Transcriptomic analysis of hepatocellular carcinoma reveals molecular features of disease progression and tumor immune biology.

Hepatocellular carcinoma (HCC) develops in the context of chronic inflammatory liver disease and has an extremely poor prognosis. An immunosuppressive tumor microenvironment may contribute to therapeutic failure in metastatic HCC. Here, we identified unique molecular signatures pertaining to HCC disease progression and tumor immunity by analyzing genome-wide RNA-Seq data derived from HCC patient tumors and non-tumor cirrhotic tissues. Unsupervised clustering of gene expression data revealed a gradual suppression of local tumor immunity that coincided with disease progression, indicating an increasingly immunosuppressive tumor environment during HCC disease advancement. IHC examination of the spatial distribution of CD8+ T cells in tumors revealed distinct intra- and peri-tumoral subsets. Differential gene expression analysis revealed an 85-gene signature that was significantly upregulated in the peri-tumoral CD8+ T cell-excluded tumors. Notably, this signature was highly enriched with components of underlying extracellular matrix, fibrosis, and epithelial-mesenchymal transition (EMT). Further analysis condensed this signature to a core set of 23 genes that are associated with CD8+ T cell localization, and were prospectively validated in an independent cohort of HCC specimens. These findings suggest a potential association between elevated fibrosis, possibly modulated by TGF-ß, PDGFR, SHH or Notch pathway, and the T cell-excluded immune phenotype. Indeed, targeting fibrosis using a TGF-ß neutralizing antibody in the STAM™ model of murine HCC, we found that ameliorating the fibrotic environment could facilitate redistribution of CD8+ lymphocytes into tumors. Our results provide a strong rationale for utilizing immunotherapies in HCC earlier during treatment, potentially in combination with anti-fibrotic therapies.

Atomic Configuration of Point Defect Clusters in Ion-Irradiated Silicon Carbide.

Silicon Carbide (SiC) is a promising cladding material for accident-tolerant fuel in light water reactors due to its excellent resistance to chemical attacks at high temperatures, which can prevent severe accident-induced environmental disasters. Although it has been known for decades that radiation-induced swelling at low temperatures is driven by the formation of black spot defects with sizes smaller than 2 nm in irradiated SiC, the structure of these defect clusters and the mechanism of lattice expansion have not been clarified and remain as one of the most important scientific issues in nuclear materials research. Here we report the atomic configuration of defect clusters using Cs-corrected transmission electron microscopy and molecular dynamics to determine the mechanism of these defects to radiation swelling. This study also provides compelling evidence that irradiation-induced point defect clusters are vacancy-rich clusters and lattice expansion results from the homogenous distribution of unrecovered interstitials in the material.

Broad expansion of optical frequency combs by self-Raman scattering in coupled-cavity self-mode-locked monolithic lasers.

Broad expansion of optical frequency comb (OFC) by the self-Raman scattering is numerically analyzed and experimentally accomplished in a coupled-cavity self-mode-locked (SML) monolithic Yb:KGW laser. The gain medium is coated to achieve the monolithic SML operation and a partially reflective mirror is further exploited to form the coupled cavity and to multiply the repetition rate up to 128.9 GHz. With a coupled reflectivity of 95%, it is experimentally found that not only the first-order but also second-order stimulated Raman scattering (SRS) can be efficiently generated. The mode-locked OFC can be consequently expanded to reach approximately 8.4 THz, leading the pulse width to be as narrow as 53 fs. At the pump power of 8.7 W, the total output power for the fundamental and the first- and second-Stokes waves can be maintained at 1.6 W. The present exploration provides a promising way to generate the ultrahigh-repetition-rate broadband OFC via the simultaneous SML and SRS processes.

Exploring transverse pattern formation in a dual-polarization self-mode-locked monolithic Yb: KGW laser and generating a 25-GHz sub-picosecond vortex beam via gain competition.

Formation of transverse modes in a dual-polarization self-mode-locked monolithic Yb: KGW laser under high-power pumping is thoroughly explored. It is experimentally observed that the polarization-resolved transverse patterns are considerably affected by the pump location in the transverse plane of the gain medium. In contrast, the longitudinal self-mode-locking is nearly undisturbed by the pump position, even under the high-power pumping. Under central pumping, a vortex beam of the Laguerre-Gaussian LGp,l mode with p = 1 and l = 1 can be efficiently generated through the process of the gain competition with a sub-picosecond pulse train at 25.3 GHz and the output power can be up to 1.45 W at a pump power of 10.0 W. Under off-center pumping, the symmetry breaking causes the transverse patterns to be dominated by the high-order Hermite-Gaussian modes. Numerical analyses are further performed to manifest the symmetry breaking induced by the off-center pumping.

Dual-comb self-mode-locked monolithic Yb:KGW laser with orthogonal polarizations.

The dependence of lasing threshold on the output transmission is numerically analyzed to find the condition for the gain-to-loss balance for the orthogonal Np and Nm polarizations with a Ng-cut Yb:KGW laser crystal. With the numerical analysis, an orthogonally polarized dual-comb self-mode-locked operation is experimentally achieved with a coated Yb:KGW crystal to form a monolithic cavity. At a pump power of 5.2 W, the average output power, the pulse repetition rate, and the pulse duration are measured to be 0.24 (0.6) W, 25.8 (25.3) GHz, and 1.06 (1.12) ps for the output along the Np (Nm) polarization.

Efficient continuous-wave self-Raman Yb:KGW laser with a shift of 89 cm⁻¹.

We demonstrated a continuous-wave (CW) self-Raman laser with high conversion efficiency by using Yb:KGW as the Raman crystal. The first Stokes line of wavelength centered at 1095.2 nm with spectral bandwidth of 8 nm and the cascaded Raman conversion wavelength at 1109.5 nm with spectral bandwidth of 3.4 nm were observed with a Raman shift of 89 cm⁻¹ with respect to the fundamental laser wavelength at 1085.0 nm with spectral bandwidth of 10 nm. The CW Raman output power of 1.7 W was attained under the diode pump power of 7.8 W which corresponds to the slope efficiency and the diode-to-Stokes optical conversion efficiency of 26.6% and 21.8%, respectively.

High-power high-repetition-rate subpicosecond monolithic Yb:KGW laser with self-mode locking.

We report on a high-power subpicosecond monolithic self-mode-locked Yb:KGW laser with the pulse repetition rate up to several tens of gigahertz. Experimental results reveal that not only the repetition rate but also the pulse width depend on the length of the laser crystal. Using a coated Yb:KGW crystal with a length of 3.36 mm, mode-locked pulses with pulse duration of 850 fs at the repetition rate of 22.4 GHz have been achieved. With an incident pump power of 10.5 W, an average output power of 3.6 W was achieved which corresponds to the optical conversion efficiency of 34.3%.

Novel genetic markers of the carbonic anhydrase II gene associated with egg production and reproduction traits in Tsaiya ducks.

In our previous cDNA microarray study, we found that the carbonic anhydrase II (CA2) gene is one of the differentially expressed transcripts in the duck isthmus epithelium during egg formation period. The aim of this study was to identify the single-nucleotide polymorphisms (SNPs) in the CA2 gene of Tsaiya ducks. The relationship of SNP genotype with egg production and reproduction traits was also investigated. A total of 317 ducks from two lines, a control line with no selection and a selected line, were employed for testing. Three SNPs (C37T, A62G and A65G) in the 3'-untranslated region of the CA2 gene were found. SNP-trait association analysis showed that SNP C37T and A62G were associated with duck egg weight besides fertility. The ducks with the CT and AG genotypes had a 1.46 and 1.62 g/egg lower egg weight as compared with ducks with the CC and AA genotypes, respectively (p < 0.05). But the ducks with CT and AG genotypes had 5.20% and 4.22% higher fertility than those with CC and AA genotypes, respectively (p < 0.05). Diplotype constructed on these three SNPs was associated with duck fertility, and the diplotype H1H4 was dominant for duck fertility. These findings might provide the basis for balanced selection and may be used in marker-assisted selection to improve egg weight and fertility simultaneously in the Tsaiya ducks.

A novel SNP of the PNRC1 gene and its association with reproductive traits in Tsaiya ducks.

Proline-rich nuclear receptor coactivator (PNRC)1 is a member of a new family of nuclear receptor coactivators capable of potentiating the transcriptional activity of nuclear receptors. The objective was to investigate the relationship between PNRC1 genotypes of single nucleotide polymorphism (SNP) and reproductive traits in ducks. Brown Tsaiya ducks (N = 305) from two lines, a control line with no selection and the selected line, were used. Polymerase chain reaction-single strand polymorphism and DNA sequencing were done to screen polymorphisms of the PNRC1 gene. A novel SNP (G98T) in 3'-untranslated region of the PNRC1 gene was identified and resulted in two genotypes, GG and GT. The frequencies of genotype GG and allele G were higher in both lines investigated. Regarding egg weight at first egg (EWFE), based on SNP trait association analysis, ducks with the GG genotype had a 4.48 g per egg greater egg weight at first egg when compared with ducks of the GT genotype in the control line (P < 0.05). In addition, this SNP was associated with the hatchability rate (HR) in the selected line; ducks with the GT genotype had a 6.70% higher hatchability rate than those with the GG genotype (P < 0.05). Therefore, we inferred that the PNRC1 gene could be a candidate locus or linked to a major gene that influenced egg weight-related and hatchability traits in Tsaiya ducks. Further investigations on additional duck populations with larger sample sizes are needed to confirm these results.

Direct enhancement of the phagocytic and bactericidal capability of abdominal macrophage of chicks by beta-1,3-1,6-glucan.

Salmonella enterica serovar Enteritidis is the major zoonotic and intracellular pathogen. Different strategies have been developed to prevent the S. Enteritidis infection. The beta-1,3-1,6-glucan of Schizophyllum commune was used as an immunological booster to determine the minimal dietary level of beta-glucan that would restrict S. Enteritidis infection through the effects of beta-glucan on the activity of macrophages and direct physical protection of the intestine. One-day-old male Single Comb White Leghorn chicks were used in all trials. In trials 1 and 2, the 0.1% beta-1,3-1,6-glucan treatment completely eliminated the viable S. Enteritidis from spleen and liver in an oral challenge of 10(8) S. Enteritidis without any harmful effect on BW, serum proteins, and immunoglobulin. Instead of a 21-d feeding period of beta-glucan, a 14-d treatment was enough to eliminate the S. Enteritidis in spleen and liver. In trial 3, an increase in the relative weight of bursa of Fabricius and phytohemagglutinin-P-inducing cutaneous basophil hypersensitivity was observed (P < 0.05). In trials 2, 3, and 4, the direct or indirect effect of beta-1,3-1,6-glucan on abdominal macrophages was examined. Sterilized 3% Sephadex G-50 was injected to induce abdominal (peritoneal) phagocytes in chicks fed with or without 0.1% beta-1,3-1,6-glucan. Significantly increased phagocytic and bactericidal capability to S. Enteritidis was found in abdominal macrophages either pretreated or in vitro treated with 0.1% beta-1,3-1,6-glucan. In conclusion, in addition to the physical properties to block S. Enteritidis entrance, 0.1% dietary beta-1,3-1,6-glucan may enhance the host defense to S. Enteritidis by directly upregulating the phagocytosis and bactericidal activity of abdominal macrophages in chicks.

Comparison of BiPAP nasal ventilation and ventilation via iron lung in severe stable COPD.

The effects of noninvasive ventilators on COPD remain controversial because of their obscure mechanisms. A randomized crossover study, using iron lung and positive pressure nasal ventilation (BiPAP) each for 40 min, was performed in 11 stable patients with severe COPD. Throughout the study, we monitored surface EMGdi, EMGst, ECG, SaO2, ETCO2, and the movements of RC and AB. Afterwards the data were replayed to calculate VT, RR, PR, VT/TI, iEMG, and phase angle. No statistically significant improvement was found in view of the above parameters. However, the percentage of iEMGst change after 40-min BiPAP ventilation, compared with the baseline, was much more significant in patients with FEV1 below 0.55 L than those with FEV1 above 0.55 L (n = 4:7, delta iEMGst -62.93 percent +/- 23.27 percent vs 32.45 percent +/- 42.79 percent, p = 0.0056). delta iEMGst correlated significantly with FEV1 during BiPAP ventilation (p < 0.05, r = 0.59). We conclude that the iEMGst during short-term BiPAP ventilation correlates with the severity of the disease.

Study on the concentrations of cerebrospinal fluid immunoglobulin G and albumin in children.

Concentrations of immunoglobulin G (IgG) and albumin in cerebrospinal fluid (CSF) and serum were measured in 118 "normal" Chinese children from birth to 15 years old to obtain the reference values for the evaluation of the blood-brain barrier (BBB) function. The values of the CSF/serum IgG ratio, CSF/serum albumin ratio and IgG index (IgG ratio/albumin ratio) were then calculated for each subject. A relation was found between the content of IgG in CSF and serum depending on age. The gradual decrease of CSF IgG and IgG ratio during the first 6 months indicated a postnatal impediment of the diffusion of IgG from the blood to the CSF. In the meanwhile the CSF/serum albumin ratio continued to drop until the age of one year. The slower slope of the decrement of the latter ratio further demonstrated the differential permeability of the BBB in favor of the shift of small molecular protein. The change of the protein permeability within the first year of life shows a characteristic of the maturational process of the BBB. Nevertheless, IgG index has no age-dependent variation throughout the childhood period. It remains constant in the absence of inflammation within the central nervous system.

A simple method for staining nuclei of mature and germinated maize pollen.

A sugar acetocarmine staining technique has been developed for staining the sperm and vegetative nucleus of mature and germinated maize pollen grains. This procedure is simple, stable and highly repeatable. The physiological properties of the mature maize pollen grains are first adjusted by using an in vitro germinating culture solution. This solution is 15% sucrose and contains 360 ppm calcium chloride dihydrate, and 120 ppm boric acid. One part fresh pollen grains is uniformly mixed with nine parts of the solution and left at room temperature for at least 5 hr. One part of this solution is then mixed with two parts of regular acetocarmine stain and left overnight. The color of this mixture is pinkish red or raspberry. The sugar in the mixture helps to increase color contrast between the pollen cytoplasm (light pink) and the nuclei (reddish purple), decreases the frequency of burst pollen, increases pollen expansion, stabilizes pollen figures and automatically seals the coverglass.

Nucleotide sequence of Lymantria dispar nuclear polyhedrosis virus polyhedrin gene.

The polyhedrin gene of the nuclear polyhedrosis virus of the gypsy moth (Lymantria dispar) (LdMNPV) was cloned and sequenced. A polyhedrin open reading frame of 735 nucleotides (nt) was identified which can code for a protein of 245 amino acids that demonstrates a high degree of similarity to other polyhedrins. The protein predicted from the nucleotide sequence shows differences in several regions to that previously sequenced from the LdMNPV polyhedrin protein. The consensus sequence AATAAGTATTTT found at the mRNA start site of baculovirus hyperexpressed genes was located 55 nt upstream from the translational start site.

Nuclear, Virescent Mutants of Zea mays L. with High Levels of Chlorophyll (a/b) Light-Harvesting Complex during Thylakoid Assembly.

We have found nuclear, recessive mutants in Zea mays L. where assembly of the major chlorophyll (a/b) light-harvesting complex (LHC) was not delayed relative to most other thylakoid protein complexes during thylakoid biogenesis. This contrasts with the normal development of maize chloroplasts (NR Baker, R Leech 1977 Plant Physiol 60: 640-644). All four mutants examined were allelic and virescent, and displayed visibly higher yields of leaf Chl fluorescence during greening. Fully greened mutants had normal leaf Chl fluorescence yield and normal levels of LHC, and grew to maturity under field conditions. Therefore, delayed LHC assembly is not an obligate feature of thylakoid differentiation.Assigning the molecular basis for the mutation should provide information concerning reguation of LHC assembly. Several possibilities are discussed. The pleiotropic mutant phenotype is not attributable to defects in thylakoid glycerolipid synthesis. Thylakoids isolated from greening mutant leaf sections had elevated glycerolipid/Chl ratios. In addition, both the molar distribution and acyl composition of four major glycerolipids were normal for developing mutant thylakoids.

Comparison of three tests for virulent Yersinia enterocolitica.

Magnesium oxalate agar was found to select against virulent types of Yersinia enterocolitica. Small colonies isolated from magnesium oxalate agar which were presumably virulent generally contained no detectable virulence-specific plasmids, did not agglutinate with virulence-specific antiserum, and exhibited various degrees of virulence in mice. Results indicate that the virulence potential of a Y. enterocolitica isolate cannot always be identified by these in vitro methods and suggest that virulence also involves other factors yet to be identified.

Identification of specific outer membrane polypeptides associated with virulent Yersinia enterocolitica.

An antiserum (WA-SAA) that agglutinates specifically with mouse virulent but not avirulent strains of Yersinia enterocolitica was used to identify virulence-associated factors by Western blot techniques. Several outer membrane polypeptides were identified only in the virulent strains, which included serotypes O:8, O:3, O:9, O:4,32, O:5,27, and O:21. These included three, and possibly four, major outer membrane polypeptides. The prominent high-molecular-weight species was demonstrated by both sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot, whereas the others were only revealed by the Western blot technique. Expression of these polypeptides correlated with antiserum agglutination reaction and the presence of a 42- and/or 82-megadalton plasmid. These polypeptides were highly temperature dependent and only slightly affected by the inclusion of 10 mM Ca2+ in the growth medium. These polypeptides were produced during both the logarithmic and stationary phases of growth at 37 degrees C. We suggest that the production of these specific polypeptides and calcium dependency may be coded for by the plasmid(s) but are regulated by independent mechanisms. These polypeptides appear to be novel markers specific for virulent strains of Y. enterocolitica and may be important to the pathogenicity of this organism.

The effect of light on morphogenesis of Dictyostelium mucoroides.

The effect of light on the production of macrocysts and sorocarps of Dictyostelium mucoroides, strain DM-7, has been studied with surface cultures grown on dilute lactose-peptone agar at 22 degrees C with Escherichia coli, strain B/r, as food bacteria. The production of sorocarps or macrocysts can be controlled by altering the light component of the environment. Far red light had no effect on macrocyst production, whereas visible light from 440 to 700 nm inhibited macrocyst production with production decreasing with increasing light intensity. Fluence response curves for macrocyst production were determined for twelve wavelengths of light between 400 and 700 nm. An action spectrum calculated from the fluence response curves shows a single major peak at about 425-430 nm.

The periodic synthesis of tubulin in the Physarum cell cycle. Characterization of Physarum tubulins by affinity for monoclonal antibodies and by peptide mapping.

Polypeptides preferentially labeled in the G2 phase of the synchronous nuclear replication cycle of Physarum macroplasmodia were compared in electrophoretic mobility and peptide map with the tubulins enriched from Physarum myxamoebae. One major and one minor fluorographic species match the myxamoebal alpha and beta chains, respectively. Thus, tubulins are among the proteins of Physarum selectively synthesized before nuclear division. A third species P, prominently labeled in premitotic plasmodia, is distinct from the two myxamoebal tubulins even though it co-polymerizes with microtubules. The nature of P remains unknown. Two rat monoclonal antibodies directed against yeast tubulin were found to bind selectively to the alpha tubulin of porcine brain. These served to confirm the assignment of the 50,000-dalton Physarum myxamoebal tubulin as an alpha-like polypeptide.

Serological relatedness of mouse-virulent Yersinia enterocolitica.

An antiserum (WA-SAA) was produced which agglutinated specifically with mouse-virulent but not with avirulent strains of Yersinia enterocolitica. Expression of the antigenic determinant(s) reaction with WA-SAA was temperature dependent; for growth temperatures of 20 to 40 degrees C, agglutination titers were lowest for cultures grown at 20 degrees C and highest for cultures grown at 35 to 40 degrees C. Addition of Ca2+ (2.5 to 10 mM) to the growth medium had little effect on the agglutination titer, and gel diffusion studies with monospecific anti-V serum indicated that V antigen was not likely to be the determinant reacting with WA-SAA. Immunohistological studies of Peyer's patches of mice infected with Y. enterocolitica WA revealed that the antigenic determinant(s) reacting with WA-SAA was expressed in vivo. The strong correlation of agglutination titer with mouse virulence and the expression in vivo of the antigenic determinant(s) reacting with WA-SAA suggest that the antigen(s) may be associated with the pathogenicity of Y. enterocolitica.