Genomic analyses of nitrogen utilization efficiency, its indicator trait blood urea nitrogen and the relationship to classical growth performance and feed efficiency traits in a Landrace × Piétrain crossbred population.

Improving the nutrient efficiency in pork production is required to reduce the resource competition between human food and animal feed regarding diet components edible for humans and to minimize emissions relevant to climate or the environment. Thereby, protein utilization efficiency and its equivalent nitrogen utilization efficiency (NUE) play a major role. Breeding for more nitrogen (N) efficient pigs bears a promising strategy to improve such traits, however, directly phenotyping NUE based on N balance data is neither cost-efficient nor straightforward and not applicable for routine evaluations. Blood urea nitrogen (BUN) levels in the pig are suitable to predict the NUE and, therefore, might be an indicator trait for NUE because BUN is a relatively easy-to-measure trait. This study investigated the suitability of NUE as a selection trait in future breeding programs. The relationships to classical growth performance and feed efficiency traits were analysed as well as the relationship to BUN to infer the role of BUN as an indicator trait to improve NUE via breeding. The analyzes were based on a Landrace F1 cross population consisting of 502 individuals who descended from 20 Piétrain sires. All animals were genotyped for 48,525 SNPs. They were phenotyped in two different fattening phases, i.e., FP1 and FP2, during the experiment. Uni- and bivariate analyses were run to estimate variance components and to determine the genetic correlation between different traits or between the same trait measured at different time points. Moderate heritabilities were estimated for all traits, whereby the heritability for NUE was h2 = 0.293 in FP1 and h2 = 0.163 in FP2 and BUN had the by far highest heritability (h2 = 0.415 in FP1 and h2 = 0.460 in FP2). The significant genetic correlation between NUE and BUN showed the potential of BUN to be considered an indicator trait for NUE. This was particularly pronounced when NUE was measured in FP1 (genetic correlations r g = - 0.631 $$ {r}_g=-0.631 $$ and r g = - 0.688 $$ {r}_g=-0.688 $$ between NUE and BUN measured in FP1 and FP2, respectively). The genetic correlations of NUE and BUN with important production traits suggest selecting pigs with high growth rates and low BUN levels to breed more efficient pigs in future breeding programs.

From Soy Waste to Bioplastics: Industrial Proof of Concept.

The global plastic waste problem is pushing for the development of sustainable alternatives, encouraged by stringent regulations combined with increased environmental consciousness. In response, this study presents an industrial-scale proof of concept to produce self-standing, transparent, and flexible bioplastic films, offering a possible solution to plastic pollution and resource valorization. We achieve this by combining amyloid fibrils self-assembled from food waste with methylcellulose and glycerol. Specifically, soy whey and okara, two pivotal protein-rich byproducts of tofu manufacturing, emerge as sustainable and versatile precursors for amyloid fibril formation and bioplastic development. An exhaustive industrial-scale feasibility study involving the transformation of 500 L of soy whey into ∼1 km (27 kg) of bioplastic films underscores the potential of this technology. To extend the practicality of our approach, we further processed a running kilometer of film at the industrial scale into transparent windows for paper-based packaging. The mechanical properties and the water interactions of the novel film are tested and compared with those of commercially used plastic films. By pioneering the large-scale production of biodegradable bioplastics sourced from food byproducts, this work not only simultaneously addresses the dual challenges of plastic pollution and food waste but also practically demonstrates the feasibility of biopolymeric building block valorization for the development of sustainable materials in real-world scenarios.

Controlling Spontaneous Orientation Polarization in Organic Semiconductors─The Case of Phosphine Oxides.

Upon film growth by physical vapor deposition, the preferential orientation of polar organic molecules can result in a nonzero permanent dipole moment (PDM) alignment, causing a macroscopic film polarization. This effect, known as spontaneous orientation polarization (SOP), was studied in the case of different phosphine oxides (POs). We investigate the control of SOP by molecular design and film-growth conditions. Our results show that using less polar POs with just one phosphor-oxygen bond yields an exceptionally high degree of SOP with the so-called giant surface potential (slope), reaching more than 150 mV nm-1 in a neat bis-4-(N-carbazol(yl)phenyl)phenyl phosphine oxide (BCPO) film grown at room temperature. Additionally, by altering the evaporation rate and substrate temperature, we are able to control the SOP magnitude over a broad range from 0 to almost 300 mV nm-1. Diluting BCPO in a nonpolar host enhances the PDM alignment only marginally, but combining temperature control with dipolar doping can result in highly aligned molecules with more than 80% of their PDMs standing upright on the substrate on average.

Optimization Strategies to Adapt Sheep Breeding Programs to Pasture-Based Production Environments: A Simulation Study.

Strong differences between the selection (indoor fattening) and production environment (pasture fattening) are expected to reduce genetic gain due to possible genotype-by-environment interactions (G × E). To investigate how to adapt a sheep breeding program to a pasture-based production environment, different scenarios were simulated for the German Merino sheep population using the R package Modular Breeding Program Simulator (MoBPS). All relevant selection steps and a multivariate pedigree-based BLUP breeding value estimation were included. The reference scenario included progeny testing at stations to evaluate the fattening performance and carcass traits. It was compared to alternative scenarios varying in the progeny testing scheme for fattening traits (station and/or field). The total merit index (TMI) set pasture-based lamb fattening as a breeding goal, i.e., field fattening traits were weighted. Regarding the TMI, the scenario with progeny testing both in the field and on station led to a significant increase in genetic gain compared with the reference scenario. Regarding fattening traits, genetic gain was significantly increased in the alternative scenarios in which field progeny testing was performed. In the presence of G × E, the study showed that the selection environment should match the production environment (pasture) to avoid losses in genetic gain. As most breeding goals also contain traits not recordable in field testing, the combination of both field and station testing is required to maximize genetic gain.

Isolation of Nuclei Tagged in Specific Cell Types (INTACT) in Arabidopsis.

Many functionally distinct plant tissues have relatively low numbers of cells that are embedded within complex tissues. For example, the shoot apical meristem (SAM) consists of a small population of pluripotent stem cells surrounded by developing leaves and/or flowers at the growing tip of the plant. It is technically challenging to collect enough high-quality SAM samples for molecular analyses. Isolation of Nuclei Tagged in specific Cell Types (INTACT) is an easily reproducible method that allows the enrichment of biotin-tagged cell-type-specific nuclei from the total nuclei pool using biotin-streptavidin affinity purification. Here, we provide a detailed INTACT protocol for isolating nuclei from the Arabidopsis SAM. One can also adapt this protocol to isolate nuclei from other tissues and cell types for investigating tissue/cell-type-specific transcriptome and epigenome and their changes during developmental programs at a high spatiotemporal resolution. Furthermore, due to its low cost and simple procedures, INTACT can be conducted in any standard molecular laboratory.

The physics of dancing peanuts in beer.

In Argentina, some people add peanuts to their beer. Once immersed, the peanuts initially sink part way down into the beer before bubbles nucleate and grow on the peanut surfaces and remain attached. The peanuts move up and down within the beer glass in many repeating cycles. In this work, we propose a physical description of this dancing peanuts spectacle. We break down the problem into component physical phenomena, providing empirical constraint of each: (i) heterogeneous bubble nucleation occurs on peanut surfaces and this is energetically preferential to nucleation on the beer glass surfaces; (ii) peanuts enshrouded in attached bubbles are positively buoyant in beer above a critical attached gas volume; (iii) at the beer top surface, bubbles detach and pop, facilitated by peanut rotations and rearrangements; (iv) peanuts containing fewer bubbles are then negatively buoyant in beer and sink; and (v) the process repeats so long as the beer remains sufficiently supersaturated in the gas phase for continued nucleation. We used laboratory experiments and calculations to support this description, including constraint of the densities and wetting properties of the beer-gas-peanut system. We draw analogies between this peanut dance cyclicity and industrial and natural processes of wide interest, ultimately concluding that this bar-side phenomenon can be a vehicle for understanding more complex, applied systems of general interest and utility.

Combinatorial Properties and Recognition of Unit Square Visibility Graphs.

Unit square visibility graphs (USV) are described by axis-parallel visibility between unit squares placed in the plane. If the squares are required to be placed on integer grid coordinates, then USV become unit square grid visibility graphs (USGV), an alternative characterisation of the well-known rectilinear graphs. We extend known combinatorial results for USGV and we show that, in the weak case (i.e., visibilities do not necessarily translate into edges of the represented combinatorial graph), the area minimisation variant of their recognition problem is NP-hard. We also provide combinatorial insights with respect to USV, and as our main result, we prove their recognition problem to be NP-hard, which settles an open question.

Approaches in Sustainable, Biobased Multilayer Packaging Solutions.

The depletion of fossil resources and the growing demand for plastic waste reduction has put industries and academic researchers under pressure to develop increasingly sustainable packaging solutions that are both functional and circularly designed. In this review, we provide an overview of the fundamentals and recent advances in biobased packaging materials, including new materials and techniques for their modification as well as their end-of-life scenarios. We also discuss the composition and modification of biobased films and multilayer structures, with particular attention to readily available drop-in solutions, as well as coating techniques. Moreover, we discuss end-of-life factors, including sorting systems, detection methods, composting options, and recycling and upcycling possibilities. Finally, regulatory aspects are pointed out for each application scenario and end-of-life option. Moreover, we discuss the human factor in terms of consumer perception and acceptance of upcycling.

Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria.

Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.

Exo- and endophytic fungi enable rapid transfer of nutrients from ant waste to orchid tissue.

The epiphytic orchid Caularthron bilamellatum sacrifices its water storage tissue for nutrients from the waste of ants lodging inside its hollow pseudobulb. Here, we investigate whether fungi are involved in the rapid translocation of nutrients. Uptake was analysed with a 15 N labelling experiment, subsequent isotope ratio mass spectrometry (IRMS) and secondary ion mass spectrometry (ToF-SIMS and NanoSIMS). We encountered two hyphae types: a thick melanized type assigned to 'black fungi' (Chaetothyriales, Cladosporiales, and Mycosphaerellales) in ant waste, and a thin endophytic type belonging to Hypocreales. In few cell layers, both hyphae types co-occurred. 15 N accumulation in both hyphae types was conspicuous, while for translocation to the vessels only Hypocreales were involved. There is evidence that the occurrence of the two hyphae types results in a synergism in terms of nutrient uptake. Our study provides the first evidence that a pseudobulb (=stem)-born endophytic network of Hypocreales is involved in the rapid translocation of nitrogen from insect-derived waste to the vegetative and reproductive tissue of the host orchid. For C. bilamellatum that has no contact with the soil, ant waste in the hollow pseudobulbs serves as equivalent to soil in terms of nutrient sources.

Is the Femoral-Epiphyseal Acetabular Roof (FEAR) index associated with hip pain in patients with hip dysplasia?

BACKGROUND: Micro instability of the hip joint has been suggested to cause pain in patients with hip dysplasia. Recently, the Femoral-Epiphyseal Acetabular Roof (FEAR) index has been developed to evaluate hip instability in patients with dysplasia. PURPOSE: To investigate associations between the FEAR index and patient-reported outcomes before and six months after periacetabular osteotomy (PAO). MATERIAL AND METHODS: Radiographs of patients with hip dysplasia who underwent PAO between 2018 and 2020 were retrospectively assessed by a radiologist and an orthopedic surgeon. Radiographic measurements indicative of hip instability (Shenton's line, FEAR index, center-edge angle of Wiberg, acetabular index of Tönnis, and the femoral neck-shaft angle) were measured. Data on hip pain, function, and quality of life were collected prospectively using the Hip dysfunction and Osteoarthritis Outcome Score (HOOS). RESULTS: A total of 222 patients were included in the study. All radiographic measurements and patient-reported outcomes improved significantly from preoperative to six months postoperative (P < 0.001). There were no differences in the change score of patient-reported outcomes between patients with a FEAR index >2° (indicative of hip instability) and patients with a FEAR index ≤2°. CONCLUSION: The FEAR index was not associated with hip pain, function, and quality of life among patients with hip dysplasia. This study did not find evidence supporting that instability defined by the FEAR index caused pain in patients with hip dysplasia.

PICLN modulates alternative splicing and light/temperature responses in plants.

Plants undergo transcriptome reprograming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. Ion Chloride nucleotide-sensitive protein (PICLN) is part of the methylosome complex in both humans and Arabidopsis (Arabidopsis thaliana), and we show here that the human PICLN ortholog rescues phenotypes of Arabidopsis picln mutants. Altered photomorphogenic and photoperiodic responses in Arabidopsis picln mutants are associated with changes in pre-mRNA splicing that partially overlap with those in PROTEIN ARGININE METHYL TRANSFERASE5 (prmt5) mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PRMT5, the main protein of the methylosome, are controlled by Arabidopsis GEMIN2. As with GEMIN2 and SM PROTEIN E1/PORCUPINE (SME1/PCP), low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.

Physical, Chemical and Biochemical Modification Approaches of Potato (Peel) Constituents for Bio-Based Food Packaging Concepts: A Review.

Potatoes are grown in large quantities and are mainly used as food or animal feed. Potato processing generates a large amount of side streams, which are currently low value by-products of the potato processing industry. The utilization of the potato peel side stream and other potato residues is also becoming increasingly important from a sustainability point of view. Individual constituents of potato peel or complete potato tubers can for instance be used for application in other products such as bio-based food packaging. Prior using constituents for specific applications, their properties and characteristics need to be known and understood. This article extensively reviews the scientific literature about physical, chemical, and biochemical modification of potato constituents. Besides short explanations about the modification techniques, extensive summaries of the results from scientific articles are outlined focusing on the main constituents of potatoes, namely potato starch and potato protein. The effects of the different modification techniques are qualitatively interpreted in tables to obtain a condensed overview about the influence of different modification techniques on the potato constituents. Overall, this article provides an up-to-date and comprehensive overview of the possibilities and implications of modifying potato components for potential further valorization in, e.g., bio-based food packaging.

Complex geometry of volcanic vents and asymmetric particle ejection: experimental insights.

Explosive volcanic eruptions eject a gas-particle mixture into the atmosphere. The characteristics of this mixture in the near-vent region are a direct consequence of the underlying initial conditions at fragmentation and the geometry of the shallow plumbing system. Yet, it is not possible to observe directly the sub-surface parameters that drive such eruptions. Here, we use scaled shock-tube experiments mimicking volcanic explosions in order to elucidate the effects of a number of initial conditions. As volcanic vents can be expected to possess an irregular geometry, we utilise three vent designs, two "complex" vents and a vent with a "real" volcanic geometry. The defining geometry elements of the "complex" vents are a bilateral symmetry with a slanted top plane. The "real" geometry is based on a photogrammetric 3D model of an active volcanic vent with a steep and a diverging vent side. Particle size and density as well as experimental pressure are varied. Our results reveal a strong influence of the vent geometry, on both the direction and the magnitude of particle spreading and the velocity of particles. The overpressure at the vent herby controls the direction of the asymmetry of the gas-particle jet. These findings have implications for the distribution of volcanic ejecta and resulting areas at risk.

NK cells with tissue-resident traits shape response to immunotherapy by inducing adaptive antitumor immunity.

T cell-directed cancer immunotherapy often fails to generate lasting tumor control. Harnessing additional effectors of the immune response against tumors may strengthen the clinical benefit of immunotherapies. Here, we demonstrate that therapeutic targeting of the interferon-γ (IFN-γ)-interleukin-12 (IL-12) pathway relies on the ability of a population of natural killer (NK) cells with tissue-resident traits to orchestrate an antitumor microenvironment. In particular, we used an engineered adenoviral platform as a tool for intratumoral IL-12 immunotherapy (AdV5-IL-12) to generate adaptive antitumor immunity. Mechanistically, we demonstrate that AdV5-IL-12 is capable of inducing the expression of CC-chemokine ligand 5 (CCL5) in CD49a+ NK cells both in tumor mouse models and tumor specimens from patients with cancer. AdV5-IL-12 imposed CCL5-induced type I conventional dendritic cell (cDC1) infiltration and thus increased DC-CD8 T cell interactions. A similar observation was made for other IFN-γ-inducing therapies such as Programmed cell death 1 (PD-1) blockade. Conversely, failure to respond to IL-12 and PD-1 blockade in tumor models with low CD49a+ CXCR6+ NK cell infiltration could be overcome by intratumoral delivery of CCL5. Thus, therapeutic efficacy depends on the abundance of NK cells with tissue-resident traits and, specifically, their capacity to produce the DC chemoattractant CCL5. Our findings reveal a barrier for T cell-focused therapies and offer mechanistic insights into how T cell-NK cell-DC cross-talk can be enhanced to promote antitumor immunity and overcome resistance.

FLOWERING LOCUS T paralogs control the annual growth cycle in Populus trees.

In temperate and boreal regions, perennials adapt their annual growth cycle to the change of seasons. These adaptations ensure survival in harsh environmental conditions, allowing growth at different latitudes and altitudes, and are therefore tightly regulated. Populus tree species cease growth and form terminal buds in autumn when photoperiod falls below a certain threshold.1 This is followed by establishment of dormancy and cold hardiness over the winter. At the center of the photoperiodic pathway in Populus is the gene FLOWERING LOCUS T2 (FT2), which is expressed during summer and harbors significant SNPs in its locus associated with timing of bud set.1-4 The paralogous gene FT1, on the other hand, is hyper-induced in chilling buds during winter.3,5 Even though its function is so far unknown, it has been suggested to be involved in the regulation of flowering and the release of winter dormancy.3,5 In this study, we employ CRISPR-Cas9-mediated gene editing to individually study the function of the FT-like genes in Populus trees. We show that while FT2 is required for vegetative growth during spring and summer and regulates the entry into dormancy, expression of FT1 is absolutely required for bud flush in spring. Gene expression profiling suggests that this function of FT1 is linked to the release of winter dormancy rather than to the regulation of bud flush per se. These data show how FT duplication and sub-functionalization have allowed Populus trees to regulate two completely different and major developmental control points during the yearly growth cycle.

The electrical signature of mafic explosive eruptions at Stromboli volcano, Italy.

Volcanic lightning is commonly observed in explosive volcanic eruptions of Volcanic Explosivity Index (VEI) > 2 and can be detected remotely providing real-time volcano monitoring information. However, little is known about the electrical activity accompanying the lower-magnitude spectrum of explosive eruptions, often involving mafic magmas. We narrow this gap in knowledge by presenting the electrical signature of the explosive activity (VEI ≤ 1) of Stromboli volcano (Italy) recorded by an electrostatic thunderstorm detector. The persistent eruptive activity of mild Strombolian explosions is occasionally interrupted by larger-scale major explosions and paroxysmal events.Here, we present electrical observations of three major explosions and unprecedented measurements of the 3 July 2019 paroxysm. The electrical signals of the major explosions show apparent similarities, with movements of charge and tens of electrical discharges, arising the question of whether these observations could be used to supplement the classification scheme of explosions on Stromboli. The electrical signals from the 3 July 2019 paroxysm exceed those from the major explosions in amplitude, discharge rate and complexity, showing characteristic variations during different phases of the eruption.These results show that also impulsive lower-magnitude explosions generate detectable electrical activity, which holds promise for monitoring low VEI activity at mafic volcanoes.

Improving the Accuracy of Multi-Breed Prediction in Admixed Populations by Accounting for the Breed Origin of Haplotype Segments.

Numerically small breeds have often been upgraded with mainstream breeds. This historic introgression predisposes the breeds for joint genomic evaluations with mainstream breeds. The linkage disequilibrium structure differs between breeds. The marker effects of a haplotype segment may, therefore, depend on the breed from which the haplotype segment originates. An appropriate method for genomic evaluation would account for this dependency. This study proposes a method for the computation of genomic breeding values for small admixed breeds that incorporate phenotypic and genomic information from large introgressed breeds by considering the breed origin of alleles (BOA) in the evaluation. The proposed BOA model classifies haplotype segments according to their origins and assumes different but correlated SNP effects for the different origins. The BOA model was compared in a simulation study to conventional within-breed genomic best linear unbiased prediction (GBLUP) and conventional multi-breed GBLUP models. The BOA model outperformed within-breed GBLUP as well as multi-breed GBLUP in most cases.

Facile fabrication of transparent high-barrier poly(lactic acid)-based bilayer films with antioxidant/antimicrobial performances.

Poly(lactic acid) (PLA) has been intended as an encouraging biopolymer for packaging purposes. Nevertheless, PLA-based films suffer from low gas barrier properties, which restrict their applications. Here, we report a facile fabrication of multi-component coating via layer deposition of cinnamaldehyde (CIN)-doped chitosan/poly(vinyl alcohol)/fish gelatin (CPF) on PLA surfaces. Different PLA/CPF ratios (100:0, 77.5:22.5, 55:45, 32.5:67.5, and 0:100) were tested, whereas the PLA55:CPF45 was selected for loading of CIN. The surface and morphology analyses of the bilayers verify that CPF layers are successfully coated on the PLA surfaces. This design improved the mechanical strength and water barrier of CPF films and simultaneously enhanced the ductility of PLA films. By deposition of CIN-doped CPF layer on a PLA substrate, the oxygen permeability decreased from 28.92 to 0.238 cm3 mm/m2 day bar, approximately 122 times lower than that of bare PLA. CIN loadings in the CPF layer endowed bilayer films with antioxidant/antimicrobial activity.