Do slow slip events trigger large and great megathrust earthquakes?

Slow slip events have been suggested to trigger subduction earthquakes. However, examples to date have been poorly recorded, occurring offshore, where data are sparse. Better understanding of slow slip events and their influence on subsequent earthquakes is critical for hazard forecasts. We analyze a well-recorded event beginning 6 months before the 2012 M w (moment magnitude) 7.6 earthquake in Costa Rica. The event migrates to the eventual megathrust rupture. Peak slip rate reached a maximum of 5 mm/day, 43 days before the earthquake, remaining high until the earthquake. However, changes in Mohr-Coulomb failure stress at the hypocenter were small (0.1 bar). Our data contradict models of earthquake nucleation that involve power law acceleration of slip and foreshocks. Slow slip events may prove useful for short-term earthquake forecasts.

Pollen limitation and inbreeding depression in an 'old rare' bumblebee-pollinated grassland herb.

Habitat fragmentation and reduction of population size have been found to negatively affect plant reproduction in 'new rare' species that were formerly common. This has been attributed primarily to effects of increased inbreeding but also to pollen limitation. In contrast, little is known about the reproduction of 'old rare' species that are naturally restricted to small and isolated habitats and thus may have developed strategies to cope with long-term isolation and small population size. Here we study the effects of pollen source and quantity on reproduction of the 'old rare' bumblebee-pollinated herb, Astragalus exscapus. In two populations of this species, we tested for pollen autodeposition, inbreeding depression and outbreeding depression. Caged plants were left unpollinated or were pollinated with pollen from the same plant, from the same population or from a distant population (50 km). Additionally, we tested for pollen limitation by pollen supplementation in four populations of different size and density. In the absence of pollinators, plants did not produce seed whereas self-pollinated plants did. This indicates a self-compatible breeding system dependent on insect pollination. Both self-pollination and, in one of the two populations, cross-pollination with pollen from plants from the distant population resulted in a lower number of seeds per flower than cross-pollination with pollen from plants from the resident population, indicating inbreeding and outbreeding depression. Pollen addition enhanced fruit set and number of seeds per flower in three of the four populations, indicating pollen limitation. The degree of pollen limitation was lowest in the smallest but densest population. Our results suggest that, similar to 'new rare' plant species, also 'old rare' species may be at risk of inbreeding depression and pollen limitation.

DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy.

Solving the structure of macromolecular complexes using transmission electron microscopy can be an arduous task. Many of the steps in this process rely strongly on the aid of pre-existing structural knowledge, and are greatly complicated when this information is unavailable. Here, we present two software tools meant to facilitate particle picking, an early stage in the single-particle processing of unknown macromolecules. The first tool, DoG Picker, is an efficient and reasonably general, particle picker based on the Difference of Gaussians (DoG) image transform. It can function alone, as a reference-free particle picker with the unique ability to sort particles based on size, or it can also be used as a way to bootstrap the creation of templates or training datasets for other particle pickers. The second tool is TiltPicker, an interactive graphical interface application designed to streamline the selection of particle pairs from tilted-pair datasets. In many respects, TiltPicker is a re-implementation of the SPIDER WEB tilted-particle picker, but built on modern computer frameworks making it easier to deploy and maintain. The TiltPicker program also includes several useful new features beyond those of its predecessor.

ExPlain: finding upstream drug targets in disease gene regulatory networks.

Different signal transduction pathways leading to the activation of transcription factors (TFs) converge at key molecules that master the regulation of many cellular processes. Such crossroads of signalling networks often appear as "Achilles Heels" causing a disease when not functioning properly. Novel computational tools are needed for analysis of the gene expression data in the context of signal transduction and gene regulatory pathways and for identification of the key nodes in the networks. An integrated computational system, ExPlain (www.biobase.de) was developed for causal interpretation of gene expression data and identification of key signalling molecules. The system utilizes data from two databases (TRANSFAC and TRANSPATH) and integrates two programs: (1) Composite Module Analyst (CMA) analyses 5'-upstream regions of co-expressed genes and applies a genetic algorithm to reveal composite modules (CMs) consisting of co-occurring single TF binding sites and composite elements; (2) ArrayAnalyzer is a fast network search engine that analyses signal transduction networks controlling the activities of the corresponding TFs and seeks key molecules responsible for the observed concerted gene activation. ExPlain system was applied to microarray data on inflammatory bowel diseases (IBD). The results obtained suggest a number of highly interesting biological hypotheses about molecular mechanisms of pathological genetic disregulation.

Allogeneic SCT for relapsed composite and transformed lymphoma using related and unrelated donors: long-term results.

Outcome is poor with conventional therapy for relapsed transformed non-Hodgkin's lymphoma (NHL). Autologous SCT has been successfully employed; however the impact of allogeneic SCT has not been well defined. We therefore studied 40 consecutive patients who received allogeneic SCT for relapsed composite and transformed NHL (25 transformed, 8 composite (same site) and 7 discordant (different sites)) with related (n=25) and unrelated donors (n=15) to evaluate long-term outcome. Conditioning was myeloablative in the majority (39 of 40). Of 40 patients, 11 survive with median follow-up of 25 months. Death occurred in similar proportions due to relapsed NHL (n=14) or treatment-related complications (transplant-related mortality, TRM; n=15). The cumulative incidence of TRM was 36% at 3 years and disease relapse was 42% at 5 years. Probability of 2- and 5-year event-free survival is 36 and 23% with overall survival 39 and 23%. Performance of SCT within 1 year of NHL diagnosis predicted improved outcome. Relapse and TRM remain significant problems in this setting, indicating the need for strategies whereby patients at high risk of transformation should be selected for early SCT, ideally before their actual transformation.

Primary therapy for adults with T-cell lymphoblastic lymphoma with hematopoietic stem-cell transplantation results in favorable outcomes.

BACKGROUND: Controversy exists regarding the role of high-dose therapy followed by stem-cell transplant (SCT) in the treatment of T-cell lymphoblastic lymphoma (T-LBL). We conducted an intention-to-treat analysis of the strategy of SCT as definitive treatment of T-LBL. PATIENTS AND METHODS: From July 1987 to March 2005, 34 adults with T-LBL were diagnosed and treated in British Columbia. Treatment, before planned SCT, consisted of a non-Hodgkin's lymphoma (NHL)/acute lymphoblastic leukemia hybrid chemotherapy protocol (28 patients) or a standard NHL chemotherapy regimen (six patients). RESULTS: Median follow-up of the 23 surviving patients is 51 months (range 13-142 months). Twenty-nine proceeded to SCT (four allogeneic, 25 autologous). For all 34 patients, 4-year overall survival (OS) and event-free survival (EFS) are 72% and 68%, respectively. For patients proceeding to SCT, the 4-year OS and EFS are 79% and 73%, respectively. All patients who received allografts are alive without disease at 38-141 months since diagnosis. For patients who received autografts, the 4-year EFS is 69%. Bone marrow involvement was a significant prognostic factor predicting for a worse survival (P = 0.02). CONCLUSION: A treatment strategy for adults with chemosensitive T-LBL that includes planned consolidation with SCT in first response produces favorable long-term outcome.

Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm.

Composite Module Analyst (CMA) is a novel software tool aiming to identify promoter-enhancer models based on the composition of transcription factor (TF) binding sites and their pairs. CMA is closely interconnected with the TRANSFAC database. In particular, CMA uses the positional weight matrix (PWM) library collected in TRANSFAC and therefore provides the possibility to search for a large variety of different TF binding sites. We model the structure of the long gene regulatory regions by a Boolean function that joins several local modules, each consisting of co-localized TF binding sites. Having as an input a set of co-regulated genes, CMA builds the promoter model and optimizes the parameters of the model automatically by applying a genetic-regression algorithm. We use a multicomponent fitness function of the algorithm which includes several statistical criteria in a weighted linear function. We show examples of successful application of CMA to a microarray data on transcription profiling of TNF-alpha stimulated primary human endothelial cells. The CMA web server is freely accessible at http://www.gene-regulation.com/pub/programs/cma/CMA.html. An advanced version of CMA is also a part of the commercial system ExPlaintrade mark (www.biobase.de) designed for causal analysis of gene expression data.

The geometry of the ribosomal polypeptide exit tunnel.

The geometry of the polypeptide exit tunnel has been determined using the crystal structure of the large ribosomal subunit from Haloarcula marismortui. The tunnel is a component of a much larger, interconnected system of channels accessible to solvent that permeates the subunit and is connected to the exterior at many points. Since water and other small molecules can diffuse into and out of the tunnel along many different trajectories, the large subunit cannot be part of the seal that keeps ions from passing through the ribosome-translocon complex. The structure referred to as the tunnel is the only passage in the solvent channel system that is both large enough to accommodate nascent peptides, and that traverses the particle. For objects of that size, it is effectively an unbranched tube connecting the peptidyl transferase center of the large subunit and the site where nascent peptides emerge. At no point is the tunnel big enough to accommodate folded polypeptides larger than alpha-helices.

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.

The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match and Patch provides increased functionality for TRANSFAC. The list of databases which are linked to the common GENE table of TRANSFAC and TRANSCompel has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD and TRANSPRO. Standard gene names from HGNC, MGI and RGD, are included for human, mouse and rat genes, respectively. With the help of InterProScan, Pfam, SMART and PROSITE domains are assigned automatically to the protein sequences of the transcription factors. TRANSCompel contains now, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based. Finally, for TRANSFAC, in respect of data growth, in particular the gain of Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. The here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.

Favorable outcome of primary mediastinal large B-cell lymphoma in a single institution: the British Columbia experience.

BACKGROUND: Primary mediastinal large B-cell lymphoma (PMBCL) is a distinct clinico-pathological subtype of diffuse large B-cell lymphoma (DLBCL). The optimal treatment is unknown, with some studies suggesting a superior outcome with dose-intensive chemotherapy regimens, and the role of radiotherapy remains ill-defined. PATIENTS AND METHODS: The British Columbia Cancer Agency lymphoma database was searched and records reviewed to identify those patients presenting with a prominent mediastinal mass and considered to be PMBCL based on the current REAL/WHO classifications. Patients were treated based on era-specific BCCA guidelines (1980-1992 MACOPB/VACOPB; 1992-2001 CHOP-type; 2001-present CHOP-R). Beginning in January 1998 involved-field radiotherapy was recommended to be routinely administered following chemotherapy. Prior to this, use of radiotherapy was individualized in advanced disease. RESULTS: In total, 153 patients with newly diagnosed PMBCL were identified between 28 July 1980 and 30 June 2003. The median age was 37 years (range 13-82) and the majority had stage I/II (74%), bulky mediastinal disease (75%). Overall (OS) and progression-free (PFS) survival at 5 years for the entire cohort were 75% and 69%, respectively. In direct comparison with a cohort of patients with DLBCL (n = 1273), OS (P = 10(-4)) and PFS (P = 0.0001) favored PMBCL. The age-adjusted International Prognostic Index (aaIPI) was not predictive of survival (P = 0.18). Five-year OS in patients < 65 years old treated with MACOPB/VACOPB, CHOP-R and CHOP-type was 87%, 81% and 71% respectively (P = 0.048). In pair-wise survival comparisons, only MACOPB/VACOPB and CHOP-type treated patients were significantly different (P = 0.016). In Cox multiple regression analysis, poor performance status remained the only predictor of survival, with treatment received demonstrating a trend to worse outcome for patients treated with CHOP-type regimens (P = 0.09). In an intention-to-treat analysis comparing the era before radiotherapy was routinely administered with after, there was no significant difference in 5-year PFS (74% versus 62%; P = 0.09) or OS (78% versus 69%; P = 0.14). CONCLUSIONS: In this single institution, population-based retrospective study, we found that PMBCL patients have excellent survival rates and a distinct plateau is observed in PFS, in striking comparison to DLBCL. The aaIPI was not predictive of survival in this population, suggesting that other prognostic models may be better suited for risk stratification. Dose-intensified chemotherapy with MACOPB or VACOPB demonstrated a trend to superior outcome over CHOP-type chemotherapy. However, further randomized studies are needed and the impact of rituximab on these comparisons must be considered. Finally, the routine addition of radiotherapy does not improve survival.

Myeloablative allografting for chronic lymphocytic leukemia: evidence for a potent graft-versus-leukemia effect associated with graft-versus-host disease.

In all, 30 patients with CLL proceeded to myeloablative allogeneic BMT using related (n=20, 67%) or unrelated (n=10) donors, at the Princess Margaret Hospital (Toronto) (n=20) or the Leukemia/BMT Program of BC (Vancouver) (n=10), from 1989 to 2001. Median (range) interval from diagnosis to BMT was 4.8 (0.3-13) years, median number of prior therapies was three and median age 48 years. The preparative regimen included total body irradiation in 15 (50%). In all, 14 of 30 patients (47%) are alive, with median (range) follow up of 4.3 (2.4-10.5) years. All are in complete remission, two following therapy for post-BMT progression. Actuarial overall (OS) and event-free survival (EFS) at 5 years is 39% (OS 48% for related donor and 20% for unrelated donor BMT); cumulative incidence of nonrelapse mortality (NRM) and relapse is 47 and 19%, respectively. Both acute (RR=0.008, P=0.01) and chronic (RR=0.006, P=0.02) Graft-versus-host disease (GVHD) were associated with markedly decreased risk of relapse. Patients receiving grafts from unrelated donors had increased NRM (RR=3.6, P=0.02) and decreased OS (RR of death=3.4, P=0.002). Allogeneic BMT has resulted in long-term EFS in approximately 40% of patients with CLL. There is evidence for a strong graft-versus-leukemia effect associated with acute and chronic GVHD, resulting in near complete protection from relapse.

Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly.

Traditionally, for biomolecular packing calculations research has focused on proteins. Besides proteins, RNA is the other large biomolecule that has tertiary structure interactions and complex packing. No one has yet quantitatively investigated RNA packing or compared its packing to that of proteins because, until recently, there were no large RNA structures. Here we address this question in detail, using Voronoi volume calculations on a set of high-resolution RNA crystal structures. We do a careful parameterization, taking into account many factors such as atomic radii, crystal packing, structural complexity, solvent, and associated protein to obtain a self-consistent, universal set of volumes that can be applied to both RNA and protein. We report this set of volumes, which we call the NucProt parameter set. Our measured values are consistent across the many different RNA structures and packing environments. When common atom types are compared between proteins and RNA, nine of 12 types show that RNA has a smaller volume and packs more tightly than protein, suggesting that close-packing may be as important for the folding of RNAs as it is for proteins. Moreover, calculated partial specific volumes show that RNA bases pack more densely than corresponding aromatic residues from proteins. Finally, we find that RNA bases have similar packing volumes to DNA bases, despite the absence of tertiary contacts in DNA. Programs, parameter sets and raw data are available online at.

Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods.

MOTIVATION: Transcription factor binding sites often differ significantly in their primary sequence and can hardly be aligned. Often one set of sites can contain several subsets of sequences that follow not just one but several different patterns. There is a need for sensitive methods to reveal multiple patterns in unaligned sets of sequences. RESULTS: We developed a novel method for analysis of unaligned sets of sequences based on kernel estimation. The method is able to reveal 'multiple local patterns'-a set of weight matrices. Every weight matrix characterizes a pattern that can be found in a significant subset of sequences under analysis. The method developed has been compared with several other methods of pattern discovery such as Gibbs sampling, MEME, CONSENSUS, MULTIPROFILER and PROJECTION. The kernel method showed the best performance in terms of how close the revealed weight matrices are to the original ones. We applied the kernel method to analyze three samples of promoters (cell-cycle, T-cells and muscle-specific). We compared the multiple patterns revealed with the TRANSFAC library of weight matrices and found a strong similarity to several weight matrices for transcription factors known to be involved in the mentioned specific gene regulation. AVAILABILITY: The program is available for on-line use at: http://www.biobase.de/cgi-bin/biobase/cbs2/bin/template.cgi?template=cbscall.html

Limited-stage mantle-cell lymphoma.

BACKGROUND: Mantle-cell lymphoma (MCL) is known to have a poor outcome, however, most patients present with advanced-stage disease. Little information is available on limited-stage MCL. PATIENTS AND METHODS: We retrospectively reviewed clinicopathological information on all patients with limited-stage MCL seen at the British Columbia Cancer Agency since 1984. RESULTS: Twenty-six patients had low bulk (<10 cm) stage IA (12 patients) or IIA (14 patients) MCL. Initial therapy was involved-field radiation therapy (RT) with or without chemotherapy (CT), 17 patients; CT alone or observation, nine patients. Fifteen patients are alive at a median follow-up of 72 months (range 14-194). Progression-free survival (PFS) at 2 and 5 years was 65% and 46%, and overall survival (OS) 86% and 70%, respectively. Five patients surviving beyond 8 years. Only age and initial use of RT significantly affected PFS. Five-year PFS for patients <60 years of age was 83%, compared with 39% for those aged >/= 60 years, P = 0.04. Patients receiving RT with or without CT (n = 17), had a 5-year PFS of 68%, compared with 11% for those not receiving RT (n = 9, P = 0.002). Receiving RT eliminated the impact of age on PFS (with RT the 5-year PFS was 83% for those aged <60 years and 57% for those >/= 60 years, P = 0.17). Although OS for the whole group was 53% at 6 years, it was 71% for those initially treated with RT, but only 25% for those not given RT (P = 0.13). CONCLUSION: In our experience, patients with limited-stage MCL had an improved PFS when treated with regimens including RT, with a trend towards improved OS. These results suggest a potentially important role for RT in limited-stage MCL.

Intra-cerebral relapse following prolonged remission after autologous stem cell transplantation for multiple myeloma.

Central nervous system (CNS) myeloma is a rare phenomenon, especially so after high-dose therapy (HDT) and stem cell transplantation. We describe a case of isolated CNS relapse of myeloma post autologous transplantation that followed a prolonged progression-free interval. Issues regarding the pathophysiology and management of this unusual complication are discussed.

Determining the minimum number of types necessary to represent the sizes of protein atoms.

MOTIVATION: Traditionally, for packing calculations people have collected atoms together into a number of distinct 'types'. These, in fact, often represent a heavy atom and its associated hydrogens (i.e. a united atom). Also, atom typing is usually done according to basic chemistry, giving rise to 20-30 protein atom types, such as carbonyl carbons, methyl groups, and hydroxyl groups. No one has yet investigated how similar in packing these chemically derived types are. Here we address this question in detail, using Voronoi volume calculations on a set of high-resolution crystal structures. RESULTS: We perform a rigorous clustering analysis with cross-validation on tens of thousands of atom volumes and attempt to compile them into types based purely on packing. From our analysis, we are able to determine a 'minimal' set of 18 atom types that most efficiently represent the spectrum of packing in proteins. Furthermore, we are able to uncover a number of inconsistencies in traditional chemical typing schemes, where differently typed atoms have almost the same effective size. In particular, we find that tetrahedral carbons with two hydrogens are almost identical in size to many aromatic carbons with a single hydrogen. AVAILABILITY: Programs available from http://geometry.molmovdb.org. CONTACT: JerryTsai@TAMU.edu; neil.voss@yale.edu; Mark.Gerstein@yale.edu SUPPLEMENTARY INFORMATION: Available at http://geometry.molmovdb.org.

Meningiomas of the cerebellopontine angle.

BACKGROUND: Meningiomas of the cerebellopontine angle (CPA), although uniform in location, are diverse with regard to the site of dural origin and displacement of neurovascular structures. A study of patients with CPA meningiomas was undertaken to gain more information regarding the relationship between site of dural attachment, clinical presentation, operative approach, and outcome. METHODS: In this report, we retrospectively review 40 patients with CPA meningiomas managed surgically. RESULTS: Common clinical presentations were hearing loss, unsteadiness, and dysequilibrium. Findings upon physical examination included hearing loss (73%), cerebellar signs (32%), trigeminal neuropathy (16%), and facial nerve dysfunction (16%). The most common site of dural origin was the petrous ridge (anterior to the IAC [26%], posterior [21%], superior [18%], and inferior [16%]). Less common sites of dural origin included the tentorium (31%), the clivus (15%), the IAC (10%), and the jugular foramen (8%). Site of dural origin determined the direction of displacement of the facial/vestibulocochlear nerve bundle. The most common microsurgical complication was facial nerve dysfunction (30%). Gross total resection was achieved in 82% of cases, whereas 18% underwent subtotal resection. Two patients died. Follow-up ranged from three months to 13 years with three recurrences. CONCLUSIONS: CPA meningiomas displace the seventh and eighth cranial nerves in various directions depending on the site of dural origin. Total surgical excision can be accomplished in the majority of cases with acceptable morbidity.

Allogeneic bone marrow transplantation for low-grade lymphoma and chronic lymphocytic leukemia.

Twenty-six patients with low-grade lymphoma (LGL) (n = 18) or chronic lymphocytic leukemia (CLL) (n = 8) received allogeneic BMTs between 1985 and 1998. Median age was 42 years, median interval from diagnosis to transplant 22 months and median number of prior treatments three. Twenty (77%) had stage IV disease; 22 (85%) had never achieved CR. Donor source was HLA matched sibling (n = 19, 73%), matched unrelated (n = 6, 23%) or syngeneic (n = 1). Conditioning therapy included total body irradiation in 23 patients and busulphan in three. Twenty-five received GVHD prophylaxis with cyclosporine A; + methotrexate (n = 19), + methylprednisolone (n = 2) or + T cell depletion of allograft +/- methotrexate (n = 4). Sixteen patients are alive, a median of 2.4 years post BMT. Death occurred due to transplant complications (n = 7) or underlying disease (n = 3). Eighteen (12 LGL, six CLL) of 22 evaluable patients (82%) achieved CR post BMT. Cumulative incidence of refractory/recurrent disease was 18% (95% confidence interval (CI) 7-42%). Overall and event-free survivals were 58% (95% CI 35-75%) and 54% (95% CI 32-72%), respectively. Allogeneic BMT for young patients with advanced LGL or CLL is feasible and can result in long-term disease-free survival.

Allografting for indolent lymphoid neoplasms.

BACKGROUND: Allogeneic bone marrow transplantation (BMT) has been used in patients with low-grade lymphoma (LGL) and chronic lymphocytic leukemia (CLL) with the goal of achieving long-term disease-free survival. PATIENTS AND METHODS: Twenty-nine patients with these diagnoses (LGL = 19, CLL = 10) received allogeneic BMT between September 1995 and January 1999. Median age was 42 (range 20-52) years. Twenty-three of twenty-nine patients (79%) were Ann Arbor or Rai stage IV at the time of transplant; twenty-four (83%) had never achieved complete remission (CR). Donor source was HLA-matched sibling (20), unrelated (8) and syngeneic (1). RESULTS: Seventeen patients are currently alive, a median of 29 months (range 1-85) post-BMT with a median KPS of 90%. Twenty-three of twenty-seven evaluable patients (85%) achieved CR post-BMT. Six patients had refractory/recurrent disease. Death occurred related to transplant complications in eight patients and underlying disease in four. Overall and event-free survival for the whole group is 51% and 44%, respectively. CONCLUSIONS: Allogeneic BMT for young patients with advanced stage LGL or CLL is a feasible strategy that can result in achievement of long-term disease-free survival.

Database of non-canonical base pairs found in known RNA structures.

Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.