Efficient processing of multiple XML twig queries

Master'sMASTER OF SCIENC

Mutational Analysis of Highly Conserved Residues in the Phage PhiC31 Integrase Reveals Key Amino Acids Necessary for the DNA Recombination

Background: Amino acid sequence alignment of phage phiC31 integrase with the serine recombinases family revealed highly conserved regions outside the catalytic domain. Until now, no system mutational or biochemical studies have been carried out to assess the roles of these conserved residues in the recombinaton of phiC31 integrase. Methodology/Principal Findings: To determine the functional roles of these conserved residues, a series of conserved residues were targeted by site-directed mutagenesis. Out of the 17 mutants, 11 mutants showed impaired or no recombination ability, as analyzed by recombination assay both in vivo and in vitro. Results of DNA binding activity assays showed that mutants (R18A, I141A, L143A,E153A, I432A and V571A) exhibited a great decrease in DNA binding affinity, and mutants (G182A/F183A, C374A, C376A/G377A, Y393A and V566A) had completely lost their ability to bind to the specific target DNA attB as compared with wild-type protein. Further analysis of mutants (R18A, I141A, L143A and E153A) synapse and cleavage showed that these mutants were blocked in recombination at the stage of strand cleavage. Conclusions/Significance: This data reveals that some of the highly conserved residues both in the N-terminus and C-terminus region of phiC31 integrase, play vital roles in the substrate binding and cleavage. The cysteine-rich motif and th

Revision of Cyprinus maomingensis Liu 1957 and the first discovery of Procypris-like cyprinid (Teleostei, Pisces) from the late Eocene of South China

Fossil cyprinids from the upper part of the upper Eocene Youganwo Formation of Maoming, Guangdong, China were first studied in 1957 by Liu, who referred the only specimen to the genus Cyprinus as a new species, C. maomingensis. And this was suggested as one of the earliest records for fossil cyprinids. Unfortunately, this specimen is poorly preserved and reveals no more morphological information than its serrated last unbranched dorsal and anal fin rays. Recently, some new specimens were unearthed from the same locality, where C. maomingensis was discovered. In addition to the serrated dorsal and anal fin rays, these new materials also show that the pattern and shape of their pharyngeal teeth obviously differ from that of Cyprinus but resemble that of Procypris. However, its number of the branched dorsal fin rays and number of vertebrae are much less than that in Procypris. Morphologically, these specimens are closer to Procypris than to Cyprinus. This is the first report of fossil Procypris-like fish, and it implies that Procypris-like fish is an early member of the Tribe Cyprinini sensu stricto (sensu Yang et al., 2010) and the origin of this group can be traced back at least to the late Eocene

Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome : Insights from the LUNG SAFE study

Publisher Copyright: © 2020 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.Background: Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study. Methods: In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 ≥ 0.60 during hyperoxemia). Results: Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55-100 mmHg) patients (P = 0.47). Conclusions: Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort. Trial registration: LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073publishersversionPeer reviewe

Seasonal variations in food resource partitioning among four sympatric gudgeon species in the upper Yangtze River

Knowledge of food resource partitioning among sympatric fish species is crucial for understanding the potential mechanisms of species coexistence. Gudgeons (Teleostei: Cyprinidae: Gobioninae) often dominate fish assemblages in the upper Yangtze River. However, little research has been conducted on their trophic interactions. In this paper, seasonal diet and feeding strategy variations of four sympatric gudgeon species, Coreius guichenoti, Coreius heterodon, Rhinogobio ventralis, and Rhinogobio cylindricus, were investigated by analysis of intestinal tract contents, aiming to explore whether food resource partitioning occurred among them. Fish specimens were collected during spring (April-May) and autumn (August-October) in 2010 in Hejiang, a free-flowing stretch of the upper Yangtze River. Coreius guichenoti, C. heterodon, and R. cylindricus showed omnivorous feeding habits, while R. ventralis exhibited an obligate carnivore feeding habit. Diet overlap among the four studied species was high, especially in spring. However, changes in feeding strategies were observed in autumn. Specifically, C. guichenoti and R. cylindricus expanded their dietary niche breadth and consumed detritus, Sinopotamidae or Hydropsychidae as important complementary food resources. In contrast, C. heterodon and R. ventralis reduced their dietary niche breadth and became more specialized on mussels (Limnoperna lacustris). These results confirmed that sympatric fish species can coexist with high diet overlap, and food resource partitioning among these species may also fluctuate with the seasons

Mitochondrial divergence suggests unexpected high species diversity in the opsariichthine fishes (Teleostei: Cyprinidae) and the revalidation of Opsariichthys macrolepis

Opsariichthine (sensu Oceanologi Et Limnologia Sinica, 1982, 13, 293-298) is a cyprinid group consisting of five genera and endemic to East Asia. Previous studies suggested that there may be many possible cryptic species in this group, but this has not been confirmed. In this study, using mitochondrial cyt b sequences on 1,388 samples and 739 haplotypes, we showed very high species diversity within this group. The results showed that phylogenetic relationships of the opsariichthine group were as ([Nipponocypris-Parazacco-Candidia] + [Zacco + Opsariichthys]), and there were multiple deep lineages within several species, flagging putative cryptic species. When a 3% genetic distance was used as a threshold for species delimitation, 35 haplogroups were found, nine haplogroups in Candidia-Parazacco-Nipponocypris group, six haplogroups in the Zacco group, and 20 haplogroups in the Opsariichthys group. We consider all of them to be putative until determination of distinct species based on the tree topology, geographic distributions, or a combination of both. In addition, two kinds of species delimitation tools, ABGD and PTP, were applied to construct molecular operational taxonomic units (MOTUs). The ABGD method revealed nine MOTUs in Candidia-Parazacco-Nipponocypris group, two MOTUs in the Zacco group, and 17 MOTUs in the Opsariichthys group. And the PTP method revealed 10 MOTUs in Candidia-Parazacco-Nipponocypris group, 10 MOTUs in the Zacco group, and 29 MOTUs in the Opsariichthys group. Therefore, there should be more species in the opsariichthine group than presently described. Based on the molecular data and morphological characteristics, we proposed Opsariichthys macrolepis as a valid species and described its morphological diagnostic characters