bluuebunny/crossref_metadata_2025 huggingface dataset:
An alignment-free model for comparison of regulatory sequences
Authors: Koohy Hashem , Dyer Nigel P. , Reid John E. , Koentges Georgy , Ott Sascha
Published: August 2010

Motivation: Some recent comparative studies have revealed that regulatory regions can retain function over large evolutionary distances, even though the DNA sequences are divergent and difficult to align. It is also known that such enhancers can drive very similar expression patterns. This poses a challenge for the in silico detection of biologically related sequences, as they can only be discovered using alignment-free methods.

Results: Here, we present a new computational framework called Regulatory Region Scoring (RRS) model for the detection of functional conservation of regulatory sequences using predicted occupancy levels of transcription factors of interest. We demonstrate that our model can detect the functional and/or evolutionary links between some non-alignable enhancers with a strong statistical significance. We also identify groups of enhancers that are likely to be similarly regulated. Our model is motivated by previous work on prediction of expression patterns and it can capture similarity by strong binding sites, weak binding sites and even the statistically significant absence of sites. Our results support the hypothesis that weak binding sites contribute to the functional similarity of sequences.

Our model fills a gap between two families of models: detailed, data-intensive models for the prediction of precise spatio-temporal expression patterns on the one side, and crude, generally applicable models on the other side. Our model borrows some of the strengths of each group and addresses their drawbacks.

Availability: The RRS source code is freely available upon publication of this manuscript: http://www2.warwick.ac.uk/fac/sci/systemsbiology/staff/ott/tools_and_software/rrs

Contact:  s.ott@warwick.ac.uk; hashem.koohy@warwick.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Recovery of depleted Baltic Sea fish stocks: a review
Authors: Aps Robert , Lassen Hans
Published: August 2010

Aps, R., and Lassen, H. 2010. Recovery of depleted Baltic Sea fish stocks: a review. – ICES Journal of Marine Science, 67: 1856–1860. Attempts to recover some depleted Baltic fish stocks between 1995 and 2008 are reviewed. Management measures aimed at recovery were adopted by competent authorities (until 2005 the International Baltic Fisheries Commission, IBSFC), including the Baltic Salmon Action Plan (1997), Long-Term Management Strategy for Cod Stocks in the Baltic Sea (1999), Long-Term Management Strategy for the Sprat Stock in the Baltic Sea (2000), Recovery Plan for Baltic Cod (2001), and the Long-Term Objectives and Strategies for the Management of Baltic Sea Herring (2000–2002). For all stocks, TACs have been set systematically more than the scientific advice based on sustainable exploitation. We interpret this as “decision overfishing”. There is also evidence of extensive underreporting of catches, which is interpreted as “implementation overfishing”. This means that a management body is knowingly maintaining a situation of overfishing. Nevertheless, measures have also been taken to combat the situation. Our analysis suggests that decision overfishing is related strongly to overcapacity of the fleets. The combination of decision overfishing and implementation overfishing, and not the management measures per se, could be the reason for the failure of depleted stocks to recover.
First Report of Group 16SrXII Phytoplasma Causing Stolbur Disease in Potato Plants in the Eastern and Southern Anatolia Regions of Turkey
Authors: Eroglu S. , Ozbek H. , Sahin F.
Published: August 2010

In recent years, a stolbur-like disease has had devastating effects on the yield and marketable quality of potato production in Erzurum (Eastern Anatolia) and Akcakale-Sanliurfa (Southern Anatolia) regions of Turkey. Potato plants exhibited several different symptoms including stunting, upward rolling of the top leaves along with reddish or purplish coloration, chlorosis, shortened internodes, swollen nodes, proliferated axillary buds, aerial tubers, and early plant decline. An extensive survey from 2003 to 2010 was performed and diseased plant samples were collected. Total genomic DNAs were isolated from the leaf mid-veins of the six different symptomatic and two symptomless plants selected. Nested-PCRs, carried out by using phytoplasma-universal primer pair P1/P7 followed by R16F2n/R16R2 (2), amplified 16S rDNA fragments (F2nR2) from only templates derived from symptomatic plants. F2nR2 PCR products from two independent symptomatic plants were cloned and sequenced from both directions with M13 universal primers. The obtained 16S rDNA sequence (GenBank Accession No HM485579) was subjected to virtual restriction fragment length polymorphism (RFLP) analysis using iphyclassifier software (3). Results indicated that the phytoplasma, here identified in association with potato plants, shared best sequence identity (99%) with members of subgroup 16SrXII-A (e.g., GenBank Accession No. EU010006). Moreover, collective RFLP pattern of potato-associated phytoplasma differed from digestion profiles of previously described 16SrXII subgroups, sharing best similarity coefficient (0.94) with the reference phytoplasma strain of subgroup 16SrXII-A (GenBank Accession No. AJ964960). Thus, it was confirmed that potato-associated phytoplasma represents a new 16SrXII subgroup (16SrXII-N). Furthermore, a new primer set (PatsecF/PatsecR) was designed for priming specific PCR-amplification of potato-associated phytoplasma 16S rDNA sequence. PCR reaction was successfully used for specifically detecting stolbur phytoplasma in infected potato plants. The use of this method may help to determine possible alternative hosts and vectors of potato phytoplasma, which is important for development of an integrated management strategy for effective control of this disease in the future. Presence of potato stolbur diseases in the Eastern Anatolia Region of Turkey has previously been reported (1). To our knowledge, this is the first report of occurrence of a 16SrXII group phytoplasma causing potato stolbur diseases caused in the Eastern and Southern Anatolia regions of Turkey.

References: (1) A. Citir. J. Turk. Phytopathol. 14:53, 1985. (2) D. E. Gundersen and I. M. Lee. Phytopathol. Mediterr. 35:144, 1996. (3)Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
Increased Severity of Foliar Diseases of Sweet Corn Infected with Maize Dwarf Mosaic and Sugarcane Mosaic Viruses
Authors: Meyer M. D. , Pataky J. K.
Published: August 2010

Maize dwarf mosaic (MDM), caused by Maize dwarf mosaic virus (MDMV) and Sugarcane mosaic virus (SCMV), is an economically important viral disease of sweet corn (Zea mays). MDM is known to increase the severity of fungal root rots and southern corn leaf blight (SCLB). The effect of infection with MDMV-A and SCMV on eight foliar diseases was evaluated on 32 sweet corn hybrids (27 MDM-susceptible hybrids and five MDM-resistant hybrids) in 2007, 2008, and 2009. Virus infection substantially increased the severity of five diseases, including: SCLB, northern corn leaf spot (NCLS), gray leaf spot (GLS), Diplodia leaf streak (DLS), and eyespot. Among MDM-susceptible hybrids, mean severity of SCLB, NCLS, GLS, DLS, and eyespot on virus-infected plants was typically double that of plants that were asymptomatic of viral infection. Three diseases were not substantially increased by MDM, including: common rust, northern corn leaf blight (NCLB), and Stewart's wilt. Virus infection appeared to affect the severity of diseases caused by necrotrophic foliar fungi that colonize mesophyll tissue. MDM did not appear to substantially affect the severity of diseases caused by pathogens that form haustoria or invade the vascular system. The extent to which SCLB severity is increased by MDM in terms of changes in level of host resistance also was determined. For MDM-susceptible hybrids, reactions to SCLB ranged from resistant to moderately susceptible in MDM-free treatments, but each of these hybrids was classified as moderately susceptible to susceptible when infected with MDMV-A and/or SCMV. The results of this experiment demonstrate the importance of breeding for MDM resistance, not only to control this important viral disease of sweet corn, but also to lower the potential for detrimental effects from several other foliar diseases that often are of minor importance on sweet corn in the absence of MDM.
Identification and Characterization of Carbendazim-Resistant Isolates of Gibberella zeae
Authors: Liu Xin , Yin Yanni , Wu Jianbing , Jiang Jinhua , Ma Zhonghua
Published: August 2010

Sensitivity of Gibberella zeae to carbendazim was determined by measuring mycelial growth in fungicide-amended media. Among 1,529 isolates tested, 31 isolates showed a high level of resistance (HR) to carbendazim (fungicide concentration that results in 50% inhibition of mycelial growth [EC50] of 10.35 to 30.26 mg a.i. liter–1) and 10 isolates were moderately resistant (MR) (EC50 of 4.50 to 7.28 mg a.i. liter–1). The remaining 1,488 isolates were sensitive to carbendazim and were unable to grow on potato dextrose agar amended with carbendazim at 2 mg a.i. liter–1. Analysis of DNA sequences of the β2-tubulin (Tub2) gene showed that all 10 MR isolates had a point mutation at codon 198 causing a replacement of glutamic acid by glutamine. At the codon position 167, the amino acid phenylalanine was replaced by tyrosine in 28 of 31 HR isolates. The remaining three HR isolates had a point mutation at codon 200 which converted phenylalanine to tyrosine. Based on these point mutations in the Tub2 gene, allele-specific polymerase chain reaction primers were developed for rapid detection of the point mutations. The rapid molecular method will be a valuable tool for the monitoring of carbendazim resistance in G. zeae. Additionally, deletion of the β1-tubulin gene (Tub1) in the HR isolate GJ33 resulted in increased resistance to carbendazim. These results indicate that Tub1 plays a role in the sensitivity of G. zeae to carbendazim.
Identification and Pathogenicity of Chrysoporthe cubensis on Eucalyptus and Syzygium spp. in South China
Authors: Chen S. F. , Gryzenhout M. , Roux J. , Xie Y. J. , Wingfield M. J. , Zhou X. D.
Published: August 2010

The genus Chrysoporthe includes important pathogens of plantation-grown Eucalyptus spp. and has been reported from several tree genera in the order Myrtales in tropical and subtropical areas of the world. During disease surveys in South China, fruiting structures typical of Chrysoporthe spp. were observed on cankers on Eucalyptus spp. and Syzygium cumini trees. The aim of this study was to confirm the identity of the Chrysoporthe cubensis infecting the Eucalyptus spp. and S. cumini and to test the pathogenicity of the fungus. Following glasshouse trials to select virulent isolates, field inoculations were undertaken to screen different commercial Eucalyptus genotypes for their susceptibility to the fungus. Isolates were characterized based on their morphology and DNA sequence data for the β-tubulin and internal transcribed spacer regions of the ribosomal DNA. Results showed that the putative pathogen represented the Asian form of C. cubensis, which occurred on numerous different Eucalyptus spp. and hybrid clones as well as S. cumini. Field inoculations showed that all six of the Eucalyptus genotypes tested are susceptible to infection by C. cubensis. Significant differences were observed between them, providing prospects to select disease-tolerant planting stock in the future.
Local Distance of Wheat Spike Infection by Released Clones of Gibberella zeae Disseminated from Infested Corn Residue
Authors: Keller Melissa D. , Waxman Katrina D. , Bergstrom Gary C. , Schmale David G.
Published: August 2010

Knowledge of the movement of Gibberella zeae (Fusarium graminearum) from a local source of inoculum in infested cereal debris is critical to the management of Fusarium head blight (FHB) of wheat. Previous spatial dissemination and infection studies were unable to completely distinguish the contributions of released inocula from those of background inocula. Clones of G. zeae were released and recaptured in five wheat fields in New York and Virginia in 2007 and 2008. Amplified fragment length polymorphisms were used to track and unambiguously identify the released clones in heterogeneous populations of the fungus recovered from infected wheat spikes collected at 0, 3, 6, and ≥24 m from small-area sources of infested corn residues. The percent recovery of the released clones decreased significantly at fairly short distances from the inoculum sources. Isolates of G. zeae recovered at 0, 3, 6, and ≥24 m from the center of source areas shared 65, 19, 13, and 5% of the genotypes of the released clones, respectively. More importantly, the incidence of spike infection attributable to released clones averaged 15, 2, 1, and <1% at 0, 3, 6, and ≥24 m from source areas, respectively. Spike infection attributable to released clones decreased an average of 90% between 3 and 6 m from area sources of inoculum, and the spike infection potential of inocula dispersed at this range did not differ significantly from background sources. Our data suggest that FHB field experiments including a cereal debris variable should incorporate debris-free borders and interplots of at least 3 m and preferably 6 m to avoid significant interplot interference from spores originating from within-field debris.
First Report of Fusarium Wilt of Lavandula pubescens Caused by Fusarium oxysporum in Saudi Arabia
Authors: Perveen K. , Bokhari N.
Published: August 2010

In November 2008, a wilt of lavender (Lavandula pubescens) seedlings was observed in the greenhouse at King Saud University, Riyadh, Saudi Arabia. Affected seedlings were wilted and the root system was poorly developed. Diseased stems developed a dark coloration that extended down to the roots. Vascular tissue of the affected seedlings appeared red or brown. Isolations consistently yielded a fungus growing from the discolored stem tissue when placed on potato dextrose agar. The macroscopic characteristics of the colony, as well as microscopic structures, were used to identify the fungus as Fusarium oxysporum (2). Oval to elliptical microconidia without septa and originating from short phialides were used to distinguish the species from F. solani (1). The fungus was authenticated by the ITCC (Indian Type Collection Centre), Indian Agricultural Research Institute, New Delhi, India, and given I.D. No. 7532.09. For conducting further experiments, healthy seedlings of L. pubescens were obtained from the botanical garden of the King Saud University and grown in steam-sterilized soil. Healthy seedlings of lavender were inoculated using a root-dip method with a conidial suspension (1 × 107 CFU/ml) of one strain of F. oxysporum obtained from infected plants. Inoculated seedlings were then transplanted into steam-sterilized soil. Plants inoculated with sterilized water (1 ml per plant) served as control treatments. Wilt symptoms and vascular discoloration in the roots and crown developed within 20 days on all plants inoculated with the pathogen, while control plants remained asymptomatic. F. oxysporum was consistently reisolated from symptomatic plants. The pathogenicity test was conducted twice. To our knowledge, this is the first report of F. oxysporum on L. pubescens in Saudi Arabia or elsewhere in the world, and this newly identified disease may be a potential threat to commercial production of lavender.

References: (1) J. F. Leslie and B. A. Summerell. Page 212 in: The Fusarium Laboratory Manual. Blackwell Publishing Professional, Hoboken, NJ, 2006. (2) P. C. Nelson et al. Clin. Microbiol. Rev. 7:479, 1994.
First Report of Tomato torrado virus Infecting Tomato in Italy
Authors: Davino S. , Bivona L. , Iacono G. , Davino M.
Published: August 2010

In 2009 and 2010, approximately 2% of plants had disease symptoms, including initial leaflet chlorosis that later developed into necrotic spots and general necroses along the leaflet. Fruit production on affected plants was substantially reduced and necroses were also present. Total RNA was extracted from five symptomatic plant samples using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) and analyzed by reverse transcription (RT)-PCR with specific primer pair: TR2F (5′ GAAGGACGAAGAGCGACTG 3′), and TR2R (5′ AAGGTAGGTATGCGTTTGC 3′) (1). The primers amplified a 575-bp fragment within the coat protein Vp23 of Tomato torrado virus (ToTV). No RT-PCR products were observed when water or asymptomatic tomato plants were used as controls. The RT-PCR products were purified and directly sequenced in both directions. Pair-wise similarity analysis confirmed the presence of ToTV with 99% similarity to isolate PRI-ToTV0301 (GenBank Accession No. DQ388880) and 98% similarity to isolate Kra (Accession No. EU652402). A representative sequence was deposited with GenBank (Accession No. GU903899). To further confirm the presence of ToTV, dsRNA analysis was conducted on all five symptomatic plants and one healthy tomato plant (2). Electrophoresis of dsRNA showed two bands of approximately 5,400 and 7,800 nucleotides long, typical of ToTV in all samples, while a third band between the other two (approximately 6,400 nt) was detected. Serological testing using double-antibody sandwich-ELISA was also conducted on the five symptomatic and 25 additional plants from the same greenhouse that displayed typical Pepino mosaic virus (PepMV) symptoms only. Antibodies used for serological testing screened for the presence of PepMV, Tomato spotted wilt virus, Cucumber mosaic virus, and Tomato mosaic virus (Loewe Biochemica, Sauerlach, Germany). These tests detected PepMV in all samples with disease symptoms typical of PepMV, and in three of the five samples with the newly described symptoms. To our knowledge, this is the first report of ToTV in Italy, and in some plants, co-infection with PepMV was likely. All ToTV-infected tomato plants in the greenhouse were destroyed.

References: (1) H. Pospieszny et al. Plant Dis. 91:1364, 2007. (2) J. Sambrook et al. Molecular Cloning. A Laboratory Manual. 2nd ed. Cold Spring Harbor Laboratory Press, Woodbury, NY, 1989.
Molecular Properties of Post‐Mortem Muscle. II. Phase Microscopy of Myofibrils from Bovine Muscle
Authors: STROMER MARVIN H. , GOLL DARREL E.
Published: August 2010

SUMMARY—

The structural appearance of homogenized myofibril suspensions from seven heifers was studied using phase microscopy at various times post‐mortem with three different extracting solutions: 1) 0.25M sucrose, 1mM ethylenedi‐aminetetraacetic acid (EDTA), 0.05M Tris‐(hydroxymethyl) aminomethane (Tris), pH 7.6; 2) 0.15M KCI, 1mM EDTA, 0.05M Tris, pH 7.6; and 3) 50% glycerol, 1miZl EDTA, 0.05M Tris, pH 7.6. Samples were examined at death and 24 hr and 312 hr post‐mortem with storage at 2 and 16°C. The 16°‐24‐hr samples exhibited a marked thickening of the A‐band, a shortening of the l‐band, and a replacement of the H‐zone by a dark line or band. The 2°.24‐hr samples showed only alternating light and dark bands of nearly equal width, which has been described as a typical supercontracted pattern. At 312 hr, more variability in banding pattern and fragmentation is encountered, but the trend is to preserve the pattern observed in the 24.hr samples. Occasionally, a narrow H‐zone is seen in the center of a thickened A‐band in the glycerol preparations sampled 312 hr post‐mortem. The results suggest that cold shortening of bovine muscle is structurally identical to contraction and substantiate the view that shortening is minimal at 16° storage temperatures.

The sucrose extracting solution consistently gave the best preservation and was used for subsequent experiments. Although banding patterns at death and in the 24‐hr samples obtained with glycerol showed reliable consistency, these preparations at times exhibited a disturbing fuzziness. Results with KCI solutions were least desirable, because of repeatedly poor structural preservation, as indicated by variability in sarcomere lengths within and between fibers, as well as lack of clarity in banding.
Reaction of Malonaldehyde with Protein
Authors: CRAWFORD DAVID L. , YU T. C. , SINNHUBER RUSSELL O.
Published: August 2010

SUMMARY—

Malonaldehyde was shown to react with bovine plasma albumin under aqueous conditions by a pH‐dependent reaction exhibiting first‐order kinetics. The maximum reaction rate observed was near pH 4.30. The reaction was shown to involve the e‐amino lysine and N‐terminal amino aspartic acid groups on the protein as judged by their loss to reaction with 1‐fluoro‐2,4‐dinitrobenzene. Malonaldehyde did not appear to participate in an intermolecular cross‐linking reaction with gelatin sols over a wide pH range. Presumptive evidence was obtained for the reaction of malonaldehyde, derived from autoxidized lipid, with the c‐amino lysine functions on bovine plasma albumin.

A nucleophilic 1,4‐addition of the free amino functions on the protein to the end carbon atom of the α,β‐unsaturated carbonyl system of the free enol of malonaldehyde to form an enamine linkage is postulated to be the mechanism for this reaction.
Effect of Refined Menhaden Oils on the Flavor and Fatty Acid Composition of Broiler Flesh
Authors: MILLER DAVID , GRUGER EDWARD H. , LEONG KAM C. , KNOBL GEORGE M.
Published: August 2010

SUMMARY—

Three menhaden oil preparations–(1) destearinated, (2) molecularly distilled triglycerides, and (3) ethyl esters of menhaden fatty acids—were fed to broilers at a 5% level to determine their effect on the flavor and fatty acid composition of the flesh. Corn oil and tallow were fed as controls. The flavor‐contributing component(s) in the menhaden oil preparations apparently resided in the fatty acids regardless of whether the preparations were fed as the triglyceride or as the ethyl ester. Four marine fatty acids (18:4ω3, 20:4ω3, 20:5ω3, and 22:5ω3),c deposited in the flesh of the broilers, were highly correlated with the occurrence of the unacceptable flavor.
Overcoming the Bacteriostatic Activity of Onion in Making Standard Plate Counts
Authors: WEI L. S. , SIREGAR J. A. , STEINBERG M. P. , NELSON A. I.
Published: August 2010

SUMMARY—

The bacteriostatic activity of onion homogenates in making standard plate counts as reported in the literature was confirmed. It was found that potassium sulfite counteracts this activity. The sulfite must be added to the blending solution instead of to the petri plate. Five‐tenths percent sulfite is sufficient and the concentration may be as high as 1.6%. Variety of onion did not appear to be a factor. This treatment was of value with both laboratory and commercially dehydrated onions. Coliform organisms were not inhibited by sulfite. It is recommended that all standard plate counts of onion be made with 0.5% K2SO8, in the blending solution.
Effect of Storage Conditions on Standard Plate Counts of Raw Onions
Authors: SIREGAR J. A. , STEINBERG M. P. , WEI L. S. , NELSON A. I.
Published: August 2010

SUMMARY—

Eight different storage conditions were applied. The storage variables were air temperature, air movement and initial bruising of the onions. Storage time was three weeks. Standard plate count and percent spoiled onions were combined into an expression termed the microbial quotient. Moving air at 34°F was the best storage condition and even bruised onions kept well. At room temperature bruised onions showed a greatly increased microbial quotient. Statistical analysis showed that air temperature and bruising were highly significant factors.
Factors Influencing the Transport of Air‐Borne Bacteria at Openings
Authors: HELDMAN D. R. , HEDRICK T. I. , HALL C. W.
Published: August 2010

SUMMARY—

The factors causing transport of air‐borne microorganisms from a high concentration space to a low concentration space were investigated in an aerosol chamber. The transport of bacterial aerosol through an opening between the compartments of the chamber was expressed in terms of a turbulent transfer coefficient.

The experimental transfer coefficients increased significantly as the ventilation rates increased from 20 to 40 ft3/min and increased slightly between 40 and 60 ft3/min. Results obtained with ventilation rate gradients ranging from − 30 to +30 ft3/min indicated that the coefficient was maximum at equal rates.

An increase in the opening height from 3 to 9 in. produced a significant decrease in the turbulent transfer coefficient. Temperature gradients ranging from −14 to +12S°F with respect to a reference temperature of 75°F resulted in an increase in the turbulent transfer coefficients from 2.09 to 8.09. The effect of temperatures between 75 and 95°F and corresponding relative humidities between 31 and 60%, on aerosol viability did not account for the entire influence of the temperature gradient on aerosol transport.
EFFECT OF QUALITY ATTRIBUTES UPON PROCESSING AND PALATABILITY CHARACTERISTICS OF COMMERCIALLY CURED HAMS
Authors: CROSS H. R. , SMITH G. C. , CARPENTER Z. L.
Published: August 2010

SUMMARY –A total of 488 fresh hams were stratified according to method of cure (regular‐cured and water‐added) and quality scores (gross morphology, color and firmness). Each ham was pumped, cured and smoked using commercial procedures. Individual weights for each ham were obtained at each stage of the processing sequence. Center slices from 50 processed hams were evaluated for muscle color, chemical composition and organoleptic properties. Among both regular‐cured and water‐added hams, gross morphology groups were not significantly (P < 0.05) related to weight gains (fresh to chilled), weight losses during the period in transit (125 km), or to flavor, saltiness, moisture (%) or pigment concentration for the combined muscles of the center slices. A comparison of individual ham muscles revealed that the biceps femoris (BF) was less tender than the semitendinosus (ST); the ST was less salty than the semimembranosus (SM) and the ST had a higher fat content on a moisture‐free basis than other muscles for both regular‐cured and water‐added hams. Significant differences (P < 0.05) among muscles for flavor and juiciness were evident for the regular‐cured hams; however, there were no significant differences for the hams in the water‐added group. There were significant differences in pigment concentration among muscles from the center‐cut slices from water‐added hams. Regular‐cured hams in gross morphology group 5 were significantly (P < 0.05) more juicy and more tender than hams in the other four quality groups. Also, center slices from hams in the high quality gross morphology group (group 5) were more uniform in muscle color, more desirable in lean color and contained more fat than hams in group 1. Regular‐cured hams in gross morphology group 5 also produced individual muscles which were more desirable in lean color (SM, BF), more flavorful (SM), more juicy (ST, BF) and more tender (ST, BF) than hams in group 1. Water‐added hams in gross morphology group 5 did not differ from hams in group 1 in any of the traits but were significantly (P < 0.05) more tender than those in group 2.
POULTRY PRODUCT QUALITY. 5. Microbiological Evaluation of Mechanically Deboned Poultry Meat
Authors: OSTOVAR K. , MacNEIL J. H. , O'DONNELL K.
Published: August 2010

SUMMARY —Samples of deboned meat from broiler necks and backs, whole fowl and turkey racks were obtained from commercial sources and examined for total aerobic counts, fecal coliforms, salmonellae, Clostridium perfringens, coagulase positive staphylococci and psychrotolerant microorganisms. The raw materials were either deboned immediately after birds were processed (conventional processing) or held in the plants at 3–5°C for 5 days prior to deboning (delayed processing). The storage studies were conducted by holding the deboned meat at 3°C for 0, 3, 6 and 12 days and at ‐15°C for periods of 3, 6 and 9 months. The total aerobic counts of delayed processed samples were shown to be higher than conventionally processed meat and remained the same throughout the storage period. In all instances, the total aerobic counts increased during the storage at 3°C. The MPN fecal coliforms were high for all samples and remained relatively the same throughout the storage period at 3°C. Freezing resulted in a significant reduction of fecal coliforms. Only six out of 54 samples were contaminated with salmonellae while four showed the presence of C. perfringens and none was contaminated with S. aureus. Pseudomonas, Achromobac‐ter and Flavobacterium dominated the psychrotolerant genera isolated in this investigation.
OCCURRENCE OF Clostridium perfringens IN BROILER PROCESSING AND FURTHER PROCESSING OPERATIONS
Authors: LILLARD H. S.
Published: August 2010

SUMMARY —Three broiler processing plants were surveyed to determine the occurrence of Clostridium perfringens in processing areas, and in further processed products. Direct plating on SPS agar and enrichment techniques were used. Samples were taken from nine points in the processing areas of two plants. The following products were examined from the further processing operations of three plants: uncooked broiler parts, cooked products, batter, flour with and without spice mixture and spice. A limited number of rolls (4) and diced meat (5) were also sampled. Results from all plants were similar. C. perfringens was isolated from the following sources in the processing area: feet, feathers, caecum, vent area, scald tank water, chill tank water, breast surface after the chill tank and neck skin from the end of the evisceration line. Though C. perfringens was found frequently on live birds coming into the plant, it was isolated in relatively small numbers from all but the feet, feathers, and caecum. With few exceptions, C. perfringens was isolated from the further processing area by enrichment techniques only. This organism was most frequently isolated from samples of flour and batter. Only 2.6% of 118 samples of cooked product were positive.
EFFECT OF OXYGEN‐ENRICHED ATMOSPHERES ON STORAGE QUALITY OF PACKAGED FRESH MEAT
Authors: DAUN HENRYK , SOLBERG MYRON , FRANKE WILLIAM , GILBERT SEYMOUR
Published: August 2010

SUMMARY —The extension of fresh meat shelf‐life is important from both practical and theoretical points of view. Color is usually used as a measure of fresh meat quality during storage. Beef top‐round slices were prepared using sanitary precautions. Meat slices were enclosed in a thermally sealed semi‐rigid polyvinyl chloride tray system of special design. Face‐to‐face meat samples were used to compare the effects of high oxygen with normal air atmospheres. One package from each pair was evacuated and the atmosphere readjusted to approximately 90% oxygen through a septum. Packages were kept at 4 ± 0.5°C and gas chromatographic readings for CO2, O2 and N2 were conducted daily. Spectrophotometric and bacteriological evaluations were made on selected pack ages during storage to determine pigment oxidation and microbial growth. Three experiments each containing six to eight pairs of samples were conducted. The generation of CO2 was observed in two periods–the first immediately after packaging and lasting for 1–2 days, after which the CO2 level remained approximately stable up to 8—9 days, when it again started to increase in correspondence with increased bacterial growth. There was more CO2 produced than O2 utilized in the stored samples. In the first stage, samples stored in oxygen‐enriched atmospheres had higher O2 uptake than samples stored in air. Microbial growth was similar in both atmospheres. Under conditions of this study, head space enrichment to about 90% oxygen prolonged acceptable meat color when compared with samples stored in an air atmosphere.
EQUILIBRIUM MOISTURE CHARACTERISTICS OF FREEZE‐DRIED BEEF COMPONENTS
Authors: PALNITKAR M. P. , HELDMAN D. R.
Published: August 2010

SUMMARY –The equilibrium moisture content isotherms of beef components and fractions were measured and analyzed. Measurements were conducted in an electrobalance system which allows continuous measurement of sample weight change during the experiment. Equilibrium moisture content isotherms were measured for water soluble and water insoluble fractions, actomyosin, connective tissue (collagen) and sarcoplasmic fraction along with raw and precooked freeze‐dried beef. The measurements were conducted at 52° and 70°F. In general, the moisture adsorption by product components was very low at low water activities when compared to the freeze‐dried product. Actomyosin adsorbed only a small amount of moisture until a water activity greater than 0.6 was exceeded. Although the influence of temperature on the magnitude of water activity was as expected, the shapes of desorption isotherms were abnormal when compared to desorption isotherms for the precooked freeze‐dried beef. A comparison of desorption isotherms for raw and precooked freeze‐dried beef revealed a similar difference. An attempt to predict product isotherms from knowledge of component isotherms and weight fractions of components revealed that predictions were significantly lower than experimental values.
NUTRITIVE AND ORGANOLEPTIC CHARACTERISTICS OF NONDAIRY IMITATION MILKS
Authors: KOSIKOWSKI FRANK V.
Published: August 2010

SUMMARY –13 nondairy imitation milk powders, concentrates and bottled beverages were analyzed for general composition, nutrients and organoleptic properties. These products were obtained from 11 domestic sources, which decreased to eight by the end of the study. Nondairy imitation milks were characterized by wide fluctuations in riboflavin (1.9–418.0 μ per 100 ml) and thiamine (0.2–54.7 μ per 100 ml), protein (0.76–3.67%) and amino acids like lysine (4.7–13.6 μmole per ml). Calcium and magnesium in all imitation milks were well below levels of the same elements in cow's milk reconstituted from whole milk powder, whereas sodium generally was much higher, almost threefold in several instances. The appearance of most nondairy imitation milks closely resembled fresh, pasteurized cow's milk, but the flavor, ascertained by three milk judges, was not similar nor as acceptable to them. Several imitation milks scored in flavor as well as or slightly better than cow's milk reconstituted from whole milk powder, but in all these instances, including the cow's milk, the flavor quality was only fair. Most imitation milks contained less protein than reconstituted cow's milk, but two contained concentrations of 3.26 and 3.67%, comparable to cow's milk. A number of nondairy imitation milks showed very low levels of calcium, riboflavin, thiamine and essential amino acids, lysine and methionine, in relation to cow's milk.
EFFECTS OF BLANCHING, CHEMICAL TREATMENTS AND FREEZING METHODS ON QUALITY OF FREEZE‐DRIED MUSHROOMS
Authors: FANG T. T. , FOOTRAKUL P. , LUH B. S.
Published: August 2010

SUMMARY –Mushrooms, Agaricus bisporus, were cut into slices about 5 mm thick. The polyphenoloxidase activity in the sliced mushrooms was inhibited by: (a) dipping in sodium metabisulfite solution containing 200 ppm SO2; (b) dipping in 2% NaCl solution; and (c) blanching in boiling water for 2 min followed by evaporative cooling. The products were frozen with Freon‐12 at –22°F for 60 sec. The frozen mushrooms were dried to 3% moisture in a Stokes freeze drier and sealed under vacuum in No. 2–1/2 cans. The freeze‐dried product made by the Freon‐dipping process was better in quality and firmer in texture than that made by the slow‐freezing process. Blanching the fresh mushrooms in boiling water for 2 min prior to freezing results in a lighter color in the freeze‐dried products after rehydration. However, the product was less attractive in flavor and texture. The blanching process caused considerable loss of water‐soluble solids and ascorbic acid. The effects of processing variables on the chemical, physical and organoleptic quality of the rehydrated products are presented.
RIPENESS SORTING OF MUSCADINE GRAPES BY USE OF LOW‐FREQUENCY VIBRATIONAL ENERGY
Authors: HAMANN DONALD D. , CARROLL DANIEL E.
Published: August 2010

SUMMARY –A method is described for sorting Muscadine grapes (Vitis rotundifolia) for ripeness by use of low‐frequency vibrational energy. The fruits of five cultivars of Muscadines were sorted into groups of increasing ripeness as the frequency of sinusoidal vibration (approximately constant energy) applied to a separatory trough was decreased from 200 to 100 cps (Hertz). The rms (root mean square) value of trough acceleration was held constant by holding the rms value of current driving the electromagnetic vibrator constant. Percent soluble solids, percent total acidity, the soluble solids to acid ratio and pH value of the juice were used as chemical parameters of ripening; these correlated highly with frequency of removal of the grapes from the trough. The coefficients of determination for these correlations varied from 0.871–0.999 with only three of the 20 (five cultivars X four chemical parameters) being below 0.9.
WARMED‐OVER FLAVOR IN COOKED MEATS
Authors: SATO KUNITO , HEGARTY GERALD R.
Published: August 2010

SUMMARY –Conditions leading to the development of warmed‐over flavor in uncured cooked meat were studied. Beef muscle which had been thoroughly extracted with water did not develop warmed‐over flavor indicating that the substance responsible for initiating the reaction was water soluble. A water extract from muscle tissue was fractionated by dialysis and column chromatography, and the various fractions were added back to water‐extracted tissue. The development of warmed‐over flavor in this system was followed by TBA analysis and odor evaluation. Heme compounds were found to have little effect on the development of warmed‐over flavor in this system. The reaction was apparently catalyzed by ferrous iron and ascorbate. It is considered that ascorbic acid functions by keeping at least a portion of the iron in the ferrous state. At higher levels ascorbic acid inhibited the reaction, possibly by upsetting a balance between ferrous and ferric iron.
COMPARISON OF MYOSINS PREPARED FROM RABBIT AND BOVINE MUSCLE IMMEDIATELY AFTER DEATH AND AFTER STORAGE AT 2°C
Authors: THOMAS J. , FREARSON N.
Published: August 2010

SUMMARY –Myosin was extracted from bovine and rabbit skeletal muscles from freshly slaughtered carcasses and after storage at 2°C for times up to 8 days. The amount of myosins extracted and ATPase activities were constant up to 2 days storage of both species. The at‐death and 2°C 24‐hr myosins of both species were homogeneous, similar in chemical composition, ATPase properties and molecular weights.
SOLUBLE INTRAMUSCULAR COLLAGEN CHARACTERISTICS FROM STRETCHED AND AGED MUSCLE
Authors: KRUGGEL WILLIAM G. , FIELD RAY A.
Published: August 2010

SUMMARY –Changes occurring during stretching and post‐mortem aging of intramuscular collagen from bovine muscle were studied. Sucrose density‐gradient ultracentrifugation analyses of denatured guanidine hydrochloride‐soluble intramuscular collagen (GSIC) indicated stretching and/or aging muscle changes the molecular structure of the collagen. The quantity of aldehyde cross‐links in native GSIC supported this finding. The yield of GSIC from stretched muscles was slightly greater than from normal muscles. A high correlation existed between quantity of each collagen chain component and muscle shear value. Stretched muscle had significantly longer sarcomeres than normal muscles, regardless of aging period. Sarcomere length and muscle tenderness were closely associated in unaged muscle.
ESTIMATION OF THE CENTRAL TEMPERATURE OF THERMALLY CONDUCTIVE FOOD IN CYLINDRICAL AND RECTANGULAR CANS DURING HEAT PROCESSING
Authors: LEONHARDT GUSTAVO FERREIRA
Published: August 2010

The author proposes a classification of cylindrical and rectangular cans in can‐shape‐groups in order to reduce the number of temperature response curves necessary to carry out an accurate estimation of the central temperature of thermally conductive foods.
ESTIMATION OF THE AVERAGE TEMPERATURE OF THERMALLY CONDUCTIVE FOOD IN CYLINDRICAL AND RECTANGULAR CANS DURING HEAT PROCESSING
Authors: LEONHARDT GUSTAVO FERREIRA
Published: August 2010

A classification of cylindrical and rectangular cans in can‐shape‐groups is proposed in order to reduce the number of temperature response curves necessary to carry out an accurate estimation of the average temperature of thermally conductive foods.
TEXTURE PROFILE ANALYSIS PARAMETERS OBTAINED BY AN INSTRON UNIVERSAL TESTING MACHINE
Authors: PELEG M.
Published: August 2010

A method for the interpretation of the force‐deformation curves obtained by the Instron Universal Testing Machine is suggested. The method provides a more specific physical meaning to the experimental parameters and treats separately the mechanical aspects of the recoverable and nonrecoverable deformations. The method also provides for the possibility of the introduction of new mechanical parameters and terms which might represent textural properties.
THE RELATIONSHIP OF CARDIAC SHEAR AND TRACE ELEMENT CONTENT TO BEEF MUSCLE TENDERNESS
Authors: VAVAK L. D. , SATTERLEE L. D. , ANDERSON P. C.
Published: August 2010

The purpose of this investigation was to determine whether mechanical shear values of the cardiac muscle could be useful in predicting skeletal muscle tenderness as measured by mechanical shear and sensory evaluation methods. The metal ion content of bovine skeletal muscle was also determined and evaluated for its ability to predict skeletal muscle tenderness. W‐B shear results indicate cardiac muscle tenderness is related to semimembranosis tenderness, but the magnitude of the correlation coefficient is not high enough for adequate prediction capabilities. However, the predictive capability of element content is very good for all three tenderness measures‐sensory panel, W‐B and rotary shear. These results indicate the good potential of this approach to tenderness prediction.
PROXIMATE ANALYSIS, FREE AMINO ACID, VITAMIN AND MINERAL CONTENT OF MICROWAVE COOKED MEAT
Authors: BALDWIN RUTH E. , KORSCHGEN BERNICE M. , RUSSELL MARY S. , MABESA LINDA
Published: August 2010

Beef, pork and lamb roasts were cooked by two 2450 MHz microwave ranges, one operated at 220V (1054W cooking power) and one at 11SV (492W cooking power) and by a conventional gas oven (163 ± 3°C). The only significant effect related to power level of microwave ranges was retention of thiamine, riboflavin and niacin which was less in meat cooked by the microwave 115 V than by the other two methods. There was a trend toward less retention of sodium, chloride, phosphorus and iron in meat cooked by microwaves than by the conventional method. Also, microwave cooking resulted in less formation of free amino acids than conventional cooking but total protein did not differ significantly.
ELECTRODIALYSIS OF RAW WHEY AND WHEY FRACTIONATED BY REVERSE OSMOSIS AND ULTRAFILTRATION
Authors: JOHNSON KEVIN T. , HILL CHARLES G.
Published: August 2010

Electrodialysis is a unit operation which removes ionic species from a solution through the use of an imposed voltage and ion‐selective membranes. The temperature, flow rate, and composition of the feed, and the applied voltage all influence the rate of ionic transport in electrodialysis systems. The effects of the aforementioned process parameters on the performance of an electrodialysis system were investigated using cottage cheese whey as the process feed. Increasing the flow rate proved to be of little value in decreasing the membrane stack resistance for a given run, but it significantly retarded the rate at which the stack resistance increased in repeated runs. The effect of increasing the total solids concentration of the whey without altering the solute composition was to increase the potential rate of demineralization through an increase in conductivity. Prefractionation of the feed by ultrafiltration enhanced the value of the whey solids by increasing the protein concentration and decreasing the ash concentration. However, the electrodialytic process was less efficient in removing the remaining ash in this case than it was in demineralizing other feeds.
CONDITIONING PECANS WITH STEAM TO IMPROVE SHELLING EFFICIENCY AND STORAGE STABILITY
Authors: FORBUS W. R. , SENTER S. D.
Published: August 2010

Inshell pecans (Curya illinoensis, cvs. Stuart and Schley) were conditioned for cracking and shelling by a 3‐min atmospheric‐steam process and by two processes used commercially. Conditioned and untreated pecans were evaluated for shelling efficiency and for storage stability of the meats. Shelling efficiency was based on percent halves obtained; and storage stability, on changes in peroxide and free fatty acid values, sensory evaluations, and Hunter a/b values during accelerated storage of the halves at 21°C‐65% RH. Steam‐treated pecans yielded 12‐17 percentage points more halves than pecans conditioned by the other processes, and 19 percentage points more halves than the untreated nuts. Halves from steam‐treated nuts were less susceptible to oxidative and hydrolytic deterioration during storage.
OAT PROTEIN CONCENTRATES FOR BEVERAGE FORTIFICATION
Authors: CLUSKEY J. E. , WU Y. V. , INGLETT G. E. , WALL J. S.
Published: August 2010

Up to 4% oat protein concentrates can fortify either neutral or acidic beverages. The concentrate was produced in good yield from both defatted and non‐defatted oat groats by alkaline extraction. If desired, the gum and water‐soluble protein fractions can be removed by a preliminary water extraction yielding a concentrate with a higher percentage of protein. Nitrogen solubility of protein concentrate from defatted groats in dilute phosphoric acid was considerably higher than one from nondefatted groats. Fortified acidic beverages (pH 3) prepared with oat concentrate from laboratory ground groats were slightly astringent in taste. However, astringency was eliminated if the concentrate was produced from commercial oat flour (heat treated during production). Milklike and breakfast‐type beverages fortified with oat protein concentrate would be nutritious, palatable and easily prepared and flavored.
LOSSES IN AVAILABLE LYSINE DURING THERMAL PROCESSING OF SOY PROTEIN MODEL SYSTEMS
Authors: JOKINEN J. E. , RElNECCIUS G. A. , THOMPSON D. R.
Published: August 2010

This study was conducted in order to develop a mathematical model for predicting lysine losses during processing of soy products. Model systems used in this study consisted of micro crystalline cellulose, glucose, sucrose, potato starch and soy protein. System composition, water activity, pH and time and temperature of heating were varied and available lysine was monitored by the fluoro‐2,4‐dinitro benzene method of Carpenter. In the first set of experiments, statistical analysis of the data obtained resulted in an equation which shows the effects of the variables used on available lysine retention: Fraction available lysine remaining = 0.58 + 0.047 pH ‐ 0.093 glucose ‐ 0.059 temperature —0.0068 time + 0.031 (water activity)2+ 0.025 aw sucrose + 0.033 sucrose starch. These data were collected at heating times well in excess of that required to destroy all reducing sugars present. Heating times were reduced in the second experiments such that kinetic data could be obtained. The average Ea was 28,500 calories/mole°K and the average reference reaction rate at 100°C (K100) was 0.036 mg lysine/min.
FLAME STERILIZATION OF SOME TOMATO PRODUCTS AND FRUITS IN 603 × 700 CANS
Authors: LEONARD SHERMAN , MARSH G. L , YORK G. K. , MERSON R. L , HEIL J. R. , WOLCOTT T. , ANSAR A.
Published: August 2010

Processing of fruits and vegetables in 603 × 700 cans for institutional use is a common commercial practice. The present time‐temperature treatments for assuring commercial sterility are often excessive and unavoidably detrimental to product quality. Using the count reduction system of process lethality evaluation, canned whole peeled tomatoes packed in juice and fruits packed in syrup were experimentally flame sterilized as rapidly in 603 × 700 cans as in 303 × 406 cans.