Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi.

The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read length compared with 454 sequencing. We explored whether Illumina sequencing improves estimates of arbuscular mycorrhizal (AM) fungal richness in plant root samples, compared with 454 sequencing. We identified AM fungi in root samples by sequencing amplicons of the SSU rRNA gene with 454 and Illumina MiSeq paired-end sequencing. In addition, we sequenced metagenomic DNA without prior PCR amplification. Amplicon-based Illumina sequencing yielded two orders of magnitude higher sequencing depth per sample than 454 sequencing. Initial analysis with minimal quality control recorded five times higher AM fungal richness per sample with Illumina sequencing. Additional quality control of Illumina samples, including restriction of the marker region to the most variable amplicon fragment, revealed AM fungal richness values close to those produced by 454 sequencing. Furthermore, AM fungal richness estimates were not correlated with sequencing depth between 300 and 30,000 reads per sample, suggesting that the lower end of this range is sufficient for adequate description of AM fungal communities. By contrast, metagenomic Illumina sequencing yielded very few AM fungal reads and taxa and was dominated by plant DNA, suggesting that AM fungal DNA is present at prohibitively low abundance in colonised root samples. In conclusion, Illumina MiSeq sequencing yielded higher sequencing depth, but similar richness of AM fungi in root samples, compared with 454 sequencing.

Trends in alkali metal hydrosulfides: a combined Fourier transform microwave/millimeter-wave spectroscopic study of KSH (X1A').

The pure rotational spectrum of KSH (X(1)A') has been measured using millimeter-wave direct absorption and Fourier transform microwave (FTMW) techniques. This work is the first gas-phase experimental study of this molecule and includes spectroscopy of KSD as well. In the millimeter-wave system, KSH was synthesized in a DC discharge from a mixture of potassium vapor, H2S, and argon; a discharge-assisted laser ablation source, coupled with a supersonic jet expansion, was used to create the species in the FTMW instrument. Five and three rotational transitions in the range 3-57 GHz were recorded with the FTMW experiment for KSH and KSD, respectively, in the K(a) = 0 component; in these data, potassium quadrupole hyperfine structure was observed. Five to six transitions with K(a) = 0-5 were measured in the mm-wave region (260-300 GHz) for the two species. The presence of multiple asymmetry components in the mm-wave spectra indicates that KSH has a bent geometry, in analogy to other alkali hydrosulfides. The data were analyzed with an S-reduced asymmetric top Hamiltonian, and rotational, centrifugal distortion, and potassium electric quadrupole coupling constants were determined for both isotopolgues. The r0 geometry for KSH was calculated to be r(S-H) = 1.357(1) Å, r(K-S) = 2.806(1) Å, and θ(M-S-H) (°) = 95.0 (1). FTMW measurements were also carried out on LiSH and NaSH; metal electric quadrupole coupling constants were determined for comparison with KSH. In addition, ab initio computations of the structures and vibrational frequencies at the CCSD(T)/6-311++G(3df,2pd) and CCSD(T)/aug-cc-pVTZ levels of theory were performed for LiSH, NaSH, and KSH. Overall, experimental and computational data suggest that the metal-ligand bonding in KSH is a combination of electrostatic and covalent forces.

The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont.

• The arbuscular mycorrhizal symbiosis is arguably the most ecologically important eukaryotic symbiosis, yet it is poorly understood at the molecular level. To provide novel insights into the molecular basis of symbiosis-associated traits, we report the first genome-wide analysis of the transcriptome from Glomus intraradices DAOM 197198. • We generated a set of 25,906 nonredundant virtual transcripts (NRVTs) transcribed in germinated spores, extraradical mycelium and symbiotic roots using Sanger and 454 sequencing. NRVTs were used to construct an oligoarray for investigating gene expression. • We identified transcripts coding for the meiotic recombination machinery, as well as meiosis-specific proteins, suggesting that the lack of a known sexual cycle in G. intraradices is not a result of major deletions of genes essential for sexual reproduction and meiosis. Induced expression of genes encoding membrane transporters and small secreted proteins in intraradical mycelium, together with the lack of expression of hydrolytic enzymes acting on plant cell wall polysaccharides, are all features of G. intraradices that are shared with ectomycorrhizal symbionts and obligate biotrophic pathogens. • Our results illuminate the genetic basis of symbiosis-related traits of the most ancient lineage of plant biotrophs, advancing future research on these agriculturally and ecologically important symbionts.

A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas.

Evolutionary relationships of 120 root-nodulating bacteria isolated from the nodules of Pisum sativum cultivated at 22 different locations of the trans-Himalayan valleys of Lahaul and Spiti in the state of Himachal Pradesh of India were studied using 16S rRNA gene PCR-RFLP, ERIC-PCR, sequencing of 16S rRNA, atpD, recA, nodC and nifH genes, carbon-source utilization pattern (BIOLOG™), and whole-cell fatty acid profiling. The results demonstrated that all isolates belonged to Rhizobium leguminosarum symbiovar viciae (Rlv). Isolates from the two valleys were clearly separated on the basis of ERIC fingerprints, carbon-source utilization pattern, and whole-cell fatty acid methyl esters. Phylogenetic analysis of atpD, recA, nodC and nifH genes revealed a common Rlv sublineage in Spiti valley. Lahaul valley isolates were represented by three sequence types of atpD and recA genes, and four sequence types of nodC and nifH genes. Genotypes from the two valleys were completely distinct, except for two Lahaul isolates that shared nodC and nifH sequences with Spiti isolates but were otherwise more similar to other Lahaul isolates. Isolates from the two highest Spiti valley sites (above 4000 m) had a distinctive whole-cell fatty acid profile. Spiti valley isolates are closely related to Rlv sublineages from Xinjiang and Shanxi provinces in China, while Lahaul valley isolates resemble cosmopolitan strains of the western world. The high mountain pass between these valleys represents a boundary between two distinct microbial populations.

Promoter methylation of Wnt5a is associated with microsatellite instability and BRAF V600E mutation in two large populations of colorectal cancer patients.

BACKGROUND: In colorectal cancer (CRC), tumour microsatellite instability (MSI) status and CpG island methylator phenotype (CIMP) status are indicators of patient outcome, but the molecular events that give rise to these outcomes remain largely unknown. Wnt5a is a critical regulator of non-canonical Wnt activity and promoter hypermethylation of this gene has emerging prognostic roles in CRC; however the frequency and prognostic significance of this epigenetic event have not been explored in the context of colorectal tumour subtype. Consequently, we investigated the frequency and prognostic significance of Wnt5a methylation in a large cohort of MSI-stratified CRCs. METHODS: Methylation was quantified in a large cohort of 1232 colorectal carcinomas from two clinically distinct populations from Canada. Associations were examined between methylation status and clinicopathlogical features, including tumour MSI status, BRAF V600E mutation, and patient survival. RESULTS: In Ontario, Wnt5a methylation was strongly associated with MSI tumours after adjustment for age, sex, and tumour location (odds ratio (OR)=4.2, 95% confidence interval (CI)=2.4-7.4, P<10(-6)) and with BRAF V600E mutation, a marker of CIMP (OR=12.3, 95% CI=6.9-21.7, P<10(-17)), but was not associated with patient survival. Concordant results were obtained in Newfoundland. CONCLUSION: Methylation of Wnt5a is associated with distinct tumour subtypes, strengthening the evidence of an epigenetic-mediated Wnt bias in CRC.

Body mass index in early adulthood and colorectal cancer risk for carriers and non-carriers of germline mutations in DNA mismatch repair genes.

BACKGROUND: Carriers of germline mutations in DNA mismatch repair (MMR) genes have a high risk of colorectal cancer (CRC), but the modifiers of this risk are not well established. We estimated an association between body mass index (BMI) in early adulthood and subsequent risk of CRC for carriers and, as a comparison, estimated the association for non-carriers. METHODS: A weighted Cox regression was used to analyse height and weight at 20 years reported by 1324 carriers of MMR gene mutations (500 MLH1, 648 MSH2, 117 MSH6 and 59 PMS2) and 1219 non-carriers from the Colon Cancer Family Registry. RESULTS: During 122,304 person-years of observation, we observed diagnoses of CRC for 659 carriers (50%) and 36 non-carriers (3%). For carriers, the risk of CRC increased by 30% for each 5 kg m(-2) increment in BMI in early adulthood (hazard ratio, HR: 1.30; 95% confidence interval, CI: 1.08-1.58; P=0.01), and increased by 64% for non-carriers (HR: 1.64; 95% CI: 1.02-2.64; P=0.04) after adjusting for sex, country, cigarette smoking and alcohol drinking (and the MMR gene that was mutated in carriers). The difference in HRs for carriers and non-carriers was not statistically significant (P=0.50). For MLH1 and PMS2 (MutLα heterodimer) mutation carriers combined, the corresponding increase was 36% (HR: 1.36; 95% CI: 1.05-1.76; P=0.02). For MSH2 and MSH6 (MutSα heterodimer) mutation carriers combined, the HR was 1.26 (95% CI: 0.96-1.65; P=0.09). There was no significant difference between the HRs for MutLα and MutSα heterodimer carriers (P=0.56). CONCLUSION: Body mass index in early adulthood is positively associated with risk of CRC for MMR gene mutation carriers and non-carriers.

Enzyme polymorphism and cyclic parthenogenesis in Daphnia magna. I. Selection and clonal diversity.

Genotype frequencies and fecundities were recorded over a period of two years for three polymorphic enzyme loci (Est, Mdh and Got) in a parthenogenetic natural population of Daphnia magna Straus (Crustacea: Cladocera). There was a large excess of heterozygotes at each locus, and some nonrandom association between loci, although 29 different three-locus genotypes were detected. There were small but significant changes in genotype frequencies that did not follow any clear seasonal cycles or overall trends, and the genotypes often differed significantly in fecundity, although the direction of the difference was not constant. These fitness differences were probably not attributable to the specific loci studied.--Models of balancing selection are of two types: segregation-balanced (e.g., heterosis) and competition-balanced (e.g., frequency dependence). Only the latter type can stabilize diversity in a clonal population. The observed selection was not heterotic, but it is not certain that it was stabilizing either. Clonal competition did not lead to victory by a single, fittest clone; genotypic diversity remained high.

Enzyme polymorphism and cyclic parthenogenesis in Daphnia magna. II. Heterosis following sexual reproduction.

Cyclical parthenogenesis exaggerates the force of selection relative to recombination and will therefore enhance interlocus effects. Observations of electrophoretic variation in a natural population of Daphnia magna Straus (Crustacea: Cladocera) are interpreted in this light. Sexual reproduction led to Hardy-Weinberg equilibrium, but heterozygote excesses rapidly developed at each of three observed loci during subsequent parthenogenesis. Homozygote fecundity was often lower than that of heterozygotes; this may have been the cause of some of the observed frequency changes. The superior fitness of the enzyme heterozygotes does not imply that selection was necessarily acting on the enzyme loci thermselves, since apparent heterosis is the expected result of linkage disequilibrium.

Proliferation, apoptosis, and survival in high-level microsatellite instability sporadic colorectal cancer.

Sporadic colorectal cancer (CRC) characterized by high-level DNA microsatellite instability (MSI-H) has a favorable prognosis. The reason for this MSI-H survival advantage is not known. The aim of this study was to correlate proliferation, apoptosis, and prognosis in CRC stratified by MSI status. The proliferative index (PI) was measured by immunohistochemical staining with the Ki-67 antibody in a selected series of 100 sporadic colorectal cancers classified according to the level of MSI as 31 MSI-H, 29 MSI-Low (MSI-L), and 40 microsatellite stable (MSS). The Ki-67 index was significantly higher in MSI-H cancers (P < 0.0001) in which the PI was 90.1 +/- 1.2% (mean +/- SE) compared with 69.5 +/- 3.1% and 69.5 +/- 2.3% in MSI-L and MSS subgroups, respectively. There was a positive linear correlation between the apoptotic index (AI) and PI (r = 0.51; P < 0.001), with MSI-H cancers demonstrating an increased AI:PI ratio indicative of a lower index of cell production. A high PI showed a trend toward predicting improved survival within MSI-H cancers (P = 0.09) but did not predict survival in MSI-L or MSS cancers. The AI was not associated with survival in any MSI subgroup. In conclusion, this is the first study to show that sporadic MSI-H cancers are characterized by a higher AI:PI ratio and increased proliferative activity compared with MSI-L and MSS cancers, and that an elevated PI may confer a survival advantage within the MSI-H subset.

Altered vascular reactivity in sickle hemoglobinopathy. A possible protective factor from hypertension.

Patients with sickle cell anemia have considerably less hypertension than the black population in general. Factor(s) offering "protection" from hypertension in these patients remain unknown. Hormonal and hemodynamic parameters involved in blood pressure regulation were evaluated in normotensive, stable sickle cell patients and black nonsickle normotensive controls. There was no difference in systolic, diastolic, or mean arterial blood pressure between the two groups. The characteristic hemodynamic findings of increased cardiac index, renal plasma flow, and plasma volume were observed in the sickle cell patients. Urinary sodium excretion was comparable on an ad libitum, high sodium, and low sodium diet. In contrast, plasma renin activity was greater in sickle cell patients at all levels of sodium intake in both supine and upright positions. These findings suggested possible altered vascular responsiveness to endogenous angiotensin II. Plethysmography revealed that sickle cell patients had greater forearm blood flow than normal controls and black nonsickle chronic anemic controls at rest, during cold stimulation, and during exercise. Forearm vascular resistance was significantly lower in the patients and did not increase with cold-induced, sympathetic-mediated stimulation. To assess these findings more directly, the pressor response to the exogenous administration of graded doses of angiotensin II and norepinephrine was measured. There was a marked decrease in the pressor response to angiotensin II but not to norepinephrine in the sickle cell patients. The findings in these studies indicate fundamental differences in blood pressure control in the sickle cell patient, probably at the vascular level.

The replicator region of the Rhizobium leguminosarum cryptic plasmid pRL8JI.

The replicator region of the cryptic plasmid pRL8JI from Rhizobium leguminosarum strain 3841 was cloned and sequenced. The recombinant plasmid (pYK3) was selected by function from a partial EcoRI library of total DNA cloned in pSUP202 and shows incompatibility with plasmid pRL8JI when conjugated into R. leguminosarum strains 3841 and its derivative 1062. The cloned insert (approximately 10.5 kb) comprises five EcoRI fragments none of which confers replicative stability when cloned individually. A single 5.0-kb BamHI fragment, that spans all five EcoRI fragments and confers replicative stability on pSUP202 in R. leguminosarum, has been sequenced. This replicator region shows organisational and sequence similarity to the replicator regions of the Agrobacterium plasmids pTiB6S3 and pRiA4b. It has three open reading frames (repA, repB, repC) and a conserved intergenic sequence.

Characterisation of rhizobia from African acacias and other tropical woody legumes using Biolog and partial 16S rRNA sequencing.

A Biolog (sole carbon source utilisation) user database of tropical and temperature rhizobial strains was created and used in conjunction with the partial 16S rRNA sequencing method to characterise 12 rhizobial isolates from African acacias and other tropical woody legumes. There was close agreement between the two methods but also some significant discrepancies. A high degree of diversity was shown in the relatively small sample of isolates, with 4 out of 5 of the currently proposed rhizobial genera represented. This is the first time Biolog has shown congruence with genotypic fingerprinting using a wide selection of rhizobial reference and test strains.

Cefotaxime: United Kingdom clinical trial results in the treatment of severe infections.

A multicentre study was carried out to assess the efficacy and tolerance of the wide-spectrum cephalosporin, cefotaxime, in the treatment of 411 hospitalized patients, most of whom were seriously ill with severe infections, including septicaemia, lower respiratory tract infection, urinary tract infections and soft tissue infection. Almost half the patients had failed to respond to previous antibacterial therapy and, in general, prognoses were poor. Patients received cefotaxime by intramusclar or/and intravenous injection in unit doses ranging from 0.5 to 2.0 g, 6 to 12 hourly, for periods up to 10 days or more. The results of clinical response in those who could be assessed showed a cure rate of 75% in 103 patients with septicaemia and over 80% in all other conditions.The bacteriological findings after treatment showed a similarly high eradication rate in a wide range of pathogens, particularly so in infections caused by E. coli, Klebsiella, H. influenzae, Proteus, Staph, aureus, staph. epidermis and Strep. pneumoniae. Useful clinical activity was also demonstrated in infections caused by moderately sensitive pathogens such a Pseudomonas and Strep. faecalis. Cefotaxime was well tolerated by the majority of patients, the commonest side-effects reported being moderate pain of short duration or phlebitis on injection, rash and diarrhoea, as with other cephalosporins. It is concluded that cefotaxime should be considered as a first line antibiotic for patients with severe infections caused by susceptible pathogens.

An integrated system for patient assessment and classification and nurse staff allocation for long term care facilities.

An integrated approach to patient classification and nurse staffing for long term care facilities is constructed, based on the quantification of patient care needs as reflected by formal assessment of a variety of key functioning status items, behavioral status indicators, and medically defined conditions. Nonlinear multiple regression techniques are employed in order to cluster these key assessment indicators in to an easily applied level of care classification method that can be used to determine placement of patients within the long term care system and to indicate the particular nursing care activities called for. Given the classification of patients into the various levels of care required (e.g., Chronic, Skilled Nursing Care, Intermediate A or B) a mixed integer/linear programming model is used to permit presentation of alternative nurse staffing strategies within a long term care facility or program. Extensions to the model portray the effects of changing budgetary, service, and legal restrictions.

A staff allocation model for mental health facilities.

This article describes a model for allocating staff within a large psychiatric hospital. The model provides an objective framework within which one can test alternative staff operating policies before making critical decisions concerning the employment of one category of personnel as opposed to another. It is based on objective data describing patient needs and staff functioning patterns, rather than subjective opinions concerning staff deployment. Besides being useful for the short-term deployment of staff and budgetary resources, it can also be used as a long-range planning tool for testing modifications in policy decisions and budget proposals. The algorithm employed, mixed-integer linear programming, is readily available; computer costs and running time are relatively minimal.

The influences of age and gender on blood ethanol concentrations in healthy humans.

OBJECTIVE: Previous cross-section studies suggested that blood ethanol concentrations (BAC) increase with age. To establish this, and to account for putative gender differences, we studied four cohorts of nonalcoholic subjects. METHOD: Fifty-seven subjects were studied: 14 men and 14 women in the young (21-40 years) and 14 men and 15 women in the old (> or = 60 years) groups. All subjects received ethanol (0.3 g/kg) on three occasions: orally (PO) after an overnight fast; PO after a standard meal; and by intravenous (IV) infusion after a standard meal. RESULTS: In all four cohorts, PO ethanol in the fasted state produced the greatest average areas under the curve (AUC) for ethanol, followed by IV ethanol and PO ethanol, both in the fed state. Pooled by age, blood ethanol AUCs were significantly greater in old subjects given PO ethanol when fasted (p = .001) and IV ethanol when fed (p < .004) but not after PO ethanol in the fed state. Pooled by gender, blood ethanol AUCs did not separate men and women in any of the experiments. Corrected for relative volumes of distribution (Vdist) among the four cohorts, only elderly women evidenced AUC values that could not be explained by Vdist alone and only in the fasted state. Both elderly men and women in the fasted state showed higher average peak ethanol levels than gender-matched younger cohorts; this effect was most pronounced in elderly women (47% vs 12%). CONCLUSIONS: The data confirm the influence of age, but fail to confirm that of gender, on blood ethanol response after a moderate dose of ethanol. They also show that feeding state can negate differences due to Vdist alone. In the fasted state, Vdist alone explains AUC and peak increases in elderly men but not in elderly women. Neither gastric metabolism nor motility account for age/BAC differences since these were independent of route. These data suggest caution for elderly drinkers or for those prescribing alcoholic beverages to elderly persons as well as for studies of ethanol ingestion that do not account for age and for feeding state.

Using tumour pathology to identify people at high genetic risk of breast and colorectal cancers.

Genes have been identified for which germline mutations are associated with high lifetime risks of breast, colorectal and other cancers. Identification of mutation carriers through genetic testing is important as it could help lower cancer incidence and mortality. The translation of genetic information into better health outcomes is expensive because of the costs of genetic counselling as well as laboratory testing. Approaches to triage for mutation screening of known genes which rely on cancer family history are not necessarily sensitive and specific or the most cost-effective. Recent population-based research has shown that the cancers and precancerous lesions arising in mutation carriers have specific molecular and morphological characteristics. People with colorectal cancer, especially those diagnosed at a young age, whose tumours exhibit microsatellite instability and some specific pathology and immunohistochemically-defined features are more likely to carry a germline mutation in one of four mismatch repair genes. Some morphological and immunohistochemically-defined features are associated with breast cancers arising in women who carry BRCA1 or BRCA2 germline mutations, especially if at a young age. Screening paradigms based on molecular and morphological features that predict mutation status, especially if focused on early-onset disease, have the potential to identify mutation carriers with greater sensitivity and specificity, and in a more cost-effective way, than those based on family history alone. Genetic testing results could help inform treatment if those affected are tested soon after diagnosis using pathology-led selection strategies to identify cases most likely to carry germline mutations. We propose how this new approach could be undertaken by having genetic testing and counselling prioritised to those with the greatest probability of carrying a germline mutation in these known cancer predisposition genes.