Whole genome sequencing of Canadian Saccharomyces cerevisiae strains isolated from spontaneous wine fermentations reveals a new Pacific West Coast Wine clade

Vineyards in wine regions around the world are reservoirs of yeast with oenological potential. Saccharomyces cerevisiae ferments grape sugars to ethanol and generates flavor and aroma compounds in wine. Wineries place a high-value on identifying yeast native to their region to develop a region-specific wine program. Commercial wine strains are genetically very similar due to a population bottleneck and in-breeding compared to the diversity of S. cerevisiae from the wild and other industrial processes. We have isolated and microsatellite-typed hundreds of S. cerevisiae strains from spontaneous fermentations of grapes from the Okanagan Valley wine region in British Columbia, Canada. We chose 75 S. cerevisiae strains, based on our microsatellite clustering data, for whole genome sequencing using Illumina paired-end reads. Phylogenetic analysis shows that British Columbian S. cerevisiae strains cluster into 4 clades: Wine/European, Transpacific Oak, Beer 1/Mixed Origin, and a new clade that we have designated as Pacific West Coast Wine. The Pacific West Coast Wine clade has high nucleotide diversity and shares genomic characteristics with wild North American oak strains but also has gene flow from Wine/European and Ecuadorian clades. We analyzed gene copy number variations to find evidence of domestication and found that strains in the Wine/European and Pacific West Coast Wine clades have gene copy number variation reflective of adaptations to the wine-making environment. The "wine circle/Region B", a cluster of 5 genes acquired by horizontal gene transfer into the genome of commercial wine strains is also present in the majority of the British Columbian strains in the Wine/European clade but in a minority of the Pacific West Coast Wine clade strains. Previous studies have shown that S. cerevisiae strains isolated from Mediterranean Oak trees may be the living ancestors of European wine yeast strains. This study is the first to isolate S. cerevisiae strains with genetic similarity to nonvineyard North American Oak strains from spontaneous wine fermentations.

Gene and pathway based burden analyses in familial lymphoid cancer cases: Rare variants in immune pathway genes

Genome-wide association studies have revealed common genetic variants with small effect sizes associated with diverse lymphoid cancers. Family studies have uncovered rare variants with high effect sizes. However, these variants explain only a portion of the heritability of these cancers. Some of the missing heritability may be attributable to rare variants with small effect sizes. We aim to identify rare germline variants associated with familial lymphoid cancers using exome sequencing. One case per family was selected from 39 lymphoid cancer families based on early onset of disease or rarity of subtype. Control data was from Non-Finnish Europeans in gnomAD exomes (N = 56,885) or ExAC (N = 33,370). Gene and pathway-based burden tests for rare variants were performed using TRAPD. Five putatively pathogenic germline variants were found in four genes: INTU, PEX7, EHHADH, and ASXL1. Pathway-based association tests identified the innate and adaptive immune systems, peroxisomal pathway and olfactory receptor pathway as associated with lymphoid cancers in familial cases. Our results suggest that rare inherited defects in the genes involved in immune system and peroxisomal pathway may predispose individuals to lymphoid cancers.

T2 FLAIR Increased Signal Intensity at the Posterior Limb of the Internal Capsule: Clinical Significance in ALS Patients

Amyotrophic lateral sclerosis (ALS) is characterized by progressive upper and lower motor neuron degeneration. A hyperintense signal on T2-weighted images along the corticospinal tract has been reported in patients with confirmed ALS. However, the specificity of this finding is under consideration, since it is also identified in healthy controls. Moreover, the correlation of this finding with disease progression has not yet been established. The purpose of our study is to evaluate the frequency with which this high signal appears in the posterior limb of the internal capsule (PLIC), compare visual with quantitative measurements, and correlate these with the progression of the disease. Our prospective clinical study included 24 patients and 51 healthy volunteers. In the ALS patient group, the diagnosis was established according to the criteria of El Escorial in the revised form of Airlee House. All patients were neurologically examined and underwent diagnostic procedures to exclude other diseases resembling ALS. The initial MRI was performed six months to two years after the onset of symptomatology. All ALS patients were clinically examined regarding their symptoms from the upper and lower motor neurons. Follow-up MRIs were performed in nine out of 24 patients over a period of six months. Signal changes in the PLIC are visually evaluated on FLAIR images, and are classified as distinct, mild or no signal change. Fractional anisotropy (FA) measurements are performed by placing a region of interest (ROI) in the PLIC bilaterally. Both findings are being compared. Mild signal changes were visualized in the PLIC in ten volunteers and seven patients. Distinct T2 FLAIR signal changes were visualized in the PLIC in seven ALS patients. No distinct signal change was visualized in the controls. Moreover this increased T2 FLAIR signal change became more accentuated with disease progress. FA measurements in patients were lower than in age-matched healthy subjects, with a further decrease with disease progression. Our findings indicate that although mild hyperintensity of the PLIC is not pathognomonic for ALS, detection of a distinct PLIC hyperintensity that gradually accentuates might actually be a sign of progressive ALS. This finding is supported by the progressively decreasing FA measurements. Larger numbers of patients need to be included and re-evaluated to obtain statistically significant results.

Spinal anesthesia: comparison of plain ropivacaine, bupivacaine and levobupivacaine for lower abdominal surgery

This study was performed to compare the anesthetic efficacy and safety of three local anesthetic agents: racemic bupivacaine and its two isomers: ropivacaine and levobupivacaine, in patients undergoing lower abdominal surgery. One hundred-twenty patients, ASA I-III, were randomized to receive an intrathecal injection of one of three local anesthetic solutions. Group A (n = 40) received 3 ml of isobaric bupivacaine 5 mg/ml (15 mg). Group B (n = 40) received 3 ml of isobaric ropivacaine 5 mg/ml (15 mg). Group C (n = 40) received 3 ml of isobaric levobupivacaine 5 mg/ml (15 mg). The onset and duration of sensory block at dermatome level T8, maximum upper spread of sensory block, time for 2-segment regression of sensory block as well as the onset, intensity and duration of motor block were recorded, as were any adverse effects, such as bradycardia, hypotension, hypoxia, tremor, nausea and/or vomiting. Time to unassisted standing up and voluntary micturition was also recorded. The onset of motor block was significantly faster in the bupivacaine group compared with that in the ropivacaine group and almost the same of that in the levobupivacaine group (P < 0.05). Ropivacaine presented a shorter duration of both motor and sensory block than bupivacaine and levobupivacaine (P < 0.05). Bupivacaine required more often the use of a vasoactive drug (ephedrine) compared to both ropivacaine and levobupivacaine and of a sympathomimetic drug (atropine) compared to the ropivacaine group.

Low RLS prevalence and awareness in central Greece: an epidemiological survey

Restless legs syndrome (RLS) is a sensorimotor disorder with a general population prevalence of 3-10%. A single, previous epidemiological study performed in south-east Europe reported the lowest prevalence rate amongst European countries. We conducted a population-based survey of RLS in central Greece. A total of 4200 subjects were randomly recruited. We used the international RLS study group criteria for diagnosis and the severity scale for severity assessment in subjects with RLS. We also included questions to assess the level of awareness of RLS in our region. A total of 3033 subjects were screened. The overall lifetime prevalence was 3.9% with a female-to-male ratio of 2.6:1. Nearly half of RLS patients reported moderate to severe intensity of symptoms. After adjustment for multiple comparisons we found no association of RLS with education level, smoking, alcohol intake, caffeine consumption, shift work, professional pesticide use or comorbid illness. Our study revealed a low level of awareness amongst the population and physicians in our region and sub-optimal management. We provide further evidence for low prevalence of RLS in south-east Europe and a low level of awareness of RLS in our region.

Soluble type II transforming growth factor-beta (TGF-beta) receptor inhibits TGF-beta signaling in COLO-357 pancreatic cancer cells in vitro and attenuates tumor formation

Human pancreatic ductal adenocarcinomas overexpress transforming growth factor-betas (TGF-betas). This overexpression has been correlated with decreased patient survival. TGF-betas bind to a type II TGF-beta receptor (TbetaRII) dimer, which heterotetramerizes with a type I TGF-beta receptor (TbetaRI) dimer, thereby activating downstream signaling.

PURPOSE AND EXPERIMENTAL DESIGN

To determine whether blocking TGF-beta actions would suppress pancreatic cancer cell growth in vivo, we expressed a soluble TbetaRII, encoding amino acids 1-159 of the extracellular domain in COLO-357 human pancreatic cancer cells. This cell line expresses all of the three mammalian TGF-beta isoforms and is growth inhibited by TGF-beta in vitro.

RESULTS

COLO-357 clones expressing soluble TbetaRII were no longer growth inhibited by exogenous TGF-beta1 and exhibited a marked decrease in their invasive capacity in vitro. When injected s.c. into athymic mice, these clones exhibited attenuated growth rates and angiogenesis and decreased levels of plasminogen activator inhibitor-1 mRNA as compared with tumors formed by sham-transfected cells.

CONCLUSIONS

These results indicate that endogenous TGF-betas can confer a growth advantage in vivo to a pancreatic cancer cell line that is growth inhibited in vitro and suggest that a soluble receptor approach can be used to block these tumorigenic effects of TGF-betas.