Understanding and interpreting community sequencing measurements of the vaginal microbiome.

Community-wide high-throughput sequencing has transformed the study of the vaginal microbiome, and clinical applications are on the horizon. Here we outline the three main community sequencing methods: (1) amplicon sequencing, (2) shotgun metagenomic sequencing, and (3) metatranscriptomic sequencing. We discuss the advantages and limitations of community sequencing generally, and the unique strengths and weaknesses of each method. We briefly review the contributions of community sequencing to vaginal microbiome research and practice. We develop suggestions for critically interpreting research results and potential clinical applications based on community sequencing of the vaginal microbiome. TWEETABLE ABSTRACT: We review the advantages and limitations of amplicon sequencing, metagenomics, and metatranscriptomics methods for the study of the vaginal microbiome.

Extracellular Tau Oligomers Produce An Immediate Impairment of LTP and Memory.

Non-fibrillar soluble oligomeric forms of amyloid-ß peptide (oAß) and tau proteins are likely to play a major role in Alzheimer's disease (AD). The prevailing hypothesis on the disease etiopathogenesis is that oAß initiates tau pathology that slowly spreads throughout the medial temporal cortex and neocortices independently of Aß, eventually leading to memory loss. Here we show that a brief exposure to extracellular recombinant human tau oligomers (oTau), but not monomers, produces an impairment of long-term potentiation (LTP) and memory, independent of the presence of high oAß levels. The impairment is immediate as it raises as soon as 20 min after exposure to the oligomers. These effects are reproduced either by oTau extracted from AD human specimens, or naturally produced in mice overexpressing human tau. Finally, we found that oTau could also act in combination with oAß to produce these effects, as sub-toxic doses of the two peptides combined lead to LTP and memory impairment. These findings provide a novel view of the effects of tau and Aß on memory loss, offering new therapeutic opportunities in the therapy of AD and other neurodegenerative diseases associated with Aß and tau pathology.

Utilizing the Canadian Emergency Department Triage and Acuity Scale (CTAS) in an oncology urgent care clinic: the university health network experience.

The Canadian Triage Acuity Score (CTAS) is a validated triage method used in Canadian emergency departments (ED) that groups patients according to severity of presenting illness (CIHI, 2005). According to Tanabe, Gimbel, Yarnold and Adams (2004), five-level triage systems can be utilized in order to benchmark with similar programs. CTAS, a five-level triage system, can also be used as an instrument to determine triage quality and to predict admission rates, hospital length of stay and diagnostic utilization (Jiminez et al., 2003). In June 2009, Princess Margaret Hospital launched REACH (Reducing Emergent and Acute Care Hospitalization), an oncology-specific urgent care clinic. In order to appropriately utilize resources, assist patients in a timely manner according to acuity, and compare and contrast data to that which is traditionally reported from our area EDs, we implemented the use of a validated triage methodology, CTAS, in this urgent care clinic. The following paper describes the University Health Network experience with utilizing CTAS in an oncology population.

Prevalencia de psoriasis secundaria a agentes biológicos en pacientes con artritis reumatoidea / Prevalence of psoriasis in patients with rheumatoid arthritis treated with biological agents

Los objetivos del estudio fueron determinar la prevalencia de psoriasis en pacientes con Artritis Reumatoidea (AR) tratados con Agentes Biológicos (AB) y analizar sus características clínicas en una población de Tucumán.Se incluyeron 284 pacientes con AR. Ciento cuarenta y ocho en tratamiento con AB y 136 pacientes en tratamiento con Drogas Modificadoras de AR (DMAR), seleccionados por muestreo aleatorio simple. De los 284 pacientes evaluados, 242 (85%) fueron de sexo femenino, edad media de 56,4 años ± 13,4, la edad media al diagnóstico de AR fue de 42,3 años ± 16,7 con un tiempo de evolución de la enfermedad de 11,9 años ± 8,5. Doscientos cuarenta y un pacientes (85%) fueron seropositivos para Factor Reumatoideo (FR). Ciento treinta y seis (48%) fueron tratados con DMAR y 148 (52%) con AB. Al comparar ambos grupos, no hubo diferencias significativas entre edad media, edad media al diagnóstico de AR y presencia de factor reumatoideo. Cinco de los 148 pacientes en tratamiento biológico desarrollaron psoriasis. La prevalencia de psoriasis cutánea fue 3,4% (IC 95% 1,1-7,7). La mayoría de los casos se presentaron como psoriasis gutata. La duración media del tratamiento hasta la aparición de psoriasis fue de 31,6 meses (DS 26,8). Un paciente teníaantecedentes familiares de psoriasis. Ningún paciente del grupo DMAR desarrolló psoriasis (p <0,0001). En 2 pacientes que suspendieron el AB hubo remisión completa de la manifestación cutánea y en 3 pacientes que mantuvieron el tratamiento las manifestaciones cutáneas persistieron. No se encontró asociación entre el desarrollo de psoriasis y edad al diagnóstico, tiempo de evolución de AR y tiempo de tratamiento con AB (p = NS). Concluimos que la prevalencia de psoriasis en pacientes tratados con AB (etanercept, adalimumab y abatacept) fue 3,4%. El desarrollo de psoriasis cutánea no se asoció a edad al diagnóstico, tiempo de evolución de AR ni tiempo de tratamiento con agentes biológicos.

The objectives of this study were to determine the prevalence of psoriasis in patients with rheumatoid arthritis (RA) who were treated with biological agents (BA) and analize its clinical features in apopulation of Tucumán. We included 284 patients with RA. One hundred and forty-eight patients received treated with AB and 136 patients were treated with disease modifying anti-rheumatic drugs (DMARD), and they were selected by simple random sampling. Of the 284 patients evaluated, 242 (85%) were female, mean age was 56.4 ± 13.4 years, mean age at diagnosis of RA was 42.3 ± 16.7 years with a mean time of disease progression of 11.9 ± 8.5 years. Two hundred and fourty-one patients (85%) were seropositive for rheumatoid factor. One hundred thirty-six patients (48%) were treated with DMARD and 148 (52%) received BA. When we compared both groups, there was no significant difference between mean age, age at diagnosis of RA and presence of rheumatoid factor.Five of 148 patients developed psoriasis in the BA group, after receiving the first BA. The prevalence of cutaneous psoriasis was 3.4% (95% CI 1.1-7.7). Most cases were presented as gutata psoriasis. The average duration of treatment to onset of psoriasis was31.6 months (SD 26.8). One patient had a family history of psoriasis. In the group with DMARD, neither patient developed psoriasis (p<0.0001). Remission of the cutaneous manifestation was observed in 2 patients that discontinued the BA and 3 maintained treatment with persistance of the symptoms. No association was found between the development of psoriasis and age at diagnosis, RA duration and treatment time with BA (p = NS). We conclude that the prevalence of psoriasis in patients treated with BA (etanercept, adalimumab and abatacept) was 3.4%. The development of skin psoriasis was not associated with age at diagnosis, RA duration or time of treatment with biological agents.

Prevalencia de psoriasis secundaria a agentes biológicos en pacientes con artritis reumatoidea / Prevalence of psoriasis in patients with rheumatoid arthritis treated with biological agents

Los objetivos del estudio fueron determinar la prevalencia de psoriasis en pacientes con Artritis Reumatoidea (AR) tratados con Agentes Biológicos (AB) y analizar sus características clínicas en una población de Tucumán.Se incluyeron 284 pacientes con AR. Ciento cuarenta y ocho en tratamiento con AB y 136 pacientes en tratamiento con Drogas Modificadoras de AR (DMAR), seleccionados por muestreo aleatorio simple. De los 284 pacientes evaluados, 242 (85%) fueron de sexo femenino, edad media de 56,4 años ± 13,4, la edad media al diagnóstico de AR fue de 42,3 años ± 16,7 con un tiempo de evolución de la enfermedad de 11,9 años ± 8,5. Doscientos cuarenta y un pacientes (85%) fueron seropositivos para Factor Reumatoideo (FR). Ciento treinta y seis (48%) fueron tratados con DMAR y 148 (52%) con AB. Al comparar ambos grupos, no hubo diferencias significativas entre edad media, edad media al diagnóstico de AR y presencia de factor reumatoideo. Cinco de los 148 pacientes en tratamiento biológico desarrollaron psoriasis. La prevalencia de psoriasis cutánea fue 3,4% (IC 95% 1,1-7,7). La mayoría de los casos se presentaron como psoriasis gutata. La duración media del tratamiento hasta la aparición de psoriasis fue de 31,6 meses (DS 26,8). Un paciente teníaantecedentes familiares de psoriasis. Ningún paciente del grupo DMAR desarrolló psoriasis (p <0,0001). En 2 pacientes que suspendieron el AB hubo remisión completa de la manifestación cutánea y en 3 pacientes que mantuvieron el tratamiento las manifestaciones cutáneas persistieron. No se encontró asociación entre el desarrollo de psoriasis y edad al diagnóstico, tiempo de evolución de AR y tiempo de tratamiento con AB (p = NS). Concluimos que la prevalencia de psoriasis en pacientes tratados con AB (etanercept, adalimumab y abatacept) fue 3,4%. El desarrollo de psoriasis cutánea no se asoció a edad al diagnóstico, tiempo de evolución de AR ni tiempo de tratamiento con agentes biológicos.(AU)

The objectives of this study were to determine the prevalence of psoriasis in patients with rheumatoid arthritis (RA) who were treated with biological agents (BA) and analize its clinical features in apopulation of Tucumán. We included 284 patients with RA. One hundred and forty-eight patients received treated with AB and 136 patients were treated with disease modifying anti-rheumatic drugs (DMARD), and they were selected by simple random sampling. Of the 284 patients evaluated, 242 (85%) were female, mean age was 56.4 ± 13.4 years, mean age at diagnosis of RA was 42.3 ± 16.7 years with a mean time of disease progression of 11.9 ± 8.5 years. Two hundred and fourty-one patients (85%) were seropositive for rheumatoid factor. One hundred thirty-six patients (48%) were treated with DMARD and 148 (52%) received BA. When we compared both groups, there was no significant difference between mean age, age at diagnosis of RA and presence of rheumatoid factor.Five of 148 patients developed psoriasis in the BA group, after receiving the first BA. The prevalence of cutaneous psoriasis was 3.4% (95% CI 1.1-7.7). Most cases were presented as gutata psoriasis. The average duration of treatment to onset of psoriasis was31.6 months (SD 26.8). One patient had a family history of psoriasis. In the group with DMARD, neither patient developed psoriasis (p<0.0001). Remission of the cutaneous manifestation was observed in 2 patients that discontinued the BA and 3 maintained treatment with persistance of the symptoms. No association was found between the development of psoriasis and age at diagnosis, RA duration and treatment time with BA (p = NS). We conclude that the prevalence of psoriasis in patients treated with BA (etanercept, adalimumab and abatacept) was 3.4%. The development of skin psoriasis was not associated with age at diagnosis, RA duration or time of treatment with biological agents.(AU)

Metabolic syndrome in Argentinean patients with systemic lupus erythematosus.

The objective was to determine the prevalence of the metabolic syndrome (MS) in patients with systemic lupus erythematosus (SLE) in Argentina, to assess the factors associated to it, and to compare the results with a control group with non-inflammatory disorders. The study included 147 patients with SLE and 119 controls. MS was defined according to criteria by the American Heart Association/National Heart, Lung, and Blood Institute (AHA/NHLBI) Scientific Statement. Demographic characteristics, Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) and Systemic Lupus International Collaborating Clinics/ACR Damage Index (SDI) were assessed as well as administration, maximum dose and cumulative dose of prednisone and hydroxychloroquine (HCQ). MS prevalence was 28.6% (CI 95%: 21.4-36.6) in patients with SLE and 16% in controls (P = 0.0019). Patients with SLE presented higher arterial hypertension frequency compared with controls (43 vs 25%, P = 0.007). When comparing lupus patients with MS (n = 41) and without MS (n = 106), no significant differences were observed regarding duration of the disease, SLEDAI or cumulative prednisone dose. Cumulative damage was associated independently with MS (OR 1.98; P = 0.021), whereas HCQ use was found to be protective (OR 0.13; P = 0.015). Patients with lupus presented higher MS prevalence than controls with non-inflammatory disorders, and occurrence of arterial hypertension was also higher. MS was associated with cumulative damage; the use of HCQ showed to be protective against presence of MS.

Compromiso cardíaco en hijos de madres con Lupus Eritematoso Sistémico (LES) / Cardiac compromise in children born from Mathers suffering from Systemic Lupus Erythematosus (SLE)

Objetivo: Analizar la presencia de trastornos de la conducción tempranos y tardíos en hijos de madres lúpicas y su asociación con anti-Ro/SSA. Material y método: Se estudiaron 41 hijos de 29 madres con LES (criterios ACR), a quienes se les realizó evaluación cardiovascular, ECG y serología para anti-Ro/SSA a los neonatos y a las madres. Se analizaron variables relacionadas al embarazo, puerperio y al LES. Resultados: La edad X de los hijos al momento de la evaluación fue 9.6 años (DS 8.8). En 29 embarazos (71%), las madres tenían diagnóstico previo de LES, tiempo de evolución de la enfermedad X 7.4 años (DS 6). Once de ellas (27%) reactivaron su enfermedad durante el embarazo. El 31% de las madres (9) fueron anti-Ro positivas. Sólo 2 niños fueron anti-Ro positivos, ninguno de ellos con lupus neonatal. Tres niños (7%) presentaron patología cardíaca al nacer: 1) Niña con bloqueo cardíaco congénito (BCC) que requirió marcapasos y falleció a los 3 años de edad por insuficiencia cardíaca secundaria a miocardiopatía dilatada; 2) Niño con bradicardia transitoria; 3) Niña con malformación cardíaca severa. Ninguno deellos fue anti-Ro positivo. La presencia de anti-Ro en madres con LES no se asoció a complicaciones del embarazo, enfermedades neonatales, patología cardíaca ni reactivación del LES (p=NS) Conclusión: En esta población de madres lúpicas, la presencia de anti-Ro/SSA no se asoció a compromiso cardíaco en sus hijos

Influencia de factores sociodemográficos en actividad de enfermedad, estadofuncional y calidad de vida de pacientes con artritis psoriásica / Influence of sociodemographic features on clinical manifestations, disease activity, functional status and quality of life of patients with psoriatic artritis

Objetivo: Determinar la influencia de factores sociodemográficos en las manifestaciones clínicas, actividad de la enfermedad, estado funcional y calidad de vida de pacientes con artritis psoriásica (APs). Métodos: Se incluyeron 148 pacientes con APs reclutados de varios centros de reumatología de Argentina. Se determinaron factores sociodemográficos: edad, sexo, raza, nivel de educación, fuentes de ingreso personal, escala de Graffar y clases sociales. Al inicio de la enfermedad se evaluaron las siguientes variables: edad al inicio, duración de la enfermedad, manifestaciones clínicas y forma clínica de presentación. La actividad de la enfermedad fue evaluada mediante número de articulaciones activas, escala visual análoga (EVA) global del paciente y BASDAI. El estado funcional y la calidad de vida de los pacientes se determinó por medio de BASFI, ASQoL y SF-12 (Versión 1.0). Para el análisis estadístico de los datos obtenidos se utilizó test de Chi-cuadrado, test exacto de Fisher y test de Kruskal-Wallis. Resultados: De los 148 pacientes, 58,8% fueron mujeres con una edad media al inicio de la enfermedad de 53,2 ± 13,6 años y una duración media de enfermedad de 9,3 ± 8,9 años. La edad al inicio, el sexo, la raza y la escala de Graffar no estuvieron asociados con manifestaciones clínicas, actividad de la enfermedad, estado funcional y calidad de vida

Genetic and epigenetic changes in mammary epithelial cells identify a subpopulation of cells involved in early carcinogenesis.

Morphologically normal foci of epithelial cells exhibiting p16 inactivation have been found in several tissues and may be precursors to cancer. Our previous work demonstrates that cells lacking p16(INK4A) activity exhibit phenotypes associated with malignancy (Romanov et al. 2001). The acquisition of genomic instability occurs through the activation of telomeric and centrosomal dysfunction. Additionally, the activation of stress pathways such as COX-2 provides these cells with the mutagenic potential to survive adverse environments as well as the ability to migrate, evade apoptosis and immune surveillance, and summon sustaining vasculature. Examination of archived tissue from women with DCIS (ductal carcinoma in situ) reveals epithelial cells that overexpress markers of premalignant stress activation pathways and mirror the distinctive expression patterns of these markers observed in vitro. These epithelial cells are found within the premalignant lesion as well as in the field of morphologically normal tissue that surrounds the lesion. Here, we show that p16(INK4A)-silenced vHMEC cells exhibit a gene expression profile which is distinct, reproducible, and extends beyond the changes mediated by p16(INK4A) inactivation. The present work suggests that cells lacking p16(INK4A) activity exhibit critical activities which allow cells to evade differentiation processes that would be expected to terminate proliferation. All of these properties are critical to malignancy. These events may be useful biomarkers to detect the earliest events in breast cancer.

Serum CA 19-9 levels as a diagnostic marker in cystic fibrosis patients with borderline sweat tests.

Patients with normal or borderline sweat tests present a diagnostic challenge. In spite of the availability of genetic analysis and measurement of nasal potential difference, there is still uncertainty in diagnosing cystic fibrosis in some patients. CA 19-9 is a tumor-associated antigen whose levels were previously found to be elevated in some cystic fibrosis patients. We investigated whether serum CA 19-9 levels can contribute to establishing the diagnosis of cystic fibrosis in patients with a borderline sweat test, and evaluated the influence of different clinical variables on CA 19-9 levels. Serum CA 19-9 levels were measured in 82 cystic fibrosis patients grouped according to their genotype and in 38 healthy individuals. Group A included 50 patients who carried two mutations previously found to be associated with a pathological sweat test and pancreatic insufficiency (DeltaF508, W1282X, G542X, N1303K, and S549R). Group B included 13 compound heterozygote cystic fibrosis patients who carried one mutation known to cause mild disease with a borderline or normal sweat test and pancreatic sufficiency (3849+10kb C-->T, 5T). Group C included 38 normal controls. Nineteen cystic fibrosis patients carried at least one unidentified mutation. An association between CA 19-9 levels and age, pulmonary function, pancreatic status, sweat chloride, previous pancreatitis, serum lipase, meconium ileus, distal intestinal obstruction, liver disease, and diabetes was investigated. The distribution of CA 19-9 levels was significantly different between the three groups ( p<0.01); high CA 19-9 levels were found in 60% (30/50) of group Apatients and in 46.6% (6/13) of group B patients, but in only 5.2% (2/38) of the controls. CA 19-9 levels were inversely related to forced expiratory volume in 1 s, while no association was found with the other clinical parameters examined. Our findings suggest that the serum CA 19-9 in cystic fibrosis patients originates in the respiratory system, and has a useful ancillary role, particularly when diagnostic uncertainty exists. Hence, the diagnosis of cystic fibrosis should be considered in patients with borderline sweat tests and high CA 19-9 levels, but normal levels do not exclude cystic fibrosis.

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking.

The catabolite activator protein (CAP) makes no direct contact with the consensus base-pair T:A at position 6 of the DNA half-site 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' but, nevertheless, exhibits strong specificity for T:A at position 6. Binding of CAP results in formation of a sharp DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site. The consensus base-pair T:A at position 6 and the consensus base-pair G:C at position 7 form a T:A/G:C step, which is known to be associated with DNA flexibility. It has been proposed that specificity for T:A at position 6 is a consequence of formation of the DNA kink between positions 6 and 7, and of effects of the T:A(6)/G:C(7) step on the geometry of DNA kinking, or the energetics of DNA kinking. In this work, we determine crystallographic structures of CAP-DNA complexes having the consensus base-pair T:A at position 6 or the non-consensus base-pair C:G at position 6. We show that complexes containing T:A or C:G at position 6 exhibit similar overall DNA bend angles and local geometries of DNA kinking. We infer that indirect readout in this system does not involve differences in the geometry of DNA kinking but, rather, solely differences in the energetics of DNA kinking. We further infer that the main determinant of DNA conformation in this system is protein-DNA interaction, and not DNA sequence.

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking.

The catabolite activator protein (CAP) sharply bends DNA in the CAP-DNA complex, introducing a DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site, 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' ("primary kink"). CAP recognizes the base-pair immediately 5' to the primary-kink site, T:A(6), through an "indirect-readout" mechanism involving sequence effects on the energetics of primary-kink formation. CAP recognizes the base-pair immediately 3' to the primary-kink site, G:C(7), through a "direct-readout" mechanism involving formation of a hydrogen bond between Glu181 of CAP and G:C(7). Here, we report that substitution of the carboxylate side-chain of Glu181 of CAP by the one-methylene-group-shorter carboxylate side-chain of Asp changes DNA binding specificity at position 6 of the DNA half site, changing specificity for T:A(6) to specificity for C:G(6), and we report a crystallographic analysis defining the structural basis of the change in specificity. The Glu181-->Asp substitution eliminates the primary kink and thus eliminates indirect-readout-based specificity for T:A(6). The Glu181-->Asp substitution does not eliminate hydrogen-bond formation with G:C(7), and thus does not eliminate direct-readout-based specificity for G:C(7).

Children and war: current understandings and future directions.

During the last decade, the number of children whose lives have been disrupted by war, oppression, terror, and other forms of conflict has grown tremendously. When the United Nations High Commission for Refugees was first established during the 1950s to provide international protection to refugees following World War II, it was estimated that there were 1.5 million refugees and displaced persons. Today there are approximately 14 million, about three-fourths of whom are women and children. Although the experiences of refugee children and adolescents vary considerably, many have witnessed or experienced the death or murder of loved ones. Upon resettlement, they face numerous challenges. Research with this population is a relatively new area of investigation, but there is evidence that many of these young people experience long-term physical and emotional health problems. In this article, current research findings are reviewed, the widespread emphasis in the literature on post-traumatic stress disorder (PTSD) is critically examined, future research directions are suggested, and implications for public health nurses are addressed.

The crystal and molecular structure of a collagen-like peptide with a biologically relevant sequence.

A detailed description of the 2.0 A structure of the triple-helical peptide, (Pro-Hyp-Gly)(3)-Ile-Thr-Gly-Ala-Arg-Gly-Leu-Ala-Gly-Pro-Hyp-Gly-(Pro-Hyp-Gly)(3), denoted as T3-785, is presented. This peptide contains a biologically relevant sequence and was designed to model the imino acid-poor 785-796 region of human type III collagen just C-terminal to the matrix metalloproteinase cleavage site. The crystal structure of the T3-785 peptide demonstrates that sequence can influence local conformational changes in triple-helical structure, in terms of superhelical pitch, hydrogen bonding pattern, and hydration patterns. The novel packing arrangement displayed by the T3-785 structure, compared with those of collagen-like peptides with more imino acid-rich sequences indicates the sequence dependence of intermolecular assemblies in collagen as well. The observed synergy between the packing arrangements and the extended hydration network indicates that hydration of the triple helix is directly related to its association with other molecules.

Checking nucleic acid crystal structures.

The program SFCHECK [Vaguine et al. (1999), Acta Cryst. D55, 191-205] is used to survey the quality of the structure-factor data and the agreement of those data with the atomic coordinates in 105 nucleic acid crystal structures for which structure-factor amplitudes have been deposited in the Nucleic Acid Database [NDB; Berman et al. (1992), Biophys. J. 63, 751-759]. Nucleic acid structures present a particular challenge for structure-quality evaluations. The majority of these structures, and DNA molecules in particular, have been solved by molecular replacement of the double-helical motif, whose high degree of symmetry can lead to problems in positioning the molecule in the unit cell. In this paper, the overall quality of each structure was evaluated using parameters such as the R factor, the correlation coefficient and various atomic error estimates. In addition, each structure is characterized by the average values of several local quality indicators, which include the atomic displacement, the density correlation, the B factor and the density index. The latter parameter measures the relative electron-density level at the atomic position. In order to assess the quality of the model in specific regions, the same local quality indicators are also surveyed for individual groups of atoms in each structure. Several of the global quality indicators are found to vary linearly with resolution and less than a dozen structures are found to exhibit values significantly different from the mean for these indicators, showing that the quality of the nucleic acid structures tends to be rather uniform. Analysis of the mutual dependence of the values of different local quality indicators, computed for individual residues and atom groups, reveals that these indicators essentially complement each other and are not redundant with the B factor. Using several of these indicators, it was found that the atomic coordinates of the nucleic acid bases tend to be better defined than those of the backbone. One of the local indicators, the density index, is particularly useful in spotting regions of the model that fit poorly in the electron density. Using this parameter, the quality of crystallographic water positions in the analyzed structures was surveyed and it was found that a sizable fraction of these positions have poorly defined electron density and may therefore not be reliable. The possibility that cases of poorly positioned water molecules are symptomatic of more widespread problems with the structure as a whole is also raised.

Protein-RNA interactions: a structural analysis.

A detailed computational analysis of 32 protein-RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein-RNA and protein-DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein-RNA complexes, backbone contacts were more dominant in the protein-DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level.

The PDB data uniformity project.

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the data uniformity project that is underway to address the inconsistency in PDB data.