Embedding machine-readable proteins interactions data in scientific articles for easy access and retrieval

Extraction of protein-protein interactions data from scientific literature remains a hard, time- and resource-consuming task. This task would be greatly simplified by embedding in the source, i.e. research articles, a standardized, synthetic, machine-readable codification for protein-protein interactions data description, to make the identification and the retrieval of such very valuable information easier, faster, and more reliable than now.
We shortly discuss how this information can be easily encoded and embedded in research papers with the collaboration of authors and scientific publishers, and propose an online demonstrative tool that shows how to help and allow authors for the easy and fast conversion of such valuable biological data into an embeddable, accessible, computer-readable codification

Influence of milk somatic cell content on Parmigiano-Reggiano cheese yield

The aim of this study was to determine the influence of the somatic cell content (SCC) of milk on Parmigiano-Reggiano cheese yield, produced in commercial cheese factories under field conditions. The study was carried out following the production of 56 batches of Parmigiano-Reggiano in 13 commercial cheese factories by processing milk collected from Italian Friesian cattle herds. The vat-milk (V-milk) used for making each cheese batch was obtained by mixing evening milk (partially skimmed following spontaneous separation of fat overnight, natural creaming) and morning milk. The batches of cheese produced were divided into 5 classes according to the SCC value of the evening milk determined prior to natural creaming (class 1, from 0 to 200 000; 2, 201 000-300 000; 3, 301 000-400 000; 4, 401 000-500 000; 5, over 501 000 cells/ml). The cheese yield was calculated as the amount of 24-h cheese, expressed in kilograms, obtained from 100 kg of V-milk (24 h ACY). The values of fat, crude protein, true protein, casein and 24 h ACY of V-milk were negatively correlated with the somatic cell score (SCS) of the evening milk. Conversely, a positive correlation was observed between chloride and SCS. Fat, protein fractions (crude protein, casein and whey proteins), P and titratable acidity of V-milk were positively correlated with its 24 h ACY, while chloride, pH and SCS showed a negative correlation. A significant drop in 24 h ACY was observed in classes 3, 4 and 5, therefore when the SCC of the evening milk exceeded 300 000 cells/ml. Finally a lower recovery of milk fat in cheese was observed as SCC of evening milk increase

Effects of Milk Storage Temperature at the Farm on the Characteristics of Parmigiano Reggiano Cheese: Chemical Composition and Proteolysis

Parmigiano Reggiano is a Protected Designation of Origin (PDO) cheese whose official production protocol provides that milk cannot be stored at less than 18 °C at the farm. The possibility of refrigerating milk at the farm is highly debated, since it should allow for the limiting of bacterial growth, thus improving the quality of the cheese. The present research aimed to study the influence of storing the milk at 9 °C on the chemical composition and proteolysis during the ripening of Parmigiano Reggiano cheese. The experimentation considered six cheese-making trials, in which both evening and morning milks were subdivided into two parts that were maintained at 9 and 20 °C. After Parmigiano Reggiano cheese-making, one of the twin wheels obtained was analyzed after 21 months of ripening. From each cheese, two different samples were taken, one from the inner zone, and the other from the outer zone. The results of the chemical analyses evidenced that milk storage at 9 °C significantly (p ≤ 0.05) influenced fat, crude protein, soluble nitrogen and peptone nitrogen contents. Nevertheless, the differences observed with respect to the cheese obtained with milk stored under standard condition were very small and should be considered within the “normal variations” of Parmigiano Reggiano chemical characteristics

Effects of somatic cell count on the gross composition, protein fractions and mineral content of individual ewe’s milk

The aim of the research was to evaluate the effect of two somatic cell content (SCC) levels (<265,000 and >265,000 cells/ml) on ewe milk composition, protein fractions and mineral content. Samples were collected during two years, from three different ewe herds. Each herd was surveyed four times per year, one per season. For each survey more than 10 individual milk samples were collected during morning milking and analysed for SCC. On the basis of the results, two individual milk samples were selected: one from a sheep with low milk SCC (up to 265.000 cells/mL; LCC) and one from a sheep with high milk SCC (over 265,000 and less than 1,000,000 cells/mL; HCC). In one herd, it was not possible to collect the milk samples in summer. So, a total of 44 ewe milk samples (22 comparative pairs) were collected. On each milk sample, crude protein, crude whey protein, casein, casein number, non protein nitrogen x 6.38, true protein, true whey protein, fat, lactose, dry matter, ash, phosphorus, calcium, magnesium and chloride were determined. Average SCC in LCC was 170,000 and 466,000 cells/ml in HCC milk. HCC milk had lower lactose (4.05 vs. 4.60 g/100 g), casein (3.91 vs. 4.28 g/100 g), phosphorus (131.31 vs. 138.81 mg/100 g), calcium (157.28 vs. 170.48 mg/100 g) and magnesium (14.59 vs. 15.30 mg/100 g) contents than LCC milk. Additionally, HCC milk had lower casein number (76.53 vs. 79.03%) and higher contents of true whey protein (1.00 vs. 0.92 g/100 g), ash (0.90 vs. 0.87 g/100 g) and chloride (103.57 vs. 93.17 mg/100 g) than LCC milk. Somatic cell content significantly affected ewe milk quality. As a result of the higher lactose, casein, phosphorus, calcium and magnesium contents, LCC milk was more suitable for cheese making than HCC milk.Key words: Ewe milk, milk quality, chemical composition, somatic cell content

New insights into the quality characteristics of milk from Modenese breed compared with Italian Friesian

This study examined the milk quality of the autochthonous cattle breed Modenese (MO) in comparison with Italian Friesian (IF), at peak and mid lactation, with the aim to support the interest in sustainability of the local cattle breeds in Europe. Forty-eight individual milk samples were collected from 11 MO and 14 IF pluriparous cows, housed in a free stall barn under similar conditions of feeding and management, at 8 and 21 weeks post-calving; daily milk yield (MY) and body condition score (BCS) were individually recorded. Breed differences were observed, being MY lower in MO cows, but BCS, titratable acidity, freezing point, casein (MC), total calcium (Ca), total phosphorus (P) and colloidal P contents were higher compared to IF cows. Time affected BCS, MY, milk protein (MP), MC, urea, casein P and the micellar content of colloidal Ca and colloidal inorganic P. A factorial analysis was performed and four common factors were obtained with a cumulative explained variance of 77.7% of the total original. MO milk showed a nutritionally interesting mineral profile and processing properties suitable for the production of typical cheese that could be interesting for improving the interest in the conservation of animal genetic resources

Effects of the Cooling Temperature at the Farm on Milk Maturation and Cheesemaking Process in the Manufacture of Parmigiano Reggiano PDO Cheese

Parmigiano Reggiano is a hard PDO cheese made from bovine raw milk, whose microbiological characteristics have important repercussions on cheese quality. According to the EU official production protocol, milk temperature at the farm must not drop below 18 °C. The present research aimed to study the effect of cooling milk at the farm at 9 °C on the characteristics of milk and on the cheesemaking process and losses during manufacture. Six cheesemaking trials were performed in two different dairies. In each of them, two cheesemakings were made in parallel: one with milk kept at 9 °C (TM9) and the other with milk kept at 20 °C (TM20). TM9 milk, in comparison with TM20, showed after the creaming process a significant reduction not only of total bacterial count but also of psychrotrophic and lipolytic bacteria. At the same time, TM9 milk showed a higher creaming capacity and, consequently, a lower fat content than TM20. TM9 vat milk had worst coagulation properties than TM20, which caused slightly higher loss of fat and curd fines into the whey. Nevertheless, these changes were too small to influence the efficiency of the cheesemaking process; conversely, maintaining milk at the farm at 9 °C led to a reduction of the number of spoilage bacteria

Characterisation of Formaggella della Valle di Scalve Cheese Produced From Cows Reared in Valley Floor Stall or in Mountain Pasture: Fatty Acids Profile and Sensory Properties

An important problem in mountain areas is the abandonment of pasture. This trend can be combated by the valorisation of typical dairy products, such as "Formaggella della Valle di Scalve", a semi-cooked traditional cheese made from whole milk in a mountain area in Italy. The aim of the present research was to compare the fatty acid (FA) profile and the sensory properties of this cheese as manufactured under different conditions: i) from the milk of cows grazing on mountain or valley pasture or fed indoors; ii) from the milk of cows fed hay or fed silage. In the first case, five cheesemaking trials were conducted during two years for each of the following situations: mountain pasture (A); pasture at the bottom of the valley (P) (about 1000m asl); stall (S). In the second case, three cheesemaking trials were conducted for each of the following situations: cows fed silage (I); cows fed hay (F). S cheese was richer in medium-chain FAs, while long-chain FAs were higher in P and A cheeses. On the other hand, long chain fatty acids (LCFA) were more abundant in P and A cheeses than in S. In general, MUFA, PUFA and, consequently, total unsaturated FA (UFA), were significantly higher in the P and A cheeses than S (UFA: 36.55 and 38.34, respectively, vs 31.13; p < 0.001), while SFA showed higher values in S (68.85 vs 63.41 and 61.68 in P and A, respectively; p < 0.001). Conjugated linoleic acid isomers (CLA) were more represented in the P and A samples (1.86 in P and 1.52 in A, vs 0.80 in S; p < 0.001); Omega 3 fatty acids, and in particular α-linolenic acid, were more abundant in P than in S cheese. In winter, the I sample (silage) presented higher percentages of myristic (C14), myristoleic (C14:1) and omega 6 acids, whereas F cheese (hay) contained higher concentrations of CLA. The triangular test of sensory analysis showed that, in general, F cheeses were judged as "sweeter" than I, with aromatic profiles characterized by higher content of 2- butanol and ethyl capronate

Cheese as Functional Food: The Example of Parmigiano Reggiano and Grana Padano

Talijanski tvrdi kuhani sirevi, kao što su Parmigiano Reggiano i Grana Padano, imaju veliku nutritivnu vrijednost. Prema definiciji Europske Unije smatraju se funkcionalnom hranom, jer sadržavaju spojeve koji imaju specifična biološka svojstva. U ovom su preglednom radu ukratko opisani ti spojevi te njihov pozitivan učinak na zdravlje, i to u nekoliko poglavlja: proteini i peptidi, masti i lipidi, ugljikohidrati i prebiotici, probiotičke bakterije, vitamini, mineralne tvari, te sastojci mliječnih proizvoda s aktivnom ulogom u prevenciji bolesti. U uzorcima sira Parmigiano Reggiano pronađeno je nekoliko peptida s dokazanim biološkim svojstvima, npr. fosfopeptidi, koji imaju sposobnost vezivanja mineralnih tvari i funkciju prijenosnika funkcionalnih skupina, peptidi s imunomodulacijskim učinkom, te peptidi s antihipertenzijskim svojstvima i sposobnošću inibicije enzima koji konvertira angiotenzin. Među lipidima su opisane uloge konjugirane linolne kiseline i drugih masnih kiselina u siru. Također su opisani oligosaharidi s prebiotičkim svojstvima i probiotičke bakterije. Na kraju je posebno naglašena iskoristivost kalcija iz sireva, što je bitno za zdravlje kostiju.Italian hard cooked types of cheese, like Parmigiano Reggiano and Grana Padano, are characterised by positive nutritional qualities. In fact, they contain substances that have particular biological activities, and therefore they can be fully considered, according to the definition given by the European Unit, as ‘functional’ foods. This short review concisely describes these components and the beneficial effects related to their activities. The description of the biologically active components has been organised in the following paragraphs: protein and peptides, fat and lipids, carbohydrates and prebiotics, probiotic bacteria, vitamins, mineral salts, and components of dairy products active in disease prevention. In particular, several known bioactive peptides were found in Parmigiano Reggiano cheese samples: for example, phosphopeptides, which are known for their mineral-binding capacity and vehiculation activity, peptides with immunomodulatory activity, and angiotensin-converting enzyme-inhibitory peptides with anti-hypertensive effects. Among lipids, the role of conjugated linoleic acid and other fatty acids present in these cheese types was taken into consideration. The presence of oligosaccharides with prebiotic properties and probiotic bacteria was also described. Finally, particular emphasis was given to highly available calcium and its impact on bone health