Broad Functional Repertoire Research Articles

Insights Gained from Including People in Our Models of Nature and Modes of Science.

Across the natural sciences, humans are typically conceptualized as external disruptors of nature rather than adaptable components of it. Historical evidence, however, challenges this dominant schema. Here, we describe the broad repertoire of ecological functions performed by people in place-based societies across the Pacific Ocean over millennia, illustrating their roles as ecosystem engineers, dispersers, bioturbators, nutrient cyclers, predators, and herbivores. By considering the reciprocal relationships between people and the ecosystems within which they are embedded, evidence of humanity's ability to experiment, learn, adapt, innovate, and sustain diverse and resilient social-ecological relationships emerges. Therefore, recognizing people as inseparable components of marine ecosystems and their millennia of engagement with coastal ocean spaces is critical to both understanding marine ecosystems and devising resilient and equitable ocean policies.

Investigating the impact of external load on muscle synergies during bipedal squats

PurposeA broad functional movement repertoire is crucial for engaging in physical activity and reducing the risk of injury, both of which are central aspects of lifelong health. As a fundamental exercise in both recreational and rehabilitative training regimes, the bipedal squat (SQBp) incorporates many everyday movement patterns. Crucially, SQBp can only be considered functional if the practitioner can meet the coordinative demands. Many factors affect coordinative aspects of an exercise, most notably external load. Since compound movements are assumed to be organized in a synergistic manner, we employed muscle synergy analysis to examine differences in muscle synergy properties between various external load levels during SQBp.MethodsTen healthy male recreational athletes were enrolled in the present study. Each participant performed three sets of ten SQBp on a smith machine at three submaximal load levels (50%, 62.5%, and 75% of 3 repetition maximum) across three non-consecutive days. Muscle activity was recorded from 12 prime movers of SQBp by way of electromyography (EMG). Muscle synergies were analyzed in terms of temporal activation patterns, i.e., waveform, as well as the relative input of each muscle into individual synergies, i.e., weight contribution.ResultsWaveforms of muscle synergies did not differ between loads. Weight contributions showed significant differences between load levels, albeit only for the gastrocnemius muscle in a single synergy.ConclusionTaken together, our results imply mostly stable spatiotemporal composition of muscle activity during SQBp, underlining the importance of technical competence during compound movement performance in athletic and rehabilitative settings.

Distinctive features of Zaprionus indianus hemocyte differentiation and function revealed by transcriptomic analysis.

Insects have specialized cell types that participate in the elimination of parasites, for instance, the lamellocytes of the broadly studied species Drosophila melanogaster. Other drosophilids, such as Drosophila ananassae and the invasive Zaprionus indianus, have multinucleated giant hemocytes, a syncytium of blood cells that participate in the encapsulation of the eggs or larvae of parasitoid wasps. These cells can be formed by the fusion of hemocytes in circulation or originate from the lymph gland. Their ultrastructure highly resembles that of the mammalian megakaryocytes. Morphological, protein expressional, and functional features of blood cells were revealed using epifluorescence and confocal microscopy. The respective hemocyte subpopulations were identified using monoclonal antibodies in indirect immunofluorescence assays. Fluorescein isothiocyanate (FITC)-labeled Escherichia coli bacteria were used in phagocytosis tests. Gene expression analysis was performed following mRNA sequencing of blood cells. D. ananassae and Z. indianus encapsulate foreign particles with the involvement of multinucleated giant hemocytes and mount a highly efficient immune response against parasitoid wasps. Morphological, protein expressional, and functional assays of Z. indianus blood cells suggested that these cells could be derived from large plasmatocytes, a unique cell type developing specifically after parasitoid wasp infection. Transcriptomic analysis of blood cells, isolated from naïve and wasp-infected Z. indianus larvae, revealed several differentially expressed genes involved in signal transduction, cell movements, encapsulation of foreign targets, energy production, and melanization, suggesting their role in the anti-parasitoid response. A large number of genes that encode proteins associated with coagulation and wound healing, such as phenoloxidase activity factor-like proteins, fibrinogen-related proteins, lectins, and proteins involved in the differentiation and function of platelets, were constitutively expressed. The remarkable ultrastructural similarities between giant hemocytes and mammalian megakaryocytes, and presence of platelets, and giant cell-derived anucleated fragments at wound sites hint at the involvement of this cell subpopulation in wound healing processes, in addition to participation in the encapsulation reaction. Our observations provide insights into the broad repertoire of blood cell functions required for efficient defense reactions to maintain the homeostasis of the organism. The analysis of the differentiation and function of multinucleated giant hemocytes gives an insight into the diversification of the immune mechanisms.

PTBP1 promotes hematopoietic stem cell maintenance and red blood cell development by ensuring sufficient availability of ribosomal constituents.

Ribosomopathies constitute a range of disorders associated with defective protein synthesis mainly affecting hematopoietic stem cells (HSCs) and erythroid development. Here, we demonstrate that deletion of poly-pyrimidine-tract-binding protein 1 (PTBP1) in the hematopoietic compartment leads to the development of a ribosomopathy-like condition. Specifically, loss of PTBP1 is associated with decreases in HSC self-renewal, erythroid differentiation, and protein synthesis. Consistent with its function as a splicing regulator, PTBP1 deficiency results in splicing defects in hundreds of genes, and we demonstrate that the up-regulation of a specific isoform of CDC42 partly mimics the protein-synthesis defect associated with loss of PTBP1. Furthermore, PTBP1 deficiency is associated with a marked defect in ribosome biogenesis and a selective reduction in the translation of mRNAs encoding ribosomal proteins. Collectively, this work identifies PTBP1 as a key integrator of ribosomal functions and highlights the broad functional repertoire of RNA-binding proteins.

Tumor-Associated Macrophages and Their Functional Transformation in the Hypoxic Tumor Microenvironment.

Tumor-associated macrophages (TAMs) are some of the most abundant immune cells within tumors and perform a broad repertoire of functions via diverse phenotypes. On the basis of their functional differences in tumor growth, TAMs are usually categorized into two subsets of M1 and M2. It is well established that the tumor microenvironment (TME) is characterized by hypoxia along with tumor progression. TAMs adopt an M1-like pro-inflammatory phenotype at the early phases of oncogenesis and mediate immune response that inhibits tumor growth. As tumors progress, anabatic hypoxia of the TME gradually induces the M2-like functional transformation of TAMs by means of direct effects, metabolic influence, lactic acidosis, angiogenesis, remodeled stroma, and then urges them to participate in immunosuppression, angiogenesis and other tumor-supporting procedure. Therefore, thorough comprehension of internal mechanism of this TAM functional transformation in the hypoxic TME is of the essence, and might provide some novel insights in hypoxic tumor immunotherapeutic strategies.

Increased Resting-State Interhemispheric Functional Connectivity of Posterior Superior Temporal Gyrus and Posterior Cingulate Cortex in Congenital Amusia.

Interhemispheric connectivity of the two cerebral hemispheres is crucial for a broad repertoire of cognitive functions including music and language. Congenital amusia has been reported as a neurodevelopment disorder characterized by impaired music perception and production. However, little is known about the characteristics of the interhemispheric functional connectivity (FC) in amusia. In the present study, we used a newly developed voxel-mirrored homotopic connectivity (VMHC) method to investigate the interhemispheric FC of the whole brain in amusia at resting-state. Thirty amusics and 29 matched participants underwent a resting-state functional magnetic resonance imaging (fMRI) scanning. An automated VMHC approach was used to analyze the fMRI data. Compared to the control group, amusics showed increased VMHC within the posterior part of the default mode network (DMN) mainly in the posterior superior temporal gyrus (pSTG) and posterior cingulate cortex (PCC). Correlation analyses revealed negative correlations between the VMHC value in pSTG/PCC and the music perception ability among amusics. Further ROC analyses showed that the VMHC value of pSTG/PCC showed a good sensibility/specificity to differentiate the amusics from the controls. These findings provide a new perspective for understanding the neural basis of congenital amusia and imply the immature state of DMN may be a credible neural marker of amusia.

Biophysical Characterization of Interaction between E. coli Alanyl-tRNA Synethase with its Promoter DNA.

Aminoacyl-tRNA Synthetases (aaRSs) are well known for their role in the translation process. Lately investigators have discovered that this family of enzymes are also capable of executing a broad repertoire of functions that not only impact protein synthesis, but extend to a number of other activities. Till date, transcriptional regulation has so far only been described in E. coli Alanyl-tRNA synthetase and it was demonstrated that alaRS binds specifically to the palindromic DNA sequence flanking the gene's transcriptional start site and thereby regulating its own transcription. In the present study, we have characterized some of the features of the alaRS-DNA binding using various biophysical techniques. To understand the role of full length protein and oligomerization of alaRS in promoter DNA binding, two mutants were constructed, namely, N700 (a monomer, containing the N-terminal aminoacylation domain but without the C-terminal part) and G674D (previously demonstrated to form full-length monomer). Protein-DNA binding study using fluorescence spectroscopy, analytical ultracentrifugation, Isothermal Titration Calorimetry was conducted. Sedimentation equilibrium studies clearly demonstrated that monomeric variants were unable to bind promoter DNA. Isothermal Calorimetry (ITC) experiment was employed for further characterization of wild type alaRS-DNA interaction. It was observed that full length E. coli Alanyl-tRNA synthetase binds specifically with its promoter DNA and forms a dimer of dimers. On the other hand the two mutant variants were unable to bind with the DNA. In this study it was concluded that full length E. coli Alanyl-tRNA synthetase undergoes a conformational change in presence of its promoter DNA leading to formation of higher order structures. However, the exact mechanism behind this binding is currently unknown and beyond the scope of this study.

Strategies to Target ISG15 and USP18 Toward Therapeutic Applications.

The interferon (IFN)-stimulated gene product 15 (ISG15) represents an ubiquitin-like protein (Ubl), which in a process termed ISGylation can be covalently linked to target substrates via a cascade of E1, E2, and E3 enzymes. Furthermore, ISG15 exerts functions in its free form both, as an intracellular and as a secreted protein. In agreement with its role as a type I IFN effector, most functions of ISG15 and ISGylation are linked to the anti-pathogenic response. However, also key roles in other cellular processes such as protein translation, cytoskeleton dynamics, exosome secretion, autophagy or genome stability and cancer were described. Ubiquitin-specific protease 18 (USP18) constitutes the major ISG15 specific protease which counteracts ISG15 conjugation. Remarkably, USP18 also functions as a critical negative regulator of the IFN response irrespective of its enzymatic activity. Concordantly, lack of USP18 function causes fatal interferonopathies in humans and mice. The negative regulatory function of USP18 in IFN signaling is regulated by various protein–protein interactions and its stability is controlled via proteasomal degradation. The broad repertoire of physiological functions and regulation of ISG15 and USP18 offers a variety of potential intervention strategies which might be of therapeutic use. Due to the high mutation rates of pathogens which are often species specific and constantly give rise to a variety of immune evasion mechanisms, immune effector systems are under constant evolutionarily pressure. Therefore, it is not surprising that considerable differences in ISG15 with respect to function and sequence exist even among closely related species. Hence, it is essential to thoroughly evaluate the translational potential of results obtained in model organisms especially for therapeutic strategies. This review covers existing and conceptual assay systems to target and identify modulators of ISG15, ISGylation, USP18 function, and protein–protein interactions within this context. Strategies comprise mouse models for translational perspectives, cell-based and biochemical assays as well as chemical probes.

The Role of Noncoding RNAs in Double-Strand Break Repair.

Genome stability is constantly threatened by DNA lesions generated by different environmental factors as well as endogenous processes. If not properly and timely repaired, damaged DNA can lead to mutations or chromosomal rearrangements, well-known reasons for genetic diseases or cancer in mammals, or growth abnormalities and/or sterility in plants. To prevent deleterious consequences of DNA damage, a sophisticated system termed DNA damage response (DDR) detects DNA lesions and initiates DNA repair processes. In addition to many well-studied canonical proteins involved in this process, noncoding RNA (ncRNA) molecules have recently been discovered as important regulators of the DDR pathway, extending the broad functional repertoire of ncRNAs to the maintenance of genome stability. These ncRNAs are mainly connected with double-strand breaks (DSBs), the most dangerous type of DNA lesions. The possibility to intentionally generate site-specific DSBs in the genome with endonucleases constitutes a powerful tool to study, in vivo, how DSBs are processed and how ncRNAs participate in this crucial event. In this review, we will summarize studies reporting the different roles of ncRNAs in DSB repair and discuss how genome editing approaches, especially CRISPR/Cas systems, can assist DNA repair studies. We will summarize knowledge concerning the functional significance of ncRNAs in DNA repair and their contribution to genome stability and integrity, with a focus on plants.

Sequence Versus Composition: What Prescribes IDP Biophysical Properties?

Intrinsically disordered proteins (IDPs) represent a distinct class of proteins and are distinguished from globular proteins by conformational plasticity, high evolvability and a broad functional repertoire. Some of their properties are reminiscent of early proteins, but their abundance in eukaryotes, functional properties and compositional bias suggest that IDPs appeared at later evolutionary stages. The spectrum of IDP properties and their determinants are still not well defined. This study compares rudimentary physicochemical properties of IDPs and globular proteins using bioinformatic analysis on the level of their native sequences and random sequence permutations, addressing the contributions of composition versus sequence as determinants of the properties. IDPs have, on average, lower predicted secondary structure contents and aggregation propensities and biased amino acid compositions. However, our study shows that IDPs exhibit a broad range of these properties. Induced fold IDPs exhibit very similar compositions and secondary structure/aggregation propensities to globular proteins, and can be distinguished from unfoldable IDPs based on analysis of these sequence properties. While amino acid composition seems to be a major determinant of aggregation and secondary structure propensities, sequence randomization does not result in dramatic changes to these properties, but for both IDPs and globular proteins seems to fine-tune the tradeoff between folding and aggregation.

Sodium channels.

In 2000, with the completion of the human genome project, nine related channels were found to comprise the complete voltage-gated sodium gene family and they were renamed NaV1.1–NaV1.9. This millennial event reflected the extraordinary impact of molecular genetics on our understanding of electrical signalling in the nervous system. In this review, studies of animal electricity from the time of Galvani to the present day are described. The seminal experiments and models of Hodgkin and Huxley coupled with the discovery of the structure of DNA, the genetic code and the application of molecular genetics have resulted in an appreciation of the extraordinary diversity of sodium channels and their surprisingly broad repertoire of functions. In the present era, unsuspected roles for sodium channels in a huge range of pathologies have become apparent.

A drug development perspective on targeting tumor-associated myeloid cells.

Despite decades of research, cancer remains a devastating disease and new treatment options are needed. Today cancer is acknowledged as a multifactorial disease not only comprising of aberrant tumor cells but also the associated stroma including tumor vasculature, fibrotic plaques, and immune cells that interact in a complex heterotypic interplay. Myeloid cells represent one of the most abundant immune cell population within the tumor stroma and are equipped with a broad functional repertoire that promotes tumor growth by suppressing cytotoxic T cell activity, stimulating neoangiogenesis and tissue remodeling. Therefore, myeloid cells have become an attractive target for pharmacological intervention. In this review, we summarize the pharmacological approaches to therapeutically target tumor-associated myeloid cells with a focus on advanced programs that are clinically evaluated. In addition, for each therapeutic strategy, the preclinical rationale as well as advantages and challenges from a drug development perspective are discussed.

KATANIN 1 Is Essential for Embryogenesis and Seed Formation in Arabidopsis.

Cytoskeletal remodeling has a fundamental role, especially during transitional developmental stages when cells rapidly adopt new forms and roles, like gametogenesis, fertilization and concomitant embryogenesis and seed formation. KATANIN 1, a microtubule severing protein, fulfills a major regulatory mechanism of dynamic microtubule turnover in eukaryotes. Herein, we show that three well-established KATANIN 1 mutants, fra2, lue1 and ktn1-2 collectively display lower fertility and seed set in Arabidopsis. These lower fertility and seed set rates of fra2, lue1 and ktn1-2 mutants were correlated to abnormalities in the development of embryo proper and seed. Such phenotypes were rescued by transformation of mutants with functional pKTN1::GFP:KTN1 construct. This study significantly expands the already broad functional repertoire of KATANIN 1 and unravels its new role in embryo and seed development. Thus, KATANIN 1 significantly contributes to the fertility and proper embryo and seed formation in Arabidopsis.

Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life.

Recent years witnessed increased interest in intrinsically disordered proteins and regions. These proteins and regions are abundant and possess unique structural features and a broad functional repertoire that complements ordered proteins. However, modern studies on the abundance and functions of intrinsically disordered proteins and regions are relatively limited in size and scope of their analysis. To fill this gap, we performed a broad and detailed computational analysis of over 6 million proteins from 59 archaea, 471 bacterial, 110 eukaryotic and 325 viral proteomes. We used arguably more accurate consensus-based disorder predictions, and for the first time comprehensively characterized intrinsic disorder at proteomic and protein levels from all significant perspectives, including abundance, cellular localization, functional roles, evolution, and impact on structural coverage. We show that intrinsic disorder is more abundant and has a unique profile in eukaryotes. We map disorder into archaea, bacterial and eukaryotic cells, and demonstrate that it is preferentially located in some cellular compartments. Functional analysis that considers over 1,200 annotations shows that certain functions are exclusively implemented by intrinsically disordered proteins and regions, and that some of them are specific to certain domains of life. We reveal that disordered regions are often targets for various post-translational modifications, but primarily in the eukaryotes and viruses. Using a phylogenetic tree for 14 eukaryotic and 112 bacterial species, we analyzed relations between disorder, sequence conservation and evolutionary speed. We provide a complete analysis that clearly shows that intrinsic disorder is exceptionally and uniquely abundant in each domain of life.

The FMRFamide-Like Peptide Family in Nematodes.

In the three decades since the FMRFamide peptide was isolated from the mollusk Macrocallista nimbosa, structurally similar peptides sharing a C-terminal RFamide motif have been identified across the animal kingdom. FMRFamide-like peptides (FLPs) represent the largest known family of neuropeptides in invertebrates. In the phylum Nematoda, at least 32 flp-genes are classified, making the FLP system of nematodes unusually complex. The diversity of the nematode FLP complement is most extensively mapped in Caenorhabditis elegans, where over 70 FLPs have been predicted. FLPs have shown to be expressed in the majority of the 302 C. elegans neurons including interneurons, sensory neurons, and motor neurons. The vast expression of FLPs is reflected in the broad functional repertoire of nematode FLP signaling, including neuroendocrine and neuromodulatory effects on locomotory activity, reproduction, feeding, and behavior. In contrast to the many identified nematode FLPs, only few peptides have been assigned a receptor and there is the need to clarify the pathway components and working mechanisms of the FLP signaling network. Here, we review the diversity, distribution, and functions of FLPs in nematodes.

The Roles of Vitamin D in Skeletal Muscle: Form, Function, and Metabolism

Beyond its established role in bone and mineral homeostasis, there is emerging evidence that vitamin D exerts a range of effects in skeletal muscle. Reports of profound muscle weakness and changes in the muscle morphology of adults with vitamin D deficiency have long been described. These reports have been supplemented by numerous trials assessing the impact of vitamin D on muscle strength and mass and falls in predominantly elderly and deficient populations. At a basic level, animal models have confirmed that vitamin D deficiency and congenital aberrations in the vitamin D endocrine system may result in muscle weakness. To explain these effects, some molecular mechanisms by which vitamin D impacts on muscle cell differentiation, intracellular calcium handling, and genomic activity have been elucidated. There are also suggestions that vitamin D alters muscle metabolism, specifically its sensitivity to insulin, which is a pertinent feature in the pathophysiology of insulin resistance and type 2 diabetes. We will review the range of human clinical, animal, and cell studies that address the impact of vitamin D in skeletal muscle, and discuss the controversial issues. This is a vibrant field of research and one that continues to extend the frontiers of knowledge of vitamin D's broad functional repertoire.

Serotonin as an integrator of leech behavior and muscle mechanical performance

The obliquely striated muscle in the leech body wall has a broad functional repertoire; it provides power for both locomotion and suction feeding. It also operates over an unusually high strain range, undergoing up to threefold changes in length. Serotonin (5-HT) may support this functional flexibility, integrating behavior and biomechanics. It can act centrally, promoting motor outputs that drive body wall movements, and peripherally, modulating the mechanical properties of body wall muscle. During isometric contractions 5-HT enhances active force production and reduces resting muscle tone. We therefore hypothesized that 5-HT would increase net work output during the cyclical contractions associated with locomotion and feeding. Longitudinal strains measured during swimming, crawling and feeding were applied to body wall muscle in vitro with the timing and duration of stimulation selected to maximize net work output. The net work output during all simulated behaviors significantly increased in the presence of 100μM 5-HT relative to the 5-HT-free control condition. Without 5-HT the muscle strips could not achieve a net positive work output during simulated swimming. The decrease in passive tension associated with 5-HT may also be important in reducing muscle antagonist work during longitudinal muscle lengthening. The behavioral and mechanical effects of 5-HT during locomotion are clearly complementary, promoting particular behaviors and enhancing muscle performance during those behaviors. Although 5-HT can enhance muscle mechanical performance during simulated feeding, low in vivo activity in serotonergic neurons during feeding may mean that its mechanical role during this behavior is less important than during locomotion.

Neocortical layer 4 as a pluripotent function linearizer

A highly effective kernel-based strategy used in machine learning is to transform the input space into a new "feature" space where nonlinear problems become linear and more readily solvable with efficient linear techniques. We propose that a similar "problem-linearization" strategy is used by the neocortical input layer 4 to reduce the difficulty of learning nonlinear relations between the afferent inputs to a cortical column and its to-be-learned upper layer outputs. The key to this strategy is the presence of broadly tuned feed-forward inhibition in layer 4: it turns local layer 4 domains into functional analogs of radial basis function networks, which are known for their universal function approximation capabilities. With the use of a computational model of layer 4 with feed-forward inhibition and Hebbian afferent connections, self-organized on natural images to closely match structural and functional properties of layer 4 of the cat primary visual cortex, we show that such layer-4-like networks have a strong intrinsic tendency to perform input transforms that automatically linearize a broad repertoire of potential nonlinear functions over the afferent inputs. This capacity for pluripotent function linearization, which is highly robust to variations in network parameters, suggests that layer 4 might contribute importantly to sensory information processing as a pluripotent function linearizer, performing such a transform of afferent inputs to a cortical column that makes it possible for neurons in the upper layers of the column to learn and perform their complex functions using primarily linear operations.

The Importance of Stem Cells and Bioengineering in Regenerative Medicine

The field of regenerative medicine is focused on the creation of functional human tissue to either model, repair or replace the damaged body part. This provides promise that in the future scientists will be able to bioengineer human tissue in vitro [1,2] that may allow the identification of novel medicines and has the potential for cell based therapies. If successful, such approaches could have a significant impact on the problem donor organ shortage for transplantation and improve patient treatment and medication. The liver is a fascinating organ, performing many processes necessary for life. In addition to its broad functional repertoire, the liver is the only human organ capable of large scale regeneration. Only 20-30% of healthy liver mass is required liver regeneration. The primary regenerative response of the liver is provided by its principal cell type, the hepatocyte. However when the liver is overloaded or chronically damaged, the hepatocyte response is inhibited, prompting the activation of a resident stem cell population. In both cases, acute and chronic liver injury may result in irreparable loss of human liver function marking the onset of liver disease. Presently the only real treatment strategy for critically failing liver function is organ transplantation. While highly successful, the shortage of donor organs limits its widespread implementation. The generation of liver tissue from a renewable resource therefore holds great promise for the development of extra-corporeal liver support devices and transplantation procedures.

Innovations in Design Through Transformation: A Fundamental Study of Transformation Principles

The act of creating a new product, system, or process is an innovation; the result of excogitation, study and experimentation. It is an inductive and/or deductive process. The inductive process involves studying systems that exist, for example, in nature, patents and products, and inducing from the behavior of these systems elemental features for innovating novel products. The deductive process involves deducing such aspects from hypothetical concepts and situations where systems or products could exist. By the application of a combined inductive and deductive approach, this paper reports on a methodology for the creation of innovative products with a broader functional repertoire than traditional designs. This breed of innovative products is coined as transformers, transforming into different configurations or according to different states. Current design theory lacks a systematic methodology for the creation of products that have the ability to transform. This paper identifies analogies in nature, patents, and products along with hypothesizing the existence of such products in different environments and situations. Transformation design principles are extracted by studying key design features and functional elements that make up a transforming product. These principles are defined and categorized according to their roles in general transformations. The principles and categorizations are then validated and applied to conceptualize transforming products as part of an innovative design process.