ASU Scholarship Showcase

Background: Meiotic recombination has traditionally been explained based on the structural requirement to stabilize homologous chromosome pairs to ensure their proper meiotic segregation. Competing hypotheses seek to explain the emerging findings of significant heterogeneity in recombination rates within and between genomes, but intraspecific comparisons of genome-wide recombination patterns are rare. The honey bee (Apis mellifera) exhibits the highest rate of genomic recombination among multicellular animals with about five cross-over events per chromatid.

Results: Here, we present a comparative analysis of recombination rates across eight genetic linkage maps of the honey bee genome to investigate which genomic sequence features are correlated with recombination rate and with its variation across the eight data sets, ranging in average marker spacing ranging from 1 Mbp to 120 kbp. Overall, we found that GC content explained best the variation in local recombination rate along chromosomes at the analyzed 100 kbp scale. In contrast, variation among the different maps was correlated to the abundance of microsatellites and several specific tri- and tetra-nucleotides.

Conclusions: The combined evidence from eight medium-scale recombination maps of the honey bee genome suggests that recombination rate variation in this highly recombining genome might be due to the DNA configuration instead of distinct sequence motifs. However, more fine-scale analyses are needed. The empirical basis of eight differing genetic maps allowed for robust conclusions about the correlates of the local recombination rates and enabled the study of the relation between DNA features and variability in local recombination rates, which is particularly relevant in the honey bee genome with its exceptionally high recombination rate.

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.

Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.

Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.

Two classes of scaling behaviours, namely the super-linear scaling of links or activities, and the sub-linear scaling of area, diversity, or time elapsed with respect to size have been found to prevail in the growth of complex networked systems. Despite some pioneering modelling approaches proposed for specific systems, whether there exists some general mechanisms that account for the origins of such scaling behaviours in different contexts, especially in socioeconomic systems, remains an open question. We address this problem by introducing a geometric network model without free parameter, finding that both super-linear and sub-linear scaling behaviours can be simultaneously reproduced and that the scaling exponents are exclusively determined by the dimension of the Euclidean space in which the network is embedded. We implement some realistic extensions to the basic model to offer more accurate predictions for cities of various scaling behaviours and the Zipf distribution reported in the literature and observed in our empirical studies. All of the empirical results can be precisely recovered by our model with analytical predictions of all major properties. By virtue of these general findings concerning scaling behaviour, our models with simple mechanisms gain new insights into the evolution and development of complex networked systems.

Honeybee workers are essentially sterile female helpers that make up the majority of individuals in a colony. Workers display a marked change in physiology when they transition from in-nest tasks to foraging. Recent technological advances have made it possible to unravel the metabolic modifications associated with this transition. Previous studies have revealed extensive remodeling of brain, thorax, and hypopharyngeal gland biochemistry. However, data on changes in the abdomen is scarce. To narrow this gap we investigated the proteomic composition of abdominal tissue in the days typically preceding the onset of foraging in honeybee workers.

In order to get a broader representation of possible protein dynamics, we used workers of two genotypes with differences in the age at which they initiate foraging. This approach was combined with RNA interference-mediated downregulation of an insulin/insulin-like signaling component that is central to foraging behavior, the insulin receptor substrate (irs), and with measurements of glucose and lipid levels.
Our data provide new insight into the molecular underpinnings of phenotypic plasticity in the honeybee, invoke parallels with vertebrate metabolism, and support an integrated and irs-dependent association of carbohydrate and lipid metabolism with the transition from in-nest tasks to foraging.

Background: Gene bodies are the most evolutionarily conserved targets of DNA methylation in eukaryotes. However, the regulatory functions of gene body DNA methylation remain largely unknown. DNA methylation in insects appears to be primarily confined to exons. Two recent studies in Apis mellifera (honeybee) and Nasonia vitripennis (jewel wasp) analyzed transcription and DNA methylation data for one gene in each species to demonstrate that exon-specific DNA methylation may be associated with alternative splicing events. In this study we investigated the relationship between DNA methylation, alternative splicing, and cross-species gene conservation on a genome-wide scale using genome-wide transcription and DNA methylation data.

Results: We generated RNA deep sequencing data (RNA-seq) to measure genome-wide mRNA expression at the exon- and gene-level. We produced a de novo transcriptome from this RNA-seq data and computationally predicted splice variants for the honeybee genome. We found that exons that are included in transcription are higher methylated than exons that are skipped during transcription. We detected enrichment for alternative splicing among methylated genes compared to unmethylated genes using fisher’s exact test. We performed a statistical analysis to reveal that the presence of DNA methylation or alternative splicing are both factors associated with a longer gene length and a greater number of exons in genes. In concordance with this observation, a conservation analysis using BLAST revealed that each of these factors is also associated with higher cross-species gene conservation.

Conclusions: This study constitutes the first genome-wide analysis exhibiting a positive relationship between exon-level DNA methylation and mRNA expression in the honeybee. Our finding that methylated genes are enriched for alternative splicing suggests that, in invertebrates, exon-level DNA methylation may play a role in the construction of splice variants by positively influencing exon inclusion during transcription. The results from our cross-species homology analysis suggest that DNA methylation and alternative splicing are genetic mechanisms whose utilization could contribute to a longer gene length and a slower rate of gene evolution.

Insect immune systems can recognize specific pathogens and prime offspring immunity. High specificity of immune priming can be achieved when insect females transfer immune elicitors into developing oocytes. The molecular mechanism behind this transfer has been a mystery. Here, we establish that the egg-yolk protein vitellogenin is the carrier of immune elicitors. Using the honey bee, Apis mellifera, model system, we demonstrate with microscopy and western blotting that vitellogenin binds to bacteria, both Paenibacillus larvae – the gram-positive bacterium causing American foulbrood disease – and to Escherichia coli that represents gram-negative bacteria. Next, we verify that vitellogenin binds to pathogen-associated molecular patterns; lipopolysaccharide, peptidoglycan and zymosan, using surface plasmon resonance. We document that vitellogenin is required for transport of cell-wall pieces of E. coli into eggs by imaging tissue sections. These experiments identify vitellogenin, which is distributed widely in oviparous species, as the carrier of immune-priming signals. This work reveals a molecular explanation for trans-generational immunity in insects and a previously undescribed role for vitellogenin.

Myoelectric artificial limbs can significantly advance the state of the art in prosthetics, since they can be used to control mechatronic devices through muscular activity in a way that mimics how the subjects used to activate their muscles before limb loss. However, surveys indicate that dissatisfaction with the functionality of terminal devices underlies the widespread abandonment of prostheses. We believe that one key factor to improve acceptability of prosthetic devices is to attain human likeness of prosthesis movements, a goal which is being pursued by research on social and human–robot interactions. Therefore, to reduce early abandonment of terminal devices, we propose that controllers should be designed so as to ensure effective task accomplishment in a natural fashion. In this work, we have analyzed and compared the performance of three types of myoelectric controller algorithms based on surface electromyography to control an underactuated and multi-degrees of freedom prosthetic hand, the SoftHand Pro.

The goal of the present study was to identify the myoelectric algorithm that best mimics the native hand movements. As a preliminary step, we first quantified the repeatability of the SoftHand Pro finger movements and identified the electromyographic recording sites for able-bodied individuals with the highest signal-to-noise ratio from two pairs of muscles, i.e., flexor digitorum superficialis/extensor digitorum communis, and flexor carpi radialis/extensor carpi ulnaris. Able-bodied volunteers were then asked to execute reach-to-grasp movements, while electromyography signals were recorded from flexor digitorum superficialis/extensor digitorum communis as this was identified as the muscle pair characterized by high signal-to-noise ratio and intuitive control. Subsequently, we tested three myoelectric controllers that mapped electromyography signals to position of the SoftHand Pro. We found that a differential electromyography-to-position mapping ensured the highest coherence with hand movements. Our results represent a first step toward a more effective and intuitive control of myoelectric hand prostheses.

Introduction: Options currently available to individuals with upper limb loss range from prosthetic hands that can perform many movements, but require more cognitive effort to control, to simpler terminal devices with limited functional abilities. We attempted to address this issue by designing a myoelectric control system to modulate prosthetic hand posture and digit force distribution.

Methods: We recorded surface electromyographic (EMG) signals from five forearm muscles in eight able-bodied subjects while they modulated hand posture and the flexion force distribution of individual fingers. We used a support vector machine (SVM) and a random forest regression (RFR) to map EMG signal features to hand posture and individual digit forces, respectively. After training, subjects performed grasping tasks and hand gestures while a computer program computed and displayed online feedback of all digit forces, in which digits were flexed, and the magnitude of contact forces. We also used a commercially available prosthetic hand, the i-Limb (Touch Bionics), to provide a practical demonstration of the proposed approach’s ability to control hand posture and finger forces.

Results: Subjects could control hand pose and force distribution across the fingers during online testing. Decoding success rates ranged from 60% (index finger pointing) to 83–99% for 2-digit grasp and resting state, respectively. Subjects could also modulate finger force distribution.

Discussion: This work provides a proof of concept for the application of SVM and RFR for online control of hand posture and finger force distribution, respectively. Our approach has potential applications for enabling in-hand manipulation with a prosthetic hand.

The concept of postural synergies of the human hand has been shown to potentially reduce complexity in the neuromuscular control of grasping. By merging this concept with soft robotics approaches, a multi degrees of freedom soft-synergy prosthetic hand [SoftHand-Pro (SHP)] was created. The mechanical innovation of the SHP enables adaptive and robust functional grasps with simple and intuitive myoelectric control from only two surface electromyogram (sEMG) channels. However, the current myoelectric controller has very limited capability for fine control of grasp forces. We addressed this challenge by designing a hybrid-gain myoelectric controller that switches control gains based on the sensorimotor state of the SHP. This controller was tested against a conventional single-gain (SG) controller, as well as against native hand in able-bodied subjects. We used the following tasks to evaluate the performance of grasp force control: (1) pick and place objects with different size, weight, and fragility levels using power or precision grasp and (2) squeezing objects with different stiffness. Sensory feedback of the grasp forces was provided to the user through a non-invasive, mechanotactile haptic feedback device mounted on the upper arm. We demonstrated that the novel hybrid controller enabled superior task completion speed and fine force control over SG controller in object pick-and-place tasks. We also found that the performance of the hybrid controller qualitatively agrees with the performance of native human hands.

Biological and robotic grasp and manipulation are undeniably similar at the level of mechanical task performance. However, their underlying fundamental biological vs. engineering mechanisms are, by definition, dramatically different and can even be antithetical. Even our approach to each is diametrically opposite: inductive science for the study of biological systems vs. engineering synthesis for the design and construction of robotic systems. The past 20 years have seen several conceptual advances in both fields and the quest to unify them. Chief among them is the reluctant recognition that their underlying fundamental mechanisms may actually share limited common ground, while exhibiting many fundamental differences. This recognition is particularly liberating because it allows us to resolve and move beyond multiple paradoxes and contradictions that arose from the initial reasonable assumption of a large common ground. Here, we begin by introducing the perspective of neuromechanics, which emphasizes that real-world behavior emerges from the intimate interactions among the physical structure of the system, the mechanical requirements of a task, the feasible neural control actions to produce it, and the ability of the neuromuscular system to adapt through interactions with the environment. This allows us to articulate a succinct overview of a few salient conceptual paradoxes and contradictions regarding under-determined vs. over-determined mechanics, under- vs. over-actuated control, prescribed vs. emergent function, learning vs. implementation vs. adaptation, prescriptive vs. descriptive synergies, and optimal vs. habitual performance. We conclude by presenting open questions and suggesting directions for future research. We hope this frank and open-minded assessment of the state-of-the-art will encourage and guide these communities to continue to interact and make progress in these important areas at the interface of neuromechanics, neuroscience, rehabilitation and robotics.