Large Repertoire Research Articles

Vocal repertoire of Azure-winged Magpies (Cyanopica cyanus): A context-associated communication system

Signals within animals’ vocal communication are considered functional referential and context-specific. Even in the absence of the context, receivers are expected to acquire the information of calls and respond specifically. Whereas the framework was supported by plenty of evidence, its exhaustivity in describing all animal vocalisations has been questioned. Here, we investigated the vocal repertoire of a cooperatively breeding species, Azure-winged Magpie (Cyanopica cyanus), to present evidence for referential signals. The results showed that Azure-winged Magpies had a relatively large vocal repertoire, consisting of twelve distinct calls. These calls were associated with the context including movement, begging for food, contact, vigilance against predators, etc. However, even the predator-specific alarm calls would induce various responses of receivers. This implies that multiple pieces of information are involved in the vocalisation, which could be utilised by the receiver to select an appropriate response based on the surroundings. Our study gives a detailed description of the context and function of the vocal repertoire in Azure-winged Magpies, laying the foundation for further investigation on the developmental mechanisms of bird vocalisations. This study also suggests that the referential signals of animal vocalisations may not be limited to the context-specific responses of receivers and need to be discussed from a broader perspective.

Characterization of Motor Unit Firing and Twitch Properties for Decoding Musculoskeletal Force in the Human Ankle Joint In Vivo.

Understanding how motor units (MUs) contribute to skeletal mechanical force is crucial for unraveling the underlying mechanism of human movement. Alterations in MU firing, contractile and force-generating properties emerge in response to physical training, ageing or injury. However, how changes in MU firing and twitch properties dictate skeletal muscle force generation in healthy and impaired individuals remains an open question. In this work, we present a MU-specific approach to identify firing and twitch properties of MU samples and employ them to decode musculoskeletal function in vivo. First, MU firing events were decomposed offline from high-density electromyography (EMG) of six lower leg muscles involved in ankle plantar-dorsi flexion.We characterized their twitch responses based on the statistical distributions of their firing properties and employed them to compute MU-specific activation dynamics. Subsequently, we decoded ankle joint moments by linking our framework to a subject-specific musculoskeletal model. We validated our approach at different ankle positions and levels of activation and compared it with traditional EMG-driven models. Our proposed MU-specific formulation achieves higher generalization across conditions than the EMG-driven models, with significantly lower coefficients of variation in torque predictions. Furthermore, our approach shows distinct neural strategies across a large repertoire of contractile conditions in different muscles. Our proposed approach may open new avenues for characterizing the relationship between MU firing and twitch properties and their influence on force capacity. This can facilitate the development of targeted rehabilitation strategies tailored to individuals with specific neuromuscular conditions.

Recording from Fly Olfactory Sensilla.

Olfactory systems detect and discriminate an enormous diversity of volatile environmental stimuli and provide important paradigms to investigate how sensory cues are represented in the brain. Key stimulus-coding events occur in peripheral olfactory sensory neurons, which typically express a single olfactory receptor-from a large repertoire encoded in the genome-with a defined ligand-response profile. These receptors convert odor ligand recognition into spatial and temporal patterns of neural activity that are transmitted to, and interpreted in, central brain regions. Drosophila provides an attractive model to study olfactory coding because it possesses a relatively simple peripheral olfactory system that displays many organizational parallels to those of vertebrates. Moreover, nearly all olfactory sensory neurons have been molecularly characterized and are accessible for physiological analysis, as they are exposed on the surface of sensory organs (antennae and maxillary palps) housed in specialized hairs called sensilla. This protocol describes how to perform recordings of odor-evoked activity from Drosophila olfactory sensilla, covering the basics of sample preparation, setting up the electrophysiology rig, assembling an odor stimulus-delivery device, and data analysis. The methodology can be used to characterize the ligand-recognition properties of most olfactory sensory neurons and the role of olfactory receptors (and other molecular components) in signal transduction.

Generation of a Large Repertoire of Monoclonal Antibodies against Dengue Virus NS1 Antigen and the Development of a Novel NS1 Detection Enzyme-Linked Immunosorbent Assay.

Commercial dengue virus (DENV) nonstructural-1 (NS1) Ag detection immunoassays often perform poorly, particularly in secondary DENV infection. To develop a highly sensitive NS1 ELISA, we generated a large repertoire of anti-DENV NS1 mouse mAbs (n = 95) that falls into 36 mAb classes based on binding specificities. The identified mAb pair, capable of efficiently detecting NS1 from four DENV serotypes in an immunoassay, was selected based on multiparametric analysis. The selected mAbs have subnanomolar affinities for NS1 with recognition sites outside the immunodominant wing domain. The assay was converted to an ELISA kit, which showed higher analytical sensitivity (3-fold to 83-fold) for NS1 from four DENV serotypes than commercial Platelia NS1 ELISA (Bio-Rad Laboratories). Compared to RT-PCR, the developed NS1 ELISA showed 78.57% (66 of 84) sensitivity, whereas Platelia NS1 ELISA showed a sensitivity of 60.71% (51 of 84). In a subgroup of RT-PCR-positive secondary dengue samples, our ELISA showed a sensitivity of 70.18% (40 of 57), whereas Platelia ELISA detected only 47.37% (27 of 57) samples. Furthermore, unlike Platelia ELISA, our test equally detected NS1 from four serotypes; Platelia ELISA performed poorly for the DENV-2 serotype, in which only 8 of 21 (38.10%) samples were detected compared with 17 of 21 (80.95%) in our ELISA. Moreover, our ELISA showed 100% specificity in 342 challenging dengue-negative samples. The large and diverse mAb repertoire generated against DENV NS1 and the appropriate selection of mAbs allowed us to establish an ELISA that can efficiently detect NS1 Ag even in secondary dengue and without serotype level bias.

Electromyography-driven model-based estimation of ankle torque and stiffness during dynamic joint rotations in perturbed and unperturbed conditions

The simultaneous modulation of joint torque and stiffness enables humans to perform large repertoires of movements, while versatilely adapting to external mechanical demands. Multi-muscle force control is key for joint torque and stiffness modulation. However, the inability to directly measure muscle force in the intact moving human prevents understanding how muscle force causally links to joint torque and stiffness. Joint stiffness is predominantly estimated via joint perturbation-based experiments in combination with system identification techniques. However, these techniques provide joint-level stiffness estimations with no causal link to the underlying muscle forces. Moreover, the need for joint perturbations limits the generalizability and applicability to study natural movements. Here, we present an electromyography (EMG)-driven musculoskeletal modeling framework that can be calibrated to match reference joint torque and stiffness profiles simultaneously via a multi-term objective function. EMG-driven models calibrated on <2 s of reference torque and stiffness data could blindly estimate reference profiles across 100 s of data not used for calibration. Model calibrations using an objective function comprising torque and stiffness terms always provided less feasible solutions than an objective function comprising solely a torque term, thereby reducing the space of feasible muscle–tendon parameters. Results also showed the proposed framework’s ability to estimate joint stiffness in unperturbed conditions, while capturing differences against stiffness profiles derived during perturbed conditions. The proposed framework may provide new ways for studying causal relationships between muscle force and joint torque and stiffness during movements in interaction with the environment, with broad implications across biomechanics, rehabilitation and robotics.

‘Tail-dipping’ to drink from an open water source in Cebus imitator (Primates: Cebidae) in a protected area of Costa Rica

Primate species demonstrate high levels of intelligence, innovation, and social learning. These characteristics give rise to a high likelihood of new behaviours occurring and being socially transmitted to other individuals within a group. Capuchin monkeys are group-living and are commonly considered to be among the most intelligent non-ape primates. They exhibit a large repertoire of complex behaviours and have been shown to be capable of innovating to problem solve. However, observations of new behaviours in wild populations are rare in comparison to captive populations. Here we describe Panamanian white-faced capuchins (Cebus imitator) carrying out a behaviour which has not been previously documented in capuchin species and may be related to predator avoidance. This behaviour was video-recorded and to our knowledge is the first record of a capuchin species using tail-dipping behaviour to access an open water source in the wild.

Characterization of the interactome profiling of Mycoplasma fermentans DnaK in cancer cells reveals interference with key cellular pathways.

Chaperone proteins are redundant in nature and, to achieve their function, they bind a large repertoire of client proteins. DnaK is a bacterial chaperone protein that recognizes misfolded and aggregated proteins and drives their folding and intracellular trafficking. Some Mycoplasmas are associated with cancers, and we demonstrated that infection with a strain of Mycoplasma fermentans isolated in our lab promoted lymphoma in a mouse model. Its DnaK is expressed intracellularly in infected cells, it interacts with key proteins to hamper essential pathways related to DNA repair and p53 functions and uninfected cells can take-up extracellular DnaK. We profile here for the first time the eukaryotic proteins interacting with DnaK transiently expressed in five cancer cell lines. A total of 520 eukaryotic proteins were isolated by immunoprecipitation and identified by Liquid Chromatography Mass Spectrometry (LC-MS) analysis. Among the cellular DnaK-binding partners, 49 were shared between the five analyzed cell lines, corroborating the specificity of the interaction of DnaK with these proteins. Enrichment analysis revealed multiple RNA biological processes, DNA repair, chromatin remodeling, DNA conformational changes, protein-DNA complex subunit organization, telomere organization and cell cycle as the most significant ontology terms. This is the first study to show that a bacterial chaperone protein interacts with key eukaryotic components thus suggesting DnaK could become a perturbing hub for the functions of important cellular pathways. Given the close interactions between bacteria and host cells in the local microenvironment, these results provide a foundation for future mechanistic studies on how bacteria interfere with essential cellular processes.

Inducing Singlet Fission in Perylene Thin Films by Molecular Contortion.

Singlet fission occurs only in a limited number of molecules, and expanding the molecular toolbox is necessary for progress. Here, we apply the molecular contortion strategy to tune singlet and triplet energies and observe changes in the excited-state dynamics that are consistent with singlet fission playing a role in thin films of contorted perylene. Perylene is a prototypical molecular chromophore, which does not undergo singlet fission in its planar form from its S1 state. The tuning of the energetics that control singlet fission through molecular contortion can be applied to a large repertoire of established molecular chromophores.

Identification of iron-responsive genes in Proteus vulgaris.

Iron is essential for almost all bacteria, and iron homeostasis is precisely controlled by the ferric uptake regulator (Fur). The Fur regulons have been well characterized in some model bacteria, yet little is known in the common opportunistic pathogen Proteus vulgaris. In this study, Fur regulon and iron-responsive genes in P. vulgaris were mainly defined by in silico and proteomic analyses. The results showed that about 250 potential Fur-regulated operons including 14 transcriptional factors were predicted, while 559 proteins exhibited differential expression in response to iron deficiency, not all being directly regulated by Fur, such as transcriptional factors lexA, recA, narL, and arcA. Collectively, these results demonstrated that Fur functioned as a global regulatory protein to repress or activate expression of a large repertoire of genes in P. vulgaris; besides, not all the iron-responsive genes were directly regulated by Fur, whereas indirectly regulated through other mechanisms such as additional transcriptional regulatory proteins.

Multidrug-Resistant High-Risk Escherichia coli and Klebsiella pneumoniae Clonal Lineages Occur in Black-Headed Gulls from Two Conservation Islands in Germany.

Multidrug-resistant (MDR) Enterobacterales, including extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae, not only emerge in healthcare settings but also in other habitats, such as livestock and wildlife. The spread of these pathogens, which often combine resistance with high-level virulence, is a growing problem, as infections have become increasingly difficult to treat. Here, we investigated the occurrence of ESBL-producing E. coli and K. pneumoniae in fecal samples from two black-headed gull colonies breeding on two nature conservation islands in Western Pomerania, Germany. In addition to cloacal samples from adult birds (n = 211) and their nestlings (n = 99) during the 2021 breeding season, collective fecal samples (n = 29) were obtained. All samples were screened for ESBL producers, which were then subjected to whole-genome sequencing. We found a total of 12 ESBL-producing E. coli and K. pneumoniae consisting of 11 E. coli and 1 K. pneumoniae, and including the international high-risk E. coli sequence types (ST)131, ST38, and ST58. Eight of the investigated strains had a MDR genotype and carried a large repertoire of virulence-associated genes, including the pap operon, which is important for urinary tract infections. In addition, we identified many genes associated with adherence, biofilm formation, iron uptake, and toxin production. Finally, our analysis revealed the close phylogenetic relationship of ST38 strains with genomes originating from human sources, underlining their zoonotic and pathogenic character. This study highlights the importance of the One Health approach, and thus the interdependence between human and animal health and their surrounding environment.

Associations between behavioral flexibility and health behavior in cardiac patients in the Do CHANGE trials.

Health behaviors (e.g., physical inactivity, poor diet) are associated with poor prognosis and mortality in cardiac patients. Changing these behaviors is challenging and only a minority of patients succeeds in this endeavor. Studies show that behavioral flexibility (defined as responding less habitually to stimuli and having a large behavioral repertoire) is a potentially important facilitator of health behaviors. The current study examines the association between behavioral flexibility and health behaviors (health responsibility, physical activity, nutrition, spiritual growth, interpersonal relations, stress management) in patients with cardiac disease. A total of 387 patients with stable cardiac disease were recruited as part of the Do Cardiac Health: Advanced New Generation Ecosystem Trials. Behavioral flexibility (via the Do Something Different Questionnaire) was assessed at baseline and health behaviors including the above described six domains (HPLP-II at baseline, at 3 months, and at 6 months. Linear mixed models were used to answer the research question. The sample consisted of predominantly male patients (n = 274/71%) with a mean age of 62 (SD = 10), diagnosed with hypertension (n = 198/51%), coronary artery disease (n = 114/30%), and/or heart failure (n = 75/19%). The analyses revealed a positive but small (r = .106-.270, B = .00-.31) association between behavioral flexibility and all self-reported health behaviors over time. This is the first study to examine the association between behavioral flexibility and health behaviors in cardiac patients. Current results showed a positive association between behavioral flexibility and health behaviors over time. More research is needed to further examine causal effects of behavioral flexibility on health behaviors. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Experiences and perception of character strengths among patients with breast cancer in China: a qualitative study

ObjectiveTo explore the patients’ experiences on character strengths that Chinese patients experience after the diagnosis of breast cancer.DesignA qualitative, exploratory study using semistructured interviews based on the patients’ lived experience...

NLR receptor networks in plants.

To fight off diverse pathogens and pests, the plant immune system must recognize these invaders; however, as plant immune receptors evolve to recognize a pathogen, the pathogen often evolves to escape this recognition. Plant-pathogen co-evolution has led to the vast expansion of a family of intracellular immune receptors-nucleotide-binding domain and leucine-rich repeat proteins (NLRs). When an NLR receptor recognizes a pathogen ligand, it activates immune signaling and thus initiates defense responses. However, in contrast with the model of NLRs acting individually to activate resistance, an emerging paradigm holds that plants have complex receptor networks where the large repertoire of functionally specialized NLRs function together to act against the large repertoire of rapidly evolving pathogen effectors. In this article, we highlight key aspects of immune receptor networks in plant NLR biology and discuss NLR network architecture, the advantages of this receptor network system, and the evolution of the NLR network in asterid plants.

Light, chromatin, action: nuclear events regulating light signaling in Arabidopsis.

The plant nucleus provides a major hub for environmental signal integration at the chromatin level. Multiple light signaling pathways operate and exchange information by regulating a large repertoire of gene targets that shape plant responses to a changing environment. In addition to the established role of transcription factors in triggering photoregulated changes in gene expression, there are eminent reports on the significance of chromatin regulators and nuclear scaffold dynamics in promoting light-induced plant responses. Here, we report and discuss recent advances in chromatin-regulatory mechanisms modulating plant architecture and development in response to light, including the molecular and physiological roles of key modifications such as DNA, RNA and histone methylation, and/or acetylation. The significance of the formation of biomolecular condensates of key light signaling components is discussed and potential applications to agricultural practices overviewed.

A brainstem map for visceral sensations

The nervous system uses various coding strategies to process sensory inputs. For example, the olfactory system uses large receptor repertoires and is wired to recognize diverse odours, whereas the visual system provides high acuity of object position, form and movement1–5. Compared to external sensory systems, principles that underlie sensory processing by the interoceptive nervous system remain poorly defined. Here we developed a two-photon calcium imaging preparation to understand internal organ representations in the nucleus of the solitary tract (NTS), a sensory gateway in the brainstem that receives vagal and other inputs from the body. Focusing on gut and upper airway stimuli, we observed that individual NTS neurons are tuned to detect signals from particular organs and are topographically organized on the basis of body position. Moreover, some mechanosensory and chemosensory inputs from the same organ converge centrally. Sensory inputs engage specific NTS domains with defined locations, each containing heterogeneous cell types. Spatial representations of different organs are further sharpened in the NTS beyond what is achieved by vagal axon sorting alone, as blockade of brainstem inhibition broadens neural tuning and disorganizes visceral representations. These findings reveal basic organizational features used by the brain to process interoceptive inputs.

Displaced Selves: Older African Adults in Forced Migration

Abstract Ageing as a refugee in an unsettled life situation increases the need for identity management due to dramatic life changes. This qualitative study, influenced by phenomenology, focuses on the stories of older adults in protracted intra-African refugee situations and the continuity and discontinuity of their identities. In line with identity process theory, we portray identities as situationally accomplished through the interplay of how one defines oneself internally and how others define one from the outside. The data, analysed by using abductive thematic analysis, consist of five semi-structured interviews with refugees in protracted refugee situations in Nairobi. We argue that older age combined with protracted migratory experiences resulted in the study participants possessing a wide array of experiences, including many losses. These, including their pre-migratory experiences, formed a large repertoire of intra-psychic, interpersonal and intergroup coping strategies to rely on when reworking their identities.

This Month in Anesthesiology

This Month in Anesthesiology

A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters

Bacteria of the phylum Acidobacteria are one of the most abundant groups across soil ecosystems, yet they are represented by comparatively few sequenced genomes, leaving gaps in our understanding of their metabolic diversity. Recently, genomes of Acidobacteria species with unusually large repertoires of biosynthetic gene clusters (BGCs) were reconstructed from grassland soil metagenomes, but the degree to which species with this trait are widespread is still unknown. To investigate this, we assembled 46 metagenome-assembled genomes recovered from permanently saturated organic-rich soils of a vernal (spring) pool ecosystem in Northern California. We obtained high and medium-quality draft genomes for three novel species from Candidatus Angelobacter (a proposed subdivision 1 Acidobacterial genus), a genus that is genomically enriched in genes for specialized metabolite biosynthesis. Acidobacteria were particularly abundant in the vernal pool sediments, and a Ca. Angelobacter species was the most abundant bacterial species detected in some samples. We identified numerous diverse biosynthetic gene clusters in these genomes, and also in five additional genomes from other publicly available soil metagenomes for other related Ca. Angelobacter species. Metabolic analysis indicates that Ca. Angelobacter likely are aerobes that ferment organic carbon, with potential to contribute to carbon compound turnover in soils. Using metatranscriptomics, we identified in situ metabolic activity and expression of specialized metabolic traits for two species from this genus. In conclusion, we expand genomic sampling of the uncultivated Ca. Angelobacter, and show that they represent common and sometimes highly abundant members of dry and saturated soil communities, with a high degree of capacity for synthesis of diverse specialized metabolites.

Epitopes mapped onto SARS-CoV-2 receptor-binding motif by five distinct human neutralising antibodies

ABSTRACT An Immune complex formation is mediated through intermolecular interactions between proteins and antigens. In the present study, in silico methods were used to locate, identify and provide valuable structural and energetic information that describes the dominant and energetically stabilising interactions found at the epitope-paratope interface of selected human antibodies, isolated from convalescent COVID-19 patients. These antibodies are directed toward the SARS-CoV-2 receptor-binding domain (RBD, i.e. residues 333–526). The analyzed immune complexes have shown strong in vitro neutralising activity against SARS-CoV-2 infection by targeting the receptor-binding motif (RBM, i.e. residues 437–508) within the viral SARS-CoV-2 spike RBD. Our data shows that residues Tyr449, Leu455, Phe456, Ala475, Phe486, Gln493, Gln498, Asn501, Gly502 and Tyr505 exhibit strong epitope capability. On another hand, the analyzed paratopes show a large repertoire of residues to recognise RBM epitopes by both the VH and VL chains within complementary determining regions (CDR), which would make it difficult to bind RBM to the human ACE2 cell receptor by residue interactions competition. Undoubtedly, our findings provide valuable structural and energetic information to those previously obtained through experimental crystallographic studies, and provides new insights about the binding interface that could provide a structural basis for rational epitope-based vaccinology.

Evolution of the nitric oxide synthase family in vertebrates and novel insights in gill development.

Nitric oxide (NO) is an ancestral key signalling molecule essential for life and has enormous versatility in biological systems, including cardiovascular homeostasis, neurotransmission and immunity. Although our knowledge of NO synthases (Nos), the enzymes that synthesize NO in vivo, is substantial, the origin of a large and diversified repertoire of nos gene orthologues in fishes with respect to tetrapods remains a puzzle. The recent identification of nos3 in the ray-finned fish spotted gar, which was considered lost in this lineage, changed this perspective. This finding prompted us to explore nos gene evolution, surveying vertebrate species representing key evolutionary nodes. This study provides noteworthy findings: first, nos2 experienced several lineage-specific gene duplications and losses. Second, nos3 was found to be lost independently in two different teleost lineages, Elopomorpha and Clupeocephala. Third, the expression of at least one nos paralogue in the gills of developing shark, bichir, sturgeon, and gar, but not in lamprey, suggests that nos expression in this organ may have arisen in the last common ancestor of gnathostomes. These results provide a framework for continuing research on nos genes' roles, highlighting subfunctionalization and reciprocal loss of function that occurred in different lineages during vertebrate genome duplications.