Studying the relationship between sequences and their corresponding three-dimensional structure assists structural biologists in solving the protein-folding problem. Despite several experimental and in-silico approaches, still understanding or decoding the three-dimensional structures from the sequence remains a mystery. In such cases, the accuracy of the structure prediction plays an indispensable role. To address this issue, an updated web server (CSSP-2.0) has been created to improve the accuracy of our previous version of CSSP by deploying the existing algorithms. It uses input as probabilities and predicts the consensus for the secondary structure as a highly accurate three-state Q3 (helix, strand, and coil). This prediction is achieved using six recent top-performing methods: MUFOLD-SS, RaptorX, PSSpred v4, PSIPRED, JPred v4, and Porter 5.0. CSSP-2.0 validation includes datasets involving various protein classes from the PDB, CullPDB, and AlphaFold databases. Our results indicate a significant improvement in the accuracy of the consensus Q3 prediction. Using CSSP-2.0, crystallographers can sort out the stable regular secondary structures from the entire complex structure, which would aid in inferring the functional annotation of hypothetical proteins. The web server is freely available at https://bioserver3.physics.iisc.ac.in/cgi-bin/cssp-2/.

The treatment of cow\'s milk protein allergy is based on the complete elimination of cow\'s milk protein from the diet. To achieve remission of symptoms and future tolerance, exclusion must be total. In formula fed infants the extensively hydrolysed formula is the most appropriate option in mild or moderate forms, while those based on amino acids are reserved for the most severe cases. The treatment time, the acquisition of tolerance and the moment for the oral provocation test will vary according to the clinical picture, the immunological mechanism involved and the age of the patient. The aim of this consensus has been to reflect the updated knowledge together with the experience of neonatologists, pediatricians, experts in allergy, nutrition and gastroenterology.
El tratamiento de la alergia a las proteínas de la leche de vaca se basa en la eliminación completa de las proteínas de leche de vaca de la dieta del niño y de la madre en los que reciben leche materna. Para lograr la remisión de los síntomas y la tolerancia futura, la exclusión debe ser total. En los niños que reciben fórmula, esta deberá tener hidrolizado extenso de proteínas en las formas leves o moderadas, mientras que aquellas a base de aminoácidos se reservan para los casos más graves. El tiempo de tratamiento, la adquisición de tolerancia y el momento para la prueba de provocación oral van a variar según el cuadro clínico, el mecanismo inmunológico implicado y la edad del paciente. El objetivo de este consenso ha sido reflejar el conocimiento actualizado junto con la experiencia de neonatólogos, pediatras, especialistas en alergia, nutrición y gastroenterología.

Antimicrobial peptides (AMPs) are promising candidates to combat pathogens that are resistant to conventional antimicrobial drugs because they operate through mechanisms that involve membrane disruption. However, the use of AMPs in clinical settings has been limited, at least in part, by their susceptibility to proteolytic degradation and their lack of selectivity toward pathogenic microbes vs mammalian cells. We recently reported on the design of α- and β-peptide oligomers structurally templated upon the naturally occurring α-helical AMP aurein 1.2. These α/β-peptide oligomers are more proteolytically stable than aurein 1.2 and have several other attributes that render them attractive as alternatives to conventional AMPs. This study describes the influence of peptide physicochemical properties on the broad-spectrum activity of aurein 1.2-based α/β-peptide mimics against nine bacterial, fungal, and mammalian cell lines. We used a partial least-squares regression (PLSR)-supervised machine learning model to quantify and visualize relationships between experimentally determined physicochemical properties (e.g., hydrophobicity, charge, and helicity) and experimentally measured cell-type-specific activities of 21 peptides in a 149-member α/β-peptide library. Using this approach, we identified several peptides that were predicted to exhibit enhanced broad-spectrum selectivity, a measure that evaluates antimicrobial activity relative to mammalian cell toxicity compared to aurein 1.2. Experimental validation demonstrated high model predictive performance, and characterization of compounds with the highest broad-spectrum selectivity revealed peptide hydrophobicity, helicity, and helical rigidity to be strong predictors of broad-spectrum selectivity. The most selective peptide identified from the model prediction has more than a 13-fold improvement in broad-spectrum selectivity than that of aurein 1.2, demonstrating the ability of using PLSR models to identify quantitative structure-function relationships for nonstandard amino acid-containing peptides. Overall, this work establishes quantifiable guidelines for the rational design of helical antimicrobial α/β-peptides and identifies promising new α/β-peptides with significantly reduced mammalian toxicities and improved antifungal and antibacterial activities relative to aurein 1.2.

Parenteral nutrition (PN) is prescribed for preterm infants until nutrition needs are met via the enteral route, but unanswered questions remain regarding PN best practices in this population.
An interdisciplinary committee was assembled to answer 12 questions concerning the provision of PN to preterm infants. The Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) process was used. Questions addressed parenteral macronutrient doses, lipid injectable emulsion (ILE) composition, and clinically relevant outcomes, including PNALD, early childhood growth, and neurodevelopment. Preterm infants with congenital gastrointestinal disorders or infants already diagnosed with necrotizing enterocolitis or PN-associated liver disease (PNALD) at study entry were excluded.
The committee reviewed 2460 citations published between 2001 and 2023 and evaluated 57 clinical trials. For most questions, quality of evidence was very low. Most analyses yielded no significant differences between comparison groups. A multicomponent oil ILE was associated with a reduction in stage 3 or higher retinopathy of prematurity (ROP) compared to an ILE containing 100% soybean oil. For all other questions, expert opinion was provided.
Most clinical outcomes were not significantly different between comparison groups when evaluating timing of PN initiation, amino acid dose, and ILE composition. Future clinical trials should standardize outcome definitions to permit statistical conflation of data, thereby permitting more evidence based recommendations in future guidelines. This guideline has been approved by the ASPEN 2022-2023 Board of Directors.

The currently dominant Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swiftly diverged into clades. To predict the probable impact of these clades, the consensus insertions/deletions (indels) and amino acid substitutions of the whole genome of clades were compared with the original SARS-CoV-2 strain. The evolutionary history of representatives of clades and lineages was inferred using the maximum-likelihood method and tested using the bootstrap method. The indels and polymorphic amino acids were found to be either clade-specific or shared among clades. The 21K clade has unique indels and substitutions, which probably represent reverted indels/substitutions. Three variations that appear to be associated with SARS-CoV-2 attenuation in the Omicron clades included a deletion in the nucleocapsid gene, a deletion in the 3\'untranslated region, and a truncation in open reading frame 8. Phylogenetic analysis showed that the Omicron clades and lineages form three separate clusters.

An experiment was conducted to test the hypothesis that increasing levels of a novel phytase increases the apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of nutrients in diets fed to young pigs. A negative control (NC) diet based on corn, soybean meal, and canola meal that contained approximately 0.83% phytate (i.e., 0.23% phytate-bound P) was formulated to be deficient in Ca, P, and standardized ileal digestible amino acids (AA). Five additional diets were formulated by adding 250, 500, 1,000, 2,000, or 4,000 phytase units/kg of the novel phytase to the NC diets. Eighteen ileal-cannulated pigs (17.81 ± 1.71 kg) were allotted to a 6 × 3 incomplete Latin square design with six diets and three 11-day periods. There were three pigs per diet in each period; therefore, there were nine replicate pigs per diet. The initial 5 d of each period was considered an adaptation period to the diet. For each period, fecal samples were collected via anal stimulation on days 6, 7, 8, and 9, whereas ileal digesta were collected on days 10 and 11 using standard procedures. Results indicated that the AID of crude protein, indispensable AA, and dispensable AA was increased (quadratic, P < 0.05) as the concentration of microbial phytase increased in the diets. Dietary inclusion of the novel phytase at 1,000 or 2,000 FTU/kg increased the AID of total AA from 73.7% to 79.8%. Increasing levels of microbial phytase increased (quadratic, P < 0.05) the AID of dry matter and minerals (i.e., Ca, P, K, Mg, Cu) in the diets. Likewise, a linear increase (P < 0.05) in the AID of ash and Na was observed as the inclusion level of phytase increased in the diets. Increasing levels of microbial phytase increased (linear, P < 0.01) the AID of gross energy (GE) and starch in the diets. A quadratic (P < 0.05) increase in the ATTD of ash, Ca, P, K, and Cu in experimental diets was observed as the concentration of microbial phytase increased in the diets. The ATTD of Mg and GE also increased (linear; P < 0.05) as concentration of dietary phytase increased. In conclusion, the novel microbial phytase used in this experiment was effective in increasing the AID of dry matter, GE, starch, minerals, and AA, as well as the ATTD of gross energy and minerals in diets formulated to be deficient in Ca, P, and AA.
The effect of microbial phytase on amino acid (AA) digestibility has been inconsistent, but in many experiments, relatively low levels of phytase were used and it is not known if greater concentrations of phytase are needed to increase AA digestibility. A novel consensus bacterial 6-phytase variant has been recently developed, but it is not known if this phytase results in increased digestibility of AA and other nutrients. Therefore, an experiment was conducted to test the hypothesis that dietary inclusion of increasing levels of the novel phytase (i.e., 0, 250, 500, 1,000, 2,000, and 4,000 phytase units/kg) increases ileal digestibility of AA and total tract digestibility of energy and minerals in diets for growing pigs. In this experiment, it was demonstrated that increasing levels of phytase increased the apparent ileal digestibility of starch, gross energy, minerals, crude protein, and AA, as well as the apparent total tract digestibility of gross energy and minerals. The impact of phytase on AA digestibility is possibly dependent on diet composition, phytate and phytase sources and concentrations, and pig maturity; however, further research is needed to confirm this.

Given the importance of poor nutrition as a cause for human chronic disease, it is surprising that nutrition receives so little attention during medical school training and in clinical practice. Specific vitamins, minerals, fatty acids, amino acids and water in the diet are essential for health, and deficiencies lead or contribute to many diseases. Proper use of the dietary guidelines and nutrition facts labeling can improve nutritional status and lead to the consumption of a healthy diet. COVID-19 has altered access to nutritious foods for millions and increased awareness of the importance of diet and immune function. An improved appreciation for nutrition will improve the outcomes of clinical care.

Vaccines based on proteins and peptides may be safer and if calculated based on many sequences, more broad-spectrum than those designed based on single strains. Physicochemical Property Consensus (PCPcon) alphavirus (AV) antigens from the B-domain of the E2 envelope protein were designed, synthesized recombinantly and shown to be immunogenic (i.e. sera after inoculation detected the antigen in dotspots and ELISA). Antibodies in sera after inoculation with B-region antigens based on individual AV species (eastern or Venezuelan equine encephalitis (EEEVcon, VEEVcon), or chikungunya (CHIKVcon) bound only their cognate protein, while those designed against multiple species (Mosaikcon and EVCcon) recognized all three serotype specific antigens. The VEEVcon and EEEVcon sera only showed antiviral activity against their related strains (in plaque reduction neutralization assays (PRNT50/80). Peptides designed to surface exposed areas of the E2-A-domain of CHIKVcon were added to CHIKVcon inocula to provide anti-CHIKV antibodies. EVCcon, based on three different alphavirus species, combined with E2-A-domain peptides from AllAVcon, a PCPcon of 24 diverse AV, generated broad spectrum, antiviral antibodies against VEEV, EEEV and CHIKV, AV with less than 35% amino acid identity to each other (>65% diversity). This is a promising start to a molecularly defined vaccine against all AV. Further study with these antigens can illuminate what areas are most important for a robust immune response, resistant to mutations in rapidly evolving viruses. The validated computational methods can also be used to design broad spectrum antigens against many other pathogen families.

Positron emission tomography (PET) has been widely used in paediatric oncology. 2-Deoxy-2-[18F]fluoro-D-glucose ([18F]FDG) is the most commonly used radiopharmaceutical for PET imaging. For oncological brain imaging, different amino acid PET radiopharmaceuticals have been introduced in the last years. The purpose of this document is to provide imaging specialists and clinicians guidelines for indication, acquisition, and interpretation of [18F]FDG and radiolabelled amino acid PET in paediatric patients affected by brain gliomas. There is no high level of evidence for all recommendations suggested in this paper. These recommendations represent instead the consensus opinion of experienced leaders in the field. Further studies are needed to reach evidence-based recommendations for the applications of [18F]FDG and radiolabelled amino acid PET in paediatric neuro-oncology. These recommendations are not intended to be a substitute for national and international legal or regulatory provisions and should be considered in the context of good practice in nuclear medicine. The present guidelines/standards were developed collaboratively by the EANM and SNMMI with the European Society for Paediatric Oncology (SIOPE) Brain Tumour Group and the Response Assessment in Paediatric Neuro-Oncology (RAPNO) working group. They summarize also the views of the Neuroimaging and Oncology and Theranostics Committees of the EANM and reflect recommendations for which the EANM and other societies cannot be held responsible.

The effect of a novel consensus bacterial 6-phytase variant (PhyG) on apparent ileal digestibility (AID) of amino acids (AA) and phosphorus (P) utilization in young broilers when added to diets with high phytate-P (PP) content without added inorganic phosphate (Pi) and deficient in digestible (dig) AA and metabolizable energy (ME) was investigated. A total of 256 Ross 308 male broilers were assigned to 4 treatments (8 birds/cage, 8 cages/treatment) in a completely randomized design. Treatments comprised a positive control (PC, 2,975 kcal/kg ME, 3.7 g/kg dig P, 2.83 g/kg PP, 8.4 g/kg Ca, 10.6 g/kg dig lysine), a negative control (NC) without added Pi (ME -68 kcal/kg, crude protein -10 g/kg, dig AA -0.1 to -0.4 g/kg, Ca -2.0 g/kg, dig P -2.2 g/kg, Na -0.4 g/kg vs. PC), and NC plus 500 or 1,000 FTU/kg of PhyG. Test diets were corn/soy/rapeseed-meal/rice-bran-based and fed from 5 to 15 d of age. Ileal digesta and tibias were collected on day 15. Excreta was collected during days 12 to 15 to determine P retention. The NC (vs. PC) reduced (P < 0.05) P retention (-10.4% units), tibia ash (-14.3% units), weight gain (-109 g), feed intake (-82 g) and increased FCR (from 1.199 to 1.504), confirming that the NC was extremely deficient in nutrients and energy. Phytase addition to the NC linearly (P < 0.001) improved performance, but did not fully recover it to the level of the PC due to the severe nutrients/energy reduction in NC. Phytase linearly increased P retention (P < 0.001), tibia ash (P < 0.001), AID of dry matter (P < 0.05), nitrogen (P < 0.01), gross energy (P < 0.05), and all 17 individual AA (P < 0.01). At 1,000 FTU/kg, phytase increased (P < 0.05) P retention vs. PC and NC (+14.5 and +24.9% units, respectively) and increased tibia ash vs. NC (+13.8% units), equivalent to PC. The NC decreased AID of Cys, Gly, Thr, and Met vs. PC (P < 0.05). At 1,000 FTU/kg, phytase increased AID of all 17 AA vs. NC (P < 0.01), equivalent to PC. At 1,000 FTU/kg, AID AA responses (above NC) ranged from +4.5% (Met) to +15.0% (Cys), being maximal for essential Thr (+10.4%) and Val (+8.2%) and non-essential Cys (+15.0%) and Gly (+10.4%). The results highlight the efficacy of PhyG at a dose level of 500 to 1,000 FTU/kg in young broilers for improving the ileal digestibility of nitrogen, AA, and energy alongside P retention and tibia ash. The performance data emphasize the need to consider digestible nutrient intake as a response variable in exogenous enzyme studies.
Microbial phytase is widely used in commercial broiler diets to improve digestion of phosphorus (P) and reduce its excretion into the environment. Phytase improves the digestion of phosphorus and other nutrients including amino acids (AA). This study evaluated the effect of a novel consensus bacterial 6-phytase variant (PhyG) added to a nutrient-reduced diet without any added inorganic P on the digestibility of nutrients including P and AA in the ileum of young broilers. Effects on P retention and bone mineralization were also assessed. Compared to an unsupplemented negative control diet, PhyG improved growth performance, P retention, bone mineralization (tibia ash), digestibility of dry matter, nitrogen, gross energy, and all 17 individual AA during 5 to 15 d post-hatch, in a dose-dependent manner (dose range 0 to 1,000 phytase units [FTU] per kilogram of feed). For some AA, the increases in digestibility with PhyG at 1,000 FTU/kg were substantial (cysteine: +15.0%, threonine:+10.4%), and for all AA were equivalent to the responses produced by a nutritionally adequate positive control (unsupplemented) diet. The results demonstrate the efficacy of PhyG to improve AA digestibility alongside growth performance, P retention, and bone mineralization in young broilers.