Quantitative reactivity profiling predicts functional cysteines in proteomes

Cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochemical functions. The absence of a consensus sequence that defines functional cysteines in proteins has hindered their discovery and characterization. Here we describe a proteomics method to profile quantitatively the intrinsic reactivity of cysteine residues en masse directly in native biological systems. Hyper-reactivity was a rare feature among cysteines and it was found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. Hyper-reactive cysteines were identified in several proteins of uncharacterized function, including a residue conserved across eukaryotic phylogeny that we show is required for yeast viability and is involved in iron-sulphur protein biogenesis. We also demonstrate that quantitative reactivity profiling can form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs.

Environmental impacts of cultured meat production

Cultured meat (i.e., meat produced in vitro using tissue engineering techniques) is being developed as a potentially healthier and more efficient alternative to conventional meat. Life cycle assessment (LCA) research method was used for assessing environmental impacts of large-scale cultured meat production. Cyanobacteria hydrolysate was assumed to be used as the nutrient and energy source for muscle cell growth. The results showed that production of 1000 kg cultured meat requires 26-33 GJ energy, 367-521 m(3) water, 190-230 m(2) land, and emits 1900-2240 kg CO(2)-eq GHG emissions. In comparison to conventionally produced European meat, cultured meat involves approximately 7-45% lower energy use (only poultry has lower energy use), 78-96% lower GHG emissions, 99% lower land use, and 82-96% lower water use depending on the product compared. Despite high uncertainty, it is concluded that the overall environmental impacts of cultured meat production are substantially lower than those of conventionally produced meat.

Effect of ammonia on the immune response of white shrimp Litopenaeus vannamei and its susceptibility to Vibrio alginolyticus

Growth of Vibrio alginolyticus was not affected by TSB medium containing ammonia-N concentration in the range of 0-20 mg l(-1). White shrimp Litopenaeus vannamei (7-12 g in the intermolt stage) were challenged with V. alginolyticus, which had been incubated for 24 h in the TSB medium containing different concentrations of ammonia-N (0, 1, 5. 10 and 20 mg l(-1)). There was no significant difference in cumulative mortality for shrimp incubated in the TSB medium containing 0, 1, 5, 10 and 20 mg l(-1)ammonia-N after 120 h of challenge. The shrimps were challenged with V. alginolyticus previously incubated in the TSB medium for 24 h, then placed in water containing concentrations of ammonia-N at 0.01 mg l(-1)(control), 1.10, 5.24, 11.10 and 21.60 mg l(-1). Mortality of shrimp in 5.24, 11.10 and 21.60 mg l(-1)was significantly higher than those in the control solution (0.01 mg l(-1)) after 48-168 h. Shrimps which had been exposed to control, 1.10, 5.24, 11.10 and 21.60 mg l(-1)ammonia-N for 7 days were examined for THC (total haemocyte count), granular cells, hyaline cells, phenoloxidase activity, release of superoxide anion, superoxide dismutase (SOD) activity, phagocytic activity and clearance efficiency to V. alginolyticus. No significant difference in THC, hyaline cells and granular cells were observed among shrimps at different ammonia-N concentrations. Phenoloxidase activity however, decreased when the shrimps were exposed to 5.24 mg l(-1)ammonia-N and greater after 7 days. The release of superoxide anion increased significantly, whereas SOD activity decreased significantly at 21.60 mg l(-1)ammonia-N. With shrimps exposed to 11.21 and 21.22 mg l(-1)ammonia-N for 7 days, phagocytic activity and clearance efficiency to V. alginolyticus significantly decreased. It is therefore suggested that ammonia in water caused a depression in the immune response and an increase in mortality of L. vannamei from the V. alginolyticus infection.

VITAMIN REQUIREMENTS OF SEVERAL CELLULOLYTIC RUMEN BACTERIA

Scott, H. W. (Ohio Agricultural Experiment Station, Wooster), and B. A. Dehority. Vitamin requirements of several cellulolytic rumen bacteria. J. Bacteriol. 89:1169-1175. 1965.-Four strains of cellulolytic bacteria recently isolated from in vitro rumen fermentations were used in this study. Nine water-soluble vitamins were tested in single-deletion and single-addition plus biotin experiments, each with and without charcoal-extracted casein hydrolysate. Bacteroides succinogenes A3C and B21a required only biotin under the above experimental conditions. Ruminococcus flavefaciens B34b showed an absolute requirement for biotin and was stimulated by p-aminobenzoic acid (PABA) in the single-deletion experiments. In the single-addition plus biotin experiments, PABA and, to a lesser extent, vitamin B(12) appeared to be required for maximal growth. The presence or absence of casein hydrolysate did not affect the vitamin requirements for the aforementioned three strains. In the single-deletion experiments, R. flavefaciens Cla showed an absolute requirement for biotin and, when casein hydrolysate was omitted, for B(12). When casein hydrolysate was present, no requirement for B(12) could be observed. In the single-addition experiments where the basal medium contained biotin and casein hydrolysate or B(12), PABA was required for maximal growth; however, the single deletion of PABA caused only slight retardation of growth. Investigation of the B(12) or casein hydrolysate requirement of Cla revealed that a mixture of purified amino acids simulating casein hydrolysate satisfied this requirement. Subsequent work indicated that this requirement could be satisfied by the amino acid methionine.

Development of a repair-enrichment broth for resuscitation of heat-injured Listeria monocytogenes and Listeria innocua

The ability of the divalent cations magnesium, iron, calcium and manganese; yeast extract; pyruvate; catalase; and the carbohydrates glucose, lactose, sucrose, esculin, fructose, galactose, maltose, and mannose to facilitate repair of heat-injured Listeria monocytogenes and Listeria innocua was evaluated. Listeria populations were injured by heating at 56 degrees C for 50 min. To determine the effects on repair, Trypticase soy broth (TSB) was supplemented with each medium component to be evaluated. Repair occurred to various degrees within 5 h in TSB supplemented with glucose, lactose, sucrose, yeast extract, pyruvate, or catalase. Chelex-exchanged TSB was supplemented with divalent cations; magnesium and iron cations were found to have a role in repair. Listeria repair broth (LRB) was formulated by utilizing the components that had the greatest impact upon repair. When incubated in LRB, heat-injured Listeria cells completed repair in 5 h. After the repair, acriflavin, nalidixic acid, and cycloheximide were added to LRB to yield final concentrations identical to those of the selective enrichment broths used in the procedures of the Food and Drug Administration and the U.S. Department of Agriculture. The efficacy of LRB in promoting repair and enrichment of heat-injured Listeria cells was compared with that of existing selective enrichment broths. Repair was not observed in the Food and Drug Administration enrichment broth, Listeria enrichment broth, or University of Vermont enrichment broth. The final Listeria populations after 24 h of incubation in selective enrichment media were 1.7 x 10(8) to 9.1 x 10(8) CFU/ml; populations in LRB consistently averaged 2.5 x 10(11) to 8.2 x 10(11) CFU/ml.

Identification of 9-hydroxyoctadecadienoic acid and other oxidized free fatty acids as ligands of the G protein-coupled receptor G2A

G2A is a G protein-coupled receptor that is predominantly expressed in lymphoid tissues and macrophages. G2A can be induced by diverse stimuli to cause cell cycle arrest in the G(2)/M phase in pro-B and T cells. G2A is also expressed in macrophages within atherosclerotic lesions, suggesting G2A involvement in atherosclerosis. Recently, G2A was discovered to possess proton-sensing ability. In this paper, we report another function of G2A, that is, as a receptor for 9-hydroxyoctadecadienoic acid (9-HODE) and other oxidized free fatty acids. G2A, expressed in CHO-K1 or HEK293 cells, showed 9-HODE-induced intracellular calcium mobilization, inositol phosphate accumulation, inhibition of cAMP accumulation, [(35)S]guanosine 5'-3-O-(thio)triphosphate binding, and MAP kinase activation. Furthermore, G2A was activated by various oxidized derivatives of linoleic and arachidonic acids, but it was weakly activated by cholesteryl-9-HODE. Oxidized phosphatidylcholine (1-palmitoyl-2-linoleoyl) when hydrolyzed with phospholipase A(2) also evoked intracellular calcium mobilization in G2A-expressing cells. These results indicate that G2A is activated by oxidized free fatty acids produced by oxidation and subsequent hydrolysis of phosphatidylcholine or cholesteryl linoleate. Thus, G2A might have a biological role in diverse pathological conditions including atherosclerosis.

Potential of chicken by-products as sources of useful biological resources

By-products from different animal sources are currently being utilised for beneficial purposes. Chicken processing plants all over the world generate large amount of solid by-products in form of heads, legs, bones, viscera and feather. These wastes are often processed into livestock feed, fertilizers and pet foods or totally discarded. Inappropriate disposal of these wastes causes environmental pollution, diseases and loss of useful biological resources like protein, enzymes and lipids. Utilisation methods that make use of these biological components for producing value added products rather than the direct use of the actual waste material might be another viable option for dealing with these wastes. This line of thought has consequently led to researches on these wastes as sources of protein hydrolysates, enzymes and polyunsaturated fatty acids. Due to the multi-applications of protein hydrolysates in various branches of science and industry, and the large body of literature reporting the conversion of animal wastes to hydrolysates, a large section of this review was devoted to this subject. Thus, this review reports the known functional and bioactive properties of hydrolysates derived from chicken by-products as well their utilisation as source of peptone in microbiological media. Methods of producing these hydrolysates including their microbiological safety are discussed. Based on the few references available in the literature, the potential of some chicken by-product as sources of proteases and polyunsaturated fatty acids are pointed out along with some other future applications.

The acquisition of tolerance toward cow's milk through probiotic supplementation: a randomized, controlled trial

BACKGROUND

Cow's milk allergy (CMA) is the most frequently diagnosed food allergy in infancy. In general, patients have a good prognosis because the majority acquire tolerance within the first years. Interventions have been proposed to accelerate tolerance and reduce morbidity. Probiotic supplementation could be effective through modulation of the immune system.

OBJECTIVE

We sought to determine whether supplementation with a combination of probiotics (Lactobacillus casei CRL431 and Bifidobacterium lactis Bb-12) accelerates tolerance to cow's milk (CM) in infants with CMA.

METHODS

We performed a double-blind, randomized, placebo-controlled trial in 119 infants with CMA. Infants received CRL431 and Bb-12 supplemented to their standard treatment of extensively hydrolyzed formula for 12 months. Primary outcome was clinical tolerance to CM at 6 and 12 months of treatment. Furthermore, we analyzed T- and B-lymphocyte subsets (CD3(+), CD3(+)CD4(+), CD3(+)CD8(+), and CD20(+)) in peripheral blood at randomization and at 12 months with flow cytometry and examined the presence of viable probiotic strains in fecal samples.

RESULTS

The cumulative percentage of tolerance to CM at 6 and 12 months was similar in both groups: 56 (77%) in the probiotics group versus 54 (81%) in the placebo group. Infants in the placebo group had higher percentages of CD3(+) and CD3(+)CD4(+) lymphocytes compared with those seen in probiotic-treated infants. Probiotic intake was confirmed because probiotics were isolated from feces more often in treated infants than in the placebo group.

CONCLUSION

Supplementation of CRL431 and Bb-12 to extensively hydrolyzed formula does not accelerate CM tolerance in infants with CMA.

Evaluation of different detection methods of biofilm formation in Staphylococcus aureus

The icaADBC gene locus of Staphylococcus aureus and its polysaccharide intercellular adhesin (PIA/PNSG) were recently identified, but biofilm formation has rarely been detected in vitro. In this study we evaluated a tissue culture plate (TCP) assay and a tube test, as well as Congo red agar, using the two basic media trypticase soy broth (TSB) and brain heart infusion (BHI) broth with different sugar supplements for detection of biofilm formation in 128 ica-positive S. aureus isolates. Of the S. aureus strains, 57.1% displayed a biofilm-positive phenotype under optimized conditions in the TCP test. The tube test correlated well with the TCP test for strongly biofilm-producing strains, whereas weak producers were not safely discriminated from biofilm-negative strains. Screening on Congo red agar displayed a strong correlation with the TCP and the tube test for only 3.8%, and is therefore not recommended for investigation of biofilm formation in S. aureus.

Flavor programming during infancy

OBJECTIVE

Although individuals differ substantially in their flavor and food preferences, the source of such differences remains a mystery. The present experimental study was motivated by clinical observations that early experience with formulas establishes subsequent preferences.

DESIGN

Infants whose parents had chosen to formula-feed them were randomized into 1 of 4 groups by the second week of life. One group was assigned to be fed a milk-based formula (Enfamil), whereas another was assigned to be fed (Nutramigen), a particularly unpleasant-tasting protein hydrolysate formula. The remaining groups were assigned to be fed Nutramigen for 3 months and Enfamil for 4 months; the timing of exposure differed between the groups. After 7 months of exposure, infants were videotaped on 3 separate days while feeding, in counterbalanced order, Enfamil, Nutramigen, and Alimentum, a novel hydrolysate formula.

RESULTS

For each of the 4 interrelated measures of behavior (intake, duration of formula feeding, facial expressions, and mothers' judgments of infant acceptance), previous exposure to Nutramigen significantly enhanced subsequent acceptance of both Nutramigen and Alimentum. Seven months of exposure led to greater acceptance than did 3 months.

CONCLUSIONS

The bases for clinical difficulties in introducing hydrolysate formulas during older infancy are clarified in this study. More broadly, variation in formula flavor provided a useful model for demonstrating experimentally the effects of long-term exposure differences on later acceptance. Such early variation, under more species-typical circumstances (eg, via exposure to different flavors in amniotic fluid and mothers' milk), may underlie individual differences in food acceptability throughout the life span.

Determination of the sequences of protein-derived peptides and peptide mixtures by mass spectrometry

Micro-quantities of protein-derived peptides have been converted into N-acetylated permethyl derivatives, and their sequences determined by low-resolution mass spectrometry without prior knowledge of their amino acid compositions or lengths. A new strategy is suggested for the mass spectrometric sequencing of oligopeptides or proteins, involving gel filtration of protein hydrolysates and subsequent sequence analysis of peptide mixtures. Finally, results are given that demonstrate for the first time the use of mass spectrometry for the analysis of a protein-derived peptide mixture, again without prior knowledge of the protein or components within the mixture.

Poly-3-hydroxybutyrate (P3HB) production by bacteria from xylose, glucose and sugarcane bagasse hydrolysate

Fifty-five bacterial strains isolated from soil were screened for efficient poly-3-hydroxybutyrate (P3HB) biosynthesis from xylose. Three strains were also evaluated for the utilization of bagasse hydrolysate after different detoxification steps. The results showed that activated charcoal treatment is pivotal to the production of a hydrolysate easy to assimilate. Burkholderia cepacia IPT 048 and B. sacchari IPT 101 were selected for bioreactor studies, in which higher polymer contents and yields from the carbon source were observed with bagasse hydrolysate, compared with the use of analytical grade carbon sources. Polymer contents and yields, respectively, reached 62% and 0.39 g g(-1) with strain IPT 101 and 53% and 0.29 g g(-1) with strain IPT 048. A higher polymer content and yield from the carbon source was observed under P limitation, compared with N limitation, for strain IPT 101. IPT 048 showed similar performances in the presence of either growth-limiting nutrient. In high-cell-density cultures using xylose plus glucose under P limitation, both strains reached about 60 g l(-1) dry biomass, containing 60% P3HB. Polymer productivity and yield from this carbon source reached 0.47 g l(-1) h(-1) and 0.22 g g(-1), respectively.

Effect of milk base and starter culture on acidification, texture, and probiotic cell counts in fermented milk processing

In the present work, the compared effect of milk base and starter culture on acidification, texture, growth, and stability of probiotic bacteria in fermented milk processing, was studied. Two strains of probiotic bacteria were used, Lactobacillus acidophilus LA5 and L. rhamnosus LR35, with two starter cultures. One starter culture consisted only of Streptococcus thermophilus ST7 (single starter culture); the other was a yogurt mixed culture with S. thermophilus ST7 and L. bulgaricus LB12 (mixed starter culture). For the milk base preparation, four commercial dairy ingredients were tested (two milk protein concentrates and two casein hydrolysates). The resulting fermented milks were compared to those obtained with control milk (without enrichment) and milk added with skim milk powder. The performance of the two probiotic strains were opposite. L. acidophilus LA5 grew well on milk but showed a poor stability during storage. L. rhamnosus LR35 grew weakly on milk but was remarkably stable during storage. With the strains tested in this study, the use of the single starter culture and the addition of casein hydrolysate gave the best probiotic cell counts. The fermentation time was of about 11 h, and the probiotic level after five weeks of storage was greater than 106 cfu/ml for L. acidophilus LA5 and 10(7) cfu/ml for L. rhamnosus LR35. However, an optimization of the level of casein hydrolysate added to milk base has to be done, in order to improve texture and flavor when using this dairy ingredient.

Colic and the effect of changing formulas: a double-blind, multiple-crossover study

This study investigated the effect of changing the formulas of colicky infants and addressed the methodologic flaws of earlier studies. Attention was paid to issues of designing a blind study, providing a washout period, and measuring and reproducing the effect. In this randomized, double-blind trial, three changes of formula were made: for each of four 4-day periods, colicky infants alternately received a casein hydrolysate formula (Nutramigen) and a formula containing cow milk. Mothers recorded crying in diaries and indicated which crying episodes they considered to have been caused by colic. Nine infants were started on Nutramigen and eight on the cow milk formula. With the first formula change there was significantly less crying and colic in infants when they were fed Nutramigen than when they were fed cow milk (p less than 0.01); with the second change there was less colic when infants were fed Nutramigen (p less than 0.05) but not significantly less crying. By the third change there were no significant differences between formulas. Further analyses demonstrated that there were more clinically meaningful positive responses (a change in crying by at least one third) to Nutramigen than to cow milk (p less than 0.05). However, only one subject had a clinically meaningful response in colic to all three formula changes. These results demonstrate that in some instances, colic improves with elimination of cow milk formula. However, the effect diminishes with time, and only infrequently is the effect reproducible.

Subfragments from the Fc fragment of human immunoglobulin G. Isolation and physicochemical charaterization

A fragment termed fragment Fc' and a related fragment termed fragment pFc' produced by the actions of papain and pepsin respectively on human immunoglobulin G have been isolated and characterized. Amino acid analyses and experiments utilizing cyanogen bromide to cleave the methionyl bonds of the Fc' and pFc' fragments make it possible to locate both fragments within the known chain structure of the immunoglobulin G molecule. The pFc' fragment is probably a non-covalently linked dimer situated at the C-terminal end of the molecule, containing about 232 amino acid residues and having a molecular weight of 26000. The Fc' fragment is a similar dimer of about 182 residues extending from near residue 14 to near residue 105 (numbered from the C-terminal end) of the gamma-chain and has a molecular weight of 21000.