A genomics-led approach to deciphering the mechanism of thiotetronate antibiotic biosynthesis

Thiolactomycin (TLM) is a thiotetronate antibiotic that selectively targets bacterial fatty acid biosynthesis through inhibition of the β-ketoacyl-acyl carrier protein synthases (KASI/II) that catalyse chain elongation on the type II (dissociated) fatty acid synthase. It has proved effective in in vivo infection models of Mycobacterium tuberculosis and continues to attract interest as a template for drug discovery. We have used a comparative genomics approach to uncover the (hitherto elusive) biosynthetic pathway to TLM and related thiotetronates. Analysis of the whole-genome sequence of Streptomyces olivaceus Tü 3010 producing the more ramified thiotetronate Tü 3010 provided initial evidence that such thiotetronates are assembled by a novel iterative polyketide synthase-nonribosomal peptide synthetase, and revealed the identity of other pathway enzymes, encoded by adjacent genes. Subsequent genome sequencing of three other thiotetronate-producing actinomycetes, including the Lentzea sp. ATCC 31319 that produces TLM, confirmed that near-identical clusters were also present in these genomes. In-frame gene deletion within the cluster for Tü 3010 from Streptomyces thiolactonus NRRL 15439, or within the TLM cluster, led to loss of production of the respective thiotetronate, confirming their identity. Each cluster houses at least one gene encoding a KASI/II enzyme, suggesting plausible mechanisms for self-resistance. A separate genetic locus encodes a cysteine desulfurase and a (thiouridylase-like) sulfur transferase to supply the sulfur atom for thiotetronate ring formation. Transfer of the main Tü 3010 gene cluster (stu gene cluster) into Streptomyces avermitilis led to heterologous production of this thiotetronate, showing that an equivalent sulfur donor can be supplied by this host strain. Mutational analysis of the Tü 3010 and TLM clusters has revealed the unexpected role of a cytochrome P450 enzyme in thiotetronate ring formation. These insights have allowed us to propose a mechanism for sulfur insertion, and have opened the way to engineering of the biosynthesis of TLM and other thiotetronates to produce novel analogues.

Enterococcus faecalis attenuates osteogenesis through activation of p38 and ERK1/2 pathways in MC3T3-E1 cells

AIM

To explore the role of Enterococcus faecalis in the proliferation, apoptosis and differentiation of osteoblasts.

METHODOLOGY

Pre-osteoblastic MC3T3-E1 cells were treated with heat-killed E. faecalis ATCC 29212 and clinical E. faecalis P25RC strains, respectively. Cell proliferation, mineralized calcium deposition, alkaline phosphatase (ALP) activity and apoptosis were assessed at various time-points. The expression levels of osteogenic-related genes including ALP, osteocalcin (OC), runt-related protein 2 (Runx2) and collagen type 1 (COL1) were also analysed throughout the duration of the experiment. Additionally, the involvement of mitogen-activated protein kinases (MAPKs) signalling pathways was analysed by Western blotting. In the presence of culture supernatant from E. faecalis-treated murine macrophages, apoptosis of MC3T3-E1 cells was detected with flow cytometry. Data were analysed using analysis of variance (anova), and P < 0.05 was considered significantly different.

RESULTS

E. faecalis significantly inhibited proliferation (P < 0.05) and also significantly induced apoptosis of MC3T3-E1 cells (P < 0.05), whilst differentiation seemed to be unaffected after 7 days of E. faecalis treatment. However, osteogenic differentiation was significantly inhibited with 21-day E. faecalis treatment (P < 0.05). The p38 and ERK1/2 phosphorylation pathways associated with mineral deposition and apoptosis were significantly activated in MC3T3-E1 cells. The culture supernatants from E. faecalis-treated macrophages induced osteoblast apoptosis.

CONCLUSIONS

E. faecalis exerted an inhibitory effect on osteogenesis in pre-osteoblastic MC3T3-E1 cells via phosphorylation of p38 and ERK1/2.

A survey of outcomes and management of patients post fragility fractures in China

We found that the fragility hip and vertebral fractures caused excess mortality rates in this Chinese female population, which was unexpectedly lower than those in western countries and other Asian countries. This was the first nationwide survey relating to post-fracture outcomes conducted among Chinese population in Mainland China.

INTRODUCTION

This study aimed to investigate the mortality, self-care ability, diagnosis, and medication treatment of osteoporosis following fragility hip and vertebral fractures through a nationwide survey among female patients aged over 50 in Mainland China.

METHODS

This was a multicenter, retrospective cohort study based on medical chart review and patient questionnaire. Female patients aged 50 or older admitted for low-trauma hip or vertebral fractures and discharged from Jan 1, 2008 to Dec 31, 2012 were followed.

RESULTS

Total of 1151 subjects of hip fracture and 842 subjects of vertebral fracture were included. The mean age was 73.4 ± 10.0, and the median of duration from index fracture to interview was 2.6 years. The overall 1-year, 2-year, 3-year, 4-year, and 5-year cumulative mortality rates were 3.5, 7.0, 11.2, 13.1, and 16.9 %, respectively. The first year mortality rates in hip (3.8 %, 95% CI 3.3-4.4 %) and vertebral fracture (3.1 %, 95% CI 2.5-3.7 %) were significantly higher than that in the general population (1.6 %). Impaired self-care ability was observed in 33.2, 40.6, and 23.8 % of overall, hip fracture, and vertebral fracture group, respectively. The overall diagnosis rate of osteoporosis was 56.8 %, and bone mineral density (BMD) measurement had never been conducted in 42.0 % among these women. After the index fracture, 69.6 % of them received supplements and/or anti-osteoporotic medications, among which 39.6 % only received calcium with/without vitamin D supplementation.

CONCLUSIONS

The osteoporotic hip and vertebral fractures caused excess mortality rates in this population of Mainland China. The current diagnosis and medical treatment following the fragility fractures is still insufficient in Mainland China.

Allelic polymorphism of KIR2DL2/2DL3 in a southern Chinese population

KIR2DL2 and KIR2DL3 segregate as alleles of the same killer cell immunoglobulin-like receptor (KIR) gene locus. They have been associated with viral infectious diseases and certain cancers and their allelic information may help to better comprehend mechanisms. The allelic polymorphism of KIR2DL2/2DL3 has been shown to influence their binding specificity and affinity to the HLA-C1 ligands. The present study aims to investigate the distribution of the allelic polymorphism of KIR2DL2/2DL3 in a southern Chinese population using sequence-specific primer polymerase chain reaction (PCR-SSP) and PCR-sequence-based typing (SBT) at the entire coding sequence. Of the 306 tested individuals, 1.96% were positive for KIR2DL2 only, 78.10% for KIR2DL3 only, and 19.93% for both KIR2DL2 and 2DL3. KIR2DL3 showed a high degree of diversity in the study population with 15 alleles detected including 8 novel ones. The predominant 2DL3 allele in the study population is 2DL3*00101 (92.81%) followed by 2DL3*00201 (24.18%), 2DL3*023 (4.25%), and 2DL3*00109 (1.31%). The remaining 11 2DL3 alleles all had a frequency below 1%. Three detected 2DL2 alleles were 2DL2*00301 (18.95%), 2DL2*00101 (3.59%), and the novel 2DL2*013 (0.33%). These results provide further insight into the KIR gene diversity in Southern Chinese and may help to better understand the role played by KIR genes in associated diseases.

A novel KIR2DL3 variant allele, KIR2DL3*032, which has arisen by a missense mutation in codon 231

The novel 2DL3*032 allele differs from the closest allele KIR2DL3*0010101 by a non-synonymous mutation in exon 7.

Cotransplantation of bone marrow mononuclear cells and umbilical cord mesenchymal stem cells in avascular necrosis of the femoral head

OBJECTIVE

We sought to investigate the therapeutic effects of cotransplantation of autologous bone marrow mononuclear cells (BMMNCs) and allogeneic umbilical cord mesenchymal stem cells (UC-MSCs) on avascular necrosis of the femoral head (ANFH).

METHODS

In all, 30 patients (49 hips; 24 males and 6 females) with ANFH were enrolled. According to the system of the Association Research Circulation Osseous, there were 24 hips in phase II and 25 hips in phase Ⅲ. Blood supply to the femoral head was evaluated by using digital subtraction angiography. Generally, 60 to 80 mL of autologous BMMNCs and 30 to 50 mL of UC-MSCs were infused into the femoral head artery. Harris scores including pain and joint function were used to evaluate the effects before and 3, 6, 9, and 12 months after transplantation. Computed tomography and radiographs were performed before and 12 months after the treatment.

RESULTS

Clinical symptoms of pain and claudication were gradually improved. After the treatment, 93.3% (28/30), 86.7% (26/30), and 86.7% (26/30) of patients showed relief of hip pain, improvement of joint function, and extended walking distances, respectively. The Harris scores were increased significantly at 3, 6, and 12 months posttransplant compared with those pretransplant. In addition, the bone lesions in 89.7% of hips (44/49) were improved as showed on computed tomography after transplantation.

CONCLUSION

Cotransplantation of autologous BMMNCs and allogeneic UC-MSCs showed therapeutic effect on ANFH without severe adverse effects.

The anomaly Cu doping effects on LiFeAs superconductors

The Cu substitution effect on the superconductivity of LiFeAs has been studied in comparison with Co/Ni substitution. It is found that the shrinking rate of the lattice parameter c for Cu substitution is much smaller than that of Co/Ni substitution. This is in conjugation with the observation of ARPES that shows almost the same electron and hole Fermi surfaces (FSs) size for undoped and Cu substituted LiFeAs sample, except for a very small hole band sinking below Fermi level with doping. This indicates that there is little doping effect at Fermi surface by Cu substitution, in sharp contrast to the more effective carrier doping effect by Ni or Co.

Activated STING in a vascular and pulmonary syndrome

BACKGROUND

The study of autoinflammatory diseases has uncovered mechanisms underlying cytokine dysregulation and inflammation.

METHODS

We analyzed the DNA of an index patient with early-onset systemic inflammation, cutaneous vasculopathy, and pulmonary inflammation. We sequenced a candidate gene, TMEM173, encoding the stimulator of interferon genes (STING), in this patient and in five unrelated children with similar clinical phenotypes. Four children were evaluated clinically and immunologically. With the STING ligand cyclic guanosine monophosphate-adenosine monophosphate (cGAMP), we stimulated peripheral-blood mononuclear cells and fibroblasts from patients and controls, as well as commercially obtained endothelial cells, and then assayed transcription of IFNB1, the gene encoding interferon-β, in the stimulated cells. We analyzed IFNB1 reporter levels in HEK293T cells cotransfected with mutant or nonmutant STING constructs. Mutant STING leads to increased phosphorylation of signal transducer and activator of transcription 1 (STAT1), so we tested the effect of Janus kinase (JAK) inhibitors on STAT1 phosphorylation in lymphocytes from the affected children and controls.

RESULTS

We identified three mutations in exon 5 of TMEM173 in the six patients. Elevated transcription of IFNB1 and other gene targets of STING in peripheral-blood mononuclear cells from the patients indicated constitutive activation of the pathway that cannot be further up-regulated with stimulation. On stimulation with cGAMP, fibroblasts from the patients showed increased transcription of IFNB1 but not of the genes encoding interleukin-1 (IL1), interleukin-6 (IL6), or tumor necrosis factor (TNF). HEK293T cells transfected with mutant constructs show elevated IFNB1 reporter levels. STING is expressed in endothelial cells, and exposure of these cells to cGAMP resulted in endothelial activation and apoptosis. Constitutive up-regulation of phosphorylated STAT1 in patients' lymphocytes was reduced by JAK inhibitors.

CONCLUSIONS

STING-associated vasculopathy with onset in infancy (SAVI) is an autoinflammatory disease caused by gain-of-function mutations in TMEM173. (Funded by the Intramural Research Program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases; ClinicalTrials.gov number, NCT00059748.).

Activated STING in a vascular and pulmonary syndrome

BACKGROUND

The study of autoinflammatory diseases has uncovered mechanisms underlying cytokine dysregulation and inflammation.

METHODS

We analyzed the DNA of an index patient with early-onset systemic inflammation, cutaneous vasculopathy, and pulmonary inflammation. We sequenced a candidate gene, TMEM173, encoding the stimulator of interferon genes (STING), in this patient and in five unrelated children with similar clinical phenotypes. Four children were evaluated clinically and immunologically. With the STING ligand cyclic guanosine monophosphate-adenosine monophosphate (cGAMP), we stimulated peripheral-blood mononuclear cells and fibroblasts from patients and controls, as well as commercially obtained endothelial cells, and then assayed transcription of IFNB1, the gene encoding interferon-β, in the stimulated cells. We analyzed IFNB1 reporter levels in HEK293T cells cotransfected with mutant or nonmutant STING constructs. Mutant STING leads to increased phosphorylation of signal transducer and activator of transcription 1 (STAT1), so we tested the effect of Janus kinase (JAK) inhibitors on STAT1 phosphorylation in lymphocytes from the affected children and controls.

RESULTS

We identified three mutations in exon 5 of TMEM173 in the six patients. Elevated transcription of IFNB1 and other gene targets of STING in peripheral-blood mononuclear cells from the patients indicated constitutive activation of the pathway that cannot be further up-regulated with stimulation. On stimulation with cGAMP, fibroblasts from the patients showed increased transcription of IFNB1 but not of the genes encoding interleukin-1 (IL1), interleukin-6 (IL6), or tumor necrosis factor (TNF). HEK293T cells transfected with mutant constructs show elevated IFNB1 reporter levels. STING is expressed in endothelial cells, and exposure of these cells to cGAMP resulted in endothelial activation and apoptosis. Constitutive up-regulation of phosphorylated STAT1 in patients' lymphocytes was reduced by JAK inhibitors.

CONCLUSIONS

STING-associated vasculopathy with onset in infancy (SAVI) is an autoinflammatory disease caused by gain-of-function mutations in TMEM173. (Funded by the Intramural Research Program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases; ClinicalTrials.gov number, NCT00059748.).

Identification of the novel KIR3DL1*01505 allele from southern Chinese Han individual

The novel KIR3DL1*01505 allele differs from the closest allele KIR3DL1*0150201 by a single silent mutation.

The Processing Behavior of Liquid Sn/Molten Polyethylene during Internal Mixing

In our study, liquid tin (Sn) was mixed with molten polyethylene using an internal mixer; the interfacial tension between the liquid Sn and molten polyethylene was measured using the deformed drop retraction method. The results showed that liquid Sn separated when the Sn content was higher than approximately 2 % by volume because of the interfacial tension of up to 167 mN/m and the 106-fold viscosity difference between the liquid Sn and the molten polyethylene. When Sn separation did not occur, the effects of the mixing time and rotary speed on the degree of mixing and the Sn particle size were analyzed using thermogravimetric analysis and scanning electron microscopy. The results showed that the effects of mixing time and rotary speed on the degree of mixing and Sn particle size can be combined as the impact of specific energy input. With increasing specific energy input, the degree of mixing initially increased and subsequently remained constant, while the Sn particle size initially decreased and subsequently remained constant. The refinement of the dispersed phase was completed with a low specific energy input, but the homogenization of the dispersed phase required a higher specific energy input to achieve completion, revealing the relationship between distributive mixing and dispersive mixing.

VNP: Interactive Visual Network Pharmacology of Diseases, Targets, and Drugs

In drug discovery, promiscuous targets, multifactorial diseases, and "dirty" drugs construct complex network relationships. Network pharmacology description and analysis not only give a systems-level understanding of drug action and disease complexity but can also help to improve the efficiency of target selection and drug design. Visual network pharmacology (VNP) is developed to visualize network pharmacology of targets, diseases, and drugs with a graph network by using disease, target or drug names, chemical structures, or protein sequence. To our knowledge, VNP is the first free interactive VNP server that should be very helpful for systems pharmacology research. VNP is freely available at http://cadd.whu.edu.cn/ditad/vnpsearch.

Anatomical research on the subacromial interval following implantation of clavicle hook plates

This article aimed to explore whether hook plate implantation significantly narrowed the subacromial space. 24 shoulder joints were implanted with clavicle hook plates. A Vernier caliper was used to measure the length and thickness of the acromion. In addition, the length and thickness of the hook of the plate were measured. The data from all measurements recorded were divided into 2 groups Group A, the length group: the length of acromion and the hook, and Group B, the thickness group: the thickness of acromion and the depth of hook. There are significant statistical differences when comparing between the subgroups within each group. The depth of the hook exceeds the thickness of the acromion (12.41±2.80 mm vs. 10.44±2.59 mm, respectively), the hook plate implantation significantly narrowed the subacromial space by 1.97±1.19 mm (p<0.01), and the length of the hook was shorter than that of the acromion by 9.75±3.64 mm (p<0.01). Our findings revealed that the hook plate with only 3 depths could not match the acromion satisfactorily and the hook plate implantation significantly narrowed the subacromial space. A hook plate with a variable depth, which can match better with patient's anatomy, is worthy of further investigation in the future.

Characterization of the novel HLA-DPA1*02:05 allele identified by sequence-based typing

The novel HLA-DPA1*02:05 variant allele differs from the closest allele DPA1*02:02:02.