Characterizing Circumgalactic Gas around Massive Ellipticals at z~0.4 - II. Physical Properties and Elemental Abundances

We present a systematic investigation of the circumgalactic medium (CGM) within projected distances d<160 kpc of luminous red galaxies (LRGs). The sample comprises 16 intermediate-redshift (z=0.21-0.55) LRGs of stellar mass M_star>1e11 M_sun. Combining far-ultraviolet Cosmic Origin Spectrograph spectra from the Hubble Space Telescope and optical echelle spectra from the ground enables a detailed ionization analysis based on resolved component structures of a suite of absorption transitions, including the full HI Lyman series and various ionic metal transitions. By comparing the relative abundances of different ions in individually-matched components, we show that cool gas (T~1e4 K) density and metallicity can vary by more than a factor of ten in in an LRG halo. Specifically, metal-poor absorbing components with <1/10 solar metallicity are seen in 50% of the LRG halos, while gas with solar and super-solar metallicity is also common. These results indicate a complex multiphase structure and poor chemical mixing in these quiescent halos. We calculate the total surface mass density of cool gas, \Sigma_cool, by applying the estimated ionization fraction corrections to the observed HI column densities. The radial profile of \Sigma_cool is best-described by a projected Einasto profile of slope \alpha=1 and scale radius r_s=48 kpc. We find that typical LRGs at z~0.4 contain cool gas mass of M_cool= (1-2) x1e10 M_sun at d<160 kpc (or as much as 4x1e10 M_sun at d<500 kpc), comparable to the cool CGM mass of star-forming galaxies. Furthermore, we show that high-ionization OVI and low-ionization absorption species exhibit distinct velocity profiles, highlighting their different physical origins. We discuss the implications of our findings for the origin and fate of cool gas in LRG halos.Comment: Accepted for publication in MNRAS after a minor revision. 23 pages, 14 figures, and a 29-page Appendix with 27 additional figure

An overview of the Phalaenopsis orchid genome through BAC end sequence analysis

<p>Abstract</p> <p>Background</p> <p><it>Phalaenopsis </it>orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC) end sequences (BESs) can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding.</p> <p>Results</p> <p>We used two BAC libraries (constructed using the <it>Bam</it>HI and <it>Hin</it>dIII restriction enzymes) of <it>Phalaenopsis equestris </it>to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the <it>Bam</it>HI and <it>Hin</it>dIII libraries, respectively), at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the <it>Phalaenopsis </it>genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp) in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6%) were predicted to represent protein-encoding regions, whereas 1,272 (23.0%) contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively), whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs) were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6%) of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or <it>Arabidopsis</it>, and even fewer mapped to the rice genome. This work will facilitate analysis of the <it>Phalaenopsis </it>genome, and will help clarify similarities and differences in genome composition between orchids and other plant species.</p> <p>Conclusion</p> <p>Using BES analysis, we obtained an overview of the <it>Phalaenopsis </it>genome in terms of gene abundance, the presence of repetitive DNA and SSR markers, and the extent of microsynteny with other plant species. This work provides a basis for future physical mapping of the <it>Phalaenopsis </it>genome and advances our knowledge thereof.</p

Paraholcoglossum and Tsiorchis, Two New Orchid Genera Established by Molecular and Morphological Analyses of the Holcoglossum Alliance

BACKGROUND: Holcoglossum is a small orchid genus of 12 species ranging from SW China to Thailand and NE India. Although molecular and morphological analyses have been performed to establish the phylogenetic relationships within this genus, the interspecific relations and its relations with allied genera, such as Rhynchostylis, Aerides and Vanda, remain unclear. METHODOLOGY/PRINCIPAL FINDINGS: In addition to morphological analysis, maximum parsimony, maximum likelihood, and Bayesian inference analyses were performed based on fragments of the nuclear ITS and chloroplast trnL-F and matK genes of 31 taxa (15 Holcoglossum, 14 Aeridinae, 2 outgroups) representing all major clades of the Holcoglossum alliance. The results suggest that Holcoglossum is triphyletic, comprising three clades: the Holcoglossum clade, its sister clade, and a distant clade more closely related to Rhynchostylis, Aerides, and Vanda than to the Holcoglossum clade. The Holcoglossum clade is further divided into three subclades; the genetic distances between these three subclades also support this delimitation. The molecular conclusion is consistent with their distinct morphological characters. CONCLUSIONS: We propose that the latter two clades comprise two new genera, Paraholcoglossum and Tsiorchis, and Holcoglossum clade divides into three sections. In addition, a new section, Holcoglossum sect. Nujiangensia, and a new species, Holcoglossum linearifolium, are proposed. Some new combinations are made, and a new scheme is provided for the classification of all species of Holcoglossum, Paraholcoglossum, and Tsiorchis

Characterizing Circumgalactic Gas around Massive Ellipticals at z ~ 0.4 I. Initial Results

We present a new Hubble Space Telescope (HST) Cosmic Origins Spectrograph (COS) absorption-line survey to study halo gas around 16 luminous red galaxies (LRGs) at z=0.21-0.55. The LRGs are selected uniformly with stellar mass Mstar>1e11 Msun and no prior knowledge of the presence/absence of any absorption features. Based on observations of the full Lyman series, we obtain accurate measurements of neutral hydrogen column density N(HI) and find that high-N(HI) gas is common in these massive quiescent halos with a median of <log N(HI)> = 16.6 at projected distances d<~160 kpc. We measure a mean covering fraction of optically-thick gas with log N(HI)>~17.2 of LLS=0.44^{+0.12}_{-0.11} at d<~160 kpc and LLS=0.71^{+0.11}_{-0.20} at d<~100 kpc. The line-of-sight velocity separations between the HI absorbing gas and LRGs are characterized by a mean and dispersion of =29 km/s and \sigma_v_{gas-gal}=171 km/s. Combining COS FUV and ground-based echelle spectra provides an expanded spectral coverage for multiple ionic transitions, from low-ionization MgII and SiII, to intermediate ionization SiIII and CIII, and to high-ionization OVI absorption lines. We find that intermediate ions probed by CIII and SiIII are the most prominent UV metal lines in LRG halos with a mean covering fraction of _{0.1}=0.75^{+0.08}_{-0.13} for W(977)>=0.1 Ang at d<160 kpc, comparable to what is seen for CIII in L* and sub-L* star-forming and red galaxies but exceeding MgII or OVI in quiescent halos. The COS-LRG survey shows that massive quiescent halos contain widespread chemically-enriched cool gas and that little distinction between LRG and star-forming halos is found in their HI and CIII content.Comment: 19 pages, 6 figures, accepted by MNRA

Comparison of Aspergillus-specific antibody cut-offs for the diagnosis of aspergillosis

BackgroundAspergillus diseases are frequently encountered in patients who are immunocompromised. Without a prompt diagnosis, the clinical consequences may be lethal. Aspergillus-specific antibodies have been widely used to facilitate the diagnosis of Aspergillus diseases. To date, universally standardized cut-off values have not been established. This study aimed to investigate the cut-off values of Aspergillus-specific antibodies and perform a narrative review to depict the geographic differences in the Taiwanese population.MethodsWe analyzed enrolled 118 healthy controls, 29 patients with invasive aspergillosis (IA), chronic pulmonary aspergillosis (CPA), and allergic bronchopulmonary aspergillosis (ABPA) and 99 with disease control, who were tested for Aspergillus fumigatus and Aspergillus niger-specific IgG and IgE using ImmunoCAP. 99 participants not fulfilling the diagnosis of IA, CPA, and ABPA were enrolled in the disease control group. The duration of retrieval of medical records from June 2018 to September 2021. Optimal cut-offs and association were determined using receiver operating characteristic curve (ROC) analysis.ResultsWe found that patients with CPA had the highest A. fumigatus-specific IgG levels while patients with ABPA had the highest A. fumigatus-specific IgE, and A. niger-specific IgG and IgE levels. In patients with CPA and ABPA, the optimal cut-offs of A. fumigatus-specific IgG and A. niger-specific IgG levels were 41.6, 40.8, 38.1, and 69.9 mgA/l, respectively. Geographic differences in the cut-off values of A. fumigatus-specific IgG were also noted. Specifically, the levels were different in eco-climatic zones.ConclusionWe identified the optimal cut-offs of Aspergillus-specific antibodies to facilitate a precise diagnosis of aspergillosis. The observed geographic differences of the antibody levels suggest that an eco-climatic-specific reference is needed to facilitate a prompt and accurate diagnosis of aspergillosis

Increased Risk for Entamoeba histolytica Infection and Invasive Amebiasis in HIV Seropositive Men Who Have Sex with Men in Taiwan

Entamoeba histolytica, morphologically identical to but genetically different from E. dispar and E. moshkovskii, is the causative agent of amebiasis. Recently there have been reports of increased risk for amebiasis among men who have sex with men (MSM) due to oral-anal sexual contact in several developed countries. In this longitudinal follow-up study, the incidence of amebiasis was determined among HIV-infected patients using serological and specific amebic antigen assays. DNA extracted from stool samples containing E. histolytica were analyzed by PCR, sequenced, and compared. Clinical manifestations and treatment response of invasive amebiasis in HIV-infected patients were reviewed. The results demonstrated that HIV-infected MSM were at significantly higher risk of amebiasis than patients from other risk groups. Clustering of E. histolytica isolates by sequencing analyses from geographically unrelated patients suggested person-to-person transmission. Despite immunosuppression, amebic liver abscesses and colitis responded favorably to metronidazole therapy. It is important to investigate in areas of high incidence of both amebiasis and HIV (sub-Saharan Africa) how generalizable these findings are