Consensus and controversies regarding follow-up after treatment with curative intent of nonmetastatic colorectal cancer: a synopsis of guidelines used in countries represented in the European Society of Coloproctology.

AIM: It is common clinical practice to follow patients for a period of years after treatment with curative intent of nonmetastatic colorectal cancer, but follow-up strategies vary widely. The aim of this systematic review was to provide an overview of recommendations on this topic in guidelines from member countries of the European Society of Coloproctology, with supporting evidence. METHOD: A systematic search of Medline, Embase and the guideline databases Trip database, BMJ Best Practice and Guidelines International Network was performed. Quality assessment included use of the AGREE-II tool. All topics with recommendations from included guidelines were identified and categorized. For each subtopic, a conclusion was made followed by the degree of consensus and the highest level of evidence. RESULTS: Twenty-one guidelines were included. The majority recommended that structured follow-up should be offered, except for patients in whom treatment of recurrence would be inappropriate. It was generally agreed that clinical visits, measurement of carcinoembryoinc antigen and liver imaging should be part of follow-up, based on a high level of evidence, although the frequency is controversial. There was also consensus on imaging of the chest and pelvis in rectal cancer, as well as endoscopy, based on lower levels of evidence and with a level of intensity that was contradictory. CONCLUSION: In available guidelines, multimodal follow-up after treatment with curative intent of colorectal cancer is widely recommended, but the exact content and intensity are highly controversial. International agreement on the optimal follow-up schedule is unlikely to be achieved on current evidence, and further research should refocus on individualized 'patient-driven' follow-up and new biomarkers.

Maternal and foetal outcomes in pregnant systemic lupus erythematosus patients: an incident cohort from a stable referral population followed during 1990-2010.

OBJECTIVES: To assess the impact of systemic lupus erythematosus (SLE) on pregnancy outcome in a cohort of incident pregnant lupus patients referred to a Danish university hospital during 1990-2010. METHOD: All pregnant lupus patients were referred to the university hospital from a stable referral area with approximately 1.4 million inhabitants. Eighty-four pregnancies in 39 women were registered using the Danish National Registry and retrospective reviewing of medical records, laboratory results, and midwifery records from the Department of Rheumatology, the Department of Obstetrics and Gynaecology, and possible other departments. Data were compared to 29 059 births during 2005-2010, covering all births from the referral area. RESULTS: The 84 SLE pregnancies resulted in 62 live births. SLE flares developed in 46.4%, pre-eclampsia in 8.3%, and HELLP syndrome in 4.8% of cases. Significantly higher rates of premature delivery (p=0.0032), caesarean section (p=0.015), hypertension (p=0.025), and intrauterine growth retardation (IUGR) (p=0.003) were found. Disease activity significantly (p=0.021) increased the risk of prematurity threefold. Antiphospholipid antibody (aPL) presence significantly (p=0.002) increased the risk of spontaneous abortion threefold. Two babies died after extreme preterm birth. Two had neonatal lupus syndrome (NLS) and one had congenital heart block (CHB). Birth weight and length were significantly lower in the SLE cohort. An unexpectedly high number of cardiac septum defects (9.7%) were observed. CONCLUSIONS: From a stable referral area, an incident cohort of SLE pregnancies were mostly successful, but maternal and foetal complications were observed in one-half and one-third of cases, respectively. Outcome risk factors were identified. A possible new observation is a high frequency of cardiac septum defects.

Impact of arbuscular mycorrhizal fungi on uranium accumulation by plants.

Contamination by uranium (U) occurs principally at U mining and processing sites. Uranium can have tremendous environmental consequences, as it is highly toxic to a broad range of organisms and can be dispersed in both terrestrial and aquatic environments. Remediation strategies of U-contaminated soils have included physical and chemical procedures, which may be beneficial, but are costly and can lead to further environmental damage. Phytoremediation has been proposed as a promising alternative, which relies on the capacity of plants and their associated microorganisms to stabilize or extract contaminants from soils. In this paper, we review the role of a group of plant symbiotic fungi, i.e. arbuscular mycorrhizal fungi, which constitute an essential link between the soil and the roots. These fungi participate in U immobilization in soils and within plant roots and they can reduce root-to-shoot translocation of U. However, there is a need to evaluate these observations in terms of their importance for phytostabilization strategies.

Role and influence of mycorrhizal fungi on radiocesium accumulation by plants.

This review summarizes current knowledge on the contribution of mycorrhizal fungi to radiocesium immobilization and plant accumulation. These root symbionts develop extended hyphae in soils and readily contribute to the soil-to-plant transfer of some nutrients. Available data show that ecto-mycorrhizal (ECM) fungi can accumulate high concentration of radiocesium in their extraradical phase while radiocesium uptake and accumulation by arbuscular mycorrhizal (AM) fungi is limited. Yet, both ECM and AM fungi can transport radiocesium to their host plants, but this transport is low. In addition, mycorrhizal fungi could thus either store radiocesium in their intraradical phase or limit its root-to-shoot translocation. The review discusses the impact of soil characteristics, and fungal and plant transporters on radiocesium uptake and accumulation in plants, as well as the potential role of mycorrhizal fungi in phytoremediation strategies.

No significant contribution of arbuscular mycorrhizal fungi to transfer of radiocesium from soil to plants.

The diffuse pollution by fission and activation products following nuclear accidents and weapons testing is of major public concern. Among the nuclides that pose a serious risk if they enter the human food chain are the cesium isotopes 137Cs and 134Cs (with half-lives of 30 and 2 years, respectively). The biogeochemical cycling of these isotopes in forest ecosystems is strongly affected by their preferential absorption in a range of ectomycorrhiza-forming basidiomycetes. An even more widely distributed group of symbiotic fungi are the arbuscular mycorrhizal fungi, which colonize most herbaceous plants, including many agricultural crops. These fungi are known to be more efficient than ectomycorrhizas in transporting mineral elements from soil to plants. Their role in the biogeochemical cycling of Cs is poorly known, in spite of the consequences that fungal Cs transport may have for transfer of Cs into the human food chain. This report presents the first data on transport of Cs by these fungi by use of radiotracers and compartmented growth systems where uptake by roots and mycorrhizal hyphae is distinguished. Independent experiments in three laboratories that used different combinations of fungi and host plants all demonstrated that these fungi do not contribute significantly to plant uptake of Cs. The implications of these findings for the bioavailability of radiocesium in different terrestrial ecosystems are discussed.

Phospho-imaging as a tool for visualization and noninvasive measurement of P transport dynamics in arbuscular mycorrhizas.

• A new method is described for monitoring hyphal 32 P transport in compartmented, monoxenic mycorrhizal root cultures. Nondestructive time-course measurements of P transport in hyphae were obtained by capturing digital autoradiograms on P-imaging screens, and comparing with growth observed by optical scanning. 32 P distribution measured by densitometry on the day of harvest closely agreed with values obtained by liquid scintillation counting after destructive harvest. • Virtually all labeled PO4 was absorbed by arbuscular mycorrhizal (AM) hyphae, but transfer to the roots appeared to be incomplete. P transport was not unidirectional towards the roots, as 32 P was also transported from the root compartment to the hyphal compartment. Net P flux rates were calculated for hyphae crossing between compartments, taking bidirectional flow into account. • Amounts of transported P were poorly correlated with extra-radical hyphal length and root d. wt, but highly correlated with the number of hyphae crossing the barrier separating the two compartments. Such correlations were highest when only hyphae with detectable protoplasmic streaming were considered. • The method was tested using radiolabeled P sources, H2 PO4 - and cytidine triphosphate (CTP), and the AM fungi, Glomus intraradices and G. proliferum. Fungal transport of 32 P from CTP was much slower than from PO4 for both fungi.

MEGA2: molecular evolutionary genetics analysis software.

UNLABELLED: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform. AVAILABILITY: http://www.megasoftware.net. CONTACT: s.kumar@asu.edu

Interactive effects of soil temperature, atmospheric carbon dioxide and soil N on root development, biomass and nutrient uptake of winter wheat during vegetative growth.

Nutrient requirements for plant growth are expected to rise in response to the predicted changes in CO(2) and temperature. In this context, little attention has been paid to the effects of soil temperature, which limits plant growth at early stages in temperate regions. A factorial growth-room experiment was conducted with winter wheat, varying soil temperature (10 degrees C and 15 degrees C), atmospheric CO(2) concentration (360 and 700 ppm), and N supply (low and high). The hypothesis was that soil temperature would modify root development, biomass allocation and nutrient uptake during vegetative growth and that its effects would interact with atmospheric CO(2) and N availability. Soil temperature effects were confirmed for most of the variables measured and 3-factor interactions were observed for root development, plant biomass components, N-use efficiency, and shoot P content. Importantly, the soil temperature effects were manifest in the absence of any change in air temperature. Changes in root development, nutrient uptake and nutrient-use efficiencies were interpreted as counterbalancing mechanisms for meeting nutrient requirements for plant growth in each situation. Most variables responded to an increase in resource availability in the order: N supply >soil temperature >CO(2).

TreeGeneBrowser: phylogenetic data mining of gene sequences from public databases.

MOTIVATION: Sequence databases represent an enormous resource of phylogenetic information, but there is a lack of tools for accessing that information in order to assess the amount of evolutionary information in these databases that may be suitable for phylogenetic reconstruction and for identifying areas of the taxonomy that are under-represented for specific gene sequences. RESULTS: We have developed TreeGeneBrowser which allows inspection and evaluation of gene sequence data for phylogenetic reconstruction. This program improves the efficiency of identification of genes that may be useful for particular phylogenetic studies and identifies taxa and taxonomic branches that are under-represented in sequence databases.

Phosphate transport by communities of arbuscular mycorrhizal fungi in intact soil cores.

• Variation in phosphate uptake capacity is reported here for natural communities of arbuscular mycorrhizal fungi associated with annual pasture plants. • Tests were made of methodology for quantifying phosphate uptake by hyphae associated with clover in soil cores from pastures containing different morphotypes of the fungi. This provided a direct measure of the phosphate uptake capacity of hyphae from 32 P-labelled soil in a root-free mesh bag inserted into the centre of intact soil cores. • Bicarbonate-extractable phosphorus in the soils ranged from very deficient to close to adequate for plant growth. Uptake of 32 P was related to an estimate of the length of hyphae formed in four of the five soils, but not to either the length or the proportion of roots colonized. In the fifth soil type, phosphate uptake by hyphae was negligible. • Phosphate uptake by natural communities of arbuscular mycorrhizal fungi in intact soil cores can be assessed directly, and is shown to be highly variable. The experimental approach could be applied widely for field investigations of phosphate uptake by hyphal networks.

Atmospheric CO(2) and mycorrhiza effects on biomass allocation and nutrient uptake of nodulated pea (Pisum sativum L.) plants.

The effect of ambient and elevated atmospheric CO(2) on biomass partitioning and nutrient uptake of mycorrhizal and non-mycorrhizal pea plants grown in pots in a controlled environment was studied. The hypothesis tested was that mycorrhizae would increase C assimilation by increasing photosynthetic rates and reduce below-ground biomass allocation by improving nutrient uptake. This effect was expected to be more pronounced at elevated CO(2) where plant C supply and nutrient demand would be increased. The results showed that mycorrhizae did not interact with atmospheric CO(2) concentration in the variables measured. Mycorrhizae did not affect photosynthetic rates, had no effect on root weight or root length density and almost no effect on nutrient uptake, but still significantly increased shoot weight and reduced root/shoot ratio at harvest. Elevated CO(2) increased photosynthetic rates with no evidence for down-regulation, increased shoot weight and nutrient uptake, had no effect on root weight, and actually reduced root/shoot ratio at harvest. Non-mycorrhizal plants growing at both CO(2) concentrations had lower shoot weight than mycorrhizal plants with similar nutritional status and photosynthetic rates. It is suggested that the positive effect of mycorrhizal inoculation was caused by an enhanced C supply and C use in mycorrhizal plants than in non-mycorrhizal plants. The results indicate that plant growth was not limited by mineral nutrients, but partially source and sink limited for carbon. Mycorrhizal inoculation and elevated CO(2) might have removed such limitations and their effects on above-ground biomass were independent, positive and additive.

How important is DNA replication for mutagenesis?

Rates of mutation and substitution in mammals are generally greater in the germ lines of males. This is usually explained as resulting from the larger number of germ cell divisions during spermatogenesis compared with oogenesis, with the assumption made that mutations occur primarily during DNA replication. However, the rate of cell division is not the only difference between male and female germ lines, and mechanisms are known that can give rise to mutations independently of DNA replication. We investigate the possibility that there are other causes of male-biased mutation. First, we show that patterns of variation at approximately 5,200 short tandem repeat (STR) loci indicate a higher mutation rate in males. We estimate a ratio of male-to-female mutation rates of approximately 1.9. This is significantly greater than 1 and supports a greater rate of mutation in males, affecting the evolution of these loci. Second, we show that there are chromosome-specific patterns of nucleotide and dinucleotide composition in mammals that have been shaped by mutation at CpG dinucleotides. Comparable patterns occur in birds. In mammals, male germ lines are more methylated than female germ lines, and these patterns indicate that differential methylation has played a role in male-biased vertebrate evolution. However, estimates of male mutation bias obtained from both classes of mutation are substantially lower than estimates of cell division bias from anatomical data. This discrepancy, along with published data indicating slipped-strand mispairing arising at STR loci in nonreplicating DNA, suggests that a substantial percentage of mutation may occur in nonreplicating DNA.

Suppression of the biocontrol agent trichoderma harzianum by mycelium of the arbuscular mycorrhizal fungus glomus intraradices in root-free soil

Trichoderma harzianum is an effective biocontrol agent against several fungal soilborne plant pathogens. However, possible adverse effects of this fungus on arbuscular mycorrhizal fungi might be a drawback in its use in plant protection. The objective of the present work was to examine the interaction between Glomus intraradices and T. harzianum in soil. The use of a compartmented growth system with root-free soil compartments enabled us to study fungal interactions without the interfering effects of roots. Growth of the fungi was monitored by measuring hyphal length and population densities, while specific fatty acid signatures were used as indicators of living fungal biomass. Hyphal 33P transport and beta-glucuronidase (GUS) activity were used to monitor activity of G. intraradices and a GUS-transformed strain of T. harzianum, respectively. As growth and metabolism of T. harzianum are requirements for antagonism, the impact of wheat bran, added as an organic nutrient source for T. harzianum, was investigated. The presence of T. harzianum in root-free soil reduced root colonization by G. intraradices. The external hyphal length density of G. intraradices was reduced by the presence of T. harzianum in combination with wheat bran, but the living hyphal biomass, measured as the content of a membrane fatty acid, was not reduced. Hyphal 33P transport by G. intraradices also was not affected by T. harzianum. This suggests that T. harzianum exploited the dead mycelium but not the living biomass of G. intraradices. The presence of external mycelium of G. intraradices suppressed T. harzianum population development and GUS activity. Stimulation of the hyphal biomass of G. intraradices by organic amendment suggests that nutrient competition is a likely means of interaction. In conclusion, it seemed that growth of and phosphorus uptake by the external mycelium of G. intraradices were not affected by the antagonistic fungus T. harzianum; in contrast, T. harzianum was adversely affected by G. intraradices.

Diversity and evolution of T-cell receptor variable region genes in mammals and birds.

The receptor of a T lymphocyte (TCR) recognizes nonself antigens in the company of major histocompatibility complex (MHC) molecules presented to it by the antigen-presenting cell. The variable region of TCR is encoded by either a concatenation of variable region (TCR-V), diversity region (TCR-D), and joining region (TCR-J) genes, or a concatenation of TCR-V and TCR-J genes. The TCR-V genes exist as a multigene family in vertebrate species. Here we study the evolutionary relationships of TCR-V genes from humans, sheep, cattle, rabbits, mice, and chicken. These six species can be classified into two groups according to the frequency of gamma(delta) T-cells in their peripheral T-cell populations. The "gamma(delta) low" group of species includes humans and mice, in which gamma(delta)T-cells constitute very limited portion of the T-cell population. The "gamma(delta) high" group includes sheep, cattle, rabbits, and chicken, in which gamma(delta) T-cells comprise up to 60% of the T-cell population. Here, we compiled TCR-V sequences from the six species and conducted a phylogenetic analysis. We identified various TCR-V gene subgroups based on the analysis. We found that humans and mice have representatives from nearly all of the subgroups identified, while other species have lost subgroups to different extent. Therefore, the gamma(delta) low species have a high degree of diversity of TCR-V genes, while gamma(delta) high species all have limited diversity of TCR-V genes. This pattern is similar to that found for immunoglobulin variable region (IGV) genes.

Patterns of reticulate evolution for the classical class I and II HLA loci.

Some alleles of the major histocompatibility complex (MHC) genes have a reticulate pattern of evolution, probably resulting from the exchange of segments by gene conversion or recombination. Here we compare the extent and patterns of reticulate evolution among the classical class I and class II loci of the human MHC using the recently developed compatibility and partition matrix methods. A complex pattern is revealed with substantial differences among loci in the extent and pattern of reticulation. Extremely high levels of reticulation are observed at HLA-B and HLA-DPB1, high levels at HLA-A and HLA-DRB1, moderate levels at HLA-C and HLA-DQB1, and low levels at HLA-DQA1. The reticulate events are concentrated in the exons encoding the highly variable, peptide-binding domains, suggesting that the sequence combinations produced by these events are maintained by natural selection.

Correlating sequence variation with HLA-A allelic families: implications for T cell receptor binding specificities.

Six families of HLA-A alleles have been previously proposed on the basis of nucleotide sequence and phylogenetic analysis. Here, sequence polymorphism has been examined at both the protein and DNA levels in a family specific manner and new minimal signatures for each of the families have been delineated. The DNA and protein sites that constitute these signatures are distributed throughout the length of the sequence and generally do not appear to act to promote structural or functional features of the molecules. This is explained by the fact that traditional signatures suffer biases where, for example, recombination products of low frequency can obscure one family's trend by introducing 'impurities' intrinsic to another family. In the absence of complete frequency data, a closer approximation of family signatures can be defined by sites that show strong correlation with the family groups. Using this description, the amino acid positions 62, 97 and 114, localized in the antigen-binding cleft are, in combination, sufficient to discriminate between the six families. Thus, while the composition of the whole cleft defines the details of antigen specificity, these sites in particular, play a key role in modulating supertype peptide specificity and T cell recognition.

The partition matrix: exploring variable phylogenetic signals along nucleotide sequence alignments.

The partition matrix is a graphical tool for comparative analysis of nucleotide sequences following alignment. It is particularly useful for investigating the divergent phylogenies of sequence regions undergoing reticulate evolution. A partition matrix is generated by determining the consistency of the parsimoniously informative sites in a set of aligned sequences with the binary partitions inferred from the sequences. Since the linear order of sites is maintained, the matrix can be used to assess whether the distribution of sites either supporting or conflicting with particular partitions changes along the length of the alignment. The usefulness of the matrix in allowing visual identification of differences in evolutionary history among regions depends on the order in which partitions are shown; several suitable ordering schemes are proposed. We demonstrate the use of the partition matrix in interpreting the evolution of the pseudoautosomal boundary region on the sex chromosome of catarrhine primates. Its routine use should help to avoid attempts to derive single phylogenies from sequences whose evolution has been reticulate and to identify the gene conversion or recombination events underlying the reticulation. The method is relatively fast. It is exploratory, and it can form the basis for more formal analysis, which we discuss.

Phosphorus effects on the mycelium and storage structures of an arbuscular mycorrhizal fungus as studied in the soil and roots by analysis of Fatty Acid signatures.

The distribution of an arbuscular mycorrhizal (AM) fungus between soil and roots, and between mycelial and storage structures, was studied by use of the fatty acid signature 16:1(omega)5. Increasing the soil phosphorus level resulted in a decrease in the level of the fatty acid 16:1(omega)5 in the soil and roots. A similar decrease was detected by microscopic measurements of root colonization and of the length of AM fungal hyphae in the soil. The fatty acid 16:1(omega)5 was estimated from two types of lipids, phospholipids and neutral lipids, which mainly represent membrane lipids and storage lipids, respectively. The numbers of spores of the AM fungus formed in the soil correlated most closely with neutral lipid fatty acid 16:1(omega)5, whereas the hyphal length in the soil correlated most closely with phospholipid fatty acid 16:1(omega)5. The fungal neutral lipid/phospholipid ratio in the extraradical mycelium was positively correlated with the level of root infection and thus decreased with increasing applications of P. The neutral lipid/phospholipid ratio indicated that at high P levels, less carbon was allocated to storage structures. At all levels of P applied, the major part of the AM fungus was found to be present outside the roots, as estimated from phospholipid fatty acid 16:1(omega)5. The ratio of extraradical biomass/intraradical biomass was not affected by the application of P, except for a decrease at the highest level of P applied.

Structural comparison of major histocompatibility complex class I molecules and homology modelling of five distinct human leukocyte antigen-A alleles.

The peptide complexes of 19 major histocompatibility complex class I alpha 1 and alpha 2 domains have been compared to identify similarities that can be interpreted as constraints necessary for the function or stability of the molecule. It was found that nearly half of the residues maintained their side-chain conformations (or had no side chain), with the remaining residues being highly solvent exposed and/or polymorphic. Seven hydrogen bonds between the molecule and peptide are conserved in all the structures and serve to orientate the ends of the peptide in the binding groove. Furthermore, the general orientations of most residue side chains in the peptide are similar. Based on these constraints, homology models for the distinct human leukocyte antigen-A alleles A*0302, A*2403, A*2603, A*3101 and A*8001 have been constructed and the implications for peptide binding discussed. The models provide a useful framework from which to engineer allele-specific peptides with a high binding affinity.

Evolution of mammalian X-linked and autosomal Pgk and Pdh E1 alpha subunit genes.

The phylogeny and substitution rates of the mammalian X chromosome-located and autosomal phosphoglycerate kinase and pyruvate dehydrogenase genes were investigated. Compatibility analysis was used to show reticulate evolution in these genes. Analysis of the marsupial, mouse, and human phosphoglycerate kinase genes suggests that at least two recombination events have taken place, one occurring about the time of the placental-marsupial split involving exons 1-5 and the other before the primate-rodent split involving exons 9-10. Similar analysis of the pyruvate dehydrogenase genes indicates a recombination event involving exons 2-3 at a time before the primate-rodent split and a gene conversion between exons 3-4 in the human somatic and testis-specific pyruvate dehydrogenase genes after the primate-rodent split. This demonstrates that genetic exchange can occur between paralogous genes at widely separated chromosomal locations. Estimation of nucleotide substitution rates in these genes confirmed a higher substitution rate in the pyruvate dehydrogenase genes. In the phosphoglycerate kinase genes, there is no difference between the substitution rates in mice and humans and between the X chromosome- and autosome-located genes. A greater substitution rate was noted in the mouse autosomal pyruvate dehydrogenase gene when compared with the other mouse and human genes. This may be a result of either directional natural selection or a relaxation of functional constraint at this specific gene.