Personalized Computational Causal Modeling of the Alzheimer Disease Biomarker Cascade

BACKGROUND

Mathematical models of complex diseases, such as Alzheimer's disease, have the potential to play a significant role in personalized medicine. Specifically, models can be personalized by fitting parameters with individual data for the purpose of discovering primary underlying disease drivers, predicting natural history, and assessing the effects of theoretical interventions. Previous work in causal/mechanistic modeling of Alzheimer's Disease progression has modeled the disease at the cellular level and on a short time scale, such as minutes to hours. No previous studies have addressed mechanistic modeling on a personalized level using clinically validated biomarkers in individual subjects.

OBJECTIVES

This study aimed to investigate the feasibility of personalizing a causal model of Alzheimer's Disease progression using longitudinal biomarker data.

DESIGN/SETTING/PARTICIPANTS/MEASUREMENTS

We chose the Alzheimer Disease Biomarker Cascade model, a widely-referenced hypothetical model of Alzheimer's Disease based on the amyloid cascade hypothesis, which we had previously implemented mathematically as a mechanistic model. We used available longitudinal demographic and serial biomarker data in over 800 subjects across the cognitive spectrum from the Alzheimer's Disease Neuroimaging Initiative. The data included participants that were cognitively normal, had mild cognitive impairment, or were diagnosed with dementia (probable Alzheimer's Disease). The model consisted of a sparse system of differential equations involving four measurable biomarkers based on cerebrospinal fluid proteins, imaging, and cognitive testing data.

RESULTS

Personalization of the Alzheimer Disease Biomarker Cascade model with individual serial biomarker data yielded fourteen personalized parameters in each subject reflecting physiologically meaningful characteristics. These included growth rates, latency values, and carrying capacities of the various biomarkers, most of which demonstrated significant differences across clinical diagnostic groups. The model fits to training data across the entire cohort had a root mean squared error (RMSE) of 0.09 (SD 0.081) on a variable scale between zero and one, and were robust, with over 90% of subjects showing an RMSE of < 0.2. Similarly, in a subset of subjects with data on all four biomarkers in at least one test set, performance was high on the test sets, with a mean RMSE of 0.15 (SD 0.117), with 80% of subjects demonstrating an RMSE < 0.2 in the estimation of future biomarker points. Cluster analysis of parameters revealed two distinct endophenotypic groups, with distinct biomarker profiles and disease trajectories.

CONCLUSION

Results support the feasibility of personalizing mechanistic models based on individual biomarker trajectories and suggest that this approach may be useful for reclassifying subjects on the Alzheimer's clinical spectrum. This computational modeling approach is not limited to the Alzheimer Disease Biomarker Cascade hypothesis, and can be applied to any mechanistic hypothesis of disease progression in the Alzheimer's field that can be monitored with biomarkers. Thus, it offers a computational platform to compare and validate various disease hypotheses, personalize individual biomarker trajectories and predict individual response to theoretical prevention and therapeutic intervention strategies.

Transcriptome analyses of leaf architecture in Sansevieria support a common genetic toolkit in the parallel evolution of unifacial leaves in monocots

Planar structures dramatically increase the surface-area-to-volume ratio, which is critically important for multicellular organisms. In this study, we utilize naturally occurring phenotypic variation among three Sansivieria species (Asperagaceae) to investigate leaf margin expression patterns that are associated with mediolateral and adaxial/abaxial development. We identified differentially expressed genes (DEGs) between center and margin leaf tissues in two planar-leaf species Sansevieria subspicata and Sansevieria trifasciata and compared these with expression patterns within the cylindrically leaved Sansevieria cylindrica. Two YABBY family genes, homologs of FILAMENTOUS FLOWER and DROOPING LEAF, are overexpressed in the center leaf tissue in the planar-leaf species and in the tissue of the cylindrical leaves. As mesophyll structure does not indicate adaxial versus abaxial differentiation, increased leaf thickness results in more water-storage tissue and enhances resistance to aridity. This suggests that the cylindrical-leaf in S. cylindrica is analogous to the central leaf tissue in the planar-leaf species. Furthermore, the congruence of the expression patterns of these YABBY genes in Sansevieria with expression patterns found in other unifacial monocot species suggests that patterns of parallel evolution may be the result of similar solutions derived from a limited developmental toolbox.

Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi

Background

Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom’s evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown.

Results

By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways.

Conclusions

The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01346-8.

From Genome Variation to Molecular Mechanisms: What we Have Learned From Yeast Mitochondrial Genomes?

Analysis of genome variation provides insights into mechanisms in genome evolution. This is increasingly appreciated with the rapid growth of genomic data. Mitochondrial genomes (mitogenomes) are well known to vary substantially in many genomic aspects, such as genome size, sequence context, nucleotide base composition and substitution rate. Such substantial variation makes mitogenomes an excellent model system to study the mechanisms dictating mitogenome variation. Recent sequencing efforts have not only covered a rich number of yeast species but also generated genomes from abundant strains within the same species. The rich yeast genomic data have enabled detailed investigation from genome variation into molecular mechanisms in genome evolution. This mini-review highlights some recent progresses in yeast mitogenome studies.

[Impact of obstructive sleep apnea on the long-term cardiovascular outcomes in patients with acute coronary syndrome]

Objective: To investigate the impact of obstructive sleep apnea (OSA) on long-term cardiovascular outcomes in patients with acute coronary syndrome (ACS). Methods: This is a single-center, prospective cohort study. Between June 2015 to January 2020, consecutive ACS patients hospitalized at Beijing Anzhen Hospital, Capital Medical University were enrolled. All patients underwent portable sleep breathing monitoring, and they were then divided into moderate/severe OSA group (apnea-hypopnea index (AHI)≥15 events/hour) and no/mild OSA group (AHI<15 events/hour). The primary endpoint was major adverse cardiac and cerebrovascular event (MACCE), defined as a composite of cardiovascular death, non-fatal myocardial infarction, non-fatal stroke, ischemia-driven revascularization and hospital admission for unstable angina or heart failure. MACCE were compared yearly by the log-rank test. Multivariable Cox regression analyses were performed to determine the independent predictors of MACCE. Results: A total of 1 927 patients with ACS were enrolled, including 1 629 males (84.5%), aged (56.4±10.5) years. Moderate/severe OSA was present in 1 014 (52.6%) patients. Compared with no/mild OSA group, moderate/severe OSA group exhibited a higher body mass index (P<0.05). Hypertension, prior PCI were more prevalent in moderate/severe OSA group (both P<0.05). The difference of ACS category between the two groups was statistically significant (P=0.021). The rate of patients who underwent PCI and the number of stents were higher in the moderate/severe OSA group. During a 5-year follow-up (median 2.9 years (IQR 1.5-3.6 years)), the cumulative incidence of MACCE was significantly higher in the moderate/severe OSA group than in the no/mild OSA group (34.0% vs. 24.0%, HR=1.346, 95%CI 1.100-1.646, log-rank P=0.004). The cumulative incidence of MACCE remained statistically higher at 4 and 5 year in the moderate/severe OSA group as compared to the no/mild OSA group (33.3% vs. 22.9%, HR=1.397, 95%CI 1.141-1.710, log-rank P=0.001; 34.0% vs. 24.0%, HR=1.341, 95%CI 1.096-1.640, log-rank P=0.004, respectively). Multivariate analysis showed that moderate/severe OSA (HR=1.312, 95%CI 1.054-1.631, P=0.015) was an independent predictor of long-term MACCE in ACS patients. Conclusions: Moderate/severe OSA is observed in more than 52% ACS patients. Moderate/severe OSA is an independent predictor of long-term MACCE.

Variable Spontaneous Mutation and Loss of Heterozygosity among Heterozygous Genomes in Yeast

Mutation and recombination are the primary sources of genetic variation. To better understand the evolution of genetic variation, it is crucial to comprehensively investigate the processes involving mutation accumulation and recombination. In this study, we performed mutation accumulation experiments on four heterozygous diploid yeast species in the Saccharomycodaceae family to determine spontaneous mutation rates, mutation spectra, and losses of heterozygosity (LOH). We observed substantial variation in mutation rates and mutation spectra. We also observed high LOH rates (1.65-11.07×10-6 events per heterozygous site per cell division). Biases in spontaneous mutation and LOH together with selection ultimately shape the variable genome-wide nucleotide landscape in yeast species.

Effects of oral sialic acid on gut development, liver function and gut microbiota in mice

Sialic acid (N-acetylneuraminic acid), a 9-carbon monosaccharide, has been widely studied in immunology, oncology and neurology. However, the effects of sialic acid on organ and intestinal development, liver function and gut microbiota were rarely studied. In this study, we found that oral sialic acid tended to increase the relative weight of liver and decreased the serum aspartate aminotransferase (GPT) activity. In addition, sialic acid treatment markedly reduced gut villus length, depth, the ratio of villus length/depth (L/D), areas, width and the number of goblet cells. Furthermore, gut microbes were changed in response to oral sialic acid, such as Staphylococcus lentus, Corynebacterium stationis, Corynebacterium urealyticum, Jeotgalibaca sp_PTS2502, Ignatzschineria indica, Sporosarcina pasteurii, Sporosarcina sp_HW10C2, Facklamia tabacinasalis, Oblitimonas alkaliphila, Erysipelatoclostridium ramosum, Blautia sp_YL58, Bacteroids thetaiotaomicron, Morganella morganii, Clostridioides difficile, Helicobacter tryphlonius, Clostridium sp_Clone47, Alistipes finegoldii, [pseudomonas]_geniculata and Pseudomonas parafulva at the species level. In conclusion, oral sialic acid altered the intestinal pathological state and microbial compositions, and the effect of sialic acid on host health should be further studied.

Evolution of a Record-Setting AT-Rich Genome: Indel Mutation, Recombination, and Substitution Bias

Genome-wide nucleotide composition varies widely among species. Despite extensive research, the source of genome-wide nucleotide composition diversity remains elusive. Yeast mitochondrial genomes (mitogenomes) are highly A + T rich, and they provide a unique opportunity to study the evolution of AT-biased landscape. In this study, we sequenced ten complete mitogenomes of the Saccharomycodes ludwigii yeast with 8% G + C content, the lowest genome-wide %(G + C) in all published genomes to date. The S. ludwigii mitogenomes have high densities of short tandem repeats but severely underrepresented mononucleotide repeats. Comparative population genomics of these record-setting A + T-rich genomes shows dynamic indel mutations and strong mutation bias toward A/T. Indel mutations play a greater role in genomic variation among very closely related strains than nucleotide substitutions. Indels have resulted in presence–absence polymorphism of tRNA^Arg (ACG) among S. ludwigii mitogenomes. Interestingly, these mitogenomes have undergone recombination, a genetic process that can increase G + C content by GC-biased gene conversion. Finally, the expected equilibrium G + C content under mutation pressure alone is higher than observed G + C content, suggesting existence of mechanisms other than AT-biased mutation operating to increase A/T. Together, our findings shed new lights on mechanisms driving extremely AT-rich genomes.

MiR-122-3p regulates the osteogenic differentiation of mouse adipose-derived stem cells via Wnt/β catenin signaling pathway

OBJECTIVE

To explore the regulatory mechanism of micro-ribonucleic acid (miR)-122-3p in the osteogenic differentiation of mouse adipose-derived stem cells (mADSCs).

MATERIALS AND METHODS

The regulatory mechanism of miR-122-3p in the osteogenic differentiation of mesenchymal stem cells was investigated through its overexpression and knockdown.

RESULTS

The overexpression of miR-122-3p inhibited the osteogenic differentiation of mADSCs. On the contrary, its knockdown promoted the osteogenic differentiation of mADSCs. The further study on the molecular mechanism of miR-122-3p regulating mADSCs' osteogenic differentiation showed that the overexpression of miR-122-3p could activate the Wingless and int-1 (WNT)/β-catenin signaling pathway, but the knockdown of miR-122-3p could repress this signaling pathway.

CONCLUSIONS

MiR-122-3p influences the osteogenic differentiation of mADSCs by modulating the WNT/β-catenin signaling pathway.

0727 Study Onthe Effect Of Obstructive Sleep Apnea-hypopnea Syndrome Onperioperative Management Inendoscopic Sinussurgerypatients

Introduction

To determine the frequency of undiagnosed OSA patients in patients received endoscopic sinus surgery (ESS) and to investigate the effect of OSA on the perioperative management in those patients.

Methods

308 patients undergoing ESS from 2017-2019 were enrolled. The patients were divided into two groups according to whether OSA was combined. STOP-Bang questionnaire scoring system was used to classify patients into high risk and low risk for OSA. The differences between perioperative management and complications between the two groups were compared.

Results

308 consecutive cases were included, 46 cases (14.9%) combined with OSA and 108 cases (35.0%) were at high risk of OSA. OSA patients have higher morbidity of hypertension (OR, 2.05; CI, 1.07-3.92; P=0.03), hyperlipidemia (OR, 2.19; CI, 1.06- 4.51; P=0.03), longer hospitalization time(7.0±2.7 vs. 5.4±3.6, P≤0.01) and higher incidence of intubation difficulties (OR, 3.74; CI,1.39-10.1; P=0.01). Patients at high risk of OSA also had increased rates of hypertension, hyperlipidemia, coronary heart disease and post-operative cardiovascular and respiratory complications.

Conclusion

OSA or high scores of STOP-Bang are associated with increased perioperative complications in ESS patients. Preoperative OSA screening should be strengthened to improve the safety and prognosis of ESS surgery.

Support

National Natural Science Foundation of China under Grant [number 81670903]; and Beijing Municipal Administration of Hospitals Ascent Plan under Grant [number DFL20150602]

The Absence of Calponin 2 in Rabbits Suggests Caution in Choosing Animal Models

While the rapid development of CRISPR/CAS9 technology has allowed for readily performing site-specific genomic editing in non-rodent species, an emerging challenge is to select the most suitable species to generate animal models for the study of human biology and diseases. Improving CRISPR/CAS9 methodology for more effective and precise editing in the rabbit genome to replicate human disease is an active area of biomedical research. Although rabbits are more closely related to humans than mice (based on DNA sequence analysis), our whole-genome protein database search revealed that rabbits have more missing human protein sequences than mice. Hence, precisely replicating human diseases in rabbits requires further consideration, especially in studies involving essential functions of the missing proteins. For example, rabbits lack calponin 2, an actin-associated cytoskeletal protein that is important in the pathogenesis of inflammatory arthritis, atherosclerosis, and calcific aortic valve disease. The justification of using rabbits as models for human biomedical research is based on their larger size and their closer phylogenetic distance to humans (based on sequence similarity of conserved genes), but this may be misleading. Our findings, which consider whole-genome protein profiling together with actual protein expressions, serve as a warning to the scientific community to consider overall conservation as well as the conservation of specific proteins when choosing an animal model to study a particular aspect of human biology prior to investing in genetic engineering.

In-vivo assessment of T cell kinetics in individuals at risk for type 1 diabetes

We previously assessed the kinetics of T cell turnover in vivo by labeling cells with ² H-H₂ O over 42 days in individuals with type 1 diabetes (T1D) and demonstrated an increased turnover of CD4 memory T cells. We have now tested T cell turnover in individuals at risk for T1D using a 3-4-day labeling protocol with ² H-glucose. We studied 30 relatives with T1D with and without autoantibodies, and 10 healthy controls. Peripheral blood mononuclear cells (PBMC) were flow-sorted into T cell subsets of interest; ² H-DNA enrichment was measured by mass spectrometry and in-vivo turnover was calculated as maximum fractional enrichment of deuterated adenosine (F_max ). Among CD4⁺ cells, F_max was highest in regulatory T cells (T_reg ), followed by effector and central memory T cells and lowest in naive cells. Similarly, CD8⁺ central and effector memory T cells had a higher turnover than CD8⁺ terminally differentiated effector memory T cells (TEMRA) and CD8⁺ -naive T cells. Relatives as a group showed significantly increased T_reg turnover by F_max compared to controls (1·733 ± 0·6784% versus 1·062 ± 0·3787%, P = 0·004), suggesting pre-existing immune dysfunction within families with T1D. However, there was no significant difference in F_max between groups according to autoantibody or glucose tolerance status. Repeat testing in 20 subjects 1 year later demonstrated relatively higher within-subject compared to between-subject variability for the measurement of F_max in various T cell subsets. The short labeling protocol with ² H-glucose should be applied in the context of a clinical trial in which the therapy is expected to have large effects on T cell turnover.

Abstract P1-18-03: Phase I trial to assess the safety, pharmacokinetics and pharmacodynamics of receptor activator of nuclear factor-κB ligand inhibitor (TK006) in patients with bone metastases from breast cancer

Background

Within the bone microenvironment, tumor cells secrete factors that stimulate osteoblasts to express and secrete receptor activator of nuclear factor-κB ligand (RANKL), which binds to its receptor RANK on the surface of osteoclasts, thus enhancing the osteoclast-mediated bone resorption and promoting skeletal complications.TK006 is a fully human monoclonal antibody that binds and inhibits RANKL, thus inhibiting osteoclast-mediated bone destruction.

Objective

To investigate the safety, pharmacokinetics and pharmacodynamics of TK006 in patients with bone metastases from breast cancer.

Patients and methods

In this dose-escalating study, patients were sequentially enrolled into 60 mg, 120 mg, 180 mg single-dosing and 120 multiple-dosing cohorts. Before making dose escalation decision, the safety of TK006 during the 14-day period after dosing in the prior cohort must be confirmed. In the three single-dosing cohorts, patients were followed up for 16 weeks after dosing. In the 120 mg multiple-dosing cohort, patents were treated with 120 mg TK006 every 4 weeks for 3 times totally, and followed up for 20 weeks after the first dosing. The primary outcome was safety profile, and the secondary outcomes were pharmacokinetics, pharmacodynamics and immunogenicity. Pharmacodynamics was measured by level of serum bone alkaline phosphatase (BALP) and urine creatinine corrected cross-linked N-telopeptides of type I collagen (uNTX/Cr).

Patients aged 18 to 65 years with breast cancer related bone metastasis were eligible. It was planned to enroll 10 subjects in each cohort for a total sample size of 40 subjects.

Result

As of May 24 2018, the common adverse events (AEs) related to treatment (≥10%) included: hypocalcemia (25.0%), limbs pain (20.0%), gamma-glutamyl transferase increased (17.5%), lactate dehydrogenase increased (12.5%), alpha-hydroxybutyric dehydrogenase increased (12.5%), aspertate aminotransferase increased (12.5%), alanine aminotransferase (10.0%),osphyalgia (10.0%) toothache (10.0%) and hypertriglyceridemia (10%). Most adverse reactions were mild or moderate except one case of grade 3 hypertriglyceridemia and two cases of grade 3 gamma-glutamyl transferase increasement. No esteonecrosis of the jaw or treatment-related SAE was reported.

In the 60 mg single-dosing cohort, a significant reduction in median uNTX/Cr was observed as early as day 1, the nadir of median uNTX/Cr was reach at day 28 and started to return towards the baseline level at day 112 (Table 1).

Only modest decreasing from baseline in median bone-specific alkaline phosphatase was observed.

Table 1.Effects of 60 mg TK006 therapy on bone turnover markers uNTX/Cr, % change from baseline, medianBALP , % change from baseline, medianD1-38.6-4.7D7-63.01.7D14-55.30.2D28-69.2-0.2D56-57.9-12.1D84-33.4-0.4D1121.3-18.7

Ostalgia was measured by visual analogue scale (VAS). In the 60 mg single-dosing cohort, scores were reduced to 2 from 5 and 3 in two patients individually. No increasing in pain was observed in the remaining 8 patients.

Conclusion

These results suggested a potential therapeutic role for TK006 in patients with bone metastases from breast cancer.

Citation Format: Mei YY, Hai TJ, Wei L, Xiang H, Hao W, Ming ZX, An LX. Phase I trial to assess the safety, pharmacokinetics and pharmacodynamics of receptor activator of nuclear factor-κB ligand inhibitor (TK006) in patients with bone metastases from breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-18-03.

Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora

Plastid genomes (plastomes) vary enormously in size and gene content among the many lineages of nonphotosynthetic plants, but key lineages remain unexplored. We therefore investigated plastome sequence and expression in the holoparasitic and morphologically bizarre Balanophoraceae. The two Balanophora plastomes examined are remarkable, exhibiting features rarely if ever seen before in plastomes or in any other genomes. At 15.5 kb in size and with only 19 genes, they are among the most reduced plastomes known. They have no tRNA genes for protein synthesis, a trait found in only three other plastid lineages, and thus Balanophora plastids must import all tRNAs needed for translation. Balanophora plastomes are exceptionally compact, with numerous overlapping genes, highly reduced spacers, loss of all cis-spliced introns, and shrunken protein genes. With A+T contents of 87.8% and 88.4%, the Balanophora genomes are the most AT-rich genomes known save for a single mitochondrial genome that is merely bloated with AT-rich spacer DNA. Most plastid protein genes in Balanophora consist of ≥90% AT, with several between 95% and 98% AT, resulting in the most biased codon usage in any genome described to date. A potential consequence of its radical compositional evolution is the novel genetic code used by Balanophora plastids, in which TAG has been reassigned from stop to tryptophan. Despite its many exceptional properties, the Balanophora plastome must be functional because all examined genes are transcribed, its only intron is correctly trans-spliced, and its protein genes, although highly divergent, are evolving under various degrees of selective constraint.

Genetic Drift and Indel Mutation in the Evolution of Yeast Mitochondrial Genome Size

Mitochondrial genomes (mitogenomes) are remarkably diverse in genome size and organization, but the origins of dynamic mitogenome architectures are still poorly understood. For instance, the mutational burden hypothesis postulates that the drastic difference between large plant mitogenomes and streamlined animal mitogenomes can be driven by their different mutation rates. However, inconsistent trends between mitogenome sizes and mutation rates have been documented in several lineages. These conflicting results highlight the need of systematic and sophisticated investigations on the evolution and diversity of mitogenome architecture. This study took advantage of the strikingly variable mitogenome size among different yeast species and also among intraspecific strains, examined sequence dynamics of introns, GC-clusters, tandem repeats, mononucleotide repeats (homopolymers) and evaluated their contributions to genome size variation. The contributions of these sequence features to mitogenomic variation are dependent on the timescale, over which extant genomes evolved from their last common ancestor, perhaps due to a combination of different turnover rates of mobile sequences, variable insertion spaces, and functional constraints. We observed a positive correlation between mitogenome size and the level of genetic drift, suggesting that mitogenome expansion in yeast is likely driven by multiple types of sequence insertions in a primarily nonadaptive manner. Although these cannot be explained directly by the mutational burden hypothesis, our results support an important role of genetic drift in the evolution of yeast mitogenomes.

[Association between hypothyroidism and sleep breathing disorders in patients with coronary heart disease]

Objective: To explore the association between hypothyroidism and sleep breathing disorders in patients with coronary heart disease (CHD). Methods: A total of 784 patients with CHD were consecutively enrolled at the Emergency & Critical Care Center of Beijing Anzhen Hospital from June 2015 to May 2017. According to thyroid function test results, patients were divided into hypothyroidism group (79 cases) and non-hypothyroidism group (705 cases). All patients had undergone sleep monitoring. The sleep apnea status was compared between the two groups. Multivariate logistic regression and linear regression models were used to analyze the association between hypothyroidism and sleep breathing disorders in patients with CHD. Results: The proportion of females, mean body weight and body mass index in the hypothyroidism group were higher than those in the non-hypothyroidism group [26.6% vs.16.2%, (78.6±11.6) kg vs. (75.7±12.0) kg, (27.7±3.2) kg/m(2) vs. (26.6±3.5) kg/m(2), all P<0.05]. Patients in hypothyroidism group had a decreased average oxygen saturation (SaO(2)) compared with patients in non-hypothyroidism group [ (93.2±2.9) % vs. (93.9±2.0) %, P=0.030]. In addition, events of hypoventilation in hypothyroidism group were significantly higher than those in non-hypothyroidism group[92.5 (45.8, 758.3) times vs. 68.0 (33.0, 125.0) times, P=0.013]. There were no significant differences in apnea hypopnea index, diagnosis of obstructive sleep apnea and other sleep breathing parameters between the two groups (P>0.05). A multiple linear regression analysis found that in patients with CHD, the correlation between hypothyroidism and average sleep SaO(2) was significant (β=-0.508, 95%CI -0.989--0.026, P=0.039). Conclusions: CHD patients with hypothyroidism had a lower sleep average SaO(2), and a higher sleep hypopnea events. There is a correlation between hypothyroidism and sleep hypoxia in patients with CHD. Clinical trial registration: clinicalTrials.gov, NCT03362385.

Origin and Spread of Spliceosomal Introns: Insights from the Fungal Clade Zymoseptoria

Spliceosomal introns are a key feature of eukaryote genome architecture and have been proposed to originate from selfish group II introns from an endosymbiotic bacterium, that is, the ancestor of mitochondria. However, the mechanisms underlying the wide spread of spliceosomal introns across eukaryotic genomes have been obscure. In this study, we characterize the dynamic evolution of spliceosomal introns in the fungal genus Zymoseptoria at different evolutionary scales, that is, within a genome, among conspecific strains within species, and between different species. Within the genome, spliceosomal introns can proliferate in unrelated genes and intergenic regions. Among conspecific strains, spliceosomal introns undergo rapid turnover (gains and losses) and frequent sequence exchange between geographically distinct strains. Furthermore, spliceosomal introns could undergo introgression between distinct species, which can further promote intron invasion and proliferation. The dynamic invasion and proliferation processes of spliceosomal introns resemble the life cycles of mobile selfish (group I/II) introns, and these intron movements, at least in part, account for the dramatic processes of intron gain and intron loss during eukaryotic evolution.

Enhanced energy transfer in heterogeneous nanocrystals for near infrared upconversion photocurrent generation

The key to produce inorganic heterogeneous nanostructures, and to integrate multiple functionalities, is to enhance or at least retain the functionalities of different components of materials. However, this ideal scenario is often deteriorated at the interface of the heterogeneous nanostructures due to lattice mismatches, resulting in downgraded performance in most hybrid nanomaterials. Here, we report that there is a narrow window in controlling temperature in a Lewis acid-base reaction process to facilitate epitaxial alignment during the synthesis of hybrid nanomaterials. We demonstrate a perfectly fused NaYF₄:Yb,Tm@ZnO heterogeneous nanostructure, in which the semiconductor ZnO shell can be epitaxially grown onto lanthanide-doped upconversion nanoparticles. By achieving a matched crystal lattice, the interface defects and crystalline grain boundaries are minimized to enable more efficient energy transfer from the upconversion nanoparticles to the semiconductor, resulting in both enhanced upconversion luminescence intensity and superior photoelectrochemical properties. This strategy provides an outstanding approach to endow lanthanide-doped upconversion nanoparticles with versatile properties.

Identification of Conflicting Selective Effects on Highly Expressed Genes

Many different selective effects on DNA and proteins influence the frequency of codons and amino acids in coding sequences. Selection is often stronger on highly expressed genes. Hence, by comparing high- and low-expression genes it is possible to distinguish the factors that are selected by evolution. It has been proposed that highly expressed genes should (i) preferentially use codons matching abundant tRNAs (translational efficiency), (ii) preferentially use amino acids with low cost of synthesis, (iii) be under stronger selection to maintain the required amino acid content, and (iv) be selected for translational robustness. These effects act simultaneously and can be contradictory. We develop a model that combines these factors, and use Akaike's Information Criterion for model selection. We consider pairs of paralogues that arose by whole-genome duplication in Saccharmyces cerevisiae. A codon-based model is used that includes asymmetric effects due to selection on highly expressed genes. The largest effect is translational efficiency, which is found to strongly influence synonymous, but not non-synonymous rates. Minimization of the cost of amino acid synthesis is implicated. However, when a more general measure of selection for amino acid usage is used, the cost minimization effect becomes redundant. Small effects that we attribute to selection for translational robustness can be identified as an improvement in the model fit on top of the effects of translational efficiency and amino acid usage.

Forty-one cases of round ligament varicosities that are easily misdiagnosed as inguinal hernias

PURPOSE

To demonstrate the benefit and safety of conservative therapy for round ligament varicosities (RLVs) that are easily misdiagnosed as inguinal hernias.

METHODS

We retrospectively analyzed clinical materials of 41 consecutive cases of RLVs diagnosed by ultrasound in a single hospital from January 2011 to December 2015. Misdiagnosis rate, clinical and sonographic features, management after diagnosis and prognosis were recorded.

RESULTS

All forty-one cases were pregnant females in their second or third trimester. Twenty-eight cases were first misdiagnosed as inguinal hernias (68.3%). Thirty cases presented as reducible swelling in the inguinal area (73.2%), and twenty-five of which were painful (61.0%). Four cases only felt pain in the inguinal area without swelling (9.7%). Seven cases had no obvious discomfort (17.1%). All cases were diagnosed as RLVs by gray-scale and color Doppler ultrasonography and justified a wait-and-see strategy. Thirty-seven cases were followed until total recovery after delivery (follow-up rate 90.2%). Swelling with or without pain disappeared spontaneously postpartum.

CONCLUSIONS

RLVs are easily misdiagnosed as inguinal hernias and color Doppler of the inguinal area is the best examination for making the correct diagnosis. Conservative therapy for RLV is beneficial and safe when assured by color Doppler.

Molecular and structural changes related to hepatitis E virus antigen and its expression in testis inducing apoptosis in Mongolian gerbil model

Hepatitis E virus (HEV) infection has been associated with a wide range of extrahepatic manifestations, so this study was designed to examine the effect and role of HEV on structural and molecular changes in the testicular tissues of Mongolian gerbils experimentally infected with swine HEV. HEV RNA was first detected in testis at 14 days post-inoculation and reached a peak between 28 and 42 days later with viral load between 3.12 and 6.23 logs/g by PCR assays. Changes including vacuolation, sloughing of germ cells, formation of multinuclear giant cells, degeneration, necrosis of tubules and damaged blood-testis barrier were observed through transmission electron microscopy. HEV ORF2 antigen was detected in the sperm cell cytoplasm along with decrease in relative protein of zonula occludens-1 through immunohistochemistry. HEV ORF3 antigen and ZO-1 protein were detectable by Western blotting. Lower (P<.05) serum testosterone and higher (P<.05) blood urea nitrogen level was observed in inoculated Mongolian gerbils. Likewise, increased (P<.05) germ cell apoptosis rate was detected with significant increased expression of Fas-L and Fas in HEV-inoculated groups at each time points. Up-regulation (P<.05 or P<.01) in mRNA level of Fas-L, Fas, Bax, Bcl-2 and caspase-3 was observed in HEV RNA-positive testes. Our study demonstrated that after experimental inoculation, HEV can be detected in testis tissues and viral proteins produce structural and molecular changes that in turn disrupt the blood-testis barrier and induce germ cell apoptosis.

Evidence of Hepatitis E virus breaking through the blood-brain barrier and replicating in the central nervous system

Neurologic dysfunctions such as Guillain-Barre' syndrome, encephalitis, meningitis and transverse myelitis occur frequently in patients with hepatitis E virus (HEV) infection, and this study was conducted to better characterize the role of HEV in the pathogenesis of neurologic disorders. Genotype 4 strain of swine HEV was used to inoculate Mongolian gerbils. Reverse transcription-nested polymerase chain reaction (RT-nPCR), ELISA, histopathology, ultrastructural pathology and enzyme immunohistochemistry method were conducted to investigate the replication and localization of HEV in the central nervous system (CNS) and the consequent pathological changes. Both positive- and negative-strand HEV RNA was detectable in brain and spinal cord from 7 to 28 dpi (days postinoculation) via RT-nPCR. Various pathological changes such as perineural invasion, neuron necrosis, microglia nodule, lymphocyte infiltration, perivascular cuff and myelin degeneration were observed in HEV-positive brains and spinal cords. Immunohistochemical (IHC) staining targeting on HEV ORF2 protein revealed positive signals concentrated mainly in the cytoplasm of neuron, ependymal epithelium and choroid plexus area. Positive area density of ZO-1 (zonula occludens-1) in brain of HEV-positive gerbils decreased, while the GFAP (glial fibrillary acidic protein) expression was upregulated compared with control groups. These results provide strong evidence that HEV is able to damage the blood-brain barrier (BBB), replicate in brain and spinal cord, and hammer the causative role of HEV in the pathogenesis of neurologic disorders.

Rapidly Translated Polypeptides Are Preferred Substrates for Cotranslational Protein Degradation

Nascent polypeptides are degraded by the proteasome concurrently with their synthesis on the ribosome. This process, called cotranslational protein degradation (CTPD), has been observed for years, but the underlying mechanisms remain poorly understood. Equally unclear are the identities of cellular proteins genuinely subjected to CTPD. Here we report the identification of CTPD substrates in the yeast Saccharomyces cerevisiae via a quantitative proteomic analysis. We compared the abundance of individual ribosome-bound nascent chains between a wild type strain and a mutant defective in CTPD. Of 1,422 proteins acquired from the proteomic analysis, 289 species are efficient CTPD substrates, with >30% of their nascent chains degraded cotranslationally. We found that proteins involved in translation, ribosome biogenesis, nuclear transport, and amino acid metabolism are more likely to be targeted for CTPD. There is a strong correlation between CTPD and the translation efficiency. CTPD occurs preferentially to rapidly translated polypeptides. CTPD is also influenced by the protein sequence length; longer polypeptides are more susceptible to CTPD. In addition, proteins with N-terminal disorder have a higher probability of being degraded cotranslationally. Interestingly, the CTPD efficiency is not related to the half-lives of mature proteins. These results for the first time indicate an inverse correlation between CTPD and cotranslational folding on a proteome scale. The implications of this study with respect to the physiological significance of CTPD are discussed.

Experimental Investigation on Curing Stress in Polymer Composite Using Digital Gradient Sensing Technique

The curing stress and deformation of epoxy resin and aramid fiber/epoxy composites was measured using Digital Gradient Sensing (DGS) technique. First, the working principle of the DGS method was explained, and the governing equations were derived based on angular deflections of light rays. Then the angle deflection of light rays due to curing stress of epoxy resin was measured, and the effect of the fiber bundle and aramid fiber fabric on the stress distribution during formation was analyzed. The experimental results show that angular deflections of light rays can be related to nonuniform distribution of curing stress in epoxy. The fiber bundles and fabric style have important effects on the curing stress distribution. These results play an important role for predicting curing stress and deformation of fiber reinforced composites.

Vibrations of thin plates with small clamped patches

Eigenvalues of fourth-order elliptic operators feature prominently in stability analysis of elastic structures. This paper considers out-of-plane modes of vibration of a thin elastic plate perforated by a collection of small clamped patches. As the radius of each patch shrinks to zero, a point constraint eigenvalue problem is derived in which each patch is replaced by a homogeneous Dirichlet condition at its centre. The limiting problem is consequently not the eigenvalue problem with no patches, but a new type of spectral problem. The discrepancy between the eigenvalues of the patch-free and point constraint problems is calculated. The dependence of the point constraint eigenvalues on the location(s) of clamping is studied numerically using techniques from numerical algebraic geometry. The vibrational frequencies are found to depend very sensitively on the number and centre(s) of the clamped patches. For a range of number of punctures, we find spatial clamping patterns that correspond to local maxima of the base vibrational frequency of the plate.

Postharvest Strategies for Managing Phytophthora Brown Rot of Citrus using Potassium Phosphite in Combination with Heat Treatments

Phytophthora brown rot, caused by several species of Phytophthora, is an economically important disease of citrus in areas with rainfall during the late stages of fruit development. Recent export restrictions of California orange fruit to China due to the presence of brown rot caused by the quarantine pathogen Phytophthora syringae have mandated more rigorous disease management. We evaluated postharvest applications with the phosphonate fungicide potassium phosphite in combination with heat treatments. In timing studies, potassium phosphite at 1,500 μg/ml was most effective when applied within 18 h after inoculation of orange fruit with P. citrophthora, reducing the incidence of decay by >96% as compared with the control. Potassium phosphite was also highly effective in inoculations with P. syringae. Heated water treatments at 60°C were consistently and highly effective in reducing the incidence of brown rot after inoculation with P. citrophthora, whereas treatments at 55 or 50°C were more variable and generally less effective. Two-stage treatments of fruit were conducted in the laboratory to simulate current packinghouse practices and to evaluate any interaction of the efficacy of potassium phosphite with treatments of two commonly used postharvest fungicides (i.e., imazalil and thiabendazole [TBZ]) or a postharvest carnauba-based fruit coating. In these studies, an aqueous imazalil-potassium phosphite (2,000 μg/ml) dip at ambient temperature that was followed by a spray treatment of imazalil and TBZ prepared in fruit coating significantly reduced the incidence of brown rot from the control. When the aqueous dip was applied at 54°C, brown rot developed in only 1% of the fruit as compared with 76% in the water control. The efficacy of potassium phosphite was also demonstrated in commercial packinghouse treatments. Based on our research, this fungicide was registered for postharvest use against brown rot of citrus and is exempt from tolerance in the United States and many other countries.

Extensive Horizontal Transfer and Homologous Recombination Generate Highly Chimeric Mitochondrial Genomes in Yeast

The frequency of horizontal gene transfer (HGT) in mitochondrial DNA varies substantially. In plants, HGT is relatively common, whereas in animals it appears to be quite rare. It is of considerable importance to understand mitochondrial HGT across the major groups of eukaryotes at a genome-wide level, but so far this has been well studied only in plants. In this study, we generated ten new mitochondrial genome sequences and analyzed 40 mitochondrial genomes from the Saccharomycetaceae to assess the magnitude and nature of mitochondrial HGT in yeasts. We provide evidence for extensive, homologous-recombination-mediated, mitochondrial-to-mitochondrial HGT occurring throughout yeast mitochondrial genomes, leading to genomes that are highly chimeric evolutionarily. This HGT has led to substantial intraspecific polymorphism in both sequence content and sequence divergence, which to our knowledge has not been previously documented in any mitochondrial genome. The unexpectedly high frequency of mitochondrial HGT in yeast may be driven by frequent mitochondrial fusion, relatively low mitochondrial substitution rates and pseudohyphal fusion to produce heterokaryons. These findings suggest that mitochondrial HGT may play an important role in genome evolution of a much broader spectrum of eukaryotes than previously appreciated and that there is a critical need to systematically study the frequency, extent, and importance of mitochondrial HGT across eukaryotes.

Aerobic Stability and Effects of Yeasts during Deterioration of Non-fermented and Fermented Total Mixed Ration with Different Moisture Levels

The present experiment evaluated the influence of moisture level and anaerobic fermentation on aerobic stability of total mixed ration (TMR). The dynamic changes in chemical composition and microbial population that occur after air exposure were examined, and the species of yeast associated with the deterioration process were also identified in both non-fermented and fermented TMR to deepen the understanding of aerobic deterioration. The moisture levels of TMR in this experiment were adjusted to 400 g/kg (low moisture level, LML), 450 g/kg (medium moisture level, MML), and 500 g/kg (high moisture level, HML), and both non-fermented and 56-d-fermented TMR were subjected to air exposure to determine aerobic stability. Aerobic deterioration resulted in high losses of nutritional components and largely reduced dry matter digestibility. Non-fermented TMR deteriorated during 48 h of air exposure and the HML treatment was more aerobically unstable. On dry matter (DM) basis, yeast populations significantly increased from 10(7) to 10(10) cfu/g during air exposure, and Candida ethanolica was the predominant species during deterioration in non-fermented TMR. Fermented TMR exhibited considerable resistance to aerobic deterioration. Spoilage was only observed in the HML treatment and its yeast population increased dramatically to 10(9) cfu/g DM when air exposure progressed to 30 d. Zygosaccharomyces bailii was the sole yeast species isolated when spoilage occurred. These results confirmed that non-fermented and fermented TMR with a HML are more prone to spoilage, and fermented TMR has considerable resistance to aerobic deterioration. Yeasts can trigger aerobic deterioration in both non-fermented and fermented TMR. C. ethanolica may be involved in the spoilage of non-fermented TMR and the vigorous growth of Z. bailii can initiate aerobic deterioration in fermented TMR.

Serological surveillance for Penicillium marneffei infection in HIV-infected patients during 2004-2011 in Guangzhou, China

Prevalence of disseminated Penicillium marneffei infection is not known in human immunodeficiency virus (HIV)-infected patients. This retrospective study aimed to evaluate the prevalence of and risk factors for disseminated P. marneffei infection in HIV-infected patients during 2004-11 in Guangzhou, China. We tested 8131 archived HIV-infected patient serum samples for P. marneffei-specific mannoprotein (Mp1p) antigen using a highly sensitive and specific ELISA that we previously established. The CD4 count of 2686 cases was determined by flow cytometry. Logistic regression was used to assess predictors of Mp1p antigenaemia. The overall prevalence of disseminated penicilliosis as detected by positive serum Mp1p antigen was 9.36% (761/8131), in good concordance with Platelia™ Aspergillus immunoassay. During 2004-11, the prevalence increased to a peak of 12.58% (158/1256) in 2010 and decreased in 2011. Penicilliosis was strongly associated with progression from HIV to AIDS (OR 4.66, 95% CI 3.94-5.51, p <0.001) and humidity (OR 1.02, 95% CI 1.01-1.03, p 0.002). Disseminated penicilliosis occurred mainly during the rainy seasons (p <0.001). For 2686 cases with known CD4 count, logistic regression showed that CD4 count of <200 cells/μL was a risk factor for penicilliosis (OR 2.90, 95% CI 1.10-7.66, p 0.032), especially when it was <50 cells/μL (OR 24.26, 95% CI 10.63-55.36, p <0.001) during which 28.06% of patients developed disseminated penicilliosis. In conclusion, approximately 9.36% of the HIV-infected patients in our study developed disseminated penicilliosis. Rapid diagnosis may be achieved by performing serological surveillance for Mp1p antigenaemia as a routine procedure for all HIV-infected patients with CD4 count of <50 cells/μL.

HGT turbulence: Confounding phylogenetic influence of duplicative horizontal transfer and differential gene conversion

Horizontal gene transfer (HGT) often leads to phylogenetic incongruence. When "duplicative HGT" introduces a second copy of a pre-existing gene, the two copies may then engage in gene conversion, leading to phylogenetically mosiac genes. When duplicative HGT is followed by differential gene conversion among descendant lineages, as under the DH-DC model, phylogenetic analysis is further complicated. To explore the effects of DH-DC on phylogeny reconstruction, we analyzed two sets of sequences: (1) an augmented set of plant mitochondrial atp1 sequences for which we recently published evidence of DH-DC; and (2) a set of simulated sequences for which we varied the extent of chimerism, the number of chimeric genes and nucleotide substitution rates. We show that the phylogenetic behavior of evolutionarily chimeric genes is highly volatile and depends on both the degree of chimerism and the number of differentially chimeric genes present in the analysis. Furthermore, we show that the presence of chimeric genes in gene trees can spuriously affect the phylogenetic position of purely native sequences, especially by attracting these sequences toward basal positions in trees. We propose the term "HGT turbulence" to describe these complex effects of evolutionarily chimeric genes on phylogenetic results.

Extensive genomic variation within clonal bacterial groups resulted from homologous recombination

Due to divergence, genetic variation is generally believed to be high among distantly related strains, low among closely related ones and little or none within the same classified clonal groups. Several recent genome-wide studies, however, revealed that significant genetic variation resides in a considerable number of genes among strains with identical MLST (Multilocus sequence typing) types and much of the variation was introduced by homologous recombination. Recognizing and understanding genomic variation within clonal bacterial groups could shed new light on the evolutionary path of infectious agents and the emergence of particularly pathogenic or virulent variants. This commentary presents our recent contributions to this line of work.

DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood

Background

The study of discrete characters is crucial for the understanding of evolutionary processes. Even though great advances have been made in the analysis of nucleotide sequences, computer programs for non-DNA discrete characters are often dedicated to specific analyses and lack flexibility. Discrete characters often have different transition rate matrices, variable rates among sites and sometimes contain unobservable states. To obtain the ability to accurately estimate a variety of discrete characters, programs with sophisticated methodologies and flexible settings are desired.

Results

DiscML performs maximum likelihood estimation for evolutionary rates of discrete characters on a provided phylogeny with the options that correct for unobservable data, rate variations, and unknown prior root probabilities from the empirical data. It gives users options to customize the instantaneous transition rate matrices, or to choose pre-determined matrices from models such as birth-and-death (BD), birth-death-and-innovation (BDI), equal rates (ER), symmetric (SYM), general time-reversible (GTR) and all rates different (ARD). Moreover, we show application examples of DiscML on gene family data and on intron presence/absence data.

Conclusion

DiscML was developed as a unified R program for estimating evolutionary rates of discrete characters with no restriction on the number of character states, and with flexibility to use different transition models. DiscML is ideal for the analyses of binary (1s/0s) patterns, multi-gene families, and multistate discrete morphological characteristics.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-320) contains supplementary material, which is available to authorized users.

mGluR3 promotes proliferation of human embryonic cortical neural progenitor cells by activating ERK1/2 and JNK2 signaling pathway in vitro

Metabotropic glutamate receptors (mGluRs) regulate the proliferation and differentiation of neural progenitor cells (NPCs) in brain; however, the mechanisms remain unknown. In this study, we investigated the effect of mGluR3 on the proliferation of human embryonic neural progenitor cells (NPCs), the expression of cyclin D1 and the activation of signaling pathways of mitogen-activated protein kinases (MAPKs). The results showed that mGluR3 agonist N-Acetylaspartylglutamate (NAAG) increased the proliferation of NPCs by increasing cell activity, diameter of neurospheres and cell division. In addition, mGluR3 siRNA decreased the NPC proliferation. The protein expressions of cyclin D1 increased with NAAG treatment and decreased after siRNA treatment. It was also found that activation of extracellular signal-regulated protein kinase (ERK) and c-Jun N-terminal protein kinase (JNK) signaling pathways were involved in the proliferation of NPCs. NAAG increased phosphorylation of ERK1/2 and JNK2 levels, and meanwhile p-p38 level decreased; but p-ERK1/2 and p-JNK2 levels decreased after siRNA treatment, and p-p38 level increased. ERK1/2 inhibitor U0126 and JNK2 inhibitor SP600125 attenuated the increase of proliferation induced by NAAG. These findings demonstrated that mGluR3 promoted the proliferation of human embryonic cortical NPCs and increased cyclin D1 expression by activating ERK1/2 and JNK2 signaling pathways in vitro, suggesting that mGluR3 may be a target molecule for regulating NPC proliferation in brain development.

Inter-observer and intra-observer variability in the diagnosis of dysplasia in patients with inflammatory bowel disease: correlation of pathological and endoscopic findings

AIM

Colonic epithelial dysplasia is deemed the precursor lesion of cancer arising in inflammatory bowel disease (IBD). It has been suggested that many dysplastic lesions could be endoscopically detected to obtain target biopsies, leading to better yield. However, the clinical impact of a diagnosis of dysplasia may be hampered by a significant degree of histological and endoscopic intra-observer and inter-observer variability. This study aimed to evaluate intra-observer and inter-observer variability in the microscopic diagnosis of dysplasia in IBD and correlate endoscopic and histological findings.

METHOD

In total, 158 cases of ulcerative colitis and 14 of Crohn's disease with dysplasia were selected from a pathology database. Slides were blindly reviewed twice by two expert gastrointestinal pathologists. Results of endoscopic examinations were extracted from the reports. The degree of intra-observer and inter-observer variability was determined by kappa statistics.

RESULTS

Overall, there was an excellent degree of histopathological inter-observer agreement (κ = 0.786). The lowest level of agreement in the dysplasia group was for indefinite dysplasia (κ = 0.251). Negative and high grade dysplasia diagnosis reached the highest level of agreement with κ values of 0.822 [95% confidence interval (CI) 0.673-0.971] and 1.00 (95% CI 0.850-1.149), respectively. Intra-observer agreement was good and increased during the latter period of the study (κ = 0.734, 95% CI 0.642-0.826). Endoscopic-histological correlation was poor among the negative endoscopies, as up to 43% of cases were diagnosed with at least focal high grade dysplasia. The endoscopic-histological correlation improved when evaluating suspicious endoscopic lesions.

CONCLUSION

Dysplasia is reliably diagnosed by expert gastrointestinal pathologists but has poor correlation with an endoscopic diagnosis of dysplasia.

Unrecognized fine-scale recombination can mimic the effects of adaptive radiation

Gene sequences can undergo accelerated nucleotide changes and rapid diversification. The rapid sequence changes can then potentially lead to phylogenetic incongruence. Recently, Bodilis et al. (2011) observed artificial phylogenetic incongruence using the Pseudomonas surface protein gene oprF, and hypothesized that it was the result of a long-branch attraction artifact ultimately caused by adaptive radiation. In this study, an alternative hypothesis, namely fine-scale recombination, was tested on the same dataset. The results reveal that regions in oprF are of different evolutionary origins, and the mosaic gene structure resulted in confounding phylogenetic signals. These findings demonstrate that unrecognized fine-scale recombination can confound the phylogenetic interpretation and emphasize the limitation of using whole genes as the unit of phylogenetic analysis.

Homologous recombination drives both sequence diversity and gene content variation in Neisseria meningitidis

The study of genetic and phenotypic variation is fundamental for understanding the dynamics of bacterial genome evolution and untangling the evolution and epidemiology of bacterial pathogens. Neisseria meningitidis (Nm) is among the most intriguing bacterial pathogens in genomic studies due to its dynamic population structure and complex forms of pathogenicity. Extensive genomic variation within identical clonal complexes (CCs) in Nm has been recently reported and suggested to be the result of homologous recombination, but the extent to which recombination contributes to genomic variation within identical CCs has remained unclear. In this study, we sequenced two Nm strains of identical serogroup (C) and multi-locus sequence type (ST60), and conducted a systematic analysis with an additional 34 Nm genomes. Our results revealed that all gene content variation between the two ST60 genomes was introduced by homologous recombination at the conserved flanking genes, and 94.25% or more of sequence divergence was caused by homologous recombination. Recombination was found in genes associated with virulence factors, antigenic outer membrane proteins, and vaccine targets, suggesting an important role of homologous recombination in rapidly altering the pathogenicity and antigenicity of Nm. Recombination was also evident in genes of the restriction and modification systems, which may undermine barriers to DNA exchange. In conclusion, homologous recombination can drive both gene content variation and sequence divergence in Nm. These findings shed new light on the understanding of the rapid pathoadaptive evolution of Nm and other recombinogenic bacterial pathogens.

Escherichia coli O104:H4 infections and international travel

We analyzed travel-associated clinical isolates of Escherichia coli O104:H4, including 1 from the 2011 German outbreak and 1 from a patient who returned from the Philippines in 2010, by genome sequencing and optical mapping. Despite extensive genomic similarity between these strains, key differences included the distribution of toxin and antimicrobial drug–resistance determinants.

Phylogenetic incongruence in E. coli O104: understanding the evolutionary relationships of emerging pathogens in the face of homologous recombination

Escherichia coli O104:H4 was identified as an emerging pathogen during the spring and summer of 2011 and was responsible for a widespread outbreak that resulted in the deaths of 50 people and sickened over 4075. Traditional phenotypic and genotypic assays, such as serotyping, pulsed field gel electrophoresis (PFGE), and multilocus sequence typing (MLST), permit identification and classification of bacterial pathogens, but cannot accurately resolve relationships among genotypically similar but pathotypically different isolates. To understand the evolutionary origins of E. coli O104:H4, we sequenced two strains isolated in Ontario, Canada. One was epidemiologically linked to the 2011 outbreak, and the second, unrelated isolate, was obtained in 2010. MLST analysis indicated that both isolates are of the same sequence type (ST678), but whole-genome sequencing revealed differences in chromosomal and plasmid content. Through comprehensive phylogenetic analysis of five O104:H4 ST678 genomes, we identified 167 genes in three gene clusters that have undergone homologous recombination with distantly related E. coli strains. These recombination events have resulted in unexpectedly high sequence diversity within the same sequence type. Failure to recognize or adjust for homologous recombination can result in phylogenetic incongruence. Understanding the extent of homologous recombination among different strains of the same sequence type may explain the pathotypic differences between the ON2010 and ON2011 strains and help shed new light on the emergence of this new pathogen.

Understanding Cr segregation at the He bubble surface in Fe

Although Cr segregation at the free Fe surface is weak, noticeable segregation of Cr at the He bubble surface in Fe has recently been observed. To understand the driving force for Cr segregation, we have carried out first-principles density functional theory calculations on the energetics of solute Cr atoms at the He bubble surface, which was modeled by a Fe/He interface. We find that both the compressive stress produced by the He bubble and the direct interfacial interaction promote Cr segregation from inside the bulk to the bubble surface, along with reduced spin polarization. Electronic structure analyses show that at the Fe/He interface, Cr is more compressible than Fe due to having more empty e(g) orbitals and, accordingly, the Fe surface gets energetically more favorable for Cr than in the bulk. On the other hand, the segregation of Cr increases the charge density at the bubble surface, and thus hinders assimilation of further He atoms.

Human exposure from dioxins in soil

Dioxins are a family of chemical compounds that has received considerable attention, both historically and currently. This article reviews scientific field studies that examine the relationship between living on soil contaminated with dioxins and the level of dioxins in people's serum, with an emphasis on the University of Michigan Dioxin Exposure Study (UMDES), the largest and most comprehensive study of its kind. These studies conclude that the levels of dioxins in serum are most strongly correlated with age, gender, body mass index, weight loss, breast feeding, and smoking. Levels of dioxins in soil are not significant predictors for dioxin concentrations in serum. The increase in serum dioxin levels that is seen with age results from historic exposure and does not represent ongoing exposure. Based on the scientific field studies conducted to date, it appears that, in the absence of the consumption of contaminated animal products, there is little evidence of ongoing exposure from contaminated soil.

Extensive genomic variation within clonal complexes of Neisseria meningitidis

Meningococcal disease is a widely distributed complex disease affecting all age categories. It can cause severe meningitis and septicemia, especially in unvaccinated infants and young children. The causative agent, Neisseria meningitidis (Nm), can be phenotypically and genetically differentiated into serogroups and sequence types (STs) and has a highly dynamic population structure. To obtain a deeper understanding of the epidemiology of Nm, we sequenced seven Nm genomes. Large-scale genomic analysis was conducted with these 7 Nm genomes, 27 additional Nm genomes from GenBank, and 4 other Neisseria genomes. We observed extensive homologous recombination in all gene functional categories among different Nm genomes. Homologous recombination is so frequent that it has resulted in numerous chimeric open reading frames, including genes in the capsule biosynthesis cluster and loci targeted by commercial vaccines. Our results reveal that, despite widespread use, evolutionary relationships inferred from the standard seven-gene multilocus sequence typing (MLST) method could not predict virulence gene content or strain phenotype. In fact, up to 28% of the virulence-associated genes could differ between strains of identical STs. Consistent with previous studies, we found that allelic recombination is also associated with alterations in antibiotic susceptibility. Overall, these findings emphasize the extensive genomic plasticity of Nm and the limitations of standard molecular methods to quantify this genotypic and phenotypic diversity.

Evidence of intra-segmental homologous recombination in influenza A virus

The evolution of influenza viruses is remarkably dynamic. Influenza viruses evolve rapidly in sequence and undergo frequent reassortment of different gene segments. Homologous recombination, although commonly seen as an important component of dynamic genome evolution in many other organisms, is believed to be rare in influenza. In this study, 256 gene segments from 32 influenza A genomes were examined for homologous recombination, three recombinant H1N1 strains were detected and they most likely resulted from one recombination event between two closely rated parental sequences. These findings suggest that homologous recombination in influenza viruses tends to take place between strains sharing high sequence similarity. The three recombinant strains were isolated at different time periods and they form a clade, indicating that recombinant strains could circulate. In addition, the simulation results showed that many recombinant sequences might not be detectable by currently existing recombinant detection programs when the parental sequences are of high sequence similarity. Finally, possible ways were discussed to improve the accuracy of the detection for recombinant sequences in influenza.