Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks

Mito‐nuclear phylogenetic discordance in Bivalvia is well known. In particular, the monophyly of Amarsipobranchia (Heterodonta + Pteriomorphia), retrieved from mitochondrial markers, contrasts with the monophyly of Heteroconchia (Heterodonta + Palaeoheterodonta), retrieved from nuclear markers. However, since oxidative phosphorylation nuclear markers support the Amarsipobranchia hypothesis instead of the Heteroconchia one, interacting subunits of the mitochondrial complexes ought to share the same phylogenetic signal notwithstanding the genomic source, which is different from the signal obtained from other nuclear markers. This may be a clue of coevolution between nuclear and mitochondrial genes. In this work we inferred the phylogenetic signal from mitochondrial and nuclear oxidative phosphorylation markers exploiting different phylogenetic approaches and added two more datasets for comparison: genes of the glycolytic pathway and genes related to the biogenesis of regulative small noncoding RNAs. All trees inferred from mitochondrial and nuclear subunits of the mitochondrial complexes support the monophyly of Amarsipobranchia, regardless of the phylogenetic pipeline. However, not every single marker agrees with this topology: this is clearly visible in nuclear subunits that do not directly interact with the mitochondrial counterparts. Overall, our data support the hypothesis of a coevolution between nuclear and mitochondrial genes for the oxidative phosphorylation. Moreover, we suggest a relationship between mitochondrial topology and different nucleotide composition between clades, which could be associated to the highly variable gene arrangement in Bivalvia

Mitochondrial genomic landscape: A portrait of the mitochondrial genome 40 years after the first complete sequence

open3noNotwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.openFormaggioni A.; Luchetti A.; Plazzi F.Formaggioni A.; Luchetti A.; Plazzi F

Physical Vulnerability Assessment Based on Fluid and Classical Mechanics to Support Cost-Benefit Analysis of Flood Risk Mitigation Strategies

The impacts of flood events that occurred in autumn 2011 in the Italian regions of Liguria and Tuscany revived the engagement of the public decision-maker to enhance the synergy of flood control and land use planning. In this context, the design of efficient flood risk mitigation strategies and their subsequent implementation critically relies on a careful vulnerability analysis of the fixed and mobile elements exposed to flood hazard. In this paper we develop computation schemes enabling dynamic vulnerability and risk analyses for a broad typological variety of elements at risk. To show their applicability, a series of prime examples are discussed in detail, e.g. a bridge deck impacted by the flood and a car, first displaced and subsequently exposed to collision with fixed objects. We hold the view that it is essential that the derivation of the computational schemes to assess the vulnerability of endangered objects should be based on classical and fluid mechanics. In such a way, we aim to complement from a methodological perspective the existing, mainly empirical, vulnerability and risk assessment approaches and to support the design of effective flood risk mitigation strategies by defusing the main criticalities within the systems prone to flood risk

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

Milk acidity, curd firming time, curd firmness and protein and fat losses in the Parmigiano- Reggiano cheesemaking

The cheese yield depends on the milk casein content and on the fat to casein ratio. The efficiency of the milk transformation depends on curd particles ("curd fines") that remain in the cooked whey and on the losses of fat and casein as it is

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 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