Analysing spatial variability in drought sensitivity of rivers using explainable artificial intelligence.

Hydrological drought can have a severe negative impact on aquatic ecosystems and human living standards. Therefore, being able to predict and gain more insights in the spatial variability in drought sensitivity of rivers is of relevance for water managers. The drought sensitivity of a river is in this study represented by four drought metrics, of which three are relative towards the ecological minimal flow. Statistical and machine learning methods were evaluated to predict these metrics for rivers in the Flanders region of Belgium based on catchment characteristics and data on human interferences. XGBoost had the best performance, with an explained variance of 80 % to 90 %. After applying explaining AI on these models, insights were obtained in the spatial variability of the drought metrics. Irrigation is the most important variable, a high percentage of irrigation leads to a higher drought sensitivity. If there are a lot of human interferences, there is a higher drought sensitivity. Many of the observed dependencies can be explained by the differences in soil infiltration capacity and transferability of water for sandy versus clay soils. No clear dependence with the amount of forest or agriculture was observed, implying that the impact of forest and agriculture on the drought sensitivity of a river is complex.

Kinetics and mechanical work done to move the body centre of mass along a curve.

When running on a curve, the lower limbs interact with the ground to redirect the trajectory of the centre of mass of the body (CoM). The goal of this paper is to understand how the trajectory of the CoM and the work done to maintain its movements relative to the surroundings (Wcom) are modified as a function of running speed and radius of curvature. Eleven participants ran at different speeds on a straight line and on circular curves with a 6 m and 18 m curvature. The trajectory of the CoM and Wcom were calculated using force-platforms measuring the ground reaction forces and infrared cameras recording the movements of the pelvis. To follow a circular path, runners overcompensate the rotation of their trajectory during contact phases. The deviation from the circular path increases when the radius of curvature decreases and speed increases. Interestingly, an asymmetry between the inner and outer lower limbs emerges as speed increases. The method to evaluate Wcom on a straight-line was adapted using a referential that rotates at heel strike and remains fixed during the whole step cycle. In an 18 m radius curve and at low speeds on a 6 m radius, Wcom changes little compared to a straight-line run. Whereas at 6 m s-1 on a 6 m radius, Wcom increases by ~25%, due to an augmentation in the work to move the CoM laterally. Understanding these adaptations provides valuable insight for sports sciences, aiding in optimizing training and performance in sports with multidirectional movements.

CysQuant: Simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry.

Protein cysteinyl thiols are susceptible to reduction-oxidation reactions that can influence protein function. Accurate quantification of cysteine oxidation is therefore crucial for decoding protein redox regulation. Here, we present CysQuant, a novel approach for simultaneous quantification of cysteine oxidation degrees and protein abundancies. CysQuant involves light/heavy iodoacetamide isotopologues for differential labeling of reduced and reversibly oxidized cysteines analyzed by data-dependent acquisition (DDA) or data-independent acquisition mass spectrometry (DIA-MS). Using plexDIA with in silico predicted spectral libraries, we quantified an average of 18% cysteine oxidation in Arabidopsis thaliana by DIA-MS, including a subset of highly oxidized cysteines forming disulfide bridges in AlphaFold2 predicted structures. Applying CysQuant to Arabidopsis seedlings exposed to excessive light, we successfully quantified the well-established increased reduction of Calvin-Benson cycle enzymes and discovered yet uncharacterized redox-sensitive disulfides in chloroplastic enzymes. Overall, CysQuant is a highly versatile tool for assessing the cysteine modification status that can be widely applied across various mass spectrometry platforms and organisms.

Shift in vacuolar to cytosolic regime of infecting Salmonella from a dual proteome perspective.

By applying dual proteome profiling to Salmonella enterica serovar Typhimurium (S. Typhimurium) encounters with its epithelial host (here, S. Typhimurium infected human HeLa cells), a detailed interdependent and holistic proteomic perspective on host-pathogen interactions over the time course of infection was obtained. Data-independent acquisition (DIA)-based proteomics was found to outperform data-dependent acquisition (DDA) workflows, especially in identifying the downregulated bacterial proteome response during infection progression by permitting quantification of low abundant bacterial proteins at early times of infection when bacterial infection load is low. S. Typhimurium invasion and replication specific proteomic signatures in epithelial cells revealed interdependent host/pathogen specific responses besides pointing to putative novel infection markers and signalling responses, including regulated host proteins associated with Salmonella-modified membranes.

Interactome of Arabidopsis ATG5 Suggests Functions beyond Autophagy.

Autophagy is a catabolic pathway capable of degrading cellular components ranging from individual molecules to organelles. Autophagy helps cells cope with stress by removing superfluous or hazardous material. In a previous work, we demonstrated that transcriptional upregulation of two autophagy-related genes, ATG5 and ATG7, in Arabidopsis thaliana positively affected agronomically important traits: biomass, seed yield, tolerance to pathogens and oxidative stress. Although the occurrence of these traits correlated with enhanced autophagic activity, it is possible that autophagy-independent roles of ATG5 and ATG7 also contributed to the phenotypes. In this study, we employed affinity purification and LC-MS/MS to identify the interactome of wild-type ATG5 and its autophagy-inactive substitution mutant, ATG5K128R Here we present the first interactome of plant ATG5, encompassing not only known autophagy regulators but also stress-response factors, components of the ubiquitin-proteasome system, proteins involved in endomembrane trafficking, and potential partners of the nuclear fraction of ATG5. Furthermore, we discovered post-translational modifications, such as phosphorylation and acetylation present on ATG5 complex components that are likely to play regulatory functions. These results strongly indicate that plant ATG5 complex proteins have roles beyond autophagy itself, opening avenues for further investigations on the complex roles of autophagy in plant growth and stress responses.

Estimation of the impact of combined sewer overflows on surface water quality in a sparsely monitored area.

Combined sewer overflows (CSOs) can have a severe negative, local impact on surface water systems. To assure good ecological surface water quality and drinking water production that meets the demands, the impact of sewer system overflows on the surrounding water bodies for current and future climate conditions needs to be assessed. Typically, integrated, detailed hydrological and hydrodynamic water quantity and quality models are used for this purpose, but often data and computational resource requirements limit their applicability. Therefore, an alternative computationally efficient, integrated water quantity and quality model of sewer systems and their receiving surface waters is proposed to assess the impact of CSOs on surface water quality in a sparsely observed area. A conceptual model approach to estimate CSO discharges is combined with an empirical model for estimating CSO pollutant concentrations based on waste water treatment plant influent observations. Both methods are compared with observations and independent results of established reference methods as to evaluate their performance. The methodology is demonstrated by modelling the current impact of CSOs on the water abstraction area of a major drinking water production centre in Flanders, Belgium. It is concluded that the proposed conceptual models achieve similar results for daily WWTP effluent and CSO frequency, whereby the accumulated CSO volume is similar to more detailed full hydrodynamic models. Further, the estimated pollutant concentrations correspond with another dataset based on high resolution sampled overflows. As a result, the proposed computational efficient method can give insights in the impact of CSOs on the water quality at a catchment level and can be used for planning monitoring campaigns or performing analyses of e.g. the current and future water availability for a data scarce areas.

Modification of the locomotor pattern when deviating from the characteristic heel-to-toe rolling pattern during walking.

PURPOSE: Humans are amongst few animals that step first on the heel, and then roll on the ball of the foot and toes. While this heel-to-toe rolling pattern has been shown to render an energetic advantage during walking, the effect of different foot contact strategies, on the neuromuscular control of adult walking gaits has received less attention. We hypothesised that deviating from heel-to-toe rolling pattern affects the energy transduction and weight acceptance and re-propulsive phases in gait along with the modification of spinal motor activity. METHODS: Ten subjects walked on a treadmill normally, then placed their feet flat on the ground at each step and finally walked on the balls of the feet. RESULTS: Our results show that when participants deviate from heel-to-toe rolling pattern strategy, the mechanical work increases on average 85% higher (F = 15.5; p < 0.001), mainly linked to a lack of propulsion at late stance. This modification of the mechanical power is related to a differential involvement of lumbar and sacral segment activation. Particularly, the delay between the major bursts of activation is on average 65% smaller, as compared to normal walking (F = 43.2; p < 0.001). CONCLUSION: Similar results are observable in walking plantigrade animals, but also at the onset of independent stepping in toddlers, where the heel-to-toe rolling pattern is not yet established. These indications seem to bring arguments to the fact that the rolling of the foot during human locomotion has evolved to optimise gait, following selective pressures from the evolution of bipedal posture.

Mutation of Arabidopsis SME1 and Sm core assembly improves oxidative stress resilience.

Alternative splicing is a key posttranscriptional gene regulatory process, acting in diverse adaptive and basal plant processes. Splicing of precursor-messenger RNA (pre-mRNA) is catalyzed by a dynamic ribonucleoprotein complex, designated the spliceosome. In a suppressor screen, we identified a nonsense mutation in the Smith (Sm) antigen protein SME1 to alleviate photorespiratory H2O2-dependent cell death in catalase deficient plants. Similar attenuation of cell death was observed upon chemical inhibition of the spliceosome, suggesting pre-mRNA splicing inhibition to be responsible for the observed cell death alleviation. Furthermore, the sme1-2 mutants showed increased tolerance to the reactive oxygen species inducing herbicide methyl viologen. Both an mRNA-seq and shotgun proteomic analysis in sme1-2 mutants displayed a constitutive molecular stress response, together with extensive alterations in pre-mRNA splicing of transcripts encoding metabolic enzymes and RNA binding proteins, even under unstressed conditions. Using SME1 as a bait to identify protein interactors, we provide experimental evidence for almost 50 homologs of the mammalian spliceosome-associated protein to reside in the Arabidopsis thaliana spliceosome complexes and propose roles in pre-mRNA splicing for four uncharacterized plant proteins. Furthermore, as for sme1-2, a mutant in the Sm core assembly protein ICLN resulted in a decreased sensitivity to methyl viologen. Taken together, these data show that both a perturbed Sm core composition and assembly results in the activation of a defense response and in enhanced resilience to oxidative stress.

Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures.

Deep learning algorithms such as AlphaFold2 predict three-dimensional protein structure with high confidence. The recent release of more than 200 million structural models provides an unprecedented resource for functional protein annotation. Here, we used AlphaFold2 predicted structures of fifteen plant proteomes to functionally and evolutionary analyze cysteine residues in the plant kingdom. In addition to identification of metal ligands coordinated by cysteine residues, we systematically analyzed cysteine disulfides present in these structural predictions. Our analysis demonstrates most of these predicted disulfides are trustworthy due their high agreement (∼96%) with those present in X-ray and NMR protein structures, their characteristic disulfide stereochemistry, the biased subcellular distribution of their proteins and a higher degree of oxidation of their respective cysteines as measured by proteomics. Adopting an evolutionary perspective, zinc binding sites are increasingly present at the expense of iron-sulfur clusters in plants. Interestingly, disulfide formation is increased in secreted proteins of land plants, likely promoting sequence evolution to adapt to changing environments encountered by plants. In summary, Alphafold2 predicted structural models are a rich source of information for studying the role of cysteines residues in proteins of interest and for protein redox biology in general.

Cysteine thiol-based post-translational modification: What do we know about transcription factors?

Reactive electrophilic species are ubiquitous in plant cells, where they contribute to specific redox-regulated signaling events. Redox signaling is known to modulate gene expression during diverse biological processes, including plant growth, development, and environmental stress responses. Emerging data demonstrates that transcription factors (TFs) are a main target of cysteine thiol-based oxidative post-translational modifications (OxiPTMs), which can alter their transcriptional activity and thereby convey redox information to the nucleus. Here, we review the significant progress that has been made in characterizing cysteine thiol-based OxiPTMs, their biochemical properties, and their functional effects on plant TFs. We discuss the underlying mechanism of redox regulation and its contribution to various physiological processes as well as still outstanding challenges in redox regulation of plant gene expression.

International collaboration to improve physiotherapists' training, Viet Nam.

Problem: Like most low- and middle-income countries, Viet Nam has a scarcity of rehabilitation professionals and lacks training programmes that meet international standards. Approach: In 2018, four Vietnamese medical universities, the Université Catholique de Louvain, the Université Libre de Bruxelles, the Humanity & Inclusion charity and World Physiotherapy agreed to collaborate on strengthening pre-service education for physiotherapists in the country. Local setting: Viet Nam has a favourable environment for nurturing rehabilitation services and education: development funds have been available; government investment is increasing; and rehabilitation education has existed for many decades. Relevant changes: The collaboration resulted in the establishment of: (i) a 4-year, competency-based, entry-level curriculum for physiotherapists (bachelor's degree); (ii) opportunities for continuing professional development; (iii) a 2-year master's programme for physiotherapy lecturers and clinical supervisors; and (iv) a national physiotherapy association. In addition, four students were supported in studying for PhD degrees. Strong collaboration and comprehensive and complementary interventions have laid the foundations for sustainable, high-quality, educational programmes for physiotherapists, which will improve access to, and the standard of, rehabilitation services in Viet Nam, thereby leading to better patient outcomes. Lessons learnt: Curricula for entry-level physiotherapy programmes should be competency-based, be actively managed by national educators and meet international standards while being responsive to local priorities. To strengthen the rehabilitation workforce, educators involved in teaching and supervising training programmes should have the skills and knowledge required. A national professional physiotherapy association should be established to provide continuing professional development for physiotherapists and to take part in international collaborations.

Analysis of ROS-Triggered Changes in the Transcriptome.

RNA sequencing is routinely used for determining transcriptome-wide expression changes during various conditions, including oxidative stress conditions. In this chapter, a basic workflow to determine differentially expressed genes between two conditions of interest is provided. After providing brief guidelines for experimental design, we provide step-by-step instructions for genome alignment of reads and differential expression analysis.

Further clinical and genetic evidence of ASC-1 complex dysfunction in congenital neuromuscular disease.

Transcriptional coregulators modulate the efficiency of transcription factors. Bi-allelic variants in TRIP4 and ASCC1, two genes that encode members of the tetrameric coregulator ASC-1, have recently been associated with congenital bone fractures, hypotonia, and muscular dystrophy in a total of 22 unrelated families. Upon exome sequencing and data repository mining, we identified six new patients with pathogenic homozygous variants in either TRIP4 (n = 4, two novel variants) or ASCC1 (n = 2, one novel variant). The associated clinical findings confirm and extend previous descriptions. Considering all patients reported to date, we provide supporting evidence suggesting that ASCC1-related disease has a more severe phenotype compared to TRIP4-related disorder regarding higher incidence of perinatal bone fractures and shorter survival.

Exploring Posttranslational Modifications with the Plant PTM Viewer.

An increasing numbed and diversity of protein posttranslational modifications are mapped by proteomics. Knowledge of modified protein sites can be of direct relevance to steer downstream functional studies, but such information can be difficult to distill from the numerous individual studies that often report modified sites in supplementary data files. In this chapter, we provide basic instructions and use cases to browse and collect plant protein modifications from over 100 studies in a user-friendly manner with the Plant PTM Viewer. The Plant PTM Viewer ( https://www.psb.ugent.be/PlantPTMViewer ) is a central resource compiling currently 24 modifications types for ten thousands of plant proteins. Next to viewing modifications for a protein of interest, we demonstrate how evolutionary conserved modifications can be retrieved using PTM Blast. In addition, modifications themselves located in a motif or sequence context of interest can be retrieved by PTM search. Altogether, these operations can be performed, are intuitive, and open for non-bioinformatic experts.

Quantifying climate change effects on future forest biomass availability using yield tables improved by mechanistic scaling.

Forests and wood products play a major role in climate change mitigation strategies and the transition from a fossil-based economy to a circular bioeconomy. Accurate estimates of future forest productivity are crucial to predict the carbon sequestration and wood provision potential of forests. Since long, forest managers have used empirical yield tables as a cost-effective and reliable way to predict forest growth. However, recent climate change-induced growth shifts raised doubts about the long-term validity of these yield tables. In this study, we propose a methodology to improve available yield tables of 11 tree species in the Netherlands and Flanders, Belgium. The methodology uses scaling functions derived from climate-sensitive process-based modelling (PBM) that reflect state-of-the-art projections of future growth trends. Combining PBM and stand information from the empirical yield tables for the region of Flanders, we found that for the period 1987-2016 stand productivity has on average increased by 13% compared to 1961-1990. Furthermore, simulations indicate that this positive growth trend is most likely to persist in the coming decades, for all considered species, climate or site conditions. Nonetheless, results showed that local site variability is equally important to consider as the in- or exclusion of the CO2 fertilization effect or different climate projections, when assessing the magnitude of forests' response to climate change. Our projections suggest that incorporating these climate change-related productivity changes lead to a 7% increase in standing stock and a 22% increase in sustainably potentially harvestable woody biomass by 2050. The proposed methodology and resulting estimates of climate-sensitive projections of future woody biomass stocks will facilitate the further incorporation of forests and their products in global and regional strategies for the transition to a climate-smart circular bioeconomy.

Hidden in plain sight: challenges in proteomics detection of small ORF-encoded polypeptides.

Genomic studies of bacteria have long pointed toward widespread prevalence of small open reading frames (sORFs) encoding for short proteins, <100 amino acids in length. Despite the mounting genomic evidence of their robust expression, relatively little progress has been made in their mass spectrometry-based detection and various blanket statements have been used to explain this observed discrepancy. In this study, we provide a large-scale riboproteogenomics investigation of the challenging nature of proteomic detection of such small proteins as informed by conditional translation data. A panel of physiochemical properties alongside recently developed mass spectrometry detectability metrics was interrogated to provide a comprehensive evidence-based assessment of sORF-encoded polypeptide (SEP) detectability. Moreover, a large-scale proteomics and translatomics compendium of proteins produced by Salmonella Typhimurium (S. Typhimurium), a model human pathogen, across a panel of growth conditions is presented and used in support of our in silico SEP detectability analysis. This integrative approach is used to provide a data-driven census of small proteins expressed by S. Typhimurium across growth phases and infection-relevant conditions. Taken together, our study pinpoints current limitations in proteomics-based detection of novel small proteins currently missing from bacterial genome annotations.

Neuromuscular Age-Related Adjustment of Gait When Moving Upwards and Downwards.

Locomotor movements are accommodated to various surface conditions by means of specific locomotor adjustments. This study examined underlying age-related differences in neuromuscular control during level walking and on a positive or negative slope, and during stepping upstairs and downstairs. Ten elderly and eight young adults walked on a treadmill at two different speeds and at three different inclinations (0°, +6°, and -6°). They were also asked to ascend and descend stairs at self-selected speeds. Full body kinematics and surface electromyography of 12 lower-limb muscles were recorded. We compared the intersegmental coordination, muscle activity, and corresponding modifications of spinal motoneuronal output in young and older adults. Despite great similarity between the neuromuscular control of young and older adults, our findings highlight subtle age-related differences in all conditions, potentially reflecting systematic age-related adjustments of the neuromuscular control of locomotion across various support surfaces. The main distinctive feature of walking in older adults is a significantly wider and earlier activation of muscles innervated by the sacral segments. These changes in neuromuscular control are reflected in a reduction or lack of propulsion observed at the end of stance in older adults at different slopes, with the result of a delay in the timing of redirection of the centre-of-mass velocity and of an unanticipated step-to-step transition strategy.

Mechanical work as a (key) determinant of energy cost in human locomotion: recent findings and future directions.

NEW FINDINGS: What is the topic of this review? This narrative review explores past and recent findings on the mechanical determinants of energy cost during human locomotion, obtained by using a mechanical approach based on König's theorem (Fenn's approach). What advances does it highlight? Developments in analytical methods and their applications allow a better understanding of the mechanical-bioenergetic interaction. Recent advances include the determination of 'frictional' internal work; the association between tendon work and apparent efficiency; a better understanding of the role of energy recovery and internal work in pathological gait (amputees, stroke and obesity); and a comprehensive analysis of human locomotion in (simulated) low gravity conditions. ABSTRACT: During locomotion, muscles use metabolic energy to produce mechanical work (in a more or less efficient way), and energetics and mechanics can be considered as two sides of the same coin, the latter being investigated to understand the former. A mechanical approach based on König's theorem (Fenn's approach) has proved to be a useful tool to elucidate the determinants of the energy cost of locomotion (e.g., the pendulum-like model of walking and the bouncing model of running) and has resulted in many advances in this field. During the past 60 years, this approach has been refined and applied to explore the determinants of energy cost and efficiency in a variety of conditions (e.g., low gravity, unsteady speed). This narrative review aims to summarize current knowledge of the role that mechanical work has played in our understanding of energy cost to date, and to underline how recent developments in analytical methods and their applications in specific locomotion modalities (on a gradient, at low gravity and in unsteady conditions) and in pathological gaits (asymmetric gait pathologies, obese subjects and in the elderly) could continue to push this understanding further. The recent in vivo quantification of new aspects that should be included in the assessment of mechanical work (e.g., frictional internal work and elastic contribution) deserves future research that would improve our knowledge of the mechanical-bioenergetic interaction during human locomotion, as well as in sport science and space exploration.