Abstract
Purpose
Alström Syndrome (AS) is an autosomal recessive hereditary disease with the characteristics of multiorgan dysfunction. Due to the heterogeneity of clinical manifestations of AS, ...genetic testing is crucial for the diagnosis of AS. Herein, we used whole-exome sequencing (WES) to determine the genetic causes and characterize the clinical features of three affected patients in two Chinese families with Alström Syndrome.
Materials and methods
Three affected patients (initially diagnosed as achromatopsia). and five asymptomatic members were recruited for both genetic and clinical tests. The complete ophthalmic examinations and systemic examinations were performed on all participants. Whole exome sequencing (WES) was performed for mutation detection. The silico analysis was also applied to predict the pathogenesis of identified pathogenic variants.
Results
In family 1, the proband showed low vision, hyperopia, photophobia, nystagmus, and total color blindness. DNA analysis revealed that she carried a compound heterozygote with two novel pathogenic variants in the
ALMS1
gene NM_015120.4:c.10379del (NP_055935.4:p.(Asp2252Tyr)) and NM_015120.4:c.11641_11642del (NP_055935.4:p.(Val3881ThrfsTer11)). Further systemic examinations showed short stature, acanthosis nigricans, and sensorineural hearing loss. In family 2, two affected siblings presented the low vision, hyperopia, photophobia, nystagmus, and total color blindness. DNA analysis revealed that they carried a same compound heterozygote with two novel pathogenic variants in the
ALMS1
gene NM_015120.4:c.10379del (NP_055935.4:p.(Asn3460IlefsTer49)), NM_015120.4:c.10819C > T (NP_055935.4:p.(Arg3607Trp)). Further systemic examinations showed obesity and mild abnormalities of lipid metabolism. According to the genetic testing results and further systemic analysis, the three affected patients were finally diagnosed as Alström Syndrome (AS).
Conclusions
We found two new compound heterozygous pathogenic variants of the
ALMS1
gene and determined the diagnosis as Alström Syndrome in three patients of two Chinese families. Our study extends the genotypic and phenotypic spectrums for ALMS1 -AS and emphasizes the importance of gene testing in assisting the clinical diagnosis for cases with phenotypic diversities, which would help the AS patients with early diagnosis and treatment to reduce future systemic damage.
Bacterial alginate lyases, which are members of several polysaccharide lyase (PL) families, have important biological roles and biotechnological applications. The mechanisms for maturation, substrate ...recognition, and catalysis of PL18 alginate lyases are still largely unknown. A PL18 alginate lyase, aly-SJ02, from Pseudoalteromonas sp. 0524 displays a β-jelly roll scaffold. Structural and biochemical analyses indicated that the N-terminal extension in the aly-SJ02 precursor may act as an intramolecular chaperone to mediate the correct folding of the catalytic domain. Molecular dynamics simulations and mutational assays suggested that the lid loops over the aly-SJ02 active center serve as a gate for substrate entry. Molecular docking and site-directed mutations revealed that certain conserved residues at the active center, especially those at subsites +1 and +2, are crucial for substrate recognition. Tyr353 may function as both a catalytic base and acid. Based on our results, a model for the catalysis of aly-SJ02 in alginate depolymerization is proposed. Moreover, although bacterial alginate lyases from families PL5, 7, 15, and 18 adopt distinct scaffolds, they share the same conformation of catalytic residues, reflecting their convergent evolution. Our results provide the foremost insight into the mechanisms of maturation, substrate recognition, and catalysis of a PL18 alginate lyase.
Hormone-sensitive lipases (HSLs) are widely distributed in microorganisms, plants, and animals. Microbial HSLs are classified into two subfamilies, an unnamed new subfamily and the GDSAG motif ...subfamily. Due to the lack of structural information, the detailed catalytic mechanism of the new subfamily is not yet clarified. Based on sequence analysis, we propose to name the new subfamily as the GTSAG motif subfamily. We identified a novel HSL esterase E25, a member of the GTSAG motif subfamily, by functional metagenomic screening, and resolved its structure at 2.05 Å. E25 is mesophilic (optimum temperature at 50 °C), salt-tolerant, slightly alkaline (optimum pH at 8.5) for its activity, and capable of hydrolyzing short chain monoesters (C2–C10). E25 tends to form dimers both in the crystal and in solution. An E25 monomer contains an N-terminal CAP domain, and a classical α/β hydrolase-fold domain. Residues Ser186, Asp282, and His312 comprise the catalytic triad. Structural and mutational analyses indicated that E25 adopts a dimerization pattern distinct from other HSLs. E25 dimer is mainly stabilized by an N-terminal loop intersection from the CAP domains and hydrogen bonds and salt bridges involving seven highly conserved hydrophilic residues from the catalytic domains. Further analysis indicated that E25 also has some catalytic profiles different from other HSLs. Dimerization is essential for E25 to exert its catalytic activity by keeping the accurate orientation of the catalytic Asp282 within the catalytic triad. Our results reveal the structural basis for dimerization and catalysis of an esterase from the GTSAG motif subfamily of the HSL family.
Background: Catalytic mechanisms of GTSAG motif subfamily enzymes of the bacterial hormone-sensitive lipases (HSLs) family are largely unknown.
Results: E25, a GTSAG motif subfamily esterase, adopts a novel dimerization pattern. Dimerization keeps the catalytic Asp282 orientation for E25 catalysis.
Conclusion: Dimerization and some catalytic profiles of E25 are distinctive from other HSLs.
Significance: Our study sheds light on protein folding and evolution of HSLs.
Abstract
Members of the marine
Roseobacter
group are ubiquitous in global oceans, but their cold-adaptive strategies have barely been studied. Here, as represented by
Loktanella salsilacus
strains ...enriched in polar regions, we firstly characterized the metabolic features of a cold-adapted
Roseobacter
by multi-omics, enzyme activities, and carbon utilization procedures. Unlike in most cold-adapted microorganisms, the TCA cycle is enhanced by accumulating more enzyme molecules, whereas genes for thiosulfate oxidation, sulfate reduction, nitrate reduction, and urea metabolism are all expressed at lower abundance when
L. salsilacus
was growing at 5 °C in comparison with higher temperatures. Moreover, a carbon-source competition experiment has evidenced the preferential use of glucose rather than sucrose at low temperature. This selective utilization is likely to be controlled by the carbon source uptake and transformation steps, which also reflects an economic calculation balancing energy production and functional plasticity. These findings provide a mechanistic understanding of how a
Roseobacter
member and possibly others as well counteract polar constraints.
Objectives
There are few studies of metagenomic next-generation sequencing (mNGS) in immunocompromised patients assisted by veno-venous extracorporeal membrane oxygenation (vv-ECMO). The present ...study is aimed to investigate the pathogen-detected effect and clinical therapy value of mNGS technologies in immunocompromised patients assisted by vv-ECMO.
Methods
Our study retrospectively enrolled 46 immunocompromised patients supported by vv-ECMO from Jan 2017 to June 2021 at the First Affiliated Hospital of Zhengzhou University, respectively. Patients were divided into the deterioration group (Group D) (n = 31) and improvement group (Group I) (n = 15) according to their outcomes. Baseline characteristics and etiological data of patients during hospitalization of 2 groups were compared. The pathogens detected by mNGS and antibiotic regimens guided by mNGS in immunocompromised patients assisted by vv-ECMO were analyzed.
Results
Compared with Group I, the deterioration patients showed a higher percentage of chronic obstructive pulmonary disease (COPD) (32.3% vs. 6.7%,
p
< 0.01) and were significantly older (47.77 ± 16.72 years vs. 32 ± 15.05 years,
p
< 0.01). Within 48 h of being ECMO assisted, the consistency of the samples detected by traditional culture and mNGS at the same time was good (traditional culture vs. mNGS detection, the positive rate of bronchoalveolar lavage fluid (BALF) culture: 26.1% vs. 30.4%; the positive rate of blood sample culture: 12.2% vs. 12.2%,
p
> 0.05). However, mNGS detected far more pathogen species and strains than conventional culture (30 strains vs. 78 strains,
p
< 0.01); the most popular pathogen was
Klebsiella pneumoniae
. Parts of patients had their antibiotic treatment adjustments, and the improvement patients showed less usage of broad-spectrum antibiotics.
Conclusions
mNGS may play a relatively important role in detecting mixed pathogens and personalized antibiotic treatment in immunocompromised patients assisted by vv-ECMO.
The climatic impacts of the Tibetan Plateau since the Neogene and the phytogeographic pattern changes of formerly widely‐distributed forest communities on the plateau remain poorly constrained. ...Today, Cercis L. (Fabaceae) is a well‐known arborescent genus typically distributed in subtropical to warm temperate zones of the Northern Hemisphere, and Paleogene fossil occurrences from Eurasia and North America show a long history of the genus in mid‐low latitudes of the Northern Hemisphere. Here, we describe a fossil species, Cercis zekuensis sp. nov. based on well‐preserved fruits from the early Miocene of the northeastern Tibetan Plateau. Detailed morphological comparison (e.g., ventral margin with a veinless wing) of extant and fossil members of Cercis and other genera confirmed validity of the present taxonomic identity. Based on the comparison with extant relatives and their climate preferences, this unexpected occurrence of thermophilic Cercis in northeastern Tibetan Plateau indicates this area had higher temperature and precipitation in the Miocene than today. Integrated with inferred (paleo‐)temperature lapse rates, this indicates a low paleoelevation of less than 2.4 km. In contrast with the present‐day alpine climate here (~3.7 km), such a low elevation facilitated a more favorable habitat with comparatively high biodiversity and warm temperate forests at that time, as were evidenced by co‐occurring megafossils. Moreover, the present existence of Cercis implies the genus was widespread in interior Asia during the early Neogene and shows its modern disjunction or diversification between eastern and central Asia was possibly shaped by the late Cenozoic regional tectonic uplift and consequential environmental deterioration.
Although protease-producing bacteria are key players in the degradation of organic nitrogen and essential for the nitrogen recycling in marine sediments, diversity of both these bacteria and their ...extracellular proteases is still largely unknown. This study investigated the diversity of the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the eutrophied Jiaozhou Bay, China through phylogenetic analysis and protease inhibitor tests. The abundance of the cultivable protease-producing bacteria was up to 10(4) cells/g in all six sediment samples. The cultivated protease-producing bacteria mostly belonged to the phyla Proteobacteria and Firmicutes with the predominant genera being Photobacterium (39.4%), Bacillus (25.8%), and Vibrio (19.7%). Protease inhibitor tests revealed that extracellular proteases secreted by the bacteria were mainly serine proteases and/or metalloproteases with relatively low proportions of cysteine proteases. This study represents the first comprehensive analysis on the diversity of protease-producing bacteria and their extracellular proteases in sediments of a eutrophic bay.
The marine osmolyte dimethylsulfoniopropionate (DMSP) is one of Earth's most abundant organosulfur molecules. Bacterial DMSP lyases cleave DMSP, producing acrylate and dimethyl sulfide (DMS), a ...climate-active gas with roles in global sulfur cycling and atmospheric chemistry. DddY is the only known periplasmic DMSP lyase and is present in β-, γ-, δ- and ε-proteobacteria. Unlike other known DMSP lyases, DddY has not been classified into a protein superfamily, and its structure and catalytic mechanism are unknown. Here, we determined the crystal structure of DddY from the γ-proteobacterium Acinetobacter bereziniae originally isolated from human clinical specimens. This structure revealed that DddY contains a cap domain and a catalytic domain with a Zn2+ bound at its active site. We also observed that the DddY catalytic domain adopts a typical β-barrel fold and contains two conserved cupin motifs. Therefore, we concluded that DddY should belong to the cupin superfamily. Using structural and mutational analyses, we identified key residues involved in Zn2+ coordination, DMSP binding and the catalysis of DMSP cleavage, enabling elucidation of the catalytic mechanism, in which the residue Tyr271 of DddY acts as a general base to attack DMSP. Moreover, sequence analysis suggested that this proposed mechanism is common to DddY proteins from β-, γ-, δ- and ε-proteobacteria. The DddY structure and proposed catalytic mechanism provide a better understanding of how DMSP is catabolized to generate the important climate-active gas DMS.
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•DddY is the only known periplasmic DMSP lyase.•Crystallographic studies indicate that DddY belongs to the cupin superfamily.•The catalytic mechanism is proposed based on structural and mutational analyses.•The proposed mechanism of DddY may have universal significance.
The improvement of the strong force between the coating and the substrate is important to make the coating for solid‐phase microextraction with good stability, durability, and reproducibility during ...thermal and solvent desorption. In this paper, zeolitic imidazolate frameworks‐90 coating was immobilized on the stainless‐steel fiber via the chemical‐bonded method with the help of polydopamine. The fiber was used for the solid‐phase microextraction of lung cancer biomarkers prior to gas chromatography‐mass spectrometry analysis. Several extraction and desorption conditions were optimized. Under the optimized conditions, the established method exhibited high enrichment factors (434–7560), low limits of detection (2.6–4.2 ng/L), wide linear ranges (0.02–30 μg/L), good repeatability (3.46%–9.37% for intra‐day, 4.11%–9.18% for inter‐day, n = 6) and reproducibility (5.37%–7.02%, n = 3). Moreover, the coated fiber is thermally stable and can be reused at least 100 cycles of extraction/desorption/conditioning without significant loss of extraction efficiency and precision. Eventually, the self‐made coated fiber combined with gas chromatography‐mass spectrometry was successfully applied to the extraction and detection of five biomarkers of lung cancer from real breath samples with a satisfactory recovery (96.6%–117.6%).
A Gram-stain-negative, aerobic, ovoid-rod-shaped bacterium, designated strain SM1903
, was isolated from surface seawater of the Mariana Trench. The strain grew at 15-37 °C (optimum, 35 °C) and with ...1-15 % (optimum, 4 %) NaCl. It hydrolysed aesculin but did not reduce nitrate to nitrite and hydrolyse Tween 80. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1903
formed a separate lineage within the family
, sharing the highest 16S rRNA gene sequence similarity with type strains of
(95.7 %) and
(95.7 %). In phylogenetic trees based on single-copy OCs and whole proteins sequences, strain SM1903
fell within a sub-cluster encompassed by
,
and
and formed a branch adjacent to
. The major cellular fatty acids were summed feature 8 (C
7
and/or C
6
), C
and 11-methyl-C
7
. The polar lipids mainly comprised phosphatidylglycerol, phosphatidylcholine, one unidentified lipid, one unidentified aminolipid, and one unidentified glycolipid. The solo respiratory quinone was ubiquinone-10. The genomic DNA G+C content of strain SM1903
was 66.0 mol%. Based on the results of phenotypic, chemotaxonomic, and phylogenetic characterization for strain SM1903
, it is considered to represent a novel species of a novel genus in the family
, for which the name
gen. nov., sp. nov. is proposed. The type strain is SM1903
(=MCCC 1K03608
=KCTC 72046
).
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