Swimming kinematics of rainbow trout behind a 3×5 cylinder array: a computationally driven experimental approach to understanding fish locomotion.

Fish in the wild often contend with complex flows that are produced by natural and artificial structures. Research into fish interactions with turbulence often investigates metrics such as turbulent kinetic energy (TKE) or fish positional location, with less focus on the specific interactions between vortex organization and body swimming kinematics. Here, we compared the swimming kinematics of rainbow trout (Oncorhynchus mykiss) holding station in flows produced by two different 3×5 cylinder arrays.

Fish couple forecasting with feedback control to chase and capture moving prey.

Predatorprey interactions are fundamental to ecological and evolutionary dynamics. Yet, predicting the outcome of such interactions-whether predators intercept prey or fail to do so-remains a challenge. An emerging hypothesis holds that interception trajectories of diverse predator species can be described by simple feedback control laws that map sensory inputs to motor outputs.

Body length determines flow refuging for rainbow trout (Oncorhynchus mykiss) behind wing dams.

Complex hydrodynamics abound in natural streams, yet the selective pressures these impose upon different size classes of fish are not well understood. Attached vortices are produced by relatively large objects that block freestream flow, which fish routinely utilize for flow refuging. To test how flow refuging and the potential harvesting of energy (as seen in Kármán gaiting) vary across size classes in rainbow trout (Oncorhynchus mykiss; fingerling, 8 cm; parr, 14 cm; adult, 22 cm; n=4 per size class), we used a water flume (4100 l; freestream flow at 65 cm s-1) and created vortices using 45 deg wing dams of varying size (small, 15 cm; medium, 31 cm; large, 48 cm).

Swimming kinematics of rainbow trout behind cylinder arrays: the effect of vortex street periodicity and turbulence kinetic energy.

Unlabelled: Fish in the wild often contend with complex flows that are produced by natural and artificial structures. Research into fish interactions with turbulence often investigates metrics such as turbulence kinetic energy (TKE) or fish positional location, with less attention paid to the specific interactions between vortex organization and body swimming kinematics. Here we compare the swimming kinematics of rainbow trout ( ) holding station in flows produced by two different 3 x 5 cylinder arrays.

Fantastic beasts and how to study them: rethinking experimental animal behavior.

Humans have been trying to understand animal behavior at least since recorded history. Recent rapid development of new technologies has allowed us to make significant progress in understanding the physiological and molecular mechanisms underlying behavior, a key goal of neuroethology. However, there is a tradeoff when studying animal behavior and its underlying biological mechanisms: common behavior protocols in the laboratory are designed to be replicable and controlled, but they often fail to encompass the variability and breadth of natural behavior.

An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria.

Regulation of CO fixation in cyanobacteria is important both for the organism and global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a distinct ATP-sensing mechanism, where a drop in ATP level allows SeXPK to divert precursors of the RuBisCO substrate away from the Calvin-Benson-Bassham cycle. Deleting the SeXPK gene increased CO fixation particularly during light-dark transitions.

Effects of n-butanol production on metabolism and the photosystem in Synecococcus elongatus PCC 7942 based on metabolic flux and target proteome analyses.

Although n-butanol (BuOH) is an ideal fuel because of its superior physical properties, it has toxicity to microbes. Previously, a Synechococcus elongatus PCC 7942 derivative strain that produces BuOH from CO was developed by introducing six heterologous genes (BUOH-SE strain). To identify the bottleneck in BuOH production, the effects of BuOH production and its toxicity on central metabolism and the photosystem were investigated.

Subtyping of major SARS-CoV-2 variants reveals different transmission dynamics based on 10 million genomes.

SARS-CoV-2 continues to evolve, causing waves of the pandemic. Up to May 2022, 10 million genome sequences have accumulated, which are classified into five major variants of concern. With the growing number of sequenced genomes, analysis of the big dataset has become increasingly challenging.

SARS-CoV-2 N protein mediates intercellular nucleic acid dispersion, a feature reduced in Omicron.

The coronavirus nucleocapsid (N) protein is known to bind to nucleic acids and facilitate viral genome encapsulation. Here we report that the N protein can mediate RNA or DNA entering neighboring cells through ACE2-independent, receptor (STEAP2)-mediated endocytosis, and achieve gene expression. The effect is more pronounced for the N protein of wild-type SARS-CoV-2 than that of the Omicron variant and other human coronaviruses.

Climate change challenges, plant science solutions.

Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g.

Evolutionary convergence of a neural mechanism in the cavefish lateral line system.

Animals can evolve dramatic sensory functions in response to environmental constraints, but little is known about the neural mechanisms underlying these changes. The Mexican tetra, , is a leading model to study genetic, behavioral, and physiological evolution by comparing eyed surface populations and blind cave populations. We compared neurophysiological responses of posterior lateral line afferent neurons and motor neurons across populations to reveal how shifts in sensory function may shape behavioral diversity.

Metabolomics-Driven Identification of the Rate-Limiting Steps in 1-Propanol Production.

The concerted effort for bioproduction of higher alcohols and other commodity chemicals has yielded a consortium of metabolic engineering techniques to identify targets to enhance performance of engineered microbial strains. Here, we demonstrate the use of metabolomics as a tool to systematically identify targets for improved production phenotypes in . Gas chromatography/mass spectrometry (GC/MS) and ion-pair LC-MS/MS were performed to investigate metabolic perturbations in various 1-propanol producing strains.

Fish-inspired segment models for undulatory steady swimming.

Many aquatic animals swim by undulatory body movements and understanding the diversity of these movements could unlock the potential for designing better underwater robots. Here, we analyzed the steady swimming kinematics of a diverse group of fish species to investigate whether their undulatory movements can be represented using a series of interconnected multi-segment models, and if so, to identify the key factors driving the segment configuration of the models. Our results show that the steady swimming kinematics of fishes can be described successfully using parsimonious models, 83% of which had fewer than five segments.

Convergence of undulatory swimming kinematics across a diversity of fishes.

Fishes exhibit an astounding diversity of locomotor behaviors from classic swimming with their body and fins to jumping, flying, walking, and burrowing. Fishes that use their body and caudal fin (BCF) during undulatory swimming have been traditionally divided into modes based on the length of the propulsive body wave and the ratio of head:tail oscillation amplitude: anguilliform, subcarangiform, carangiform, and thunniform. This classification was first proposed based on key morphological traits, such as body stiffness and elongation, to group fishes based on their expected swimming mechanics.

Corollary discharge enables proprioception from lateral line sensory feedback.

Animals modulate sensory processing in concert with motor actions. Parallel copies of motor signals, called corollary discharge (CD), prepare the nervous system to process the mixture of externally and self-generated (reafferent) feedback that arises during locomotion. Commonly, CD in the peripheral nervous system cancels reafference to protect sensors and the central nervous system from being fatigued and overwhelmed by self-generated feedback.

Body Caudal Undulation Measured by Soft Sensors and Emulated by Soft Artificial Muscles.

We propose the use of bio-inspired robotics equipped with soft sensor technologies to gain a better understanding of the mechanics and control of animal movement. Soft robotic systems can be used to generate new hypotheses and uncover fundamental principles underlying animal locomotion and sensory capabilities, which could subsequently be validated using living organisms. Physical models increasingly include lateral body movements, notably back and tail bending, which are necessary for horizontal plane undulation in model systems ranging from fish to amphibians and reptiles.

The Philosophy of Outliers: Reintegrating Rare Events Into Biological Science.

Individual variation in morphology, physiology, and behavior has been a topic of great interest in the biological sciences. While scientists realize the importance of understanding diversity in individual phenotypes, historically the "minority" results (i.e.

Identification of COVID-19 B-cell epitopes with phage-displayed peptide library.

Background: Coronavirus disease 19 (COVID-19) first appeared in the city of Wuhan, in the Hubei province of China. Since its emergence, the COVID-19-causing virus, SARS-CoV-2, has been rapidly transmitted around the globe, overwhelming the medical care systems in many countries and leading to more than 3.3 million deaths.

Activity of Posterior Lateral Line Afferent Neurons during Swimming in Zebrafish.

Sensory systems gather cues essential for directing behavior, but animals must decipher what information is biologically relevant. Locomotion generates reafferent cues that animals must disentangle from relevant sensory cues of the surrounding environment. For example, when a fish swims, flow generated from body undulations is detected by the mechanoreceptive neuromasts, comprising hair cells, that compose the lateral line system.