Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution

Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.

POS0051 THE IMPACT OF COVID-19 ON RHEUMATOLOGY TRAINING: RESULTS FROM THE COVID-19 GLOBAL RHEUMATOLOGY ALLIANCE TRAINEE SURVEY

Background:

The COVID-19 pandemic has disrupted healthcare delivery and education of physicians, including rheumatology trainees.

Objectives:

To assess the impact of the COVID-19 pandemic on the clinical experiences, research opportunities, and well-being of rheumatology trainees.

Methods:

A voluntary, anonymous, web-based survey was administered in English, Spanish, or French from 19/08/2020 to 05/10/2020. Adult and paediatric rheumatology trainees worldwide in training in 2020 were invited to participate via social media and email. Using multiple choice questions, Likert scales, and free text answers, we assessed trainee patient care activities, redeployment, research, and well-being.

Results:

The 302 respondents were from 33 countries, with most (83%, 252/302) in adult rheumatology training. Many trainees (45%, 135/300) reported an increase in non-rheumatology clinical work (e.g. care of COVID-19 patients), with 52% of these (70/135) also continuing rheumatology clinical work. COVID-19 redeployment was not optional for 68% (91/134).

Trainees reported a negative impact of the pandemic in their growth in rheumatology (Figure 1). They also reported a substantial impact on several training areas: outpatient clinics (79%, 238/302), inpatient consultations (59%, 177/302), formal teaching (55%, 167/302), procedures (53%, 147/302), teaching opportunities (52%, 157/302), and ultrasonography (36%, 110/302), with 87-96% perceiving a negative impact on these areas. Only 54% (159/294) reported feeling comfortable with their level of clinical supervision during the pandemic (Figure 1).

Many trainees (46%, 128/280) reported changes in research experiences during the pandemic; 39% (110/285) reported that COVID-19 negatively affected their ability to continue their pre-pandemic research and 50% (142/285) reported difficulty maintaining research goals (Figure 1).

Some rheumatology trainees reported having health condition(s) putting them at high risk for COVID-19 (10%, 30/302) and 14% of trainees (41/302) reported having had COVID-19 (Table 1). Only 53% (160/302) reported feeling physically safe in the workplace while 25% (76/302) reported not feeling physically safe; reasons included lack of training about COVID-19, lack of comfort in the clinical setting, insufficient personal protective equipment, immunocompromised state, and pregnancy. Half (151/302) reported burnout and 68% (204/302) an increase in stress from work during the pandemic (Figure 1), whilst 25% (75/302) reported that changes to their training programme negatively impacted their physical health.

Conclusion:

The COVID-19 pandemic has negatively impacted the experience of rheumatology training as well as the well-being of trainees globally. Our data highlight concerns for rheumatology trainees including research opportunities and clinical care which should be a focus for curriculum planning.

Figure 1.

Rheumatology trainee perceptions of pandemic impact and changes in training programme.

Table 1.

Estimated hazard ratios, adjusted for age and gender, for individuals with rheumatoid arthritis

Europen = 89ROWn = 213Combinedn = 302Disability1 (1)9 (4)10 (3)High risk7 (8)23 (11)30 (10)Pregnant4 (5)15 (7)19 (6)Shielding/Quarantining12 (13)70 (33)82 (27)Acquired COVID-1920 (22)21 (10)41 (14)

Disclosure of Interests:

Kristen Young: None declared, Su-Ann Yeoh: None declared, Michael Putman: None declared, Elizabeth Graef: None declared, Francis Berenbaum: None declared, Richard Conway: None declared, Rebecca Grainger Speakers bureau: Speaker fees from Abbvie, Janssen, Novartis, Pfizer, Cornerstones, all not related to this work, Consultant of: Consultancy fees from Abbvie, Janssen, Novartis, Pfizer, Cornerstones, all not related to this work, Grant/research support from: Travel assistance from Pfizer, not related to this work, Adam Kilian: None declared, Maximilian Konig: None declared, Jean Liew Grant/research support from: Research grant from Pfizer unrelated to this manuscript, Pedro M Machado Speakers bureau: Speaker fees from Abbvie, BMS, Celgene, Eli Lilly, Janssen, MSD, Novartis, Orphazyme, Pfizer, Roche and UCB, all unrelated to this manuscript, Consultant of: Consulting fees from Abbvie, BMS, Celgene, Eli Lilly, Janssen, MSD, Novartis, Orphazyme, Pfizer, Roche and UCB, all unrelated to this manuscript, Sebastian E. Sattui: None declared, Jeffrey Sparks Consultant of: Consultancy for Bristol-Myers Squibb, Gilead, Inova Diagnostics, Optum, and Pfizer unrelated to this manuscript, Grant/research support from: Research support from Bristol-Myers Squibb unrelated to this manuscript, Paul Sufka: None declared, Manuel Ugarte-Gil Grant/research support from: Research grants from Janssen and Pfizer unrelated to this manuscript, Laura Upton: None declared, Zachary Wallace: None declared, Jinoos Yazdany Consultant of: Consultancy for Astra Zeneca, Eli Lilly, and Pfizer, not related to this work, Grant/research support from: Research grants from Gilead and Pfizer, not related to this work, Arundathi Jayatilleke: None declared.

AB0674 RAPID ADOPTION OF TELEMEDICINE IN RHEUMATOLOGY TRAINING: RESULTS FROM THE COVID-19 GLOBAL RHEUMATOLOGY ALLIANCE TRAINEE SURVEY

Background:

The COVID-19 pandemic led to a rapid increase in remote consultations in rheumatology care. Due to the potential impact of this change on rheumatology clinical training, we investigated trainees’ experiences with telemedicine.

Objectives:

To assess the impact of telemedicine use during the COVID-19 pandemic on rheumatology training, including supervision.

Methods:

A voluntary, anonymous web-based survey was administered in English, Spanish, or French from 19/08/2020 to 05/10/2020. Adult and paediatric rheumatology trainees worldwide in training in 2020 were invited to participate via social media and email. Using multiple choice questions, Likert scales, and free text answers, we collected data regarding prior and current telemedicine use, training, and supervision.

Results:

302 respondents from 33 countries completed the survey, with most (83%, 252/302) in adult rheumatology training. Reported use of telemedicine increased from 13% (39/302) pre-pandemic to 82% (247/302) (Table 1). European trainees predominantly utilised audio-only compared to trainees from the rest of the world (ROW) who predominantly utilised audio-video telemedicine.

Most trainees continued to evaluate new patients using telemedicine (65%, 161/247). A larger proportion of trainees were comfortable using telemedicine to evaluate follow-up (69% 170/247) versus new patients (25%, 41/161) (Figure 1).

Only 32% (97/302) were trained in telemedicine, with the highest proportion among United States (US) trainees (59%, 69/116); subjects included software, clinical skills, and billing. The majority of trainees found this helpful (92%, 89/97).

Supervision was most frequently in the form of verbal discussion after the consultation (Table 1); 24% (59/247) had no telemedicine supervision during the pandemic. In general, trainees found telemedicine negatively impacted their supervision (51%, 123/242) and clinical teaching quality (70%, 171/244); only 9% reported a positive impact on these areas.

Conclusion:

Adoption of telemedicine during the COVID-19 pandemic has led to areas of concern for rheumatology trainees including inadequate supervision and clinical teaching. Our results suggest a need for education on evaluation of new patients using telemedicine, increasing telemedicine training, and ensuring adequate supervisory arrangements.

Table 1.

Telemedicine use, supervision, and training by region. Data is presented as n (%). Rest of the world (ROW) data includes Asia (50), Central and South America (23), Canada (12), Australia (8), and Africa (4).

Europen = 89USn = 116ROWn = 97Combinedn = 302Telemedicine usePre-pandemic15 (17)9 (8)15 (15)39 (13)During pandemic64 (72)112 (97)71 (73)247 (82)Telemedicine modalitypre-pandemicAudio-only14 (93)3 (33)8 (53)25 (64)Audio-video1 (7)7 (78)7 (47)15 (38)Telemedicine modality during pandemicAudio-only56 (88)47 (42)51 (72)154 (62)Audio-video7 (11)100 (89)29 (41)136 (55)Supervisionpre-pandemicReal-time observation (part of visit)0 (0)4 (44)3 (20)7 (18)Real-time observation (full visit)0 (0)2 (22)2 (13)4 (10)Verbal discussion after8 (53)3 (33)7 (47)18 (46)Written communication after0 (0)0 (0)1 (7)1 (3)None7 (47)2 (22)5 (33)14 (36)Supervision during pandemicReal-time observation (part of visit)2 (3)54 (48)15 (21)71 (29)Real-time observation (full visit)3 (5)32 (29)8 (11)43 (17)Verbal discussion after32 (50)65 (58)28 (39)125 (51)Written communication after7 (11)15 (13)9 (13)31 (13)None28 (44)9 (8)22 (31)59 (24)Figure 1.

Rheumatology trainee comfort levels in using telemedicine during the pandemic.

Disclosure of Interests:

Su-Ann Yeoh: None declared, Kristen Young: None declared, Michael Putman: None declared, Elizabeth Graef: None declared, Francis Berenbaum: None declared, Richard Conway: None declared, Rebecca Grainger Speakers bureau: Speaker fees from Abbvie, Janssen, Novartis, Pfizer, Cornerstones, all not related to this work, Consultant of: Consultancy fees from Abbvie, Janssen, Novartis, Pfizer, Cornerstones, all not related to this work, Grant/research support from: Travel assistance from Pfizer, not related to this work, Adam Kilian: None declared, Maximilian Konig: None declared, Jean Liew Grant/research support from: Research grant from Pfizer unrelated to this manuscript, Pedro M Machado Speakers bureau: Speaker fees from Abbvie, BMS, Celgene, Eli Lilly, Janssen, MSD, Novartis, Orphazyme, Pfizer, Roche and UCB, all unrelated to this manuscript, Consultant of: Consulting fees from Abbvie, BMS, Celgene, Eli Lilly, Janssen, MSD, Novartis, Orphazyme, Pfizer, Roche and UCB, all unrelated to this manuscript, Sebastian E. Sattui: None declared, Jeffrey Sparks Consultant of: Consultancy for Bristol-Myers Squibb, Gilead, Inova Diagnostics, Optum, and Pfizer unrelated to this manuscript, Grant/research support from: Research support from Bristol-Myers Squibb unrelated to this manuscript, Paul Sufka: None declared, Manuel Ugarte-Gil Grant/research support from: Research grants from Janssen and Pfizer unrelated to this manuscript, Laura Upton: None declared, Zachary Wallace: None declared, Jinoos Yazdany Consultant of: Consultancy for Astra Zeneca, Eli Lilly, and Pfizer, not related to this work, Grant/research support from: Research grants from Gilead and Pfizer, not related to this work, Arundathi Jayatilleke: None declared

Prolegomenon to the thought style of the new history of psychology

The present article provides an introduction to the new history of psychology within the framework of critical perspective while offering some methodological solutions for contemporary historical research in psychology. We propose a new model of research for conducting studies in the history of psychology. This approach is predominantly concerned with reconstructing crypto thought styles, acknowledging the existence of peripheral sources of knowledge about human psychological life, and revealing hidden lines of inquiry, which will be presented using a contextual approach to the history of psychology. In this analysis, psychological knowledge will be treated as a product of social activities that occur un-der specific historical conditions and define the scope of psychological research. The proposed to examine history of psychology and investigative practice in a specific context will allow for deeper insight into the world’s history of psychology and provide new methods for studying psychological schools of thought and ideas established on the periphery of mainstream psychology. Finally, we offer words of encouragement for scholars engaging in a context-specific study of psychological thought and efforts made towards grasping the reality of a local soul.

Development of Diversity Arrays Technology markers as a tool for rapid genomic assessment in Nile tilapia, Oreochromis niloticus

The development of genomic markers is described for Nile tilapia, Oreochromis niloticus, using the Diversity Arrays Technology (DArT) genotype-by-sequencing platform. A total of 13 215 single nucleotide polymorphism (SNP) markers and 12 490 silicoDArT (dominant) markers were identified from broodstock of two selective breeding programs [Genetically Improved Farmed Tilapia (GIFT) strain from Malaysia and the Abbassa strain from Egypt]. Over 10 000 SNPs were polymorphic in either strain, and 2985 and 3087 showed strain-specific polymorphisms for the GIFT and Abbassa strains respectively. We demonstrate the potential utility of these markers for rapid genomic screening and use in breeding programs.

DArT whole genome profiling provides insights on the evolution and taxonomy of edible Banana (Musa spp.)

BACKGROUND AND AIMS

Dessert and cooking bananas are vegetatively propagated crops of great importance for both the subsistence and the livelihood of people in developing countries. A wide diversity of diploid and triploid cultivars including AA, AB, AS, AT, AAA, AAB, ABB, AAS and AAT genomic constitutions exists. Within each of this genome groups, cultivars are classified into subgroups that are reported to correspond to varieties clonally derived from each other after a single sexual event. The number of those founding events at the basis of the diversity of bananas is a matter of debate.

METHODS

We analysed a large panel of 575 accessions, 94 wild relatives and 481 cultivated accessions belonging to the section Musa with a set of 498 DArT markers previously developed.

KEY RESULTS

DArT appeared successful and accurate to describe Musa diversity and help in the resolution of cultivated banana genome constitution and taxonomy, and highlighted discrepancies in the acknowledged classification of some accessions. This study also argues for at least two centres of domestication corresponding to South-East Asia and New Guinea, respectively. Banana domestication in New Guinea probably followed different schemes that those previously reported where hybridization underpins the emergence of edible banana. In addition, our results suggest that not all wild ancestors of bananas are known, especially in M. acuminata subspecies. We also estimate the extent of the two consecutive bottlenecks in edible bananas by evaluating the number of sexual founding events underlying our sets of edible diploids and triploids, respectively.

CONCLUSIONS

The attribution of clone identity to each sample of the sets allowed the detection of subgroups represented by several sets of clones. Although morphological characterization of some of the accessions is needed to correct potentially erroneous classifications, some of the subgroups seem polyclonal.

Derivation and Application of an Algorithm for the Numerical Calculation of the Local Orientation of Nematic Liquid Crystals

Starting from a relaxation equation for the alignment tensor, an algorithm is derived which allows the numerical calculation of the dynamic and static behavior of the director field n with the correct nematic symmetry property, where n and - n are equivalent. As a first application, a two-dimensional problem is treated where the typical nematic defects with half-integer winding numbers only occur when the algorithm with the correct nematic symmetry property is used. Furthermore, the method is applied to the static and dynamic behavior of a Frederiks cell with strong and weak anchoring.

Radiation hybrid QTL mapping of Tdes2 involved in the first meiotic division of wheat

Since the dawn of wheat cytogenetics, chromosome 3B has been known to harbor a gene(s) that, when removed, causes chromosome desynapsis and gametic sterility. The lack of natural genetic diversity for this gene(s) has prevented any attempt to fine map and further characterize it. Here, gamma radiation treatment was used to create artificial diversity for this locus. A total of 696 radiation hybrid lines were genotyped with a custom mini array of 140 DArT markers, selected to evenly span the whole 3B chromosome. The resulting map spanned 2,852 centi Ray with a calculated resolution of 0.384 Mb. Phenotyping for the occurrence of meiotic desynapsis was conducted by measuring the level of gametic sterility as seeds produced per spikelet and pollen viability at booting. Composite interval mapping revealed a single QTL with LOD of 16.2 and r (2) of 25.6 % between markers wmc326 and wPt-8983 on the long arm of chromosome 3B. By independent analysis, the location of the QTL was confirmed to be within the deletion bin 3BL7-0.63-1.00 and to correspond to a single gene located ~1.4 Mb away from wPt-8983. The meiotic behavior of lines lacking this gene was characterized cytogenetically to reveal striking similarities with mutants for the dy locus, located on the syntenic chromosome 3 of maize. This represents the first example to date of employing radiation hybrids for QTL analysis. The success achieved by this approach provides an ideal starting point for the final cloning of this interesting gene involved in meiosis of cereals.

Development of a genetic linkage map for Sharon goatgrass (Aegilops sharonensis) and mapping of a leaf rust resistance gene

Aegilops sharonensis (Sharon goatgrass), a diploid wheat relative, is known to be a rich source of disease resistance genes for wheat improvement. To facilitate the transfer of these genes into wheat, information on their chromosomal location is important. A genetic linkage map of Ae. sharonensis was constructed based on 179 F2 plants derived from a cross between accessions resistant (1644) and susceptible (1193) to wheat leaf rust. The linkage map was based on 389 markers (377 Diversity Arrays Technology (DArT) and 12 simple sequence repeat (SSR) loci) and was comprised of 10 linkage groups, ranging from 2.3 to 124.6 cM. The total genetic length of the map was 818.0 cM, with an average interval distance between markers of 3.63 cM. Based on the chromosomal location of 115 markers previously mapped in wheat, the four linkage groups of A, B, C, and E were assigned to Ae. sharonensis (S(sh)) and homoeologous wheat chromosomes 6, 1, 3, and 2. The single dominant gene (designated LrAeSh1644) conferring resistance to leaf rust race THBJ in accession 1644 was positioned on linkage group A (chromosome 6S(sh)) and was flanked by DArT markers wpt-9881 (at 1.9 cM distal from the gene) and wpt-6925 (4.5 cM proximal). This study clearly demonstrates the utility of DArT for genotyping uncharacterized species and tagging resistance genes where pertinent genomic information is lacking.

Identification and mapping of a leaf rust resistance gene in barley line Q21861

Barley line Q21861 possesses an incompletely dominant gene (RphQ) for resistance to leaf rust caused by Puccinia hordei. To investigate the allelic and linkage relations between RphQ and other known Rph genes, F2 populations from crosses between Q21861 and donors of Rph1 to Rph14 (except for Rph8) were evaluated for leaf rust reaction at the seedling stage. Results indicate that RphQ is either allelic with or closely linked to the Rph2 locus. A doubled haploid population derived from a cross between Q21861 and SM89010 (a leaf rust susceptible line) was used for molecular mapping of the resistance locus. Bulked segregant analysis was used to identify markers linked to RphQ, using random amplified polymorphic DNAs (RAPDs), restriction fragment length polymorphisms (RFLPs), and sequence tagged sites (STSs). Of 600 decamer primers screened, amplified fragments generated by 9 primers were found to be linked to the RphQ locus; however, only 4 of them were within 10 cM of the target. The RphQ locus was mapped to the centromeric region of chromosome 7, with a linkage distance of 3.5 cM from the RFLP marker CDO749. Rrn2, an RFLP clone from the ribosomal RNA intergenic spacer region, was found to be very closely linked with RphQ, based on bulked segregant analysis. An STS marker, ITS1, derived from Rrn2, was also closely linked (1.6 cM) to RphQ.

Development of wild barley (Hordeum chilense)-derived DArT markers and their use into genetic and physical mapping

Diversity arrays technology (DArT) genomic libraries were developed from H. chilense accessions to support robust genotyping of this species and a novel crop comprising H. chilense genome (e.g., tritordeums). Over 11,000 DArT clones were obtained using two complexity reduction methods. A subset of 2,209 DArT markers was identified on the arrays containing these clones as polymorphic between parents and segregating in a population of 92 recombinant inbred lines (RIL) developed from the cross between H. chilense accessions H1 and H7. Using the segregation data a high-density map of 1,503 cM was constructed with average inter-bin density of 2.33 cM. A subset of DArT markers was also mapped physically using a set of wheat-H. chilense chromosome addition lines. It allowed the unambiguous assignment of linkage groups to chromosomes. Four segregation distortion regions (SDRs) were found on the chromosomes 2H(ch), 3H(ch) and 5H(ch) in agreement with previous findings in barley. The new map improves the genome coverage of previous H. chilense maps. H. chilense-derived DArT markers will enable further genetic studies in ongoing projects on hybrid wheat, seed carotenoid content improvement or tritordeum breeding program. Besides, the genetic map reported here will be very useful as the basis to develop comparative genomics studies with barley and model species.

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.

New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L

Nutritional benefits of cultivated oat (Avena sativa L., 2n = 6x = 42, AACCDD) are well recognized; however, seed protein levels are modest and resources for genetic improvement are scarce. The wild tetraploid, A. magna Murphy et Terrell (syn A. maroccana Gdgr., 2n = 4x = 28, CCDD), which contains approximately 31% seed protein, was hybridized with cultivated oat to produce a domesticated A. magna. Wild and cultivated accessions were crossed to generate a recombinant inbred line (RIL) population. Although these materials could be used to develop domesticated, high-protein oat, mapping and quantitative trait loci introgression is hindered by a near absence of genetic markers. Objectives of this study were to develop high-throughput, A. magna-specific markers; generate a genetic linkage map based on the A. magna RIL population; and map genes controlling oat domestication. A Diversity Arrays Technology (DArT) array derived from 10 A. magna genotypes was used to generate 2,688 genome-specific probes. These, with 12,672 additional oat clones, produced 2,349 polymorphic markers, including 498 (21.2%) from A. magna arrays and 1,851 (78.8%) from other Avena libraries. Linkage analysis included 974 DArT markers, 26 microsatellites, 13 SNPs, and 4 phenotypic markers, and resulted in a 14-linkage-group map. Marker-to-marker correlation coefficient analysis allowed classification of shared markers as unique or redundant, and putative linkage-group-to-genome anchoring. Results of this study provide for the first time a collection of high-throughput tetraploid oat markers and a comprehensive map of the genome, providing insights to the genome ancestry of oat and affording a resource for study of oat domestication, gene transfer, and comparative genomics.

Development of a molecular linkage map of pearl millet integrating DArT and SSR markers

Pearl millet is an important component of food security in the semi-arid tropics and is assuming greater importance in the context of changing climate and increasing demand for highly nutritious food and feed. Molecular tools have been developed and applied for pearl millet on a limited scale. However, the existing tool kit needs to be strengthened further for its routine use in applied breeding programs. Here, we report enrichment of the pearl millet molecular linkage map by exploiting low-cost and high-throughput Diversity Arrays Technology (DArT) markers. Genomic representation from 95 diverse genotypes was used to develop a DArT array with circa 7,000 clones following PstI/BanII complexity reduction. This array was used to genotype a set of 24 diverse pearl millet inbreds and 574 polymorphic DArT markers were identified. The genetic relationships among the inbred lines as revealed by DArT genotyping were in complete agreement with the available pedigree data. Further, a mapping population of 140 F(7) Recombinant Inbred Lines (RILs) from cross H 77/833-2 × PRLT 2/89-33 was genotyped and an improved linkage map was constructed by integrating DArT and SSR marker data. This map contains 321 loci (258 DArTs and 63 SSRs) and spans 1148 cM with an average adjacent-marker interval length of 3.7 cM. The length of individual linkage groups (LGs) ranged from 78 cM (LG 3) to 370 cM (LG 2). This better-saturated map provides improved genome coverage and will be useful for genetic analyses of important quantitative traits. This DArT platform will also permit cost-effective background selection in marker-assisted backcrossing programs as well as facilitate comparative genomics and genome organization studies once DNA sequences of polymorphic DArT clones are available.

Genetic map of triticale compiling DArT, SSR, and AFLP markers

A set of 90 doubled haploid (DH) lines derived from F(1) plants that originated from a cross between × Triticosecale Wittm. 'Saka3006' and ×Triticosecale Wittm. 'Modus', via wide crossing with maize, were used to create a genetic linkage map of triticale. The map has 21 linkage groups assigned to the A, B, and R genomes including 155 simple sequence repeat (SSR), 1385 diversity array technology (DArT), and 28 amplified fragment length polymorphism (AFLP) markers covering 2397 cM with a mean distance between two markers of 4.1 cM. Comparative analysis with wheat consensus maps revealed that triticale chromosomes of the A and B genomes were represented by 15 chromosomes, including combinations of 2AS.2AL#, 2AL#2BL, 6AS.6AL#, and 2BS.6AL# instead of 2A, 2B, and 6A. In respect to published maps of rye, substantial rearrangements were found also for chromosomes 1R, 2R, and 3R of the rye genome. Chromosomes 1R and 2R were truncated and the latter was linked with 3R. A nonhomogeneous distribution of markers across the triticale genome was observed with evident bias (48%) towards the rye genome. This genetic map may serve as a reference linkage map of triticale for efficient studies of structural rearrangements, gene mapping, and marker-assisted selection.

High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT)

Implementation of molecular methods in hop (Humulus lupulus L.) breeding is dependent on the availability of sizeable numbers of polymorphic markers and a comprehensive understanding of genetic variation. However, use of molecular marker technology is limited due to expense, time inefficiency, laborious methodology and dependence on DNA sequence information. Diversity arrays technology (DArT) is a high-throughput cost-effective method for the discovery of large numbers of quality polymorphic markers without reliance on DNA sequence information. This study is the first to utilise DArT for hop genotyping, identifying 730 polymorphic markers from 92 hop accessions. The marker quality was high and similar to the quality of DArT markers previously generated for other species; although percentage polymorphism and polymorphism information content (PIC) were lower than in previous studies deploying other marker systems in hop. Genetic relationships in hop illustrated by DArT in this study coincide with knowledge generated using alternate methods. Several statistical analyses separated the hop accessions into genetically differentiated North American and European groupings, with hybrids between the two groups clearly distinguishable. Levels of genetic diversity were similar in the North American and European groups, but higher in the hybrid group. The markers produced from this time and cost-efficient genotyping tool will be a valuable resource for numerous applications in hop breeding and genetics studies, such as mapping, marker-assisted selection, genetic identity testing, guidance in the maintenance of genetic diversity and the directed breeding of superior cultivars.

Development and assessment of DArT markers in triticale

Triticale (X Triticosecale Wittm.) is a hybrid derived by crossing wheat (Triticum sp.) and rye (Secale sp.). Till date, only a limited number of simple sequence repeat (SSRs) markers have been used in triticale molecular analyses and there is a need to identify dedicated high-throughput molecular markers to better exploit this crop. The objective of this study was to develop and evaluate diversity arrays technology (DArT) markers in triticale. DArT marker technology offers a high level of multiplexing. Development of new markers from triticale accessions was combined with mining the large collection of previously developed markers in rye and wheat. Three genotyping arrays were used to analyze a collection of 144 triticale accessions. The polymorphism level ranged from 8.6 to 23.8% for wheat and rye DArT markers, respectively. Among the polymorphic markers, rye markers were the most abundant (3,109) followed by wheat (2,214) and triticale (719). The mean polymorphism information content values were 0.34 for rye DArT markers and 0.37 for those from triticale and wheat. High correlation was observed between similarity matrices derived from rye, triticale, wheat and combined marker sets, as well as for the cophenetic values matrices. Cluster analysis revealed genetic relationships among the accessions consistent with the agronomic and pedigree information available. The newly developed triticale DArT markers as well as those originated from rye and wheat provide high quality markers that can be used for diversity analyses and might be exploited in a range of molecular breeding and genomics applications in triticale.

Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)

Pigeonpea (Cajanus cajan), an important food legume crop in the semi-arid regions of the world and the second most important pulse crop in India, has an average crop productivity of 780 kg/ha. The relatively low crop yields may be attributed to non-availability of improved cultivars, poor crop husbandry and exposure to a number of biotic and abiotic stresses in pigeonpea growing regions. Narrow genetic diversity in cultivated germplasm has further hampered the effective utilization of conventional breeding as well as development and utilization of genomic tools, resulting in pigeonpea being often referred to as an 'orphan crop legume'. To enable genomics-assisted breeding in this crop, the pigeonpea genomics initiative (PGI) was initiated in late 2006 with funding from Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative, which was further expanded with financial support from the US National Science Foundation's Plant Genome Research Program and the Generation Challenge Program. As a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries. For instance, 25 mapping populations segregating for a number of biotic and abiotic stresses have been developed or are under development. An 11X-genome coverage bacterial artificial chromosome (BAC) library comprising of 69,120 clones have been developed of which 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated. A variety of molecular markers have been developed from BESs, microsatellite or simple sequence repeat (SSR)-enriched libraries and mining of ESTs and genomic amplicon sequencing. Of about 21,000 SSRs identified, 6,698 SSRs are under analysis along with 670 orthologous genes using a GoldenGate SNP (single nucleotide polymorphism) genotyping platform, with large scale SNP discovery using Solexa, a next generation sequencing technology, is in progress. Similarly a diversity array technology array comprising of ca. 15,000 features has been developed. In addition, >600 unique nucleotide binding site (NBS) domain containing members of the NBS-leucine rich repeat disease resistance homologs were cloned in pigeonpea; 960 BACs containing these sequences were identified by filter hybridization, BES physical maps developed using high information content fingerprinting. To enrich the genomic resources further, sequenced soybean genome is being analyzed to establish the anchor points between pigeonpea and soybean genomes. In addition, Solexa sequencing is being used to explore the feasibility of generating whole genome sequence. In summary, the collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecular tools in pigeonpea and should significantly benefit pigeonpea genetics and breeding. As these efforts come to fruition, and expanded (depending on funding), pigeonpea would move from an 'orphan legume crop' to one where genomics-assisted breeding approaches for a sustainable crop improvement are routine.

Fourteen years of surveillance of HIV-1 prevalence among pregnant women attending antenatal care clinics in western Uganda

This study monitored long-term temporal trends in HIV-1 prevalence in antenatal clinic attendees living in western Uganda. Semi-annual data collection was done from 1991 to 2004. For each woman the following data were recorded: HIV-1 status, age, educational status, marital status, occupation and parity. The results show that the overall HIV-1 prevalence was 15.3% during the entire time period (urban 21.3%, semi-urban 12.7% and rural 7.1%). Between 1991 and 2004, we observed a gradual decline in the HIV-1 prevalence. The decline was most pronounced in urban women aged 15-19 years old and least pronounced in rural women aged 20-24 years. Women above 25 years of age did not show any decline in HIV-1 prevalence over time. The declining HIV-1 prevalence in the younger age groups (15-24 years) likely represents a declining risk for acquiring HIV infection as we have previously shown in the urban sub-sample of this data set.

The genetic diversity of UK, US and Australian cultivars of Triticum aestivum measured by DArT markers and considered by genome

The genetic diversity of UK, US and Australian wheat varieties over the period of modern plant breeding is estimated using diversity array technology markers. Diversity is assessed by both genetic distance between varieties, by AMOVA and as the volumes of multi-dimensional convex hulls estimated from principal co-ordinate analysis. At the whole genome level the three populations are genetically distinct; this is also true of the B genome. However, the US and Australian D genomes are found to occupy the same region of diversity space and the A genomes for these countries are partially overlapping. The use of high-density genotyping with a common marker set allows an unprecedented direct comparison between the diversities of the national populations, between individual genomes and the fluctuation of diversity over time. The highest genetic diversity amongst varieties is reported in the Australian population followed by the US, which in turn is more diverse than the UK. However the average diversity of loci is higher in the US set than in the Australian. Non-random fluctuations in genetic diversity over time are observed.

Selective p38MAPK isoform expression and activation in antineutrophil cytoplasmatic antibody-associated crescentic glomerulonephritis: role of p38MAPKalpha

OBJECTIVE

Crescentic glomerulonephritis (crGN) is a frequent and life-threatening manifestation of antineutrophil cytoplasmatic antibody-associated vasculitis. Up-regulation of proinflammatory cytokines contributes to renal damage by activation of p38 mitogen-activated protein kinases (MAPKs). However, it is unclear which of the four p38MAPK isoforms are expressed, activated and hence of major importance in crGN.

METHODS

Kidney biopsies of patients with antineutrophil cytoplasmatic antibody-positive crGN and control samples were investigated for the expression and phosphorylation of p38MAPK isoforms and downstream target kinase MAPKAP2 by immunohistochemistry. Expression and functional activation of p38MAPK isoforms by TNF was also assessed in a human podocyte cell line by reverse transcription-polymerase chain reaction, immunoblotting and kinase array.

RESULTS

Strong expression of p38MAPKalpha, beta and gamma isoforms was found in glomerular podocytes and crescents. Infiltrating leucocytes showed predominant p38MAPKalpha expression. Activation of p38MAPK and its downstream mediator MAPKAP2 was found in crGN confined to glomerular podocytes, crescents and inflammatory infiltrates. Interestingly, corticosteroid treatment before kidney biopsy diminished p38MAPK activation in crGN. Activated p38MAPK co-localised with alpha, beta and gamma isoforms in podocytes and crescents, while leucocytes showed mainly p38MAPKalpha activation. In a human podocyte cell line mRNA and protein of all four p38MAPK isoforms was expressed but only p38MAPKalpha was activated upon challenge with TNF.

CONCLUSIONS

This study shows selective p38MAPK isoform expression and activation in crGN. Podocytes and podocyte-induce crescent formation is the main source of p38MAPK activation in crGN. TNF is a potent and selective activator of the alpha-isoform in podocytes, which therefore appears as a main contributor to proinflammatory signalling in the glomerulum of crGN.

Analysis of patient load data from the 2003 Cricket World Cup in South Africa

Objectives. The purpose of this study was to evaluate the patient presentation data for spectators attending the opening ceremony and all the 2003 Cricket World Cup matches played in South Africa in order to provide organisers with the basis of a sound medical care plan for mass gatherings of a similar nature. Methods. During the 2003 Cricket World Cup, data were collected on the spectators presenting to the medical facilities during the opening ceremony and the 42 matches played in South Africa. Data included the total number of patient presentations and the category of illness or injury. This information was used to determine the venue accommodation rate and the patient presentation rate. The illness/injury data were classified into the following categories: (i) heat-related illness; (ii) blisters/scrapes/ bruises; (iii) headache; (iv) fractures/sprains/lacerations; (v) eye injuries; (vi) abdominal pain; (vii) insect bite; (viii) allergy-related illness; (ix) cardiac disorders, chest pains; (x) pulmonary disorder/shortness of breath; (xi) syncope; (xii) weakness/dizziness; (xiii) alcohol/drug-related conditions; (xiv) seizure; (xv) cardiac arrest; (xvi) obstetric/ gynaecological disorder; and (xvii) other. Results. The total number of patients who presented to the medical stations was 2 118, with a mean of 50 (range 14 - 91) injuries per match. The mean for the patient presentation rate was 4/1 000 spectators. The most frequently encountered illness or injury was headache (954 patients, 45%), followed by fractures, sprains and lacerations (351 patients, 16%). South African Journal of Sports Medicine Vol. 18 (2) 2006: pp. 52-56

Diagnostic microbial microarrays in soil ecology

Soil microbial communities are responsible for important physiological and metabolic processes. In the last decade soil microorganisms have been frequently analysed by cultivation-independent techniques because only a minority of the natural microbial communities are accessible by cultivation. Cultivation-independent community analyses have revolutionized our understanding of soil microbial diversity and population dynamics. Nevertheless, many methods are still laborious and time-consuming, and high-throughput methods have to be applied in order to understand population shifts at a finer level and to be better able to link microbial diversity with ecosystems functioning. Microbial diagnostic microarrays (MDMs) represent a powerful tool for the parallel, high-throughput identification of many microorganisms. Three categories of MDMs have been defined based on the nature of the probe and target molecules used: phylogenetic oligonucleotide microarrays with short oligonucleotides against a phylogenetic marker gene; functional gene arrays containing probes targeting genes encoding specific functions; and community genome arrays employing whole genomes as probes. In this review, important methodological developments relevant to the application of the different types of diagnostic microarrays in soil ecology will be addressed and new approaches, needs and future directions will be identified, which might lead to a better insight into the functional activities of soil microbial communities.

The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases

Stem rust caused by Puccinia graminis f. sp. tritici was among the most devastating diseases of barley in the northern Great Plains of the U.S. and Canada before the deployment of the stem rust-resistance gene Rpg1 in 1942. Since then, Rpg1 has provided durable protection against stem rust losses in widely grown barley cultivars (cvs.). Extensive efforts to clone Rpg1 by synteny with rice provided excellent flanking markers but failed to yield the gene because it does not seem to exist in rice. Here we report the map-based cloning and characterization of Rpg1. A high-resolution genetic map constructed with 8,518 gametes and a 330-kb bacterial artificial chromosome contig physical map positioned the gene between two crossovers approximately 0.21 centimorgan and 110 kb apart. The region including Rpg1 was searched for potential candidate genes by sequencing low-copy probes. Two receptor kinase-like genes were identified. The candidate gene alleles were sequenced from resistant and susceptible cvs. Only one of the candidate genes showed a pattern of apparently functional gene structure in the resistant cvs. and defective gene structure in the susceptible cvs. identifying it as the Rpg1 gene. Rpg1 encodes a receptor kinase-like protein with two tandem protein kinase domains, a novel structure for a plant disease-resistance gene. Thus, it may represent a new class of plant resistance genes.

[Concepts in discussion groups in psychiatric outpatient care - an individual "Patchwork Design"? Results of a qualitative investigation]

OBJECTIVE

Research on concepts of discussion groups in the outpatient psychiatrist care is accounted for on the background of its practical relevance and the simultaneous lack of specialist literature.

METHODS

Using qualitative proceedings, the subjective concepts of the discussion leaders concerning origin and feasibility are investigated, compared and put in relation to the specialist literature.

RESULTS

Varied concepts and executed actions that were newly worked out at every one time, partly moulded rather on an individual than on subject-specific criteria and that are thus only restrictedly convertible become obvious.

CONCLUSIONS

In order to secure the quality of this work further research concerning the development of scientifically founded concepts and educational offers as well as the transfer of relevant scientific cognition from the clinical sector are suggested.

Genetic diversity of Plasmodium falciparum and its relationship to parasite density in an area with different malaria endemicities in West Uganda

Field populations of Plasmodium falciparum can be effectively genotyped by PCR-amplification of selected fragments of the Merozoite Surface Proteins 1 and 2 (MSP1 and MSP2). Genetic diversity of P. falciparum populations in areas with different transmission levels (holo- vs. mesoendemic) was investigated in Kabarole District, West Uganda. 225 samples positive for P. falciparum were analysed by amplification of polymorphic regions and classified according to prevalence of allelic families. A large number of alleles was detected for each locus: 22 for MSP1 block 2 and 24 for MSP2 and, 175 (78%) of MSP1 alleles and 143 (64%) of MSP2 showed multiple infections within a range of 2-8 clones. Significant differences between holoendemic and mesoendemic areas in regards of population structure and number of multiclonal infections of P. falciparum were not apparent. However, a significant correlation between parasite density, selected MSP2 loci and differences between parasite density in monoclonal vs. multiclonal infections occurred. Multiplicity of infection was age-dependent.

Diversity arrays: a solid state technology for sequence information independent genotyping

Here we present the successful application of the microarray technology platform to the analysis of DNA polymorphisms. Using the rice genome as a model, we demonstrate the potential of a high-throughput genome analysis method called Diversity Array Technology, DArT'. In the format presented here the technology is assaying for the presence (or amount) of a specific DNA fragment in a representation derived from the total genomic DNA of an organism or a population of organisms. Two different approaches are presented: the first involves contrasting two representations on a single array while the second involves contrasting a representation with a reference DNA fragment common to all elements of the array. The Diversity Panels created using this method allow genetic fingerprinting of any organism or group of organisms belonging to the gene pool from which the panel was developed. Diversity Arrays enable rapid and economical application of a highly parallel, solid-state genotyping technology to any genome or complex genomic mixtures.

The MetaFam Server: a comprehensive protein family resource

MetaFam is a comprehensive relational database of protein family information. This web-accessible resource integrates data from several primary sequence and secondary protein family databases. By pooling together the information from these disparate sources, MetaFam is able to provide the most complete protein family sets available. Users are able to explore the interrelationships among these primary and secondary databases using a powerful graphical visualization tool, MetaFamView. Additionally, users can identify corresponding sequence entries among the sequence databases, obtain a quick summary of corresponding families (and their sequence members) among the family databases, and even attempt to classify their own unassigned sequences. Hypertext links to the appropriate source databases are provided at every level of navigation. Global family database statistics and information are also provided. Public access to the data is available at http://metafam.ahc.umn.edu/.

Lateralization of visuospatial processing in the bottlenose dolphin (Tursiops truncatus)

Two adult female bottlenose dolphins were tested for cerebral asymmetries in the visuospatial domain. The animals learned under binocular conditions a three-choice spatial discrimination task with three hoops positioned along a line in the middle of the tank. During a correct trial the dolphins had to swim from a starting position at the tanks wall through one of the hoops, come back to the starting position, choose another hoop, swim back to start and finally swim through the third hoop. For such a trial to be correct, the animals had to swim through all three hoops in any sequence without omitting or re-using one of them. After reaching criterion binocularly, monocular trials (one eye covered with an adherent suction cup) were introduced where the dolphins carried out the same task alternatingly under left or right eye seeing conditions. For both animals, the right eye performance was clearly superior to that of the left eye. Binocular and right eye performances were similar. As a result of the complete decussation at the optic nerve, this right eye superiority suggests a left-hemispheric dominance for the processing of visuospatial information. This is a remarkable deviation from the usual right hemisphere advantage for these kind of tasks found in different species of mammals and birds.

Recombinant human interleukin 10 in the treatment of patients with mild to moderately active Crohn's disease. The Interleukin 10 Inflammatory Bowel Disease Cooperative Study Group

BACKGROUND & AIMS

Interleukin 10 (IL-10) is an anti-inflammatory, immunomodulatory cytokine that regulates mucosal inflammation. This study evaluated the safety, tolerance, and efficacy of recombinant human IL-10 (rhuIL-10) for mild to moderately active Crohn's disease.

METHODS

We conducted a 24-week multicenter, prospective, randomized, double-blind, placebo-controlled, and sequential-escalating-dose study. Ninety-five patients with Crohn's Disease Activity Index of 200-350, not presently undergoing corticosteroid, mesalamine, or immunosuppressive therapy, were treated with subcutaneous rhuIL-10 (1, 5, 10, or 20 microg/kg) or placebo once daily for 28 consecutive days. Patients were followed up for 20 weeks after treatment. Evaluation of safety and tolerance was the first objective, and efficacy was the second objective.

RESULTS

Adverse effects were dose-related, mild-to-moderate in severity, and reversible. Asymptomatic and reversible anemia and thrombocytopenia were observed at higher doses. No withdrawal or delayed adverse effects were evident during 20 weeks of follow-up. At the end of treatment (day 29), intent-to-treat analysis showed that 23.5% (confidence interval [CI], 6.8%-49.9%) of patients receiving 5 micro/kg rhuIL-10 experienced clinical remission and endoscopic improvement; 0% (CI, 0%-14.8%) of patients in the placebo group did. Higher doses of recombinant human IL-10 were less effective than 5 microg/kg. No rhuIL-10 serum accumulation and no antibody against IL-10 were detected after 4 weeks.

CONCLUSIONS

Subcutaneous rhuIL-10 administered daily for 28 days to patients with mild to moderately active Crohn's disease is safe, well-tolerated, and shows clinical and endoscopic improvement.

PANAL: an integrated resource for Protein sequence ANALysis

SUMMARY

We present PANAL, an integrated resource for protein sequence analysis. The tool allows the user to simultaneously search a protein sequence for motifs from several databases, and to view the result as an intuitive graphical summary.

Physical mapping of the barley stem rust resistance gene rpg4

The barley stem rust resistance gene rpg4 was physically and genetically localized on two overlapping BAC clones covering an estimated 300-kb region of the long arm of barley chromosome 7(5H). Initially, our target was mapped within a 6.0-cM region between the previously described flanking markers MWG740 and ABG391. This region was then saturated by integrating new markers from several existing barley and rice maps and by using BAC libraries of barley cv. Morex and rice cv. Nipponbare. Physical/genetic distances in the vicinity of rpg4 were found to be 1.0 Mb/cM, which is lower than the average for barley (4 Mb/cM) and lower than that determined by translocation breakpoint mapping (1.8 Mb/cM). Synteny at high resolution levels has been established between the region of barley chromosome 7(5H) containing the rpg4 locus and the subtelomeric region of rice chromosome 3 between markers S16474 and E10757. This 1.7-cM segment of the rice genome was covered by two overlapping BAC clones, about 250 kb of total length. In barley the markers S16474 and E10757 genetically delimit rpg4, lying 0.6 cM distal and 0.4 cM proximal to the locus, respectively.

The hTERTalpha splice variant is a dominant negative inhibitor of telomerase activity

The telomerase catalytic subunit (hTERT) is an essential component of the holoenzyme complex that adds telomeric repeats to the ends of human chromosomes. Maintenance of telomeres by telomerase or another mechanism is required for cell immortalization, and loss of telomeric DNA has been proposed as a trigger for cellular senescence. Available evidence suggests that regulation of telomerase activity primarily depends on transcriptional control of hTERT. However, several human tissues as well as some normal cell strains have been shown to express low levels of hTERT mRNA even though they lack telomerase activity. We have previously identified six splice variants of hTERT, including a "deletion" variant (hTERTalpha) that is missing conserved residues from the catalytic core of the protein. Several of the deletion variants have been detected in normal and developing human tissues. We now show that hTERTalpha inhibits endogenous telomerase activity, which results in telomere shortening and chromosome end-to-end fusions. Telomerase inhibition induced a senescence-like state in HT1080 cells and apoptosis in a jejunal fibroblast cell line. These results suggest a possible role for hTERT splice variants in the regulation of telomerase activity.

Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region

In the course of map-based cloning of the barley stem rust resistance gene Rpg1, we identified a rice bacterial artificial chromosome (BAC) containing the Rpg1 flanking markers. Based on the excellent gene order colinearity between barley and rice in this region, we expected that this rice BAC would contain the barley Rpg1 homologue. In order to identify the putative rice homologue, we sequenced ca. 35 kb of the rice BAC at random and then an additional 33 kb of contiguous sequence between the two most closely spaced Rpg1 flanking markers. Sequence analysis revealed a total of 15 putative genes, 5 within the 33-kb contiguous region. A rice Rpg1 homologue was not identified, although a gene encoding a hypothetical polypeptide with similarity to a membrane protein could not be eliminated as a candidate. Surprisingly, four of the genes identified in the 33-kb contiguous rice sequence showed a high degree of similarity with genes on Arabidopsis chromosome 4. The genome regions harboring these genes showed some relatedness, but many rearrangements were also evident. These data suggest that some genes have remained linked even over the long evolutionary separation of Arabidopsis and rice, as has also been reported for mammals and invertebrates.

Synteny with rice: analysis of barley malting quality QTLs and rpg4 chromosome regions

The barley (Hordeum vulgare L.) chromosome 1 centromere region contains two adjacent overlapping quantitative trait loci (QTLs) for malting quality traits, and the chromosome 7L subtelomere region contains the stem rust (causal agent Puccinia graminis f.sp. tritici) resistance gene rpg4. To facilitate the saturation mapping of these two target regions, a synteny-based approach was employed. Syntenic relationships between the barley target regions and the rice (Oryza sativa) genome were established through comparative mapping. The barley chromosome 1 centromere region was found to be syntenic with rice chromosome 8 and parts of rice chromosomes 3 and 10. A 6- to 15-fold difference in genetic distance between barley and rice in the syntenic region was observed, owing to the apparent suppressed recombination in the barley chromosome 1 centromere region. Barley chromosome 7L was found to be syntenic with rice chromosome 3. The establishment of synteny with rice in the two target regions allows well-established and characterized rice resources to be utilized in fine mapping and map-based cloning studies.Key words: genome synteny, quantitative trait loci, QTL, disease resistance gene, Triticeae.

Isolation of a candidate human telomerase catalytic subunit gene, which reveals complex splicing patterns in different cell types

Telomerase is a multicomponent reverse transcriptase enzyme that adds DNA repeats to the ends of chromosomes using its RNA component as a template for synthesis. Telomerase activity is detected in the germline as well as the majority of tumors and immortal cell lines, and at low levels in several types of normal cells. We have cloned a human gene homologous to a protein from Saccharomyces cerevisiae and Euplotes aediculatus that has reverse transcriptase motifs and is thought to be the catalytic subunit of telomerase in those species. This gene is present in the human genome as a single copy sequence with a dominant transcript of approximately 4 kb in a human colon cancer cell line, LIM1215. The cDNA sequence was determined using clones from a LIM1215 cDNA library and by RT-PCR, cRACE and 3'RACE on mRNA from the same source. We show that the gene is expressed in several normal tissues, telomerase-positive post-crisis (immortal) cell lines and various tumors but is not expressed in the majority of normal tissues analyzed, pre-crisis (non-immortal) cells and telomerase-negative immortal (ALT) cell lines. Multiple products were identified by RT-PCR using primers within the reverse transcriptase domain. Sequencing of these products suggests that they arise by alternative splicing. Strikingly, various tumors, cell lines and even normal tissues (colonic crypt and testis) showed considerable differences in the splicing patterns. Alternative splicing of the telomerase catalytic subunit transcript may be important for the regulation of telomerase activity and may give rise to proteins with different biochemical functions.

Towards map-based cloning of the barley stem rust resistance genes Rpg1 and rpg4 using rice as an intergenomic cloning vehicle

The barley stem rust resistance genes Rpg1 and rpg4 were mapped in barley on chromosomes 1P and 7M, respectively and the syntenous rice chromosomes identified as 6P and 3P by mapping common probes in barley and rice. Rice yeast artificial chromosome (YAC), bacterial artificial chromosome (BAC) and cosmid clones were used to isolate probes mapping to the barley Rpg1 region. The rice BAC isolated with the pM13 probe was a particularly excellent source of probes. A high-resolution map of the Rpg1 region was established with 1400 gametes yielding a map density of 3.6 markers per 0.1 cM. A detailed physical map was established for the rice BAC fragment containing the Rpg1-flanking markers pM13 and B24. This fragment covers a barley genetic distance of 0.6 cM and a rice DNA physical distance of ca. 70 kb. The distribution of barley cross-overs in relation to the rice DNA physical distances was extremely uneven. The barley genetic distance between the pM13 marker and Rpg1 was 0.1 cM per ca. 55 kb, while on the proximal side it was 0.5 cm per ca. 15 kb. Three probes from the distal end of the pM13 BAC mapped 3.0 cm proximal of Rpg1 and out of synteny with rice. These experiments confirm the validity of using large insert rice clones as probe sources to saturate small barley (and other large genome cereals) genome regions with markers. They also establish a note of caution that even in regions of high microsynteny, there may be small DNA fragments that have transposed and are no longer in syntenous positions.

Photoinduced refractive-index change in Sm(+2)/Sm(+3) codoped aluminosilicate fiber by irradiation of an Ar-ion laser

A Sm(+2)/Sm(+3) codoped aluminosilicate glass optical fiber was fabricated by use of modified chemical-vapor deposition in conjunction with an aerosol-delivery technique. A permanent index change of 7.6 x 10(-5) was induced in the fiber by irradiation of 1 W of multiline output from an Ar-ion laser. Bleaching of a broad absorption band of Sm(+2) in the visible range was also observed, and it is believed that photoionization of Sm(+2)? Sm(+3)+e plays an important role in the induced photorefractivity.

High dose naloxone does not improve cerebral or myocardial blood flow during cardiopulmonary resuscitation in pigs

In a prospective, randomized, placebo-controlled, double-blind trial we tested the hypothesis that naloxone given during cardiopulmonary resuscitation (CPR) enhances cerebral and myocardial blood flow. Twenty-one anesthetized, normoventilated pigs were instrumented for measurements of right atrial and aortic pressures, and regional organ blood flow (radiolabeled microspheres). After 5 min of untreated fibrillatory arrest, CPR was commenced using a pneumatic chest compressor/ventilator. With onset of CPR, an i.v. bolus of 40 micrograms/kg b.w. of epinephrine was given, followed by an infusion of 0.4 micrograms/kg per min. After 5 min of CPR, either naloxone, 10 mg/kg b.w. (group N, n = 11) or normal saline (group S, n = 10) was given i.v. Prior to, and after 1, 15, and 30 min of CPR, hemodynamic and blood flow measurements were obtained. After 30 min of CPR, mean arterial pressure was significantly higher in group N (26 +/- 5 vs. 13 +/- 3 mmHg, P < 0.05). Groups did not differ with respect to myocardial perfusion pressure or arterial blood gases at any time during the observation period. Regional brain and heart blood flows were not different between N and S at any point of measurement. We conclude that high-dose naloxone does not augment cerebral or myocardial blood flow during prolonged closed-chest CPR.