Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural manipulations of a shelter resource reveal underlying preference functions in a shell-dwelling cichlid fish

Many animals can modify the environments in which they live, thereby changing the selection pressures they experience. A common example of such niche-construction is the use, creation, or modification of environmental resources for use as nests or shelters. Because these resources often have correlated structural elements, it can be difficult to disentangle the relative contribution of these elements to resource choice, and the preference functions underlying niche-construction behaviour remain hidden. Here, we present an experimental paradigm that uses 3D-scanning, -modelling, and -printing to create replicas of structures that differ with respect to key structural attributes. We show that a niche-constructing, shelldwelling cichlid fish, Neolamprologus multifasciatus, has strong open-ended preference functions for exaggerated shell replicas. Fish preferred shells that were fully intact and either enlarged, lengthened, or had widened apertures. Shell intactness was the most important structural attribute, followed by shell length, then aperture width. We disentangle the relative roles of different shell attributes, which are tightly correlated in the wild, but nevertheless differentially influence shelter choice and therefore niche construction in this species. We highlight the broad utility of our approach when compared to more traditional methods (e.g. two-choice tasks) for studying animal decision-making in a range of contexts.
A Systematic Protein Turnover Map for Decoding Protein Degradation

Protein degradation is mediated by an expansive and complex network of protein modification and degradation enzymes. Matching degradation enzymes with their targets and determining globally which proteins are degraded by the proteasome or lysosome/vacuole has been a major challenge. Further, an integrated view of protein degradation for cellular pathways has been lacking. Here we present a novel analytical platform that combines systematic gene deletions with quantitative measures of protein turnover to deconvolve protein degradation pathways for S. cerevisiae. The resulting turnover map (T-MAP) reveals target candidates of nearly all E2 and E3 ubiquitin ligases and identifies the primary degradation routes for most proteins. We further mined this T-MAP to identify new substrates of ER-associated Degradation (ERAD) involved in sterol biosynthesis and to uncover novel regulatory nodes for sphingolipid biosynthesis. The T-MAP approach should be broadly applicable to the study of other cellular processes and systems, including mammalian systems. One Sentence Summary A systematic, global map of protein turnover for a large set of yeast mutants reveals scope and specificity of degradation pathways and identifies novel regulatory nodes for lipid metabolism.
The extracellular matrix phenome across species

Extracellular matrices are essential for cellular and organismal function. Recent genome-wide and phenome-wide association studies started to reveal a broad spectrum of phenotypes associated with genetic variants. However, the phenome or spectrum of all phenotypes associated with genetic variants in extracellular matrix genes is unknown. Here, we analyzed over two million recorded genotype-to-phenotype relationships across hundreds of species to define their extracellular matrix phenomes. By using previously defined matrisomes of humans, mice, zebrafish, Drosophila, and C. elegans, we found that the extracellular matrix phenome comprises of 3-10% of the entire phenome. Collagens (COL1A1, COL2A1) and fibrillin (FBN1) are each associated with more than 150 distinct phenotypes in humans, whereas collagen COL4A1, Wnt- and sonic hedgehog (shh) signaling are predominantly associated in other species. We determined the phenotypic fingerprints of matrisome genes and found that MSTN, CTSD, LAMB2, HSPG2, and COL11A2 and their corresponding orthologues have the most phenotypes across species. Out of the 42’558 unique matrisome genotype-to-phenotype relationships across the five species with defined matrisomes, we have constructed interaction networks to identify the underlying molecular components connecting with orthologues phenotypes and with novel phenotypes. Thus, our networks provide a framework to predict unassessed phenotypes and their potential underlying molecular interactions. These frameworks inform on matrisome genotype-to-phenotype relationships and potentially provide a sophisticated choice of biological model system to study human phenotypes and diseases. Highlights 7.6% of the human phenome originates from variations in matrisome genes 11’671 phenotypes are linked to matrisome genes of humans, mice, zebrafish, Drosophila, and C. elegans Expected top ECM phenotypes are developmental, morphological and structural phenotypes Nonobvious top ECM phenotypes include immune system, stress resilience, and age-related phenotypes
Essential roles for deubiquitination in Leishmania life cycle progression

The parasitic protozoan Leishmania requires proteasomal, autophagic and lysosomal proteolytic pathways to enact the extensive cellular remodelling that occurs during its life cycle. The proteasome is essential for parasite proliferation, yet little is known about the requirement for ubiquitination/deubiquitination processes in growth and differentiation. Activity-based protein profiling of L. mexicana C12, C19 and C65 deubiquitinating cysteine peptidases (DUBs) revealed DUB activity remains relatively constant during differentiation of procyclic promastigote to amastigote. However, when Bar-seq was applied to a pool of 16 DUB null mutants created in promastigotes using CRISPR-Cas9, significant loss of fitness was observed during differentiation and intracellular infection. DUBs 4, 7, and 13 are required for successful transformation from metacyclic promastigote to amastigote and DUBs 3, 5, 6, 10, 11 and 14 are required for normal amastigote proliferation in mice. DUBs 1, 2, 12 and 16 are essential for promastigote viability and the essential role of DUB2 in establishing infection was demonstrated using DiCre inducible gene deletion in vitro and in vivo. DUB2 is found in the nucleus and interacts with nuclear proteins associated with transcription/chromatin dynamics, mRNA splicing and mRNA capping. DUB2 has broad linkage specificity, cleaving all the di-ubiquitin chains except for Lys27 and Met1. Our study demonstrates the crucial role that DUBs play in differentiation and intracellular survival of Leishmania and that amastigotes are exquisitely sensitive to disruption of ubiquitination homeostasis. Author Summary Leishmania parasites require a variety of protein degradation pathways to enable the parasite to transition through the various life cycle stages that occur in its insect and mammalian hosts. Several enzymes involved in protein degradation in Leishmania are known to be essential, including a multi-protein complex, the proteasome, but little is known about how proteins are targeted to the proteasome for degradation. Here, we analyse components of the deubiqutination pathway, including twenty cysteine peptidases (DUBs) that remove the posttranslational modifier ubiquitin from substrates tagged for proteasomal degradation. We used chemical probes to measure active enzymes in parasite lysates and genome engineering to create DUB gene deletion mutants. We identified some DUBs that are essential for parasite viability and some that are required for life cycle progression. We carried out a detailed analysis of the essential DUB2, which has broad deubiquitinase activity and is found in the nucleus. This enzyme interacts with nuclear proteins associated with transcription/chromatin dynamics, mRNA splicing and mRNA capping. This work demonstrates the important role that DUBs play in Leishmania in vivo infection and further validates DUBs as potential drug targets in this parasite.
The m6A reader Ythdf restricts axonal growth in Drosophila through target selection modulation of the Fragile X mental retardation protein

N6-methyladenosine (m6A) regulates a variety of physiological processes through modulation of RNA metabolism. The modification is particularly enriched in the nervous system of several species, and its dysregulation has been associated with neurodevelopmental defects and neural dysfunctions. In Drosophila, loss of m6A alters fly behavior albeit the underlying mechanism and the role of m6A during nervous system development have remained elusive. Here we find that impairment of the m6A pathway leads to axonal overgrowth and misguidance at larval neuromuscular junctions as well as in the adult mushroom bodies. We identify Ythdf as the main m6A reader in the nervous system being required for limiting axonal growth. Mechanistically, we show that Ythdf directly interacts with Fragile X mental retardation protein to inhibit the translation of key transcripts involved in axonal growth regulation. Altogether, this study demonstrates that the m6A pathway controls development of the nervous system by modulating Fmr1 target selection.
Dystroglycan proteolysis is conformationally-regulated and disrupted by disease-associated mutations

The adhesion receptor dystroglycan provides a critical mechanical link between the extracellular matrix (ECM) and the actin cytoskeleton to help muscle cells withstand contraction and neural cells maintain the blood brain barrier. Disrupting the link is associated with diseases such as cancer and muscular dystrophy. Proteolysis of dystroglycan by Matrix Metalloproteases (MMPs) also breaks the mechanical anchor and is amplified in several pathogenic states. We use a combination of biochemical and cell-based assays to show that dystroglycan proteolysis is conformationally regulated by an extracellular, juxtamembrane “proteolysis domain”, comprised of tandem Ig-like and SEA-like domains. The intact proteolysis domain is resistant to MMP cleavage, but structurally-disruptive muscular dystrophy-related mutations sensitize dystroglycan to proteolysis. Moreover, increased dystroglycan proteolysis correlates with faster cell migration, linking proteolysis to a disease-relevant cellular phenotype. Intriguingly, previously uncharacterized cancer-associated mutations that map to the proteolysis domain similarly lead to increases in proteolysis and rates of cell migration, potentially revealing a new pathogenic mechanism in cancer.
JNK signaling regulates oviposition in the malaria vector Anopheles gambiae

The reproductive fitness of the Anopheles gambiae mosquito represents a promising target to prevent malaria transmission. The ecdysteroid hormone 20-hydroxyecdysone (20E), transferred from male to female during copulation, is key to An. gambiae reproductive success as it licenses females to oviposit eggs developed after blood feeding. Here we show that 20E-triggered oviposition in these mosquitoes is regulated by the stress- and immune-responsive c-Jun N-terminal kinase (JNK). The heads of mated females exhibit a transcriptional signature reminiscent of a JNK-dependent wounding response, while mating—or injection of virgins with exogenous 20E—selectively activates JNK in the same tissue. RNAi-mediated depletion of JNK pathway components inhibits oviposition in mated females, whereas JNK activation by silencing the JNK phosphatase puckered induces egg laying in virgins. Together, these data identify JNK as a potential conduit linking stress responses and reproductive success in the most important vector of malaria.
Wide awake at bedtime? The effects of caffeine on sleep and circadian timing in teenagers - a randomized crossover trial

Background Adolescents frequently consume caffeine with unknown consequences on sleep and circadian rhythms. In adults, the evidence indicates that caffeine acutely reduces homeostatic sleep pressure and delays the circadian timing system. Objective Here, we investigated the acute effects of caffeine intake on the developing sleep-wake regulatory system of teenagers. Design In a double-blind randomized crossover laboratory study, 18 teenagers (16.1 ± 1 years old, pubertal development scale [PDS]: 2.76 ± 0.35) ingested 80 mg caffeine (vs placebo) four hours prior to bedtime. Until bedtime, participants regularly filled in the Karolinska Sleepiness Scale and gave saliva samples to measure melatonin secretion. During nighttime, we quantified homeostatic sleep need by the electroencephalographically derived amount of slow wave sleep duration (SWS). After sleep, participants rated sleep quality by the Leeds Sleep Evaluation Questionnaire. Results While participants felt less sleepy after caffeine vs. placebo (P=0.038), their ratings of sleep quality were not strongly affected by the treatment. However, objectively, SWS was on average reduced by ∼20 min after caffeine vs. placebo (P=0.026). This caffeine-induced reduction was more pronounced in those individuals with more SWS under placebo (regression: P=0.042; standardized beta=0.622, P=0.011), even if controlling for habitual caffeine intake or pubertal stage (PDS). In melatonin onsets we observed both delays and advances in response to caffeine. This variance could partly be explained by differences in relative dose (i.e., mg caffeine/kg of bodyweight): the higher the relative dose, the more likely were delays (regression: P=0.01; standardized beta=0.592, P=0.01). Conclusions In teenagers, evening caffeine intake of already 80 mg (i.e. ∼8fl oz of common energy drinks) is sufficient to promote alertness at the costs of subsequent sleep. These costs might be more pronounced in adolescents with a higher need for SWS. Moreover, caffeine might disturb the circadian timing system, consequently hampering the balanced interplay of sleep-wake regulatory components. Sources of Support Marie-Heim-Voegtlin Grant of the Swiss National Science Foundation (SNSF) PMPDP1_171364
Glycoengineering of NK cells with glycan ligands of CD22 and selectins for B-cell lymphoma therapy

CD22, a member of Siglec family of sialic acid binding proteins, has restricted expression on B cells. Antibody-based agents targeting CD22 or CD20 (Rituxan™) on B lymphoma and leukemia cells exhibit clinical efficacy for treating these malignancies, but also attack normal B cells leading to immune deficiency. Here, we report a chemoenzymatic glycocalyx editing strategy to introduce high-affinity and specific CD22 ligands onto NK-92MI and cytokine-induced killer (CIK) cells to achieve tumor-specific CD22 targeting. These CD22-ligand modified cells exhibited significantly enhanced tumor cell binding and killing in vitro without harming healthy B cells. For effective lymphoma cell killing in vivo we further functionalized CD22 ligand-modified NK-92MI cells with the E-selectin ligand sialyl Lewis X to promote trafficking to bone marrow. The cells containing the ligands of both CD22 and selectins resulted in the efficient suppression of B lymphoma in a xenograft model. Our results suggest that NK cells modified with glycan ligands to CD22 and selectins promote both targeted killing of B lymphoma cells and improved trafficking to sites where the cancer cells reside, respectively.
Crystal structures of the sheeppoxvirus encoded inhibitor of apoptosis SPPV14 bound to Hrk and Bax BH3 peptides

Programmed death of infected cells is used by multicellular organisms to counter viral infections. Sheeppoxvirus encodes for SPPV14, a potent inhibitor of Bcl-2 mediated apoptosis. We reveal the structural basis of apoptosis inhibition by determining crystal structures of SPPV14 bound to BH3 motifs of proapoptotic Bax and Hrk. The structures show that SPPV14 engages BH3 peptides using the canonical ligand binding groove. Unexpectedly, Arg84 from SPPV14 forms an ionic interaction with the conserved Asp in the BH3 motif in a manner that replaces the canonical ionic interaction seen in almost all host Bcl-2:BH3 motif complexes. These results reveal the flexibility of virus encoded Bcl-2 proteins to mimic key interactions from endogenous host signalling pathways to retain BH3-binding and pro-survival functionality.
Designing Topographically Textured Microparticles for Induction and Modulation of Osteogenesis in Mesenchymal Stem Cell Engineering

Mesenchymal stem cells have been the focus of intense research in bone development and regeneration. We demonstrate the potential of microparticles as modulating moieties of osteogenic response by utilizing their architectural features. Topographically textured microparticles of varying microscale features were produced by exploiting phase-separation of a readily-soluble sacrificial component from polylactic acid. The influence of varying topographical features on primary human mesenchymal stem cell attachment, proliferation and markers of osteogenesis was investigated. In the absence of osteoinductive supplements, cells cultured on textured microparticles exhibited notably increased expression of osteogenic markers relative to conventional smooth microparticles. They also exhibited varying morphological, attachment and proliferation responses. Significantly altered gene expression and metabolic profiles were observed, with varying histological characteristics in vivo. This study highlights how tailoring topographical design offers cell-instructive 3D microenvironments which allow manipulation of stem cell fate by eliciting the desired downstream response without use of exogenous osteoinductive factors.
Noise propagation in metabolic pathways: the role of growth-mediated feedback

Metabolic networks are known to deal with the chemical reactions responsible to fuel cellular activities with energy and carbon source and, as a matter of fact, to set the growth rate of the cell. To this end, feedback and regulatory networks play a crucial role to handle adaptation to external perturbations and internal noise. In this work, a cellular resource is assumed to be activated at the end of a metabolic pathway, by means of a cascade of transformations. Such a cascade is triggered by the catalytic action of an enzyme that promotes the first transformation. The final product is responsible for the cellular growth rate modulation. This mechanism acts in feedback at the enzymatic level, since the enzyme (as well as all species) is subject to dilution, with the dilution rate set by growth. Enzymatic production is modeled by the occurrence of noisy bursts: a Stochastic Hybrid System is exploited to model the network and to investigate how such noise propagates on growth fluctuations. A major biological finding is that, differently from other models of metabolic pathways disregarding growth-mediated feedback, fluctuations in enzyme levels do not produce only local effects, but propagate up to the final product (hence to the growth rate). Furthermore, the delay provided by the cascade length helps in reducing the impact of enzymatic noise on to growth fluctuations. Analytical results are supported by Monte Carlo simulations.
Causal relationship between the right auditory cortex and speech-evoked frequency-following response: Evidence from combined tDCS and EEG

Speech-evoked frequency-following response (FFR) reflects the neural encoding of speech periodic information in the human auditory systems. FFR is of fundamental importance for pitch and speech perception and serves as clinical biomarkers for various auditory and language disorders. While it is suggested that the main neural source of FFR is in the auditory brainstem, recent studies have shown a cortical contribution to FFR predominantly in the right hemisphere. However, it is still unclear whether auditory cortex and FFR are causally related. The aim of this study was to establish this causal relationship using a combination of transcranial direct current stimulation (tDCS) and scalp-recorded electroencephalography (EEG). We applied tDCS over the left and right auditory cortices in right-handed normal-hearing participants and examined the after-effects of tDCS on FFR using EEG during monaural listening to a repeatedly-presented speech syllable. Our results showed that: (1) before tDCS was applied, participants had greater FFR magnitude when they listened to speech from the left than the right ear, illustrating right-lateralized hemispheric asymmetry for FFR; (2) anodal and cathodal tDCS applied over the right, but not left, auditory cortex significantly changed FFR magnitudes compared to the sham stimulation; specifically, such after-effects occurred only when participants listened to speech from the left ear, emphasizing the right auditory cortical contributions along the contralateral pathway. The current finding thus provides the first causal evidence that validates the relationship between the right auditory cortex and speech-evoked FFR and should significantly extend our understanding of speech encoding in the brain. Significance Statement Speech-evoked frequency-following response (FFR) is a neural activity that reflects the brain’s encoding of speech periodic features. The FFR has great fundamental and clinical importance for auditory processing. Whilst convention maintains that FFR derives mainly from the brainstem, it has been argued recently that there are additional contributions to FFR from the auditory cortex. Using a combination of tDCS, that altered neural excitability of auditory cortices, and EEG recording, the present study provided the first evidence to validate a causal relationship between the right auditory cortex and speech-evoked FFR. The finding supports the right-asymmetric auditory cortical contributions to processing of speech periodicity and advances our understanding of how speech signals are encoded and analysed along the central auditory pathways.
Wireless recording from unrestrained monkeys reveals motor goal encoding beyond immediate reach in frontoparietal cortex

System neuroscience of motor cognition regarding the space beyond immediate reach mandates free, yet experimentally controlled movements. We present an experimental environment (Reach Cage) and a versatile visuo-haptic interaction system (MaCaQuE) for investigating goal-directed whole-body movements of unrestrained monkeys. Two rhesus monkeys conducted instructed walk-and-reach movements towards targets flexibly positioned in the cage. We tracked 3D multi-joint arm and head movements using markerless motion capture. Movements show small trial-to-trial variability despite being unrestrained. We wirelessly recorded 192 broad-band neural signals from three cortical sensorimotor areas simultaneously. Single unit activity is selective for different reach and walk-and-reach movements. Walk-and-reach targets could be decoded from premotor and parietal but not motor cortical activity during movement planning. The Reach Cage allows systems-level sensorimotor neuroscience studies with full-body movements in a configurable 3D spatial setting with unrestrained monkeys. We conclude that the primate frontoparietal network encodes reach goals beyond immediate reach during movement planning.
Dentate gyrus population activity during immobility supports formation of precise memories

The hippocampal dentate gyrus is an important relay conveying sensory information from the entorhinal cortex to the hippocampus proper. During exploration, the dentate gyrus has been proposed to act as a pattern separator. However, the dentate gyrus also shows structured activity during immobility and sleep. The properties of these activity patterns at cellular resolution, and their role in hippocampal-dependent memory processes have remained unclear. Using dual-color in-vivo two-photon Ca2+ imaging, we show that in immobile mice dentate granule cells generate sparse, synchronized activity patterns associated with entorhinal cortex activation. These population events are structured and modified by changes in the environment; and they incorporate place- and speed cells. Importantly, they recapitulate population patterns evoked during self-motion. Using optogenetic inhibition during immobility, we show that granule cell activity during immobility is required to form dentate gyrus-dependent spatial memories. These data suggest that memory formation is supported by dentate gyrus replay of population codes of the current environment.