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The need for automated and efficient systems for tracking full animal pose has increased with the complexity of behavioral data and analyses. Here we introduce LEAP (LEAP estimates animal pose), a deep-learning-based method for predicting the positions of animal body parts. This framework consists of a graphical interface for labeling of body parts and training the network. LEAP offers fast prediction on new data, and training with as few as 100 frames results in 95% of peak performance. We validated LEAP using videos of freely behaving fruit flies and tracked 32 distinct points to describe the pose of the head, body, wings and legs, with an error rate of <3% of body length. We recapitulated reported findings on insect gait dynamics and demonstrated LEAP’s applicability for unsupervised behavioral classification. Finally, we extended the method to more challenging imaging situations and videos of freely moving mice.

Gut symbiotic bacteria have a substantial impact on host physiology and ecology. However, the contribution of gut microbes to host fitness during long-term low-temperature stress is still unclear. This study examined the role of gut microbiota in host low-temperature stress resistance at molecular and biochemical levels in the oriental fruit fly Bactrocera dorsalis. The results showed that after the gut bacteria of flies were removed via antibiotic treatment, the median survival time was significantly decreased to approximately 68% of that in conventional flies following exposure to a temperature stress of 10°C. Furthermore, we found that Klebsiella michiganensis BD177 is a key symbiotic bacterium, whose recolonization in antibiotic treated (ABX) flies significantly extended the median survival time to 160% of that in the ABX control, and restored their lifespan to the level of conventional flies. Notably, the relative levels of proline and arginine metabolites were significantly downregulated by 34- and 10-fold, respectively, in ABX flies compared with those in the hemolymph of conventional flies after exposure to a temperature stress of 10°C whereas recolonization of ABX flies by K. michiganensis BD177 significantly upregulated the levels of proline and arginine by 13- and 10- fold, respectively, compared with those found in the hemolymph of ABX flies. qPCR analysis also confirmed that K. michiganensis-recolonized flies significantly stimulated the expression of transcripts from the arginine and proline metabolism pathway compared with the ABX controls, and RNAi mediated silencing of two key genes Pro-C and ASS significantly reduced the survival time of conventional flies, postexposure low-temperature stress. We show that microinjection of L-arginine and L-proline into ABX flies significantly increased their survival time following exposure to temperature stress of 10°C. Transmission electron microscopy (TEM) analysis further revealed that low-temperature stress caused severe destruction in cristae structures and thus resulted in abnormal circular shapes of mitochondria in ABX flies gut, while the recolonization of live K. michiganensis helped the ABX flies to maintain mitochondrial functionality to a normal status, which is important for the arginine and proline induction. Our results suggest that gut microbiota plays a vital role in promoting the host resistance to low-temperature stress in B. dorsalis by stimulating its arginine and proline metabolism pathway.

Artificial Intelligence (AI) and automation are fostering more sustainable and effective solutions for a wide spectrum of agricultural problems. Pest management is a major challenge for crop production that can benefit from machine learning techniques to detect and monitor specific pests and diseases. Traditional monitoring is labor intensive, time demanding, and expensive, while machine learning paradigms may support cost-effective crop protection decisions. However, previous studies mainly relied on morphological images of stationary or immobilized animals. Other features related to living animals behaving in the environment (e.g., walking trajectories, different postures, etc.) have been overlooked so far. In this study, we developed a detection method based on convolutional neural network (CNN) that can accurately classify in real-time two tephritid species (Ceratitis capitata and Bactrocera oleae) free to move and change their posture. Results showed a successful automatic detection (i.e., precision rate about 93%) in real-time of C. capitata and B. oleae adults using a camera sensor at a fixed height. In addition, the similar shape and movement patterns of the two insects did not interfere with the network precision. The proposed method can be extended to other pest species, needing minimal data pre-processing and similar architecture.

Mutations in the ubiquitin ligase parkin are responsible for a familial form of Parkinson’s disease. Parkin and the PINK1 kinase regulate a quality-control system for mitochondria. PINK1 phosphorylates ubiquitin on the outer membrane of damaged mitochondria, thus leading to recruitment and activation of parkin via phosphorylation of its ubiquitin-like (Ubl) domain. Here, we describe the mechanism of parkin activation by phosphorylation. The crystal structure of phosphorylated Bactrocera dorsalis (oriental fruit fly) parkin in complex with phosphorylated ubiquitin and an E2 ubiquitin-conjugating enzyme reveals that the key activating step is movement of the Ubl domain and release of the catalytic RING2 domain. Hydrogen/deuterium exchange and NMR experiments with the various intermediates in the activation pathway confirm and extend the interpretation of the crystal structure to mammalian parkin. Our results rationalize previously unexplained Parkinson’s disease mutations and the presence of internal linkers that allow large domain movements in parkin.

While research into the biology of animal behaviour has primarily focused on the central nervous system, cues from peripheral tissues and the environment have been implicated in brain development and function 1 . There is emerging evidence that bidirectional communication between the gut and the brain affects behaviours including anxiety, cognition, nociception and social interaction 1 – 9 . Coordinated locomotor behaviour is critical for the survival and propagation of animals, and is regulated by internal and external sensory inputs 10 , 11 . However, little is known about how the gut microbiome influences host locomotion, or the molecular and cellular mechanisms involved. Here we report that germ-free status or antibiotic treatment results in hyperactive locomotor behaviour in the fruit fly Drosophila melanogaster . Increased walking speed and daily activity in the absence of a gut microbiome are rescued by mono-colonization with specific bacteria, including the fly commensal Lactobacillus brevis . The bacterial enzyme xylose isomerase from L. brevis recapitulates the locomotor effects of microbial colonization by modulating sugar metabolism in flies. Notably, thermogenetic activation of octopaminergic neurons or exogenous administration of octopamine, the invertebrate counterpart of noradrenaline, abrogates the effects of xylose isomerase on Drosophila locomotion. These findings reveal a previously unappreciated role for the gut microbiome in modulating locomotion, and identify octopaminergic neurons as mediators of peripheral microbial cues that regulate motor behaviour in animals. Female Drosophila that lack a microbiota are hyperactive, and xylose isomerase from Lactobacillus brevis is sufficient to reverse this effect.

Ceratitis capitata (Wiedemann) and Anastrepha fraterculus (Wiedemann) (both Diptera: Tephritidae) cause severe economic losses to fruit production; thus, it is important to know the population fluctuations of these pests that share the same habitat and compete for similar niches, as well as to know their relationship with fruit infestation, all of which are fundamental components for understanding how to manage the risks of infestation in farms with a diversity of susceptible hosts. In the present research, the spatio-temporal distribution of C. capitata and A. fraterculus in 3 fruit farms was analyzed together with the incidence of fruit damage in different host species and cultivars. Seventy-nine Jackson traps baited with trimedlure and 88 McPhail traps baited with Torula yeast were monitored from Sep 2014 to Jun 2016, and a total of 5,700 fruits were sampled during the 2 seasons. The Spearman correlation coefficient between captures and fruit infestation was calculated, and maps of accumulated captures and fruit infestation distribution were built by site and season. Population fluctuation and fruit infestation were plotted for both fruit fly species, whereas population fluctuation discriminated by sex was analyzed for C. capitata. The Spearman correlation coefficient between C. capitata captures in McPhail traps during the 2 wk prior to harvest and the percentage of infested fruits was 0.62 (P = 0.0001), whereas for Jackson traps it was 0.34 (P = 0.02). The correlation between A. fraterculus captures in McPhail traps and fruit infestation was 0.59 (P = 0.0001). The variation observed in the number of adults and fruit infestation of both pest species between sites and host species groups is discussed.

Background The olive fruit fly, Bactrocera oleae , is the most important pest in the olive fruit agribusiness industry. This is because female flies lay their eggs in the unripe fruits and upon hatching the larvae feed on the fruits thus destroying them. The lack of a high-quality genome and other genomic and transcriptomic data has hindered progress in understanding the fly’s biology and proposing alternative control methods to pesticide use. Results Genomic DNA was sequenced from male and female Demokritos strain flies, maintained in the laboratory for over 45 years. We used short-, mate-pair-, and long-read sequencing technologies to generate a combined male-female genome assembly (GenBank accession GCA_001188975.2). Genomic DNA sequencing from male insects using 10x Genomics linked-reads technology followed by mate-pair and long-read scaffolding and gap-closing generated a highly contiguous 489 Mb genome with a scaffold N50 of 4.69 Mb and L50 of 30 scaffolds (GenBank accession GCA_001188975.4). RNA-seq data generated from 12 tissues and/or developmental stages allowed for genome annotation. Short reads from both males and females and the chromosome quotient method enabled identification of Y-chromosome scaffolds which were extensively validated by PCR. Conclusions The high-quality genome generated represents a critical tool in olive fruit fly research. We provide an extensive RNA-seq data set, and genome annotation, critical towards gaining an insight into the biology of the olive fruit fly. In addition, elucidation of Y-chromosome sequences will advance our understanding of the Y-chromosome’s organization, function and evolution and is poised to provide avenues for sterile insect technique approaches.

During gastrulation, physical forces reshape the simple embryonic tissue to form the complex body plans of multicellular organisms 1 . These forces often cause large-scale asymmetric movements of the embryonic tissue 2 , 3 . In many embryos, the gastrulating tissue is surrounded by a rigid protective shell 4 . Although it is well-recognized that gastrulation movements depend on forces that are generated by tissue-intrinsic contractility 5 , 6 , it is not known whether interactions between the tissue and the protective shell provide additional forces that affect gastrulation. Here we show that a particular part of the blastoderm tissue of the red flour beetle ( Tribolium castaneum ) tightly adheres in a temporally coordinated manner to the vitelline envelope that surrounds the embryo. This attachment generates an additional force that counteracts tissue-intrinsic contractile forces to create asymmetric tissue movements. This localized attachment depends on an αPS2 integrin (inflated), and the knockdown of this integrin leads to a gastrulation phenotype that is consistent with complete loss of attachment. Furthermore, analysis of another integrin (the αPS3 integrin, scab) in the fruit fly ( Drosophila melanogaster ) suggests that gastrulation in this organism also relies on adhesion between the blastoderm and the vitelline envelope. Our findings reveal a conserved mechanism through which the spatiotemporal pattern of tissue adhesion to the vitelline envelope provides controllable, counteracting forces that shape gastrulation movements in insects. In the red flour beetle ( Tribolium castaneum ) and fruit fly ( Drosophila melanogaster ), spatiotemporally coordinated integrin-dependent attachments between the blastoderm and vitelline envelope counteract tissue-intrinsic contractile forces to create asymmetric movements of embryonic tissue.

Bactrocera oleae Rossi causes important agricultural losses in olive growing regions. Despite its economic relevance, the expansion history and biogeography of B. oleae and other olive-feeding fruit flies remain unclear. We used mitogenomic data of Bactrocera species from a broad geographic range to explore possible historical biogeographic patterns in B. oleae and other olive-feeding fruit flies. Our data suggest that (1) the transition from stenophagy on Oleaceae to oligophagy on Olea most likely occurred in Africa more than 6 million years ago (MYA), and (2) the subsequent transition to monophagy on Olea europaea took place in Asia or in Africa in the Early Pleistocene. Our results support equally the hypotheses that the ancestors of modern B. oleae underwent two waves of migration from Asia to Africa or that they zigzagged between Asia and Africa.