Although the treatment technology of sulfamethoxazole has been investigated widely, there are various issues such as the high cost, inefficiency, and secondary pollution which restricted its application. Bioflocculant, as a novel method, is proposed to improve the removal efficiency of PPCPs, which has an advantage over other methods. Bioflocculant MFX, composed by high polymer polysaccharide and protein, is the metabolism product generated and secreted by Klebsiella sp. In this paper, MFX is added to 1 mg/L sulfanilamide aqueous solution substrate, and the removal ratio is evaluated. According to literatures review, for MFX absorption of sulfanilamide, flocculant dosage, coagulant-aid dosage, pH, reaction time, and temperature are considered as influence parameters. The result shows that the optimum condition is 5 mg/L bioflocculant MFX, 0.5 mg/L coagulant aid, initial pH 5, and 1 h reaction time, and the removal efficiency could reach 67.82%. In this condition, MFX could remove 53.27% sulfamethoxazole in domestic wastewater, and the process obeys Freundlich equation. R2 value equals 0.9641. It is inferred that hydrophobic partitioning is an important factor in determining the adsorption capacity of MFX for sulfamethoxazole solutes in water; meanwhile, some chemical reaction probably occurs.
Hydrogen sulfide (H2S) has historically been considered to be a toxic gas, an environmental and occupational hazard. However, with the discovery of its presence and enzymatic production through precursors of L-cysteine and homocysteine in mammalian tissues, H2S has recently received much interest as a physiological signaling molecule. H2S is a gaseous messenger molecule that has been implicated in various physiological and pathological processes in mammals, including vascular relaxation, angiogenesis, and the function of ion channels, ischemia/reperfusion (I/R), and heart injury. H2S is an endogenous neuromodulator and present studies show that physiological concentrations of H2S enhance NMDA receptor-mediated responses and aid in the induction of hippocampal long-term potentiation. Moreover, in the field of neuronal protection, physiological concentrations of H2S in mitochondria have many favorable effects on cytoprotection.
Gait analysis is widely used in detecting human walking disorders. Current gait analysis methods like video- or optical-based systems are expensive and cause invasion of human privacy. This article presents a self-developed low-cost body inertial-sensing network, which contains a base station, three wearable inertial measurement nodes, and the affiliated wireless communication protocol, for practical gait discrimination between hemiplegia patients and asymptomatic subjects. Every sensing node contains one three-axis accelerometer, one three-axis magnetometer, and one three-axis gyroscope. Seven hemiplegia patients (all were abnormal on the right side) and 7 asymptomatic subjects were examined. The three measurement nodes were attached on the thigh, the shank, and the dorsum of the foot, respectively (all on the right side of the body). A new method, which does not need to obtain accurate positions of the sensors, was used to calculate angles of knee flexion/extension and foot in the gait cycle. The angle amplitudes of initial contact, toe off, and knee flexion/extension were extracted. The results showed that there were significant differences between the two groups in the three angle amplitudes examined (−0.52±0.98° versus 6.94±2.63°, 28.33±11.66° versus 47.34±7.90°, and 26.85±8.6° versus 50.91±6.60°, respectively). It was concluded that the body inertial-sensing network
platform provided a practical approach for wearable biomotion acquisition and was effective for discriminating gait symptoms between hemiplegia and asymptomatic subjects.
gait analysis; body sensor network; hemiplegia
Rheumatoid arthritis (RA), a chronic autoimmune disease, affects sufferers in many different ways. Treatment of this chronic condition is particularly challenging. Traditional Chinese Medicine (TCM) provides alternatives. Bizhongxiao decoction (BZX) is a TCM complex, which has been used clinically for many years to treat RA. The purpose of this study is to compare the effects of BZX decoction and its dismantled formulae on IL-1 and TNF-1 levels in rats with RA, and to elucidate its mechanism of action.
Ninety healthy normal female SD rats were randomly divided into six groups: normal (control), model, BZX decoction, and the three dismantled formulae (I: heat-clearing and detoxication, II: dissipating dampness, and III: blood circulation promotion). Apart from the normal (control) group, the rats in each group were injected subcutaneously with bovine type II collagen and complete Freund adjuvant to establish a collagen-induced arthritis model, so that inhibition of foot swelling in the rats by BZX decoction and its dismantled formulae could be observed. Immunohistochemistry was used to assess the levels of the inflammatory cytokines IL-1 and TNF in synovial joints at various time points.
Twenty-one days after the model was established, the levels of TNF and IL-1 were significantly higher in the model group, BZX decoction group and dismantled formula groups I, II and III than in the normal controls (P < 0.05). The levels of these cytokines were significantly higher in the model group than the BZX decoction or the three dismantled formula groups (P <0.01). At longer times, the TNF and IL-1 levels in model group rose gradually; those in the BZX decoction and dismantled formula groups were gradually reduced. The cytokine levels in the BZX decoction group were lower than in the three dismantled formula groups and continued to decline.
BZX decoction and the three dismantled formulae examined down-regulated the inflammatory factors IL-1 and TNF in collagen-induced arthritis rat models, but BZX exerted the strongest effect.
Bizhongxiao decoction; Rheumatoid arthritis; Interleukin-1; Tumor necrosis factor
In the past years, a few methods have been developed to translate human EEG to music. In 2009, PloS One 4 e5915, we developed a method to generate scale-free brainwave music where the amplitude of EEG was translated to music pitch according to the power law followed by both of them, the period of an EEG waveform is translated directly to the duration of a note, and the logarithm of the average power change of EEG is translated to music intensity according to the Fechner's law. In this work, we proposed to adopt simultaneously-recorded fMRI signal to control the intensity of the EEG music, thus an EEG-fMRI music is generated by combining two different and simultaneous brain signals. And most importantly, this approach further realized power law for music intensity as fMRI signal follows it. Thus the EEG-fMRI music makes a step ahead in reflecting the physiological process of the scale-free brain.
To compare stress levels among residents in large Chinese cities between 2001 and 2008.
Survey data were collected in three mainland Chinese capital cities in two waves, in 2001 and 2008, respectively. Participants were recruited through a multi-stage stratified sampling process. Stress was assessed using the Perceived Stress Scale, Chinese version (CPSS). Descriptive methods were used to estimate mean stress levels and associated 95% confidence intervals. Estimates were adjusted by post-stratification weights.
Indicating stable stress levels, respective adjusted mean stress scores for the combined samples of study participants were 23.90 (95%CI: 23.68–24.12) in 2001 and 23.69 (95%CI: 23.38–24.01) in 2008. A lower stress level in 2008 than in 2001 manifested among residents who were under 25 years of age; female; with a college or higher level education; divorced, widowed, or separated; members of the managerial and clerical group; students or army personnel; or with an annual income of at least 30,000 RMB.
The overall stress level did not change among the combined sample of residents in the three Chinese study cities between 2001 and 2008. However, levels remained high and varied across social strata, and may have reflected a national trend among urban residents. Findings indicate a need for a new health policy, and call for the design and implementation of evidence-based interventions that target the highest-risk groups.
MtDNA haplogroups could have important implication for understanding of the relationship between the mutations of the mitochondrial genome and diseases. Distribution of a variety of diseases among these haplogroups showed that some of the mitochondrial haplogroups are predisposed to disease. To examine the susceptibility of mtDNA haplogroups to ROU, we sequenced the mtDNA HV1, HV2 and HV3 in Chinese ROU.
MtDNA haplogroups were analyzed in the 249 cases of ROU patients and the 237 cases of healthy controls respectively by means of primer extension analysis and DNA sequencing. Haplogroups G1 and H were found significantly more abundant in ROU patients than in healthy persons, while haplogroups D5 and R showed a trend toward a higher frequency in control as compared to those in patients. The distribution of C-stretch sequences polymorphism in mtDNA HV1, HV2 and HV3 regions was found in diversity.
For the first time, the relationship of mtDNA haplogroups and ROU in Chinese was investigated. Our results indicated that mtDNA haplogroups G1 and H might constitute a risk factor for ROU, which possibly increasing the susceptibility of ROU. Meanwhile, haplogroups D5 and R were indicated as protective factors for ROU. The polymorphisms of C-stretch sequences might being unstable and influence the mtDNA replication fidelity.
We report an incarcerated internal hernia in a huge irreducible parastomal hernia-"hernia within hernia." A 70-year-old obese woman with diabetes who underwent an abdomino-perineal resection 20 years ago was admitted to our hospital with 20 years history of a huge irreducible bulge, 25 cm in diameter. An internal hernia due to an adhesive band extending from the sac wall to proximal colon was found in the parastomal hernia sac during an emergency laparotomy. We cut off the distal colon and relocated the colostomy stoma. The patient was discharged uneventfully 2 weeks after the surgery and was readmitted to have a further laparoscopic hernia repair 8 months later. Unfortunately, an unrecognized enterotomy occurred during the secondary surgery that led to an additional laparotomy during which the mesh was not contaminated by the bowel contents and was kept in place. At 22-month follow-up, there were no evidences of recurrence.
Ventral hernia; Incarceration; Intestinal obstruction; Herniorrhaphy
Somatosensory evoked potentials (SSEPs) have been established as an electrophysiological tool for the prognostication of neurological outcome in patients with hypoxic-ischemic brain injury. The early and late responses in SSEPs reflect the sequential activation of neural structures along the somatosensory pathway. This study reports that the SSEP can be separated into early (short-latency, SL) and late (long-latency, LL) responses using Independent Component Analysis (ICA), based on the assumption that these components are generated from different neural sources. Moreover, this source separation into the SL and LL components allows analysis of electrophysiological response to brain injury, even when the SSEPs are severely distorted and SL and LL components get mixed. With the help of ICA decomposition and corrected peak estimation, the latency of LL-SSEP is shown to be predictive of long-term neurological outcome. Further, it is shown that the recovery processes of SL- and LL-SSEPs follow different dynamics, with the SL-SSEP restored earlier than LL-SSEP. We predict that the SL- and LL-SSEPs reflect the timing of the progression of evoked response through the thalamocortical pathway and as such respond differently depending upon injury and recovery of the thalamic and cortical regions, respectively.
Somatosensory Evoked Potential; short/long-latency; brain ischemia; Independent Component Analysis; thalamocortical
The purpose of the current study was to identify potential ligands and develop a novel diagnostic test to highly pathogenic avian influenza A virus (HPAI), subtype H5N1 viruses using phage display technology. The H5N1 viruses were used as an immobilized target in a biopanning process using a 12-mer phage display random peptide library. After five rounds of panning, three phages expressing peptides HAWDPIPARDPF, AAWHLIVALAPN or ATSHLHVRLPSK had a specific binding activity to H5N1 viruses were isolated. Putative binding motifs to H5N1 viruses were identified by DNA sequencing. In terms of the minimum quantity of viruses, the phage-based ELISA was better than antiserum-based ELISA and a manual, semi-quantitative endpoint RT-PCR for detecting H5N1 viruses. More importantly, the selected phages bearing the specific peptides to H5N1 viruses were capable of differentiating this virus from other avian viruses in enzyme-linked immunosorbent assays.
Hydrogen sulfide (H2S), the third physiologically relevant gaseous molecule, is recognized increasingly as an anti-inflammatory mediator in various inflammatory conditions. Herein, we explored the effects and mechanisms of sodium hydrosulfide (NaHS, a H2S donor) on tumor necrosis factor (TNF)-α-induced human umbilical vein endothelial cells (HUVEC) dysfunction.
Methodology and Principal Findings
Application of NaHS concentration-dependently suppressed TNF-α-induced mRNA and proteins expressions of intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1), mRNA expression of P-selectin and E-selectin as well as U937 monocytes adhesion to HUVEC. Western blot analysis revealed that the expression of the cytoprotective enzyme, heme oxygenase-1 (HO-1), was induced and coincident with the anti-inflammatory action of NaHS. Furthermore, TNF-α-induced NF-κB activation assessed by IκBα degradation and p65 phosphorylation and nuclear translocation and ROS production were diminished in cells subjected to treatment with NaHS.
H2S can exert an anti-inflammatory effect in endothelial cells through a mechanism that involves the up-regulation of HO-1.
Phosphoinositide 3-kinase γ (PI3Kγ) is a critical mediator of directional cell movement. Here, we sought to characterize the role of PI3Kγ in mediating the different steps of PMN trafficking in the lung.
In a murine model of LPS-induced lung injury, PMN migration into the different lung compartments was determined in PI3Kγ gene-deficient (PI3Kγ−/−) and wildtype mice. Bone marrow chimeras were created to characterize the role of PI3Kγ on hematopoietic vs. non-hematopoietic cells. A small molecule PI3Kγ inhibitor was tested in vitro and in vivo.
PMN adhesion to the pulmonary endothelium and transendothelial migration into the lung interstitium was enhanced in PI3Kγ−/− mice. However, transepithelial migration into the alveolar space was reduced in these mice. When irradiated PI3Kγ−/− mice were reconstituted with bone marrow from wildtype mice, migratory activity into the alveolar space was restored partially. A small molecule PI3Kγ inhibitor reduced chemokine-induced PMN migration in vitro when PMNs or epithelial cells but not when endothelial cells were treated. The inhibitor also reduced LPS-induced PMN migration in vivo.
We conclude that PI3Kγ is required for transepithelial but not for transendothelial migration in LPS-induced lung injury. Inhibition of PI3Kγ activity may be effective at curbing excessive PMN infiltration in lung injury.
Acute lung injury; chemotaxis; inflammation; Polymorphonuclear leukocytes; transmigration
Directed cell migration mediates physiological and pathological processes. In particular, immune cell trafficking in tissues is crucial for inducing immune responses and is coordinated by multiple environmental cues such as chemoattractant gradients. Although the chemotaxis mechanism has been extensively studied, how cells integrate multiple chemotactic signals for effective trafficking and positioning in tissues is not clearly defined. Results from previous neutrophil chemotaxis experiments and modeling studies suggested that ligand-induced homologous receptor desensitization may provide an important mechanism for cell migration in competing chemoattractant gradients. However, the previous mathematical model is oversimplified to cell gradient sensing in one-dimensional (1-D) environment. To better understand the receptor desensitization mechanism for chemotactic navigation, we further developed the model to test the role of homologous receptor desensitization in regulating both cell gradient sensing and migration in different configurations of chemoattractant fields in two-dimension (2-D). Our results show that cells expressing normal desensitizable receptors preferentially orient and migrate toward the distant gradient in the presence of a second local competing gradient, which are consistent with the experimentally observed preferential migration of cells toward the distant attractant source and confirm the requirement of receptor desensitization for such migratory behaviors. Furthermore, our results are in qualitative agreement with the experimentally observed cell migration patterns in different configurations of competing chemoattractant fields.
Chemokines mediate the trafficking and positioning of lymphocytes in lymphoid tissues that is crucial for immune surveillance and immune responses. In particular, a CCR7 ligand, CCL21, plays important roles in recruiting T cells to secondary lymphoid tissues (SLT). Furthermore, CCL21 together with another CCR7 ligand, CCL19, direct the navigation and compartmentation of T cells within SLT. However, the distinct roles of these two chemokines for regulating cell trafficking and positioning are not clear. In this study, we explore the effect of co-existing CCL19 and CCL21 concentration fields on guiding T cell migration. Using microfluidic devices that can configure single and superimposed chemokine fields we show that under physiological gradient conditions, human peripheral blood T cells chemotax to CCL21 but not CCL19. Furthermore, T cells migrate away from the CCL19 gradient in a uniform background of CCL21. This repulsive migratory response is predicted by mathematical modeling based on the competition of CCL19 and CCL21 for CCR7 signaling and the differential ability of the two chemokines for desensitizing CCR7. These results suggest a new combinatorial guiding mechanism by CCL19 and CCL21 for the migration and trafficking of CCR7 expressing leukocytes.
Coronary artery disease (CAD) is the leading cause of death worldwide and is commonly caused by a constellation of risk factors called the metabolic syndrome. We characterized a family with autosomal dominant early CAD, features of the metabolic syndrome (hyperlipidemia, hypertension, and diabetes), and osteoporosis. These traits showed genetic linkage to a short segment of chromosome 12p, in which we identified a missense mutation in LRP6, which encodes a co-receptor in the Wnt signaling pathway. The mutation, which substitutes cysteine for arginine at a highly conserved residue of an epidermal growth factor–like domain, impairs Wnt signaling in vitro. These results link a single gene defect in Wnt signaling to CAD and multiple cardiovascular risk factors.
Currently, a number of yeast genomes with different physiological features have been sequenced and annotated, which provides invaluable information to investigate yeast genetics, evolutionary mechanism, structure and function of gene families.
YeastWeb is a novel database created to provide access to gene families derived from the available yeast genomes by assigning the genes into putative families. It has many useful features that complement existing databases, such as SGD, CYGD and Génolevures: 1) Detailed computational annotation was conducted with each entry with InterProScan, EMBOSS and functional/pathway databases, such as GO, COG and KEGG; 2) A well established user-friendly environment was created to allow users to retrieve the annotated genes and gene families using functional classification browser, keyword search or similarity-based search; 3) Workset offers users many powerful functions to manage the retrieved data efficiently, associate the individual items easily and save the intermediate results conveniently; 4) A series of comparative genomics and molecular evolution analysis tools are neatly implemented to allow users to view multiple sequence alignments and phylogenetic tree of gene families. At present, YeastWeb holds the gene families clustered from various MCL inflation values from a total of 13 available yeast genomes.
Given the great interest in yeast research, YeastWeb has the potential to become a useful resource for the scientific community of yeast biologists and related researchers investigating the evolutionary relationship of yeast gene families. YeastWeb is available at http://centre.bioinformatics.zj.cn/Yeast/.
This paper proposes a method to translate human EEG into music, so as to represent mental state by music. The arousal levels of the brain mental state and music emotion are implicitly used as the bridge between the mind world and the music. The arousal level of the brain is based on the EEG features extracted mainly by wavelet analysis, and the music arousal level is related to the musical parameters such as pitch, tempo, rhythm, and tonality. While composing, some music principles (harmonics and structure) were taken into consideration. With EEGs during various sleep stages as an example, the music generated from them had different patterns of pitch, rhythm, and tonality. 35 volunteers listened to the music pieces, and significant difference in music arousal levels was found. It implied that different mental states may be identified by the corresponding music, and so the music from EEG may be a potential tool for EEG monitoring, biofeedback therapy, and so forth.
Aim. To construct a recombinant eukaryotic expression plasmid containing human calcitonin (hCT) gene and express the gene in murine fibroblast NIH3T3 cells. Materials and Methods. A murine Igκ-chain leader sequence and hCT gene were synthesized and cloned into pCDNA3.0 to form the pCDNA3.0-Igκ-hCT eukaryotic expression vector, which was transfected into NIH3T3 cells. The mRNA and protein expressions and secretion of hCT were detected. Primarily cultured osteoclasts were incubated with the supernatant of pCDNA3.0-Igk-hCT-transfected NIH3T3 cells, and their numbers were counted and morphology observed.
Results. The expression and secretion of hCT were successfully detected in pCDNA3.0-Igk-hCT-transfected NIH3T3 cells. The number of osteoclasts was decreased and the cells became crumpled when they were incubated with the supernatant of pCDNA3.0-Igk-hCT-transfected NIH3T3 cells.
Conclusion. A recombinant eukaryotic expression vector containing hCT gene was successfully constructed and expressed in NIH3T3 cells. The secreted recombinant hCT inhibited the growth and morphology of osteoclasts.
There is growing interest in the relation between the brain and music. The appealing similarity between brainwaves and the rhythms of music has motivated many scientists to seek a connection between them. A variety of transferring rules has been utilized to convert the brainwaves into music; and most of them are mainly based on spectra feature of EEG.
In this study, audibly recognizable scale-free music was deduced from individual Electroencephalogram (EEG) waveforms. The translation rules include the direct mapping from the period of an EEG waveform to the duration of a note, the logarithmic mapping of the change of average power of EEG to music intensity according to the Fechner's law, and a scale-free based mapping from the amplitude of EEG to music pitch according to the power law. To show the actual effect, we applied the deduced sonification rules to EEG segments recorded during rapid-eye movement sleep (REM) and slow-wave sleep (SWS). The resulting music is vivid and different between the two mental states; the melody during REM sleep sounds fast and lively, whereas that in SWS sleep is slow and tranquil. 60 volunteers evaluated 25 music pieces, 10 from REM, 10 from SWS and 5 from white noise (WN), 74.3% experienced a happy emotion from REM and felt boring and drowsy when listening to SWS, and the average accuracy for all the music pieces identification is 86.8%(κ = 0.800, P<0.001). We also applied the method to the EEG data from eyes closed, eyes open and epileptic EEG, and the results showed these mental states can be identified by listeners.
The sonification rules may identify the mental states of the brain, which provide a real-time strategy for monitoring brain activities and are potentially useful to neurofeedback therapy.
The Ensembl Trace Archive (http://trace.ensembl.org/) and the EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/), known together as the European Nucleotide Archive, continue to see growth in data volume and diversity. Selected major developments of 2007 are presented briefly, along with data submission and retrieval information. In the face of increasing requirements for nucleotide trace, sequence and annotation data archiving, data capture priority decisions have been taken at the European Nucleotide Archive. Priorities are discussed in terms of how reliably information can be captured, the long-term benefits of its capture and the ease with which it can be captured.
The EMBL Nucleotide Sequence Database () at the EMBL European Bioinformatics Institute, UK, offers a large and freely accessible collection of nucleotide sequences and accompanying annotation. The database is maintained in collaboration with DDBJ and GenBank. Data are exchanged between the collaborating databases on a daily basis to achieve optimal synchrony. Webin is the preferred tool for individual submissions of nucleotide sequences, including Third Party Annotation, alignments and bulk data. Automated procedures are provided for submissions from large-scale sequencing projects and data from the European Patent Office. In 2006, the volume of data has continued to grow exponentially. Access to the data is provided via SRS, ftp and variety of other methods. Extensive external and internal cross-references enable users to search for related information across other databases and within the database. All available resources can be accessed via the EBI home page at . Changes over the past year include changes to the file format, further development of the EMBLCDS dataset and developments to the XML format.
The EMBL Nucleotide Sequence Database () at the EMBL European Bioinformatics Institute, UK, offers a comprehensive set of publicly available nucleotide sequence and annotation, freely accessible to all. Maintained in collaboration with partners DDBJ and GenBank, coverage includes whole genome sequencing project data, directly submitted sequence, sequence recorded in support of patent applications and much more. The database continues to offer submission tools, data retrieval facilities and user support. In 2005, the volume of data offered has continued to grow exponentially. In addition to the newly presented data, the database encompasses a range of new data types generated by novel technologies, offers enhanced presentation and searchability of the data and has greater integration with other data resources offered at the EBI and elsewhere. In stride with these developing data types, the database has continued to develop submission and retrieval tools to maximise the information content of submitted data and to offer the simplest possible submission routes for data producers. New developments, the submission process, data retrieval and access to support are presented in this paper, along with links to sources of further information.
Confocal laser scanning microscopy was used to observe the spatio-temporal expression of the pathway-specific gene redD during S. coelicolor cell cultivation. The corresponding mutant S. coelicolor lyqRY1522 carrying redD::eyfp in the chromosome was constructed. The temporal expression results of the fusion protein during submerged cultivation demonstrated that expression of redD began in the transition phase, continuing through the exponential growth phase to the stationary phase, and reached maximum in the stationary phase. On the other hand, redD was expressed only in substrate mycelia during solid-state culture, while aerial mycelia remained essentially non-fluorescent throughout culture. Results demonstrated that the expression pattern of redD coincides with that of the biosynthesis of the antibiotics during culture, revealing a direct correlation between the spatio-temporal distribution of regulatory gene expression and second metabolism.
Streptomyces coelicolor; EYFP; Temporal and spatial expression; Pathway-specific gene redD
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences and annotation from available public sources. The database is part of an international collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged daily between the collaborating institutes to achieve swift synchrony. Webin is the preferred tool for individual submissions of nucleotide sequences, including Third Party Annotation (TPA) and alignments. Automated procedures are provided for submissions from large-scale sequencing projects and data from the European Patent Office. New and updated data records are distributed daily and the whole EMBL Nucleotide Sequence Database is released four times a year. Access to the sequence data is provided via ftp and several WWW interfaces. With the web-based Sequence Retrieval System (SRS) it is also possible to link nucleotide data to other specialist molecular biology databases maintained at the EBI. Other tools are available for sequence similarity searching (e.g. FASTA and BLAST). Changes over the past year include the removal of the sequence length limit, the launch of the EMBLCDSs dataset, extension of the Sequence Version Archive functionality and the revision of quality rules for TPA data.
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/), maintained at the European Bioinformatics Institute (EBI), incorporates, organizes and distributes nucleotide sequences from public sources. The database is a part of an international collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged between the collaborating databases on a daily basis to achieve optimal synchrony. The web-based tool, Webin, is the preferred system for individual submission of nucleotide sequences, including Third Party Annotation (TPA) and alignment data. Automatic submission procedures are used for submission of data from large-scale genome sequencing centres and from the European Patent Office. Database releases are produced quarterly. The latest data collection can be accessed via FTP, email and WWW interfaces. The EBI’s Sequence Retrieval System (SRS) integrates and links the main nucleotide and protein databases as well as many other specialist molecular biology databases. For sequence similarity searching, a variety of tools (e.g. FASTA and BLAST) are available that allow external users to compare their own sequences against the data in the EMBL Nucleotide Sequence Database, the complete genomic component subsection of the database, the WGS data sets and other databases. All available resources can be accessed via the EBI home page at http://www.ebi.ac.uk.