Establishing and managing a periodontal biobank for research: the sharing of experience

Periodontal bio-repositories, which allow banking of clinically validated human data and biological samples, provide an opportunity to derive biomarkers for periodontal diagnosis, prognosis and therapeutic activities which are expected to improve patient management. This article presents the establishing of the Malaysian Periodontal Database and Biobank System (MPDBS) which was initiated in 2011 with the aim to facilitate periodontal research. Partnerships were established with collaborating centres. Policies on specimen access, authorship and acknowledgement policies were agreed upon by all participating centres before the initiation of the periodontal biobank. Ethical approval for the collection of samples and data were obtained from institutional ethics review boards. A broad-based approach for informed consent was used, which covered areas related to quality of life impacts, genetics and molecular aspects of periodontal disease. Sample collection and processing was performed using a standardized protocol. Biobanking resources such as equipment and freezers were shared with the Malaysian Oral Cancer Database and Tissue Bank System (MOCDTBS). In the development of the MPDBS, challenges that were previously faced by the MOCDTBS were considered. Future challenges in terms of ethical and legal issues will be faced when international collaborations necessitate the transportation of specimens across borders.

Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus

Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified.

The risk of surgical site infection and re-admission in obese patients undergoing total joint replacement who lose weight before surgery and keep it off post-operatively

This study evaluated whether obese patients who lost weight before their total joint replacement and kept it off post-operatively were at lower risk of surgical site infection (SSI) and re-admission compared with those who remained the same weight. We reviewed 444 patients who underwent a total hip replacement and 937 with a total knee replacement who lost weight pre-operatively and sustained their weight loss after surgery. After adjustments, patients who lost weight before a total hip replacement and kept it off post-operatively had a 3.77 (95% confidence interval (CI) 1.59 to 8.95) greater likelihood of deep SSIs and those who lost weight before a total knee replacement had a 1.63 (95% CI 1.16 to 2.28) greater likelihood of re-admission compared with the reference group. These findings raise questions about the safety of weight management before total replacement of the hip and knee joints.

The risk of surgical site infection and re-admission in obese patients undergoing total joint replacement who lose weight before surgery and keep it off post-operatively

This study evaluated whether obese patients who lost weight before their total joint replacement and kept it off post-operatively were at lower risk of surgical site infection (SSI) and re-admission compared with those who remained the same weight.

We reviewed 444 patients who underwent a total hip replacement and 937 with a total knee replacement who lost weight pre-operatively and sustained their weight loss after surgery. After adjustments, patients who lost weight before a total hip replacement and kept it off post-operatively had a 3.77 (95% confidence interval (CI) 1.59 to 8.95) greater likelihood of deep SSIs and those who lost weight before a total knee replacement had a 1.63 (95% CI 1.16 to 2.28) greater likelihood of re-admission compared with the reference group.

These findings raise questions about the safety of weight management before total replacement of the hip and knee joints.

Cite this article: Bone Joint J 2014;96-B:629–35.

A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: applications in genetic dissection of qualitative and quantitative traits

Background

Dense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive molecular breeding, and map-based gene cloning. This report describes the construction of the first B. napus consensus map consisting of a 1,359 anchored array based genotyping platform; Diversity Arrays Technology (DArT), and non-DArT markers from six populations originating from Australia, Canada, China and Europe. We aligned the B. napus DArT sequences with genomic scaffolds from Brassica rapa and Brassica oleracea, and identified DArT loci that showed linkage with qualitative and quantitative loci associated with agronomic traits.

Results

The integrated consensus map covered a total of 1,987.2 cM and represented all 19 chromosomes of the A and C genomes, with an average map density of one marker per 1.46 cM, corresponding to approximately 0.88 Mbp of the haploid genome. Through in silico physical mapping 2,457 out of 3,072 (80%) DArT clones were assigned to the genomic scaffolds of B. rapa (A genome) and B. oleracea (C genome). These were used to orientate the genetic consensus map with the chromosomal sequences. The DArT markers showed linkage with previously identified non-DArT markers associated with qualitative and quantitative trait loci for plant architecture, phenological components, seed and oil quality attributes, boron efficiency, sucrose transport, male sterility, and race-specific resistance to blackleg disease.

Conclusions

The DArT markers provide increased marker density across the B. napus genome. Most of the DArT markers represented on the current array were sequenced and aligned with the B. rapa and B. oleracea genomes, providing insight into the Brassica A and C genomes. This information can be utilised for comparative genomics and genomic evolution studies. In summary, this consensus map can be used to (i) integrate new generation markers such as SNP arrays and next generation sequencing data; (ii) anchor physical maps to facilitate assembly of B. napus genome sequences; and (iii) identify candidate genes underlying natural genetic variation for traits of interest.

p190-B RhoGAP regulates the functional composition of the mesenchymal microenvironment

Hematopoiesis is regulated by components of the microenvironment, so-called niche. Here, we show that p190-B GTPase-activating protein (p190-B) deletion in mice causes hematopoietic failure during ontogeny, in p190-B(-/-) fetal liver and bones, and in p190-B(+/-) adult bones and spleen. These defects are non-cell autonomous, as we previously showed that transplantation of p190-B(-/-) hematopoietic cells into wild-type (WT) hosts leads to normal hematopoiesis. Coculture of mesenchymal stem (MSC)/progenitor cells and wild-type bone marrow (BM) cells reveals that p190-B(-/-) MSCs are dysfunctional in supporting hematopoiesis owing to impaired Wnt signaling. Furthermore, p190-B loss causes alteration in BM niche composition, including abnormal colony-forming unit (CFU)-fibroblast, CFU-adipocyte and CFU-osteoblast numbers. This is due to altered MSC lineage fate specification to osteoblast and adipocyte lineages. Thus, p190-B organizes a functional mesenchymal/microenvironment for normal hematopoiesis during development.

Mal-united fracture of calcaneum treated with lateral decompression

Fracture calcaneum is commonly complicated with mal-union. Mal-union is usually presented with broadening of the lateral wall of the calcaneum, irregularity of the sub-talar joint and loss of the vertical height of the body of calcaneum with varus rotation. In this study twenty three (n=23) patients underwent a lateral decompression for pain on lateral aspect of foot on walking and tip toeing, secondary to a mal-united calcaneal fracture with or without sub-talar intra-articular involvement. Almost every patient had ballooned out body of calcaneum with impingement of peroneal tendon sheath with its content and lateral heel pain as a result of deformity. So in current study the operative procedure selected was excision of a lateral calcaneal bony mass and decompression of the peroneal tendon to relieve pain. Peroneal tenogram was a routine procedure before surgery to detect presence and site of blockade within tendon sheath. The average follow-up was for a period of 31.6 months. Result was assessed according to American Orthopaedic Foot and Ankle Society (AOFAS) Ankle-Hind foot Scale. Two patients (n=2, 8.69%) had excellent (Category 1) result, seventeen (n=17, 73.9%) were good (Category 2), two (n=2, 8.69%) were fair (Category 3) and rest two (n=2, 8.69%) were with poor (Category 4) outcome. Every four out of five patients got back painless Heel and Ankle after surgery. The results suggest that the lateral decompression procedure is a technically simpler yet viable alternative to late sub-talar fusion for lateral pain following a mal-united fracture of calcaneum.

Genetic and physical mapping of flowering time loci in canola (Brassica napus L.)

We identified quantitative trait loci (QTL) underlying variation for flowering time in a doubled haploid (DH) population of vernalisation-responsive canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum and aligned them with physical map positions of predicted flowering genes from the Brassica rapa genome. Significant genetic variation in flowering time and response to vernalisation were observed among the DH lines from Skipton/Ag-Spectrum. A molecular linkage map was generated comprising 674 simple sequence repeat, sequence-related amplified polymorphism, sequence characterised amplified region, Diversity Array Technology, and candidate gene based markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 20 loci, localised on ten different chromosomes. These loci each accounted for between 2.4 and 28.6% of the total genotypic variation for first flowering and response to vernalisation. However, identification of consistent QTL was found to be dependant upon growing environments. We compared the locations of QTL with the physical positions of predicted flowering time genes located on the sequenced genome of B. rapa. Some QTL associated with flowering time on A02, A03, A07, and C06 may represent homologues of known flowering time genes in Arabidopsis; VERNALISATION INSENSITIVE 3, APETALA1, CAULIFLOWER, FLOWERING LOCUS C, FLOWERING LOCUS T, CURLY LEAF, SHORT VEGETATIVE PHASE, GA3 OXIDASE, and LEAFY. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for low rainfall areas, via marker-assisted selection.

Genetic and physical mapping of flowering time loci in canola (Brassica napus L.)

We identified quantitative trait loci (QTL) underlying variation for flowering time in a doubled haploid (DH) population of vernalisation-responsive canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum and aligned them with physical map positions of predicted flowering genes from the Brassica rapa genome. Significant genetic variation in flowering time and response to vernalisation were observed among the DH lines from Skipton/Ag-Spectrum. A molecular linkage map was generated comprising 674 simple sequence repeat, sequence-related amplified polymorphism, sequence characterised amplified region, Diversity Array Technology, and candidate gene based markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 20 loci, localised on ten different chromosomes. These loci each accounted for between 2.4 and 28.6% of the total genotypic variation for first flowering and response to vernalisation. However, identification of consistent QTL was found to be dependant upon growing environments. We compared the locations of QTL with the physical positions of predicted flowering time genes located on the sequenced genome of B. rapa. Some QTL associated with flowering time on A02, A03, A07, and C06 may represent homologues of known flowering time genes in Arabidopsis; VERNALISATION INSENSITIVE 3, APETALA1, CAULIFLOWER, FLOWERING LOCUS C, FLOWERING LOCUS T, CURLY LEAF, SHORT VEGETATIVE PHASE, GA3 OXIDASE, and LEAFY. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for low rainfall areas, via marker-assisted selection.

Diagnostic options for radiative divertor feedback control on NSTX-U

A radiative divertor technique is used in present tokamak experiments and planned for ITER to mitigate high heat loads on divertor plasma-facing components (PFCs) to prevent excessive material erosion and thermal damage. In NSTX, a large spherical tokamak with lithium-coated graphite PFCs and high divertor heat flux (q(peak) ≤ 15 MW/m(2)), radiative divertor experiments have demonstrated a significant reduction of divertor peak heat flux simultaneously with good core H-mode confinement using pre-programmed D(2) or CD(4) gas injections. In this work diagnostic options for a new real-time feedback control system for active radiative divertor detachment control in NSTX-U, where steady-state peak divertor heat fluxes are projected to reach 20-30 MW/m(2), are discussed. Based on the NSTX divertor detachment measurements and analysis, the control diagnostic signals available for NSTX-U include divertor radiated power, neutral pressure, spectroscopic deuterium recombination signatures, infrared thermography of PFC surfaces, and thermoelectric scrape-off layer current. In addition, spectroscopic "security" monitoring of possible confinement or pedestal degradation is recommended. These signals would be implemented in a digital plasma control system to manage the divertor detachment process via an actuator (impurity gas seeding rate).

Identification and characterization of candidate Rlm4 blackleg resistance genes in Brassica napus using next-generation sequencing

A thorough understanding of the relationships between plants and pathogens is essential if we are to continue to meet the agricultural needs of the world's growing population. The identification of genes underlying important quantitative trait loci is extremely challenging in complex genomes such as Brassica napus (canola, oilseed rape or rapeseed). However, recent advances in next-generation sequencing (NGS) enable much quicker identification of candidate genes for traits of interest. Here, we demonstrate this with the identification of candidate disease resistance genes from B. napus for its most devastating fungal pathogen, Leptosphaeria maculans (blackleg fungus). These two species are locked in an evolutionary arms race whereby a gene-for-gene interaction confers either resistance or susceptibility in the plant depending on the genotype of the plant and pathogen. Preliminary analysis of the complete genome sequence of Brassica rapa, the diploid progenitor of B. napus, identified numerous candidate genes with disease resistance characteristics, several of which were clustered around a region syntenic with a major locus (Rlm4) for blackleg resistance on A7 of B. napus. Molecular analyses of the candidate genes using B. napus NGS data are presented, and the difficulties associated with identifying functional gene copies within the highly duplicated Brassica genome are discussed.

Suction elevator for ear surgery

An instrument has been designed to combine a suction and an elevator for use in ear surgery.

Molecular mapping of qualitative and quantitative loci for resistance to Leptosphaeria maculans causing blackleg disease in canola (Brassica napus L.)

Blackleg, caused by Leptosphaeria maculans, is one of the most important diseases of oilseed and vegetable crucifiers worldwide. The present study describes (1) the construction of a genetic linkage map, comprising 255 markers, based upon simple sequence repeats (SSR), sequence-related amplified polymorphism, sequence tagged sites, and EST-SSRs and (2) the localization of qualitative (race-specific) and quantitative (race non-specific) trait loci controlling blackleg resistance in a doubled-haploid population derived from the Australian canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum using the whole-genome average interval mapping approach. Marker regression analyses revealed that at least 14 genomic regions with LOD ≥ 2.0 were associated with qualitative and quantitative blackleg resistance, explaining 4.6-88.9 % of genotypic variation. A major qualitative locus, designated RlmSkipton (Rlm4), was mapped on chromosome A7, within 0.8 cM of the SSR marker Xbrms075. Alignment of the molecular markers underlying this QTL region with the genome sequence data of B. rapa L. suggests that RlmSkipton is located approximately 80 kb from the Xbrms075 locus. Molecular marker-RlmSkipton linkage was further validated in an F(2) population from Skipton/Ag-Spectrum. Our results show that SSR markers linked to consistent genomic regions are suitable for enrichment of favourable alleles for blackleg resistance in canola breeding programs.

Macular pigment optical density in wet age-related macular degeneration among Indians

PURPOSE

To estimate the value of macular pigment optical density (MPOD) in adult south Indian population with wet age-related macular degeneration (AMD).

METHODS

A total of 33 patients with wet AMD and 29 age-matched controls >50 years of age underwent MPOD measurement with the macular densitometer. The patients were also tested for their dietary intake of carotenoids, smoking history, and lifetime UV exposure.

RESULTS

The mean MPOD values in the Indian population with wet AMD was 0.23 (95% CI: 0.18-0.29) vs control was 0.43 (95% CI: 0.37-0.49), P<0.0001, at 0.5° eccentricity. Ex-smokers had a lower MPOD than non-smokers (0.16 (0.09-0.23) vs 0.28 (0.22-0.34), P=0.026) and the lowest level of carotenoids intake had 48% lower MPOD than the highest level (0.14 (0.08-0.21) vs 0.33 (0.24-0.43), P=0.012). There was no significant age-related decline or gender variation in MPOD.

CONCLUSION

This study establishes the MPOD in adult Indian population with wet AMD, with a lack of macular pigment in association with wet AMD.

Treatment consent capacity in patients with traumatic brain injury across a range of injury severity

OBJECTIVE

To investigate medical decision-making capacity (MDC) in patients with acute traumatic brain injury (TBI) across a range of injury severity.

METHODS

We evaluated MDC cross-sectionally 1 month after injury in 40 healthy controls and 86 patients with TBI stratified by injury severity (28 mild [mTBI], 15 complicated mild [cmTBI], 43 moderate/severe [msevTBI]). We compared group performance on the Capacity to Consent to Treatment Instrument and its 5 consent standards (expressing choice, reasonable choice, appreciation, reasoning, understanding). Capacity impairment ratings (no impairment, mild/moderate impairment, severe impairment) on the consent standards were also assigned to each participant with TBI using cut scores referenced to control performance.

RESULTS

One month after injury, the mTBI group performed equivalently to controls on all consent standards. In contrast, the cmTBI group was impaired relative to controls on the understanding standard. No differences emerged between the mTBI and cmTBI groups. The msevTBI group was impaired on almost all standards relative to both control and mTBI groups, and on the understanding standard relative to the cmTBI group. Capacity compromise (mild/moderate or severe impairment ratings) on the 3 clinically complex standards (understanding, reasoning, appreciation) occurred in 10%-30% of patients with mTBI, 50% of patients with cmTBI, and 50%-80% of patients with msevTBI.

CONCLUSIONS

One month following injury, MDC is largely intact in patients with mTBI, but is impaired in patients with cmTBI and msevTBI. Impaired MDC is prevalent in acute TBI and is strongly related to injury severity.

Association between various types of obesity and macular pigment optical density

PURPOSE

To elucidate the association between macular pigment optical density (MPOD) and various types of obesity in the South-Indian population.

PATIENTS AND METHODS

In total, 300 eyes of 161 healthy volunteers of South-Indian origin were studied. MPOD was measured psychophysically at 0.25°, 0.50°, 1.00°, and 1.75° eccentricities from fovea. Anthropometric measurements included waist circumference (WC) and waist-to-hip ratio (WHR) and body mass index (BMI). Using the WHO Expert Consultation guidelines, obesity was defined based on BMI alone (BMI ≥ 23 kg/m(2)), based on WC alone (WC ≥ 90 cm for men and ≥ 80 cm for women), and based on WHR alone (≥ 0.90 for men and ≥ 0.85 for women). Isolated generalized obesity was defined as increased BMI and normal WC. Isolated abdominal obesity was defined as increased WC and normal BMI. Combined obesity was defined as increased BMI and increased WC.

RESULTS

Mean MPOD at all eccentricities was not significantly different between men and women. Mean MPOD values did not significantly differ in various types of obesity, when compared with the normal subjects. On subgroup analysis, in age group ≥ 60 years, mean MPOD values were significantly higher in subjects with obesity based on BMI (0.61 vs 0.41, P=0.036), obesity based on WHR (0.67 vs 0.41, P=0.007), and isolated generalized obesity (0.66 vs 0.41, P=0.045) in comparison with normal subjects at 0.25° eccentricity.

CONCLUSION

We found lack of an association between MPOD and obesity in the South-Indian population. A similar finding was also noted on age group- and gender-wise analyses.

Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.)

We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines ‘Lynx-037DH’ and ‘Monty-028DH’. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed.