cells.

The differentiation of embryonic stem cells is initiated by a gradual loss of pluripotency-associated transcripts and induction of differentiation genes. Accordingly, the detection of differentially expressed genes at the early stages of differentiation could assist the identification of the causal genes that either promote or inhibit differentiation. The previous methods of identifying differentially expressed genes by comparing different cell types would inevitably include a large portion of genes that respond to, rather than regulate, the differentiation process. We demonstrate through the use of biological replicates and a novel statistical approach that the gene expression data obtained without prior separation of cell types are informative for detecting differentially expressed genes at the early stages of differentiation. Applying the proposed method to analyze the differentiation of murine embryonic stem cells, we identified and then experimentally verified Smarcad1 as a novel regulator of pluripotency and self-renewal. We formalized this statistical approach as a statistical test that is generally applicable to analyze other differentiation processes.

Short-term seasonal variability in 7Be wet deposition in a semiarid ecosystem of central Argentina.

The (7)Be wet deposition has been intensively investigated in a semiarid region at San Luis Province, Argentina. From November 2006 to May 2008, the (7)Be content in rainwater was determined in 58 individual rain events, randomly comprising more than 50% of all individual precipitations at the sampling period. (7)Be activity concentration in rainwater ranged from 0.7+/-0.3 Bq l(-1) to 3.2+/-0.7 Bq l(-1), with a mean value of 1.7 Bq l(-1) (sd=0.53 Bq l(-1)). No relationship was found between (7)Be content in rainwater and (a) rainfall amount, (b) precipitation intensity and (c) elapsed time between events. (7)Be ground deposition was found to be well correlated with rainfall amount (R=0.92). For the precipitation events considered, the (7)Be depositional fluxes ranged from 1.1 to 120 Bq m(-2), with a mean value of 32.7 Bq m(-2) (sd=29.9 Bq m(-2)). The annual depositional flux was estimated at 1140+/-120 Bq m(-2)y(-1). Assuming the same monthly deposition pattern and that the (7)Be content in soil decreases only through radioactive decay, the seasonal variation of (7)Be areal activity density in soil was estimated. Results of this investigation may contribute to a valuable characterization of (7)Be input in the explored semiarid ecosystem and its potential use as tracer of environmental processes.

Development of a tandem-electrostatic-quadrupole accelerator facility for BNCT.

In this work we describe the present status of an ongoing project to develop a tandem-electrostatic-quadrupole (TESQ) accelerator facility for accelerator-based (AB) BNCT at the Atomic Energy Commission of Argentina in Buenos Aires. The project final goal is a machine capable of delivering 30 mA of 2.4 MeV protons to be used in conjunction with a neutron production target based on the (7)Li(p,n)(7)Be reaction slightly beyond its resonance at 2.25 MeV. These are the specifications needed to produce sufficiently intense and clean epithermal neutron beams, based on the (7)Li(p,n)(7)Be reaction, to perform BNCT treatment for deep-seated tumors in less than an hour. An electrostatic machine is the technologically simplest and cheapest solution for optimized AB-BNCT. The machine being designed and constructed is a folded TESQ with a high-voltage terminal at 1.2 MV intended to work in air. Such a machine is conceptually shown to be capable of transporting and accelerating a 30 mA proton beam to 2.4 MeV. The general geometric layout, its associated electrostatic fields, and the acceleration tube are simulated using a 3D finite element procedure. The design and construction of the ESQ modules is discussed and their electrostatic fields are investigated. Beam transport calculations through the accelerator are briefly mentioned. Likewise, work related to neutron production targets, strippers, beam shaping assembly and patient treatment room is briefly described.

Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells.

We introduce the GibbsModule algorithm for de novo detection of cis-regulatory motifs and modules in eukaryote genomes. GibbsModule models the coexpressed genes within one species as sharing a core cis-regulatory motif and each homologous gene group as sharing a homologous cis-regulatory module (CRM), characterized by a similar composition of motifs. Without using a predetermined alignment result, GibbsModule iteratively updates the core motif shared by coexpressed genes and traces the homologous CRMs that contain the core motif. GibbsModule achieved substantial improvements in both precision and recall as compared with peer algorithms on a number of synthetic and real data sets. Applying GibbsModule to analyze the binding regions of the Krüppel-like factor (KLF) transcription factor in embryonic stem cells (ESCs), we discovered a motif that differs from a previously published KLF motif identified by a SELEX experiment, but the new motif is consistent with mutagenesis analysis. The SOX2 motif was found to be a collaborating motif to the KLF motif in ESCs. We used quantitative chromatin immunoprecipitation (ChIP) analysis to test whether GibbsModule could distinguish functional and nonfunctional binding sites. All seven tested binding sites in GibbsModule-predicted CRMs had higher ChIP signals as compared with the other seven tested binding sites located outside of predicted CRMs. GibbsModule is available at (http://biocomp.bioen.uiuc.edu/GibbsModule).

Characterisation of uranium(VI) sorption by two environmental fungal species using gamma spectrometry.

Uranium(VI) sorption by two highly uranium-resistant air-borne fungi in a low-pH medium was measured by means of gamma spectrometry. Growth kinetics and stoichiometry of the two fungal species were also studied. Results show acceptable growth rates in synthetic medium with glucose and ammonia as carbon and nitrogen sources, respectively. Typical oxidative metabolism of carbohydrates was found. In vivo uptake of the radionuclide was negligible, but biosorption dry biomass presented a remarkable performance. The fungal strains showed potential for use in bioremediation.

210Pb dating of sediments in a heavily contaminated drainage channel to the La Plata estuary in Buenos Aires, Argentina.

Concentrations of (210)Pb and (137)Cs in sediment samples collected from two cores at a drainage channel to the La Plata river estuary in Buenos Aires, Argentina, were measured using ultralow-background detection systems. The (210)Pb data were used to determine the rate of sediment accumulation of the sites. These results were correlated with some heavy metal (chromium and lead) concentrations of the samples in an attempt to characterize the historical input of contaminants due to the industrial development, which has taken place in this area over the last century. The (137)Cs measurements demonstrate that cesium dating is not adequate in regions of the southern hemisphere.

137Cs contamination in tea and yerba mate in South America.

Gamma-ray spectra from more than 50 samples of food products available in stores of Buenos Aires city were measured using a germanium detector. Activity concentrations of 137Cs up to 10 Bq/kg were found in tea and yerba mate manufactured in Apóstoles, Argentina. Further measurements of tea leaves, yerba mate leaves and soils, all coming from a cultivated area in that region, also show the presence of 137Cs contamination. The results suggest that the area was fertilized with a product that originated in a region affected by the fallout from the Chernobyl nuclear plant accident.

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.

Using high-density oligonucleotide arrays representing essentially all nonrepetitive sequences on human chromosomes 21 and 22, we map the binding sites in vivo for three DNA binding transcription factors, Sp1, cMyc, and p53, in an unbiased manner. This mapping reveals an unexpectedly large number of transcription factor binding site (TFBS) regions, with a minimal estimate of 12,000 for Sp1, 25,000 for cMyc, and 1600 for p53 when extrapolated to the full genome. Only 22% of these TFBS regions are located at the 5' termini of protein-coding genes while 36% lie within or immediately 3' to well-characterized genes and are significantly correlated with noncoding RNAs. A significant number of these noncoding RNAs are regulated in response to retinoic acid, and overlapping pairs of protein-coding and noncoding RNAs are often coregulated. Thus, the human genome contains roughly comparable numbers of protein-coding and noncoding genes that are bound by common transcription factors and regulated by common environmental signals.

Smoothness of ablation on acrylic by four different excimer lasers.

PURPOSE: There are many different excimer laser devices available for photoablative refractive surgery. Smoothness of ablation may vary with different excimer lasers systems. METHODS: Ablations were performed on polymethylmethacrylate (PMMA) plates of 8 x 4 x 0.5 cm, with four different excimer lasers: VISX-Star, Coherent Schwind Keratom I/II, Chiron Technolas Keracor 117C (Plano Scan), and the Nidek EC-5000, to determine and compare the homogeneity and smoothness of the surface. Ten -3.00 D samples, ten -6.00 D samples, and ten -9.00 D samples were ablated with each laser. The PMMA discs were examined with optical microscopy, documented by photographs, and each sample was measured quantitatively using a Hommel-Werkel rugosimeter. We used the same PMMA material throughout. RESULTS: Statistically significant differences in smoothness were found between the Chiron Technolas 117C and the VISX-Star, Nidek and VISX-Star, and Coherent Schwind and VISX-Star in the homogeneities achieved by ablating -3.00 D. Ablations of -6.00 D resulted in homogeneities that were statistically significantly different: Chiron Technolas 117C with the other three devices, the Nidek EC-5000 with the VISX-Star, and the Coherent-Schwind with the VISX-Star. In the ablations for -9.00 D, statistically significant differences in homogeneity were found between the Chiron Technolas 117C and Nidek, between the Chiron and VISX-Star, between the Coherent Schwind and VISX-Star, and between the Nidek and VISX-Star. The laser with the scanning spot system was smoother. CONCLUSION: Scanning spot technology produced smooth ablations even up to -9.00 D.