Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana

The plant Arabidopsis thaliana (Arabidopsis) has become an important model species for the study of many aspects of plant biology. The relatively small size of the nuclear genome and the availability of extensive physical maps of the five chromosomes provide a feasible basis for initiating sequencing of the five chromosomes. The YAC (yeast artificial chromosome)-based physical map of chromosome 4 was used to construct a sequence-ready map of cosmid and BAC (bacterial artificial chromosome) clones covering a 1.9-megabase (Mb) contiguous region, and the sequence of this region is reported here. Analysis of the sequence revealed an average gene density of one gene every 4.8 kilobases (kb), and 54% of the predicted genes had significant similarity to known genes. Other interesting features were found, such as the sequence of a disease-resistance gene locus, the distribution of retroelements, the frequent occurrence of clustered gene families, and the sequence of several classes of genes not previously encountered in plants.

Homeosis and intestinal tumours in Cdx2 mutant mice

In Drosophila, disturbing the expression of the homeobox gene caudal causes a severe disruption in body segmentation and global body patterning. There are three mouse homologues of Drosophila caudal: Cdx1 (ref. 2), Cdx2 (ref. 3) and Cdx4 (ref. 4). We have generated a null mutation of murine Cdx2 by homologous recombination. Cdx2 homozygote null mutants die between 3.5 and 5.5 days post coitum (d.p.c.). Cdx2 heterozygote mutants exhibit a variable phenotype, with many showing tail abnormalities or stunted growth. Skeletal analysis demonstrates a homeotic shift of vertebrae and compatible malformations of the ribs. Within the first three months of life, 90% of Cdx2 heterozygotes develop multiple intestinal adenomatous polyps, particularly in the proximal colon. These polyps occasionally contain areas of true metaplasia. In contrast to the surrounding intestinal epithelium, the neoplastic cells do not express Cdx2 from the remaining allele. These results suggest that Cdx2 mutation is the primary event in the genesis of some intestinal tumours.

Expression of Cdx-2 in the mouse embryo and placenta: possible role in patterning of the extra-embryonic membranes

Three mouse homologues of the Drosophila homeotic gene Caudal (Cad) have been described. They are currently designated Cdx-1, Cdx-2, and Cdx-4. Cdx-1 and 2 are both strongly expressed in the adult mid- and hindgut, while Cdx-1 and 4 have been shown to be activated in the embryonic primitive streak. Using a polyclonal antibody against a fusion protein containing the amino terminal 109 amino acids of murine Cdx-2, we here describe the topographical location of the gene product from early cleavage to 12.5 days of embryonic development. Cdx-2 expression begins at 3.5 days and is confined to the trophectoderm, being absent from the inner cell mass. Subsequently, staining is located in the extra-embryonic ectoderm adjacent to the epiblast, but sparing the more superficially placed polar, as well as the mural trophoblastic cells. Continuing expression in the fetal membranes involves the chorion, the allantoic bud, and, at even later stages, the spongiotrophoblast. From 8.5 days, Cdx-2 begins to be expressed in embryonic tissues, principally (unlike Cdx-1) in the posterior part of the gut from its earliest formation, as well as in the tail bud and in the caudal part of the neural tube. Cdx-2 is, therefore, transcribed well before any other membrane of the Cad homologue group and of the related Hox-C group; its expression in the extra-embryonic membranes and in the hindgut reflects the phylogenetic relationship between the cloaca and the chorio-allantois and suggests the possibility that homeobox genes may be involved in placental development and/or patterning.

Chemoradiation for the treatment of epidermoid anal cancer: 13-year follow-up of the first randomised UKCCCR Anal Cancer Trial (ACT I)

Background:

The first UKCCCR Anal Cancer Trial (1996) demonstrated the benefit of chemoradiation over radiotherapy (RT) alone for treating epidermoid anal cancer, and it became the standard treatment. Patients in this trial have now been followed up for a median of 13 years.

Methods:

A total of 577 patients were randomised to receive RT alone or combined modality therapy using 5-fluorouracil and mitomycin C. All patients were scheduled to receive 45 Gy by external beam irradiation. Patients who responded to treatment were recommended to have boost RT, with either an iridium implant or external beam irradiation. Data on relapse and deaths were obtained until October 2007.

Results:

Twelve years after treatment, for every 100 patients treated with chemoradiation, there are an expected 25.3 fewer patients with locoregional relapse (95% confidence interval (CI): 17.5–32.0 fewer) and 12.5 fewer anal cancer deaths (95% CI: 4.3–19.7 fewer), compared with 100 patients given RT alone. There was a 9.1% increase in non-anal cancer deaths in the first 5 years of chemoradiation (95% CI +3.6 to +14.6), which disappeared by 10 years.

Conclusions:

The clear benefit of chemoradiation outweighs an early excess risk of non-anal cancer deaths, and can still be seen 12 years after treatment. Only 11 patients suffered a locoregional relapse as a first event after 5 years, which may influence the choice of end points in future studies.

Prevalence of malnutrition on admission to four hospitals in England. The Malnutrition Prevalence Group

AIMS

The primary objective was to estimate prevalence of malnutrition on admission to four hospitals. Secondary objectives included assessing the relationship between nutritional status and length of hospital stay, numbers of new prescriptions, new infections and disease severity.

METHODS

We entered eligible patients according to predefined quotas for elective and emergency admissions to 23 specialties. We measured height, weight, Body Mass Index and anthropometrics, and recorded history of unintentional weight loss. Patients who had lost > or = 10% of their body weight, had a Body Mass Index <20, or had a Body Mass Index <20 with one anthropometric measurement <15th centile were considered malnourished.

RESULTS

Of 1611 eligible patients, 761 did not participate; 269 were too ill; 256 could not be weighed; and 236 refused consent. Eight hundred and fifty were subsequently evaluated. Prevalence of malnutrition on admission was 20%. Length of stay, new prescriptions and infections and disease severity were significantly higher in the malnourished.

CONCLUSIONS

One patient in every five admitted to hospital is malnourished. Although this figure is unacceptably high, it may underestimate true prevalence. Malnutrition was associated with increased length of stay, new prescriptions and infections. Malnutrition may also have contributed to disease severity.

Social network theory in the behavioural sciences: potential applications

Social network theory has made major contributions to our understanding of human social organisation but has found relatively little application in the field of animal behaviour. In this review, we identify several broad research areas where the networks approach could greatly enhance our understanding of social patterns and processes in animals. The network theory provides a quantitative framework that can be used to characterise social structure both at the level of the individual and the population. These novel quantitative variables may provide a new tool in addressing key questions in behavioural ecology particularly in relation to the evolution of social organisation and the impact of social structure on evolutionary processes. For example, network measures could be used to compare social networks of different species or populations making full use of the comparative approach. However, the networks approach can in principle go beyond identifying structural patterns and also can help with the understanding of processes within animal populations such as disease transmission and information transfer. Finally, understanding the pattern of interactions in the network (i.e. who is connected to whom) can also shed some light on the evolution of behavioural strategies.

Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9

The kinetics and thermodynamics of the folding of the homologous four-helix proteins Im7 and Im9 have been characterised at pH 7.0 and 10 degrees C. These proteins are 60 % identical in sequence and have the same three-dimensional structure, yet appear to fold by different kinetic mechanisms. The logarithm of the folding and unfolding rates of Im9 change linearly as a function of urea concentration and fit well to an equation describing a two-state mechanism (with a folding rate of 1500 s-1, an unfolding rate of 0. 01 s-1, and a highly compact transition state that has approximately 95 % of the native surface area buried). By contrast, there is clear evidence for the population of an intermediate during the refolding of Im7, as indicated by a change in the urea dependence of the folding rate and the presence of a significant burst phase amplitude in the refolding kinetics. Under stabilising conditions (0.25 M Na2SO4, pH 7.0 and 10 degrees C) the folding of Im9 remains two-state, whilst under similar conditions (0.4 M Na2SO4, pH 7.0 and 10 degrees C) the intermediate populated during Im7 refolding is significantly stabilised (KUI=125). Equilibrium denaturation experiments, under the conditions used in the kinetic measurements, show that Im7 is significantly less stable than Im9 (DeltaDeltaG 9.3 kJ/mol) and the DeltaG and m values determined accord with those obtained from the fit to the kinetic data. The results show, therefore, that the population of an intermediate in the refolding of the immunity protein structure is defined by the precise amino acid sequence rather than the global stability of the protein. We discuss the possibility that the intermediate of Im7 is populated due to differences in helix propensity in Im7 and Im9 and the relevance of these data to the folding of helical proteins in general.

Food intolerance and the irritable bowel syndrome

Two hundred patients (156 women) with the irritable bowel syndrome were treated with dietary exclusion for three weeks. Of the 189 who completed this study, 91 (48.2%) showed symptomatic improvement. Subsequent challenge with individual foods showed that 73 of these 91 responders were able to identify one or more food intolerances and 72 remained well on a modified diet during the follow up period (mean (SD), 14.7 (7.98) months). Of the 98 patients who showed no symptomatic improvement after three weeks of strict exclusion only three were symptomatically well at follow up (mean (SD), 12.48 (8.09 months). There was no close correlation between response and symptom complex. There was a wide range of food intolerance. The majority (50%) identified two to five foods which upset them (range 1-14). The foods most commonly incriminated were dairy products (40.7%) and grains (39.4%).

Assortative interactions and social networks in fish

The mechanisms underpinning the structure of social networks in multiple fish populations were investigated. To our knowledge this is the first study to provide replication of social networks and therefore probably the first that allows general conclusions to be drawn. The social networks were all found to have a non-random structure and exhibited 'social cliquishness'. A number of factors were observed to contribute to this structuring. Firstly, social network structure was influenced by body length and shoaling tendency, with individuals interacting more frequently with conspecifics of similar body length and shoaling tendency. Secondly, individuals with many social contacts were found to interact with each other more often than with other conspecifics, a phenomenon known as a 'positive degree correlation'. Finally, repeated interactions between pairs of individuals occurred within the networks more often than expected by random interactions. The observed network structures will have ecological and evolutionary implications. For example, the occurrence of positive degree correlations suggests the possibility that pathogens and information (that are socially transmitted) could spread very fast within the populations. Furthermore, the occurrence of repeated interactions between pairs of individuals fulfils an important pre-requisite for the evolution of reciprocal altruism.

Consensus recommendations on calf- and herd-level passive immunity in dairy calves in the United States

Passive immunity in calves is evaluated or quantified by measuring serum or plasma IgG or serum total protein within the first 7 d of age. While these measurements inform about circulating concentrations of this important protein, they are also a proxy for evaluating all of the additional benefits of colostral ingestion. The current individual calf standard for categorizing dairy calves with successful passive transfer or failure of passive transfer of immunity are based on serum IgG concentrations of ≥10 and <10 g/L, respectively. This cutoff was based on higher mortality rates in calves with serum IgG <10 g/L. Mortality rates have decreased since 1991, but the percentage of calves with morbidity events has not changed over the same time period. Almost 90% of calves sampled in the USDA National Animal Health Monitoring System's Dairy 2014 study had successful passive immunity based on the dichotomous standard. Based on these observations, a group of calf experts were assembled to evaluate current data and determine if changes to the passive immunity standards were necessary to reduce morbidity and possibly mortality. In addition to the USDA National Animal Health Monitoring System's Dairy 2014 study, other peer-reviewed publications and personal experience were used to identify and evaluate potential standards. Four options were evaluated based on the observed statistical differences between categories. The proposed standard includes 4 serum IgG categories: excellent, good, fair, and poor with serum IgG levels of ≥25.0, 18.0-24.9, 10.0-17.9, and <10 g/L, respectively. At the herd level, we propose an achievable standard of >40, 30, 20, and <10% of calves in the excellent, good, fair, and poor categories, respectively. Because serum IgG concentrations are not practical for on-farm implementation, we provide corresponding serum total protein and %Brix values for use on farm. With one-third of heifer calves in 2014 already meeting the goal of ≥25 g/L serum IgG at 24 h of life, this achievable standard will require more refinement of colostrum management programs on many dairy farms. Implementation of the proposed standard should further reduce the risk of both mortality and morbidity in preweaned dairy calves, improving overall calf health and welfare.

Personality in the context of social networks

There is great interest in environmental effects on the development and evolution of animal personality traits. An important component of an individual's environment is its social environment. However, few studies look beyond dyadic relationships and try to place the personality of individuals in the context of a social network. Social network analysis provides us with many new metrics to characterize the social fine-structure of populations and, therefore, with an opportunity to gain an understanding of the role that different personalities play in groups, communities and populations regarding information or disease transmission or in terms of cooperation and policing of social conflicts. The network position of an individual is largely a consequence of its interactive strategies. However, the network position can also shape an individual's experiences (especially in the case of juveniles) and therefore can influence the way in which it interacts with others in future. Finally, over evolutionary time, the social fine-structure of animal populations (as quantified by social network analysis) can have important consequences for the evolution of personalities-an approach that goes beyond the conventional game-theoretic analyses that assumed random mixing of individuals in populations.

Structural and mechanistic basis of immunity toward endonuclease colicins

The crystal structure of the cytotoxic endonuclease domain from the bacterial toxin colicin E9 in complex with its cognate immunity protein Im9 reveals that the inhibitor does not bind at the active site, the core of which comprises the HNH motif found in intron-encoded homing endonucleases, but rather at an adjacent position leaving the active site exposed yet unable to bind DNA because of steric and electrostatic clashes with incoming substrate. Although its mode of action is unorthodox, Im9 is a remarkably effective inhibitor since it folds within milliseconds and then associates with its target endonuclease at the rate of diffusion to form an inactive complex with sub-femtomolar binding affinity. This hyperefficient mechanism of inhibition could be well suited to other toxic enzyme systems, particularly where the substrate is a polymer extending beyond the boundaries of the active site.

The DNA sequence and biological annotation of human chromosome 1

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.

Synthesis, biological evaluation, and preliminary structure-activity considerations of a series of alkylphenols as intravenous anesthetic agents

Following our discovery of the intravenous (iv) anesthetic activity of 2,6-diethylphenol in mice, a series of alkylphenols was examined in this species and the most active analogues were further evaluated in rabbits. The synthesis of compounds which were not commercially available was accomplished by adaptations of standard ortho-alkylation procedures for phenols. Structure-activity relationships were found to be complex, but, in general, potency and kinetics appeared to be a function of both the lipophilic character and the degree of steric hindrance exerted by ortho substituents. The most interesting compounds were found in the 2,6-dialkyl series, and the greatest potency was associated with 2,6-di-sec-alkyl substitution. In particular, 2,6-diisopropylphenol (ICI 35 868) emerged as a candidate for further development and has subsequently been shown to be an effective iv anesthetic agent in man.

Translationally controlled tumor protein: a protein identified in several nontumoral cells including erythrocytes

The translationally controlled tumor protein (TCTP) is a growth-related protein which is regulated at the translational level. It is present in mammals, higher plants and Saccharomyces cerevisiae. This study was undertaken to localize and further characterize the TCTP in human cell lysates using two-dimensional gel electrophoresis, monoclonal antibodies, and 45Ca-gel overlay. TCTP was found in several healthy and tumoral cells including erythrocytes, hepatocytes, macrophages, platelets, keratinocytes, erythroleukemia cells, gliomas, melanomas, hepatoblastomas, and lymphomas. It could not be detected in kidney and renal cell carcinoma (RCC). A monoclonal antibody raised against TCTP detected three isoforms likely due to post-translational modifications. A calcium binding property was found as well as heat stability and cytoplasmic localization. The high degree of homology from plants to man and its expression in many tissues suggests that TCTP most likely has a cell housekeeping function.

Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes

Bacteria producing endonuclease colicins are protected against their cytotoxic activity by virtue of a small immunity protein that binds with high affinity and specificity to inactivate the endonuclease. DNase binding by the immunity protein occurs through a "dual recognition" mechanism in which conserved residues from helix III act as the binding-site anchor, while variable residues from helix II define specificity. We now report the 1.7 A crystal structure of the 24.5 kDa complex formed between the endonuclease domain of colicin E9 and its cognate immunity protein Im9, which provides a molecular rationale for this mechanism. Conserved residues of Im9 form a binding-energy hotspot through a combination of backbone hydrogen bonds to the endonuclease, many via buried solvent molecules, and hydrophobic interactions at the core of the interface, while the specificity-determining residues interact with corresponding specificity side-chains on the enzyme. Comparison between the present structure and that reported recently for the colicin E7 endonuclease domain in complex with Im7 highlights how specificity is achieved by very different interactions in the two complexes, predominantly hydrophobic in nature in the E9-Im9 complex but charged in the E7-Im7 complex. A key feature of both complexes is the contact between a conserved tyrosine residue from the immunity proteins (Im9 Tyr54) with a specificity residue on the endonuclease directing it toward the specificity sites of the immunity protein. Remarkably, this tyrosine residue and its neighbour (Im9 Tyr55) are the pivots of a 19 degrees rigid-body rotation that relates the positions of Im7 and Im9 in the two complexes. This rotation does not affect conserved immunity protein interactions with the endonuclease but results in different regions of the specificity helix being presented to the enzyme.

Plasma protein map: an update by microsequencing

The reference plasma protein map, obtained with immobilized pH gradients in the first dimension of two-dimensional electrophoresis, is presented. By microsequencing, more than 40 polypeptide chains were identified. The new polypeptides and previously known proteins are listed in a table and labeled on the protein map, thus providing an update of the human plasma two-dimensional gel database.