Differentiating molecular etiologies of Angelman syndrome through facial phenotyping using deep learning

Angelman syndrome (AS) is caused by several genetic mechanisms that impair the expression of maternally‐inherited UBE3A through deletions, paternal uniparental disomy (UPD), UBE3A pathogenic variants, or imprinting defects. Current methods of differentiating the etiology require molecular testing, which is sometimes difficult to obtain. Recently, computer‐based facial analysis systems have been used to assist in identifying genetic conditions based on facial phenotypes. We sought to understand if the facial‐recognition system DeepGestalt could find differences in phenotype between molecular subtypes of AS. Images and molecular data on 261 individuals with AS ranging from 10 months through 32 years were analyzed by DeepGestalt in a cross‐validation model with receiver operating characteristic (ROC) curves generated. The area under the curve (AUC) of the ROC for each molecular subtype was compared and ranked from least to greatest differentiable phenotype. We determined that DeepGestalt demonstrated a high degree of discrimination between the deletion subtype and UPD or imprinting defects, and a lower degree of discrimination with the UBE3A pathogenic variants subtype. Our findings suggest that DeepGestalt can recognize subclinical differences in phenotype based on etiology and may provide decision support for testing.     

Development and evaluation of NucliSens basic kit NASBA for diagnosis of parainfluenza virus infection with 'end-point' and 'real-time' detection

New methods for the detection of human parainfluenza viruses (HPIVs) were developed. These were based on nucleic acid sequence-based amplification (NASBA) and utilised the NucliSens Basic Kit. Primers and probes were selected from the haemagglutinin neuraminidase (HN) gene of HPIV1, HPIV2 and HPIV3, and from the phosphoprotein (P) of HPIV4a and -4b. Synthetic RNA, titrated control virus stocks and respiratory specimens (n=44) were utilised to evaluate performance of the assays. Detection of NASBA products was by probe hybridisation and electrochemiluminescence (ECL) ('end-point' detection) or using molecular beacons ('real-time' detection). The assays using ECL detection proved to be both sensitive and specific. Typically, less than or equal to 100 RNA copies or one TCID(50) input was detectable with no cross-reaction between the specific HPIV assays and other respiratory viruses. Results for clinical samples were concordant with those obtained by 'conventional' procedures by classical viral diagnostic methods. 'Real-time' detection utilised probes specific for either HPIV1 or HPIV3 with similar performance characteristics to the assays with 'end-point' detection. The feasibility of multiplexing targets together was confirmed using a combined HPIV1 and HPIV3 assay with good results for ECL and molecular beacon detection on control material and clinical samples.     

Cigarette smoke prevents apoptosis through inhibition of caspase activation and induces necrosis

Emphysema is characterized by enlargement of the distal airspaces in the lungs due to destruction of alveolar walls. Alveolar endothelial and epithelial cell apoptosis induced by cigarette smoke is thought to be a possible mechanism for this cell loss. In contrast, our studies show that cigarette smoke condensate (CSC) induces necrosis in alveolar epithelial cells and human umbilical vein endothelial cells. Furthermore, study of the cell death pathway in a model system using Jurkat cells revealed that in addition to inducing necrosis, CSC inhibited apoptosis induced by staurosporine or Fas ligation, with both effects prevented by the antioxidants glutathione and dithiothreitol. Time course experiments revealed that CSC inhibited an early step in the caspase cascade, whereby caspase-3 was not activated. Moreover, cell-free reconstitution of the apoptosome in cytoplasmic extracts from CSC-treated cells, by addition of cytochrome-c and dATP, did not result in activation of caspases-3 or -9. Thus, smoke treatment may alter the levels of pro- and antiapoptogenic factors downstream of the mitochondria to inhibit active apoptosome formation. Therefore, unlike previous studies, cell death in response to cigarette smoke by necrosis and not apoptosis may be responsible for the loss of alveolar walls and inflammation observed in emphysema.     

Adaptive Wiener Filtering for Improved Acquisition of Distortion Product Otoacoustic Emissions

An innovative acoustic noise canceling method using adaptive Wiener filtering (AWF) was developed for improved acquisition of distortion product otoacoustic emissions (DPOAEs). The system used one microphone placed in the test ear for the primary signal. Noise reference signals were obtained from three different sources: (a) pre-stimulus response from the test ear microphone, (b) post-stimulus response from a microphone placed near the head of the subject and (c) post-stimulus response obtained from a microphone placed in the subjects nontest ear. In order to improve spectral estimation, block averaging of a different number of single sweep responses was used. DPOAE data were obtained from 11 ears of healthy newborns in a well-baby nursery of a hospital under typical noise conditions. Simultaneously obtained recordings from all three microphones were digitized, stored and processed off-line to evaluate the effects of AWF with respect to DPOAE detection and signal-to-noise ratio (SNR) improvement. Results show that compared to standard DPOAE processing, AWF improved signal detection and improved SNR. © 1998 Biomedical Engineering Society. PAC98: 4364Jb, 4360-c, 8790+y     

Ganglion cell density and oil droplet distribution in the retina of brown-eared bulbul (Hysipetes amaurotis)

This study was intended to determine the number and density of both retinal ganglion cells and the oil droplets of cone photoreceptor cells in brown-eared bulbul (Hysipetes amaurotis). For this study birds were killed with proper dose of anesthetic (pentobarbital, 30 mg/kg), and the eyes were removed from the orbital cavity to isolate the retina. For the ganglion cell study retinal whole-mount specimens were prepared and stained with 0.1% cresyl violet. The different types of oil droplets were counted from color microphotographs of freshly prepared retinal samples. The mean total number of ganglion cells was estimated at approximately 2.5×10⁶; with an average density of 16 523 cells/mm². Two high-density areas, namely the central area (CA) and the dorso-temporal area (DTA), are located in the central and dorso-temporal retinas, respectively, in bulbuls (24 032 cells/mm² in the CA; 23 113 cells/mm² in the DTA). Small ganglion cells persisted in the highest density areas, whereas the largest soma sizes were found in the lowest density areas of the retina. Four types of different colored oil droplets — red, orange, green and clear — were identified with an average density of 29 062/mm². Among the different colors, the green oil droplets had a significantly higher population (13 083/mm²) than the others across the retina. The central retina had a significantly higher number of all types of oil droplets, at a density of 60 552/mm². The density and size of the different colored oil droplets were inversely related across the regions of the retina. Taken together, it is concluded that the CA of the retina is an excellent quality area for visual perception due to peak density of ganglion cells and oil droplets. Moreover, each specific oil droplet makes a distinct contribution to visual perception, thereby ensuring that the bird has a retina that best matches its natural environment and feeding behavior.     

Molecular and genetic characterizations of five pathogenic and two non-pathogenic monoclonal antiphospholipid antibodies

Antiphospholipid syndrome (APS) is an autoimmune disease that is characterized by thrombosis, recurrent fetal loss and thrombocytopenia. Antiphospholipid antibodies, detected by enzyme-linked immunoabsorbent assays (aCL) and/or in vitro blood clotting assays (LAC) are strongly associated with APS. Both the molecular structures used by pathogenic antiphospholipid antibodies and the genetic mechanisms leading to their production are unknown. We describe here the variable region genes of seven IgG antiphospholipid antibodies derived from two APS patients. Of these, five are pathogenic as defined in a mouse model of thrombosis and two are not. Analyses of the expressed variable region genes show no preferential V gene usage. However, similar to anti-DNA antibodies, pathogenic antiphospholipid antibodies contain an increased number of arginine residues in the third complimentarity-determining region (CDR3) of their H chains. The increased accumulation of arginine residues in the V(H) CDR3 may act to enhance antigen binding, promote disease and point to the importance of the H chain in the pathogenic potential of certain antiphospholipid antibodies.     

Use of Antibodies in Lymphocyte Secretions for Detection of Subclinical Tuberculosis Infection in Asymptomatic Contacts

We have previously demonstrated that Mycobacterium bovis BCG-specific immunoglobulin G antibodies in lymphocyte secretions (ALS) can be employed as a marker for active tuberculosis (TB). We aimed to determine whether the ALS method allows detection of subclinical TB infection in asymptomatic individuals. A prospective study of family contacts (FCs) of patients with active TB and healthy controls was performed. Thirteen of 42 FCs had high ALS responses, including 6 FCs who subsequently developed active TB. No correlation was observed between the tuberculin skin test and the ALS responses in the FCs (r = 0.1, P = 0.23). Among patients with active TB, BCG-specific ALS responses steadily declined from the time of diagnosis through 6 months following antimycobacterial chemotherapy (P = 0.001). The ALS assay enabled detection of infection in exposed symptom-free contacts, who are at greater risk for developing active TB. The method may also allow discrimination between effective treatment of active infection and suboptimal response to therapy.     

The (α2→8)-Linked Polysialic Acid Capsule and Lipooligosaccharide Structure Both Contribute to the Ability of Serogroup B Neisseria meningitidis To Resist the Bactericidal Activity of Normal Human Serum

The molecular basis for the resistance of serogroup B Neisseria meningitidis to the bactericidal activity of normal human sera (NHS) was examined with a NHS-resistant, invasive serogroup B meningococcal isolate and genetically and structurally defined capsule-, lipooligosaccharide (LOS)-, and sialylation-altered mutants of the wild-type strain. Expression of the (α2→8)-linked polysialic acid serogroup B capsule was essential for meningococcal resistance to NHS. The very NHS-sensitive phenotype of acapsular mutants (99.9 to 100% killed in 10, 25, and 50% NHS) was not rescued by complete LOS sialylation or changes in LOS structure. However, expression of the capsule was necessary but not sufficient for a fully NHS-resistant phenotype. In an encapsulated background, loss of LOS sialylation by interrupting the α2,3 sialyltransferase gene, lst, increased sensitivity to 50% NHS. In contrast, replacement of the lacto-N-neotetraose α-chain (Galβ1-4GlcNAcβ1-3Galβ1-4Glc) with glucose extensions (Glc_N) in a galE mutant resulted in a strain resistant to killing by 50% NHS at all time points. Encapsulated meningococci expressing a Hep₂(GlcNAc)→KDO₂→lipid A LOS without an α-chain demonstrated enhanced sensitivity to 50% NHS (98% killed at 30 min) mediated through the antibody-dependent classical complement pathway. Encapsulated LOS mutants expressing truncated Hep₂→KDO₂→lipid A and KDO₂→lipid A structures were also sensitive to 50% NHS (98 to 100% killed at 30 min) but, unlike the wild-type strain and mutants with larger oligosaccharide structures, they were killed by hypogammaglobulinemic sera. These data indicate that encapsulation is essential but that the LOS structure contributes to the ability of serogroup B N. meningitidis to resist the bactericidal activity of NHS.Serogroup B Neisseria meningitidis (the meningococcus) is an obligate human pathogen and remains a leading cause of fulminant septicemia and meningitis. In addition to sporadic outbreaks, large epidemics of serogroup B meningococcal disease continue to occur in many parts of the world, including South America, the United States Pacific Northwest, Western Europe, and New Zealand (4, 22). After penetrating upper respiratory tract mucosal surfaces, N. meningitidis must survive and multiply in the bloodstream to cause sepsis, meningitis, and other manifestations of invasive meningococcal disease. A major mechanism inhibiting or preventing the multiplication of meningococci in the blood is the complement-mediated bactericidal activity of human sera (17, 39). The importance of this activity in the prevention of systemic meningococcal disease is reinforced by host factors that alter bactericidal activity and increase the risk for development of invasive disease. These factors include the absence of bactericidal antibodies against meningococci (17, 18, 45), deficiencies in the complement cascade (13), and the presence of blocking immunoglobulin A antibodies that inhibit the bactericidal activity of human sera (19). The bactericidal activity of human sera against meningococci is also used as a surrogate marker for assessing meningococcal vaccine efficacy.Meningococci have evolved mechanisms that protect them from the bactericidal activity of human sera. Invasive serogroup B meningococcal strains recovered from blood and cerebrospinal fluid often resist being killed by human sera (48). The molecular basis for resistance has been attributed to the expression by this organism of an (α2→8)-linked polysialic acid capsule and a short-chained lipooligosaccharide (LOS) with terminal sialic acid residues (23, 34, 35). Meningococci isolated from the bloodstream in invasive disease, in contrast to nasopharyngeal isolates, are heavily encapsulated (9) and express the L3,7,9 LOS immunotypes (28). These immunotypes have a lacto-N-neotetraose originating from HepI of the inner core, which may be terminally sialylated (34, 62). However, the experimental data defining the precise contributions of the capsule, LOS sialylation, and LOS structure to the ability of serogroup B meningococci to resist the bactericidal activity of human sera is conflicting (11, 15, 20, 21, 27, 37, 63–65).LOS epitopes are immunogenic in infants and children and induce protective bactericidal antibodies in convalescent sera (10, 12). These bactericidal LOS antibodies appear to be directed at conserved low-molecular-weight LOS epitopes (10, 12). LOS is also a component of new serogroup B outer membrane vesicle (OMV) vaccines and is proposed as a basis for other new meningococcal vaccines (1–3, 50). Although changes in the structure of LOS are known to influence the amount and epitopes of bactericidal and other functional antibodies elicited by OMV vaccines (2), the precise LOS structure(s) to include in these and other LOS-containing meningococcal vaccines is uncertain.To help understand the basis for meningococcal survival following mucosal invasion and to facilitate development of meningococcal vaccines which may contain LOS, we created a series of genetically and structurally defined capsule-, sialylation-, and LOS-altered mutants of the serogroup B meningococcal strain NMB. We used these mutants to study the contributions of the capsule, LOS sialylation, and changes in LOS structure to meningococcal resistance to the bactericidal activity of normal human sera (NHS).     

Reduced susceptibility to dextran sulphate sodium-induced colitis in the interleukin-2 heterozygous (IL-2) mouse

Summary Mice homozygous for an inactivation of the interleukin-2 (IL-2) gene develop a T-cell dependent colitis. Heterozygous (IL-2+/-) mice are clinically healthy but have been shown to express reduced levels of IL-2 in the colon. Splenocytes from the IL-2+/- mice had a poorer proliferative response to polyclonal T-cell activation and these mice have reduced numbers of intestinal regulatory T cells (CD4+ CD25+ cells) when compared to wild type mice. When exposed to dextran sulphate sodium (DSS) IL-2+/- mice showed a markedly reduced susceptibility to DSS-induced colitis. While DSS treatment caused a marked increase in both CD4+ and CD8+ colonic T cells expressing increased levels of IL-2, IL-4, and IL-10 in wild type mice none of these changes were seen in IL-2+/- mice. On the contrary, cytokine expression in intestinal T cells of IL-2+/- mice was actually reduced after DSS treatment. These results suggest that reduced levels of IL-2 leads to attenuated activation and function of intestinal T cells in IL-2+/- mice and a failure to react adequately to DSS exposure.