Intake of high quantities of dietary proteins sourced from dairy, meat or plants can affect body weight and metabolic health in humans. To improve our understanding of how this may be achieved, we reviewed the data related to the availability of nutrients and metabolites in the faeces, circulation and urine. All protein sources (≥20% by energy) increased faecal levels of branched chain fatty acids and ammonia, and decreased the levels of butyrate. There were metabolites responding to dairy and meat proteins (branch chain amino acids) as well as dairy and plant proteins (p-cresol), which were increased in faecal matter. Specific to dairy protein intake, the faecal levels of acetate, indole and phenol were increased, whereas plant protein intake specifically increased the levels of kynurenine and tyramine. Meat protein intake increased the faecal levels of methionine, cysteine and alanine, and decreased the levels of propionate and acetate. The metabolite profile in the faecal matter following dairy protein intake mirrored availability in circulation or urine. These findings provide an understanding of the contrasting gut versus systemic effects of different dietary proteins, which we know to show different physiological effects. In this regard, we provide directions to determining the mechanisms for the effects of different dietary proteins.

Graph theory, a branch of mathematics that focuses on the study of graphs (networks of nodes and edges), provides a robust framework for analysing the structural and functional properties of biomolecules. By leveraging molecular dynamics (MD) simulations, atoms or groups of atoms can be represented as nodes, while their dynamic interactions are depicted as edges. This network-based approach facilitates the characterization of properties such as connectivity, centrality, and modularity, which are essential for understanding the behaviour of molecular systems. This review details the application and development of graph theory-based models in studying biomolecular systems. We introduce key concepts in graph theory and demonstrate their practical applications, illustrating how innovative graph theory approaches can be employed to design biomolecular systems with enhanced functionality. Specifically, we explore the integration of graph theoretical methods with MD simulations to gain deeper insights into complex biological phenomena, such as allosteric regulation, conformational dynamics, and catalytic functions. Ultimately, graph theory has proven to be a powerful tool in the field of molecular dynamics, offering valuable insights into the structural properties, dynamics, and interactions of molecular systems. This review establishes a foundation for using graph theory in molecular design and engineering, highlighting its potential to transform the field and drive advancements in the understanding and manipulation of biomolecular systems.

Barley is one of the most consumed cereals, with many different cultivars available worldwide. Like other crops, its yield has been affected by climate change and soil degradation. This work proposes controlled-release protein-based matrices with incorporated zinc to improve barley seed germination and zinc content in the plant. Thus, the main objective of this study was to investigate the use of controlled-release protein-based matrices for massive crops, such as barley. Different barley cultivars of barley were studied: Barke, Golden Promise, Morex, WB-200, WB379, and WB-446. The seeds of each cultivar were also analyzed in order to explain the behavior of plants observed during the growth. To this end, the physico-chemical (FT-IR, Raman spectroscopy, and Zn concentration) and microstructural (SEM) properties of the different seeds were firstly evaluated to establish differences between the studied cultivars. In addition, the use of controlled-release soybean protein-based matrices without zinc (M) or with zinc incorporated (MZ) was evaluated as fertilizers in the different barley cultivars. In this sense, the use of these matrices as a zinc carrier improved seed germination and zinc content in the plants, indicating that the use of matrices improves the amount of zinc assimilated by the crops (up to 30 and 50% with M and MZ, respectively) and allows the proper root growth of all cultivars of barley. In conclusion, this article shows the potential of controlled-release protein-based matrices as substitutes for conventional fertilization.

Hydrophobic forces are known to have a crucial part not only in the conformation of the three-dimensional structure of proteins, but also in the build-up of DNA–protein complexes. Electric forces also play an important role both in the tertiary as well in the quaternary structure of macromolecular associations. Sometimes both hydrophobic and electric interactions add up their strengths to accomplish these structures but in most cases they act in opposite directions. This fact, together with being overall interactions with different ranges, provides a nuanced equilibrium also modulated by the need to comply with steric hindrances and geometric frustration effects. This review focuses on the utility of using the hydrophobic and electrical dipole moment vectors to describe the interactions that give rise to the structures of biological macromolecules. Although different definitions of both electric dipole and hydrophobic moments have been described in the literature, results obtained in biological assemblies demonstrate the principle of the biological membrane model. According to this model, postulated by our group, biological macromolecules tend to associate by aligning their hydrophobic moments in a similar manner to phospholipids in a membrane. Examples of both closed and open structures are used to assess the predictability of our model. We seek agreement between our results with those described in the current literature. The review ends with possible future projections using this formalism.

Tetraspanins are a superfamily of transmembrane proteins that in flatworms have structural roles in the development, maturation or stability of the tegument. Several tetraspanins are considered as potential candidates for vaccines or drugs against helminths. Monopisthocotylean monogeneans are ectoparasites of fish that are health hazards for farmed fish. The aim of this study was to identify in silico putative tetraspanins in the genomic datasets of four monopisthocotylean species. The analysis predicted and classified 40 tetraspanins in Rhabdosynochus viridisi, 39 in Scutogyrus longicornis, 22 in Gyrodactylus salaris and 13 in Neobenedenia melleni, belonging to 13 orthologous groups. The high divergence of tetraspanins made it difficult to annotate their function. However, a conserved group was identified in different metazoan taxa. According to this study, metazoan tetraspanins can be divided into 17 monophyletic groups. Of the 114 monogenean tetraspanins, only seven were phylogenetically close to tetraspanins from non-platyhelminth metazoans, which suggests that this group of proteins shows rapid sequence divergence. The similarity of the monopisthocotylean tetraspanins was highest with trematodes, followed by cestodes and then free-living platyhelminths. In total, 27 monopisthocotylean-specific and 34 flatworm-specific tetraspanins were identified. Four monogenean tetraspanins were orthologous to TSP-1, which is a candidate for the development of vaccines and a potential pharmacological target in trematodes and cestodes. Although studies of tetraspanins in parasitic flatworms are scarce, this is an interesting group of proteins for the development of new methods to control monogeneans.

Declining nutrient densities of crops in the past 50–70 years have been attributed to unsound agricultural practices and plant breeding focus on yield rather than quality. Few studies have quantified the soil and nutritional quality of grains in organic and conventional farms and reported results are scarce and inconsistent. The Rodale Institute's Farming Systems Trial (FST) was established in 1981 to quantify the effects of long-term organic and conventional grain cropping systems and tillage practices. A 2014 study to quantify effects on the nutrient density of oat grains was integrated into three systems within the long-term trial: organic manure-based (MNR), organic legume-based (LEG), and conventional synthetic input-based (CNV), split between tilled (T) and no-till (NT) practices. Oat grains with hulls removed were analyzed for minerals (n = 24), vitamins (n = 24), amino acids (n = 24) and proteins (n = 24), while soil samples to a depth of 10 cm were analyzed for elemental minerals, and total carbon (C), nitrogen (N) and sulfur (S). Organic systems increased six out ten soil minerals whose concentrations were influenced by cropping systems: aluminum (Al), iron (Fe), chromium (Cr), calcium (Ca), barium (B) and strontium (Sr). All essential amino acids were greater in oat grains under LEG systems compared with other systems except lysine, histidine and methionine. Both LEG systems also increased 12 out of 13 non-essential amino acids in oat grains. Total oat N, C and S required for amino acid synthesis tended to be greater in organic systems. Soil N, C and S were highly correlated with total oat amino acids under organic systems compared to CNV. Organic LEG had significantly greater vitamin B1 than MNR and CNV. These results suggest that nutrient concentrations of oat grains were greater in organic systems compared to CNV systems, and the increase could be partially explained by the long-term soil management differences between the systems.

Native chicory inulin is one of the promising alternatives to replace antibiotic growth promoters in young animals. Several potential mechanisms of prebiotic action have been proposed, such as modification of the intestinal microbiota composition leading to improved epithelial integrity and gut mucosal immunity of the host. The current study was focused on inulin effect on the large intestinal proteome and its implications for gut barrier functions. Therefore, we used proteomic techniques to determine changes in the large intestinal mucosa proteome of growing pigs after 40-day supplementation with native chicory inulin. The experiment was performed on 24 piglets fed from the 10th day of life an unsupplemented cereal-based diet or inulin-enriched diets (1% or 3%) with an average degree of polymerisation ≥ 10. At the age of 50 days, animals were sacrificed and tissue samples were collected from the cecum, and proximal and distal colon. Feeding diets supplemented with both levels of native inulin increased cecal and colonic expression of molecular chaperones, protein foldases and antioxidant proteins, which are collectively responsible for maintaining mucosal cell integrity as well as protecting against endotoxins and reactive oxygen species. This may confirm the beneficial effect of inulin on the gut health in growing pigs.

The strong, long-range electrostatic forces described by Coulomb's law disappear for ions in water, and the behavior of these ions is instead controlled by their water affinity – a weak, short-range force which arises from their charge density. This was established experimentally in the mid-1980s by size-exclusion chromatography on carefully calibrated Sephadex® G-10 (which measures the effective volume and thus the water affinity of an ion) and by neutron diffraction with isotopic substitution (which measures the density and orientation of water molecules near the diffracting ion and thus its water affinity). These conclusions have been confirmed more recently by molecular dynamics simulations, which explicitly model each individual water molecule. This surprising change in force regime occurs because the oppositely charged ions in aqueous salt solutions exist functionally as ion pairs (separated by 0, 1 or 2 water molecules) as has now been shown by dielectric relaxation spectroscopy; this cancels out the strong long-range electrostatic forces and allows the weak, short-range water affinity effects to come to the fore. This microscopic structure of aqueous salt solutions is not captured by models utilizing a macroscopic dielectric constant. Additionally, the Law of Matching Water Affinity, first described in 1997 and 2004, establishes that contact ion pair formation is controlled by water affinity and is a major determinant of the solubility of charged species since only a net neutral species can change phases.

The characterisation of proteome and peptidome of adolescent mothers’ breast milk brings important information to both mother’s and infant’s health; however, it has not been investigated. Bioactive peptides derived from milk proteins have numerous functions. The bioactivity of breast milk peptides includes anti-inflammatory and antimicrobial activities and regulation of gastrointestinal function. We aimed to characterise the proteome and peptidome of mature breast milk of adolescent mothers and investigate whether it is affected by lactational period. We used a combination of electrophoretic and nano-scale LC-quadrupole time-of-flight MS/MS (nLC-Q-TOF-MS/MS) techniques and bioinformatics to explore the proteome of human skimmed milk expressed by lactating adolescents in two groups according to postpartum period (up to 3 and over 5 weeks postpartum). This is the first study that analysed the proteome of adolescent mothers’ breast milk produced during two periods of lactation using 1D-electrophoresis combined with nLC-Q-TOF-MS/MS analysis. Our results showed that the protein composition of adolescent milk varies independently of lactation stage and showed high inter-individual variation. A total of 424 proteins were identified in skimmed milk, of which 137 proteins were common to both groups. Most of the peptides found in adolescents’ breast milk were not derived from major proteins in milk. Association maps showed several interactions between groups of peptides that pointed to the relevance of breast milk peptides to neonatal defensive system.

There is lack of evidence on the differential impact of maternal macronutrient consumption: carbohydrates (CHO), fats and protein on birth weight. We investigated the association between maternal dietary macronutrient intakes and their sub-components such as saccharides and fatty acids and birth weight. This analyses included 1,196 women with singleton pregnancies who were part of the CAffeine and REproductive health study in Leeds, UK between 2003 and 2006. Women were interviewed in each trimester. Dietary information was collected twice using a 24-h dietary recall about 8–12 weeks and 13–27 weeks of gestation. Multiple linear regression models adjusted for alcohol and smoking in trimester 1, showed that each additional 10 g/d CHO consumption was associated with an increase of 4 g (95 % CI 1, 7; P=0·003) in birth weight. Conversely, an additional 10 g/d fat intake was associated with a lower birth weight of 8 g (95 % CI 0, 16; P=0·04) when we accounted for energy contributing macronutrients in each model, and maternal height, weight, parity, ethnicity, gestational age at delivery and sex of the baby. There was no evidence of an association between protein intake and birth weight. Maternal diet in trimester 2 suggested that higher intakes of glucose (10 g/d) and lactose (1 g/d) were both associated with higher birth weight of 52 g (95 % CI 4, 100; P=0·03) and 5 g (95 % CI 2, 7; P<0·001) respectively. These results show that dietary macronutrient composition during pregnancy is associated with birth weight outcomes. An appropriately balanced intake of dietary CHO and fat during pregnancy could support optimum birth weight.

A foundation diet, an intermediate blend and a summit diet were formulated with different levels of soyabean meal, casein and crystalline amino acids to compare ‘slow’ and ‘rapid’ protein diets. The diets were offered to male Ross 308 chicks from 7 to 28 d post-hatch and assessed parameters included growth performance, nutrient utilisation, apparent digestibility coefficients and disappearance rates of starch and protein (N) in four small intestinal segments. Digestibility coefficients and disappearance rates of sixteen amino acids in three small intestinal segments and amino acid concentrations in plasma from portal and systemic circulations from the foundation and summit diets were determined. The dietary transition significantly accelerated protein (N) disappearance rates in the distal jejunum and ileum. The transition from foundation to summit diets significantly increased starch digestibility coefficients in the ileum and disappearance rates in all four small intestinal segments. These starch responses were associated with significant enhancements in nutrient utilisation. The dietary transition linearly increased digestibility coefficients and disappearance rates of amino acids in the majority of cases. The summit diet increased plasma concentrations of five amino acids but decreased those of four amino acids relative to the foundation diet to significant extents. Plasma concentrations of free amino acids were higher in the portal than systemic circulations. Rapid protein disappearance rates advantaged poultry performance and influenced post-enteral availability of amino acids. If the underlying mechanisms are to be identified, further research into the impact of protein digestive dynamics on broiler performance is required but appears justified.

A total of ten experimental diets with protein concentrations ranging from 154 to 400 g/kg and two lipid levels (46 and 85 g/kg) with identical energy densities were offered to 240 male Ross 308 broilers from 7 to 28 d post-hatch. Growth performance was monitored and nutrient utilisation (apparent metabolisable energy (AME), N-corrected AME (AMEn), AME daily intake, AME:gross energy ratios, N retention) was determined. The weight gain response of broiler chickens to dietary protein concentrations in diets containing high and low lipid levels was diverse, with the relevant quadratic regressions being significantly different (P<0·05). With low lipid levels, the predicted maximum weight gain of 1809 g/bird equated to 342 g/kg dietary protein, whereas, for high lipid levels the predicted maximum weight gain of 1694 g/bird equated to 281 g/kg dietary protein. AME was linearly correlated with dietary protein concentration but regressions in diets with different lipid content were not significantly different (P>0·05). AMEn was also linearly (P<0·0001) increased with dietary protein concentrations but regressions in diets with low and high lipid content were significantly different (P<0·03). Carcass protein content increased linearly with dietary protein content in diets containing high lipid concentrations (r 0·933, P<0·0001); by contrast, this relationship was quadratic (R2=0·93, P<0·0001) in diets with low lipid levels. In conclusion, predictably, the effects of dietary protein concentrations on broiler performance were profound; however, the impact of dietary protein on performance in broiler chickens was modified by dietary lipid concentrations.

No study has analysed how protein intake from early childhood to young adulthood relate to adult BMI in a single cohort. To estimate the association of protein intake at 2, 11, 15, 19 and 22 years with age- and sex-standardised BMI at 22 years (early adulthood), we used linear regression models with dietary and anthropometric data from a Filipino birth cohort (1985–2005, n 2586). We used latent growth curve analysis to identify trajectories of protein intake relative to age-specific recommended daily allowance (intake in g/kg body weight) from 2 to 22 years, then related trajectory membership to early adulthood BMI using linear regression models. Lean mass and fat mass were secondary outcomes. Regression models included socioeconomic, dietary and anthropometric confounders from early life and adulthood. Protein intake relative to needs at age 2 years was positively associated with BMI and lean mass at age 22 years, but intakes at ages 11, 15 and 22 years were inversely associated with early adulthood BMI. Individuals were classified into four mutually exclusive trajectories: (i) normal consumers (referent trajectory, 58 % of cohort), (ii) high protein consumers in infancy (20 %), (iii) usually high consumers (18 %) and (iv) always high consumers (5 %). Compared with the normal consumers, ‘usually high’ consumption was inversely associated with BMI, lean mass and fat mass at age 22 years whereas ‘always high’ consumption was inversely associated with male lean mass in males. Proximal protein intakes were more important contributors to early adult BMI relative to early-childhood protein intake; protein intake history was differentially associated with adulthood body size.

This study examined the effect of including different dietary proportions of starch, protein and lipid, in diets balanced for digestible energy, on the utilisation efficiencies of dietary energy by barramundi (Lates calcarifer). Each diet was fed at one of three ration levels (satiety, 80 % of initial satiety and 60 % of initial satiety) for a 42-d period. Fish performance measures (weight gain, feed intake and feed conversion ratio) were all affected by dietary energy source. The efficiency of energy utilisation was significantly reduced in fish fed the starch diet relative to the other diets, but there were no significant effects between the other macronutrients. This reduction in efficiency of utilisation was derived from a multifactorial change in both protein and lipid utilisation. The rate of protein utilisation deteriorated as the amount of starch included in the diet increased. Lipid utilisation was most dramatically affected by inclusion levels of lipid in the diet, with diets low in lipid producing component lipid utilisation rates well above 1·3, which indicates substantial lipid synthesis from other energy sources. However, the energetic cost of lipid gain was as low as 0·65 kJ per kJ of lipid deposited, indicating that barramundi very efficiently store energy in the form of lipid, particularly from dietary starch energy. This study defines how the utilisation efficiency of dietary digestible energy by barramundi is influenced by the macronutrient source providing that energy, and that the inclusion of starch causes problems with protein utilisation in this species.

In the present work, it is shown that thermodynamically feasible polymerization of cyanomethanol, which can be formed from formaldehyde and hydrogen cyanide, can lead to synthesis of polypeptides as well as to the previously reported synthesis of RNA. If the polymerization takes place on a one-dimensional feature of a mineral, such as for example a crack on its surface, the concept of quasi-chirality is introduced to describe the adsorbed polypeptide. This, in principle, would lead to formation of proteins that are completely homochiral in their alpha carbon groups. The concept of quasi-chirality can also be introduced in the condensation of glycine under similar conditions to form a polypeptide. This again leads to proteins completely chiral in their alpha carbon groups.