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Discovering the entire list of human ciliary genes would help in the diagnosis of cilia-related human disorders known as ciliopathy, but at present the genetic diagnosis of many ciliopathies (over 30%) is far from complete (Bachmann-Gagescu et al., 2015; Knopp et al., 2015; Paff et al., 2018). In a theory, many independent approaches may uncover the whole list of ciliary genes, but 30% of the genes on the ciliary gene list are still ciliary candidate genes (van Dam et al., 2019; Vasquez et al., 2021). All of these cutting-edge techniques, however, have relied on a different single strategy to discover ciliary candidate genes. Because different methodologies demonstrated distinct capabilities with varying quality, categorizing the ciliary candidate genes in the ciliary gene list without further evidence has been difficult. Here, we present a method for predicting ciliary capacity of each human gene that incorporates diverse methodologies (single-cell RNA sequencing, protein-protein interactions (PPIs), comparative genomics, transcription factor (TF)-network analysis, and text mining). By integrating multiple approaches, we reveal previously undiscovered ciliary genes. Our method, CilioGenics, outperforms other approaches that are dependent on a single method. Our top 500 gene list contains 256 new candidate ciliary genes, with 31 experimentally validated. Our work suggests that combining several techniques can give useful evidence for predicting the ciliary capability of all human genes.

Rapid and low-cost sequencing, as well as computer analysis, have facilitated the diagnosis of many genetic diseases, resulting in a substantial rise in the number of disease-associated genes. However, genetic diagnosis of many disorders remains problematic due to the lack of interpretation for many genetic variants, especially missenses, the infeasibility of high-throughput experiments on mammals, and the shortcomings of computational prediction technologies. Additionally, the available mutant databases are not well-utilized. Toward this end, we usedCaenorhabditis elegansmutant resources to delineate the functions of eight missense variants (V444I, V517D, E610K, L732F, E817K, H873P, R1105K, and G1205E) and two stop codons (W937stop and Q1434stop), including several matching variants (MatchVar) with human in ciliopathy associated IFT-140 (also called CHE-11)//IFT140 (intraflagellar transport protein 140). Moreover, MatchVars carryingC. elegansmutants, including IFT-140(G680S) and IFT-140(P702A) for the human (G704S) (dbSNP: rs150745099) and P726A (dbSNP: rs1057518064 and a conflicting variation) were created using CRISPR/Cas9. IFT140 is a key component of IFT complex A (IFT-A), which is involved in the retrograde transport of IFT along cilia and the entrance of G protein-coupled receptors (GPCRs) into cilia. Functional analysis of all ten variants revealed that P702A and W937stop, but not others phenocopied the ciliary phenotypes (short cilia, IFT accumulations, mislocalization of membrane proteins, and cilia entry of non-ciliary proteins) of the IFT-140 null mutant, indicating that both P702A and W937stop are phenotypic inC. elegans. Our functional data offered experimental support for interpreting human variants, by using ready-to-use mutants carrying MatchVars and generating MatchVars with CRISPR/Cas9.

The availability of genetic variants, together with phenotypic annotations from model organisms, facilitates comparing these variants with equivalent variants in humans. However, existing databases and search tools do not make it easy to scan for equivalent variants, namely “matching variants” (MatchVars) between humans and other organisms. Therefore, we developed an integrated search engine called ConVarT (http://www.convart.org/) for matching variants between humans, mice, andC. elegans. ConVarT incorporates annotations (including phenotypic and pathogenic) into variants, and these previously unexploited phenotypic MatchVars from mice andC. eleganscan give clues about the functional consequence of human genetic variants. Our analysis shows that many phenotypic variants in different genes from mice andC. elegans, so far, have no counterparts in humans, and thus, can be useful resources when evaluating a relationship between a new human mutation and a disease.

ConVarT (https://convart.org/) is a search engine for searching for conjugate variants between humans and other species. The search engine is based on matching conjugate variants called MatchVars between species. Matching equivalent variants requires correct alignment of orthologous proteins with the use of multiple sequence alignments (MSA). Indeed, the ConVarT pipeline has performed over a million MSAs and integrated variants and variant-specific annotations (pathogenicity, phenotypic variants; etc.) into the corresponding positions on MSAs. When a clinically relevant variant is discovered whose functional relevance is unknown, ConVarT offers clinician scientists the possibility to search for a MatchVar in other species and to look for functional data on that variant. Fortunately, ConVarT enables users to paste a protein sequence in FASTA format to search for human orthologous proteins. A pairwise sequence alignment (PSA) is then performed between the provided protein sequence and the human orthologous protein, allowing users to visualize human variants on the PSA. Here, we describe the step-by-step usage of ConVarT. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Searching matching variants (MatchVar) with gene/protein identifiers. Basic Protocol 2: Searching with a FASTA sequence. Alternate Protocol: Search with gene name in multiple species. Basic Protocol 3: Search genes associated with a disease.

Gene therapy studies have been of great importance in the elimination of genetic diseases, and the capability of the CRISPR/Cas9 genome editing technique to correct genetic defects has shown great promise. As DNA-based Cas9 nuclease delivery is preferable because of its low cost and higher stability, effective vector-based CRISPR/Cas9 administration is urgently needed. Here, we used the multicellular organism Caenorhabditis elegans to optimize the polymer-mediated DNA delivery system to generate mutants with CRISPR/Cas9. Toward this end, the cationically quaternized polymer of POEGMA-b-P4VP (POEGMA-b-QP4VP) as a carrier of CRISPR/Cas9 components was first synthesized, followed by the formation of plasmid DNA-polymer complex called polyplexes. 1H NMR, Zeta-Sizer, Scanning Electron Microscopy (SEM) analysis, and gel retardation experiments confirmed the polyplexes formation, including pRF4 (Roller) and sgRNA dpy-10, which were then incubated with C. elegans. The polymer-mediated delivery system facilitated the generation of transgenic Roller animals and heritable Dumpy mutants with CRISPR/Cas9. Our study for the first time demonstrated optimized administration of CRISPR/Cas 9 components to C. elegans.

The correct intraflagellar transport (IFT) assembly at the ciliary base and the IFT turnaround at the ciliary tip are key for the IFT to perform its function, but we still have poor understanding about how these processes are regulated. Here, we identify WDR31 as a new ciliary protein, and analysis from zebrafish and Caeno-rhabditis elegans reveals the role of WDR31 in regulating the cilia morphology. We find that loss of WDR-31 together with RP-2 and ELMD-1 (the sole ortholog ELMOD1-3) results in ciliary accumu-lations of IFT Complex B components and KIF17 kinesin, with fewer IFT/BBSome particles traveling along cilia in both anterograde and retrograde directions, suggesting that the IFT/BBSome entry into the cilia and exit from the cilia are impacted. Furthermore, anterograde IFT in the middle segment travels at increased speed in wdr-31;rpi-2;elmd-1. Remarkably, a non-ciliary protein leaks into the cilia of wdr-31;rpi-2;elmd-1, possibly because of IFT de-fects. This work reveals WDR31-RP-2-ELMD-1 as IFT and BBSome trafficking regulators. National Institutes of Health (NIH) - USA P40 OD010440 Abdullah Gul University Scienti fic Research Project Coordination Unit TOA-2018-110 German Research Foundation (DFG) INST 2388/62-1

C. elegans EGL-36 displays extensive similarity to human KCNC proteins, the conserved potassium channel subfamily KV3 (the Shaw subfamily). This potassium channel subfamily contains four genes KCNC1, KCNC2, KCNC3, and KCNC4 encoding KV3.1 (Shaker), KV3.2 (Shab), KV3.3 (Shaw), and KV3.4 (Shal), respectively. Previous studies have demonstrated that C. elegans EGL-36 is expressed in the egg-laying muscles, ventral cord neurons, and the subset of ciliated sensory neurons including ADEL, ADER, PHB through its subcellular localization in the ciliated sensory neurons remains unknown (Elkes et al. 1997; Johnstone et al. 1997). To observe the subcellular localization of EGL-36 in the ciliated sensory neurons in C. elegans, we tagged green fluorescent protein (GFP) at the C-termini of EGL-36 with a cilia-specific promoter. We observed overexpressed EGL-36::GFP in the subsets of sensory neurons in the head and tail including PHB sensory neurons in the tail but not in the PHA sensory neuron, which is in line with previous findings (Elkes et al. 1997; Johnstone et al. 1997) (Figure 1A). Confocal laser scanning microscopy shows that EGL-36::GFP is predominantly located at the base of the cilium. The EGL-36::GFP signal can be found in the neuronal cell body, with weak dendrite staining, where they may function in the dendritic excitability (Figure 1A).

We report the identification of C. elegans F42G8.19 as the ortholog of human CEP41. This conclusion was based on database searches, reciprocal BLAST analysis, and cilia-specific localization. To look for the orthologous gene of human CEP41 in C. elegans, we used three databases: the model organism Alliance of Genome Resources (https://www.alliancegenome.org/, Release 3.2.0), OrthoList 2 (http://ortholist.shaye-lab.org/, Release 2017), and ConVarT (https://convart.org/, Release 2020) (Kim et. al., 2018; Pir et. al., 2021). On the Alliance of Genome Resources and ConVarT, we discovered that C. elegans F42G8.19 is the ortholog of human CEP41. To validate this conclusion, we ran a manual reciprocal BLAST analysis (the Reciprocal Best Hits BLAST (RBHB)). The protein-protein BLAST (BLASTp) search of human CEP41 protein sequence (NP 061188.1) revealed F42G8.19 as the top C. elegans hit (Altschul et. al., 1990). In the following step, the protein sequence from the best hit C. elegans F42G8.19 (NP_001294206.1) was compared to human proteins, with human CEP41 emerging as the best match. C. elegans F42G8.19 encodes a 182-amino-acid protein that is shorter than the 373-amino-acid human CEP41 protein (Figure 1A). We subsequently performed the amino acid alignments of human CEP41 (169–373 amino acid) and C. elegans F42G8.19 (1–182 amino acid), which revealed over 24 % identity to each other (Figure 1A). We eventually determined whether C. elegans F42G8.19 has a rhodanese domain as human CEP41 (169-266 aa), and our query showed that C. elegans F42G8.19 has a rhodanese domain (30-121 aa) (Figure 1A) (Lee et. al., 2012). Taken together, our analysis revealed that C. elegans F42G8.19 is orthologous to human CEP41, and C. elegans F42G8.19 was therefore assigned CEPH-41 (CEntrosomal Protein Homolog 41).

The term “ciliopathy” refers to a group of over 35 rare disorders characterized by defective cilia and many overlapping clinical features, such as hydrocephalus, cerebellar vermis hypoplasia, polydactyly, and retinopathy. Even though many genes have been implicated in ciliopathies, the genetic pathogenesis in certain cases remains still undisclosed. Here, we identified a homozygous truncating variant in WDR31 in a patient with a typical ciliopathy phenotype encompassing congenital hydrocephalus, polydactyly, and renal agenesis. WDR31 is an evolutionarily conserved protein that localizes to the cilium and cilia-related compartment. Analysis from zebrafish supports the role of WDR31 in regulating the cilia morphology. The CRISPR/Cas9 knock-in (p.Arg261del) C. elegans model of the patient variant (p.Arg268*) reproduced several cilia-related defects observed in wdr-31 null mutants. Mechanistic analysis from C. elegans revealed that WDR-31 functions redundantly with ELDM-1 (ELMOD protein) and RPI-2 (RP2) to regulate the IFT trafficking through controlling the cilia entry of the BBSome. This work revealed WDR31 as a new ciliopathy protein that regulates IFT and BBSome trafficking.

The correct intraflagellar transport (IFT) assembly at the ciliary base and the IFT turnaround at the ciliary tip are key for the IFT to perform its function, but we still have poor understanding about how these processes are regulated. Here, we identify WDR31 as a new ciliary protein, and analysis from zebrafish andCaenorhabditis elegansreveals the role ofWDR31in regulating the cilia morphology. We find that loss of WDR-31 together with RP-2 and ELMD-1 (the sole ortholog ELMOD1-3) results in ciliary accumulations of IFT Complex B components and KIF17 kinesin, with fewer IFT/BBSome particles traveling along cilia in both anterograde and retrograde directions, suggesting that the IFT/BBSome entry into cilia and exit from cilia are impacted. Furthermore, anterograde IFT in the middle segment travel at increased speed inwdr-31;rpi-2;elmd-1. Remarkably, a non-ciliary protein leaks into cilia ofwdr-31;rpi-2;elmd-1possible due to IFT defects. This work reveals WDR31-RP-2-ELMD-1 as IFT and BBSome trafficking regulators.

SummarySequence alignment is an excellent way to visualize the similarities and differences between DNA, RNA, or protein sequences, yet it is currently difficult to jointly view sequence alignment data with genetic variations, modifications such as post-translational modifications, and annotations (i.e. protein domains). Here, we develop the MSABrowser tool that makes it easy to co-visualize genetic variations, modifications, and annotations on the respective positions of amino acids or nucleotides in pairwise or multiple sequence alignments. MSABrowser is developed entirely in JavaScript and works on any modern web browser at any platform, including Linux, Mac OS X, and Windows systems without any installation. MSABrowser is also freely available for the benefit of the scientific community.Availability and implementationMSABrowser is released as open-source and web-based software under GNU General Public License, version 3.0 (GPLv3). The visualizer, documentation, all source codes, and examples are available athttp://thekaplanlab.github.io/and GitHub repositoryhttps://github.com/thekaplanlab/msabrowser.Supplementary informationSupplementary data are available online.

Glutamylation is a post-translational modification found on tubulin that can alter the interaction between microtubules (MTs) and associated proteins. The molecular mechanisms regulating tubulin glutamylation in response to the environment are not well understood. Here, we show that in the sensory cilia of Caenorhabditis elegans, tubulin glutamylation is upregulated in response to various signals such as temperature, osmolality, and dietary conditions. Similarly, tubulin glutamylation is modified in mammalian photoreceptor cells following light adaptation. A tubulin glutamate ligase gene ttll-4, which is essential for tubulin glutamylation of axonemal MTs in sensory cilia, is activated by p38 MAPK. Amino acid substitution of TTLL-4 has revealed that a Thr residue (a putative MAPKphosphorylation site) is required for enhancement of tubulin glutamylation. Intraflagellar transport (IFT), a bidirectional trafficking system specifically observed along axonemal MTs, is required for the formation, maintenance, and function of sensory cilia. Measurement of the velocity of IFT particles revealed that starvation accelerates IFT, which was also dependent on the Thr residue of TTLL-4. Similarly, starvation-induced attenuation of avoidance behaviour from high osmolality conditions was also dependent on ttll-4. Our data suggest that a novel evolutionarily conserved regulatory system exists for tubulin glutamylation in sensory cilia in response to the environment. National Bio-Resource Project of the MEXT, Japan National Center for Research Resources, National Institutes of Health (NIH) JSPS KAKENHI 25116712 -25293044 -25440082 -12J06986 MEXT Project for Creation of Research Platforms and Sharing of Advanced Research Infrastructure MEXT JASSO Otsuka Toshimi Foundation Takeda Science Foundation

Lim, Sungwoo/0000-0002-4890-0396 WOS:000418429800007 PubMed: 28369953 Objective: This article presents data on the burden of periodontal diseases in Turkish adults aged 35 years or older. Methods: Within each region of Turkey, a rural and an urban area or city were selected in 2009-10 using a probability proportional to size method. In the selected towns, local officials who were familiar with their communities assisted in recruiting subjects. Loss of Attachment (LOA) was measured at six sites around each tooth present in the mouth, excluding third molars. Additionally, the Community Periodontal Index was used to assess the severity of periodontal diseases around 12 index teeth. Self-reported data on key risk factors were also collected. Weights were computed using a raking ratio adjustment procedure and used in all analyses. Results: Almost all examined adults had some loss of periodontal attachment. The proportion of those with more than 3 mm LOA ranged from 43 percent in 35-44 year olds to 91 percent in those aged 65+ years. Among females, older age, low education status, smoking 11-40+ cigarettes a day, being employed, and presence of high number of missing tooth surfaces were associated with LOA>3 mm. Among males LOA >3 mm was associated with older age, use of alcohol, and unemployment. The CPI data did not yield the same associations with periodontal diseases and risk factors. Conclusions: Periodontal diseases in Turkish adults are highly prevalent. A tailored common risk factor health promotion program is recommended to reduce the burden of periodontal infection in Turkey.

Objective: To evaluate and compare the normative and subjective need for orthodontic treatment within different age groups in Turkey. Methods: One thousand and sixteen patients from seven different demographic regions of Turkey (Marmara, Black Sea, East Anatolia, Southeastern Anatolia, Mediterranean, Aegean, and Central Anatolia Region) (mean age ± SD: 12.80 ± 3.57 years) were randomly selected and divided into six age groups (7-8,9-10,11-12,13-14,15-16, and 17-18 year-olds) and categorized according to the dental health component (DHC) of the index for orthodontic treatment need (IOTN). Additionally, the patients were asked to indicate the photograph that was most similar to their own dentition from the 10-point scale of the aesthetic component of IOTN. Results: The DHC of IOTN was not significantly different between the six age groups (P > 0.05). However, no/slight need (aesthetic component 1-4) for orthodontic treatment according to AC of IOTN was significantly higher in 13-14,15-16, and 17-18 age groups than 7-8, 9-10, and 11-12 age groups (P < 0.05). No sex differences were found in both DHC and aesthetic component of IOTN between age groups (P > 0.05). Conclusion: The normative need distribution was homogeneous within all the age groups according to DHC. However, the subjective need for orthodontic treatment was higher in the younger age groups. © 2018 Nigerian Journal of Clinical Practice | Published by Wolters Kluwer - Medknow.

Purpose: To assess the correlation between toothbrushing (TB) and the common biological (HDL) and quality-of-life-related risk factors for noncommunicable diseases (NCDs) and communicable diseases among patients with diabetes mellitus type 2 (DM2). Materials and Methods: The present study is part of a prospective intervention study among DM2 patients (n = 200), randomly selected from the outpatient clinics, Istanbul, Turkey. The assessed variables were: TB, self-reported gingival bleeding (SRGB), HDL, BMI, body-fat proportion, modified quality of life scale (WHOQOL-BrefPhPs). Descriptive statistics, frequency distributions, Spearman rank correlation, the chi-square test and factor analysis were applied. Results: A minority of the patients brushed their teeth twice a day or more (27%) and reported no gingival bleeding (37%). Favourable HDL and high WHOQOL-BrefPhPs were 77% and 57%, respectively. A majority of patients had unhealthy BMI (83%) and body-fat proportions (63%). SRGB was negatively correlated with WHOQOL-BrefPhPs (rs = -0.24, p < 0.05) and TB (rs = -0.25, p < 0.01). The patients who reported less than daily TB were more likely to have unfavourable HDL and low WHOQOL-BrefPhPs (32% vs 54%) than those brushing their teeth daily (17% vs 35%, p < 0.05). Principal component analysis revealed two clusters: 'healthy weight' (WHOQOL-BrefPhPs, TB, BMI) and 'oral health' (SRGB, HDL). Conclusion: The present results demonstrate a correlation between TB and biological and quality-of-life-related risk markers of NCDs and communicable diseases. There seems to be a need to increase the awareness of the significance TB's potential intermediatory role between NCDs and communicable diseases. © Quintessenz all rights reserved.

The aim of this study was to compare the impact of case-based learning (CBL) and lecture-based learning (LBL) on fourth-year dental students' clinical decision making by using the Structure of Observed Learning Outcome (SOLO) taxonomy. Participants in the study were fourth-year dental students (n=55) in academic year 2012-13 taught in a large-group LBL context and fourth-year dental students (n=54) in academic year 2013-14 taught with the CBL methodology; both took place in the oral diseases course at Yeditepe University Faculty of Dentistry, Istanbul, Turkey. All eligible students participated, for a 100 percent response rate. A real case was presented to the students in both groups to assess their clinical decision making on the topic of oral diseases. Their performance was evaluated with the SOLO taxonomy. Student t-test was used for statistical evaluation, and significance was set at the p

BERBER, BURAK/0000-0001-5136-5323; Berber, Burak/0000-0002-6843-8450; doluca, osman/0000-0003-0412-6148; Kaplan, Oktay Ismail/0000-0002-8733-0920 WOS:000388016900010 PubMed: 27596596 Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns.

The aim of this study was to evaluate differences with regard to local anesthesia education in Turkish dental schools. Questionnaires designed to collect information about local anesthesia education were sent to the heads of the Departments of Oral and Maxillofacial Surgery of seventeen Turkish dental schools. Eleven returned the completed survey for a response rate of 64 percent. It was determined that dental schools begin the theoretical part of their local anesthesia (LA) curricula during the first half of the third year. Most dental schools start teaching the practical aspects during the second half of the third year on average-half a year after the beginning of the theoretical background. The first injection in humans, usually a fellow student (82 percent), is mostly supervised by an oral and maxillofacial surgeon. The number of injections under supervision usually depends upon the individual capabilities of the student. None of the schools said they required permission of a medical ethics committee for injections on fellow students. Seventy-three percent of the schools said they were satisfied with their current LA teaching and were not planning to make any changes. Overall, LA teaching programs showed minor variations across the surveyed Turkish dental schools.

Purpose: To assess the role of toothbrushing self-efficacy (TBSE) in toothbrushing (TB) behaviour and diabetes management, measured in terms of HbA1c knowledge, quality of life, BMI, self-reported health and physical activity among Turkish type-II-diabetes (DM2) patients. Materials and Methods: A pilot study using self-administered health questionnaires was conducted among a random sample of 60 patients (aged 40 to 70 years) in Istanbul, Turkey. The assessed variables were: TBSE, TB, glycated haemoglobin (HbA1c) knowledge, quality of life, BMI, self-reported health and physical activity. Descriptive statistics, frequency distributions, Pearson's correlation, the chi-square test and MANOVA were applied. Results: Almost half of the patients reported low TBSE (mean ? 53%). and TB once a day (54%). Most (77%) did not know their HA1C level and they were overweight (42%) and obese (32%). Almost half of the patients reported good quality of life (> mean, 55%), being physically active (51%) and in good health (mean < 46%). The patients reporting high levels of TBSE were more likely to know their HbA1c (OR = 10.5: 95%CI = 1.01-103.24) and to report better health (OR = 10.0: 95%CI = 1.80-55.63) and were less likely to be obese (OR = 0.16: 95%CI = 0.02-1.00) (P < 0.05). There was a strong correlation between TBSE and TB (rs = 0.61, P < 0.01). Conclusion: The present study underlines the need for TBSE-integrated common health promotion for oral health and DM2, considering the relation of TBSE, HbA1c, BMI and toothbrushing.