A scalable framework for the discovery of functional helicase substrates and helicase-driven regulatory switches.

Helicases are ubiquitous motor enzymes that remodel nucleic acids (NA) and NA-protein complexes in key cellular processes. To explore the functional repertoire and specificity landscape of helicases, we devised a screening scheme-Helicase-SELEX (Systematic Evolution of Ligands by EXponential enrichment)-that enzymatically probes substrate and cofactor requirements at global scale. Using the transcription termination Rho helicase of Escherichia coli as a prototype for Helicase-SELEX, we generated a genome-wide map of Rho utilization (Rut) sites. The map reveals many features, including promoter- and intrinsic terminator-associated Rut sites, bidirectional Rut tandems, and cofactor-dependent Rut sites with inverted G > C skewed compositions. We also implemented an H-SELEX variant where we used a model ligand, serotonin, to evolve synthetic Rut sites operating in vitro and in vivo in a ligand-dependent manner. Altogether, our data illustrate the power and flexibility of Helicase-SELEX to seek constitutive or conditional helicase substrates in natural or synthetic NA libraries for fundamental or synthetic biology discovery.

Cryo-EM structure of transcription termination factor Rho from Mycobacterium tuberculosis reveals bicyclomycin resistance mechanism.

The bacterial Rho factor is a ring-shaped motor triggering genome-wide transcription termination and R-loop dissociation. Rho is essential in many species, including in Mycobacterium tuberculosis where rho gene inactivation leads to rapid death. Yet, the M. tuberculosis Rho [MtbRho] factor displays poor NTPase and helicase activities, and resistance to the natural Rho inhibitor bicyclomycin [BCM] that remain unexplained. To address these issues, we solved the cryo-EM structure of MtbRho at 3.3 Šresolution. The MtbRho hexamer is poised into a pre-catalytic, open-ring state wherein specific contacts stabilize ATP in intersubunit ATPase pockets, thereby explaining the cofactor preference of MtbRho. We reveal a leucine-to-methionine substitution that creates a steric bulk in BCM binding cavities near the positions of ATP γ-phosphates, and confers resistance to BCM at the expense of motor efficiency. Our work contributes to explain the unusual features of MtbRho and provides a framework for future antibiotic development.

A Large Insertion Domain in the Rho Factor From a Low G + C, Gram-negative Bacterium is Critical for RNA Binding and Transcription Termination Activity.

Rho-dependent termination of transcription (RDTT) is a critical regulatory mechanism specific to bacteria. In a subset of species including most Actinobacteria and Bacteroidetes, the Rho factor contains a large, poorly conserved N-terminal insertion domain (NID) of cryptic function. To date, only two NID-bearing Rho factors from high G + C Actinobacteria have been thoroughly characterized. Both can trigger RDTT at promoter-proximal sites or with structurally constrained transcripts that are unsuitable for the archetypal, NID-less Rho factor of Escherichia coli (EcRho). Here, we provide the first biochemical characterization of a NID-bearing Rho factor from a low G + C bacterium. We show that Bacteroides fragilis Rho (BfRho) is a bona fide RNA-dependent NTPase motor able to unwind long RNA:DNA duplexes and to disrupt transcription complexes. The large NID (~40% of total mass) strongly increases BfRho affinity for RNA, is strictly required for RDTT, but does not promote RDTT at promoter-proximal sites or with a structurally constrained transcript. Furthermore, the NID does not preclude modulation of RDTT by transcription factors NusA and NusG or by the Rho inhibitor bicyclomycin. Although the NID contains a prion-like Q/N-rich motif, it does not spontaneously trigger formation of ß-amyloids. Thus, despite its unusually large RNA binding domain, BfRho behaves more like the NID-less EcRho than NID-bearing counterparts from high G + C Actinobacteria. Our data highlight the evolutionary plasticity of Rho's N-terminal region and illustrate how RDTT is adapted to distinct genomic contents.

Computer modeling of whole-cell voltage-clamp analyses to delineate guidelines for good practice of manual and automated patch-clamp.

The patch-clamp technique and more recently the high throughput patch-clamp technique have contributed to major advances in the characterization of ion channels. However, the whole-cell voltage-clamp technique presents certain limits that need to be considered for robust data generation. One major caveat is that increasing current amplitude profoundly impacts the accuracy of the biophysical analyses of macroscopic ion currents under study. Using mathematical kinetic models of a cardiac voltage-gated sodium channel and a cardiac voltage-gated potassium channel, we demonstrated how large current amplitude and series resistance artefacts induce an undetected alteration in the actual membrane potential and affect the characterization of voltage-dependent activation and inactivation processes. We also computed how dose-response curves are hindered by high current amplitudes. This is of high interest since stable cell lines frequently demonstrating high current amplitudes are used for safety pharmacology using the high throughput patch-clamp technique. It is therefore critical to set experimental limits for current amplitude recordings to prevent inaccuracy in the characterization of channel properties or drug activity, such limits being different from one channel type to another. Based on the predictions generated by the kinetic models, we draw simple guidelines for good practice of whole-cell voltage-clamp recordings.

Molecular investigation of a RSV outbreak in a geriatric hospital.

BACKGROUND: Acquired infections in hospitalized elderly people are a growing concern. In long-term care facilities with multiple staff and visitor contacts, virus outbreaks are a common challenge for infection prevention teams. Although several studies have reported nosocomial RSV outbreaks in long term care facilities, molecular epidemiology data are scarce. METHODS: RSV RNA was detected in respiratory samples from 19 patients in a long-term care hospital for elderly in Paris in March 2019 over a 3 weeks period. Genotyping was performed using nucleotide sequencing. Sociodemographic and clinical characteristics of cases part of a unique cluster, were retrospectively reviewed. RESULTS: Molecular investigation of theses RSV cases, revealed a unique cluster of 12 nosocomial cases in 2 adjacent wards. Mean age of these outbreak's cases was 89. All patients had underlying medical conditions. Seven exhibited lower respiratory symptoms and three experienced decompensation of underlying chronic heart condition. Two patients died. CONCLUSIONS: This case report highlights the importance of RSV in causing substantial disease in elderly in case of nosocomial outbreak and the contributions of molecular epidemiology in investigation and management of such outbreak.

A Simple Fluorescence Microplate Assay to Monitor RNA-DNA Hybrid Unwinding by the Bacterial Transcription Termination Factor Rho.

Transcription termination factor Rho contributes to shape the transcriptomes of many bacteria and is essential in a large subset of them. Although the transcription termination function of Rho is not always easy to reconstitute and to study in vitro, assays based on the ATP-dependent RNA-DNA hybrid unwinding activity of the factor can prove useful to dissect Rho mechanisms or to seek new antibiotics targeting Rho. However, current in vitro assays of Rho helicase activity are time-consuming, as they usually require radiolabeling of the hybrid substrates and analysis of reaction products by gel electrophoresis. Here, we describe a fluorescence-based microplate assay that informs on Rho helicase activity in a matter of minutes and allows the multiplexed analysis of conditions required for primary biochemical characterization or for drug screening.

Antenatal diagnosis of absence of septum pellucidum.

The absence of septum pellucidum (ASP) is a rare disease, which affects the structure of the brain. It is either isolated or associated with various congenital brain malformations. The diagnosis of ASP can be performed by second-trimester ultrasound. When the ASP is isolated, prenatal counseling is optimistic regarding neurological outcome, but there is a 20% risk of septo-optic dysplasia in the neonate.

Prenatal sonographic description of fetuses affected by pyruvate dehydrogenase or pyruvate carboxylase deficiency.

OBJECTIVE: Pyruvate dehydrogenase deficiency (PDHD) and pyruvate carboxylase deficiency (PCD) are diseases with severe neonatal forms, and their low prevalence makes them difficult to diagnose during pregnancy. Our objective was to describe prenatal ultrasound features that may be suggestive of these diagnoses. METHODS: We analyzed 3 cases from our institution and reviewed 12 published cases of PDHD and 6 cases of PCD, recording all of the ultrasound signs, as well as magnetic resonance findings when available. Because of the small number of cases of PCD, we also included postnatal signs that could have been observed during imaging during pregnancy, for a total of 11 cases of PCD. RESULTS: We conclude that PDHD can be suggested in the presence of ventriculomegaly or paraventricular cysts, associated with an abnormality of the cerebral parenchyma such as abnormal gyration or involvement of the corpus callosum. Pyruvate carboxylase deficiency can be suggested in the presence of ventriculomegaly, frontal horn impairment associated with subependymal, and paraventricular cysts. CONCLUSION: When confronted to the ultrasound abnormalities we described, and after eliminating the most frequent etiologies, a metabolic deficiency should be considered. Furthermore, the hereditary character of these diseases makes that it is important to send the family with genetic advice in particular in case of history of a fetal death in utero or a death neonatal unexplained.

Isonatric Dialysis Biofeedback in Hemodiafiltration with Online Regeneration of Ultrafiltrate in Hypertensive Hemodialysis Patients: A Randomized Controlled Study.

UNLABELLED: Dialysis biofeedback in hemodiafiltration with online regeneration of ultrafiltrate (HFR) could help to improve arterial hypertension. We evaluated the impact of isonatric HFR (HFR-iso) on hypertension control compared to conventional HFR. Forty-seven hemodialysis patients were included and randomized (ratio 2/1) HFR-iso versus HFR during 24 dialysis sessions. In the HFR-iso group (32 patients, 768 dialysis sessions), the predialytic systolic blood pressure (BP) decreased from S1 to S24 of 9 ± 20 mm Hg and increased of 5 ± 24 mm Hg in the HFR group (15 patients, 360 dialysis sessions), variation that differed between the 2 groups (x0394;S1-S24, p = 0.035; interaction group*time, p = 0.012). The diastolic BP (HFR-iso -3 ± 14 mm Hg vs. HFR 5 ± 13 mm Hg; p = 0.088), the DDD of antihypertensive treatment and the dry weight did not vary significantly during the study. Number of sessions complicated by symptomatic hypotension was similar in the 2 groups. HFR-iso improved BP control without increasing dialysis hypotension episodes. SHORT SUMMARY: In this multicenter, open-label, controlled, randomized study, we evaluated the impact of dialysis biofeedback in HFR on arterial hypertension compared to conventional HFR. We observed that HFR-iso improved arterial BP control without increasing dialysis hypotension episodes.

Sarcoma-like pyogenic granuloma of the thumb and respiratory restrictive syndrome in a non-compliant hemodialysis patient.

Pyogenic granuloma is a benign vascular tumor of the skin or mucosae usually observed after irritative processes. We report the case of a non-compliant hemodialysis patient with severe hyperparathyroidism who rapidly developed growing pyogenic granuloma of the distal part of the left thumb. This tumor mimicked sarcoma and caused recurrent bleeding during hemodialysis sessions. Hand radiograph revealed an osteolytic lesion compatible with a brown tumor. Among other brown tumors, several of those found in the ribs were responsible of a severe respiratory restrictive deficit. This report highlights the difficulty to choose the adequate treatment of severe hyperparathyroidism, and discusses the benefit/risk balance of performing parathyroidectomy.

Comparison between ultrasound and magnetic resonance imaging in assessment of fetal cytomegalovirus infection.

OBJECTIVE: To evaluate whether fetal brain magnetic resonance imaging (MRI) adds useful information to the one obtained by ultrasound in fetuses with cytomegalovirus (CMV) infection. METHODS: MRI and ultrasonographic findings were analyzed retrospectively in 38 fetuses with proven congenital CMV infection. Both techniques were performed on the same week at a mean gestational age of 33 weeks (24-37). The referral indications were maternal seroconversion (n = 19), and ultrasound findings (n = 19). The results were compared with the fetopathologic examination in cases with fetal death or termination of pregnancy (TOP) or the infant's neurological examination. RESULTS: The 38 cases were classified into three groups, depending on ultrasound findings at referral. Group 1: no ultrasound features (n = 11); group 2: extracerebral features without cerebral abnormalities at ultrasound (n = 13); group 3: presence of cerebral features at ultrasound (n = 14). In group 1, MRI was always normal. In group 2, MRI revealed cerebral features in six cases (46%). In group 3, MRI always confirmed the lesions seen at ultrasound and highlighted other cerebral features. CONCLUSIONS: MRI can provide important additional information with regard to abnormal gyration, cerebellar hypoplasia, or abnormal signal in white matter. It is certainly useful in the assessment of fetuses with extracerebral features without brain abnormalities detected with ultrasounds. If the fetal ultrasound is strictly normal in an infected fetus, MRI may not detect brain anomalies; however, it seems difficult to not perform this noninvasive procedure.

Neocortical neuronal arrangement in LIS1 and DCX lissencephaly may be different.

In type I or classical lissencephaly, two genetic causes, namely the LIS1 gene mapping at 17p13.3 and the DCX (doublecortin on X) gene mapping at Xq22.3 are involved. These are considered to act during corticogenesis on radial migratory pathways. The prevailing view is that heterozygous mutations in the LIS1 gene and hemizygous mutations in the DCX gene produce similar histological pattern. The present detailed neuropathological study in two unrelated fetuses with respectively a mutation in the LIS1 and the DCX genes do not confirm this view. In LIS1 mutation, the cortical ribbon displays a characteristic inverted organization, also called "four layered cortex" while in DCX mutation, the cortex displays a roughly ordered "six layered" lamination. Our hypothesis is that mutations of the LIS1 and DCX genes, may not affect the same neuronal arrangement in the neocortex. Because the pathology of proven XLIS is rarely documented, further detailed neuropathological analysis in other cases identified through molecular study would be of a great help in the recognition of neuronal population involved in these migrational disorders and their underlying molecular mechanism.

Fetal CT.

INTRODUCTION: Fetal CT is helpful in the diagnosis of bony anomalies, particularly with 3D reconstructions. DISCUSSION: Because of the potential risks of irradiation, CT should not be performed before 32 weeks' gestation and should be restricted to a carefully selected group of patients.

Prenatal diagnosis of diastematomyelia.

INTRODUCTION: Diastematomyelia, also termed split cord malformation, is a form of occult spinal dysraphism characterized by a cleft in the spinal cord. Prenatal diagnosis of this anomaly is possible by ultrasonography (US), and fetal MRI can be used to diagnose the type of diastematomyelia precisely. Diastematomyelia can be isolated or associated with other dysraphisms, segmental anomalies of the vertebral bodies, or visceral malformations (horseshoe or ectopic kidney, utero-ovarian malformation, and anorectal malformation). We present three cases of fetal diastematomyelia investigated using a multimodal prenatal work-up (US, MRI, 3D-CT). CASES: The first case, detected at 20 weeks' gestation, had a lumbar meningocele. At 30 weeks' gestation, direct US visualization revealed the division of the spinal cord into two hemicords. This patient illustrates an isolated type II diastematomyelia with a favorable prognosis. The second case, detected at 22 weeks' gestation, presented with disorganization of bony process of the vertebral column with a midline echogenic bony spur, asymmetrical hemicords, and a foot malposition. Fetal MRI at 26 weeks' gestation and CT/3D reconstructed at 32 weeks' gestation confirmed a type I diastematomyelia with orthopedic malposition. The third case, detected at 22 weeks' gestation, presented with widening of the lumbar canal and scoliosis. Prenatal work-up (US, MRI) disclosed other visceral malformations (pelvic kidney), which led to the assumption of a complex polymalformative syndrome. The pregnancy was terminated. Fetopathologic examination disclosed even more visceral malformations (anal atresia and unicorn uterus).

Validation of a suprasternal pressure transducer for apnea classification during sleep.

STUDY OBJECTIVES: To validate a new method of evaluation of respiratory efforts during polysomnographic recordings. SETTING: NA PARTICIPANTS: 26 patients with sleep apnea syndrome, either during diagnostic assessment (n=16) or under nasal continuous positive airway pressure (n=10). METHODS: This method consists of measuring suprastemal pressure by a pressure transducer placed over the trachea above the sternal notch (Pst). It was compared to the reference method (ie, esophageal pressure) during the same polysomnogram. RESULTS: The analysis was based on 3,261 episodes of apnea, classified as obstructive in 2,556 cases, mixed in 347 cases, and central in 358 cases according to the esophageal pressure monitor. The concordance between the two methods was very good, with a sensitivity of Pst of 99.4% for the detection of apneas with respiratory efforts and a specificity of 93.6%. Twenty-three (6.4%) of the 358 central apneas were classified by Pst as apneas with respiratory efforts and 18 of the 353 central apneas classified by Pst were actually apneas with respiratory efforts on the esophageal pressure monitor. CONCLUSION: The suprasternal pressure transducer, which presents a good sensitivity and a good specificity for identification of respiratory efforts, can be used to classify apneas during polysomnographic recordings in clinical practice.