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M Caccamo

Publications and source records attributed to M Caccamo.

9 recordsLinked to original sources

Ensembl 2007.

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of chordate genome sequences. Over the past year the number of genomes available from Ensembl has increased from 15 to 33, with the addition of sites for the mammalian genomes of elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat and european hedgehog; the fish genomes of stickleback and medaka and the second example of the genomes of the sea squirt (Ciona savignyi) and the mosquito (Aedes aegypti). Some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology/paralog annotations based on gene trees.

Animals↗

Ensembl 2006.

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased from 4 to 19, with the addition of the mammalian genomes of Rhesus macaque and Opossum, the chordate genome of Ciona intestinalis and the import and integration of the yeast genome. The year has also seen extensive improvements to both data analysis and presentation, with the introduction of a redesigned website, the addition of RNA gene and regulatory annotation and substantial improvements to the integration of human genome variation data.

Animals↗

Interaction of brine concentration, brine temperature, and presalting on salt penetration in Ragusano cheese.

Thirty-one 3.6-kg blocks of Ragusano cheese were made on each of 6 different days (in different weeks) starting with a different batch of milk on each day. On d 1, 3, and 5, the cheeses were not presalted and on d 2, 4, and 6, all cheeses were presalted (PS). One of the 31 blocks of cheese was selected at random for analysis before brine salting (i.e., on d 0). The remaining 30 blocks were randomly divided into 2 groups of 15 blocks each; one group was placed in 18% brine (18%B) and the other group was placed in saturated brine (SB). For the 15 blocks within each of the 2 brine concentrations (BC), 5 blocks were placed in a brine tank at 12 degrees C, 5 at 15 degrees C, and 5 at 18 degrees C, and submerged for 24 d. The research objective was to determine the combined impacts (i.e., interactions) of PS the curd before stretching, BC (SB vs. 18%B), and brine temperature (BT; 12, 15, and 18 degrees C) on salt uptake, moisture content, and yield of Ragusano cheese. Although BC, BT, and PS each had their own separate impacts on salt uptake, there was little interaction of these effects on salt uptake when they were used in combination. The PS most quickly delivered salt to the interior of the cheese and was the most effective approach to salting for controlling early gas formation. There were strong separate impacts of BC, BT, and PS on cheese moisture content, moisture loss, and net weight loss, with BC having the largest separate impact on these parameters. Reducing BT reduced salt content and increased moisture, but the effects were small. The more important effect of reduced BT was to reduce growth of gas forming bacteria. The 18%B produced higher moisture, and less moisture and weight loss than SB. The effect of interactions of BC, BT, and PS on moisture loss and net weight loss were small. To achieve the maximum benefit from the various approaches to salting for controlling early gas formation in Ragusano cheese, PS combined with slightly lower BT (i.e., 15 degrees C instead of 18 degrees C) should be used. Although using 18%B instead of SB did increase salt uptake, the point at which improved salt uptake occurred due to use of 18%B did not provide benefit in prevention of early gas formation, as reported separately. However, use of 18%B instead of SB provided a 9.98% increase in cheese yield due to reduced moisture loss during brining; this would be very attractive to cheese makers. The increase in yield needs to be balanced against the risk of growth of undesirable bacteria in the 18%B and the creation of another cheese quality defect.

Animals↗

Ensembl 2005.

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.

Animals↗

Ensembl 2004.

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.

Animals↗

Measurement of gas holes and mechanical openness in cheese by image analysis.

A method to measure the amount of the surface area of cheese slices occupied by gas holes was developed to reflect the relative gas production among different cheeses. A digital camera mounted on a copy stand with lighting was used to make digital images of each slice of cheese. A commercial digital image analysis software program was used and an algorithm was written to measure the area of the image of the cheese slice occupied by holes. The image was cropped and scanned to determine which color channel produced the best image contrast. The MATLAB program allowed the user to eliminate mechanical openness or false holes and then to scan the image to produce a percent distribution of pixels in the image as a function of pixel intensity. The user then determined a threshold value to differentiate pixels that were in holes from those representing areas with no holes. The percentage of the total surface area occupied by holes was calculated. The coefficient of variation of the method ranged from 2.43% with gas holes of about 1% of the surface of the cheese slice to a coefficient of variation of 0.92% with gas holes of about 6.8% of the surface area of the cheese slice. Examples of applications of this method are given for Emmental, Ragusano, and Cheddar cheeses. The method can be used as a tool in research studies to correlate the amount of gas production with manufacturing conditions or as a quality control tool in cheese manufacturing.

Cheese↗

Influence of brine concentration, brine temperature, and presalting on early gas defects in raw milk pasta filata cheese.

Thirty-one 3.8-kg blocks of Ragusano cheese were made on each of 6 d starting with a different batch of raw milk on each day. On d 1, 3, and 5, cheeses were not presalted and on d 2, 4, and 6, all cheeses were presalted. Before brine salting, one of the 31 blocks of cheese was selected at random for analysis (i.e., at d 0). The remaining 30 blocks were randomly divided into 2 batches of 15 blocks each, one group was placed in 18% brine, and the other group was placed in saturated brine. For the 15 blocks within each of the 2 brine concentrations, 5 blocks each were placed in brine tanks at 12, 15, and 18 degrees C. Cheese blocks were sampled immediately before brine salting (d 0) and after 1, 4, 8, 16, and 24 d of brine salting. Presalting the curd with 2% added salt before stretching reduced the coliform count in the cheese by 1.41 log and resulted in a major reduction in early gas formation. Across all treatments in the present study, the average reduction in gas formation due to presalting was 75%. Reducing brine temperature had the second largest impact on reducing gas production, but did not reduce the coliform count in the cheese. Reducing brine temperature from 18 to 12 degrees C made a larger reduction in early gas formation in cheeses that were not presalted (from 6.8 to 1.8% gas holes, respectively) than in cheeses that were presalted (from 1.9 to 0.5% gas holes, respectively). To achieve the same absolute level of gas production in the nonpre-salted cheese as was achieved in presalted cheese in combination with 18 degrees C brine, the brine temperature for the nonpresalted cheese had to be lowered from 18 to 12 degrees C. Reducing brine concentration, although effective at increasing the rate of salt penetration into the block, did not have any impact on coliform count and had minimal impact on reducing gas production. The condition where reducing brine concentration was able to make a reduction in gas production was for cheeses that were not presalted and brined at 18 degrees C. Presalting is a very simple and practical approach to reducing the problem of early gas formation in combination with strategies to improve milk quality and cheese making conditions. Further work is needed to understand the impact of different levels of presalting on death of coliforms and gas production in the cheese.

Cheese↗