Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.

Accurate prediction of quantitative traits with failed SNP calls in canola and maize

In modern plant breeding, genomic selection is becoming the gold standard to select superior genotypes in large breeding populations that are only partially phenotyped. Many breeding programs commonly rely on single-nucleotide polymorphism (SNP) markers to capture genome-wide data for selection candidates. For this purpose, SNP arrays with moderate to high marker density represent a robust and cost-effective tool to generate reproducible, easy-to-handle, high-throughput genotype data from large-scale breeding populations. However, SNP arrays are prone to technical errors that lead to failed allele calls. To overcome this problem, failed calls are often imputed, based on the assumption that failed SNP calls are purely technical. However, this ignores the biological causes for failed calls-for example: deletions-and there is increasing evidence that gene presence-absence and other kinds of genome structural variants can play a role in phenotypic expression. Because deletions are frequently not in linkage disequilibrium with their flanking SNPs, permutation of missing SNP calls can potentially obscure valuable marker-trait associations. In this study, we analyze published datasets for canola and maize using four parametric and two machine learning models and demonstrate that failed allele calls in genomic prediction are highly predictive for important agronomic traits. We present two statistical pipelines, based on population structure and linkage disequilibrium, that enable the filtering of failed SNP calls that are likely caused by biological reasons. For the population and trait examined, prediction accuracy based on these filtered failed allele calls was competitive to standard SNP-based prediction, underlying the potential value of missing data in genomic prediction approaches. The combination of SNPs with all failed allele calls or the filtered allele calls did not outperform predictions with only SNP-based prediction due to redundancy in genomic relationship estimates.

Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation

In a cross between two homozygous Brassica napus plants of synthetic and natural origin, we demonstrate that novel structural genome variants from the synthetic parent cause immediate genome diversification among F1 offspring. Long read sequencing in twelve F1 sister plants revealed five large-scale structural rearrangements where both parents carried different homozygous alleles but the heterozygous F1 genomes were not identical heterozygotes as expected. Such spontaneous rearrangements were part of homoeologous exchanges or segmental deletions and were identified in different, individual F1 plants. The variants caused deletions, gene copy-number variations, diverging methylation patterns and other structural changes in large numbers of genes and may have been causal for unexpected phenotypic variation between individual F1 sister plants, for example strong divergence of plant height and leaf area. This example supports the hypothesis that spontaneous de novo structural rearrangements after de novo polyploidization can rapidly overcome intense allopolyploidization bottlenecks to re-expand crops genetic diversity for ecogeographical expansion and human selection. The findings imply that natural genome restructuring in allopolyploid plants from interspecific hybridization, a common approach in plant breeding, can have a considerably more drastic impact on genetic diversity in agricultural ecosystems than extremely precise, biotechnological genome modifications.

Discovery of stripe rust resistance with incomplete dominance in wild emmer wheat using bulked segregant analysis sequencing

Durable crop disease resistance is an essential component of global food security. Continuous pathogen evolution leads to a breakdown of resistance and there is a pressing need to characterize new resistance genes for use in plant breeding. Here we identified an accession of wild emmer wheat (Triticum turgidum ssp. dicoccoides), PI 487260, that is highly resistant to multiple stripe rust isolates. Genetic analysis revealed resistance was conferred by a single, incompletely dominant gene designated as Yr84. Through bulked segregant analysis sequencing (BSA-Seq) we identified a 52.7 Mb resistance-associated interval on chromosome 1BS. Detected variants were used to design genetic markers for recombinant screening, further refining the interval of Yr84 to a 2.3-3.3 Mb in tetraploid wheat genomes. This interval contains 34 candidate genes encoding for protein domains involved in disease resistance responses. Furthermore, KASP markers closely-linked to Yr84 were developed to facilitate marker-assisted selection for rust resistance breeding.

Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids

Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.

Local Duplication of TIR-NBS-LRR Gene Marks Clubroot Resistance in Brassica napus cv. Tosca

Clubroot, caused by Plasmodiophora brassicae infection, is a disease of growing importance in cruciferous crops, including oilseed rape (Brassica napus). The affected plants exhibit prominent galling of the roots that impairs their capacity for water and nutrient uptake, which leads to growth retardation, wilting, premature ripening, or death. Due to the scarcity of effective means of protection against the pathogen, breeding of resistant varieties remains a crucial component of disease control measures. The key aspect of the breeding process is the identification of genetic factors associated with variable response to the pathogen exposure. Although numerous clubroot resistance loci have been described in Brassica crops, continuous updates on the sources of resistance are necessary. Many of the resistance genes are pathotype-specific, moreover, resistance breakdowns have been reported. In this study, we characterize the clubroot resistance locus in the winter oilseed rape cultivar "Tosca." In a series of greenhouse experiments, we evaluate the disease severity of P. brassicae-challenged "Tosca"-derived population of doubled haploids, which we genotype with Brassica 60 K array and a selection of SSR/SCAR markers. We then construct a genetic map and narrow down the resistance locus to the 0.4 cM fragment on the A03 chromosome, corresponding to the region previously described as Crr3. Using Oxford Nanopore long-read genome resequencing and RNA-seq we review the composition of the locus and describe a duplication of TIR-NBS-LRR gene. Further, we explore the transcriptomic differences of the local genes between the clubroot resistant and susceptible, inoculated and control DH lines. We conclude that the duplicated TNL gene is a promising candidate for the resistance factor. This study provides valuable resources for clubroot resistance breeding programs and lays a foundation for further functional studies on clubroot resistance.

Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single-nucleotide polymorphism (SNP). In recent years, there have been a number of studies associating large chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloguing small- (30-10 000 bp) to mid-scale (10 000-30 000 bp) SV and their impact on evolution and adaptation-related traits in plants. This might be attributed to complex and highly duplicated nature of plant genomes, which makes them difficult to assess using high-throughput genome screening methods. Here, we describe how long-read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small- to mid-scale SV in a major allopolyploid crop species, Brassica napus. We found that up to 10% of all genes were affected by small- to mid-scale SV events. Nearly half of these SV events ranged between 100 bp and 1000 bp, which makes them challenging to detect using short-read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco-geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium-coverage long-read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement.

Oxford Nanopore sequencing: new opportunities for plant genomics?

DNA sequencing was dominated by Sanger's chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. However, today's long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.

Gene presence-absence variation associates with quantitative Verticillium longisporum disease resistance in Brassica napus

Although copy number variation (CNV) and presence-absence variation (PAV) have been discovered in selected gene families in most crop species, the global prevalence of these polymorphisms in most complex genomes is still unclear and their influence on quantitatively inherited agronomic traits is still largely unknown. Here we analyze the association of gene PAV with resistance of oilseed rape (Brassica napus) against the important fungal pathogen Verticillium longisporum, as an example for a complex, quantitative disease resistance in the strongly rearranged genome of a recent allopolyploid crop species. Using Single Nucleotide absence Polymorphism (SNaP) markers to efficiently trace PAV in breeding populations, we significantly increased the resolution of loci influencing V. longisporum resistance in biparental and multi-parental mapping populations. Gene PAV, assayed by resequencing mapping parents, was observed in 23-51% of the genes within confidence intervals of quantitative trait loci (QTL) for V. longisporum resistance, and high-priority candidate genes identified within QTL were all affected by PAV. The results demonstrate the prominent role of gene PAV in determining agronomic traits, suggesting that this important class of polymorphism should be exploited more systematically in future plant breeding.

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus

Rapeseed (Brassica napus), the second most important oilseed crop globally, originated from an interspecific hybridization between B. rapa and B. oleracea. After this genome collision, B. napus underwent extensive genome restructuring, via homoeologous chromosome exchanges, resulting in widespread segmental deletions and duplications. Illicit pairing among genetically similar homoeologous chromosomes during meiosis is common in recent allopolyploids like B. napus, and post-polyploidization restructuring compounds the difficulties of assembling a complex polyploid plant genome. Specifically, genomic rearrangements between highly similar chromosomes are challenging to detect due to the limitation of sequencing read length and ambiguous alignment of reads. Recent advances in long read sequencing technologies provide promising new opportunities to unravel the genome complexities of B. napus by encompassing breakpoints of genomic rearrangements with high specificity. Moreover, recent evidence revealed ongoing genomic exchanges in natural B. napus, highlighting the need for multiple reference genomes to capture structural variants between accessions. Here we report the first long-read genome assembly of a winter B. napus cultivar. We sequenced the German winter oilseed rape accession 'Express 617' using 54.5x of long reads. Short reads, linked reads, optical map data and high-density genetic maps were used to further correct and scaffold the assembly to form pseudochromosomes. The assembled Express 617 genome provides another valuable resource for Brassica genomics in understanding the genetic consequences of polyploidization, crop domestication, and breeding of recently-formed crop species.

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus

Rapeseed (Brassica napus), the second most important oilseed crop globally, originated from an interspecific hybridization between B. rapa and B. oleracea. After this genome collision, B. napus underwent extensive genome restructuring, via homoeologous chromosome exchanges, resulting in widespread segmental deletions and duplications. Illicit pairing among genetically similar homoeologous chromosomes during meiosis is common in recent allopolyploids like B. napus, and post-polyploidization restructuring compounds the difficulties of assembling a complex polyploid plant genome. Specifically, genomic rearrangements between highly similar chromosomes are challenging to detect due to the limitation of sequencing read length and ambiguous alignment of reads. Recent advances in long read sequencing technologies provide promising new opportunities to unravel the genome complexities of B. napus by encompassing breakpoints of genomic rearrangements with high specificity. Moreover, recent evidence revealed ongoing genomic exchanges in natural B. napus, highlighting the need for multiple reference genomes to capture structural variants between accessions. Here we report the first long-read genome assembly of a winter B. napus cultivar. We sequenced the German winter oilseed rape accession 'Express 617' using 54.5x of long reads. Short reads, linked reads, optical map data and high-density genetic maps were used to further correct and scaffold the assembly to form pseudochromosomes. The assembled Express 617 genome provides another valuable resource for Brassica genomics in understanding the genetic consequences of polyploidization, crop domestication, and breeding of recently-formed crop species.

Connecting genome structural variation with complex traits in crop plants

Structural genome variation is a major determinant of useful trait diversity. We describe how genome analysis methods are enabling discovery of trait-associated structural variants and their potential impact on breeding. As our understanding of complex crop genomes continues to grow, there is growing evidence that structural genome variation plays a major role in determining traits important for breeding and agriculture. Identifying the extent and impact of structural variants in crop genomes is becoming increasingly feasible with ongoing advances in the sophistication of genome sequencing technologies, particularly as it becomes easier to generate accurate long sequence reads on a genome-wide scale. In this article, we discuss the origins of structural genome variation in crops from ancient and recent genome duplication and polyploidization events and review high-throughput methods to assay such variants in crop populations in order to find associations with phenotypic traits. There is increasing evidence from such studies that gene presence-absence and copy number variation resulting from segmental chromosome exchanges may be at the heart of adaptive variation of crops to counter abiotic and biotic stress factors. We present examples from major crops that demonstrate the potential of pangenomic diversity as a key resource for future plant breeding for resilience and sustainability.

A comparative assessment of fluoride concentration available in saliva using daily prescribed topical fluoride agents

Objective:

To assess the availability of fluoride concentration in saliva following the use of fluoride mouthrinse and dentifrice.

Materials and Methods:

The experiment was carried out in 7–15 year-old school children of Chandigarh (n = 90). The children were nonfluoride users. Baseline saliva samples were collected. The subjects were exposed to two test agents, i.e., fluoride mouthrinse (0.05%, 225 ppm F) and dentifrice (1000 ppm F) for 7 days and on the day 8, saliva samples were collected over a 20 hrs period. Wash out period of 3^1/2 months was there before the subjects were exposed to the second test agent. Fluoride in saliva was estimated using fluoride ion-specific electrode. Written informed consent was taken.

Statistical Analysis:

Kolmogorov–Smirnov test was applied to test the normality of the variables. Mann–Whitney U-test was used to compare the fluoride concentration available in saliva at respective time intervals subsequent to use of the two test agents.

Results:

Fluoride concentration was elevated in saliva compared to baseline for both the test agents. Fluoride mouthrinse (0.05% sodium fluoride [NaF]) and dentifrice (1000 ppm monofluorophosphate [MFP]) showed a biphasic clearance. Peak in saliva occurred at 15 mins postuse. Night-time use resulted in higher concentration of fluoride in saliva compared to baseline. There was statistically significantly higher fluoride concentration available in saliva for the dentifrice at 5 hrs, 10 hrs, and 20 hrs postuse (P < 0.05).

Conclusion:

Subsequent to the use of NaF (0.05%) daily mouthrinse and MFP dentifrice (1000 ppm) the fluoride concentration in saliva remained elevated to a level of 0.12 ppm for mouthrinse and 0.14 ppm for dentifrice compared to baseline (0.03 ppm) up to 20 hrs postuse. The therapeutic window though not yet established but suggested is 0.1–1 ppm for prevention of demineralization, indicating that daily use of fluoride mouthrinse and dentifrice provides fluoride concentration in saliva for the prevention of demineralization.

Effect of oral-transmucosal midazolam sedation on anxiety levels of 3-4 years old children during a Class II restorative procedure

AIM

A double-blind randomized control trial was conducted to assess the effect of oral-transmucosal midazolam sedation on changes in anxiety levels of precooperative children during a Class II amalgam restorative procedure.

METHODOLOGY

A sample of 40 healthy, American Society of Anesthesiologists I, children aged 3-4 years having at least one carious primary mandibular molar requiring a Class II amalgam restoration with no previous dental history were randomly divided into experimental and control groups comprising of 20 children each. The children in the experimental group (Group I) received 0.5 mg/kg body weight of midazolam mixed in strawberry syrup and those in the control group (Group II) received the same syrup mixed in saline, 15 min prior to the restorative procedure. Routine nonpharmacological behavior management techniques were used in both groups. The anxiety levels were recorded using Venham's anxiety scale at the start and end of each procedural step.

RESULTS

There was a significant (P < 0.001) reduction in the anxiety levels of children in the experimental group on entry into the operatory compared with the control group. Introduction of each fear evoking stimuli showed a somewhat similar increase in anxiety levels in the two groups. In spite of a similar trend, the anxiety levels remained much lower in Group I than in Group II.

CONCLUSION

Midazolam in conjunction with behavior management is more helpful in relaxing the child initially than behavior management alone, thus increasing the chances of successful and easy accomplishment of further treatment steps.

Progressive changes in arch width from primary to early mixed dentition period: a longitudinal study

OBJECTIVE

The present study was conducted to evaluate, on a longitudinal basis, the changes in intercanine and intermolar widths form the primary to the early mixed dentition periods.

MATERIALS AND METHODS

A total of 38 children aged 4-5 years, with normal occlusion without any proximal caries or any dental anomalies, were selected. The impressions were recorded and casts were prepared. Intercanine and intermolar widths were measured on these dental casts with the help of a digital vernier calliper. After 3 years follow-up, the impressions were recorded again and dental casts were prepared. Intercanine and intermolar widths were measured again at this stage and were compared with the baseline data using the paired t-test and the chi square test.

RESULTS

There is a significant increase in the intercanine (3.93 + 1.70 mm) and intermolar width (1.49 + 1.77 mm) during the transition period from primary to early mixed dentition in both the arches and both the sexes. The gender-wise comparison showed a greater increase in males than in females, but this was not statistically significant.

CONCLUSION

A thorough knowledge of growth changes during various stages of the mixed dentition period are important for a pediatric dentist to make an accurate diagnosis and treatment planning during preventive and interceptive orthodontics.

A study of influence of sugars on the modulations of dental plaque pH in children with rampant caries, moderate caries and no caries

The present study is undertaken to find out the pH of resting plaque in children with no caries, moderate caries and rampant caries and to determine the modulations of plaque pH with different sugar solution rinses viz: sucrose, glucose and fructose. The study was carried out on forty five children, in the age group of 3-10 years (25 males and 20 females). The child was given 10 ml of test solution and was asked to rinse and swish it in the mouth for a period of 30 sec. Plaque samples were taken from 20 different spots after 5, 10, 20 and 30 min of the rinse and pH values of all the samples were determined. Results show that there was a statistically significant (P<0.05) difference between the pH values of plaque at different intervals of time with sucrose, fructose and glucose solution rinse in children with moderate caries, rampant caries as compared to the caries free group. Sucrose was found to be highly cariogenic in all the children with a greater potentiating effect in moderate and rampant caries. Glucose also appeared to have a cariogenic role while fructose had the least of it all.

In vivo remineralization of artificial enamel carious lesions using a mineral-enriched mouthrinse and a fluoride dentifrice: a polarized light microscopic comparative evaluation

BACKGROUND

Remineralization process is accelerated by the presence of fluoride ions in the oral environment, but this mechanism of caries reversal will be further enhanced if the concentration of calcium, phosphate and fluoride ions is supersaturated with respect to that of oral fluids.

AIM

This in vivo study was carried out to evaluate and compare the remineralizing efficacy of a urea-based mineral-enriched mouthrinse and a fluoridated dentifrice using an in vivo intraoral appliance model and polarized light microscopic evaluation technique.

MATERIALS AND METHODS

The specimens were prepared from sound teeth and artificial caries was produced using an artificial caries medium in vitro and enamel specimens were inserted in removable orthodontic appliances that were to be worn by 14 children of 10-15 years of age. They were divided into three groups - nonfluoridated dentifrice, fluoridated dentifrice and mineral-enriched mouthrinse groups. After the 6-month experimental period, during which the enamel specimens inserted in the intraoral appliance were subjected to one of the agents (either fluoride, nonfluoride dentifrice or mouthrinse) in vivo, the specimens were retrieved from the patients and were evaluated using the polarized light microscopic technique.

OBSERVATIONS AND RESULTS

On analysis, mineral gain occurred in all groups, viz. nonfluoride dentifrice group, fluoride dentifrice and mineral-enriched mouthrinse group. However, it was found to be complete in the mouthrinse group, i.e. both at the surface and at the subsurface (67%), while in the fluoridated dentifrice group, 43% of the samples showed mineral gain in both zones. In the nonfluoridated dentifrice group also, remineralization occurred but was limited either to the surface or the subsurface zone.

CONCLUSIONS

Urea-based mineral-enriched mouthrinse was shown to be more efficacious in the process of remineralization of artificial carious lesions.

Natural prevalence of antibody titers to glucosyltransferase of Streptococcus mutans in serum in high and low caries active children

In this investigation, serum immunoglobulin G (IgG) and immunoglobulin A (IgA) titers, as well as total immunoglobulin concentration (IgG + IgA + IgM), were found to be raised with the increase in the number of dental caries. Only the total serum antibody titer in high dental caries (HDC) group was found to be significantly raised as compared to no dental carries (NDC) group. Although the IgG and IgA titers were raised in blood with the increased number of caries, the results were not statistically significant. However, we could not find any correlation between serum antibodies and dental caries except that there was an increased trend of serum antibodies to GTF with the increased number of carious lesions.

Comparison of validity of DIAGNOdent with conventional methods for detection of occlusal caries in primary molars using the histological gold standard: an in vivo study

AIM

This study was conducted to compare the in vivo effectiveness of DIAGNOdent with other conventional methods (visual, tactile and bitewing radiographs) for the detection of occlusal caries in primary molars. Another objective of the study was to calculate new cut-off limits for the detection of caries by DIAGNOdent in primary teeth.

MATERIALS AND METHODS

Eighty-four primary molars in 52 children (aged 8-12 years), which were indicated for extraction, were selected and evaluated for dental caries using DIAGNOdent, visual and tactile examination and bitewing radiographs. Histological examination of the sections, prepared subsequent to extraction of the teeth, served as the gold standard for comparison of the above-mentioned methods.

RESULTS

When considering enamel caries, values obtained for sensitivity, specificity and accuracy were 48.15, 100 and 49.40% for visual examination, 48.15, 100.00 and 49.40% for tactile examination, 49.38, 50.00 and 49.40% for bitewing radiographs, 85.19, 50.00 and 84.34% for DIAGNOdent scores interpreted according to manufacturer's cut-off limits and 81.48, 100.00 and 81.93% for DIAGNOdent scores interpreted according to newly formulated cut-off limits, respectively. At dentin caries cut-off levels, the values of sensitivity, specificity and accuracy for visual examination were 52.78, 89.36 and 73.49%; 50.00, 91.49 and 73.49% for tactile examination; 30.56, 82.98 and 60.24% for bitewing radiographs; 72.22, 76.60 and 74.70% for DIAGNOdent scores when interpreted according to manufacturer's cut-off limits and 77.48, 74.47 and 75.90%, respectively, for the DIAGNOdent scores when interpreted according to the newly formulated cut-off limits.

CONCLUSIONS

DIAGNOdent showed higher sensitivity and accuracy as compared with other conventional methods for detection of enamel caries, whereas for detection of dentinal caries, even though the sensitivity was high, accuracy of the DIAGNOdent device was similar to other conventional caries diagnostic methods.

Natural prevalence of antibody titres to GTF of S. mutans in saliva in high and low caries active children

The present study was conducted to find out the role of natural immunity against dental caries. Whole stimulated saliva of various caries from active children was collected. Antigen glucosyltransferase (GTF) was prepared from Streptococcus mutans serotype C and the antibody titre was estimated using ELISA. Salivary IgG, s-IgA and total immunoglobulins (IgG + s-IgA+ IgM) concentration were assayed. The result showed an increased level of salivary IgG concentration with the increased number of dental caries, which was not statistically significant. But there were significant decrease of s-IgA titre as well as total immunoglobulin concentration in saliva with the increased number of dental caries. This study showed that because of lack of local immunity the children are more prone to dental caries.

Orthodontic management of faciolingual horizontally impacted maxillary central incisor

This paper describes the successful alignment of a horizontally impacted maxillary central incisor positioned high in the vestibule, in a 15-year-old girl, by purely orthodontic means. A unique and innovative technique for traction was employed so as to cause minimal injury to the neighboring soft tissue. The article is a step forward in establishing the predictability of orthodontic alignment in management of such cases, which may become the method of choice over extractions or surgical repositionings.

Early class III occlusal tendency in children and its selective management

Class III malocclusion may develop in children as a result of an inherent growth abnormality, i.e., true class III malocclusion, or as a result of premature occlusal contacts causing forward functional shift of the mandible, which is known as pseudo class III malocclusion. These cases, if not treated at the initial stage of development, interfere with normal growth of the skeletal bases and may result in severe facial deformities. The treatment should be carried out as early as possible with the aim of permitting normal growth. This paper deals with the selection of an appropriate treatment approach from the various current options available for early intervention in children developing class III occlusal tendencies; the different clinical features are depicted in the three case reports.

Evaluation of a mixture of zinc oxide, calcium hydroxide, and sodium fluoride as a new root canal filling material for primary teeth

Endodontic treatment was performed on 25 pulpally involved mandibular primary molars in 4 to 9-year-old children; the root canals were obturated with a new root canal filling material consisting of a mixture of calcium hydroxide, zinc oxide, and 10% sodium fluoride solution, using hand-operated lentulo-spirals. All cases were evaluated clinically every 3 months and also radiographically every 6 months to assess the success of the treatment; we also examined the resorption of the root canal filling material from the root canals and the status of overpushed material, if any, as the tooth resorbed with the passage of time. At 6 months, endodontic treatment in 2 of the 25 teeth had failed and one tooth had exfoliated; the remaining 22 teeth were without any signs or symptoms. At the end of 2 years, 14 teeth could be evaluated; out of these 12 had physiologically exfoliated. It was observed that the rate of resorption of this new root canal obturating mixture was quite similar to the rate of physiologic root resorption in primary teeth. In three cases, where there was an overpush of the mixture, a gradual partial resorption was noted.

Distribution of malocclusion types among thumb suckers seeking orthodontic treatment

The present study was conducted to evaluate the influence of thumb sucking and its duration on the type of malocclusion. A total of 410 North Indian individuals between ages 12-30 years, 161 males and 249 females were examined. A specially designed proforma was used to record the detailed history of the individual. Among the etiological factors it was found that history of thumb sucking was present in 13.9% and significantly related to Class II div 1 malocclusion. When thumb sucking exceeded 18 months, it was found statistically significant (P < 0.1) in Class II skeletal malocclusion, in open bite (P < 0.1) and in extreme overjet (P < 0.5).

CONCLUSION

If thumb sucking is not treated early, it can cause skeletal Class II malocclusion, anterior open bite and excessive overjet.

Epidemiology of dental caries in Chandigarh school children and trends over the last 25 years

The prevalence of dental caries in 6, 9, 12 and 15-year-old school children of Chandigarh, selected on a randomized basis was evaluated using Moller's criteria (1966) and correlated with the various risk factors. The mean deft was found to be 4.0 +/- 3.6 in 6 year old and 4.61 +/- 3.14 in 9 year old, whereas the mean DMFT in 12 and 15 year old was found to be 3.03 +/- 2.52 and 3.82 +/- 2.85 respectively. The high prevalence of dental caries in these children was attributed to the lack of use of fluoride toothpaste (80% children), lack of knowledge about etiology of dental caries (98%) and frequency of sugar exposures up to more than five times per day (30%).

Is tongue thrust that develops during orthodontic treatment an unrecognized potential road block?

The role of tongue thrust has often been suspected, long debated and largely dispelled as a primary etiological factor of malocclusion. However, tongue thrust may contribute to poor occlusal intercuspation both during and after treatment. A tongue thrust may also develop during orthodontic mechanotherapy as a result of the transient creation of intra and interarch spaces and this little recognized phenomenon was found to occur in many randomly followed cases. In many instances, this seemingly adaptive and secondary response of the tongue posture and function may persist and thereafter impede the resolution of intra and interarch problems.

Comparative evaluation of endodontic management of teeth with unformed apices with mineral trioxide aggregate and calcium hydroxide

PURPOSE

The purpose of this study was to compare mineral trioxide aggregate (MTA) and calcium hydroxide (Ca(OH)2) for their efficacies and time taken for formation of apical biological calcific barriers and resolution of periapical radiolucencies, if present at baseline, in teeth with unformed apices.

METHODS

Twenty nonvital permanent maxillary incisors with unformed apices, stratified according to the size of periapical radiolucencies and stage of root development, were equally allocated to MTA and Ca(OH)2 groups. In group 1 (MTA group), after 7 days of disinfection with Ca(OH)2, MTA was packed into the apical one third of the root canals and obturation with gutta percha (GP) was performed in 90% (9/10) of cases within 15 to 30 days. In group 2 (Ca(OH)2 group), obturation was performed following clinical and radiographic depiction of the apical stop.

RESULTS

The mean time taken for apical biological barrier formation was 3 +/- 2.9 months for group 1 and 7 +/- 2.5 months for group 2 (P=.008). The periapical radiolucencies were resolved in 4.6 +/- 1.5 months for group 1 and 4.4 +/- 1.3 months for group 2 (P=.83). The total treatment was completed in 0.75 +/- 0.4859 months and 7 +/- 2.5 months for groups 1 and 2, respectively.

CONCLUSION

The 2 materials were found to be equally efficacious in the management of nonvital teeth with unformed apices. Time taken to complete the treatment and the biological barrier formation in group 1 was significantly less than that for group 2. The healing time for periapical radiolucencies was almost identical.

An esthetic point of view in very young children

Extensive carious breakdown of primary anterior teeth to the cervical level and their loss in very young children invariably leads to lack of confidence and self-esteem and may cause psychological problems. The present paper deals with the management of three such cases by means of biological restorations, anterior fixed space maintainer and over-dentures.

Winged maxillary central incisors with unusual morphology: a unique presentation and early treatment

Winged incisors are a well-recognized clinical finding. In this report, the disorder is briefly reviewed and a unique case of winging of the two maxillary central incisors having unusual morphology in an eight-year six-month-old boy is presented. The two winged maxillary central incisors were derotated using an anterior sectional wire inserted into a pair of twin brackets, one bonded to each of the two central incisors, and reciprocal anchorage.

Folic acid and phenytoin induced gingival overgrowth--is there a preventive effect

The role of folic acid (5mg/day) in combination with oral hygiene measures (group II) vis-a-vis oral hygiene measures alone (group I) in prevention of phenytoin-induced gingival overgrowth was investigated in a one-year follow-up study on sixty, 8-13-year-old epileptic children receiving phenytoin. The allocation of the children to the two groups was done alternately. In these children, at baseline, plaque (Silness & Löe), gingivitis (Löe & Silness) and probing depths of gingival sulcus were recorded. These parameters were re-evaluated at 3-monthly intervals when gingival overgrowth was also recorded (Modified Harris & Ewalt Index). It was seen that, after a period of one year, gingival overgrowth occurred in 60 and 50 percent children of groups I & II respectively and its development, too, was delayed in group II. More cases (93 percent) in group II exhibited minimal overgrowth as against 78 percent in group I. The study concluded that systemic folic acid prescribed along with phenytoin delays the onset and reduces the incidence and severity of gingival overgrowth induced by phenytoin.

Incidence of phenytoin induced gingival overgrowth in epileptic children: a six month evaluation

Thirty children aged 8-13 years with epileptic disorders and receiving mono-drug therapy with Phenytoin, were selected from the Departments of Pediatrics and Neurology of PGIMER, Chandigarh to evaluate the development of gingival overgrowth induced by phenytoin over a period of six months. These children were evaluated at baseline at three monthly intervals for a period of six months for plaque (Silness and Loe, 1964), gingivitis (Loe and Silness, 1963) and probing depth of the gingival sulcus. Gingival overgrowth was noted as and when it developed using modified version of Harris and Ewalt Index, 1942. No attempt was made to modify the childrens' prevailing oral habits. The results indicated that gingival overgrowth in 57% of the children was in the mesio-distal dimension of the gingival papillae and occurred within six months of initiation of therapy with Phenytoin.

Prevalence and severity of dental caries and treatment needs among population in the Eastern states of India

The present epidemiological investigation was conducted on a total sample of 2067 individuals in the age groups of 5-6, 15-16 and 30-35 years belonging to urban (U) and rural (R) areas of three states of eastern region of India viz. West Bengal (U & Rn = 361 & 359), Orissa (U & Rn = 351 & 351) and Sikkim (U & Rn = 323 & 321). Dental caries recording was done according to WHO index 1983. The point prevalence of dental caries, deft/DMFT and defs among all the three age groups in the urban and rural areas of three states revealed common pattern i.e. (i) Dental caries was higher in 5-6 year old children (U & R - W.B. = 52.4% & 48.3%, Orissa = 56.0% & 48.7% and Sikkim = 61.8% and 22.0% exception) as compared to 15-16 years (U & R.- WB. = 21.0% & 15.2%, Orissa = 18.3% & 19.8%, and Sikkim = 30.1% & 17.9%) and 30-35 year old individuals (U & R WB = 19.4% & 18.1% Orissa = 24.3% & 20.1% and Sikkim 29.9% & 24.5%) in West Bengal, Orissa and Sikkim respectively, (ii) dental caries was higher in urban as compared to rural areas. The decayed (d/D) component contributed maximum to total deft/DMFT and defs/DMFS score, followed by e/M (missing due to caries) and f/F component (filling) which was negligible or absent. Teeth requiring various type of treatment found that one or two surface fillings were maximum followed by others. Fluoride content of drinking water was negligible (0.004 - 0.011 ppm).

Silver amalgam versus resin modified GIC class-II restorations in primary molars: twelve month clinical evaluation

The purpose of this study was to compare the clinical efficacy of resin modified GIC with amalgam as a restorative material, in Class-II cavities of primary molars. Restorations were evaluated at four, eight, and twelve months for their marginal integrity, anatomic form and development of recurrent caries. When each parameter was considered separately, there was no difference in the success rate between the two groups, except development of recurrent caries significantly less (p<0.05) in RMGIC group(4.7%) compared to amalgam group (12.5%) at twelve month follow up. However, the cumulative success rate at 12 month was found to be significantly higher (p<0.05) in RMGIC (Fuji II LC) group(83.1%) compared to amalgam(72%).

A mixture of Ca(OH)2 paste and ZnO powder as a root canal filling material for primary teeth: a preliminary study

The present pilot study was conducted on five primary mandibular second molars requiring endodontic treatment to evaluate the clinical and radiographic success of root canal filling material which was a mixture of calcium hydroxide paste (1 cm), Zinc oxide powder (15 gms) and distilled water using hand operated lentulo spirals. All the five cases on clinical evaluation after 2,4,6,9, and 12 months were found to be asymptomatic with no history of pain, tenderness or abnormal mobility. Immediate post-operative radiographic evaluation revealed adequate root canal filling in all cases. The obturated material remained upto the apex of root canals till the beginning of physiologic root resorption. The roots of the primary teeth as well as the filling material mentioned above were seen to resorb at the same rate in one case.

Management of wide open apices in non-vital permanent teeth with Ca(OH)2 paste

A retrospective study on 15 non-vital immature incisor teeth was done using Ca(OH)2 Pulpdent paste. A success rate of 100 percent was achieved within one year. The variables influencing the time taken for apexification were also evaluated. The teeth were followed up to a period of 24 months. It was found that older children having narrow open apex had a shorter treatment time than the younger children (NS); teeth without periapical infection showed some amount of root growth and closing of apex that was faster than those with periapical infection (p < 0.001). The calcified bridge formed following apexification is a porous structure. This investigation provides information about the time taken and procedure required to achieve apical barrier formation in non-vital immature incisors.

Trend of dental caries in children of Chandigarh over the last sixteen years

The trend of dental caries in Chandigarh school children over a sixteen year period, studied by almost the same authors and using the same recording criteria of WHO reveals a continuous decline in 12 and 15 year children but a slight increase in the dental caries status of 5-6 year children. In 1977, the mean DMFT of 12 and 15 year children was 3.88 and 4.74 respectively. In 1985, it decreased to 1.38 in 15 year olds (12 year children not recorded) and in 1993 it marginally decreased to 1.12 +/- 1.35, much lower than the figure of 3.88 in 1977. In 5-6 year children, mean dmft/dmfs of 2.69 +/- 1.45 and 6.06 +/- 9.77 was found to be slightly higher as compared to the earlier caries prevalence figures (deft + DMFT-2.6 in 1977 and 2.26 in 1985).

Remineralizing efficacy of a mineral enriched mouth rinse and fluoridated dentifrice on artificial carious lesions: an in vivo scanning electron microscopic study

This comparative investigation was carried out to evaluate the remineralization potential on early artificial carious lesions under Scanning Electron Microscope (SEM) of a Mineral enriched mouthrinse and a fluoridated dentifrice using an in-vivo intra-oral removable appliance model. This findings revealed that the remineralization was found to have occurred in almost all the samples (in children) using non-fluoridated, fluoridated dentifrices as well as those using mineral enriched mouthrinse. However the qualitative analysis of the remineralization revealed that in case of non-fluoridated dentifrice group, the prismatic holes showed deposition of granular, variable sized particles with uneven distribution, while in fluoridated dentifrice group, deposits were found to have partially but more densely filled up the prism cores. In case of mineral enriched mouthrinse group these deposits were found to be in the form of amorphous globular precipitate.

Calcium hydroxide as a root canal filling material in primary teeth--a pilot study

A pilot study was carried out in five mandibular primary molars using calcium hydroxide (Ca(OH)2) Paste as root canal filling material to find out an alternative to the routinely used zinc oxide eugenol (ZnOE), which is non-resorbable and causes deflection of succedaneous teeth. The six month clinical and radiographic follow-up carried out at 2 months interval, revealed that the treated teeth with Ca(OH)2 as root canal filling material were successful, showing no pain and tenderness to percussion. A tendency for decrease in size of radiolucency was seen. Two teeth showed complete healing of the periradicular radiolucency. Depletion of Ca(OH)2 paste was seen from the root canals even prior to physiological resorption of roots in 2 out of 5 treated teeth.

Scientific rationale and cost effectiveness of routine use of rubber dam in clinical practice

The rubber dam was first developed and put to use in the 19th century by S.C. Barnum. Since then, the use of the rubber dam in dentistry has become mandatory especially during root canal treatment. Various irrigation solutions which are used during root canal treatment have toxic effects on the soft tissues around the teeth. This can be prevented or minimized when rubber dam is put to use. Similarly for esthetic dentistry, optimum results are obtained if the working area is protected from contamination by saliva.

Role of trace elements Se and Li in drinking water on dental caries experience

An epidemiological survey of dental caries using modified Moller's index (1966) carried out in 483 children (aged 7-17 years) of rural areas--Talwandi Kalan, Dhanansu and Bhatian (District Ludhiana) of Punjab with almost similar F levels in their drinking water supply, similar socio-economic status, environmental factors/demographic parameters and dietary habits revealed wide variations in the prevalence and severity of dental caries. Further investigation extended to evaluate the concentrations of various trace elements Se, Li, Zn, Cu, Fe and Mn in drinking water to find out the disparity of dental caries status, revealed that the higher figures of prevalence and severity of dental caries observed in Dhanansu and Bhatian as compared to Talwandi Kalan could be attributed to the presence of Se in drinking water supply of these areas which was not detectable in the water supply of Talwandi Kalan. On the contrary, the concentration of Li in water supply of Talwandi Kalan with low caries was found to be higher compared to that of Dhanansu and Bhatian with higher dental caries in children population.

Management of natal/neonatal/early infancy teeth

The natal, neonatal and early infancy teeth predominantly being of the normal series of primary dentition, the management should aim at preservation of these teeth for esthetics and maintenance of space for eruption of permanent successor. The treatment method should take into consideration (a) trauma to child's oral tissue or mother's breast (b) mobility and (c) danger of inhalation. Trauma was noted in 10 percent, mobility and danger of inhalation in 94 percent. Extraction carried out in 97 percent of 50 children with natal/neonatal/early infancy teeth showed that the neighbouring primary teeth tended to move into the extraction space. Eruption of the permanent successors to natal/neonatal teeth was not delayed, rather in some instances the eruption was found to be enhanced as compared to contralateral incisor as noted in unilaterally occurring natal/neonatal teeth. The mandibular anterior arch collapse was not permanent as the successors erupted uncrowded. The paper discusses the method and timing of extraction. From the immunological and hematological point of view the best time for extraction was calculated to be 7-25 days of birth.

Placental transfer of fluoride in pregnant women consuming optimum fluoride in drinking water

The study was conducted on 25 healthy women residing in optimum fluoride areas, who were to deliver normally through vaginal route, to correlate the maternal and cord plasma fluoride levels and evaluate the placental transfer of fluoride. A wide variation was found in the maternal and cord plasma fluoride levels. In only 8 percent of the cases the fluoride levels in cord plasma were higher than maternal plasma. It was deduced that the placenta allows passive diffusion of fluoride from mother to foetus and does not act as a barrier.

Interrelationship between sugar and dental caries--a study in child population of Orissa

An epidemiological study on interrelationship between dental caries and sugar consumption conducted on 1265 children in the age of 5-15 years revealed a positive association of dental caries experience with total sugar exposures, between meal sugar exposures and at meal sugar exposures. As the total increased from 3 to 4 in a day, a corresponding jump of 1 deft+DMFT and 2 defs+DMFS was noted, which was clinically and statistically significant. It was deduced that total sugar exposures per day should be limited to 3, out of which two should be at meal time and one between meals.

Orbital and sinus inflammation with secondary optic neuropathy

Optic neuropathy with simultaneous orbital and sinus inflammation is a diagnostic dilemma. Although sinus inflammation was described previously as causative in some cases of optic neuritis, the relatively high rate of asymptomatic sinus opacification in radiologic studies of the general population (as high as 13%) makes this a diagnosis of exclusion. We describe a patient who had optic neuropathy associated with simultaneous orbital and sinus inflammation. Although definitive determination of etiology may not be made without tissue biopsy, cases suspected of having a bacterial etiology may benefit from an initial 48-hour trial of intravenous antibiotics before initiation of systemic corticosteroids.

NaF iontophoresis, an alternative to cavity lining--an in vivo study

The study carried out on 30 teeth in 28 patients of 12-16 years to assess NaF iontophoresis as an alternative to cavity lining revealed that out of 25 cavities which were sensitive to air, water jet and exploration (14 mild, 9 moderate and 2 severe), in 20 cavities the sensitivity decreased to nil, in 9 to mild and in one to moderate following iontophoresis. It was found that in all the cases, the first application of iontophoresis decreased the sensitivity by 50-60 percent and the second by 70-90 percent. Immediately after silver filling there was no sensitivity in 25 teeth, whereas 4 were mildly and one moderately sensitive. After a six month follow up in 24 patients who reported, all the teeth were comfortable.

Apexification: follow-up after 6-12 years

Thirty 'apexified' immature permanent anterior teeth treated utilising Ca(OH)2 as root canal dressing assessed clinically and radiographically after greater than 6 less than or equal to 12 years revealed that in 15 teeth bridge remained the same; in 10 consolidated, while in 3 it decreased. Periapical radiolucency reappeared in one case, while in two it was questionable but clinically the teeth were comfortable; these cases were ones showing decrease in bridge consolidation: two teeth had been extracted during this observation period by some dentists because of complaint of discolouration.

Intercomparison of prevalence and severity of dental caries using two recording systems

Dental caries was recorded using WHO index (1983) and Moller's index (1966) in 1265 children in the age group of 5, 8, 11 and 15 years to determine the conversion and correlation figures, so as to facilitate cross comparison and quick appraisal where either of the systems have been used in epidemiological studies. The results revealed that dental caries was recorded higher with Moller's index as compared to the WHO index; on an average the difference was fourteen percent in point prevalence, one deft + DMFT and one and a half defs + DMFS.