Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity.

BACKGROUND: Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterised by hypotonia, ataxia, cognitive impairment, abnormal eye movements, respiratory control disturbances and a distinctive mid-hindbrain malformation. JS demonstrates substantial phenotypic variability and genetic heterogeneity. This study provides a comprehensive view of the current genetic basis, phenotypic range and gene-phenotype associations in JS. METHODS: We sequenced 27 JS-associated genes in 440 affected individuals (375 families) from a cohort of 532 individuals (440 families) with JS, using molecular inversion probe-based targeted capture and next-generation sequencing. Variant pathogenicity was defined using the Combined Annotation Dependent Depletion algorithm with an optimised score cut-off. RESULTS: We identified presumed causal variants in 62% of pedigrees, including the first B9D2 mutations associated with JS. 253 different mutations in 23 genes highlight the extreme genetic heterogeneity of JS. Phenotypic analysis revealed that only 34% of individuals have a 'pure JS' phenotype. Retinal disease is present in 30% of individuals, renal disease in 25%, coloboma in 17%, polydactyly in 15%, liver fibrosis in 14% and encephalocele in 8%. Loss of CEP290 function is associated with retinal dystrophy, while loss of TMEM67 function is associated with liver fibrosis and coloboma, but we observe no clear-cut distinction between JS subtypes. CONCLUSIONS: This work illustrates how combining advanced sequencing techniques with phenotypic data addresses extreme genetic heterogeneity to provide diagnostic and carrier testing, guide medical monitoring for progressive complications, facilitate interpretation of genome-wide sequencing results in individuals with a variety of phenotypes and enable gene-specific treatments in the future.

Quaternary deepwater paleoceanography.

During the past decade, geochemical paleoceanographers have begun to explore the changes in the circulation of the deep ocean that occurred during the glacial-interglacial cycles of the earth's recent history. The deep ocean was significantly colder during the glacial maximum. The distributions of biologically utilized elements (such as carbon and phosphorus) were significantly different as well; higher concentrations of these elements occurred in the deep (>2500 meters depth) North Atlantic, and lower concentrations occurred in the upper (<2500 meters depth) waters of the North Atlantic and possibly in all of the major ocean basins. In contrast, relatively subtle changes have been observed in the radiocarbon ages of deep waters. Slow deepwater changes are statistically linked to variations in the earth's orbit, but rapid changes in deepwater circulation also have occurred. Deepwater chemistry and circulation changes may control the variability in atmospheric CO(2) levels that have been documented from studies of air bubbles in polar ice cores.

Deep Circulation of the North Atlantic over the Last 200,000 Years: Geochemical Evidence.

Variations in the cadmium/calcium ratio of North Atlantic Deep Water are recorded in the fossil shells of benthic foraminifera. The oceanic distribution of cadmium is similar to that of the nutrients, hence the cadmium/calcium ratio in shells records temporal variations in nutrient distributions. Data from a North Atlantic sediment core show that over the past 200,000 years there has been a continuous supply of nutrient-depleted waters into the deep North Atlantic. The intensity of this source relative to nutrient-enriched southern waters diminished by about a factor of 2 during severe glaciations. This evidence combined with carbon isotope data indicates that the continental carbon inventory may have been less variable than previously suggested.

Phosphate depletion in the western North Atlantic Ocean.

Surface waters of the subtropical Sargasso Sea contain dissolved inorganic phosphate (DIP) concentrations of 0.2 to 1.0 nanomolar, which are sufficiently low to result in phosphorus control of primary production. The DIP concentrations in this area (which receives high inputs of iron-rich dust from arid regions of North Africa) are one to two orders of magnitude lower than surface levels in the North Pacific (where eolian iron inputs are much lower and water column denitrification is much more substantial). These data indicate a severe relative phosphorus depletion in the Atlantic. We hypothesize that nitrogen versus phosphorus limitation of primary production in the present-day ocean may be closely linked to iron supply through control of dinitrogen (N2) fixation, an iron-intensive metabolic process. Although the oceanic phosphorus inventory may set the upper limit for the total amount of organic matter produced in the ocean over geological time scales, at any instant in geological time, oceanic primary production may fall below this limit because of a persistent insufficient iron supply. By controlling N2 fixation, iron may control not only nitrogen versus phosphorus limitation but also carbon fixation and export stoichiometry and hence biological sequestration of atmospheric carbon dioxide.

Chronology of anthropogenic impacts reconstructed from sediment records of trace metals and Pb isotopes in Todos os Santos Bay (NE Brazil).

The evolution of the impacts of anthropogenic activities in Todos os Santos Bay was evaluated by profiles of trace metals and Pb isotopes determined in sediment cores. Fluxes of metals increased up to 12, 4 and 2 times for Cu, Pb, and Zn, respectively, compared to those recorded in the beginning of the 20th century. Stable Pb isotopes identified a decommissioned lead smelter and burning of fossil fuels as the main sources of Pb. Most metals showed minor to moderate enrichment factors (EF<4), but Cu and Pb were highly enriched (EF=28 and 6, respectively) at the Aratu harbor. Temporal changes in sediments were associated to different activities, namely Pb smelting, burning of fossil fuels, maritime traffic, petroleum related activities, inputs of domestic effluents, and changes in land uses. The effects of the implementation of environmental policies to improve the waters of the bay could not be identified in the evaluated cores.

Determination of the effect of brand and product identification on consumer palatability ratings of ground beef patties.

The objective of this study was to determine the effect of brand and product identification on consumer palatability ratings of ground beef patties. Six treatments were used in the study: 90/10 Certified Angus Beef (CAB) ground sirloin, 90/10 ground beef, 80/20 CAB ground chuck, 80/20 ground chuck, 80/20 ground beef, and 73/27 CAB ground beef. Ground beef was processed into 151.2-g patties using a patty former with 2 consecutively formed patties assigned to blind consumer testing and the following 2 assigned to informed testing. Following cooking to 74°C, patties were cut into quarters and served to consumers. Consumers ( = 112) evaluated samples in 2 rounds for tenderness, juiciness, flavor liking, texture liking, and overall liking. Each trait was also rated as either acceptable or unacceptable. In the first round of testing, samples were blind evaluated, with no information about the treatments provided to consumers, but in the second round, product type and brand were disclosed prior to sample evaluation. Additionally, texture profile and shear force analyses were performed on patties from each treatment. Few differences were observed for palatability traits during blind consumer testing; however, during informed testing, 90/10 CAB ground sirloin was rated greatest ( < 0.05) for all palatability traits other than juiciness. Also, 90/10 CAB ground sirloin had increased ( < 0.05; (consumer informed score - consumer blind score)/consumer blind score) ratings for tenderness (17.4%), juiciness (36.5%), flavor liking (23.3%), texture liking (18.2%), and overall liking (24.7%) due to brand disclosure. Increased ( < 0.05) ratings were found for CAB products for multiple traits due to treatment disclosure, whereas the only non-CAB-branded product that received increased ( < 0.05) ratings during informed testing was 90/10 ground beef for tenderness and juiciness. Texture results indicated that decreased fat level increased hardness, cohesiveness, gumminess, and chewiness. These results indicate that when sampling ground beef without brand and product information, few consumers find differences in eating quality among ground beef treatments; however, when consumers are aware of the brand, fat level, and subprimal blend prior to sampling, these factors have a large impact on consumer eating satisfaction.

The effect of branding on consumer palatability ratings of beef strip loin steaks.

The objective of this study was to determine the influence of knowing the brand or USDA grade on consumer palatability ratings of beef strip loin steaks. Strip loins were selected to represent 5 USDA grades and brands, USDA Select, Choice, Prime, Certified Angus Beef (CAB; upper 2/3 Choice), and Select, from carcasses of cattle classified as Angus on the basis of phenotype. After 21 d of aging, 2.5-cm-thick steaks were cut, consecutively cut steaks were paired for consumer evaluation. Consumer panelists ( = 112) evaluated samples for tenderness, juiciness, flavor liking, and overall liking. Additionally, consumers rated each palatability trait as either acceptable or unacceptable. Samples were fed in 2 rounds on the same day: blind and informed testing. In the first round, blind testing, consumers were served 1 sample from each treatment, with no product information provided. In the second round, consumers were informed of the brand or quality grade prior to sampling. During blind testing, CAB rated similar ( > 0.05) to Choice for all palatability traits; however, CAB rated greater ( < 0.05) than Choice for all traits during informed testing. Additionally, Angus Select and Select were rated similar > 0.05) for all traits when tested blind, but Angus Select was rated greater ( < 0.05) than Select for flavor and overall liking when brand was declared. When comparing blind and informed ratings, Angus Select and CAB had greater ( < 0.05) ratings for juiciness, flavor liking, and overall liking, and Prime had increased ( < 0.05) ratings for flavor liking and overall liking because of brand disclosure. However, ratings for Choice and Select samples were unaffected ( > 0.05) when brand was disclosed. Brand knowledge increased ( < 0.05) the percentage of Prime samples rated as acceptable for flavor and the percentage of Angus Select samples rated as acceptable for flavor and overall liking. Conversely, there was no difference ( > 0.05) in the percentage of Choice and Select samples rated as acceptable for all palatability traits. These data indicate that Prime, CAB, and Angus Select steaks receive an increase in consumer palatability perception, or "brand lift," which does not occur for Choice and Select beef.

Shelf life of fresh meat products under LED or fluorescent lighting.

Enhanced pork loin chops, beef longissimus lumborum steaks, semimembranosus steaks (superficial and deep portions), ground beef, and ground turkey were displayed under light emitting diode (LED) and fluorescent (FLS) lighting in two multi-shelf, retail display cases with identical operating parameters. Visual and instrumental color, internal product temperature, case temperature, case cycling, thiobarbituric acid reactive substances (TBARS), and Enterobacteriaceae and aerobic plate counts were evaluated. Under LED, beef products (except the deep portion of beef semimembranosus steaks) showed less (P<0.05) visual discoloration. Pork loin chops had higher (P<0.05) L* values for LED lighting. Other than beef longissimus lumborum steaks, products displayed under LED lights had colder internal temperatures than products under FLS lights (P<0.05). Under LED, pork loin chops, ground turkey, and beef semimembranosus steaks had higher (P<0.05) values for TBARS. LED provides colder case and product temperatures, more case efficiency, and extended color life by at least 0.5d for longissimus and semimembranosus steaks; however, some LED cuts showed increased lipid oxidation.

Empirical support for psychological profiles observed in multiple sclerosis.

Though increasing attention is being paid to psychological aspects of multiple sclerosis, much research continues to examine patients as differing in quantity rather than quality of psychological abnormality or response. Cluster analysis was used to identify distinctive psychological profiles in a large sample of patients with multiple sclerosis. It employed three measures, carefully chosen to capture the main responses historically observed in multiple sclerosis. These measures were (1) the patient's physical disability-impairment, assessed by a neurologist; (2) physical disability-impairment as perceived and reported by the patient; and (3) self-reported psychological well-being (or distress) independent of physical signs and symptoms. The optimal solution from the cluster analysis separated the 99 patients into 10 clusters, which were collapsed into four profiles, consistent with the labels "depression," "denial," "exaggerated somatic," and "severity-related." These data give strong empirical support to the existence of discrete and distinctive coping styles in multiple sclerosis.

7-Aroyl-2,3-dihydrobenzo[b]furan-3-carboxylic acids and 7-benzoyl-2,3-dihydrobenzo[b]thiophene-3-carboxylic acids as analgesic agents.

The synthesis of a series of 7-aroyl-2,3-dihydrobenzo[b]furan-3-carboxylic acids and 7-benzoyl-2,3-dihydrobenzo[b]thiophene-3-carboxylic acids is described. The isomeric 4-benzoyl-1,3-dihydrobenzo[c]furan-1-carboxylic acid was also prepared. Compounds were evaluated for analgesic activity in the mouse phenyl-p-quinone-induced writhing test. Selected compounds were tested for their ability to produce gastric damage in fasted mice and for inhibition of prostaglandin synthetase activity in vitro. Zomepirac was used as a reference. Structure-activity relationships are discussed. One of the compounds, 7-benzoyl-5-chloro-2,3-dihydrobenzo[b]furan-3-carboxylic acid (2c), combined potent analgesic activity with low gastric irritancy.

The antiemetic activity of granisetron against cytostatic-treatment-induced emesis in 10- to 13-week-old ferrets.

The antiemetic activity of granisetron was examined in ferrets aged 10-13 weeks. Emesis was induced by exposure to either whole-body X-irradiation (50 Gy over 10.4 min) or cyclophosphamide (80 mg/kg i.v.) plus doxorubicin (6 mg/kg i.v.). Following exposure to whole-body X-irradiation, the young ferrets vomited with a similar latency to vomit and severity of emesis to that shown by adult animals. Granisetron (0.5 mg/kg i.v.) significantly reduced (P < or = 0.05) the number of vomits and retches and two out of four animals were completely protected. Following injection of cyclophosphamide and doxorubicin, the young ferrets showed a reduced emetic response compared to adult animals. Following a dose of granisetron (0.5 mg/kg i.v.), only one out of four ferrets vomited compared to four out of four in the control group. Further experiments showed that cisplatin (12.5 mg/kg i.v.) was unable to induce vomiting in the young ferret (n = 2). Granisetron (0.5 mg/kg i.v.) was well tolerated by the young ferret and was able to reduce significantly or completely abolish emesis induced by cytostatic treatment. The data support the use of granisetron in pediatric patients and clinical trials are currently underway in this patient population.

The effect of a novel, non-steroidal anti-inflammatory compound, nabumetone (BRL 14777), on cellular infiltration into 24-hour polyvinyl sponge implants in the rat, compared with some steroidal and non-steroidal anti-inflammatory drugs.

The time-course of cell migration into saline-soaked sponge implants over 5 days showed peak polymorphonuclear leucocyte (PMNL) infiltration at 24 h. In common with the corticosteroids dexamethasone and hydrocortisone, and the non-steroidal anti-inflammatory drugs indomethacin, (+)-naproxen, BW 755C and benoxaprofen, nabumetone decreased cell migration into the sponges. PMNLs and mononuclear cells were reduced at 24 h, and there was a parallel decrease in exudate levels of the lysosomal acid hydrolase beta-N-acetyl glucosaminidase [NAG ECB, 3, 2, 1, 30]. Impregnation of sponges with lambda-carrageenan (1%) caused a 2-3 fold increase in cell numbers, with a relatively greater proportion of PMNLs; drug effects were more marked in these implants.

BRL 20459, a novel topically active non-steroidal anti-inflammatory drug.

BRL 20459 is a novel compound which displays anti-inflammatory activity when applied topically in the croton oil and cantharadin rat ear inflammation models. The compound does not inhibit uv-induced erythema in the guinea-pig or granuloma formation in the cotton pellet test in the rat. BRL 20459 does not inhibit prostaglandin synthesis nor does it interact with corticosteroid receptors in the thymus. In contrast to hydrocortisone, BRL 20459 did not cause thymus involution or reduce body weight gain in rats. BRL 20459 would seem to have a different mechanism of action to hydrocortisone, but this mechanism is as yet unknown.

Nabumetone (BRL 14777, 4-[6-methoxy-2-naphthyl]-butan-2-one): a new anti-inflammatory agent.

Nabumetone is a compound of novel structure which displays acute anti-inflammatory activity in the carrageenan-induced oedema model in rats and the ultraviolet-induced erythema model in guinea-pigs. Its activity in these tests is greater than that of aspirin but less than that of naproxen and indomethacin. In the cotton pellet-induced granuloma model in the rat, the compound is active and produces no signs of toxicity at doses much greater than the lowest effective dose, unlike aspirin, naproxen or indomethacin. Nabumetone is also active in the adjuvant-induced arthritis test in rats. In contrast to aspirin, indomethacin and naproxen, the compound is well tolerated by the stomach of fasted rats at doses in excess of those with anti-inflammatory activity. These findings could be linked to the relatively poor ability of nabumetone to inhibit the synthesis of prostaglandins in vitro and to its non-acidic structure. The compound has greater mild analgesic activity than paracetamol, is equi-active with phenylbutazone, but less active than aspirin, naproxen and indomethacin. Nabumetone also has antipyretic activity in the rabbit. No interactions with the hypothalamic-pituitary-adrenal axis have been found.

Refrigerated shelf life of vacuum-packaged, previously frozen ostrich meat.

Previously frozen ostrich meat was evaluated over 28 days to determine the refrigerated shelf life. Intact steaks and ground meat from three ostrich carcasses were vacuum-packaged, frozen to -40°C for 5 days, and stored in a 0°C walk-in cooler. Instrumental analysis of CIE L*a*b* values indicated that ostrich meat was very dark in color, initially and over time. Microbial growth stayed slightly below 1.0 × 10(7) CFU/g for up to 21 days of refrigerated storage. Sensorially evaluated color showed an increase (p <0.05) in darkness over time. Percentage of browning increased (p<0.05) over time from 1% initially to 55% for intact steaks and 75% for ground meat by 28 days. Sensory aroma scores significantly (p<0.05) changed over time, with unacceptable aroma occurring by 14 days. Previously frozen, vacuum-packaged ostrich meat stored under refrigerated conditions should be used within 10 days.

Physicochemical and microbiological properties of selected rice flour-based batters for fried chicken drumsticks.

Rice flour-based batter (RFBB) formulations for chicken drumstick coating were developed as an alternative for traditional wheat flour-based batter (WFBB). Physicochemical properties and storage stability of selected RFBB were evaluated and compared to WFBB. Batter pickup of RFBB formulated in combination with oxidized corn starch and methylcellulose (MC) was not significantly different from that of WFBB. In contrast, batters with only rice and corn flour (60:40% flour weight) exhibited significantly higher pickup. Rice flour batter with 15% oxidized corn starch had the lowest batter pickup. All RFBB exhibited (P < 0.05) lower oil absorption than WFBB. The TBA values of RFBB and WFBB increased (P < 0.05) with increased frozen storage time at -40 C for 90 d. The RFBB with MC exhibited the lowest TBA values, whereas WFBB had the highest values. Microstructural analysis revealed that freezing caused structural deterioration of all batters, but the RFBB with MC exhibited less freezing tolerance than other samples. The total plate counts of immediately fried or frozen fried chicken stored for 90 d were less than 1 log cfu/g sample. The RFBB with 5% oxidized corn starch and MC can replace WFBB on fried drumsticks. Additionally, RFBB results in a healthier product due to lower fat absorption.

Effects of subprimal type, quality grade, and aging time on display color of ground beef patties.

A factorial design was used to evaluate the effects of two subprimal types (chuck roll and knuckle), two quality grades (Premium Choice and Select), and three vacuum-storage aging times before processing (7, 21, and 42d) ground beef patty display color attributes. Patties from chuck roll and Premium Choice subprimals had brighter red visual color scores, less discoloration, and higher L*, a*, b*, and chroma values than those from knuckle and Select subprimals, respectively. With an increased display time, patties became darker red, more discolored, and had decreased L*, a*, b*, and chroma values. Therefore, aging Premium Choice chuck rolls for less time (fewer than 21d) could maximize display color life.

Recurrent de novo mutations implicate novel genes underlying simplex autism risk.

Autism spectrum disorder (ASD) has a strong but complex genetic component. Here we report on the resequencing of 64 candidate neurodevelopmental disorder risk genes in 5,979 individuals: 3,486 probands and 2,493 unaffected siblings. We find a strong burden of de novo point mutations for these genes and specifically implicate nine genes. These include CHD2 and SYNGAP1, genes previously reported in related disorders, and novel genes TRIP12 and PAX5. We also show that mutation carriers generally have lower IQs and enrichment for seizures. These data begin to distinguish genetically distinct subtypes of autism important for aetiological classification and future therapeutics.

Efficacy of home-style dehydrators for reducing Salmonella on whole-muscle chicken.

Home-style dehydrators commonly used by consumers have limited relative humidity (RH) and temperature control. To evaluate the effect of dehydrator load on temperature and RH and subsequent reduction of Salmonella on whole-muscle chicken, chicken breasts were rolled and cut into samples (1 to 2 mm thick, 6 by 6 cm(2)) and inoculated with a five-strain Salmonella cocktail. The samples were allowed to air dry for 15 min and then were loaded into home-style three-tray (3T) or five-tray (5T) dehydrators, with 12 chicken pieces per tray. No difference (P > 0.05) was observed in RH or temperature between the 3T and 5T dehydrators. Peak RH was 38% and gradually deceased to 8.5% after 6 h of drying. Temperatures peaked at 57 °C after 6 h of drying. Dehydrator load had no effect (P > 0.05) on lethality for Salmonella. A reduction of 3.3 ± 0.2 log CFU/cm(2) was observed after 6 h of drying. However, sample location affected Salmonella reduction (P < 0.05). Samples from the bottom tray had a 1.5-log reduction, whereas samples from the top and middle trays had 4.1- and 3.9-log reductions, respectively. The water activity of samples after 6 h of drying was 0.71 ± 0.17 regardless of tray location or dehydrator type. When chicken was dried in home-style dehydrators, increasing the dehydrator load did not increase RH or achieve greater Salmonella lethality. Tray location had a significant impact on Salmonella lethality. Adequate reduction of Salmonella on chicken was not achieved when chamber temperatures were below 57 °C with limited RH throughout drying.

Evaluation of sample preparation methods for water activity determination in jerky and kippered beef: a research note.

Commercially available packaged whole muscle beef jerky, chopped and formed beef jerky, and kippered beef steak were obtained from retail stores to determine the effect of two sample preparation methods on water activity (a(w)). Intact samples were prepared by cutting product into a hexagonal shape with a 3.2 cm diameter. Diced samples were prepared by cutting the product into 0.4 x 0.4 cm squares. Whole muscle jerky a(w) was higher (0.016 units; P<0.001) using the intact method compared to the diced method. There was no difference (P>0.05) in a(w) levels between the two preparation methods for chopped and formed jerky or kippered beef steak. An intact sample preparation method is recommended for a(w) determination of whole muscle jerky to obtain a more conservative value, especially if a(w) is near the margin of safety.