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BACKGROUND: While studies have investigated relationships among learning motivation, social presence, and cognitive presence, there appear to be no studies on the inclusion of industry talks and the theory of inventive problem-solving (TRIZ) in strengthening engineering students’ learning motivation, social presence, and cognitive presence within a blended learning setting. OBJECTIVE: This study investigated the influence of industry talks and TRIZ on learning motivation, social presence, and cognitive presence in a blended learning environment. METHODS: Data samples were obtained from 98 engineering students in a blended learning course and analysed using Spearman’s correlation test, regression, ANOVA, and t-test. RESULTS: Findings suggested that TRIZ and industry talks strongly, positively, and significantly correlated with learning motivation, social presence, and cognitive presence. A well-rounded learning experience compounded of TRIZ and industry talks significantly affected learning motivation, social presence, and cognitive presence, thereby enhancing students’ programme outcome (PO) achievement. CONCLUSIONS: These findings can be attributed to the students’ independent learning capabilities with TRIZ and industry talks. Analogically, embracing TRIZ and industry talks helps turn blended learning into a “sweet instead of bitter pill to swallow” for engineering students in the face of the COVID-19 pandemic.

Small and medium-sized enterprises (SMEs) are constantly under pressure to grow. This pressure forces everyone involved to think about how best to run their business. Although there is much research on SME growth, previous research is fragmented and only addresses internal or external enablers. This study aims to construct an interaction model for all enablers that promote sustainable SME growth. An interpretive structural modeling (ISM) analysis is conducted to formulate an interaction model of enablers for SME growth. The results show that both internal and external enablers are crucial for SME growth. This study shows that the following internal enablers that are interrelated and strongly influence SME growth are MS (managerial skills), EO (entrepreneurial orientation), and OwS (ownership structure). In addition, external enablers such as CIL (customer involvement and location) and GS (government support) also play an important role in improving the performance of other factors for SME growth. In addition, this study also provides a guide for formulating strategies for SME sustainability. Effective policy formulation must be based on a correct understanding of the interdependence between enablers as a unified model of interaction. The interaction between the enablers highlighted and the level of the model would be helpful to all shareholders in finding appropriate strategies for SME growth.

Studies show that heavy machinery operators are exposed to risk factors of musculoskeletal diseases. However, there has yet to be a study investigating the grip analysis of heavy machinery control levers. This preliminary study aims to investigate the grip analysis of a system that emulates the push–pull operations, handle shapes, and resistance of wheel loader control lever systems. The system was designed, analysed, and optimised using Autodesk Inventor 2019 before fabrication and testing. It underwent usability testing for estimated and perceived grip force analysis (ergonomics analysis). The tests measured estimated force using a sensor glove, and perceived force using the Borg CR10 scale. The data were analysed using regression and paired t-tests. The findings suggested that pulling and high resistance factors required higher estimated force (339.50 N) and perceived force (5.625) than pushing and low resistance factors in manoeuvring the system (p < 0.05). The cylindrical handle required more estimated force (339.50 N) but less perceived force (4.5) than the spherical handle due to ergonomic design considerations (p < 0.05). Although there were inaccuracies in force measurement methods, the perceived method was still effective for data collection, since it is challenging to measure grip force in a real situation with heavy machinery. While this study was only a simulation, it provided researchers with ideas that may solve problems in the manipulation of heavy machinery control levers.

DRG1 is a highly conserved member of a class of GTPases implicated in ribosome biogenesis and translation. The expression of mammalian DRG1 is elevated in the central nervous system during development, and its function has been implicated in fundamental cellular processes including protein synthesis and cellular proliferation. Using exome sequencing, we identified rare and likely pathogenic germline DRG1 variants including three stop-gained p.Gly54*, p.Arg140*, p.Lys263* and a p.Asn248Phe missense variant. These alleles segregate recessively in four affected individuals from three unrelated families and cause a neurodevelopmental disorder with global developmental delay, microcephaly, short stature and craniofacial anomalies. Using functional assays, we show that these loss-of-function variants: 1) severely disrupt DRG1 mRNA/protein stability in patient-derived fibroblasts, 2) impair it’s GTPase activity in vitro and 3) compromise it’s binding to partner protein ZC3H15. Consistent with the importance of DRG1 in humans, targeted inactivation of Drg1 in mice resulted in pre-weaning lethality. Our work highlights the importance of DRG1 GTPase activity for normal development and underscores the significance of translation factor GTPases in human physiology and homeostasis.

ObjectiveUse next-generation sequencing (NGS) technology to improve our diagnostic yield in patients with suspected genetic disorders in the Asian setting.DesignA diagnostic study conducted between 2014 and 2019 (and ongoing) under the Singapore Undiagnosed Disease Program. Date of last analysis was 1 July 2019.SettingInpatient and outpatient genetics service at two large academic centres in Singapore.PatientsInclusion criteria: patients suspected of genetic disorders, based on abnormal antenatal ultrasound, multiple congenital anomalies and developmental delay. Exclusion criteria: patients with known genetic disorders, either after clinical assessment or investigations (such as karyotype or chromosomal microarray).InterventionsUse of NGS technology—whole exome sequencing (WES) or whole genome sequencing (WGS).Main outcome measures(1) Diagnostic yield by sequencing type, (2) diagnostic yield by phenotypical categories, (3) reduction in time to diagnosis and (4) change in clinical outcomes and management.ResultsWe demonstrate a 37.8% diagnostic yield for WES (n=172) and a 33.3% yield for WGS (n=24). The yield was higher when sequencing was conducted on trios (40.2%), as well as for certain phenotypes (neuromuscular, 54%, and skeletal dysplasia, 50%). In addition to aiding genetic counselling in 100% of the families, a positive result led to a change in treatment in 27% of patients.ConclusionGenomic sequencing is an effective method for diagnosing rare disease or previous ‘undiagnosed’ disease. The clinical utility of WES/WGS is seen in the shortened time to diagnosis and the discovery of novel variants. Additionally, reaching a diagnosis significantly impacts families and leads to alteration in management of these patients.

Multinational studies have reported monogenic etiologies in 25%-30% of children with steroid-resistant nephrotic syndrome. Such large studies are lacking in Asia. We established Deciphering Diversities: Renal Asian Genetics Network (DRAGoN) and aimed to describe the genetic and clinical spectrums in Asians. We prospectively studied a cohort of 183 probands with suspected genetic glomerulopathies from South and Southeast Asia, of whom 17% had positive family history. Using multi-gene panel sequencing, we detected pathogenic variants in 26 (14%) probands, of whom one-third had COL4A4 or COL4A5 variants (n = 9, 5%). Of those with COL4A5 defects, only 25% had features suggestive of Alport syndrome. Besides traditional predictors for genetic disease (positive family history and extrarenal malformations), we identified novel predictors, namely older age (6.2 vs. 2.4 years; p = 0.001), hematuria (OR 5.6; 95% CI 2.1-14.8; p 0.001), and proteinuria in the absence of nephrotic syndrome (OR 4.6; 95% CI 1.8-11.8; p = 0.001) at first manifestation. Among patients who first presented with proteinuria without nephrotic syndrome, the genetic diagnostic rates were60% when a second risk factor (positive family history or extrarenal manifestation) co-existed. The genetic spectrum of glomerulopathies appears different in Asia. Collagen IV genes may be included in sequencing panels even when suggestive clinical features are absent.

Erratum in Publisher Correction: Discovery of a genetic module essential for assigning left-right asymmetry in humans and ancestral vertebrates. Szenker-Ravi E, Ott T, Khatoo M, Moreau de Bellaing A, Goh WX, Chong YL, Beckers A, Kannesan D, Louvel G, Anujan P, Ravi V, Bonnard C, Moutton S, Schoen P, Fradin M, Colin E, Megarbane A, Daou L, Chehab G, Di Filippo S, Rooryck C, Deleuze JF, Boland A, Arribard N, Eker R, Tohari S, Ng AY, Rio M, Lim CT, Eisenhaber B, Eisenhaber F, Venkatesh B, Amiel J, Crollius HR, Gordon CT, Gossler A, Roy S, Attie-Bitach T, Blum M, Bouvagnet P, Reversade B.Nat Genet. 2022 Jun;54(6):906. doi: 10.1038/s41588-022-01053-8.PMID: 35304595 No abstract available.; International audience; The vertebrate left-right axis is specified during embryogenesis by a transient organ: the left-right organizer (LRO). Species including fish, amphibians, rodents and humans deploy motile cilia in the LRO to break bilateral symmetry, while reptiles, birds, even-toed mammals and cetaceans are believed to have LROs without motile cilia. We searched for genes whose loss during vertebrate evolution follows this pattern and identified five genes encoding extracellular proteins, including a putative protease with hitherto unknown functions that we named ciliated left-right organizer metallopeptide (CIROP). Here, we show that CIROP is specifically expressed in ciliated LROs. In zebrafish and Xenopus, CIROP is required solely on the left side, downstream of the leftward flow, but upstream of DAND5, the first asymmetrically expressed gene. We further ascertained 21 human patients with loss-of-function CIROP mutations presenting with recessive situs anomalies. Our findings posit the existence of an ancestral genetic module that has twice disappeared during vertebrate evolution but remains essential for distinguishing left from right in humans.

The RYR1 gene codes for a ryanodine receptor which is a calcium release channel in the skeletal muscle sarcoplasmic reticulum. It is associated with Malignant Hyperthermia (MH) and congenital myopathies including Central Core Disease (CCD), Multiminicore Disease (MMD) and Congenital Fibre-Type Disproportion (CFTD). There is currently little information on the epidemiology of RYR1 variants in Asians. Our study aims to describe the RYR1 variant landscape in a Singapore cohort unselected for RYR1-associated conditions. Data was retrieved from the SG10K pilot project, where whole genome sequencing was performed on volunteers unselected and undetermined for RYR1-associated conditions. Variants were classified based on pathogenicity using databases ClinVar and InterVar. Allele frequencies of pathogenic variants were compared between Chinese, Indians and Malays. Using databases ExAC, GnomAD and GenomeAsia 100k study, we further compared local allele frequencies to those in Europe, America and Asia. Data was analysed using R Commander. Significant P value was set at p RYR1 variants were missense mutations. We identified four pathogenic and four likely pathogenic RYR1 variants. All were related to the aforementioned RYR1-associated conditions. There were 6 carriers of RYR1 pathogenic variants amongst 4810 individuals, corresponding to an allele frequency of 0.06%. The prevalence of pathogenic variants was the highest amongst Indians (4 in 1127 individuals) (p = 0.030). Majority of pathogenic and likely pathogenic mutations were missense and located in mutational hotspots. These variants also occurred at higher frequencies in Asians than globally. This study describes the variant landscape of the RYR1 gene in Singapore. This knowledge will facilitate genetic screening for RYR1-related conditions.

Stepladders are compact, foldable ladders with flat steps and a platform. Despite all the research and design efforts, there are still limitations in terms of the multifunctionality, usability and simplicity of stepladders and related variants. By combining ideas, features and functions from patent literature, existing products and scientific journals, this study aims to conceptualise a multifunctional stepladder for improved usability. Five concepts are created, which are screened and evaluated against a set of criteria to select the best concept for improved usability, divided into three categories: simplicity, effectiveness and efficiency. The result is a versatile invention that functions as a stepladder, walker, wheelchair and Pilates chair, suitable for older people and caregivers in nursing homes. It allows medical records or supplies to be retrieved from high places without the need for inappropriate aids. The invention can replace wheelchairs and walkers and converts into a Pilates chair to provide a mobile exercise option for older people. The concept offers older people flexibility and independence in terms of mobility and healthcare, while saving space in the nursing home. Further design studies, prototyping and testing are needed before this idea can go into production.

BackgroundTheRYR1gene codes for a ryanodine receptor which is a calcium release channel in the skeletal muscle sarcoplasmic reticulum. It is associated with Malignant Hyperthermia (MH) and several congenital myopathies including Central Core Disease (CCD), Multiminicore Disease (MMD) and Congenital Fibre-Type Disproportion (CFTD). There is currently little information on the epidemiology ofRYR1variants in Asians. Our study aims to describe theRYR1variant landscape in a Singapore cohort unselected forRYR1-associated conditions.MethodsData was retrieved from the SG10K pilot project, where whole genome sequencing was performed on volunteers unselected and undetermined forRYR1-associated conditions. Variants were classified based on pathogenicity using databases ClinVar and InterVar. Allele frequencies of pathogenic variants were compared between Chinese, Indians and Malays. Using databases ExAC, GnomAD and GenomeAsia 100k study, we further compared local allele frequencies to those in Europe, America and Asia.ResultsMajority of theRYR1variants were missense mutations. We identified four pathogenic and four likely pathogenicRYR1variants. All were related to the aforementionedRYR1-associated conditions. There were 6 carriers ofRYR1pathogenic variants amongst 4810 individuals, corresponding to an allele frequency of 0.06%. The prevalence of pathogenic variants was the highest amongst Indians (4 in 1127 individuals). Majority of pathogenic and likely pathogenic mutations were missense and located in mutational hotspots. These variants also occurred at higher frequencies in Asians than globally.ConclusionThis study describes the variant landscape of theRYR1gene in Singapore. This knowledge will facilitate local efforts in developing precision medicine.

Genetics intersects with environmental, cultural, and social factors in the development of addictive disorders. This study reports the feasibility of whole-exome sequencing of trios (subject and two family members) to discover potential genetic variants in the development of substance use disorders (SUD). Family trios were recruited from the National Addictions Management Service in Singapore during the 2016–2018 period. Recruited subjects had severe alcohol use disorder (AUD) or opioid use disorder (OUD), with nicotine dependence (ND) and a family history of addictive disorders. Demographic characteristics and severity of addiction were captured. Whole-exome sequencing (WES) and analysis were performed on salivary samples collected from the trios. WES revealed variants in several genes in each individual and disruptive protein mutations in most. Variants were identified in genes previously associated with SUDs, such as Pleckstrin homology domain-containing family M member 3 (PLEKHM3), coiled-coil serine-rich protein 1 (CCSER1), LIM and calponin homology domains-containing protein 1 (LIMCH1), dynein axonemal heavy chain 8 (DNAH8), and the taste receptor type 2 member 38 (TAS2R38) involved in the perception of bitterness. The feasibility study suggests that subjects with a severe addiction profile, polysubstance use, and family history of addiction may often harbor gene variants that may predispose them to SUDs. This study could serve as a model for future precision medicine-based personalized interventional strategies for behavioral addictions and SUDs and for the discovery of potentially pathogenic genetic variants.

Analysis of tissue from a 34-years-old male patient from Austrian origin with a history of multiple fractures associated with painful episodes over the carpal, tarsal and at the end of the long bones respectively is presented. Radiographic images and axial 3DCT scans showed widespread defects in trabecular bone architecture and ill-defined cortices over these skeletal sites in the form of discrete cystic-like lesions. Family history indicated two sisters (one half and one full biological sisters) also with a history of fractures. Whole exome sequencing revealed two heterozygous missense mutations in TYROBP (MIM 604142; NM_003332.3) gene encoding for a cell-surface adaptor protein, which is part of a signaling complex triggering activation of immune responses. It is expressed in cells of the ectoderm cell linage such as NK and dendritic cells, macrophages, monocytes, myeloid cells, microglia cells and osteoclasts. The phenotype and genotype of the patient were consistent with the diagnosis of Nasu-Hakola disease (NHD) (OMIM 221770). Investigations at the bone material level of a transiliac bone biopsy sample from the patient using polarized light microscopy and backscatter electron imaging revealed disordered lamellar collagen fibril arrangement and extensively increased matrix mineralization. These findings are the first bone material data in a patient with NHD and point toward an osteoclast defect involvement in this genetic condition.

Developmental epileptic encephalopathies are devastating disorders characterized by intractable epileptic seizures and developmental delay. Here, we report an allelic series of germline recessive mutations in UGDH in 36 cases from 25 families presenting with epileptic encephalopathy with developmental delay and hypotonia. UGDH encodes an oxidoreductase that converts UDP-glucose to UDP-glucuronic acid, a key component of specific proteoglycans and glycolipids. Consistent with being loss-of-function alleles, we show using patients’ primary fibroblasts and biochemical assays, that these mutations either impair UGDH stability, oligomerization, or enzymatic activity. In vitro, patient-derived cerebral organoids are smaller with a reduced number of proliferating neuronal progenitors while mutant ugdh zebrafish do not phenocopy the human disease. Our study defines UGDH as a key player for the production of extracellular matrix components that are essential for human brain development. Based on the incidence of variants observed, UGDH mutations are likely to be a frequent cause of recessive epileptic encephalopathy., German Research Foundation (DFG); European Union (European Union); NEUROMICS Network; International Coordination Action (ICA); Fund for Scientific Research Flanders (FWO); Netherlands Organization for Scientific Research (ZONMW VIDI); National Medical Research Council, Singapore; A Strategic Positioning Fund on Genetic Orphan Diseases (GODAFIT); Industry Alignment Fund on Singapore Childhood Undiagnosed Diseases Program (SUREKids); Biomedical Research Council, A*STAR; Diana and Steve Marienhoff Fashion Industries Guild Endowed Fellowship in Pediatric Neuromuscular Diseases; Fondazione Bambino Gesù (Vite Coraggiose); Canadian Institutes of Health Research; Natural Sciences and Engineering Research Council of Canada; Eurocores Program EuroEPINOMICS; University of Antwerp Research Fund; FRAXA Foundation; Brain & Behavior Research Foundation, NARSAD Young Investigator Grant

Shwachman-Diamond syndrome (SDS) is a rare multisystem ribosomal biogenesis disorder characterized by exocrine pancreatic insufficiency, hematologic abnormalities and bony abnormalities. About 90% of patients have biallelic mutations in SBDS gene. Three additional genes-EFL1, DNAJC21 and SRP54 have been reported in association with a SDS phenotype. However, the cause remains unknown for ~10% of patients. Herein, we report a 6-year-old Chinese boy, who presented in the neonatal period with pancytopenia, liver transaminitis with hepatosplenomegaly and developmental delay, and subsequently developed pancreatic insufficiency complicated by malabsorption and poor growth. Exome sequencing identified a novel de novo heterozygous variant in EIF6 (c.182G>T, p.Arg61Leu). EIF6 protein inhibits ribosomal maturation and is removed in the late steps of ribosomal maturation by SBDS and EFL1 protein. Given the interaction of EIF6 with SBDS and EFL1, we postulate heterozygous variants in EIF6 as a novel cause of Shwachman-Diamond-like phenotype. We compared the phenotype of our patient with those in patients with mutation in SBDS, EFL1, DNAJC21, and SRP54 genes to support this association. Identification of more cases of this novel phenotype would strengthen the association with the genetic etiology.

Ermin is an actin-binding protein found almost exclusively in the central nervous system (CNS) as a component of myelin sheaths. Although Ermin has been predicted to play a role in the formation and stability of myelin sheaths, this has not been directly examined in vivo. Here we show that Ermin is essential for myelin sheath integrity and normal saltatory conduction. Loss of Ermin in mice caused de-compacted and fragmented myelin sheaths and led to slower conduction along with progressive neurological deficits. RNA sequencing of the corpus callosum, the largest white matter structure in the CNS, pointed to inflammatory activation in aged Ermin-deficient mice, which was corroborated by increased levels of microgliosis and astrogliosis. The inflammatory milieu and myelin abnormalities were further associated with increased susceptibility to immune-mediated demyelination insult in Ermin knockout mice. Supporting a possible role of Ermin deficiency in inflammatory white matter disorders, a rare inactivating mutation in the ERMN gene was identified in multiple sclerosis patients. Our findings demonstrate a critical role for Ermin in maintaining myelin integrity. Given its near exclusive expression in myelinating oligodendrocytes, Ermin deficiency represents a compelling “inside-out” model of inflammatory dysmyelination and may offer a new paradigm for the development of myelin stability-targeted therapies.

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A germline homozygous loss-of-function mutation in NUAK2 causes human fetal death due to anencephaly. Our functional tests establish that NUAK2, operating on the Hippo signaling axis, is an essential kinase that regulates cytoskeletal processes that govern cell shape during neural tube closure., Failure of neural tube closure during embryonic development can result in anencephaly, one of the most common birth defects in humans. A family with recurrent anencephalic fetuses was investigated to understand its etiology and pathogenesis. Exome sequencing revealed a recessive germline 21-bp in-frame deletion in NUAK2 segregating with the disease. In vitro kinase assays demonstrated that the 7–amino acid truncation in NUAK2, a serine/threonine kinase, completely abrogated its catalytic activity. Patient-derived disease models including neural progenitor cells and cerebral organoids showed that loss of NUAK2 activity led to decreased Hippo signaling via cytoplasmic YAP retention. In neural tube–like structures, endogenous NUAK2 colocalized apically with the actomyosin network, which was disrupted in patient cells, causing impaired nucleokinesis and apical constriction. Our results establish NUAK2 as an indispensable kinase for brain development in humans and suggest that a NUAK2-Hippo signaling axis regulates cytoskeletal processes that govern cell shape during neural tube closure., Graphical Abstract

This paper offers an interdisciplinary exploration linking the narratives of disaster studies and civil engineering programme in a Malaysian context. In Malaysia, civil engineers play a pivotal role in advancing the nation and people through the construction of infrastructure. This includes highways, buildings and dam construction. These constructions are heavily related to human beings and society at large. However, current literature indicates that civil engineers in Malaysia lack the ability to understand the narratives of trauma especially in cases of manmade and natural disasters. This is due to the fact that most civil engineering programmes focus on technical knowledge while little emphasis is given to trauma studies. Hence, this case study aims to link trauma studies and hydrometeorological disasters in Malaysia. Drawing theoretical frameworks from the work of the trauma narrative expert Cathy Caruth, this project aims to take her conceptual undertaking of trauma narratives to add on, compliment and strengthen the existing curriculum. The crux of this project involves civil engineering students in engaging with trauma narratives of disaster victims. The methodology is a narrative technique to capture the elements of trauma that can be represented in many forms. The paper reports on challenges and reflections as well as methodological constraints from this case study. It concludes with a promising integration of narrative technique in the curriculum.

Innovations in food manufacturing support the agenda for sustainable development goal 9 (SDG9) on industry, innovation and infrastructure. Pursuant to this goal, this study aims to develop an automated multi-spit lamb rotisserie machine that potentially improves the lamb-roasting productivity for small and medium enterprises (SMEs). The conceptualisation involved patents, scholarly literature and product reviews of lamb-roasting devices. The design and analysis are performed using Autodesk Inventor 2019. A scaled-down prototype is developed and tested with (1) roasting output, (2) roasting time and (3) temperature stability tests. The data for test (1) are analysed by comparing the means between control and experimental groups. The data for tests (2) and (3) are analysed using the t-test and Mann–Whitney U test, respectively. Significant differences are observed in tests (1) and (2), with outcomes being in favour of the proposed invention. The prototype cooks 92.27% faster with 700% more meat than a regular lamb roaster. It also cooks at a stable temperature. The cost analysis indicated that this invention could be sold at USD 278 if mass-produced. The design is structurally simple, inexpensive and easy to manufacture, allowing SMEs that rely on traditional spit-based machines to enhance their ability in producing roast lamb.

Summary Huntington disease (HD) is a dominant neurodegenerative disorder caused by a CAG repeat expansion in HTT. Here we report correction of HD human induced pluripotent stem cells (hiPSCs) using a CRISPR-Cas9 and piggyBac transposon-based approach. We show that both HD and corrected isogenic hiPSCs can be differentiated into excitable, synaptically active forebrain neurons. We further demonstrate that phenotypic abnormalities in HD hiPSC-derived neural cells, including impaired neural rosette formation, increased susceptibility to growth factor withdrawal, and deficits in mitochondrial respiration, are rescued in isogenic controls. Importantly, using genome-wide expression analysis, we show that a number of apparent gene expression differences detected between HD and non-related healthy control lines are absent between HD and corrected lines, suggesting that these differences are likely related to genetic background rather than HD-specific effects. Our study demonstrates correction of HD hiPSCs and associated phenotypic abnormalities, and the importance of isogenic controls for disease modeling using hiPSCs., Graphical Abstract, Highlights • A CRISPR-Cas9 and PiggyBac-based approach allows efficient correction of HD hiPSCs • The corrected hiPSCs can be differentiated into synaptically active neurons • Correction of HD gene mutation reverses a number of phenotypic abnormalities • Isogenic hiPSCs help distinguish mutation from genetic background-related effects, Pouladi and colleagues show that genetic correction of HD human induced pluripotent stem cells using a CRISPR-Cas9 and piggyBac transposon-based approach rescues a number of phenotypic abnormalities in derived neural cells, including increased susceptibility to growth factor withdrawal and deficits in mitochondrial respiration, and helps distinguish HD-specific from genetic background-related molecular and cellular phenotypes.

In five separate families, we identified nine individuals affected by a previously unidentified syndrome characterized by growth retardation, spine malformation, facial dysmorphisms, and developmental delays. Using homozygosity mapping, array CGH, and exome sequencing, we uncovered bi-allelic loss-of-function CDK10 mutations segregating with this disease. CDK10 is a protein kinase that partners with cyclin M to phosphorylate substrates such as ETS2 and PKN2 in order to modulate cellular growth. To validate and model the pathogenicity of these CDK10 germline mutations, we generated conditional-knockout mice. Homozygous Cdk10-knockout mice died postnatally with severe growth retardation, skeletal defects, and kidney and lung abnormalities, symptoms that partly resemble the disease's effect in humans. Fibroblasts derived from affected individuals and Cdk10-knockout mouse embryonic fibroblasts (MEFs) proliferated normally; however, Cdk10-knockout MEFs developed longer cilia. Comparative transcriptomic analysis of mutant and wild-type mouse organs revealed lipid metabolic changes consistent with growth impairment and altered ciliogenesis in the absence of CDK10. Our results document the CDK10 loss-of-function phenotype and point to a function for CDK10 in transducing signals received at the primary cilia to sustain embryonic and postnatal development., NIH, the National Cancer Institute; Center for Cancer Research; Strategic Positioning Fund for the Genetic Orphan Diseases program; Industry Alignment Fund for the Singapore Childhood Undiagnosed Diseases program from the A*STAR (Agency for Science, Technology, and Research) Biomedical Research Council; A*STAR Biomedical Research Council

ObjectiveTo investigate the possible involvement of germline mutations in a neurologic condition involving diffuse white matter lesions.MethodsThe patients were 3 siblings born to healthy parents. We performed homozygosity mapping, whole-exome sequencing, site-directed mutagenesis, and immunoblotting.ResultsAll 3 patients showed clinical manifestations of ataxia, behavioral and mood changes, premature hair loss, memory loss, and lower back pain. In addition, they presented with inflammatory-like features and recurrent rhinitis. MRI showed abnormal diffuse demyelination lesions in the brain and myelitis in the spinal cord. We identified an insertion in high-temperature requirement A (HTRA1), which showed complete segregation in the pedigree. Functional analysis showed the mutation to affect stability and secretion of truncated protein.ConclusionsThe patients' clinical manifestations are consistent with cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL; OMIM #600142), which is known to be caused by HTRA1 mutations. Because some aspects of the clinical presentation deviate from those reported for CARASIL, our study expands the spectrum of clinical consequences of loss-of-function mutations in HTRA1.

Natural-killer/T-cell lymphoma (NKTL) is a rare subset of non-Hodgkin lymphoma that demonstrates a unique geographic distribution, with higher prevalence in Asia compared to the West1. While cure remains achievable in early-stage disease, the prognosis for advanced-stage NKTL is dismal2. Recently, some progress has been made in uncovering the molecular pathogenesis of NKTL. In a genome-wide association study, strong correlations between HLA-DPB1 single-nucleotide polymorphisms and NKTL susceptibility were discovered, implicating altered antigen processing and presentation to CD4-positive T-lymphocytes in this Epstein-Barr virus (EBV)-associated malignancy3. Next generation sequencing also revealed recurrent somatic mutations such as TP53, JAK3, STAT3 and DDX3X in NKTL4,5. In this paper, we report a pair of male siblings from a non-consanguineous Chinese family who were diagnosed with NKTL, and provide initial evidence for novel recessive germline mutations in FAM160A1 identified through next-generation sequencing. The index patient was 35 years old, when he presented with nasal blockage in March 2013. 18-FDG-PET/CT imaging revealed an 18-FDG-avid nasal mass infiltrating into the palate, as well as enlarged cervical lymph nodes. Biopsy of the mass showed abnormal lymphoid cells positive for CD56 by immunohistochemistry (IHC) as well as EBV-encoded RNA (EBER) by in-situ hybridization. He was diagnosed with stage IIA extranodal NKTL, nasal type, and treated with 4 cycles of bortezomib-GIFOX (gemcitabine, ifosfamide and oxaliplatin) as part of a clinical trial followed by radiotherapy to the nasal region. He had primary-refractory disease and was further treated with 4 cycles of SMILE (dexamethasone, methotrexate, ifosfamide, l-asparaginase, and etoposide) followed by high-dose chemotherapy and autologous stem cell transplantation. He progressed and received ruxolitinib off-label, followed by RAD001 (mTOR inhibitor) and LBH589B (histone deacetylase inhibitor) as part of another clinical trial. He then had radiotherapy to an ulcerating penile lesion before he died of progressive disease 27 months after diagnosis (Supplementary Table 1). His younger brother was 18 years old, when diagnosed with NKTL affecting the nasal floor in 1998 following a bout of epistaxis. He received 6 cycles of CHOP (cyclophosphamide, doxorubicin, vincristine, and prednisone) with high-dose methotrexate and went into complete remission. Three years later he was diagnosed with chronic myeloid leukemia, for which he received hydroxyurea. In 2004, he had a relapse of NKTL and received ESHAP (etoposide, prednisolone, cytarabine and cisplatin), total body irradiation and allogeneic bone marrow transplant. He died of transplant-related complications 6 years from diagnosis. These siblings have an older brother unaffected by any hematological malignancy. Their father died of a non-malignant condition in his fifties and their mother remains well at the age of 68 years. Among their first-degree relatives, none were known to be inflicted with hematologic malignancies (Fig. ​(Fig.11). Open in a separate window Fig. 1 Clinical characterization of brothers with familial NKTL. a 18-FDG-PET/CT image depicting a large nasal mass infiltrating into the palate, of which biopsy showed abnormal lymphoid cells positive for Epstein-Barr virus encoded RNA (EBER) by in situ hybridization. b, c Inheritance modelling identified homozygous germline mutations of FAM160A1 c.2827 C > T in both affected brothers, heterozygous carriage in their mother and paternal aunt, and homozygous wildtype in their healthy older brother. d, e The non-synonymous substitution at FAM160A1 c.2827 C > T results in an amino-acid alteration from arginine to cysteine (p.R943C). Patterns and frequencies of known mutations in other cancer types are shown

Objective To investigate the possible involvement of germline mutations in a neurologic condition involving diffuse white matter lesions. Methods The patients were 3 siblings born to healthy parents. We performed homozygosity mapping, whole-exome sequencing, site-directed mutagenesis, and immunoblotting. Results All 3 patients showed clinical manifestations of ataxia, behavioral and mood changes, premature hair loss, memory loss, and lower back pain. In addition, they presented with inflammatory-like features and recurrent rhinitis. MRI showed abnormal diffuse demyelination lesions in the brain and myelitis in the spinal cord. We identified an insertion in high-temperature requirement A (HTRA1), which showed complete segregation in the pedigree. Functional analysis showed the mutation to affect stability and secretion of truncated protein. Conclusions The patients' clinical manifestations are consistent with cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL; OMIM #600142), which is known to be caused by HTRA1 mutations. Because some aspects of the clinical presentation deviate from those reported for CARASIL, our study expands the spectrum of clinical consequences of loss-of-function mutations in HTRA1.

Background Cenani-Lenz Syndactyly (CLS) syndrome is a rare autosomal recessive disorder characterized by syndactyly and oligodactyly of fingers and toes, disorganization and fusion of metacarpals, metatarsals and phalanges, radioulnar synostosis and mesomelic shortness of the limbs, with lower limbs usually being much less affected than upper limbs. Case presentation we report here two patients, born to consanguineous Sri Lankan parents, present with bilateral postaxial oligodactyly limited to upper limbs. While the proband has no noticeable facial dysmorphism, renal impairments or cognitive impairments, his affected sister displays a few mild facial dysmorphic features. Whole exome sequencing of the proband showed a novel deleterious homozygous mutation (c.1348A > G) in the LRP4 gene, resulting in an Ile450-to-Val (I450V) substitution. Conclusion This recessive mutation in LRP4 confirmed the diagnosis of CLS syndrome in two patients present with isolated hand syndactyly. This is the first reported case of CLS syndrome in a family of Sri Lankan origin. Electronic supplementary material The online version of this article (10.1186/s12881-018-0646-1) contains supplementary material, which is available to authorized users.

Arthrogryposis multiplex congenita (AMC) is a developmental condition characterized by multiple joint contractures resulting from reduced or absent fetal movements. Through genetic mapping of disease loci and whole-exome sequencing in four unrelated multiplex families presenting with severe AMC, we identified biallelic loss-of-function mutations in LGI4 (leucine-rich glioma-inactivated 4). LGI4 is a ligand secreted by Schwann cells that regulates peripheral nerve myelination via its cognate receptor ADAM22 expressed by neurons. Immunolabeling experiments and transmission electron microscopy of the sciatic nerve from one of the affected individuals revealed a lack of myelin. Functional tests using affected individual-derived iPSCs showed that these germline mutations caused aberrant splicing of the endogenous LGI4 transcript and in a cell-based assay impaired the secretion of truncated LGI4 protein. This is consistent with previous studies reporting arthrogryposis in Lgi4-deficient mice due to peripheral hypomyelination. This study adds to the recent reports implicating defective axoglial function as a key cause of AMC.

Background: Acute myeloid leukemia (AML) with double-mutated CEBPA (dmCEBPA) occurred in about 10% of AML and it is usually associated with normal karyotype AML. It is classified as a favorable risk AML with an estimated 5 years overall survival in excess of 50%. Patients who achieved complete remission (CR) with induction chemotherapy will be consolidated with chemotherapy. Around 40% of the patients would suffer a relapse and required further salvage chemotherapy followed by allogeneic stem cell transplant. Co-mutations occurred frequently in dmCEBPA AML with TET2 being the most commonly co-mutated (34%) followed by GATA1 mutation (21%), WT1(13.7%), DNMT3a (9.6%), ASXL1 (9.5%), NRAS (8.4%) and other less common genes. Only TET2 mutation appeared to have negative impact on prognosis. In this study, we explore the relapse cases with Whole-Exome sequencing (WES) and compared with a control case (Chemo-responsive dmCEBPA AML who is in continuous complete remission (CCR)). We aimed to identify novel mutations not previously reported and with potential as new prognostic marker as well as therapeutic target for further exploration. Method: We identified 3 relapsed dmCEBPA AML cases from our leukemia cell bank and compared with a case of chemo-responsive dmCEBPA AML who is still in CCR at 8 years follow-up. Duration of prior CR for case #1, #2 and #3 were 10 months, 1 year 9 month and 1 year 10 months. WES was performed for all 4 cases. In each case, the variants were annotated using the IonReporter software and an additional customized script that annotates for variant population frequency, genotype-phenotype associations and computational missense prediction tools. Variants were filtered by removing all reference calls, intergenic variants and variants not present in the chemoresponsive case. Only exonic and non-synonymous variants were considered. Next, we look for variants with a phenotype-genotype association common with the AML phenotype by looking for variants with "Leukemia" terms listed in OMIM. In addition, in order to identify novel mutations not presently associated with AML, we identified variants that had a "Pathogenic" entry in ClinVar. Results: All 4 cases revealed the typical CEBPA mutants with VAF exceeding 40% except one with germline mutation. When compared with the chemo-responsive case, KIT was mutated in 2 out of 3 relapse cases. WNT10A was mutated in all 3 cases. The details of the mutated genes are presented in Table 1 (see below). WNT10A gene encodes for a secretory signaling protein in the WNT family of structurally related genes that are involved WNT-beta-catenin-TCF signaling pathway. WNT10A is strongly expressed in cell lines of promyelocytic leukemia. Beta-catenin, the downstream target of the WNT signaling pathway, is highly expressed in poor prognostic AML cells (Staal et al. Nature review Immun 2008). The Gly213 residue is highly evolutionary conserved in vertebrate with a PhyloP score of 9.8. Both missense variants Gly213Ser and Arg171Cys are computationally predicted be damaging (DANN score 0.99). However, these 2 variants are fairly common in the East Asian population (gnomAD_EAS MAF G213S 2.7% & R171C 1.5%). Both variants are ACMG guidelines classified as Variants of Unknown Significance (VUS). KIT gene encodes for the proto-oncogene c-kit. Mutations in c-kit are associated with mastocytosis and AML. Both variants occur within the kinase domain (exon 17) of KIT. Asp816Val variant has been linked to poorer prognosis and worse outcome on AML patients. Both missense variants are computationally predicted to be damaging (DANN score 0.99). Both Asp816Val and Asn822Lys are AMCG classified as Likely Pathogenic and VUS respectively. Conclusion: With stringent criteria of filtering in WES of relapsed dmCEBPA cases, when compared with the control, we found that KIT was mutated in 2 out of 3 cases, while WNT10A was mutated in all 3 cases. Though the sample number was small, these findings would warrant further evaluation in larger cohort of dmCEBPA AML and interrogation in pre-clinical model. Table 1. Disclosures No relevant conflicts of interest to declare.

The increasing demand for specialised instruction or lexis for Non-Native English Speakers (NNES) in various disciplines has brought about extensive research of specialized vocabulary in academic texts which help learners to make acquainted with their discourse communities. The word list which consists of the most essential words or known as “building blocks” in the specialized field is regarded as one of the most significant prerequisites in terms of curriculum development. This research emphasizes on the most frequently used engineering academic vocabulary in the form of an engineering technology word list developed using locally written Malaysian engineering technology textbooks for vocational programmes in upper secondary education. The frequently used engineering technology words are selected from the vocational-programme engineering corpus (VPEC) to enhance English for Engineering Purposes (EEP) learning. A word list named Engineering Technology Word List (ETWL) is developed and it is a valuable resource to English for Engineering Purposes (EEP) in Malaysia. The introduction of this word list can be a source of reference where key vocabulary can be accessed for curriculum development in vocational programmes. Besides that, in order for the publishers and EEP textbook writers to further advance the arrangement of vocabulary in developing EEP material, the ETWL should be the key reference.

TWINKLE (c10orf2) gene is responsible for autosomal dominant progressive external ophthalmoplegia (PEO). In rare cases, additional features such as muscle weakness, peripheral neuropathy, ataxia, cardiomyopathy, dysphagia, dysphonia, cataracts, depression, dementia, parkinsonism, and hearing loss have been reported in association with heterozygous mutations of the TWINKLE gene.We have studied a large Iranian family with myopathy, dysphonia, dysphagia, and behavior change in addition to PEO in affected members.We identified a missense mutation c.1121GA in the c10orf2 gene in all affected members. Early death is a novel feature seen in affected members of this family that has not been reported to date.The association of PEO, myopathy, dysphonia, dysphagia, behavior change and early death has not been previously reported in the literature or other patients with this mutation.

Summary The bacterial pathogen Xanthomonas campestris pv. campestris co-ordinates virulence factor production and biofilm dispersal through a diffusible signal factor (DSF)-mediated cell–cell communication mechanism. The RpfC/RpfG two-component system plays a key role in DSF signal transduction and appears to modulate downstream DSF regulon by changing intracellular content of cyclic dimeric GMP (c-di-GMP), an unusual nucleotide second messenger. Here we show that Clp, a conserved global regulator showing a strong homology to the cAMP nucleotide receptor protein Crp of Escherichia coli, is essential for DSF regulation of virulence factor production but not for biofilm dispersal. Deletion of clp in Xcc changed the transcriptional expression of 299 genes including a few encoding transcription factors. Further genetic and microarray analysis led to identification of a homologue of the transcriptional regulator Zur, and a novel TetR-type transcription factor FhrR. These two regulatory factors regulated different sets of genes within Clp regulon. These results outline a hierarchical signalling network by which DSF modulates different biological functions, and may also provide a clue on how the novel nucleotide signal can be coupled to its downstream regulatory networks.

Background: Endocrine-cerebro-osteodysplasia (ECO) syndrome [MIM:612651] caused by a recessive mutation (p.R272Q) in Intestinal cell kinase (ICK) shows significant clinical overlap with ciliary disorders. Similarities are strongest between ECO syndrome, the Majewski and Mohr-Majewski short-rib thoracic dysplasia (SRTD) with polydactyly syndromes, and hydrolethalus syndrome. In this study, we present a novel homozygous ICK mutation in a fetus with ECO syndrome and compare the effect of this mutation with the previously reported ICK variant on ciliogenesis and cilium morphology. Results: Through homozygosity mapping and whole-exome sequencing, we identified a second variant (c.358G > T; p.G120C) in ICK in a Turkish fetus presenting with ECO syndrome. In vitro studies of wild-type and mutant mRFP-ICK (p.G120C and p.R272Q) revealed that, in contrast to the wild-type protein that localizes along the ciliary axoneme and/or is present in the ciliary base, mutant proteins rather enrich in the ciliary tip. In addition, immunocytochemistry revealed a decreased number of cilia in ICK p.R272Q-affected cells. Conclusions: Through identification of a novel ICK mutation, we confirm that disruption of ICK causes ECO syndrome, which clinically overlaps with the spectrum of ciliopathies. Expression of ICK-mutated proteins result in an abnormal ciliary localization compared to wild-type protein. Primary fibroblasts derived from an individual with ECO syndrome display ciliogenesis defects. In aggregate, our findings are consistent with recent reports that show that ICK regulates ciliary biology in vitro and in mice, confirming that ECO syndrome is a severe ciliopathy., Dutch Kidney Foundation (KOUNCIL consortium project CP11.18 to HHA) and the Netherlands Organization for Health Research and Development (ZonMW Veni-91613008 to HHA) and the Netherlands Organization for Scientific research (NWO Vici-016130664 to RR). This work was also funded by a Strategic Positioning Fund on Genetic Orphan Diseases from A*STAR, Singapore, and the Scientific and Technological Research Council of Turkey (TÜBİTAK) (TUBITAK) by 112S398 to HK (E-RARE network CRANIRARE-2)

CC-BY-NC-SA; International audience; Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

Introduction: Natural-killer/T-cell lymphoma (NKTL) is a rare subset of non-Hodgkin's lymphoma that is more prevalent in Asia than in the West. We report a case of two brothers who were diagnosed with NKTL and died of their disease at 23 and 37 years old respectively, and further investigations performed to determine the underlying genetic basis to their disease. Methods Both patients were recruited into the Singapore lymphoma study where retrieval of their clinical data and biospecimens had been approved by the Singhealth instititutional review board. Their clinical courses are described using information from electronic medical records. For the older brother we extracted tumor DNA from a patient-derived xenograft (PDX), and DNA from a buccal swab and peripheral blood (PB) sample. In the younger brother DNA was extracted from normal and tumor tissue from archived formalin fixed paraffin embedded (FFPE) samples. DNA from the unaffected mother, older brother and paternal aunt were obtained from PB and buccal swab samples. We performed whole exome sequencing (WES) on the younger affected brother's tumor, the older affected brother's, mother's and unaffected brother's blood sample. Subsequent analysis of variants took into account autosomal recessive (AR), X-linked recessive (XR) and autosomal dominant (AD) inheritance models. Candidate genes are validated using Sanger sequencing. Microarray on the older affected brother and 12 sporadic NKTL cases were analyzed. Results The older affected brother was 35 years old when he presented with left nasal blockage in March 2013. He was diagnosed with stage IIA NKTL and treated with 4 cycles of bortezomib-GIFOX as part of a clinical trial followed by radiotherapy to the nasal region. He had primary refractory disease and was further treated with 4 cycles of SMILE followed by high dose chemotherapy and autologous stem cell transplantation (HDC/ASCT). He progressed and received off-label ruxolitinib, and everolimus/HDAC inhibitor as part of a clinical trial. He then had radiotherapy to an ulcerating penile lesion before he died of progressive disease 27months after diagnosis. The younger affected brother was 18 years old when he was diagnosed with NKTL in 1998. He received 6 cycles of CHOP with intravenous high-dose methotrexate and intrathecal methotrexate and went into remission. Three years later, he was diagnosed with chronic myeloid leukemia and 6 years later, he had a relapse of NKTL for which he received ESHAP, TBI and allogeneic bone marrow transplant. He died of transplant related complication 6 years after diagnosis. They both have an older unaffected brother. Their father died of non-malignant condition in his fifties and their mother remains well. They have no other relatives with hematologic malignancy. We have identified several candidate variants and genes on WES that are being validated and functional studies are ongoing. GEP shows 234 genes that are significantly upregulated in the affected brother's tumor compared to 12 sporadic NKTL tumors including p53 and 12 genes that were significantly downregulated including CTLA4 and virus entry pathways. Conclusion: We describe a case of two brothers with a rare lymphoma and the ongoing efforts in elucidating the genetic basis of their disease. To the best of our knowledge this is the first study of its kind to be presented. Disclosures No relevant conflicts of interest to declare.