A novel LncRNA-based prognostic score reveals TP53-dependent subtype of lung adenocarcinoma with poor survival

The prognostic signatures play an essential role in the era of personalised therapy for cancer patients including lung adenocarcinoma (LUAD). Long noncoding RNA (LncRNA), a relatively novel class of RNA, has shown to play a crucial role in all the areas of cancer biology. Here, we developed and validated a robust LncRNA-based prognostic signature for LUAD patients using three different cohorts. In the discovery cohort, four LncRNAs were identified with 10% false discovery rate and a hazard ratio of >10 using univariate Cox regression analysis. A risk score, generated from the four LncRNAs’ expression, was found to be a significant predictor of survival in the discovery and validation cohort (p = 9.97 × 10 ⁻⁸ and 1.41 × 10 ⁻³, respectively). Further optimisation of four LncRNAs signature in the validation cohort, generated a three LncRNAs prognostic score (LPS), which was found to be an independent predictor of survival in both the cohorts ( p = 1.00 × 10 ⁻⁶ and 7.27 × 10 ⁻⁴, respectively). The LPS also significantly divided survival in clinically important subsets, including Stage I ( p = 9.00 × 10 ⁻⁴ and 4.40 × 10 ⁻², respectively), KRAS wild-type (WT), KRAS mutant ( p = 4.00 × 10 ⁻³ and 4.30 × 10 ⁻², respectively) and EGFR WT ( p = 2.00 × 10 ⁻⁴). In multivariate analysis LPS outperformed, eight previous prognosticators. Further, individual members of LPS showed a significant correlation with survival in microarray data sets. Mutation analysis showed that high-LPS patients have a higher mutation rate and inactivation of the TP53 pathway. In summary, we identified and validated a novel LncRNA signature LPS for LUAD.     

Late-life plasma proteins associated with prevalent and incident frailty: A proteomic analysis

Proteomic approaches have unique advantages in the identification of biological pathways that influence physical frailty, a multifactorial geriatric syndrome predictive of adverse health outcomes in older adults. To date, proteomic studies of frailty are scarce, and few evaluated prefrailty as a separate state or examined predictors of incident frailty. Using plasma proteins measured by 4955 SOMAmers in the Atherosclerosis Risk in Community study, we identified 134 and 179 proteins cross-sectionally associated with prefrailty and frailty, respectively, after Bonferroni correction (p < 1 × 10⁻⁵) among 3838 older adults aged ≥65 years, adjusting for demographic and physiologic factors and chronic diseases. Among them, 23 (17%) and 82 (46%) were replicated in the Cardiovascular Health Study using the same models (FDR p < 0.05). Notably, higher odds of prefrailty and frailty were observed with higher levels of growth differentiation factor 15 (GDF15; p_prefrailty = 1 × 10⁻¹⁵, p_frailty = 2 × 10⁻¹⁹), transgelin (TAGLN; p_prefrailty = 2 × 10⁻¹², p_frailty = 6 × 10⁻²²), and insulin-like growth factor-binding protein 2 (IGFBP2; p_prefrailty = 5 × 10⁻¹⁵, p_frailty = 1 × 10⁻¹⁵) and with a lower level of growth hormone receptor (GHR, p_prefrailty = 3 × 10⁻¹⁶, p_frailty = 2 × 10⁻¹⁸). Longitudinally, we identified 4 proteins associated with incident frailty (p < 1 × 10⁻⁵). Higher levels of triggering receptor expressed on myeloid cells 1 (TREM1), TAGLN, and heart and adipocyte fatty-acid binding proteins predicted incident frailty. Differentially regulated proteins were enriched in pathways and upstream regulators related to lipid metabolism, angiogenesis, inflammation, and cell senescence. Our findings provide a set of plasma proteins and biological mechanisms that were dysregulated in both the prodromal and the clinical stage of frailty, offering new insights into frailty etiology and targets for intervention.     

Leveraging related health phenotypes for polygenic prediction of impulsive choice,impulsive action,and impulsive personality traits in 1534 European ancestry community adults

Impulsivity refers to a number of conceptually related phenotypes reflecting self-regulatory capacity that are considered promising endophenotypes for mental and physical health. Measures of impulsivity can be broadly grouped into three domains, namely, impulsive choice, impulsive action, and impulsive personality traits. In a community-based sample of ancestral Europeans (n = 1534), we conducted genome-wide association studies (GWASs) of impulsive choice (delay discounting), impulsive action (behavioral inhibition), and impulsive personality traits (UPPS-P), and evaluated 11 polygenic risk scores (PRSs) of phenotypes previously linked to self-regulation. Although there were no individual genome-wide significant hits, the neuroticism PRS was positively associated with negative urgency (adjusted R² = 1.61%, p = 3.6 × 10⁻⁷) and the educational attainment PRS was inversely associated with delay discounting (adjusted R² = 1.68%, p = 2.2 × 10⁻⁷). There was also evidence implicating PRSs of attention-deficit/hyperactivity disorder, externalizing, risk-taking, smoking cessation, smoking initiation, and body mass index with one or more impulsivity phenotypes (adjusted R²s: 0.35%–1.07%; FDR adjusted ps = 0.05–0.0006). These significant associations between PRSs and impulsivity phenotypes are consistent with established genetic correlations. The combined PRS explained 0.91%–2.46% of the phenotypic variance for individual impulsivity measures, corresponding to 8.7%–32.5% of their reported single-nucleotide polymorphism (SNP)-based heritability, suggesting a non-negligible portion of the SNP-based heritability can be recovered by PRSs. These results support the predictive validity and utility of PRSs, even derived from related phenotypes, to inform the genetics of impulsivity phenotypes.     

Comparison of mandibular bone mineral density in osteoporotic, osteopenic and normal elderly edentulous subjects measured by the dual-energy X-ray absorptiometry technique

doi: 10.1111/j.1741‐2358.2012.00625.x Comparison of mandibular bone mineral density in osteoporotic, osteopenic and normal elderly edentulous subjects measured by the dual‐energy X‐ray absorptiometry technique Objective: The aim of this study was to compare the mandibular body bone mineral density according to bone mineral density status of spine and femur measured by dual‐energy X‐ray absorptiometry (DXA) technique in elderly edentulous individuals. Background: One of the factors that affect the survival rate of implants is bone mineral density (BMD) of the jaws. Materials and methods: Fifty edentulous elderly patients’ (27 women and 23 men) spine, femur and the mandibular body BMDs were measured using DXA technique. BMD scans of the AP lumbar spine (L2–L3) and femur were classified using World Health Organisation criteria for bone mass. Results: There was a statistically significant difference between the normal femur group’s–osteoporosis group’s mandibular body BMD (p = 0.001) and femoral osteopaenia group’s–osteoporosis group’s mandibular body BMD (p < 0.001). The femoral osteoporosis group’s mandibular body BMDs were lower than those of both the normal femoral and the femoral osteopaenia group subjects’. Conclusion: Classification of edentulous mandibles according to low and high bone mineral densities is a problem in implant dentistry. The results of this study demonstrated that femoral bone mineral density status may be used to provide preliminary information about the bone mineral density of the mandibular body region in elderly edentulous subjects.     

A 16-mRNA signature optimizes recurrence-free survival prediction of Stages II and III gastric cancer

High-throughput messenger RNA (mRNA) analysis has become a powerful tool for exploring tumor recurrence or metastasis mechanisms. Here, we constructed a signature to predict the recurrence risk of Stages II and III gastric cancer (GC) patients. A least absolute shrinkage and selection operator method Cox regression model was utilized to construct the signature. Using this method, a 16-mRNA signature was identified to be associated with the relapse-free survival of Stages II and III GCs in training dataset GSE62254 (n = 194). Then this signature was validated in an independent Gene Expression Omnibus cohort GSE26253 (n = 297) and a dataset of The Cancer Genome Atlas (TCGA; n = 235). This classifier could successfully screen out the high-risk Stages II and III GCs in the training cohort (hazard ratio [HR] = 40.91; 95% confidence interval [CI] = 5.58–299.7; p < .0001). Analysis in two independent validation cohorts yielded consistent results (GSE26253: HR = 1.69, 95% CI = 1.17–2.43,; p = .0045; TCGA: HR = 2.01, 95% CI = 1.13–3.56, p = .0146). Cox regression analyses revealed that the risk score derived from this signature was an independent risk factor in Stages II and III GCs. Besides, a nomogram was constructed to serve clinical practice. Through gene set variation analysis, we found several gene sets associated with chemotherapeutic drug resistance and tumor metastasis significantly enriched in high-risk patients. In summary, this 16-mRNA signature can be used as a powerful tool for prognostic evaluation and help clinicians identify high-risk patients.     

Aged-Related Changes in Body Composition and Association between Body Composition with Bone Mass Density by Body Mass Index in Chinese Han Men over 50-year-old

Objectives

Aging, body composition, and body mass index (BMI) are important factors in bone mineral density (BMD). Although several studies have investigated the various parameters and factors that differentially influence BMD, the results have been inconsistent. Thus, the primary goal of the present study was to further characterize the relationships of aging, body composition parameters, and BMI with BMD in Chinese Han males older than 50 years.

Methods

The present study was a retrospective analysis of the body composition, BMI, and BMD of 358 Chinese male outpatients between 50 and 89 years of age that were recruited from our hospital between 2009 and 2011. Qualified subjects were stratified according to age and BMI as follows: 50–59 (n = 35), 60–69 (n = 123), 70–79 (n = 93), and 80–89 (n = 107) years of age and low weight (BMI: < 20 kg/m²; n = 21), medium weight (20 ≤ BMI < 24 kg/m²; n = 118), overweight (24 ≤ BMI < 28 kg/m²; n = 178), and obese (BMI ≥ 28 kg/m²; n = 41). Dual-energy X-ray absorptiometry (DEXA) was used to assess bone mineral content (BMC), lean mass (LM), fat mass (FM), fat-free mass (FFM), lumbar spine (L1-L4) BMD, femoral neck BMD, and total hip BMD. Additionally, the FM index (FMI; FM/height²), LM index (LMI; LM/height²), FFM index (FFMI; [BMC+LM]/height²), percentage of BMC (%BMC; BMC/[BMC+FM+LM] × 100%), percentage of FM (%FM; FM/[BMC+FM+LM] × 100%), and percentage of LM (%LM; LM/(BMC+FM+LM) × 100%) were calculated. Osteopenia or osteoporosis was identified using the criteria and T-score of the World Health Organization.

Results

Although there were no significant differences in BMI among the age groups, there was a significant decline in height and weight according to age (p < 0.0001 and p = 0.0002, respectively). The LMI and FFMI also declined with age (both p < 0.0001) whereas the FMI exhibited a significant increase that peaked in the 80-89-years group (p = 0.0145). Although the absolute values of BMC and LM declined with age (p = 0.0031 and p < 0.0001, respectively), there was no significant difference in FM. In terms of body composition, there were no significant differences in %BMC but there was an increase in %FM (p < 0.0001) and a decrease in %LM (p < 0.0001) with age. The femoral neck and total hip BMD significantly declined with age (p < 0.0001 and p = 0.0027, respectively) but there were no differences in L1-L4. BMD increased at all sites (all p < 0.01) as BMI increased but there were declines in the detection rates of osteoporosis and osteopenia (both p < 0.001). A logistic regression revealed that when the medium weight group was given a BMI value of 1, a decline in BMI was an independent risk factor of osteoporosis or osteopenia, while an increase in BMI was a protective factor for BMD. At the same time, BMD in L1-L4 exhibited a significant positive association with FMI (p = 0.0003) and the femoral neck and total hip BMDs had significant positive associations with FFMI and LMI, respectively (both p < 0.0001).

Conclusions

These data indicate that LMI and FFMI exhibited significant negative associations with aging in Chinese Han males older than 50 years, whereas FMI had a positive association. BMD in the femoral neck and total hip declined with age but an increased BMI was protective for BMD. LMI and FFMI were protective for BMD in the femoral neck and total hip.     

Growth rates of young-of-year shovelnose sturgeon in the Upper Missouri River

Information on growth during the larval and young‐of‐year life stages in natural river environments is generally lacking for most sturgeon species. In this study, methods for estimating ages and quantifying growth were developed for field‐sampled larval and young‐of‐year shovelnose sturgeon Scaphirhynchus platorynchus in the upper Missouri River. First, growth was assessed by partitioning samples of young‐of‐year shovelnose sturgeon into cohorts, and regressing weekly increases in cohort mean length on sampling date. This method quantified relative growth because ages of the cohorts were unknown. Cohort increases in mean length among sampling dates were positively related (P < 0.05, r² > 0.59 for all cohorts) to sampling date, and yielded growth rate estimates of 0.80–2.95 mm day⁻¹ (2003) and 0.44–2.28 mm day⁻¹ (2004). Highest growth rates occurred in the largest (and earliest spawned) cohorts. Second, a method was developed to estimate cohort hatch dates, thus age on date of sampling could be determined. This method included quantification of post‐hatch length increases as a function of water temperature (growth capacity; mm per thermal unit, mm TU⁻¹), and summation of mean daily water temperatures to achieve the required number of thermal units that corresponded to post‐hatch lengths of shovelnose sturgeon on sampling dates. For six of seven cohorts of shovelnose sturgeon analyzed, linear growth models (r² ≥ 0.65, P < 0.0001) or Gompertz growth models (r² ≥ 0.83, P < 0.0001) quantified length‐at‐age from hatch through 55 days post‐hatch (98–100 mm). Comparisons of length‐at‐age derived from the growth models indicated that length‐at‐age was greater for the earlier‐hatched cohorts than later‐hatched cohorts. Estimated hatch dates for different cohorts were corroborated based on the dates that newly‐hatched larval shovelnose sturgeon were sampled in the drift. These results provide the first quantification of growth dynamics for field‐sampled age‐0 shovelnose sturgeon in a natural river environment, and provide an accurate method for estimating age of wild‐caught individuals. Methods of age determination used in this study have applications to sturgeons in other regions, but require additional testing and validation.     

Heart rates of Atlantic salmon Salmo salar during a critical swim speed test and subsequent recovery

In this study, heart rate (HR) bio-loggers were implanted in the abdominal cavity of 12 post-smolt Atlantic salmon Salmo salar weighing 1024 ± 31 g and acclimated to 12°C sea water. One week after the surgical procedure, a critical swim speed (U_crit) test was performed on tagged and untagged conspecifics, whereafter tagged fish were maintained in their holding tanks for another week. The U_crit was statistically similar between tagged and untagged fish (2.67 ± 0.04 and 2.74 ± 0.05 body lengths s⁻¹, respectively) showing that the bio-logger did not compromise the swimming performance. In the pre-swim week, a diurnal cycle was apparent with HR peaking at 65 beats min⁻¹ during the day and approaching 40 beats min⁻¹ at night. In the U_crit test, HR increased approximately exponentially with swimming speed until a plateau was reached at the final speed before fatigue with a maximum of 85.2 ± 0.7 beats min⁻¹. During subsequent recovery tagged fish could be divided into a surviving group (N = 8) and a moribund group (N = 4). In surviving fish HR had fully recovered to pre-swim levels after 24 h, including reestablishment of a diurnal HR cycle. In moribund fish HR never recovered and remained elevated at c. 80 beats min⁻¹ for 4 days, whereafter they started dying. We did not identify a proximal cause of death in moribund fish, but possible explanations are discussed. Tail beat frequency (TBF) was also measured and showed a more consistent response to increased swimming speeds. As such, when exploring correlations between HR, TBF and metabolic rates at different swimming speeds, TBF provides better predictions. On the contrary, HR measurements in free swimming fish over extended periods of time are useful for other purposes such as assessing the accumulative burden of various stressors and recovery trajectories from exhaustive exercise.     

Peripheral blood monocyte-expressed ANXA2 gene is involved in pathogenesis of osteoporosis in humans

Low bone mineral density (BMD) is a risk factor of osteoporosis and has strong genetic determination. Genes influencing BMD and fundamental mechanisms leading to osteoporosis have yet to be fully determined. Peripheral blood monocytes (PBM) are potential osteoclast precursors, which could access to bone resorption surfaces and differentiate into osteoclasts to resorb bone. Herein, we attempted to identify osteoporosis susceptibility gene(s) and characterize their function(s), through an initial proteomics discovery study on PBM in vivo, and multiscale validation studies in vivo and in vitro. Utilizing the quantitative proteomics methodology LC-nano-ESI-MS(E), we discovered that a novel protein, i.e. ANXA2, was up-regulated twofold in PBM in vivo in Caucasians with extremely low BMD (cases) versus those with extremely high BMD (controls) (n = 28, p < 0.05). ANXA2 gene up-regulation in low BMD subjects was replicated at the mRNA level in PBM in vivo in a second and independent case-control sample (n = 80, p < 0.05). At the DNA level, we found that SNPs in the ANXA2 gene were associated with BMD variation in a 3(rd) and independent case-control sample (n = 44, p < 0.05), as well as in a random population sample (n = 997, p < 0.05). The above integrative evidence strongly supports the concept that ANXA2 is involved in the pathogenesis of osteoporosis in humans. Through a follow-up cellular functional study, we found that ANXA2 protein significantly promoted monocyte migration across an endothelial barrier in vitro (p < 0.001). Thus, elevated ANXA2 protein expression level, as detected in low BMD subjects, probably stimulates more PBM migration through the blood vessel walls to bone resorption surfaces in vivo, where they differentiate into higher number of osteoclasts and resorb bone at higher rates, thereby decreasing BMD. In conclusion, this study identified a novel osteoporosis susceptibility gene ANXA2, and suggested a novel pathophysiological mechanism, mediated by ANXA2, for osteoporosis in humans.     

Determination of trace carvedilol by solid substrate–room temperature phosphorimetry,based on its activating effect on hypochlorite‐oxidizing amaranth using sodium dodecyl benzene sulphonate as sensitizer

This work proposes a simple and sensitive solid substrate–room temperature phosphorimetry (SS–RTP) for the selective determination of carvedilol (CV). The method is based on the sensitizing effect of sodium dodecyl benzene sulphonate (SDBS) on CV to activate the oxidation between NaClO and amaranth, resulting in the intense quenching of room temperature phosphorescence (RTP) of the system. Compared with non‐SDBS system, the reduction of phosphorescence intensity (ΔI_p) with SDBS is 16.5 times higher and is directly proportional to the content of CV, covering a wide range 0.080–16.00 fg/spot. The regression equation of the working curve can be expressed as ΔI_p = 0.7780 + 7.057 m_CV (fg/spot) (correlation coefficient (r) = 0.9976, n = 8), with a detection limit (LD) of 0.020 fg/spot (corresponding concentration is 5.1 × 10⁻¹⁴ g/mL, sample volume is 0.40 μL/spot). This sensitive method has also been applied to determine trace CV in human plasma and the results agreed with synchronous fluorimetry (SF). The activation energy (E) and rate constant (k) of this activating reaction were 69.04 kJ/mol and 3.580 × 10⁻⁴ s⁻¹, respectively. The reaction mechanism is also discussed. Copyright © 2011 John Wiley & Sons, Ltd.     

Evolution of iron and oxygen biogeochemical cycles during the Precambrian

Iron (Fe) is an essential element for life, and its geochemical cycle is intimately linked to the coupled history of life and Earth's environment. The accumulated geologic records indicate that ferruginous waters existed in the Precambrian oceans not only before the first major rise of atmospheric O₂ levels (Great Oxidation Event; GOE) during the Paleoproterozoic, but also during the rest of the Proterozoic. However, the interactive evolution of the biogeochemical cycles of O₂ and Fe during the Archean–Proterozoic remains ambiguous. Here, we develop a biogeochemical model to investigate the coupled biogeochemical evolution of Fe–O₂–P–C cycles across the GOE. Our model demonstrates that the marine Fe cycle was less sensitive to changes in the production rate of O₂ before the GOE (atmospheric pO₂ < 10⁻⁶ PAL; present atmospheric level). When the P supply rate to the ocean exceeds a certain threshold, the GOE occurs and atmospheric pO₂ rises to ~10⁻³–10⁻¹ PAL. After the GOE, the marine Fe(II) concentration is highly sensitive to atmospheric pO₂, suggesting that the marine redox landscape during the Proterozoic may have fluctuated between ferruginous conditions and anoxic non-ferruginous conditions with sulfidic water masses around continental margins. At a certain threshold value of atmospheric pO₂ of ~0.3% PAL, the primary oxidation pathway of Fe(II) shifts from the activity of Fe(II)-utilizing anoxygenic photoautotrophs in sunlit surface waters to abiotic process in the deep ocean. This is accompanied by a shift in the primary deposition site of Fe(III) hydroxides from the surface ocean to the deep sea, providing a plausible mechanistic explanation for the observed cessation of iron formations during the Proterozoic.     

The changing times of Europe's largest remaining commercially harvested population of eel Anguilla anguilla L.

This study quantifies the processes involved in regulating the European eel population of Lough Neagh, a lake in Northern Ireland. The relationship between glass eel input and silver eel output for the 1923–1997 cohorts was best described by a Beverton–Holt stock recruitment model. Glass eel input time series was not complete and was thus derived from the relationship between catches elsewhere in Europe and Lough Neagh, together with the addition of stocked glass eel. Silver eel output was the sum of silver eel escapement, catch and yellow eel catch converted to silver eel equivalents. Natural mortality increased with glass eel density, ranging from 0.017 to 0.142 year⁻¹. The mean carrying capacity increased from ≈3.25 M silver eels (≈26 kg ha⁻¹) for the 1923–1943 cohorts to ≈5.0 M (≈40 kg ha⁻¹) for the 1948–1971 cohorts before regressing back to ≈3.25 M. The total silver eel output was highest during the late 1970s/early 1980s at 35–45 kg ha⁻¹ year⁻¹ and lowest during the early years of the 20th century and is currently at 10–15 kg ha⁻¹ year⁻¹. The findings are discussed in relation to (a) the ecological changes that have occurred within the lough, associated with eutrophication and the introduction of roach (Rutilus rutilus L.), and (b) the decline of the wider European eel stock across its distribution range. The findings from this study have relevance for the wider management of the European eel stock.     

Pooling analysis reveals that galectin-1 is a reliable prognostic biomarker in various cancers

Galectin-1 is reported to be upregulated in various human cancers. However, the relationship between galectin-1 expression and cancer prognosis has not been systematically assessed. In this study, we searched PubMed, Web of Science, and Embase to collect all relevant studies and a meta-analysis was performed. We found that increased galectin-1 expression was associated with tumor size (odds ratio [OR] = 1.75; 95% confidence interval [CI]: 1.06–2.89; p = 0.029), clinical stage (OR = 3.89; 95% CI: 2.40–6.31; p < 0.001), and poorer differentiation (OR = 1.39; 95% CI: 1.14–1.69; p = 0.001), but not with age (OR = 1.07; 95% CI: 0.82–1.39; p = 0.597), sex (OR = 0.89; 95% CI: 0.74–1.07; p = 0.202), or lymph node metastasis (OR = 2.57; 95% CI: 0.98–6.78; p = 0.056). In addition, we found that high galectin-1 expression levels were associated with poor overall survival (HR = 2.12; 95% CI: 1.71–2.64; p < 0.001). The results were further validated using The Cancer Genome Atlas data set. Moreover, high galectin-1 expression was significantly associated with disease-free survival (hazard ratio [HR] = 1.60; 95% CI: 1.17–2.19; p = 0.003), progression-free survival (HR = 1.93; 95% CI: 1.65–2.25; p < 0.001), and cancer-specific survival (HR = 1.82; 95% CI: 1.30–2.55; p < 0.001). Our meta-analysis demonstrated that galectin-1 might be a useful common biomarker for predicting prognosis in patients with cancer.     

Vitamin D Receptor Gene Variants Susceptible to Osteoporosis in Arab Post-Menopausal Women

Post-menopausal osteoporosis (PMO) is a multifactorial bone disorder in elderly women. Various vitamin D receptor (VDR) gene variants have been studied and associated with osteoporosis in other populations, but not in a homogenous Arab ethnic group. Herein, the current study explores the association between VDR polymorphisms and susceptibility to osteoporosis in Saudi postmenopausal women. In total, 600 Saudi postmenopausal women (N = 300 osteoporosis; N = 300 control) were genotyped for VDR gene variants (rs7975232, rs1544410, rs731236) using TaqMan^® SNP genotyping assays. Bone mineral density (BMD) for the lumbar spine and femur was assessed using dual-energy X-ray absorptiometry (DEXA). The heterozygous frequency distributions AC of rs7975232, CT of rs1544410, and AG of rs731236 were significantly higher in the osteoporosis group than controls (p < 0.05). Heterozygous AC of rs7975232 (1.6; 95% CI 1.1–2.3; p < 0.023), CT of rs1544410 (1.6; 95% CI 1.1–2.4; p < 0.022), and AG of rs731236 (1.6; 95% CI 1.1–2.4; p < 0.024) were significantly associated with increased risk of osteoporosis, independent of age and BMI. In conclusion, VDR gene variants rs7975232, rs1544410, rs731236 had a significant effect on BMD and were associated with osteoporosis risk in Saudi postmenopausal women.     

The study of renin–angiotensin–aldosterone in experimental diabetes mellitus

It is generally accepted that hypertension and other vascular pathologies increase in diabetes mellitus (DM) patients as a result of the renin–angiotensin–aldosterone (RAA) system. In this study, changes in the renin‐angiotensin‐aldosterone (RAA) system level was determined in Streptozotocin (STZ)‐injected rats. A total of 46 female Wistar albino rats (180–220 g body weight) was utilized in these experiments. STZ was given intraperitoneally to induce diabetes in rats. Streptozotocin (60 mg kg⁻¹ body weight) was dissolved in 0·1 m citrate–‐phosphate buffer (pH 4–5). The non‐diabetic rats were injected with sterilized buffer alone to act as a control group. Blood glucose levels were 398±8·2 mg dl⁻¹, 488±11·75 mg dl⁻¹ and 658±29·6 mg dl⁻¹ at days 3, 12 and 30 respectively. The level of plasma renin activity (PRA) was measured as 7·69±1·07 ng ml⁻¹ h⁻¹; 1·82±0·22 ng ml⁻¹ h⁻¹ and 0·67±0·12 ng ml⁻¹ h⁻¹ at days 3, 12 and 30, respectively. These values showed that the PRA levels are decreased with increased time period. Serum angiotensin converting enzyme (ACE, E.C. 3.4.15.1) levels were increased at days 12 and 30 (p<0·05 and p<0·005), whereas serum aldosterone levels were increased at days 3 and 12 (p<0·05). The level of urea and creatinine increased at days 12 and 30 (p<0·05 and p<0·005, respectively) when compared to the control group. The data from these experiments indicate that the PRA level decreased whereas ACE activity level increased in diabetic rats compared with the control. Aldosterone levels increased at the first stage of the experiment, but then decreased by the end of the experiment as a result of changes in renin and ACE levels. Copyright © 1999 John Wiley & Sons, Ltd.     

Performance of different methods for testing polymyxin B: comparison of broth microdilution,agar dilution and MIC test strip in mcr-1 positive and negative Escherichia coli

Antimicrobial susceptibility testing with the last-resort antibiotics polymyxins (polymyxin B and colistin) is associated with several methodological issues. Currently, broth microdilution (BMD) is recommended for colistin and polymyxin B. BMD is laborious and the utility of alternative methods needs to be evaluated for polymyxin B susceptibility testing. In this study, using BMD as a reference method, the performance of agar dilution (AD) and MIC test strips (MTS) were evaluated in polymyxin B susceptibility testing. BMD, AD and MTS were used to determine MICs of 193 clinical isolates of Escherichia coli. Seventy-nine were positive for the polymyxin resistance gene mcr-1. Method performances were evaluated based on pair-wise agreements with the reference method (BMD) and statistical testing. AD and MTS showed an unacceptable number of very major errors (VMEs) compared with BMD, 9·3 and 10·7%, respectively. The essential agreement (EA) was low for AD (49·7%), but high for MTS (97·8%). However, statistical testing showed that MTS tended to yield a one-step lower MIC (P < 0·01) compared with BMD. The discordances observed with MTS and AD in comparison with BMD for polymyxin B susceptibility testing for E. coli suggest their inapplicability in routine testing. A large number of isolates clustered around the susceptibility breakpoint (2–4 mg l⁻¹) and several mcr-1 positive isolates (17%) were determined as susceptible with BMD. A screening breakpoint for mcr-1 of 2 mg l⁻¹ should also be considered.     

Large contributions of coupled protonation equilibria to the observed enthalpy and heat capacity changes for ssDNA binding to Escherichia coli SSB protein

Many macromolecular interactions, including protein‐nucleic acid interactions, are accompanied by a substantial negative heat capacity change, the molecular origins of which have generated substantial interest. We have shown previously that temperature‐dependent unstacking of the bases within oligo(dA) upon binding to the Escherichia coli SSB tetramer dominates the binding enthalpy, ΔH_obs, and accounts for as much as a half of the observed heat capacity change, ΔC_p. However, there is still a substantial ΔC_p associated with SSB binding to ssDNA, such as oligo(dT), that does not undergo substantial base stacking. In an attempt to determine the origins of this heat capacity change, we have examined by isothermal titration calorimetry (ITC) the equilibrium binding of dT(pT)₃₄ to SSB over a broad pH range (pH 5.0–10.0) at 0.02 M, 0.2 M NaCl and 1 M NaCl (25°C), and as a function of temperature at pH 8.1. A net protonation of the SSB protein occurs upon dT(pT)₃₄ binding over this entire pH range, with contributions from at least three sets of protonation sites (pK_a1 = 5.9–6.6, pK_a2 = 8.2–8.4, and pK_a3 = 10.2–10.3) and these protonation equilibria contribute substantially to the observed ΔH and ΔC_p for the SSB‐dT(pT)₃₄ interaction. The contribution of this coupled protonation (∼ −260 to −320 cal mol⁻¹ K⁻¹) accounts for as much as half of the total ΔC_p. The values of the “intrinsic” ΔC_p,0 range from −210 ± 33 cal mol⁻¹ °K⁻¹ to −237 ± 36 cal mol⁻¹K⁻¹, independent of [NaCl]. These results indicate that the coupling of a temperature‐dependent protonation equilibria to a macromolecular interaction can result in a large negative ΔC_p, and this finding needs to be considered in interpretations of the molecular origins of heat capacity changes associated with ligand‐macromolecular interactions, as well as protein folding. Proteins 2000;Suppl 4:8–22. © 2000 Wiley‐Liss, Inc.     

Association between vitamin D receptor gene polymorphisms and bone mineral density in Chinese women

Vitamin D receptor (VDR) is implicated in the regulation of bone mineral density (BMD). In this study, we performed a meta-analysis to evaluate the association between the VDR BsmI (rs1544410) and ApaI (rs7975232) polymorphisms and BMD in Chinese women. Literature was retrieved from PubMed and other databases. The studies on the association between VDR BsmI and ApaI genotypes and BMD at the lumbar spine, the femoral neck, the trochanter or the Ward’s triangle in Han Chinese women were included in this meta-analysis. Pooled BMD differences and 95% confidence intervals (CIs) were calculated using random- or fixed- effects model. Twenty-five eligible studies, which included 4,075 Chinese women, were identified. No significant difference was observed for either genotype when the meta-analysis was limited to premenopausal women. In postmenopausal women, BMD differences were significant for BB vs. Bb [−0.029 (95% CI −0.056, −0.002) g/m², P = 0.037] at the femoral neck, AA vs. Aa [−0.029 (95% CI −0.051, −0.006) g/m², P = 0.012] at the lumbar spine, and Aa vs. aa [0.022(95% CI 0.011, 0.033) g/m², P = 0.000] at the trochanter. These results suggest a modest but statistically significant association between VDR BsmI and ApaI polymorphisms and BMD in Chinese postmenopausal women, with higher BMD in heterozygous subjects. More epidemiological and mechanistic studies are needed to further investigate the role of VDR gene polymorphisms in regulating BMD and osteoporosis in the future.     

The CRISPLD2 gene is involved in cleft lip and/or cleft palate in a Chinese population

BACKGROUND: Nonsyndromic cleft lip and/or cleft palate (NSCLP) are common congenital anomalies in humans, the etiologies of which are complex and associated with both genetic and environmental factors. Previous data suggested single nucleotide polymorphisms (SNPs) of rs1546124, rs4783099, and rs16974880 of the CRISPLD2 gene were associated with an increased risk of NSCLP; however, subsequent studies have yielded conflicting results. This study aims to evaluate the associations of the aforementioned polymorphisms with NSCLP in a Northwestern Chinese population. METHODS: Three CRISPLD2 SNPs were genotyped in a case‐control study (n = 907), including 444 NSCLP patients and 463 healthy individuals, using polymerase chain reaction–denaturing high‐performance liquid chromatography (PCR‐DHPLC). RESULTS: The genotype and allele frequencies of rs1546124 (odds ratio [OR], 2.30; 95% confidence interval [CI], 1.58–3.34; p = 1 × 10⁻⁵) and rs4783099 (OR, 0.73; 95% CI, 0.54–1.00; p = 0.05) were different in NSCLP patients compared with controls. Furthermore, the CC genotype at rs1546124 was associated with increased risk for cleft lip with or without cleft palate (CL/P; OR, 2.11; 95% CI, 1.41–3.15; p_correct = 1.5 × 10⁻⁴) and for cleft palate only (CPO; OR, 2.93; 95% CI, 1.69–5.07; p_correct = 5.4 × 10⁻⁴), whereas the T allele of rs4783099 was associated with decreased risk for CPO. Further gender stratification showed that the statistical association of these two loci is mainly in the male patients, and not in female patients. CONCLUSION: Our results suggest that the CRISPLD2 gene contributes to the etiology of NSCLP in the Northwestern Chinese population. SNP rs1546124 is significantly related to NSCLP, associated with both CL/P and CPO groups, and SNP rs4783099 is significantly associated with CPO. Birth Defects Research (Part A) 2011. © 2011 Wiley‐Liss, Inc.