Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeting the nociceptive somatosensory system with AAV9 and AAV2retro viral vectors

Adeno-associated viral (AAV) vectors allow for site-specific and time-dependent genetic manipulation of neurons. However, for successful implementation of AAV vectors, major consideration must be given to the selection of viral serotype and route of delivery for efficient gene transfer into the cell type being investigated. Here we compare the transduction pattern of neurons in the somatosensory system following injection of AAV9 or AAV2retro in the parabrachial complex of the midbrain, the spinal cord dorsal horn, the intrathecal space, and the colon. Transduction was evaluated based on Cre-dependent expression of tdTomato in transgenic reporter mice, following delivery of AAV9 or AAV2retro carrying identical constructs that drive the expression of Cre/GFP. The pattern of distribution of tdTomato expression indicated notable differences in the access of the two AAV serotypes to primary afferent neurons via peripheral delivery in the colon and to spinal projections neurons via intracranial delivery within the parabrachial complex. Additionally, our results highlight the superior sensitivity of detection of neuronal transduction based on reporter expression relative to expression of viral products.
Interactions between TULP3 tubby domain cargo site and ARL13B amphipathic helix promote lipidated protein transport to cilia

The tubby family protein–TULP3 coordinates with the intraflagellar transport complex-A (IFT-A) in trafficking certain transmembrane proteins to cilia. These transmembrane cargoes have short motifs that are necessary and sufficient for TULP3-mediated trafficking. However, whether TULP3 regulates trafficking of membrane-associated proteins is not well understood. Here we show that TULP3 is required for transport of the atypical GTPase ARL13B into cilia, and for ciliary enrichment of ARL13B-dependent farnesylated and myristoylated proteins. ARL13B transport requires TULP3 binding to IFT-A core but not to phosphoinositides, unlike transmembrane cargo transport that requires binding to both by TULP3. A conserved lysine in TULP3’s tubby domain mediates direct ARL13B binding and trafficking of lipidated and transmembrane cargoes. An N-terminal amphipathic helix in ARL13B flanking the palmitoylation site mediates binding to TULP3 and directs trafficking to cilia even in absence of palmitoylation and RVxP sorting motif. Therefore, TULP3 transports transmembrane proteins and ARL13B into cilia by capture of short sequences through a shared tubby domain site.
The Plasmodium NOT1-G Paralogue Acts as an Essential Nexus for Sexual Stage Maturation and Parasite Transmission

Productive transmission of malaria parasites hinges upon the execution of key transcriptional and post-transcriptional regulatory events. While much is now known about how specific transcription factors activate or repress sexual commitment programs, far less is known about the production of a preferred mRNA homeostasis following commitment and through the host-to-vector transmission event. Here we show that Plasmodium parasites have taken the unique approach to duplicate the NOT1 scaffold protein of the CAF1/CCR4/Not complex in order to dedicate one paralogue for essential transmission functions. Moreover, this NOT1-G paralogue is central to the sex-specific functions previously associated with its interacting partners, as deletion of not1-g in Plasmodium yoelii leads to a comparable or complete arrest phenotype for both male and female parasites. We show that, consistent with its role in other eukaryotes, PyNOT1-G localizes to cytosolic puncta throughout much of the Plasmodium life cycle. PyNOT1-G is essential to both the complete maturation of male gametes and to the continued development of the fertilized zygote originating from female parasites. Comparative transcriptomics of wild-type and pynot1-g- parasites shows that loss of PyNOT1-G leads to transcript dysregulation preceding and during gametocytogenesis, and shows that PyNOT1-G acts to preserve mRNAs that are critical to sexual and early mosquito stage development. Finally, we demonstrate that the tristetraprolin-binding domain, which acts as the typical organization platform for RNA decay (TTP) and RNA preservation (ELAV/HuR) factors is dispensable for PyNOT1-G’s essential blood stage functions but impacts host-to-vector transmission. Together, we conclude that Plasmodium has created and adapted a NOT1-G paralogue to fulfill the complex transmission requirements of both male and female parasites.
The effect of progressive heat acclimation on change in body heat content in young males

Heat acclimation improves the physiological capacity to dissipate heat. As previous studies have only relied upon core temperature and local heat loss measurements, it remains unclear the extent to which whole‐body heat loss, and therefore body heat storage is altered during heat acclimation. Using direct calorimetry, we examined whole‐body heat exchange during progressive increases in the requirement for heat loss during and following a 14‐day heat acclimation protocol. Six young males (Mean±SD, age: 23±3yrs) performed intermittent exercise (3×30‐min bouts of cycling at 300, 350, and 400 W·m−2separated by 10 min rest period) in dry heat (35°C, 20% relative humidity [RH]) prior to (day 0), during (day 7), and at the end (day 14) of a 14‐day heat acclimation. On days 1–6 and 8–13, subjects cycled for 90 min (~50% VO2max) in the heat (40°C, 20% RH). Despite a similar requirement between test days, significantly lower increases in evaporative heat loss were observed for the final exercise bout in days 0 (P=0.01) and 7 (P=0.02) relative to day 14. After 7 days of acclimation, the ΔHb following the exercise did not significantly decrease from day 0 (673±165 vs. 449±109 kJ, p=0.112). However, on day 14 the ΔHb was significantly reduced compared to day 0 (363±64 vs. 673±165 kJ, p=0.04). These data suggest that 14 days is necessary to achieve sufficient heat acclimation to significantly reduce heat storage during exercise in the heat. Support: Deep Mining Research Consortium (Dr. Glen P. Kenny)
Temporary prey storage along swarm columns of army ants: an adaptive strategy for successful raiding?

While pillaging the brood of other ant colonies, Eciton army ants accumulate prey in piles, or caches, along their foraging trails. Widely documented, these structures have historically been considered as byproducts of heavy traffic or aborted relocations of the ants’ temporary nest, or bivouac. However, we recently observed that caches of the hook-jawed army ant, Eciton hamatum, appeared independently from heavy traffic or bivouac relocations. In addition, the flow of prey through caches varied based on the quantity of prey items workers transported. As this suggested a potential adaptive function, we developed agent-based simulations to compare raids of caching and non-caching virtual army ants. We found that caches increased the amount of prey that relatively low numbers of raiders were able to retrieve. However, this advantage became less conspicuous - and generally disappeared - as the number of raiders increased. Based on these results, we hypothesize that caches maximize the amount of prey that limited amounts of raiders can retrieve, especially as prey colonies coordinately evacuate their brood. In principle, caches also allow workers to safely collect multiple prey items and efficiently transport them to the bivouac. Further field observations are needed to test this and other hypotheses emerging from our study.
Species’ traits and exposure as a future lens for quantifying seabird bycatch vulnerability in global fisheries

Fisheries bycatch, the incidental mortality of non-target species, is a global threat to seabirds and a major driver of their declines worldwide. Identifying the most vulnerable species is core to developing sustainable fisheries management strategies that aim to improve conservation outcomes. To advance this goal, we present a preliminary vulnerability framework that integrates dimensions of species’ exposure, sensitivity, and adaptive capacity to fisheries bycatch to classify species into five vulnerability classes. The framework combines species’ traits and distribution ranges for 341 seabirds, along with a spatially resolved fishing effort dataset. Overall, we find most species have high vulnerability scores for the sensitivity and adaptive capacity dimensions. By contrast, exposure is more variable across species, and thus the median scores calculated within seabird families is low. We further find 46 species have high exposure to fishing activities, but are not identified as vulnerable to bycatch, whilst 133 species have lower exposure, but are vulnerable to bycatch. Thus, the framework has been valuable for revealing patterns between and within the vulnerability dimensions. Still, further methodological development, additional traits, and greater availability of threat data are required to advance the framework and provide a new lens for quantifying seabird bycatch vulnerability that complements existing efforts, such as the International Union for Conservation of Nature (IUCN) Red List.
A Neural Model of RNA Splicing: Learning Motif Distances with Self-Attention and Toeplitz Max Pooling

Alternative RNA splicing is an important regulator of tissue development and specificity, and a relevant mechanism in cancer progression. There exists a strong motivation to disentangle the rules that govern RNA splicing, in part because this knowledge may one day yield new clinically relevant diagnostic tools and therapeutics. It is no easy to task to reverse engineer how the splicesome machinery choreographs the removal and addition of RNA elements following transcription. Here, we propose an interpretable neural network called the Toeplitz ATtention Architecture (TATA), which learns distance-dependent motif interactions through a novel Toeplitz max pool layer that captures the relative distance between interacting CNN filters. TATA is a completely transparent “clear-box” solution: every model parameter is human-interpretable. We validate TATA on simulated data, then apply it to real data to identify putative cis-regulatory elements that interact with primary RNA splice sites.
Survey and molecular detection of Sri Lankan cassava mosaic virus in Thailand

Cassava plantations in an area of 458 ha spanning five provinces along the Thailand– Cambodia border were surveyed from October 2018 to July 2019 to determine the prevalence of cassava mosaic disease (CMD) caused by Sri Lankan cassava mosaic virus (SLCMV) in the region. CMD prevalence was 40% in the whole area and 80% in Prachinburi, 43% in Sakaeo, 37% in Burium, 25% in Surin, and 19% in Sisaket provinces. Disease severity was generally scored as 2–3. The highest average disease severity was in Sakaeo province (3.7), followed by Buriram (3.6), Prachinburi (2.88), Surin (2.5), and Sisaket (2.4) provinces. Asymptomatic plants were identified in Surin (12%), Prachinburi (5%), Sakaeo (0.2%), and Buriram (0.1%) by PCR analysis. Interestingly, cassava cultivars CMR-89 and Rayong 11 were susceptible to CMD. In approximately 95% of cases, the infection was transmitted by whitefly (Bemisia tabaci), which had a high population density in Prachinburi but was sparse in Surin, with the largest populations observed in May and June. Nucleotide sequencing of the mitochondrial cytochrome oxidase 1 (mtCO1) gene of whitefly (Bemisia tabaci) in Thailand revealed a similarity to the Asia II 1 whitefly gene. Furthermore, the AV1 gene—which encodes the capsid protein—showed 90% nucleotide identity with SLCMV. Phylogenetic analysis of completed nucleotide sequences of DNA-A and DNA-B components of the SLCMV genome determined by rolling circle amplification (RCA) indicated that they were similar to the nucleotide sequence of SLCMV isolates from Thailand, Vietnam, and Cambodia. These results provide important insights into the distribution, impact, and spread of CMD and SLCMV in Thailand.
Distinct movement patterns generate stages of spider web building

The geometric complexity and stereotypy of spider webs have long generated interest in their algorithmic origin. Like other examples of animal architecture, web construction is the result of several assembly phases that are driven by distinct behavioral stages coordinated to build a successful structure. Manual observations have revealed a range of sensory cues and movement patterns used during web construction, but methods to systematically quantify the dynamics of these sensorimotor patterns are lacking. Here, we apply an analytical pipeline to quantify web-making behavior of the orb-weaver Uloborus diversus. Position tracking revealed stereotyped stages of construction that could occur in typical or atypical progressions across individuals. Using an unsupervised clustering approach, we identified general and stage-specific leg movements. A Hierarchical Hidden Markov Model revealed that stages of web-building are characterized by stereotyped sequences of actions largely shared across individuals, regardless of whether these stages progress in a typical or atypical fashion. Web stages could be predicted based on action-sequences alone, revealing that web-stages are a physical manifestation of underlying behavioral phases. Highlights Spider centroid trajectories indicate stereotyped progression of web-building stages. Unsupervised movement clustering reveals a shared set of movements which correspond to previously defined behaviors that define web-making across individuals. Stages of web-building use both stage-specific and non-specific behaviors. Stereotyped and distinct action sequences are predictive of stages of web-building.
On the sparsity of fitness functions and implications for learning

Significance The properties of proteins and other biological molecules are encoded in large part in the sequence of amino acids or nucleotides that defines them. Increasingly, researchers estimate functions that map sequences to a particular property using machine learning and related statistical approaches. However, an important question remains unanswered: How many experimental measurements are needed in order to accurately learn these “fitness” functions? We leverage perspectives from the fields of biophysics, evolutionary biology, and signal processing to develop a theoretical framework that enables us to make progress on answering this question. We demonstrate that this framework can be used to make useful calculations on real-world data and suggest how these calculations may be used to guide experiments. Fitness functions map biological sequences to a scalar property of interest. Accurate estimation of these functions yields biological insight and sets the foundation for model-based sequence design. However, the fitness datasets available to learn these functions are typically small relative to the large combinatorial space of sequences; characterizing how much data are needed for accurate estimation remains an open problem. There is a growing body of evidence demonstrating that empirical fitness functions display substantial sparsity when represented in terms of epistatic interactions. Moreover, the theory of Compressed Sensing provides scaling laws for the number of samples required to exactly recover a sparse function. Motivated by these results, we develop a framework to study the sparsity of fitness functions sampled from a generalization of the NK model, a widely used random field model of fitness functions. In particular, we present results that allow us to test the effect of the Generalized NK (GNK) model’s interpretable parameters—sequence length, alphabet size, and assumed interactions between sequence positions—on the sparsity of fitness functions sampled from the model and, consequently, the number of measurements required to exactly recover these functions. We validate our framework by demonstrating that GNK models with parameters set according to structural considerations can be used to accurately approximate the number of samples required to recover two empirical protein fitness functions and an RNA fitness function. In addition, we show that these GNK models identify important higher-order epistatic interactions in the empirical fitness functions using only structural information.
Subcellular micropatterning for visual immunoprecipitation reveals differences in cytosolic protein complexes downstream the EGFR

Analysis of protein-protein interactions in living cells by protein micropatterning is currently limited to the spatial arrangement of transmembrane proteins and their corresponding downstream molecules. Here we present a robust method for visual immunoprecipitation of cytosolic protein complexes by use of an artificial transmembrane bait construct in combination with micropatterned antibody arrays on cyclic olefin polymer (COP) substrates. The method was used to characterize Grb2-mediated signalling pathways downstream the epidermal growth factor receptor (EGFR). Ternary protein complexes (Shc1:Grb2:SOS1 and Grb2:Gab1:PI3K) were identified and we found that EGFR downstream signalling is based on constitutively bound (Grb2:SOS1 and Grb2:Gab1) as well as on agonist-dependent protein associations with transient interaction properties (Grb2:Shc1 and Grb2:PI3K). Spatiotemporal analysis further revealed significant differences in stability and exchange kinetics of protein interactions. Furthermore, we could show that this approach is well suited to study the efficacy and specificity of SH2 and SH3 protein domain inhibitors in a live cell context. Altogether, this method represents a significant enhancement of quantitative subcellular micropatterning approaches as an alternative to standard biochemical analyses.
Phosphatidylinositol 3-kinase-independent synthesis of PtdIns(3,4)P2 by a phosphotransferase

Despite their comparatively low abundance, phosphoinositides play a central role in membrane traffic and signalling. PtdIns(3,4,5)P3 and PtdIns(3,4)P2 are uniquely important, as they promote cell growth, survival, and migration. Pathogenic organisms have developed means to subvert phosphoinositide metabolism to promote successful infection and their survival within host organisms. We demonstrate that PtdIns(3,4)P2 is generated in host cells by effectors of the enteropathogenic bacteria Salmonella and Shigella. Pharmacological, gene silencing and heterologous expression experiments revealed that, remarkably, the biosynthesis of PtdIns(3,4)P2 occurs independently of phosphoinositide 3-kinases. Instead, we found that the Salmonella effector SopB, heretofore believed to be a phosphatase, generates PtdIns(3,4)P2 de novo via a phosphotransferase/phosphoisomerase mechanism. Recombinant SopB is capable of generating PtdIns(3,4)P2 from PtdIns(4,5)P2 in a cell-free system. Through a remarkable instance of convergent evolution, bacterial effectors acquired the ability to synthesize 3-phosphorylated phosphoinositides by an ATP- and kinase-independent mechanism, thereby subverting host signaling to gain entry and even provoke oncogenic transformation.
Distinct mechanoreceptor pezo-1 isoforms modulate food intake in the nematode Caenorhabditis elegans

Two PIEZO mechanosensitive cation channels, PIEZO1 and PIEZO2, have been identified in mammals, where they are involved in numerous sensory processes. While structurally similar, PIEZO channels are expressed in distinct tissues and exhibit unique properties. How different PIEZOs transduce force, how their transduction mechanism varies, and how their unique properties match the functional needs of the tissues they are expressed in remain all-important unanswered questions. The nematode Caenorhabditis elegans has a single PIEZO ortholog (pezo-1) predicted to have twelve isoforms. These isoforms share many transmembrane domains but differ in those that distinguish PIEZO1 and PIEZO2 in mammals. We used transcriptional and translational reporters to show that putative promoter sequences immediately upstream of the start codon of long pezo-1 isoforms predominantly drive GFP expression in mesodermally derived tissues (such as muscle and glands). In contrast, sequences upstream of shorter pezo-1 isoforms resulted in GFP expression primarily in neurons. Putative promoters upstream of different isoforms drove GFP expression in different cells of the same organs of the digestive system. The observed unique pattern of complementary expression suggests that different isoforms could possess distinct functions within these organs. We used mutant analysis to show that pharyngeal muscles and glands require long pezo-1 isoforms to respond appropriately to the presence of food. The number of pezo-1 isoforms in C. elegans, their putative differential pattern of expression, and roles in experimentally tractable processes make this an attractive system to investigate the molecular basis for functional differences between members of the PIEZO family of mechanoreceptors.
Testing the maintenance of natural responses to survival-relevant calls in the conservation breeding population of a critically endangered corvid (Corvus hawaiiensis)

Abstract Vocal communication serves an important role in driving many animals’ social interactions and ultimately their survival. However, both the structure of and responses towards natural vocal behavior can be lost or subject to alteration under human care. Determining if animals in conservation breeding programs exhibit and respond appropriately to species-specific vocalizations is therefore important for ensuring their survival and persistence post-release. We tested whether the endangered ‘alalā ( Corvus hawaiiensis ), which is extinct in nature, has retained their natural responses to vocal calls that were previously linked to survival and reproduction in the wild. We conducted our studies on breeding populations derived from a small number of founding ‘alalā maintained under human care since their extinction in the wild in 2002. We presented pairs of ‘alalā with alarm, territorial intrusion, and two types of control playback calls (a non-threatening territorial maintenance call and a novel heterospecific call). ‘Alalā were significantly more likely to approach the speaker following alarm call playback than other call types, and was more likely to respond to territorial intrusion calls with the same aggressive territorial calls. Males were more likely to make these aggressive calls than females, mirroring their roles in territory defense. We also found individual consistency in the level of vocal behavior response across all call types, indicating that some individuals are more vocal than others. These results are encouraging, showing that ‘alalā exhibit relevant, species-specific behaviors despite generations under human care. They do illustrate, however, that not all individuals respond appropriately, so animals’ responses to vocal stimuli may be an important factor to consider in determining the release suitability of individuals. Significance statement Effective communication is crucial to the survival of many animals, but can erode without natural selection. Therefore, testing the flexibility and maintenance of communication and vocal responses in contexts where animals are isolated from conspecifics or from survival consequences, such as in conservation breeding centers, can help determine species’ susceptibility to communication loss. We used playbacks of survival-related conspecific calls to test if ‘alalā ( Corvus hawaiiensis ) retained species-specific responses to these calls after generations under human care. We found that birds maintained a species-level natural response; however, these natural responses were not consistent across individuals, suggesting that some birds may not be well equipped to survive in the wild without additional training or care.