Polymorphism and divergence at the 5' flanking region of the sex- determining locus, Sry, in mice

We have investigated patterns of evolution in the nonrecombining portion of the Y chromosome in mice by comparing levels of polymorphism within Mus domesticus with levels of divergence between M. domesticus and M. spretus. A 1,277-bp fragment of noncoding sequence flanking the sex determining locus (Sry) was PCR amplified, and 1,063 bases were sequenced and compared among 20 M. domesticus and 1 M. spretus. Two polymorphic base substitutions and two polymorphic insertion/deletion sites were identified within M. domesticus; nucleotide diversity was estimated to be 0.1%. Divergence between M. domesticus and M. spretus for this region (1.9%) was slightly lower than the average divergence of single-copy nuclear DNA for these species. Comparison of levels of polymorphism and divergence at Sry with levels of polymorphism and divergence in the mitochondrial DNA control region provided no evidence of a departure from the expectations of neutral molecular evolution. These findings are consistent with the presumed lack of function for much of the Y chromosome.      

Determinants of VO2max in rats after high-intensity sprint training

The hemodynamic response to maximal exercise was determined in rats that were subjected to high-intensity sprint training (HIST) and rats that served as sedentary controls. Training consisted of five 1-min bouts of treadmill running at work loads (15% grade, 97 m/min) in excess of the animals' maximal O2 uptake (VO2max) interspersed with 90 s of rest. Training was performed 6 days/wk for 6 wk. After the training regimen, all rats were acutely instrumented with catheters in the right carotid artery and right ventricle. O2 uptakes, hemodynamic parameters, arterial and mixed venous O2 concentrations, blood gases, and acid-base status were determined at rest and during submaximal and maximal exercise. Results demonstrated that VO2max of HIST rats was significantly greater than that found for sedentary control rats. This increase in VO2max was due to an increase in maximal cardiac output (Qmax), since maximal arteriovenous O2 difference was similar between trained and sedentary rats. The increase in Qmax was due to an increase in maximal stroke volume (SVmax), because maximal heart rate in trained rats was similar to that in sedentary control rats. Citrate synthase and phosphofructokinase activities measured in the white gastrocnemius, plantaris, and soleus muscles of trained and sedentary rats were similar. These results suggest that the increase in VO2max produced with HIST in rats is strongly linked to an increase in central cardiac function as indicated by an increase in Qmax and SVmax.     

Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon

Metagenomic analysis of colonic mucosa-associated microbes has been complicated by technical challenges that disrupt or alter community structure and function. In the present study, we determined the feasibility of laser capture microdissection (LCM) of intact regional human colonic mucosa-associated microbes followed by phi29 multiple displacement amplification (MDA) and massively parallel sequencing for metagenomic analysis. Samples were obtained from the healthy human subject without bowel preparation and frozen sections immediately prepared. Regional mucosa-associated microbes were successfully dissected using LCM with minimal contamination by host cells, their DNA extracted and subjected to phi29 MDA with a high fidelity, prior to shotgun sequencing using the GS-FLX DNA sequencer. Metagenomic analysis of approximately 67 million base pairs of DNA sequences from two samples revealed that the metabolic functional profiles in mucosa-associated microbes were as diverse as those reported in feces, specifically the representation of functional genes associated with carbohydrate, protein, and nucleic acid utilization. In summary, these studies demonstrate the feasibility of the approach to study the structure and metagenomic profiles of human intestinal mucosa-associated microbial communities at small spatial scales.     

Signature of mid‐Pleistocene lineages in the European silver fir (Abies alba Mill.) at its geographic distribution margin

In a conservation and sustainable management perspective, we identify the ecological, climatic, and demographic factors responsible for the genetic diversity patterns of the European silver fir (Abies alba Mill.) at its southwestern range margin (Pyrenees Mountains, France, Europe). We sampled 45 populations throughout the French Pyrenees and eight neighboring reference populations in the Massif Central, Alps, and Corsica. We genotyped 1,620 individuals at three chloroplast and ten nuclear microsatellite loci. We analyzed within‐ and among‐population genetic diversity using phylogeographic reconstructions, tests of isolation‐by‐distance, Bayesian population structure inference, modeling of demographic scenarios, and regression analyses of genetic variables with current and past environmental variables. Genetic diversity decreased from east to west suggesting isolation‐by‐distance from the Alps to the Pyrenees and from the Eastern to the Western Pyrenees. We identified two Pyrenean lineages that diverged from a third Alpine–Corsica–Massif Central lineage 0.8 to 1.1 M years ago and subsequently formed a secondary contact zone in the Central Pyrenees. Population sizes underwent contrasted changes, with a contraction in the west and an expansion in the east. Glacial climate affected the genetic composition of the populations, with the western genetic cluster only observed in locations corresponding to the coldest past climate and highest elevations. The eastern cluster was observed over a larger range of temperatures and elevations. All demographic events shaping the current spatial structure of genetic diversity took place during the Mid‐Pleistocene Transition, long before the onset of the Holocene. The Western Pyrenees lineage may require additional conservation efforts, whereas the eastern lineage is well protected in in situ gene conservation units. Due to past climate oscillations and the likely emergence of independent refugia, east–west oriented mountain ranges may be important reservoir of genetic diversity in a context of past and ongoing climate change in Europe.     

Altered regional blood flow responses to submaximal exercise in older rats.

Maximal aerobic capacity and the ability to sustain submaximal exercise (Ex) declines with advancing age. Whether altered muscle blood flow (BF) plays a mechanistic role in these effects remains to be resolved. The present investigation determined the effects of aging on the hemodynamic and regional BF response to submaximal Ex in rats. Heart rate (HR), mean arterial pressure (MAP), and BF to different organs (kidneys, splanchnic organs, and 28 hindlimb muscles) were determined at rest and during submaximal treadmill Ex (20 m/min, 5% grade) with radiolabeled microspheres in young (Y; 6-8 mo old, 339 +/- 8 g, n = 9) and old (O; 27-29 mo old, 504 +/- 18 g, n = 7) Fischer 344 x Brown Norway rats. Results demonstrated that HR, MAP, and BF to the pancreas, small and large intestine, and total hindlimb musculature were similar between Y and O rats at rest. BF to the kidneys, spleen, and stomach were 33, 60, and 43% lower, respectively, in O compared with Y rats. BF to the total hindlimb musculature increased (P < 0.05) during Ex and was similar for both Y and O rats (Y: 16 +/- 3 to 124 +/- 7 vs. O: 20 +/- 3 to 137 +/- 12 ml.min-1.100 g-1). However, in O vs. Y rats, BF was reduced in 6 (highly oxidative) and elevated in 8 (highly glycolytic) of the 28 individual hindquarter muscles or muscle parts examined (P < 0.05). During Ex, BF to the spleen and stomach decreased (P < 0.05) from rest in Y rats, whereas BF decreased in the kidneys, pancreas, spleen, stomach, as well as the small and large intestines of O rats. In conclusion, these data demonstrate that, despite similar increases in total hindlimb BF in Y and O rats during submaximal Ex, there is a profound BF redistribution from highly oxidative to highly glycolytic muscles.     

Very different performance of the power Doppler modalities of several ultrasound machines ascertained by a microvessel flow phantom

Introduction

In many patients with rheumatoid arthritis (RA) subclinical disease activity can be detected with ultrasound (US), especially using power Doppler US (PDUS). However, PDUS may be highly dependent on the type of machine. This could create problems both in clinical trials and in daily clinical practice. To clarify how the PDUS signal differs between machines we created a microvessel flow phantom.

Methods

The flow phantom contained three microvessels (150, 1000, 2000 microns). A syringe pump was used to generate flows. Five US machines were used. Settings were optimised to assess the lowest detectable flow for each US machine.

Results

The minimal detectable flow velocities showed very large differences between the machines. Only two of the machines may be able to detect the very low flows in the capillaries of inflamed joints. There was no clear relation with price. One of the lower-end machines actually performed best in all three vessel sizes.

Conclusions

We created a flow phantom to test the sensitivity of US machines to very low flows in small vessels. The sensitivity of the power Doppler modalities of 5 different machines was very different. The differences found between the machines are probably caused by fundamental differences in processing of the PD signal or internal settings inaccessible to users. Machines considered for PDUS assessment of RA patients should be tested using a flow phantom similar to ours. Within studies, only a single machine type should be used.     

Promoter hypermethylation using 24-gene array in early head and neck cancer: Better outcome in oral than in oropharyngeal cancer

Silencing of tumor suppressor genes (TSGs) by DNA promoter hypermethylation is an early event in carcinogenesis and a potential target for personalized cancer treatment. In head and neck cancer, little is known about the role of promoter hypermethylation in survival. Using methylation specific multiplex ligation-dependent probe amplification (MS-MLPA) we investigated the role of promoter hypermethylation of 24 well-described genes (some of which are classic TSGs), which are frequently methylated in different cancer types, in 166 HPV-negative early oral squamous cell carcinomas (OSCC), and 51 HPV-negative early oropharyngeal squamous cell carcinomas (OPSCC) in relation to clinicopathological features and survival. Early OSCC showed frequent promoter hypermethylation in RARB (31% of cases), CHFR (20%), CDH13 (13%), DAPK1 (12%), and APC (10%). More hypermethylation (≥ 2 genes) independently correlated with improved disease specific survival (hazard ratio 0.17, P = 0.014) in early OSCC and could therefore be used as prognostic biomarker. Early OPSCCs showed more hypermethylation of CDH13 (58%), TP73 (14%), and total hypermethylated genes. Hypermethylation of two or more genes has a significantly different effect on survival in OPSCC compared with OSCC, with a trend toward worse instead of better survival. This could have a biological explanation, which deserves further investigation and could possibly lead to more stratified treatment in the future.