Identification and characterization of microsatellite markers from the tropical sea cucumber, Stichopus horrens (Selenka)

Tropical commercial sea cucumber Stichopus horrens is extensively distributed throughout the tropical Indo-Pacific region, and wild stocks have been severely depleted over the past decade. In this study, we used the microsatellite enrichment library of S. horrens to identify and characterize 13 microsatellite loci, including 11 polymorphic loci and 2 monomorphic loci. Among the 11 polymorphic loci, the number of alleles was 3-8. The observed and expected heterozygosity varied from 0.1364 to 0.8966 and from 0.1653 to 0.7551, respectively. Additionally, all 11 polymorphic loci showed moderate and high polymorphism with the polymorphism information content (0.271-0.7311). A total of 9 polymorphic loci were in Hardy-Weinberg equilibrium, except for 2 loci (adjusted P = 0.004545). Linkage disequilibrium was not detected in any pairs of polymorphic loci. The present study will be useful for studying genetic structure, population conservation, and breeding of wild S. horrens; moreover, our results contribute to the phylogeny and evolutionary research of Holothuroidea.

Modelling the natural history of Huntington's disease progression

BACKGROUND

The lack of reliable biomarkers to track disease progression is a major problem in clinical research of chronic neurological disorders. Using Huntington's disease (HD) as an example, we describe a novel approach to model HD and show that the progression of a neurological disorder can be predicted for individual patients.

METHODS

Starting with an initial cohort of 343 patients with HD that we have followed since 1995, we used data from 68 patients that satisfied our filtering criteria to model disease progression, based on the Unified Huntington's Disease Rating Scale (UHDRS), a measure that is routinely used in HD clinics worldwide.

RESULTS

Our model was validated by: (A) extrapolating our equation to model the age of disease onset, (B) testing it on a second patient data set by loosening our filtering criteria, (C) cross-validating with a repeated random subsampling approach and (D) holdout validating with the latest clinical assessment data from the same cohort of patients. With UHDRS scores from the past four clinical visits (over a minimum span of 2 years), our model predicts disease progression of individual patients over the next 2 years with an accuracy of 89-91%. We have also provided evidence that patients with similar baseline clinical profiles can exhibit very different trajectories of disease progression.

CONCLUSIONS

This new model therefore has important implications for HD research, most obviously in the development of potential disease-modifying therapies. We believe that a similar approach can also be adapted to model disease progression in other chronic neurological disorders.

Randomised clinical trial: the clinical efficacy and safety of an alginate-antacid (Gaviscon Double Action) versus placebo, for decreasing upper gastrointestinal symptoms in symptomatic gastroesophageal reflux disease (GERD) in China

BACKGROUND

There is a paucity of large-scale studies evaluating the clinical benefit of the Gaviscon Double Action (DA) alginate-antacid formulation for treating gastroesophageal reflux disease (GERD) symptoms.

AIM

Randomised double-blind placebo-controlled parallel-group study to evaluate efficacy and safety of Gaviscon DA in reducing heartburn, regurgitation and dyspepsia symptoms in individuals with mild-to-moderate GERD in China.

METHODS

Participants with symptomatic GERD (n = 1107) were randomised to receive Gaviscon DA or placebo (two tablets four times daily) for seven consecutive days. The primary endpoint compared the change in Reflux Disease Questionnaire (RDQ) score for the GERD (heartburn + regurgitation) dimension between Gaviscon DA and placebo. Secondary endpoints compared the change in RDQ scores for individual heartburn, regurgitation and dyspepsia dimensions, overall treatment evaluation (OTE) scores and incidence of adverse events (AEs).

RESULTS

Mean RDQ GERD scores: 2.51 for Gaviscon DA and 2.50 for placebo at baseline; 1.25 for Gaviscon DA and 1.46 for placebo post treatment. Gaviscon DA was statistically superior to placebo in reducing GERD and dyspepsia RDQ scores [least-squares mean (LSM) difference: GERD -0.21, P < 0.0001; dyspepsia -0.18, P = 0.0004], despite a substantial placebo response. The Gaviscon DA group reported more favourable overall treatment responses than the placebo group across all OTE categories (P < 0.0001). Superior relief of GERD symptoms was observed both in those with non-erosive and those with erosive reflux disease (LSM difference -0.14 [P = 0.038] and -0.29 [P < 0.0001] respectively). Incidence of AEs was similar in both groups.

CONCLUSION

Gaviscon DA tablets provide effective and safe reduction in acid reflux and dyspepsia symptoms in Chinese individuals with mild-to-moderate GERD. ClinicalTrials.gov: NCT01869491.

Screening adherence and cancer risk perceptions in colorectal cancer survivors with Lynch-like syndrome

Cancer screening recommendations for patients with Lynch-like syndrome (LLS) are not well defined. We evaluated adherence to Lynch syndrome (LS) screening recommendations, cancer risk perceptions, and communication within the families among colorectal cancer (CRC) survivors with LLS. Thirty-four participants with LLS completed a questionnaire about risk perception, adherence to LS screening recommendations, and communication with relatives. Clinical data were obtained from medical records. Most participants (76%) believed they should undergo colonoscopy every 1-2 years. Only 41% correctly interpreted their genetic tests as uninformative negative or as variant of unknown significance for LS. Less than half had had an upper gastrointestinal endoscopy for screening purpose. Among female participants, 86% had been screened for endometrial cancer (EC) and 71% for ovarian cancer. Most participants had informed relatives about the CRC diagnosis and advised them to undergo CRC screening, but only 50% advised female relatives to be screened for EC and only one-third advised relatives to have genetic counseling. Most CRC survivors with LLS follow the same cancer screening recommended for LS patients but do not understand the meaning of LLS. Greater care must be devoted to communicating the implications of nondiagnostic germline mutation testing among patients with LLS.

Observation of Z_{c}(3900)^{0} in e^{+}e^{-}→π^{0}π^{0}J/ψ

Using a data sample collected with the BESIII detector operating at the BEPCII storage ring, we observe a new neutral state Z_{c}(3900)^{0} with a significance of 10.4σ. The mass and width are measured to be 3894.8±2.3±3.2  MeV/c^{2} and 29.6±8.2±8.2  MeV, respectively, where the first error is statistical and the second systematic. The Born cross section for e^{+}e^{-}→π^{0}π^{0}J/ψ and the fraction of it attributable to π^{0}Z_{c}(3900)^{0}→π^{0}π^{0}J/ψ in the range E_{c.m.}=4.19-4.42  GeV are also determined. We interpret this state as the neutral partner of the four-quark candidate Z_{c}(3900)^{±}.

Observation and Spin-Parity Determination of the X(1835) in J/ψ→γK_{S}^{0}K_{S}^{0}η

We report an observation of the process J/ψ→γX(1835)→γK_{S}^{0}K_{S}^{0}η at low K_{S}^{0}K_{S}^{0} mass with a statistical significance larger than 12.9σ using a data sample of 1.31×10^{9} J/ψ events collected with the BESIII detector. In this region of phase space the K_{S}^{0}K_{S}^{0} system is dominantly produced through the f_{0}(980). By performing a partial wave analysis, we determine the spin parity of the X(1835) to be J^{PC}=0^{-+}. The mass and width of the observed X(1835) are 1844±9(stat)_{-25}^{+16}(syst)  MeV/c^{2} and 192_{-17}^{+20}(stat)_{-43}^{+62}(syst)  MeV, respectively, which are consistent with the results obtained by BESIII in the channel J/ψ→γπ^{+}π^{-}η^{'}.

Isolation and characterization of microsatellite markers of sea cucumber Stichopus horrens

Curry fish (Stichopus horrens) is a tropical holothurian species and is widely distributed in the India-West Pacific. In the present study, 9 polymorphic microsatellite loci were isolated and characterized for S. horrens. These loci were tested in 30 individuals from Hainan Island in China. The number of alleles ranged from 2 to 5. The polymorphism information content ranged from 0.348-0.584. The levels of observed and expected heterozygosities varied from 0.1500-0.8000 and from 0.2014-0.5000, respectively. Most loci were in Hardy-Weinberg equilibrium, except HCS1-27 and HCS2-7, after sequential Bonferroni's correction, and no significant linkage disequilibrium was detected for any pairwise combination of loci. These polymorphic microsatellite loci will be useful for studying population structure and conservation strategy design for S. horrens.

Development and characterization of microsatellite markers for molecular genetic diversity in Atrina pectinata

The pen shell, Atrina pectinata, is an economically valuable species that is widely distributed along the coastal waters of temperate and tropical areas, mainly growing in the Indian and Pacific Oceans. Eight novel microsatellite loci from the genome of A. pectinata were developed using fast isolation by amplified fragment length polymorphism of sequence containing repeats. The loci were screened in 30 wild individuals. The results showed that the number of alleles per locus and the polymorphism information content ranged from 2-6 and from 0.233-0.447, respectively. Observed and expected heterozygosities varied from 0.2069-0.7931 and 0.1887-0.5124, respectively. No significant deviations from Hardy-Weinberg equilibrium were detected. These microsatellite loci will be useful for further population studies of genetic diversity, population structure assessment, and conservation of A. pectinata.

Observation of the ψ(1 3D2) State in e+e-→π+π-γχc1 at BESIII

We report the observation of the X(3823) state in the process e+e-→π+π-X(3823)→π+π-γχc1 with a statistical significance of 6.2σ, in data samples at center-of-mass energies sqrt[s]=4.230, 4.260, 4.360, 4.420, and 4.600 GeV collected with the BESIII detector at the BEPCII electron positron collider. The measured mass of the X(3823) state is (3821.7±1.3±0.7)  MeV/c2, where the first error is statistical and the second systematic, and the width is less than 16 MeV at the 90% confidence level. The products of the Born cross sections for e+e-→π+π-X(3823) and the branching ratio B[X(3823)→γχc1,c2] are also measured. These measurements are in good agreement with the assignment of the X(3823) state as the ψ(1 3D2) charmonium state.

Patient-controlled analgesia at the end of life at a pediatric oncology institution

BACKGROUND

Patient controlled anesthesia (PCA) is increasingly used to manage pain in pediatric cancer patients and is important in the treatment of escalating pain at the end of life. The description of the use of opioid PCA in this population has been limited.

PROCEDURE

This retrospective chart review of the last 2 weeks of life addressed the following objectives: (1) to describe the patient population treated with opioid PCA; (2) to describe the morphine-equivalent doses (MED) (mg/kg/day); and (3) to describe the pain scores (PS).

RESULTS

Twenty-eight percent of inpatients used opioid PCA for pain control during the last 2 weeks of life. The mean MED (mg/kg/day) (SD) at 2 weeks prior and the day of death were 10.7 (17.9) and 19 (25.8). The mean MED increased over the last 2 weeks of life for all patients and across age groups and cancer diagnoses (all P < 0.05). The mean MED was significantly higher in the younger age group (age <13 vs. age ≥ 13) on the day of death (P < 0.04). There was a significant change in mean PS over the last 2 weeks of life (P < 0.001), with the highest PS on the day before death. The most frequently used concurrent medications were benzodiazepines (91%).

CONCLUSIONS

Children and young adults with cancer experience high opioid requirements and significant dose increases during the last 2 weeks of life. Additionally, PS increase toward the end of life. Opioid rotation and addition of adjuvant medications merit consideration in the context of escalating opioid requirements.

Joint effects of gray matter atrophy and altered functional connectivity on cognitive deficits in amnestic mild cognitive impairment patients

BACKGROUND

Gray matter (GM) atrophy and disrupted intrinsic functional connectivity (IFC) are often present in patients with amnestic mild cognitive impairment (aMCI), which shows high risk of developing into Alzheimer's disease. Little is known, however, about the relationship between GM atrophy and altered IFC, and whether they are related to cognitive decline.

METHOD

A total of 30 aMCI and 26 cognitively normal (CN) subjects were recruited for this study. Optimized voxel-based morphometric and resting-state functional connectivity magnetic resonance imaging approaches were performed to measure the GM volumes (GMVs) and atrophy-related IFC, respectively. Multivariate linear regression analysis was used to examine the effects of GM atrophy and IFC on cognitive performance across subjects, after controlling for the effects of age, education, gender and group.

RESULTS

Compared with CN subjects, aMCI subjects showed significantly reduced GMVs and decreased IFC in the frontal-parietal and medial temporal lobe systems. Multivariate regression analysis further demonstrated that the GMVs and decreased IFC simultaneously affected the cognitive function. Specifically, GMVs were positively correlated with cognitive performances, including global cognition and episodic memory, and showed a strong trend in correlation between GMVs and non-episodic memory, whilst IFC was positively correlated with the above three cognitive measures, across all subjects. In addition, significant correlation was found between GMVs and altered IFC strength across all subjects.

CONCLUSIONS

Our findings demonstrated that GMVs and IFC jointly contribute to cognitive performance, and combining quantitative information about GMVs and the strength of functional connectivity may serve as an indicator of cognitive deficits in non-demented elderly.

Development and characterization of new microsatellite markers of Fenneropenaeus penicillatus

Thirteen new polymorphic microsatellite markers in Fenneropenaeus penicillatus were isolated and characterized. The polymorphism of the thirteen microsatellite markers was tested by 30 individuals from Lianjiang, China. It showed that the number of al-leles per locus ranged from 3 to 6 and the Polymorphism Information Content (PIC) was from 0.324 to 0.706. The observed and expected heterozygosities were 0.3217-0.8023 and 0.1977-0.6783, respectively. Only one loci (LJ-19) deviated significantly from Hardy-Weinberg equilibrium (HWE) (P < 0.00385) after Bonferroni correction, while the other twelve markers were in HWE after Bonferroni correction (P > 0.00385). The thirteen polymorphic microsatellite markers could pro-vide more genetic data for further research on cultivation and recovery of F. penicillatus.

Screening and characterization of novel polymorphic microsatellite markers from sea cucumber Holothuria leucospilota

The sea cucumber Holothuria leucospilota has high me-dicinal value and rich nutritional edible value, and thus is a commercially important aquatic product in China. Microsatellite loci were developed and screened using a fast isolation protocol and amplified fragment length polymorphism of sequences containing repeats. In this study, 16 novel polymorphic microsatellite markers in H. leucospilota were identified, and the relevant genetic variability index was assessed using 30 individu-als from a wild population. The polymorphic information content ranged from 0.183 to 0.668, and the number of alleles per locus varied from 3 to 5. The observed and expected heterozygosities were 0.0370-0.5000 and 0.0776-0.6250, respectively. With the exception of 3 loci (Y1-15, Y11-1, and Y28), the polymorphic loci were in Hardy-Weinberg equilibrium (P > 0.003125). These polymorphic microsatellite loci will contribute to studies of genetic diversity, the research of population structure, and the design of conservation strategies for H. leucospilota.

Isolation and characterization of polymorphic microsatellite loci in the sea cucumber Holothuria scabra

The sea cucumber Holothuria scabra is an endangered species. In this study, nine new polymorphic microsatellite loci were developed and tested in 30 individuals. The number of alleles ranged from 2 to 5, and the observed and expected heterozygosities ranged from 0.1200 to 0.7391 and from 0.2408 to 0.5983, respectively. No loci significantly deviated from the Hardy-Weinberg equilibrium af-ter a Bonferroni correction, and no significant linkage disequilibrium was found between pairs of loci. These polymorphic microsatellite loci will be useful in studying the genetic diversity of H. scabra and its conservation.

Diagnostic value of aberrant gene methylation in stool samples for colorectal cancer or adenomas: a meta-analysis

AIM

Many studies have reported detection of aberrant methylation of genes in stool sample for early colorectal cancer (CRC) or adenomas had high sensitivity and specificity, but still remained controversial. We aimed to evaluate the diagnostic value of stool testing for markers of CRC and adenomas.

METHODS

Medline, EMbase, Web of Science, the Cochrane Library, and EMbase were systematically searched. Meta-analysis was performed using a random effects model with sensitivity, specificity, diagnostic OR (DOR), area under the summary ROC curves (SROC) and their 95% confidence interval (95% CI).

RESULTS

A total of 13 studies including 716 patients with CRC 220 cases of adenoma and 414 healthy controls were eligible for final analysis. The sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and DOR for the detection of CRC were 0.78 (95% CI: 0.75-0.82), 0.90 (95% CI: 0.91-0.96), 9.612 (95% CI: 6.761-13.666), 0.243 (95% CI: 0.176-0.336), and 48.21 (95% CI: 28.24-82.30), respectively. The sensitivity and specificity for the detection of adenoma were 0.63 (95% CI: 0.56-0.69) and 0.93 (95% CI: 0.90-0.96), respectively. The area under the SROC curve was 0.9438 and 0.9385 in CRC and adenoma detection, respectively.

CONCLUSION

Fecal gene methylation testing as a noninvasive method can be used as a screening measurement for CRC or colorectal adenoma with high sensitivity and specificity.

Non-invasive prenatal testing for trisomies 21, 18 and 13: clinical experience from 146,958 pregnancies

OBJECTIVES

To report the clinical performance of massively parallel sequencing-based non-invasive prenatal testing (NIPT) in detecting trisomies 21, 18 and 13 in over 140,000 clinical samples and to compare its performance in low-risk and high-risk pregnancies.

METHODS

Between 1 January 2012 and 31 August 2013, 147,314 NIPT requests to screen for fetal trisomies 21, 18 and 13 using low-coverage whole-genome sequencing of plasma cell-free DNA were received. The results were validated by karyotyping or follow-up of clinical outcomes.

RESULTS

NIPT was performed and results obtained in 146,958 samples, for which outcome data were available in 112,669 (76.7%). Repeat blood sampling was required in 3213 cases and 145 had test failure. Aneuploidy was confirmed in 720/781 cases positive for trisomy 21, 167/218 cases positive for trisomy 18 and 22/67 cases positive for trisomy 13 on NIPT. Nine false negatives were identified, including six cases of trisomy 21 and three of trisomy 18. The overall sensitivity of NIPT was 99.17%, 98.24% and 100% for trisomies 21, 18 and 13, respectively, and specificity was 99.95%, 99.95% and 99.96% for trisomies 21, 18 and 13, respectively. There was no significant difference in test performance between the 72,382 high-risk and 40,287 low-risk subjects (sensitivity, 99.21% vs. 98.97% (P = 0.82); specificity, 99.95% vs. 99.95% (P = 0.98)). The major factors contributing to false-positive and false-negative NIPT results were maternal copy number variant and fetal/placental mosaicism, but fetal fraction had no effect.

CONCLUSIONS

Using a stringent protocol, the good performance of NIPT shown by early validation studies can be maintained in large clinical samples. This technique can provide equally high sensitivity and specificity in screening for trisomy 21 in a low-risk, as compared to high-risk, population.

Optimization of SCoT-PCR reaction system in Dactylis glomerata by orthogonal design

The effects of 5 factors (template DNA, Mg(2+), dNTPs, Taq DNA polymerase, and primer) on the polymerase chain reaction (PCR) were investigated to optimize the start codon targeted polymor-phism (SCoT)-PCR system of Dactylis glomerata L., using an orthogo-nal design L16 (4(5)). A suitable SCoT-PCR system for D. glomerata was established; the 20 μL reaction volume contained 3.0 mM Mg(2+), 0.2 mM dNTPs, 1.0 U Taq DNA polymerase, 0.2 μM primer, 20 ng tem-plate DNA, and 2 μL 10X buffer. Each factor had a different effect on the amplification reaction, and the concentration of dNTPs had the larg-est effect on the SCoT-PCR system. We tested 10 orchardgrass samples to determine and verify the stability of the reaction system. The results showed that amplified bands from diverse materials were clear, stable, and rich in polymorphisms, indicating that the optimized system was very stable.