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-β, PDGFR, SHH or Notch pathway, and the T cell-excluded immune phenotype. Indeed, targeting fibrosis using a TGF-β 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.

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%.

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.

Mating types and macrocyst formation in Dictyostelium

Macrocysts have been found among strains of Dictyostelium rosarium Raper and Cavender (K. B. Raper and J. C. Cavender, J. Elisha Mitchell Sci. Soc. 84:31-47, 1968). Strains that exhibit mating capabilities could be classified into one of three mating types: A1, A2, or A3. Each mating type was self-incompatible but cross-compatible with the other two types in most cases. No self-fertile strain was observed. Wet conditions, darkness, and moderate nutrient particularly favored macrocyst production; opposite conditions generally favored asexual sorocarp formation. Macrocyst development followed the same morphogenetic pattern reported previously for other species of Dictyostelium. Cultures exposed to light in stages prior to precyst appearance could be switched from macrocyst to sorocarp development. In contrast, precysts always developed into macrocysts despite the presence of light. There appeared to be an "all-or-none" phenomenon in macrocyst production, suggesting that transformation to macrocysts occurred once certain light-sensitive critical factors had reached a threshold level. Intimate association of cells of mating pairs appeared to be essential for macrocyst formation, and no mating hormones were detected.

Periodic synthesis of microtubular proteins in the cell cycle of Physarum

Periodic polypeptide labeling over the naturally synchronous nuclear replication cycle of Physarum polycephalum was analyzed by fluorography of two-dimensional electropherograms. Two sets of polypeptides, denoted as P and Q, showed strong periodicity; they were maximally labeled just prior to mitosis. This periodicity was shown to reflect synthesis rather than turnover or recovery. Both P and Q copolymerized with porcine microtubular proteins and displayed electrophoretic properties similar to those of porcine tubulins. The significance of the periodic synthesis of these microtubular proteins is discussed as a possible component within the chain of events that establishes the high mitotic synchrony of Physarum syncytia.

Nucleoside Diphosphate Sugar-Starch Glucosyl Transferase Activity of wx Starch Granules

Starch granule preparations from the endosperm tissue of all waxy maize (Zea mays L.) mutants tested have low and approximately equal capability to incorporate glucose from adenosine diphosphate glucose into starch. As the substrate concentration is reduced, however, the activity of waxy preparations relative to nonmutant increases until, at the lowest substrate concentration utilized (0.1 muM), the activity of the waxy preparations is nearly equal to that of the nonmutant preparation. The apparent K(m) (adenosine diphosphate glucose) for starch granule preparations from wx-C/wx-C/wx-C endosperms was 7.1 x 10(-5) M, which is compared to 3 x 10(-3) M for preparations from nonwaxy endosperms. Starch granule preparations from three other waxy mutants of independent mutational origin have levels of enzymic activity approximately equal to wx-C at a given substrate concentration giving rise to similar apparent K(m) estimates. We conclude that there is in maize endosperm starch granules a second starch granule-bound glycosyl transferase, whose presence is revealed when mutation eliminates activity of the more active glucosyl transferase catalyzing the same reaction.