Alternatives to Carbon Dioxide in Two Phases for the Improvement of Broiler Chickens' Welfare during Stunning

This study evaluated the exposure to gas mixtures of carbon dioxide (CO2) associated with nitrogen (N2) as alternatives to CO2 in two phases to improve the welfare of broiler chickens at slaughter. Broilers were exposed to one of three treatments: 40C90C (1st phase: <40% CO2 for 2 min; 2nd phase: >90% CO2 and <2% O2 for 2 min, n = 92), 40C60N (40% CO2, 60% N2, and <2% O2 for 4 min, n = 79), or 20C80N (20% CO2, 80% N2, and <2% O2 for 4 min, n = 72). Brain activity (EEG) was assessed to determine the onset of loss of consciousness (LOC) and death. Behavioural assessment allowed for characterisation of an aversive response to the treatments and confirmed loss of posture (LOP) and motionlessness as behavioural proxies of LOC and brain death in 40C60N and 20N80C. However, the lack of quality of the EEG traces obtained in 40C90C did not allow us to determine the onset of LOC and brain death for this treatment. The onset of LOC in 40C60N was found at 19 s [14-30 s] and in 20C80N at 21 s [16-37 s], whereas a LOP was seen at 53 s [26-156 s] in 40C90C. Birds showed brain death in 40C60N at 64 s [43-108 s] and in 20C80N at 70 s [45-88 s]), while they became motionless in 40C90C at 177 s [89-212 s]. The 40C90C birds not only experienced more events of aversive behaviours related to mucosal irritation, dyspnoea, and breathlessness during induction to unconsciousness but were at risk of remaining conscious when the CO2 concentration was increased in the 2nd phase (known to cause severe pain). From an animal welfare point of view, 40C60N proved to be the least aversive of the three treatments tested, followed by 20C80N and 40C90C.

Time to Loss of Behavioral and Brainstem Responses of Ducks following Non-Stunned Slaughter

Simple Summary

For routine poultry slaughter, animals are stunned prior to the act of slaughter to prevent pain and distress. Halal slaughter requires either reversible or no stunning before performance of the neck cut. This study measured how long it takes for ducks to lose consciousness following non-stunned slaughter in a commercial processing plant. The study found that ducks take up to 383 s to lose consciousness. The performance of a cut higher on the neck resulted in a faster time to loss of consciousness. This study is the first investigation of the time to loss of consciousness following non-stunned slaughter of ducks in commercial conditions. These results could be used to improve the welfare of ducks during non-stunned slaughter, such as recommending a higher neck cut and ensuring appropriate waiting periods between slaughter and birds entering the scalding tanks.

Abstract

Non-stunned slaughter has been extensively described for other farmed species but there has been limited research on waterfowl. The study assessed 34 White Pekin ducks (Anas platyrhynchos) (study 1) in a non-stunned halal slaughterhouse in Brazil for time to loss of consciousness using various behavioral and brainstem indices (balance, cranial nerve reflexes, and muscle tension) and assessed the relationship between extent of clotting, location of neck cut, level of damage to neck vessels/tissues, and the time to onset of unconsciousness. In addition, operator practices were separately observed and neck pathology following the cut was examined in 217 carcasses after bleeding (study 2). In study 1 following the neck cut there was a wide variation between birds in the time to loss of behavioral and brainstem indices, ranging from 20 to 334 and 20 to 383 s for neck and beak tension, respectively. The median time to loss of balance following the neck cut was 166 ± 14 (22–355) seconds. There was a moderate correlation (R = 0.60 and 0.62) between distance of the neck cut and time to loss of balance and neck tension, respectively. This is the first investigation of the time to loss of consciousness following non-stunned slaughter of ducks in commercial conditions. The findings could be used to improve the welfare of ducks during non-stunned slaughter, such as recommending performance of the neck cut closer to the jaw line and ensuring appropriate waiting periods between slaughter and birds entering the scalding tanks.

On-farm culling methods used for pigs

The culling of injured and non-viable pigs (Sus scrofa) (neonate to breeding stock) is a routine and necessary procedure on most farms. Usually, pigs are culled using one of the following methods: blunt-force trauma (manual and mechanical), captive-bolt stunners, electrical stunning and electrocution or carbon dioxide. Manual blunt-force trauma is one of the most widely used methods due to its low or absent operational and investment costs. However, as a method, it has serious limitations, which include the risk of incomplete concussion, pain, and distress. Manual blunt-force trauma is also aesthetically unpleasant to operators and wider society. To address these issues there has been significant recent research into the development of alternatives to manual blunt-force trauma, these include: captive-bolt stunners, on-farm, gas-based controlled atmosphere systems, low atmospheric pressure systems and electrical stunning. Some of these are currently in commercial use while others are still in the developmental phase. This review brings together the relevant research in this field, evaluating the methods in terms of mechanism of action (mechanical and physiological), effectiveness and animal welfare.

The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification

Modern biology produces data at a staggering rate. Yet, much of these biological data is still isolated in the text, figures, tables and supplementary materials of articles. As a result, biological information created at great expense is significantly underutilised. The protein motif biology field does not have sufficient resources to curate the corpus of motif-related literature and, to date, only a fraction of the available articles have been curated. In this study, we develop a set of tools and a web resource, 'articles.ELM', to rapidly identify the motif literature articles pertinent to a researcher's interest. At the core of the resource is a manually curated set of about 8000 motif-related articles. These articles are automatically annotated with a range of relevant biological data allowing in-depth search functionality. Machine-learning article classification is used to group articles based on their similarity to manually curated motif classes in the Eukaryotic Linear Motif resource. Articles can also be manually classified within the resource. The 'articles.ELM' resource permits the rapid and accurate discovery of relevant motif articles thereby improving the visibility of motif literature and simplifying the recovery of valuable biological insights sequestered within scientific articles. Consequently, this web resource removes a critical bottleneck in scientific productivity for the motif biology field. Database URL: http://slim.icr.ac.uk/articles/.

Electroencephalographic assessment of pneumatically powered penetrating and non-penetrating captive-bolt stunning of bulls

The electroencephalographic (EEG) responses of 31 bulls (zebu crossbred cattle) stunned with either pneumatically powered Jarvis penetrating (PCB) or non-penetrating captive bolt (NPCB) was examined. Animals were organized into two treatment groups: PCB (n = 20); and NPCB (n = 11) stunning, both using airline pressures of 220 psi (1517 kPa). All bulls shot with PCB (n = 20/20) had patterns of EEG activity that were inconsistent with consciousness. Of the cattle shot with NPCB 82% (n = 9/11) showed waveforms suggesting complete unconsciousness. After stunning two NPCB bulls had periods of normal EEG activity and maintenance (Ptot, delta, theta, beta) or increased (alpha) spectral power compared to pre-treatment values, indicating incomplete concussion. The study showed that pneumatic PCB stunning was effective in rendering all bulls unconscious, while NPCB was less effective. This highlights the potential animal welfare risks associated with NPCB compared to PCB stunning of mature bulls in commercial abattoirs.

Evaluation of brain damage resulting from penetrating and non-penetrating stunning in Nelore Cattle using pneumatically powered captive bolt guns

Brain damage resulting from penetrating and non-penetrating stunning of Nelore cattle using pneumatically powered captive bolt guns was evaluated. Heads were shot using penetrating captive bolt gun with 160 psi (P1; n = 10), 175 psi (P2; n = 10), 190 psi (P3; n = 12), and non-penetrating operating with 220 psi (NP; n = 10). Skin and bone thickness, bolt penetration angle, bolt penetration depth, haemorrhage over the cerebral hemispheres and laceration were assessed. Only P1 had shots that failed to perforate the skull (n = 2; 20%). Bolt penetration depth and haemorrhage over the right cerebral hemisphere was significantly (P ≤ 0.05) greater for P3. Subarachnoid haemorrhage over the frontal, parietal and occipital lobes was higher for NP. Lacerations were observed only for penetrating gun in the cortical region of frontal and parietal lobes. Subarachnoid haemorrhage surrounding the brainstem and laceration in the midbrain and pons was only found for P3. Thus, penetrating captive bolt gun operating with 190 psi is more effective to achieve unconsciousness.

Electroencephalographic assessment of concussive non-penetrative captive bolt stunning of turkeys

1. The aim of this study was to evaluate the electroencephalographic (EEG) and behavioural responses of turkeys stunned with three different concussive non-penetrative captive-bolt guns prior to slaughter. 2. A total of 31 slaughter weight ex-breeding female turkeys (29 weeks of age; mean body weight 13.32 ± SD 0.65 kg) were stunned with the Cash Poultry Killer (CPK) (n = 10), Turkey Euthanasia Device (TED) (n = 10) and Zephyr EXL (n = 11). 3. Mean peak kinetic energy was highest for the CPK compared to the TED and Zephyr EXL (75.9 ± 4.5, 28.4 ± 0.4 and 24.4 ± 0.7 J, respectively). 4. A total of 29 (94%) of the turkeys were rendered unconscious following captive bolt stunning, with total power of the EEG (Ptot) significantly reduced from baseline values (reductions of 67% CPK, 84% TED and 76% Zephyr EXL, p < 0.01) and waveforms becoming isoelectric after periods of transitional EEG. However, two birds shot with the CPK and Zephyr EXL had periods of behavioural/reflexes (rhythmic respiration, nictitating membrane reflex, neck tension) and EEG activity (43-47 and 36-60 + s after the shot, respectively) indicating incomplete concussion and return of consciousness. In one bird, the shot was incorrectly positioned (Zephyr EXL), while the other appeared to be related to a defective cartridge (CPK). 5. In conclusion, all three captive bolt gun models were effective in producing unconsciousness in turkeys, provided they were positioned correctly and power loads performed according to their specifications.

Efficiency of low versus high airline pressure in stunning cattle with a pneumatically powered penetrating captive bolt gun

The efficiency of stunning cattle was assessed in 443 animals (304 pure Zebu and 139 crossbred cattle), being mainly mature bulls and cows. Cattle were stunned using a Jarvis pneumatically powered penetrating captive bolt gun operating with low (160-175psi, N=82) and high (190psi, N=363) airline pressure, which was within the manufactures specifications. Signs of brain function and the position of the shots on the heads were recorded after stunning. Velocity of the captive bolt and its physical parameters were calculated. Cattle shot with low pressures showed more rhythmic respiration (27 vs. 8%, P<0.001), less tongue protrusion (4 vs. 12%, P=0.03) and less masseter relaxation (22 vs. 48%, P<0.001). There was an increased frequency of shots in the ideal position when cattle were shot with the low compared to high airline pressures (15.3 vs. 3.1%). Bolt velocity and its physical parameters were significantly (P<0.01) higher when using high pressure. Airline pressures below 190psi are inappropriate when shooting adult Zebu beef cattle with pneumatically powered penetrating captive bolt guns.

Assessment of the effectiveness of head only and back-of-the-head electrical stunning of chickens

The study assesses the effectiveness of reversible head-only and back-of-the-head electrical stunning of chickens using 130–950 mA per bird at 50 Hz AC.

Three trials were conducted to compare both stunning systems: (a) behavioural assessment of return of consciousness, (b) insensibility to thermal pain, and (c) assessment of return of brain activity with visually evoked potentials (VEPs).

Assessment of behaviour suggested that the period of unconsciousness following head-only electrical stunning was shorter in hens compared to broilers.

Stunning across the back-of-the-head delayed the time to return of brainstem function compared to stunning with standard head-only electrodes. Additionally, back-of-the-head stunning produced a more prolonged period of electroanalgesia compared to head-only.

Based on examination of return of brain function with VEPs in hens, back-of-the-head stunning produced a shorter-lasting stun than standard head-only. However, even for standard head-only, the stun was notably shorter than previously reported. In some birds, brain function had returned within 9 s after the end of stunning.

The results suggest that some birds may recover consciousness prior to or during the neck cut. Based on these findings, back-of-the-head stunning and standard head-only stunning of hens should not be recommended without further development.

The identification of short linear motif-mediated interfaces within the human interactome

MOTIVATION

Eukaryotic proteins are highly modular, containing multiple interaction interfaces that mediate binding to a network of regulators and effectors. Recent advances in high-throughput proteomics have rapidly expanded the number of known protein-protein interactions (PPIs); however, the molecular basis for the majority of these interactions remains to be elucidated. There has been a growing appreciation of the importance of a subset of these PPIs, namely those mediated by short linear motifs (SLiMs), particularly the canonical and ubiquitous SH2, SH3 and PDZ domain-binding motifs. However, these motif classes represent only a small fraction of known SLiMs and outside these examples little effort has been made, either bioinformatically or experimentally, to discover the full complement of motif instances.

RESULTS

In this article, interaction data are analysed to identify and characterize an important subset of PPIs, those involving SLiMs binding to globular domains. To do this, we introduce iELM, a method to identify interactions mediated by SLiMs and add molecular details of the interaction interfaces to both interacting proteins. The method identifies SLiM-mediated interfaces from PPI data by searching for known SLiM-domain pairs. This approach was applied to the human interactome to identify a set of high-confidence putative SLiM-mediated PPIs.

AVAILABILITY

iELM is freely available at http://elmint.embl.de

CONTACT

toby.gibson@embl.de

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Electroencephalographic responses to concussive non-penetrative captive-bolt stunning in halothane - anaesthetised calves

AIM

To investigate the electroencephalographic (EEG) and cardiovascular responses of halothane-anaesthetised calves to non-penetrative captive-bolt stunning.

METHODS

Ten calves were minimally anaesthetised with halothane, using an established anaesthesia protocol. The EEG, blood pressure and electrocardiogram (ECG) were recorded before and after non-penetrative captive-bolt stunning. Visual inspection and alterations in the total power of the EEG (Ptot) were used to investigate the effects of stunning.

RESULTS

Captive-bolt stunning significantly altered cerebrocortical function in all animals. In four animals, Ptot decreased immediately following stunning and remained low throughout the recording period. In another five animals, Ptot responded to stunning in a biphasic manner characterised by an immediate decrease followed by a transient increase and then a final decrease to values similar to those of the non-biphasic animals.

CONCLUSIONS

Non-penetrative captive-bolt stunning significantly altered cerebrocortical function in halothane-anaesthetised calves. The changes in cerebrocortical function would be sufficient to produce insensibility within 0 to 14 seconds in conscious animals.

Amelioration of electroencephalographic responses to slaughter by non-penetrative captive-bolt stunning after ventral-neck incision in halothane - anaesthetised calves

AIM

To investigate the ability of non-penetrative captive-bolt stunning delivered after ventral-neck incision to ameliorate responses to noxious stimulation associated with slaughter by ventral-neck incision in halothane-anaesthetised calves.

METHODS

Seven calves were minimally anaesthetised with halothane, using an established anaesthesia protocol. Electroencephalographic (EEG) indices of cerebrocortical activity were measured in response to ventral-neck incision followed 5 seconds later by non-penetrative captive-bolt stunning. Changes in heart rate and arterial blood pressure were measured and instances of occlusion of the carotid arteries were also noted.

RESULTS

After ventral-neck incision there were periods of an active EEG in some calves, which ceased after non-penetrative captive-bolt stunning in most of the animals. Two calves had periods of active EEG following stunning. Arterial blood pressure decreased significantly after neck incision in all calves, including three with occlusion of the carotid arteries.

CONCLUSIONS

Non-penetrative captive-bolt stunning after ventral-neck incision resulted in the cessation of functional cortical activity in the majority of calves. This procedure prevented the development of cerebrocortical responses to ventral-neck incision, demonstrated elsewhere, which would be painful in conscious animals subjected to this procedure. In addition, instances of carotid arterial occlusion had no significant effect on the decrease in arterial blood pressure.

A re-evaluation of the need to stun calves prior to slaughter by ventral-neck incision : an introductory review

Commercial slaughter of farm livestock usually employs an extensive incision that severs the soft tissues of the neck including the major blood vessels supplying and draining the brain. It is intended to cause a catastrophic decrease in cerebral blood flow with rapid onset of unconsciousness or insensibility. The tissues of the neck are innervated with nociceptive nerve fibres and their transection will cause a barrage of sensory impulses. Consciousness, and therefore the ability of the animal to feel pain and experience distress after the incision, may persist for 60 seconds or longer in cattle. These observations suggest that livestock may experience pain and distress during the period before they become unconscious (insensible). Psychological shock and fear may also be associated with the extensive tissue damage and blood loss. Pre-incision stunning has been adopted as a precautionary measure to prevent suffering. However, the question remains: How intense and noxious are these experiences? Recent methodological developments related to quantitative analysis of the electroencephalogram (EEG) allow the experience of pain to be assessed more directly than has hitherto been possible. This methodology has now been applied to the question of the slaughter of calves by ventral-neck incision. The new information demonstrates clearly for the first time that the act of slaughter by ventral-neck incision is associated with noxious stimulation that would be expected to be perceived as painful in the period between the incision and loss of consciousness. These data provide further support for the value of stunning in preventing pain and distress in animals subjected to this procedure.

Clustal W and Clustal X version 2.0

SUMMARY

The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.

AVAILABILITY

The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/

Clustal W and Clustal X version 2.0

SUMMARY

The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.

AVAILABILITY

The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/

Validation of the acute electroencephalographic responses of calves to noxious stimulus with scoop dehorning

AIM

To validate use of the electroencephalogram (EEG) and a minimal anaesthesia model for assessment of noxious sensory input caused by scoop dehorning of calves.

METHODS

Twenty Friesian heifers weighing 125-178 kg were maintained under light general anaesthesia using halothane and an established protocol (minimal anaesthesia model). They were then dehorned using a scoop dehorner either with (DH+LA) or without (DH) a lignocaine ring block, and changes in the EEG and electrocardiogram (ECG) recorded. Median frequency (F50), 95% spectral edge frequency (F95) and total power (Ptot) were derived from the EEG data.

RESULTS

There were significant increases in the F50 (p<0.01) and F95 (p<0.01), and a decrease in Ptot (p<0.01) following dehorning in the DH group, but there were no changes in the DH+LA group. Transient bradycardia in the first 75 sec following dehorning was recorded in the DH group compared with both pre-treatment values in the same group and with the DH+LA group (p<0.001). Tachycardia was evident by 15 min after dehorning in the DH but not the DH+LA group.

CONCLUSIONS

The results validate use of the EEG and a minimal anaesthesia model for assessment of noxious sensory inputs in cattle.

Factors influencing occupant-to-seat belt interaction in far-side crashes

Seat belt interaction with a far-side occupant's shoulder and thorax is critical to governing excursion towards the struck-side of the vehicle in side impact. In this study, occupant-to-belt interaction was simulated using a modified MADYMO human model and finite element belts. Quasi-static tests with volunteers and dynamic sled tests with PMHS and WorldSID were used for model validation and comparison. Parameter studies were then undertaken to quantify the effect of impact direction, seat belt geometry and pretension on occupant-to-seat belt interaction. Results suggest that lowering the D-ring and increasing pretension reduces the likelihood of the belt slipping off the shoulder. Anthropometry was also shown to influence restraint provided by the shoulder belt. Furthermore, the belt may slip off the occupant's shoulder at impact angles greater than 40 degrees from frontal when no pretension is used. However, the addition of pretension allowed the shoulder to engage the belt in all impacts from 30 to 90 degrees.

RuNAway Disease: A two cycle model for transmissible spongiform encephalopathies (TSEs) wherein SINE proliferation drives PrP overproduction

BACKGROUND

Despite decades of research, the agent responsible for transmitting spongiform encephalopathies (TSEs) has not been identified. The Prion hypothesis, which dominates the field, supposes that modified host PrP protein, termed PrPSc, acts as the transmissible agent. This model fits the observation that TSE diseases elicit almost no immune reaction. Prion transmission has not been verified, however, as it has not been possible to produce pure PrPSc aggregates. One long-standing objection to the Prion model is the observation that TSE disease agents show classical genetic behaviours, such as reproducible strain variation, while also responding to selection for novel traits such as adaptation to new hosts. Moreover, evidence has been steadily accumulating that infectious titre is decoupled from the quantity (or even the presence) of PrPSc deposits. Rather awkwardly for the Prion hypothesis, PrP0/0 knockout mice have been found to incubate and transmit TSE agents (despite themselves being refractory to TSE disease).

HYPOTHESIS

In this article, a new scheme, RuNAway, is proposed whereby uncontrolled proliferation of a type of parasitic gene, the small dispersed repeat sequences (SINEs), in somatic cells induces overproduction of PrP with pathogenic consequences. The RuNAway scheme involves twin tandem positive feedback loops: triggering the second loop leads to the pathogenic disease. This model is consistent with the long latency period and much shorter visible disease progression typical of TSEs.

The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly

Much has been learned about the cellular pathology of Friedreich's ataxia, a recessive neurodegenerative disease resulting from insufficient expression of the mitochondrial protein frataxin. However, the biochemical function of frataxin has remained obscure, hampering attempts at therapeutic intervention. To predict functional interactions of frataxin with other proteins we investigated whether its gene specifically co-occurs with any other genes in sequenced genomes. In 56 available genomes we identified two genes with identical phylogenetic distributions to the frataxin/cyaY gene: hscA and hscB/JAC1. These genes have not only emerged in the same evolutionary lineage as the frataxin gene, they have also been lost at least twice with it, and they have been horizontally transferred with it in the evolution of the mitochondria. The proteins encoded by hscA and hscB, the chaperone HSP66 and the co-chaperone HSP20, have been shown to be required for the synthesis of 2Fe-2S clusters on ferredoxin in proteobacteria. JAC1, an ortholog of hscB, and SSQ1, a paralog of hscA, have been shown to be required for iron-sulfur cluster assembly in mitochondria of Saccharomyces cerevisiae. Combining data on the co-occurrence of genes in genomes with experimental and predicted cellular localization data of their proteins supports the hypothesis that frataxin is directly involved in iron-sulfur cluster protein assembly. They indicate that frataxin is specifically involved in the same sub-process as HSP20/Jac1p.

The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation

The SAND domain is a conserved sequence motif found in a number of nuclear proteins, including the Sp100 family and NUDR. These are thought to play important roles in chromatin-dependent transcriptional regulation and are linked to many diseases. We have determined the three-dimensional (3D) structure of the SAND domain from Sp100b. The structure represents a novel alpha/beta fold, in which a conserved KDWK sequence motif is found within an alpha-helical, positively charged surface patch. For NUDR, the SAND domain is shown to be sufficient to mediate DNA binding. Using mutational analyses and chemical shift perturbation experiments, the DNA binding surface is mapped to the alpha-helical region encompassing the KDWK motif. The DNA binding activity of wild type and mutant proteins in vitro correlates with transcriptional regulation activity of full length NUDR in vivo. The evolutionarily conserved SAND domain defines a new DNA binding fold that is involved in chromatin-associated transcriptional regulation.

Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries

Expressed sequence tags (ESTs) are randomly sequenced cDNA clones. Currently, nearly 3 million human and 2 million mouse ESTs provide valuable resources that enable researchers to investigate the products of gene expression. The EST databases have proven to be useful tools for detecting homologous genes, for exon mapping, revealing differential splicing, etc. With the increasing availability of large amounts of poorly characterised eukaryotic (notably human) genomic sequence, ESTs have now become a vital tool for gene identification, sometimes yielding the only unambiguous evidence for the existence of a gene expression product. However, BLAST-based Web servers available to the general user have not kept pace with these developments and do not provide appropriate tools for querying EST databases with large highly spliced genes, often spanning 50 000-100 000 bases or more. Here we describe Gene2EST (http://woody.embl-heidelberg.de/gene2est/), a server that brings together a set of tools enabling efficient retrieval of ESTs matching large DNA queries and their subsequent analysis. RepeatMasker is used to mask dispersed repetitive sequences (such as Alu elements) in the query, BLAST2 for searching EST databases and Artemis for graphical display of the findings. Gene2EST combines these components into a Web resource targeted at the researcher who wishes to study one or a few genes to a high level of detail.

An estimate of large-scale sequencing accuracy

The accuracy of large-scale DNA sequencing is difficult to estimate without redundant effort. We have found that the mobile genetic element IS10, a component of the transposon Tn10, has contaminated a significant number of clones in the public databases, as a result of the use of the transposon in bacterial cloning strain construction. These contaminations need to be annotated as such. More positively, by defining the range of sequence variation in IS10, we have been able to determine that the rate of sequencing errors is very low, most likely surpassing the stated aim of one error or less in ten thousand bases.

Object-oriented parsing of biological databases with Python

MOTIVATION

While database activities in the biological area are increasing rapidly, rather little is done in the area of parsing them in a simple and object-oriented way.

RESULTS

We present here an elegant, simple yet powerful way of parsing biological flat-file databases. We have taken EMBL, SWISSPROT and GENBANK as examples. EMBL and SWISS-PROT do not differ much in the format structure. GENBANK has a very different format structure than EMBL and SWISS-PROT. Extracting the desired fields in an entry (for example a sub-sequence with an associated feature) for later analysis is a constant need in the biological sequence-analysis community: this is illustrated with tools to make new splice-site databases. The interface to the parser is abstract in the sense that the access to all the databases is independent from their different formats, since parsing instructions are hidden.

Homology-based method for identification of protein repeats using statistical significance estimates

Short protein repeats, frequently with a length between 20 and 40 residues, represent a significant fraction of known proteins. Many repeats appear to possess high amino acid substitution rates and thus recognition of repeat homologues is highly problematic. Even if the presence of a certain repeat family is known, the exact locations and the number of repetitive units often cannot be determined using current methods. We have devised an iterative algorithm based on optimal and sub-optimal score distributions from profile analysis that estimates the significance of all repeats that are detected in a single sequence. This procedure allows the identification of homologues at alignment scores lower than the highest optimal alignment score for non-homologous sequences. The method has been used to investigate the occurrence of eleven families of repeats in Saccharomyces cerevisiae, Caenorhabditis elegans and Homo sapiens accounting for 1055, 2205 and 2320 repeats, respectively. For these examples, the method is both more sensitive and more selective than conventional homology search procedures. The method allowed the detection in the SwissProt database of more than 2000 previously unrecognised repeats belonging to the 11 families. In addition, the method was used to merge several repeat families that previously were supposed to be distinct, indicating common phylogenetic origins for these families.

Evidence in favour of ancient octaploidy in the vertebrate genome

Vertebrate genomes are larger than invertebrates and show evidence of extensive gene duplication, including many collinear chromosomal segments. On the basis of this intra-genomic synteny, it has been proposed that two rounds of whole genome duplication (octaploidy) occurred early in the vertebrate lineage. Recently, this early vertebrate octaploidy has been challenged on the basis of gene trees. We report new linkage groups encompassing the matrilin (MATN), syndecan (SDC), Eyes Absent (EYA), HCK kinase and SRC kinase paralogous gene quartets. In contrast to other studies, the sequence trees are weakly supportive of ancient octaploidy. It is concluded that there is no strong evidence against the octaploidy, provided that consecutive genome duplication was rapid.

Examination of cyanine intercalation dyes for rapid and sensitive detection of DNA fragments by capillary electrophoresis

Recently, a series of cyanine dyes has been developed that are reported to offer superior fluorescence upon intercalation relative to ethidium bromide (EB). The dimeric cyanine dyes, such as POPO-3 (Molecular Probes, Eugene, OR, U.S.A.), are reported to offer the highest fluorescence enhancement of the cyanine dyes. Although POPO-3 does offer an improvement in sensitivity, achieving reproducible, high-efficiency results by employing pre-column, on-column, and postcolumn labeling strategies proved to be problematic. Evaluation of the labeling rate of these dimeric dyes indicates that perhaps the most limiting factor to using this dye for rapid CE analysis of DNA fragments is the apparent slow rate at which the dye fully intercalates into the DNA structure. Use of the monomeric analog PO-PRO-3 (Molecular Probes) resulted in much better separations and low limits of defection when employed for on-column intercalation. However, we find that the kinetics are too slow to employ this dye in a sheath flow cell for postcolumn derivatization.

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.

Examination of band dispersion during size-selective capillary electrophoresis separations of DNA fragments

Versatile capillary electrophoresis instrumentation that permits the rapid and precise translation of a laser fluorometric detection zone along the capillary wall has been used to examine the factors which cause band broadening during size-selective separations of DNA fragments. Separations are performed using capillaries containing entangled polymer solutions. The scanning capabilities of this instrumentation facilitates the determination of diffusion coefficients under static conditions without the need to discontinue and reapply an electric field. The ability to rapidly translate the detection zone along the column allows the monitoring of the separation at various points along the capillary which enables the examination of the sources of band dispersion under kinetic conditions. Results from experiments utilizing various concentrations of both high and low molecular mass methyl cellulose polymers as sieving media are presented. It is shown that axial diffusion, even when adjusted for kinetic conditions using the Einstein relationship, does not account for the total observed band variance. Possible explanations for this behavior are presented.

Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction

Friedreich's ataxia is the most common inherited spinocerebellar ataxia. A decade of linkage and physical mapping studies have culminated in the identification of the Friedreich's ataxia gene. The presence of homologues in purple bacterial genomes, but not in other bacteria, allows us to infer a mitochondrial location for frataxin (Friedreich's ataxia protein) on the basis of bacterial phylogeny. Frataxin possesses a non-globular N-terminus domain providing a candidate mitochondrial targeting peptide. Clues to the function of frataxin are provided by the mitochondrial location, a clinically similar ataxia with vitamin E deficiency, and certain neuropathies with mitochondrial DNA instability caused by mutations in nuclear genes.

PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames

DNA translation frames can be disrupted for several reasons, including: (i) errors in sequence determination; (ii) RNA processing, such as intron removal and guide RNA editing; (iii) less commonly, polymerase frameshifting during transcription or ribosomal frameshifting during translation. Frameshifts frequently confound computational activities involving homologous sequences, such as database searches and inferences on structure, function or phylogeny made from multiple alignments. A dynamic alignment algorithm is reported here which compares a protein profile (a residue scoring matrix for one or more aligned sequences) against the three translation frames of a DNA strand, allowing frameshifting. The algorithm has been incorporated into a new package, WiseTools, for comparison of biological sequences. A protein profile can be compared against either a DNA sequence or a protein sequence. The program PairWise may be used interactively for alignment of any two sequence inputs. SearchWise can perform combinations of searches through DNA or protein databases by a protein profile or DNA sequence. Routine application of the programs has revealed a set of database entries with frameshifts caused by errors in sequence determination.

Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome

The KH module is a sequence motif found in a number of proteins that are known to be in close association with RNA. Experimental evidence suggests a direct involvement of KH in RNA binding. The human FMR1 protein, which has two KH domains, is associated with fragile X syndrome, the most common inherited cause of mental retardation. Here we present the three-dimensional solution structure of the KH module. The domain consists of a stable beta alpha alpha beta beta alpha fold. On the basis of our results, we suggest a potential surface for RNA binding centered on the loop between the first two helices. Substitution of a well-conserved hydrophobic residue located on the second helix destroys the KH fold; a mutation of this position in FMR1 leads to an aggravated fragile X phenotype.

Using CLUSTAL for multiple sequence alignments

We have tested CLUSTAL W in a wide variety of situations, and it is capable of handling some very difficult protein alignment problems. If the data set consists of enough closely related sequences so that the first alignments are accurate, then CLUSTAL W will usually find an alignment that is very close to ideal. Problems can still occur if the data set includes sequences of greatly different lengths or if some sequences include long regions that are impossible to align with the rest of the data set. Trying to balance the need for long insertions and deletions in some alignments with the need to avoid them in others is still a problem. The default values for our parameters were tested empirically using test cases of sets of globular proteins where some information as to the correct alignment was available. The parameter values may not be very appropriate with nonglobular proteins. We have argued that using one weight matrix and two gap penalties is too simplistic to be of general use in the most difficult cases. We have replaced these parameters with a large number of new parameters designed primarily to help encourage gaps in loop regions. Although these new parameters are largely heuristic in nature, they perform surprisingly well and are simple to implement. The underlying speed of the progressive alignment approach is not adversely affected. The disadvantage is that the parameter space is now huge; the number of possible combinations of parameters is more than can easily be examined by hand. We justify this by asking the user to treat CLUSTAL W as a data exploration tool rather than as a definitive analysis method. It is not sensible to automatically derive multiple alignments and to trust particular algorithms as being capable of always getting the correct answer. One must examine the alignments closely, especially in conjunction with the underlying phylogenetic tree (or estimate of it) and try varying some of the parameters. Outliers (sequences that have no close relatives) should be aligned carefully, as should fragments of sequences. The program will automatically delay the alignment of any sequences that are less than 40% identical to any others until all other sequences are aligned, but this can be set from a menu by the user. It may be useful to build up an alignment of closely related sequences first and to then add in the more distant relatives one at a time or in batches, using the profile alignments and weighting scheme described earlier and perhaps using a variety of parameter settings. We give one example using SH2 domains. SH2 domains are widespread in eukaryotic signalling proteins where they function in the recognition of phosphotyrosine-containing peptides. In the chapter by Bork and Gibson ([11], this volume), Blast and pattern/profile searches were used to extract the set of known SH2 domains and to search for new members. (Profiles used in database searches are conceptually very similar to the profiles used in CLUSTAL W: see the chapters [11] and [13] for profile search methods.) The profile searches detected SH2 domains in the JAK family of protein tyrosine kinases, which were thought not to contain SH2 domains. Although the JAK family SH2 domains are rather divergent, they have the necessary core structural residues as well as the critical positively charged residue that binds phosphotyrosine, leaving no doubt that they are bona fide SH2 domains. The five new JAK family SH2 domains were added sequentially to the existing alignment of 65 SH2 domains using the CLUSTAL W profile alignment option. Figure 6 shows part of the resulting alignment. Despite their divergent sequences, the new SH2 domains have been aligned nearly perfectly with the old set. No insertions were placed in the original SH2 domains. In this example, the profile alignment procedure has produced better results than a one-step full alignment of all 70 SH2 domains, and in considerably less time. (ABSTRACT TRUNCATED)

Dystrophin and utrophin: the missing links!

There is considerable sequence homology between dystrophin and utrophin, both at the protein and DNA level, and consequently it was assumed that their domain structures and functions would be similar. As more of the detailed biochemical and cell biological properties of these two proteins become known, so it becomes clear that there are subtle if not significant differences between them. We review recent findings and present new hypotheses into the structural and functional properties of the actin-binding domain, central coiled-coil region and regulatory/membrane protein-binding regions of dystrophin and utrophin.