Synthetic symbiosis combining plasmid displacement enables rapid construction of phenotype-stable strains

Plasmid-based microbial systems have been a major workhorse for chemical and pharmaceutical production. The biosafety issues and elevated industrial cost of antibiotic usage have led to the development of alternative strategies for plasmid selection and maintenance. Such strategies, including auxotrophy complementation, post-segregational killing, operator-repressor and RNA-based interactions often require extensive engineering of various elements and may result in extra metabolic burden in the cells. Herein, we report a design of synthetic symbiosis combining plasmid displacement to construct a phenotype-stable microbial system. By sequestrating an endogenous essential gene folP, cells obtained long-term plasmid maintenance with minimum cost. The phenotype performance was also inherited for up to 80 generations demonstrated by the production of salicylic acid in Escherichia coli. Meanwhile, the temperature-induced curing method of the intermediate plasmids enables rapid engineering. This design can lead to broad applications as a reliable and convenient plasmid-based expression system.

Development and validation of nomograms predicting survival in Chinese patients with triple negative breast cancer

Background

Triple negative breast cancer (TNBC) is an aggressive and heterogeneous disease. Nomograms predicting outcomes of TNBC are needed for risk management.

Methods

Nomograms were based on an analysis of 296 non-metastatic TNBC patients treated at Sun Yat-sen Memorial Hospital from 2002 to 2014. The end points were disease-free survival (DFS) and overall survival (OS). Predictive accuracy and discriminative ability were evaluated by concordance index (C-index), area under the curve (AUC) and calibration curve, and compared with the American Joint Committee on Cancer (AJCC) staging system, PREDICT and CancerMath. Models were subjected to bootstrap internal validation and external validation using independent cohorts of 191 patients from the second Xiangya Hospital and Peking University Shenzhen Hospital between 2007 and 2012.

Results

On multivariable analysis of training cohort, independent prognostic factors were stromal tumor-infiltrating lymphocytes (TILs), tumor size, node status, and Ki67 index, which were then selected into the nomograms. The calibration curves for probability of DFS and OS showed optimal agreement between nomogram prediction and actual observation. The C-index of nomograms was significantly higher than that of the seventh and eighth AJCC staging system for predicting DFS (training: 0.743 vs 0.666 (P = 0.003) and 0.664 (P = 0.024); validation: 0.784 vs 0.632 (P = 0.02) and 0.607 (P = 0.002)) and OS (training: 0.791 vs 0.683 (P = 0.004) and 0.677 (P < 0.001); validation: 0.783 vs 0.656 (P = 0.006) and 0.606 (P = 0.001)). Our nomograms had larger AUCs compared with PREDICT and CancerMath. In addition, the nomograms showed good performance in stratifying different risk groups of patients both in the training and validation cohorts.

Conclusion

We have developed novel and practical nomograms that can provide individual prediction of DFS and OS for TNBC based on stromal TILs, tumor size, node status, and Ki67 index. Our nomograms may help clinicians in risk consulting and selection of long term survivors.

Electronic supplementary material

The online version of this article (10.1186/s12885-019-5703-4) contains supplementary material, which is available to authorized users.

Increased diagnostic yield by reanalysis of data from a hearing loss gene panel

Background

Congenital hearing loss affects approximately 1–2 infants out of every 1000, with 50% of the cases resulting from genetic factors. Targeted gene panels have been widely used for genetic diagnosis of hearing loss. This study aims to reveal new diagnoses via reanalyzing historical data of a multigene panel, and exam the reasons for new diagnoses.

Methods

A total of 210 samples were enlisted, including clinical reports and sequencing data of patients with congenital/prelingual hearing loss who were referred to clinical genetic testing from October 2014 to June 2017. All variants listed on the original clinical reports were reinterpreted according to the standards and guidelines recommended by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP). Expanded analysis of raw data were performed in undiagnosed cases.

Results

Re-analysis resulted in nine new diagnoses, improving the overall diagnostic rate from 39 to 43%. New diagnoses were attributed to newly published clinical evidence in the literature, adoption of new interpretation guidelines and expanded analysis range.

Conclusion

This work demonstrates benefits of reanalysis of targeted gene panel data, indicating that periodical reanalysis should be performed in clinical practice.

Electronic supplementary material

The online version of this article (10.1186/s12920-019-0531-6) contains supplementary material, which is available to authorized users.

Sensing single atoms in a cavity using a broadband squeezed light

We investigate a single atom cavity-QED system directly driven by a broadband squeezed light. We demonstrate how the squeezed radiation can be used to sense the presence of a single atom in a cavity. This happens by transferring one of the photons from the field in a state with an even number of photons to the atom and thereby populating an odd number of Fock states. Specifically, the presence of the atom is sensed by remarkable changing in the presence of one photon and the loss of squeezing of the cavity field. A complete study of quantum fluctuations and the excitation of multiphoton transitions is given.

Biting pain reproduced by the Tooth Slooth: an aid for early diagnosis of cracked tooth

OBJECTIVE

The purpose of this study was to find a reliable method to reproduce biting pain to facilitate an early diagnosis of cracked tooth and to verify the feasibility of the Tooth Slooth in diagnosing a cracked tooth.

METHOD AND MATERIALS

In this study, 46 intact teeth diagnosed as cracked teeth were selected. Patients were asked to bite wet cotton rolls and the Tooth Slooth, and clinical findings were recorded. The difference in the relevance ratio between these two bite test methods was determined.

RESULTS

The relevance ratio of biting pain by the Tooth Slooth and wet cotton rolls was 91.3% and 32.6%, respectively. There was a statistically significant difference between these two bite tests (P < .001).

CONCLUSIONS

Within the limitations of this study, the relevance ratio of biting pain by the Tooth Slooth was significantly higher than that of the wet cotton rolls. The Tooth Slooth was a reliable method to reproduce biting pain and was useful for early diagnosis of cracked teeth.

Does the radiologist need to rescan the breast lesion to validate the final BI-RADS US assessment made on the static images in the diagnostic setting?

Purpose: To assess whether radiologist needs to rescan the breast lesion to validate the final American College of Radiology (ACR) Breast Imaging Reporting and Data System (BI-RADS) ultrasonography (US) assessment made on the static images in the diagnostic setting.

Patients and methods: Image data on 1,070 patients with 1,070 category 3–5 breast lesions with a pathological diagnosis scanned between January and June 2016 were included. Both real-time and static image assessments were acquired for each lesion. The diagnostic performance was evaluated by receiver operating characteristic (ROC) curves. The positive predictive values (PPVs) of each category in the two groups were calculated according to the ACR BI-RADS manual and compared. Kappas were determined for agreement on two assessment approaches.

Results: The sensitivity, specificity, PPV, and negative predictive value for real-time US were 98.9%, 58.2%, 44.8% and 99.4%, and for static images were 98.9%, 57.1%, 44.1% and 99.3%, respectively. The performance of the two groups was not significantly different (areas under ROCs: 0.786 vs 0.780, P=0.566) if the final assessment was only dichotomized as negative (category 3) and positive (categories 4 and 5). All PPVs of each category for each assessment were within the reference range provided by the ACR in 2013 except subcategory 4B (reference range: >10% and ≤50%) of static image evaluation, which was also significantly higher than that of real-time assessment (54.8% vs 40.7%, P=0.037). The overall agreement of the two approaches was moderate (κ=0.43–0.56 according to different detailed assessment).

Conclusion: Both static image and real-time assessment had similar diagnostic performance if only the treatment recommendations were considered, that is, follow-up or biopsy. However, as for subcategory 4B lesions without obviously benign or malignant US features, real-time scanning by the interpreter is recommended to obtain a more accurate BI-RADS assessment after assessing static images.

Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases

Background

Exome sequencing (ES) has been successfully applied in clinical detection of single nucleotide variants (SNVs) and small indels. However, identification of copy number variants (CNVs) using ES data remains challenging. The purpose of this study is to understand the contribution of CNVs and copy neutral runs of homozygosity (ROH) in molecular diagnosis of patients referred for ES.

Methods

In a cohort of 11,020 consecutive ES patients, an Illumina SNP array analysis interrogating mostly coding SNPs was performed as a quality control (QC) measurement and for CNV/ROH detection. Among these patients, clinical chromosomal microarray analysis (CMA) was performed at Baylor Genetics (BG) on 3229 patients, either before, concurrently, or after ES. We retrospectively analyzed the findings from CMA and the QC array.

Results

The QC array can detect ~ 70% of pathogenic/likely pathogenic CNVs (PCNVs) detectable by CMA. Out of the 11,020 ES cases, the QC array identified PCNVs in 327 patients and uniparental disomy (UPD) disorder-related ROH in 10 patients. The overall PCNV/UPD detection rate was 5.9% in the 3229 ES patients who also had CMA at BG; PCNV/UPD detection rate was higher in concurrent ES and CMA than in ES with prior CMA (7.2% vs 4.6%). The PCNVs/UPD contributed to the molecular diagnoses in 17.4% (189/1089) of molecularly diagnosed ES cases with CMA and were estimated to contribute in 10.6% of all molecularly diagnosed ES cases. Dual diagnoses with both PCNVs and SNVs were detected in 38 patients. PCNVs affecting single recessive disorder genes in a compound heterozygous state with SNVs were detected in 4 patients, and homozygous deletions (mostly exonic deletions) were detected in 17 patients. A higher PCNV detection rate was observed for patients with syndromic phenotypes and/or cardiovascular abnormalities.

Conclusions

Our clinical genomics study demonstrates that detection of PCNV/UPD through the QC array or CMA increases ES diagnostic rate, provides more precise molecular diagnosis for dominant as well as recessive traits, and enables more complete genetic diagnoses in patients with dual or multiple molecular diagnoses. Concurrent ES and CMA using an array with exonic coverage for disease genes enables most effective detection of both CNVs and SNVs and therefore is recommended especially in time-sensitive clinical situations.

Electronic supplementary material

The online version of this article (10.1186/s13073-019-0639-5) contains supplementary material, which is available to authorized users.

Case report and novel treatment of an autosomal recessive Leigh syndrome caused by short-chain enoyl-CoA hydratase deficiency

Short chain enoyl-CoA hydratase (SCEH) deficiency leads to a severe form of autosomal recessive Leigh syndrome with inevitable neurological decline and early mortality. SCEH is most notably involved in valine catabolism, a deficiency of which results in various metabolic alterations, including increased levels of the highly reactive metabolite 2-methacrylyl-CoA. With no proven treatments available to date, it has been speculated that patients may respond to a valine restricted diet and/or N-acetylcysteine supplementation, as suggested by early studies of a very similar inborn error of metabolism, 3-hydroxyisobutyryl-CoA hydrolase deficiency. We describe a patient with typical Leigh syndrome clinical findings and identified compound heterozygous variants in ECSH1. Valine-restricted diet was initiated at 6 months of age and N-acetylcysteine supplementation at 9 months with subsequent improvement in growth and slow progress in developmental milestones. However, at 15 months, the patient aspirated during a breakthrough seizure from which he did not recover and died soon after from related complications. This report highlights some of the challenges that remain in the management and treatment of SCEH deficiency, while demonstrating that a valine restricted diet and N-acetylcysteine can be safely administered with the potential for clinical improvement.

Incidentally identified genetic variants in arrhythmogenic right ventricular cardiomyopathy-associated genes among children undergoing exome sequencing reflect healthy population variation

BACKGROUND

With expanding use of clinical whole exome sequencing (WES), genetic variants of uncertain significance are increasingly identified. As pathologic mutations in genes associated with arrhythmogenic right ventricular cardiomyopathy (ARVC) carry a risk of sudden death, determining the diagnostic relevance of incidentally identified variants associated with these genes is critical.

METHODS

WES variants from a large, predominantly pediatric cohort (N = 7,066 probands) were obtained for nine ARVC-associated genes (Baylor Miraca). For comparison, a control cohort was derived from the gnomAD database and an ARVC case cohort (N = 1,379 probands) was established from ARVC cases in the literature. Topologic mapping was performed and signal-to-noise analysis was conducted normalizing WES, or case variants, against control variant frequencies. Retrospective chart review was performed of WES cases evaluated clinically (Texas Children's Hospital).

RESULTS

Incidentally identified variants occurred in 14% of WES referrals and localized to genes which were rare among ARVC cases yet similar to controls. Amino acid-level signal-to-noise analysis of cases demonstrated "pathologic hotspots" localizing to critical domains of PKP2 and DSG2 while WES variants did not. PKP2 ARM7 and ARM8 domains and DSG2 N-terminal cadherin-repeat domains demonstrated high pathogenicity while normalized WES variant frequency was low. Review of clinical data available on WES referrals demonstrated none with evidence of ARVC among variant-positive individuals.

CONCLUSIONS

Incidentally identified variants are common among pediatric WES testing with gene frequencies similar to "background" variants. Incidentally identified variants are unlikely to be pathologic.

Biallelic loss-of-function P4HTM gene variants cause hypotonia, hypoventilation, intellectual disability, dysautonomia, epilepsy, and eye abnormalities (HIDEA syndrome)

PURPOSE

A new syndrome with hypotonia, intellectual disability, and eye abnormalities (HIDEA) was previously described in a large consanguineous family. Linkage analysis identified the recessive disease locus, and genome sequencing yielded three candidate genes with potentially pathogenic biallelic variants: transketolase (TKT), transmembrane prolyl 4-hydroxylase (P4HTM), and ubiquitin specific peptidase 4 (USP4). However, the causative gene remained elusive.

METHODS

International collaboration and exome sequencing were used to identify new patients with HIDEA and biallelic, potentially pathogenic, P4HTM variants. Segregation analysis was performed using Sanger sequencing. P4H-TM wild-type and variant constructs without the transmembrane region were overexpressed in insect cells and analyzed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and western blot.

RESULTS

Five different homozygous or compound heterozygous pathogenic P4HTM gene variants were identified in six new and six previously published patients presenting with HIDEA. Hypoventilation, obstructive and central sleep apnea, and dysautonomia were identified as novel features associated with the phenotype. Characterization of three of the P4H-TM variants demonstrated yielding insoluble protein products and, thus, loss-of-function.

CONCLUSIONS

Biallelic loss-of-function P4HTM variants were shown to cause HIDEA syndrome. Our findings enable diagnosis of the condition, and highlight the importance of assessing the need for noninvasive ventilatory support in patients.

A toolkit for genetics providers in follow-up of patients with non-diagnostic exome sequencing

There are approximately 7,000 rare diseases affecting 25-30 million Americans, with 80% estimated to have a genetic basis. This presents a challenge for genetics practitioners to determine appropriate testing, make accurate diagnoses, and conduct up-to-date patient management. Exome sequencing (ES) is a comprehensive diagnostic approach, but only 25%-41% of the patients receive a molecular diagnosis. The remaining three-fifths to three-quarters of patients undergoing ES remain undiagnosed. The Stanford Center for Undiagnosed Diseases (CUD), a clinical site of the Undiagnosed Diseases Network, evaluates patients with undiagnosed and rare diseases using a combination of methods including ES. Frequently these patients have non-diagnostic ES results, but strategic follow-up techniques identify diagnoses in a subset. We present techniques used at the CUD that can be adopted by genetics providers in clinical follow-up of cases where ES is non-diagnostic. Solved case examples illustrate different types of non-diagnostic results and the additional techniques that led to a diagnosis. Frequent approaches include segregation analysis, data reanalysis, genome sequencing, additional variant identification, careful phenotype-disease correlation, confirmatory testing, and case matching. We also discuss prioritization of cases for additional analyses.

Loss-of-function mutations in Lysyl-tRNA synthetase cause various leukoencephalopathy phenotypes

OBJECTIVE

To expand the clinical spectrum of lysyl-tRNA synthetase (KARS) gene-related diseases, which so far includes Charcot-Marie-Tooth disease, congenital visual impairment and microcephaly, and nonsyndromic hearing impairment.

METHODS

Whole-exome sequencing was performed on index patients from 4 unrelated families with leukoencephalopathy. Candidate pathogenic variants and their cosegregation were confirmed by Sanger sequencing. Effects of mutations on KARS protein function were examined by aminoacylation assays and yeast complementation assays.

RESULTS

Common clinical features of the patients in this study included impaired cognitive ability, seizure, hypotonia, ataxia, and abnormal brain imaging, suggesting that the CNS involvement is the main clinical presentation. Six previously unreported and 1 known KARS mutations were identified and cosegregated in these families. Two patients are compound heterozygous for missense mutations, 1 patient is homozygous for a missense mutation, and 1 patient harbored an insertion mutation and a missense mutation. Functional and structural analyses revealed that these mutations impair aminoacylation activity of lysyl-tRNA synthetase, indicating that defective KARS function is responsible for the phenotypes in these individuals.

CONCLUSIONS

Our results demonstrate that patients with loss-of-function KARS mutations can manifest CNS disorders, thus broadening the phenotypic spectrum associated with KARS-related disease.

Extracutaneous manifestations in phacomatosis cesioflammea and cesiomarmorata: Case series and literature review

Phacomatosis pigmentovascularis (PPV) comprises a family of rare conditions that feature vascular abnormalities and melanocytic lesions that can be solely cutaneous or multisystem in nature. Recently published work has demonstrated that both vascular and melanocytic abnormalities in PPV of the cesioflammea and cesiomarmorata subtypes can result from identical somatic mosaic activating mutations in the genes GNAQ and GNA11. Here, we present three new cases of PPV with features of the cesioflammea and/or cesiomarmorata subtypes and mosaic mutations in GNAQ or GNA11. To better understand the risk of potentially occult complications faced by such patients we additionally reviewed 176 cases published in the literature. We report the frequency of clinical findings, their patterns of co-occurrence as well as published recommendations for surveillance after diagnosis. Features assessed include: capillary malformation; dermal and ocular melanocytosis; glaucoma; limb asymmetry; venous malformations; and central nervous system (CNS) anomalies, such as ventriculomegaly and calcifications. We found that ocular findings are common in patients with phacomatosis cesioflammea and cesiomarmorata. Facial vascular involvement correlates with a higher risk of seizures (p = .0066). Our genetic results confirm the role of mosaic somatic mutations in GNAQ and GNA11 in phacomatosis cesioflammea and cesiomarmorata. Their clinical and molecular findings place these conditions on a clinical spectrum encompassing other GNAQ and GNA11 related disorders and inform recommendations for their management.

Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel

PURPOSE

To provide a validated method to confidently identify exon-containing copy-number variants (CNVs), with a low false discovery rate (FDR), in targeted sequencing data from a clinical laboratory with particular focus on single-exon CNVs.

METHODS

DNA sequence coverage data are normalized within each sample and subsequently exonic CNVs are identified in a batch of samples, when the target log₂ ratio of the sample to the batch median exceeds defined thresholds. The quality of exonic CNV calls is assessed by C-scores (Z-like scores) using thresholds derived from gold standard samples and simulation studies. We integrate an ExonQC threshold to lower FDR and compare performance with alternate software (VisCap).

RESULTS

Thirteen CNVs were used as a truth set to validate Atlas-CNV and compared with VisCap. We demonstrated FDR reduction in validation, simulation, and 10,926 eMERGESeq samples without sensitivity loss. Sixty-four multiexon and 29 single-exon CNVs with high C-scores were assessed by Multiplex Ligation-dependent Probe Amplification (MLPA).

CONCLUSION

Atlas-CNV is validated as a method to identify exonic CNVs in targeted sequencing data generated in the clinical laboratory. The ExonQC and C-score assignment can reduce FDR (identification of targets with high variance) and improve calling accuracy of single-exon CNVs respectively. We propose guidelines and criteria to identify high confidence single-exon CNVs.

Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability

Acetylation of the lysine residues in histones and other DNA-binding proteins plays a major role in regulation of eukaryotic gene expression. This process is controlled by histone acetyltransferases (HATs/KATs) found in multiprotein complexes that are recruited to chromatin by the scaffolding subunit transformation/transcription domain-associated protein (TRRAP). TRRAP is evolutionarily conserved and is among the top five genes intolerant to missense variation. Through an international collaboration, 17 distinct de novo or apparently de novo variants were identified in TRRAP in 24 individuals. A strong genotype-phenotype correlation was observed with two distinct clinical spectra. The first is a complex, multi-systemic syndrome associated with various malformations of the brain, heart, kidneys, and genitourinary system and characterized by a wide range of intellectual functioning; a number of affected individuals have intellectual disability (ID) and markedly impaired basic life functions. Individuals with this phenotype had missense variants clustering around the c.3127G>A p.(Ala1043Thr) variant identified in five individuals. The second spectrum manifested with autism spectrum disorder (ASD) and/or ID and epilepsy. Facial dysmorphism was seen in both groups and included upslanted palpebral fissures, epicanthus, telecanthus, a wide nasal bridge and ridge, a broad and smooth philtrum, and a thin upper lip. RNA sequencing analysis of skin fibroblasts derived from affected individuals skin fibroblasts showed significant changes in the expression of several genes implicated in neuronal function and ion transport. Thus, we describe here the clinical spectrum associated with TRRAP pathogenic missense variants, and we suggest a genotype-phenotype correlation useful for clinical evaluation of the pathogenicity of the variants.

Quantum photonic transistor controlled by an atom in a Floquet cavity-QED system

The photon transmission of a Floquet cavity quantum electrodynamic (QED) system containing three periodically modulated cavities interacting with a two-level atom is investigated. The input-output relations and the second-order correlation functions of the output fields are calculated. The system demonstrates the feature of a quantum photonic transistor, i.e., the photon transmission is controlled by the quantum states of the atom. This device can be used as a building block for various quantum information processing.

Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies

PURPOSE

Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes from a clinical exome perspective.

METHODS

We retrospectively studied patients referred for clinical exome sequencing (CES, N = 10,698). Patients with causative variants in novel or recently described cohesinopathy genes were enrolled for phenotypic characterization.

RESULTS

Pathogenic or likely pathogenic single-nucleotide and insertion/deletion variants (SNVs/indels) were identified in established disease genes including NIPBL (N = 5), SMC1A (N = 14), SMC3 (N = 4), RAD21 (N = 2), and HDAC8 (N = 8). The phenotypes in this genetically defined cohort skew towards the mild end of CdLS spectrum as compared with phenotype-driven cohorts. Candidate or recently reported cohesinopathy genes were supported by de novo SNVs/indels in STAG1 (N = 3), STAG2 (N = 5), PDS5A (N = 1), and WAPL (N = 1), and one inherited SNV in PDS5A. We also identified copy-number deletions affecting STAG1 (two de novo, one of unknown inheritance) and STAG2 (one of unknown inheritance). Patients with STAG1 and STAG2 variants presented with overlapping features yet without characteristic facial features of CdLS.

CONCLUSION

CES effectively identified disease-causing alleles at the mild end of the cohensinopathy spectrum and enabled characterization of candidate disease genes.

De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome

BACKGROUND

Neurodevelopmental disorders are genetically and phenotypically heterogeneous encompassing developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), structural brain abnormalities, and neurological manifestations with variants in a large number of genes (hundreds) associated. To date, a few de novo mutations potentially disrupting TCF20 function in patients with ID, ASD, and hypotonia have been reported. TCF20 encodes a transcriptional co-regulator structurally related to RAI1, the dosage-sensitive gene responsible for Smith-Magenis syndrome (deletion/haploinsufficiency) and Potocki-Lupski syndrome (duplication/triplosensitivity).

METHODS

Genome-wide analyses by exome sequencing (ES) and chromosomal microarray analysis (CMA) identified individuals with heterozygous, likely damaging, loss-of-function alleles in TCF20. We implemented further molecular and clinical analyses to determine the inheritance of the pathogenic variant alleles and studied the spectrum of phenotypes.

RESULTS

We report 25 unique inactivating single nucleotide variants/indels (1 missense, 1 canonical splice-site variant, 18 frameshift, and 5 nonsense) and 4 deletions of TCF20. The pathogenic variants were detected in 32 patients and 4 affected parents from 31 unrelated families. Among cases with available parental samples, the variants were de novo in 20 instances and inherited from 4 symptomatic parents in 5, including in one set of monozygotic twins. Two pathogenic loss-of-function variants were recurrent in unrelated families. Patients presented with a phenotype characterized by developmental delay, intellectual disability, hypotonia, variable dysmorphic features, movement disorders, and sleep disturbances.

CONCLUSIONS

TCF20 pathogenic variants are associated with a novel syndrome manifesting clinical characteristics similar to those observed in Smith-Magenis syndrome. Together with previously described cases, the clinical entity of TCF20-associated neurodevelopmental disorders (TAND) emerges from a genotype-driven perspective.

The Effectiveness and Safety of Utilizing Mobile Phone-Based Programs for Rehabilitation After Lumbar Spinal Surgery: Multicenter, Prospective Randomized Controlled Trial

Background

Rehabilitation is crucial for postoperative patients with low back pain (LBP). However, the implementation of traditional clinic-based programs is limited in developing countries, such as China, because of the maldistribution of medical resources. Mobile phone–based programs may be a potential substitute for those who have no access to traditional rehabilitation.

Objective

The aim of this study was to examine the efficacy of mobile phone–based rehabilitation systems in patients who underwent lumbar spinal surgery.

Methods

Patients who accepted spinal surgeries were recruited and randomized into 2 groups of rehabilitation treatments: (1) a mobile phone–based eHealth (electronic health) program (EH) or (2) usual care treatment (UC). The primary outcomes were (1) function and pain status assessed by the Oswestry Disability Index (ODI) and (2) the visual analog scale (VAS). Secondary outcomes were (1) general mental health and (2) quality of life (Likert scales, EuroQol-5 Dimension health questionnaire, and 36-item Short-Form Health Survey). All the patients were assessed preoperatively and then at 3, 6, 12, and 24 months postoperatively.

Results

A total of 168 of the 863 eligible patients were included and randomized in this study. Our analysis showed that the improvement of primary outcomes in the EH group was superior to the UC group at 24 months postoperatively (ODI mean 7.02, SD 3.10, P<.05; VAS mean 7.59, SD 3.42, P<.05). No significant difference of primary outcomes was found at other time points.

A subgroup analysis showed that the improvements of the primary outcomes were more significant in those who completed 6 or more training sessions each week throughout the trial (the highest compliance group) compared with the UC group at 6 months (ODI mean 17.94, SD 5.24, P<.05; VAS mean 19.56, SD 5.27, P<.05), 12 months (ODI mean 13.39, SD 5.32, P<.05; VAS mean 14.35, SD 5.23, P<.05), and 24 months (ODI mean 18.80, SD 5.22, P<.05; VAS mean 21.56, SD 5.28, P<.05).

Conclusions

This research demonstrated that a mobile phone–based telerehabilitation system is effective in self-managed rehabilitation for postoperative patients with LBP. The effectiveness of eHealth was more evident in participants with higher compliance. Future research should focus on improving patients’ compliance.

Trial Registration

Chinese Clinical Trial Registry ChiCTR-TRC-13003314; http://www.chictr.org.cn/showproj.aspx?proj=6245 (Archived by WebCite at http://www.webcitation.org/766RAIDNc)

[Impaired hypoxic ventilatory response and related factors in Han and Uygur patients with obstructive sleep apnea-hypopnea syndrome]

Objective: To investigate the respiratory central hypoxia response and its related factors in Han and Uygur patients with obstructive sleep apnea hypopnea syndrome (OSAHS). Methods: One hundred and sixty six OSAHS patients were selected from Jan. 2016 to Dec. 2016 in Department of Respiratory and Critical Care Medicine, Kelamayi Central Hospital, including 69 cases of Han nationality and 97 cases of Uygur nationality. Seventy-three healthy subjects of Uygur nationality were enrolled as the control group. All of them under went sleep monitoring, nocturnal oxygen saturation (SaO(2)), pulmonary function and respiratory central hypoxia response. Results: The 3 groups were matched for age, gender, body mass index(BMI) and apnea-hypopnea index(AHI). The Uygur patients had a higher oxygen desaturation index (ODI4) [(30±22) per hour vs (18±17) per hour ] than Han patients of the same age and BMI. Compared to Han patients, Uygur patients had weaker hypoxic responsiveness [(-0.41±0.23) L·min(-1)·%(-1) vs (-0.36±0.22) L·min(-1)·%(-1,) P<0.05], and the difference still existed after adjusting for AHI [(-0.31±0.21) L·min(-1)·%(-1) vs (-0.41±0.22) L·min(-1)·%(-1,) P<0.05] in mild OSAHS, but this difference was not significant in severe OSAHS. Conclusions: The central hypoxic response in Uygur OSAHS patients was lower than that in Han OSAHS patients and normal controls.

Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA

Current non-invasive prenatal screening is targeted toward the detection of chromosomal abnormalities in the fetus^1,2. However, screening for many dominant monogenic disorders associated with de novo mutations is not available, despite their relatively high incidence³. Here we report on the development and validation of, and early clinical experience with, a new approach for non-invasive prenatal sequencing for a panel of causative genes for frequent dominant monogenic diseases. Cell-free DNA (cfDNA) extracted from maternal plasma was barcoded, enriched, and then analyzed by next-generation sequencing (NGS) for targeted regions. Low-level fetal variants were identified by a statistical analysis adjusted for NGS read count and fetal fraction. Pathogenic or likely pathogenic variants were confirmed by a secondary amplicon-based test on cfDNA. Clinical tests were performed on 422 pregnancies with or without abnormal ultrasound findings or family history. Follow-up studies on cases with available outcome results confirmed 20 true-positive, 127 true-negative, zero false-positive, and zero-false negative results. The initial clinical study demonstrated that this non-invasive test can provide valuable molecular information for the detection of a wide spectrum of dominant monogenic diseases, complementing current screening for aneuploidies or carrier screening for recessive disorders.

MiR-19a mediates the negative regulation of the NF-κB pathway in lipopolysaccharide-induced endometritis by targeting TBK1

OBJECTIVE

In both humans and animals, endometritis is severe inflammation of the uterus, and it causes great economic losses in dairy cow production. MicroRNAs have been reported to play an important role in various inflammatory diseases. However, the regulatory mechanisms of miR-19a in endometritis remain unclear. Thus, the aims of this study are to investigate the role of miR-19a in a mouse model of lipopolysaccharide (LPS)-induced endometritis and elucidate the possible mechanisms in bovine endometrial epithelial cells (bEECs).

METHODS AND RESULTS

Histological analysis showed that LPS induced severe pathological changes, suggesting that the endometritis mouse model was well established. The qPCR assay indicated that miR-19a expression in the uterine tissues of mice with endometritis and in bEECs with LPS stimulation was significantly reduced. The overexpression of miR-19a significantly decreased the expression of inflammatory cytokines (TNF-α, IL-6 and IL-1β) and the phosphorylation of NF-κB p65 and IκBα. Similar results were also obtained following the knockdown of TBK1. Furthermore, a dual luciferase reporter assay further validated that miR-19a inhibited TBK1 expression by binding directly to the 3'-UTR of TBK1.

CONCLUSION

We demonstrated that miR-19a has anti-inflammatory effects and mediates the negative regulation of the NF-κB Pathway in LPS-induced endometritis by targeting TBK1.

Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay

SMARCC2 (BAF170) is one of the invariable core subunits of the ATP-dependent chromatin remodeling BAF (BRG1-associated factor) complex and plays a crucial role in embryogenesis and corticogenesis. Pathogenic variants in genes encoding other components of the BAF complex have been associated with intellectual disability syndromes. Despite its significant biological role, variants in SMARCC2 have not been directly associated with human disease previously. Using whole-exome sequencing and a web-based gene-matching program, we identified 15 individuals with variable degrees of neurodevelopmental delay and growth retardation harboring one of 13 heterozygous variants in SMARCC2, most of them novel and proven de novo. The clinical presentation overlaps with intellectual disability syndromes associated with other BAF subunits, such as Coffin-Siris and Nicolaides-Baraitser syndromes and includes prominent speech impairment, hypotonia, feeding difficulties, behavioral abnormalities, and dysmorphic features such as hypertrichosis, thick eyebrows, thin upper lip vermilion, and upturned nose. Nine out of the fifteen individuals harbor variants in the highly conserved SMARCC2 DNA-interacting domains (SANT and SWIRM) and present with a more severe phenotype. Two of these individuals present cardiac abnormalities. Transcriptomic analysis of fibroblasts from affected individuals highlights a group of differentially expressed genes with possible roles in regulation of neuronal development and function, namely H19, SCRG1, RELN, and CACNB4. Our findings suggest a novel SMARCC2-related syndrome that overlaps with neurodevelopmental disorders associated with variants in BAF-complex subunits.

Biting pain reproduced by the Tooth Slooth: an aid for early diagnosis of cracked tooth

OBJECTIVE

The purpose of this study was to find a reliable method to reproduce biting pain to facilitate an early diagnosis of cracked tooth and to verify the feasibility of the Tooth Slooth in diagnosing a cracked tooth.

METHOD AND MATERIALS

In this study, 46 intact teeth diagnosed as cracked teeth were selected. Patients were asked to bite wet cotton rolls and the Tooth Slooth, and clinical findings were recorded. The difference in the relevance ratio between these two bite test methods was determined.

RESULTS

The relevance ratio of biting pain by the Tooth Slooth and wet cotton rolls was 91.3% and 32.6%, respectively. There was a statistically significant difference between these two bite tests (P < .001).

CONCLUSIONS

Within the limitations of this study, the relevance ratio of biting pain by the Tooth Slooth was significantly higher than that of the wet cotton rolls. The Tooth Slooth was a reliable method to reproduce biting pain and was useful for early diagnosis of cracked teeth.

Antisense RNA Elements for Downregulating Expression

Antisense RNA (asRNA) technology is an important tool for downregulating gene expression. When applying this strategy, the asRNA interference efficiency is determined by several elements including scaffold design, loop size, and relative abundance. Here, we take the Escherichia coli gene fabD encoding malonyl-CoA-[acyl-carrier-protein] transacylase as an example to describe the asRNA design with reliable and controllable interference efficiency. Real-time PCR and fluorescence assay methods are introduced to detect the interference efficiency at RNA level and protein level, respectively.

Green Tea Extract Ameliorates Ischemia-Induced Retinal Ganglion Cell Degeneration in Rats

PURPOSE

Oxidative stress induced by reduced blood circulation is a critical pathological damage to retinal ganglion cells (RGCs) in glaucoma. We previously showed that green tea extract (GTE) and its catechin constituents alleviate sodium iodate-induced retinal degeneration in rats. Here, we investigated the therapeutic effect of GTE on ischemia-induced RGC degeneration in rats.

METHODS

RGC degeneration was induced by ischemic reperfusion in adult Fischer F344 rats. Green tea extract (Theaphenon E) was intragastrically administered 4 times within 48 hours after ischemia. RGC survival, pupillary light reflex, expressions of cell apoptosis, oxidative stress, and inflammation-related proteins were studied.

RESULTS

Ischemic reperfusion significantly induced apoptotic RGCs, RGC loss, and larger constricted pupil area compared to the untreated normal rats. Expressions of activated caspase-3 and caspase-8, Sod2, and inflammation-related proteins as well as p38 phosphorylation were significantly upregulated in the ischemia-injured rats. Compared to the saline-fed ischemic rats, significantly higher number of surviving RGCs, less apoptotic RGCs, and smaller constricted pupil area were observed in the GTE-fed ischemic rats. GTE also reduced the increased protein expressions caused by ischemic injury but enhanced the Jak phosphorylation in the retina. Notably, green tea extract did not affect the survival of RGCs in the uninjured normal rats.

CONCLUSIONS

In summary, GTE offers neuroprotection to RGCs under ischemic challenge, suggesting a potential therapeutic strategy for glaucoma and optic neuropathies.

Biallelic loss of function variants in PPP1R21 cause a neurodevelopmental syndrome with impaired endocytic function

Next-generation sequencing (NGS) has been instrumental in solving the genetic basis of rare inherited diseases, especially neurodevelopmental syndromes. However, functional workup is essential for precise phenotype definition and to understand the underlying disease mechanisms. Using whole exome (WES) and whole genome sequencing (WGS) in four independent families with hypotonia, neurodevelopmental delay, facial dysmorphism, loss of white matter, and thinning of the corpus callosum, we identified four previously unreported homozygous truncating PPP1R21 alleles: c.347delT p.(Ile116Lysfs*25), c.2170_2171insGGTA p.(Ile724Argfs*8), c.1607dupT p.(Leu536Phefs*7), c.2063delA p.(Lys688Serfs*26) and found that PPP1R21 was absent in fibroblasts of an affected individual, supporting the allele's loss of function effect. PPP1R21 function had not been studied except that a large scale affinity proteomics approach suggested an interaction with PIBF1 defective in Joubert syndrome. Our co-immunoprecipitation studies did not confirm this but in contrast defined the localization of PPP1R21 to the early endosome. Consistent with the subcellular expression pattern and the clinical phenotype exhibiting features of storage diseases, we found patient fibroblasts exhibited a delay in clearance of transferrin-488 while uptake was normal. In summary, we delineate a novel neurodevelopmental syndrome caused by biallelic PPP1R21 loss of function variants, and suggest a role of PPP1R21 within the endosomal sorting process or endosome maturation pathway.

Repulsive Casimir force between hyperbolic metamaterials

The Casimir force between electric and magnetic hyperbolic metamaterial slabs is investigated. Due to hyperbolic dispersion, the electromagnetic features of these metamaterials along the optical axis are different from those perpendicular to the optical axis; consequently, these features contribute differently to the Casimir effect. The repulsive Casimir force is formed between electric and magnetic hyperbolic metamaterial slabs; moreover, hyperbolic dispersion can enhance the repulsive effect. However, by utilizing the extremely anisotropic behavior of hyperbolic metamaterials and changing the separation distance between the two slabs, the restoring Casimir force emerges. Additionally, by considering the dispersion of both the permittivity and the permeability of hyperbolic metamaterials, the Casimir force reaches several equilibrium points at different separation distances. Furthermore, the Casimir force at room temperature is discussed. Although the temperature can weaken the effect of the restoring Casimir force, stable equilibria may remain upon choosing suitable filling factors. This work shows that hyperbolic metamaterials have potential applications in micro- and nanoelectromechanical systems, especially for maintaining stability and overcoming adhesion problems.

Loss of tubulin deglutamylase CCP1 causes infantile-onset neurodegeneration

A set of glutamylases and deglutamylases controls levels of tubulin polyglutamylation, a prominent post-translational modification of neuronal microtubules. Defective tubulin polyglutamylation was first linked to neurodegeneration in the Purkinje cell degeneration (pcd) mouse, which lacks deglutamylase CCP1, displays massive cerebellar atrophy, and accumulates abnormally glutamylated tubulin in degenerating neurons. We found biallelic rare and damaging variants in the gene encoding CCP1 in 13 individuals with infantile-onset neurodegeneration and confirmed the absence of functional CCP1 along with dysregulated tubulin polyglutamylation. The human disease mainly affected the cerebellum, spinal motor neurons, and peripheral nerves. We also demonstrate previously unrecognized peripheral nerve and spinal motor neuron degeneration in pcd mice, which thus recapitulated key features of the human disease. Our findings link human neurodegeneration to tubulin polyglutamylation, entailing this post-translational modification as a potential target for drug development for neurodegenerative disorders.

Microbial biomarkers of common tongue coatings in patients with gastric cancer

PURPOSE

The study aims to explore the characteristic microorganisms of the common tongue coatings in patients with gastric cancer (GC).

METHODS

A total of 115 GC patients were assigned to four groups: White-thin coating (W-thin) group, White-thick coating (W-thick) group, Yellow-thin coating (Y-thin) group and Yellow-thick coating (Y-thick) group. Thirty-five healthy volunteers with White-thin coating were recruit as controls. High-throughput sequencing was used to describe the microbial community of the tongue coatings based on 16S rRNA and 18S rRNA genes. Multi-factors statistical analysis was carried out to present the microbial biomarkers of the tongue coating in GC patients.

RESULTS

At bacterial phylum level, Saccharibacteria had higher relative abundance in W-thick group than W-thin group, Proteobacteria was more abundant in W-thin group than Y-thick group and less abundant in Y-thick group than Y-thin group. At fungal genus level, Guehomyces and Aspergillus presented to be significantly different among the common tongue coatings. Forteen significantly increased taxa were sorted out as the microbial biomarkers of common tongue coatings by LEfSe and ROC analysis. At species level, bacterial Capnocytophaga leadbetteri and fungal Ampelomyces_sp_IRAN_1 may be the potential biomarkers of W-thin coating, four bacterial species (Megasphaera micronuciformis, Selenomonas sputigena ATCC 35185, Acinetobacter ursingii, Prevotella maculosa) may be the potential biomarkers of W-thick coating. In general, the white coatings held more complex commensal relationship than the yellow coatings.

CONCLUSION

The common tongue coating owned characteristic microorganisms and special commensal relationship in the GC patients.

Reliable detection of subchromosomal deletions and duplications using cell-based noninvasive prenatal testing

Objective

To gather additional data on the ability to detect subchromosomal abnormalities of various sizes in single fetal cells isolated from maternal blood, using low‐coverage shotgun next‐generation sequencing for cell‐based noninvasive prenatal testing (NIPT).

Method

Fetal trophoblasts were recovered from approximately 30 mL of maternal blood using maternal white blood cell depletion, density‐based cell separation, immunofluorescence staining, and high‐resolution scanning. These trophoblastic cells were picked as single cells and underwent whole genome amplification for subsequent genome‐wide copy number analysis and genotyping to confirm the fetal origin of the cells.

Results

Applying our fetal cell isolation method to a series of 125 maternal blood samples, we detected on average 4.17 putative fetal cells/sample. The series included 15 cases with clinically diagnosed fetal aneuploidies and five cases with subchromosomal abnormalities. This method was capable of detecting findings that were 1 to 2 Mb in size, and all were concordant with the microarray or karyotype data obtained on a fetal sample. A minority of fetal cells showed evidence of genome degradation likely related to apoptosis.

Conclusion

We demonstrate that this cell‐based NIPT method has the capacity to reliably diagnose fetal chromosomal abnormalities down to 1 to 2 Mb in size.

What is already known about this topic?

Fetal trophoblastic cells can be isolated from maternal blood and be used for the detection of fetal aneuploidies and copy number variants. The data on the detection of subchromosomal deletions and duplications is currently limited.

What does this study add?

Cell‐based NIPT can be used for the detection of copy number abnormalities of greater than or equal to 1 Mb in the fetus by low‐coverage next‐generation sequencing after single cell whole genome amplification. Data are provided here for five cases in which different subchromosomal deletions and duplications ranging from 1.2 to 18.9 Mb were detected in single cells.

KCTD7 deficiency defines a distinct neurodegenerative disorder with a conserved autophagy-lysosome defect

OBJECTIVE

Several small case series identified KCTD7 mutations in patients with a rare autosomal recessive disorder designated progressive myoclonic epilepsy (EPM3) and neuronal ceroid lipofuscinosis (CLN14). Despite the name KCTD (potassium channel tetramerization domain), KCTD protein family members lack predicted channel domains. We sought to translate insight gained from yeast studies to uncover disease mechanisms associated with deficiencies in KCTD7 of unknown function.

METHODS

Novel KCTD7 variants in new and published patients were assessed for disease causality using genetic analyses, cell-based functional assays of patient fibroblasts and knockout yeast, and electron microscopy of patient samples.

RESULTS

Patients with KCTD7 mutations can exhibit movement disorders or developmental regression before seizure onset, and are distinguished from similar disorders by an earlier age of onset. Although most published KCTD7 patient variants were excluded from a genome sequence database of normal human variations, most newly identified patient variants are present in this database, potentially challenging disease causality. However, genetic analysis and impaired biochemical interactions with cullin 3 support a causal role for patient KCTD7 variants, suggesting deleterious alleles of KCTD7 and other rare disease variants may be underestimated. Both patient-derived fibroblasts and yeast lacking Whi2 with sequence similarity to KCTD7 have impaired autophagy consistent with brain pathology.

INTERPRETATION

Biallelic KCTD7 mutations define a neurodegenerative disorder with lipofuscin and lipid droplet accumulation but without defining features of neuronal ceroid lipofuscinosis or lysosomal storage disorders. KCTD7 deficiency appears to cause an underlying autophagy-lysosome defect conserved in yeast, thereby assigning a biological role for KCTD7. Ann Neurol 2018;84:774-788.

Controllable radiation properties of a driven exciton-biexciton quantum dot couples to a graphene sheet

We investigate the radiation properties of a driven exciton-biexciton structure quantum dot placed close to a graphene sheet. The study of the Purcell factor then demonstrates the tunability of light-matter coupling, which in turn provides the possibility to control the steady-state populations. As the result, dipole transitions can be selectively enhanced and asymmetry in the resonance fluorescence can be observed. Meanwhile, both quadratures can exhibit two-mode squeezing at the Rabi sideband frequencies. A further study shows that although the increase in the environment temperature has a destructive influence on the population imbalance, squeezing occurs even at room temperature. Due to the flexibility in controlling the resonance fluorescence spectrum and producing two-mode squeezed states, our proposal would have potential applications in quantum information and other quantum research fields.

Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder

Background

Exome sequencing is now being incorporated into clinical care for pediatric and adult populations, but its integration into prenatal diagnosis has been more limited. One reason for this is the paucity of information about the clinical utility of exome sequencing in the prenatal setting.

Methods

We retrospectively reviewed indications, results, time to results (turnaround time, TAT), and impact of exome results for 146 consecutive “fetal exomes” performed in a clinical diagnostic laboratory between March 2012 and November 2017. We define a fetal exome as one performed on a sample obtained from a fetus or a product of conception with at least one structural anomaly detected by prenatal imaging or autopsy. Statistical comparisons were performed using Fisher’s exact test.

Results

Prenatal exome yielded an overall molecular diagnostic rate of 32% (n = 46/146). Of the 46 molecular diagnoses, 50% were autosomal dominant disorders (n = 23/46), 41% were autosomal recessive disorders (n = 19/46), and 9% were X-linked disorders (n = 4/46). The molecular diagnostic rate was highest for fetuses with anomalies affecting multiple organ systems and for fetuses with craniofacial anomalies. Out of 146 cases, a prenatal trio exome option designed for ongoing pregnancies was performed on 62 fetal specimens, resulting in a diagnostic yield of 35% with an average TAT of 14 days for initial reporting (excluding tissue culture time). The molecular diagnoses led to refined recurrence risk estimates, altered medical management, and informed reproductive planning for families.

Conclusion

Exome sequencing is a useful diagnostic tool when fetal structural anomalies suggest a genetic etiology, but other standard prenatal genetic tests did not provide a diagnosis.

Electronic supplementary material

The online version of this article (10.1186/s13073-018-0582-x) contains supplementary material, which is available to authorized users.

Phenotypic expansion in DDX3X - a common cause of intellectual disability in females

De novo variants in DDX3X account for 1–3% of unexplained intellectual disability (ID) cases and are amongst the most common causes of ID especially in females. Forty‐seven patients (44 females, 3 males) have been described. We identified 31 additional individuals carrying 29 unique DDX3X variants, including 30 postnatal individuals with complex clinical presentations of developmental delay or ID, and one fetus with abnormal ultrasound findings. Rare or novel phenotypes observed include respiratory problems, congenital heart disease, skeletal muscle mitochondrial DNA depletion, and late‐onset neurologic decline. Our findings expand the spectrum of DNA variants and phenotypes associated with DDX3X disorders.

Opening of the CLC-3 chloride channel induced by dihydroartemisinin contributed to early apoptotic events in human poorly differentiated nasopharyngeal carcinoma cells

Nasopharyngeal carcinoma (NPC) is a specific type of head and neck cancer that is prevalent in Southeast Asia. Dihydroartemisinin (DHA), a semisynthetic derivative of artemisinin, has specific anticancer activity. Here, we aimed to investigate the role of the CLC-3 chloride channel in the anticancer effect of DHA in poorly differentiated NPC CNE-2Z cells. First, we observed that DHA could specifically inhibit the proliferation, induce apoptosis, and increase cleaved caspase-3 expression in the CNE-2Z cells. Then, we found that DHA could activate chloride channels, which led to Cl^- efflux and apoptotic volume decrease (AVD) in the early stage in the CNE-2Z cells. DHA also specifically increased CLC-3 chloride channel protein expression in the CNE-2Z cells. Silencing of the CLC-3 protein expression depleted the Cl^- currents, and decreased the AVD capacity and cell apoptosis induced by DHA. Finally, we revealed that the [Ca²⁺ ]_i increased after around 6 hours of treatment with DHA, which was also inhibited by silencing of the CLC-3 protein expression. Our data demonstrated that the selective antitumor activities of DHA in NPC may occur through the specific activation of the CLC-3 Cl^- channel, leading to Cl^- efflux, and induced AVD, then led to [Ca²⁺ ]_i accumulation and caspase-3 activation, and finally induced apoptosis. The activation of the CLC-3 chloride channel played an essential and proximal upstream role in the antitumor activities of DHA.

Magnoflorine Ameliorates Lipopolysaccharide-Induced Acute Lung Injury via Suppressing NF-κB and MAPK Activation

Acute lung injury (ALI) which is featured by a strong pulmonary inflammation, is a major cause of morbidity and mortality in critically ill patients. Magnoflorine, a quaternary alkaloid isolated from Chinese herb Magnolia or Aristolochia, has been reported to have potent anti-inflammatory properties. However, the effect of magnoflorine on lipopolysaccharide (LPS)-induced ALI in mice has not been reported. The purpose of the present study is to investigate the anti-inflammatory effect of magnoflorine on LPS-induced ALI and elucidate its possible molecular mechanisms in RAW264.7 cells. The results of histopathological changes as well as the myeloperoxidase (MPO) activity indicated that magnoflorine significantly alleviated the lung injury induced by LPS. In addition, qPCR results showed that magnoflorine dose-dependently decreased the expression of pro-inflammatory cytokines TNF-α, IL-1β, and IL-6. Immunofluorescence assay also confirmed that the level of Toll-like receptor 4 (TLR4) induced by LPS was inhibited by magnoflorine treatment. Further experiments were performed using Western blotting to detect the expression of related proteins in the NF-κB and MAPK signaling pathways. The results showed that magnoflorine suppressed the levels of phosphorylated p65, IκBα, p38, ERK, and JNK. In conclusion, all data indicate that magnoflorine could protect against LPS-induced inflammation in ALI at least partially by inhibiting TLR4-mediated NF-κB and MAPK signaling pathways.

The Potential Therapeutic Role of miR-223 in Bovine Endometritis by Targeting the NLRP3 Inflammasome

Bovine endometritis affects milk production and reproductive performance in dairy cows and causes serious economic loss. The underlying molecular mechanisms or signaling pathways of bovine endometritis remain unclear. In this study, we attempted to determine the expression mechanism of mir-223 in endometritis of dairy cows and evaluate its potential therapeutic value. We first confirmed that there was an increased level of miR-223 in endometritis, and then, an LPS-induced bovine endometrial epithelial cell (BEND) line was used to mimic the inflammatory model in vitro. Our data showed that activation of NF-κB promoted the transcription of miR-223, thus inhibiting activation of the inflammatory mediator NLRP3 and its mediation of IL-1β production to protect against inflammatory damage. Meanwhile, in vivo studies showed that inhibition of mir-223 resulted in an enhanced pathology of mice during LPS-induced endometritis, while overexpression of mir-223 attenuated the inflammatory conditions in the uterus. In summary, our study highlights that miR-223 serves both to constrain the level of NLRP3 activation and to act as a protective factor in the inflammatory response and thus provides a future novel therapeutic modality for active flares in cow endometritis and other inflammatory diseases.

Approaches to carrier testing and results disclosure in translational genomics research: The clinical sequencing exploratory research consortium experience

Background

Clinical genome and exome sequencing (CGES) is primarily used to address specific clinical concerns by detecting risk of future disease, clarifying diagnosis, or directing treatment. Additionally, CGES makes possible the disclosure of autosomal recessive and X‐linked carrier results as additional secondary findings, and research about the impact of carrier results disclosure in this context is needed.

Methods

Representatives from 11 projects in the clinical sequencing exploratory research (CSER) consortium collected data from their projects using a structured survey. The survey focused on project characteristics, which variants were offered and/or disclosed to participants as carrier results, methods for carrier results disclosure, and project‐specific outcomes. We recorded quantitative responses and report descriptive statistics with the aim of describing the variability in approaches to disclosing carrier results in translational genomics research projects.

Results

The proportion of participants with carrier results was related to the number of genes included, ranging from 3% (three genes) to 92% (4,600 genes). Between one and seven results were disclosed to those participants who received any positive result. Most projects offered participants choices about whether to receive some or all of the carrier results. There were a range of approaches to communicate results, and many projects used separate approaches for disclosing positive and negative results.

Conclusion

Future translational genomics research projects will need to make decisions regarding whether and how to disclose carrier results. The CSER consortium experience identifies approaches that balance potential participant interest while limiting impact on project resources.

IRF2BPL Is Associated with Neurological Phenotypes

Interferon regulatory factor 2 binding protein-like (IRF2BPL) encodes a member of the IRF2BP family of transcriptional regulators. Currently the biological function of this gene is obscure, and the gene has not been associated with a Mendelian disease. Here we describe seven individuals who carry damaging heterozygous variants in IRF2BPL and are affected with neurological symptoms. Five individuals who carry IRF2BPL nonsense variants resulting in a premature stop codon display severe neurodevelopmental regression, hypotonia, progressive ataxia, seizures, and a lack of coordination. Two additional individuals, both with missense variants, display global developmental delay and seizures and a relatively milder phenotype than those with nonsense alleles. The IRF2BPL bioinformatics signature based on population genomics is consistent with a gene that is intolerant to variation. We show that the fruit-fly IRF2BPL ortholog, called pits (protein interacting with Ttk69 and Sin3A), is broadly detected, including in the nervous system. Complete loss of pits is lethal early in development, whereas partial knockdown with RNA interference in neurons leads to neurodegeneration, revealing a requirement for this gene in proper neuronal function and maintenance. The identified IRF2BPL nonsense variants behave as severe loss-of-function alleles in this model organism, and ectopic expression of the missense variants leads to a range of phenotypes. Taken together, our results show that IRF2BPL and pits are required in the nervous system in humans and flies, and their loss leads to a range of neurological phenotypes in both species.

Vacuum induced transparency in metamaterials

For the cavity-based electromagnetically induced transparent (EIT), as the coherent driving field is enhanced by the optical cavity, the weak probe field can propagate through the atomic ensemble without absorption even if the driving field is weak. The extreme case of vacuum in the cavity is called "vacuum-induced transparency" (VIT) to distinguish it from the cavity EIT. Here we construct a new kind of cavity made of Metamaterials, i.e. ε-negative (EN) and μ-negative (MN) slabs, and study the VIT phenomena of the atomic ensemble doped within it. When the impedances of the MN and EN slabs are matched to each other and the dissipation of the material is small, it behaves as a surface plasmon cavity with a huge Q factor. And the VIT phenomenon in this cavity appears. By adjusting the position of atoms, the coupling strength between the atom and the structure could be changed. Two kinds of extremes of VIT, the coherent population trapping (CPT) and the Autler-Townes splitting (ATS), can be achieved in this system easily. Our proposal could be used in the realization of ultra-strong coupling and integrated devices on quantum memory or optical switch.

Safety and efficacy of PLGA(Ag-Fe3O4)-coated dental implants in inhibiting bacteria adherence and osteogenic inducement under a magnetic field

Introduction

The placement of dental implants is performed in a contaminated surgical field in the oral cavity, which may lead to implant failure. Bacterial adhesion and proliferation (Streptococcus mutans, Porphyromonas gingivalis) often lead to implant infections. Although Ag nanoparticles hold great promise for a broad spectrum of antibacterial activities, their runoff from dental implants compromises their antibacterial efficacy and potentially impairs osteoblast proliferation. Thus, this aspect remains a primary challenge and should be controlled.

Materials and methods

In this study, PLGA(Ag-Fe₃O₄) was modified on the implanted tooth surface and was characterized by transmission electron microscopy, X-ray diffraction, and Fourier transform infrared spectroscopy. The magnetic and antibacterial properties were also determined.

Results

Results showed that Ag successfully bonded with Fe₃O₄, and Ag-Fe₃O₄ not only exerted superparamagnetism but also exhibited antibacterial activity almost identical to silver nanoparticles (nano-Ag). The PLGA(Ag-Fe₃O₄) coating could significantly maintain the antibacterial activity and avoid bacterial adhesion to the implant. Compared with the blank control group, PLGA(Ag-Fe₃O₄) under magnetic field-coated samples had a significantly lower amount of colonized S. mutans (P<0.01). Osteoblast proliferation results showed that the coated samples did not exhibit cytotoxicity and could promote osteoblast proliferation as shown by MTT, alkaline phosphatase, and the nucleolar organizer region count.

Conclusion

We developed a novel Ag biologically compatible nanoparticle in this study without compromising the nano-Ag antibacterial activity, which provided continuous antibacterial action.