Flavour formation by lactic acid bacteria and biochemical flavour profiling of cheese products

Flavour development in dairy fermentations, most notably cheeses, results from a series of (bio)chemical processes in which the starter cultures provide the enzymes. Particularly the enzymatic degradation of proteins (caseins) leads to the formation of key-flavour components, which contribute to the sensory perception of dairy products. More specifically, caseins are degraded into peptides and amino acids and the latter are major precursors for volatile aroma compounds. In particular, the conversion of methionine, the aromatic and the branched-chain amino acids are crucial. A lot of research has focused on the degradation of caseins into peptides and free amino acids, and more recently, enzymes involved in the conversion of amino acids were identified. Most data are generated on Lactococcus lactis, which is the predominant organism in starter cultures used for cheese-making, but also Lactobacillus, Streptococcus, Propionibacterium and species used for surface ripening of cheeses are characterised in their flavour-forming capacity. In this paper, various enzymes and pathways involved in flavour formation will be highlighted and the impact of these findings for the development of industrial starter cultures will be discussed.     

Identification, cloning, and characterization of a Lactococcus lactis branched-chain alpha-keto acid decarboxylase involved in flavor formation

The biochemical pathway for formation of branched-chain aldehydes, which are important flavor compounds derived from proteins in fermented dairy products, consists of a protease, peptidases, a transaminase, and a branched-chain alpha-keto acid decarboxylase (KdcA). The activity of the latter enzyme has been found only in a limited number of Lactococcus lactis strains. By using a random mutagenesis approach, the gene encoding KdcA in L. lactis B1157 was identified. The gene for this enzyme is highly homologous to the gene annotated ipd, which encodes a putative indole pyruvate decarboxylase, in L. lactis IL1403. Strain IL1403 does not produce KdcA, which could be explained by a 270-nucleotide deletion at the 3' terminus of the ipd gene encoding a truncated nonfunctional decarboxylase. The kdcA gene was overexpressed in L. lactis for further characterization of the decarboxylase enzyme. Of all of the potential substrates tested, the highest activity was observed with branched-chain alpha-keto acids. Moreover, the enzyme activity was hardly affected by high salinity, and optimal activity was found at pH 6.3, indicating that the enzyme might be active under cheese ripening conditions.     

Synthesis and purification of fluorinated benzimidazole and benzene nucleoside-5'-triphosphates

The expression "universal base" is very often used to express hybridization properties and recognition patterns of nucleosides. Their behaviour in biological applications, however, is of great interest regarding, e.g.,' their incorporation by polymerases. The 4,6-difluorobenzimidazole and the 2,4-difluorobenzene nucleoside analogues have proven to be universal bases that do not discriminate between the four natural nucleobases in RNA duplexes. Therefore, we synthesized the corresponding triphosphates to evaluate their behavior in polymerase catalyzed reactions and to investigate their ability to serve as substrates for the T7 RNA polymerase.     

A model to estimate risk of infection with human herpesvirus 8 associated with transfusion from cross-sectional data

In cross-sectional studies of infectious diseases, the data typically consist of: age at the time of study, status (presence or absence) of infection, and a chronology of events possibly associated with the disease. Motivated by a study of how human herpesvirus 8 (HHV-8) is transmitted among children with sickle cell anemia in Uganda, we have developed a flexible parametric approach for combining current-status data with a history of blood transfusions. We model heterogeneity in transfusion-associated risk by a child-specific random effect. We present an extension of the model to accommodate the fact that there is no gold standard for HHV-8 infection and infection status was assessed by a serological assay. The parameters are estimated via maximum likelihood. Finally, we present results from applying various parameterizations of the model to the Ugandan study.     

Intracellular distribution of oxidized proteins and proteasome in HT22 cells during oxidative stress

The production of free radicals and the resulting oxidative damage of cellular structures are always connected with the formation of oxidized proteins. The 20S proteasome is responsible for recognition and degradation of oxidatively damaged proteins. No detailed studies on the intracellular distribution of oxidized proteins during oxidative stress and on the distribution of the proteasome have been performed until now. Therefore, we used immunocytochemical methods to measure protein carbonyls, a form of protein oxidation products, and proteasome distribution within cells. Both immunocytochemical methods of measurement are semiquantitative and the load of oxidized proteins is increased after various oxidative stresses explored, with the highest increase in the perinuclear region of the cell. Distribution of the proteasome and the total protein content revealed the highest concentration of both in the nucleus. No redistribution of the proteasome during oxidative stress occurs. The normalized ratio of protein carbonyls to protein content was formed, indicating the highest concentration of oxidized proteins in the cytosolic region near the cell membrane. By forming the protein oxidation-to-proteasome ratio it was concluded that the highest load of oxidized proteins to the proteasome takes place in the cytosol, independent of the oxidant explored.     

Combo: a whole genome comparative browser

SUMMARY: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization perspectives. The perpendicular (dot plot) view provides a dot plot of genome alignments synchronized with a display of genome annotations along each axis. The parallel view displays two genome annotations horizontally, synchronized through a panel displaying local alignments as trapezoids. Users can zoom to any resolution, from whole chromosomes to individual bases. They can select, highlight and view detailed information from specific alignments and annotations. Combo is an organism agnostic and can import data from a variety of file formats. AVAILABILITY: Combo is integrated as part of the Argo Genome Browser which also provides single-genome browsing and editing capabilities. Argo is written in Java, runs on multiple platforms and is freely available for download at http://www.broad.mit.edu/annotation/argo/.     

The Vertical Pattern of Rooting and Nutrient Uptake at Different Altitudes of a South Ecuadorian Montane Forest

The vertical pattern of root length densities (RLD) of fine roots (<2 mm in diameter) and nitrogen (N) uptake potential were determined at different altitudes (1,900, 2,400, and 3,000 m a.s.l.) of a tropical montane forest in order to improve our knowledge about the depth distribution of nutrient uptake in this ecosystem. At higher altitudes, precipitation rate and frequency of fog were higher than at lower altitudes while mean annual air temperature decreased with increasing altitude. Soils were always very acid with significantly lower pH at a depth of 0.0–0.3 m in mineral soil at 3,000 m (2.8–2.9) than at 1,900 and 2,400 m (3.1–3.5). The vertical distribution of RLD was very similar both during the dry and the rainy season. During the dry season the percentage of root length in the organic layer increased from 51% at 1,900 m to 61% at 2,400 m and 76% at 3,000 m. At 3,000 m, RLD was markedly higher in the upper 0.05 m than in the remaining organic layer, whereas at 1,900 m and 2,400 m RLD were similar in all depths of the organic layer. In mineral soil, RLD decreased to a greater degree with increasing soil depth at the upper two study sites than at 1,900 m. The relative N uptake potential from different soil layers (RNUP) was determined by ¹⁵N enrichment of leaves after application of ¹⁵N enriched ammonium sulphate at various soil depths. RNUP closely followed fine root distribution confirming the shallower pattern of nutrient uptake at higher altitudes. RNUP was very similar for trees, shrubs and herbs, but shallower for saplings which obtained N only from the organic layer at both altitudes. Liming and fertilizing (N, P, K, Mg) of small patches in mineral soil had no significant impact on fine root growth. We conclude that the more superficial nutrient uptake ability at higher altitudes may be partly related to increased nutrient input from canopy by leaching. However, the specific constraints for root growth in the mineral soil of tropical montane forests warrant further investigations.