Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of finfish farms on pelagic protist communities in a semi-closed stratified embayment

Coastal aquaculture operations for feed additive species results in the release of waste into the surrounding environment, with the potential for adverse environmental change. Ubiquitous pelagic protists are sensitive to environmental changes making them potential sentinels for detecting and monitoring impacts. This study used 18S rRNA high-throughput amplicon sequencing as a molecular tool to study the pelagic protist community, with the aim of evaluating their potential as bioindicators of aquaculture activity in a low-oxygen, highly stratified marine embayment. Sampling occurred at three different depths along a distance gradient from two leases and at three control sites. Our results showed that the diversity and composition of both phytoplankton and other protist communities were more strongly influenced by depth stratification than the aquaculture activity. Nonetheless, differential abundance and machine learning analyses revealed a suite of potential bioindicators for aquaculture activity; this included the phytoplankton taxa Chrysophyceae, Gymnodiniphycidae (Gyrodinium), Cryptomonadales and Ciliophora (Philasterides armatalis, Plagiopylida, and Strombidium). Among the other protists, ciliates were also more abundant in closer proximity to the leases in both surface and bottom samples. Overall, our findings indicated that the use of 18S rRNA sequencing of protist communities is a promising tool for identifying environmental changes from aquaculture in the water column.
Psychometric and subcortical neurometric measures of temporal discrimination in rhesus macaques

Temporal envelope fluctuations are abundant in nature and are critical for perception of complex sounds. While psychophysical sinusoidal amplitude modulation (SAM) processing studies have characterized the perception of SAM, and neurophysiological studies report a subcortical transformation from temporal to rate-based code, no studies have characterized this transformation in unanesthetized animals or in nonhuman primates. To address this, we recorded single-unit responses and compared derived neurometric measures in the cochlear nucleus (CN) and inferior colliculus (IC) to psychometric measures of modulation frequency (MF) discrimination in macaques. IC and CN neurons often exhibited tuned responses to SAM in their rate and spike-timing. Neurometric thresholds spanned a large range (2-200 Hz Δ MF). The lowest 40% of IC thresholds were less than or equal to psychometric thresholds, regardless of which code was used, while CN thresholds were greater than psychometric thresholds. Discrimination at 10-20 Hz could be explained by indiscriminately pooling 30 units in either structure, while discrimination at higher MFs was best explained by more selective pooling. This suggests that pooled brainstem activity was sufficient for AM discrimination. Psychometric and neurometric thresholds decreased as a function of stimulus duration, but IC and CN thresholds were greater and more variable than behavior at durations less than 500 ms. This slower subcortical temporal integration compared to behavior was consistent with a drift diffusion model which reproduced individual differences in performance and can constrain future neurophysiological studies of temporal integration. These measures provide an account of AM perception at the neurophysiological, computational, and behavioral levels. Significance statement Listening in everyday environments tasks the brain with extracting information from sound envelopes. This process involves both sensory encoding and decision-making. Different neural codes for envelope representation have been well characterized in the auditory midbrain and cortex, but studies of the brainstem have usually been conducted in anesthetized rodents or cats. Moreover, these candidate neural codes have been studied in isolation from the decision-making process. In this study, we found that population activity in the primate subcortical auditory system contains sufficient information for discriminating sound envelope and applied a biologically plausible model of decision-making to sound envelope discrimination performance from rhesus macaques, a species with great phylogenetic and perceptual similarity to humans.
Evaluating material-driven regeneration in a tissue engineered human in vitro bone defect model

Advanced in vitro human bone defect models can contribute to the evaluation of materials for in situ bone regeneration, addressing both translational and ethical concerns regarding animal models. In this study, we attempted to develop such a model to study material-driven regeneration, using a tissue engineering approach. By co-culturing human umbilical vein endothelial cells (HUVECs) with human bone marrow-derived mesenchymal stromal cells (hBMSCs) on silk fibroin scaffolds with in vitro critically sized defects, the growth of vascular-like networks and three-dimensional bone-like tissue was facilitated. After a model build-up phase of 28 days, materials were artificially implanted and HUVEC and hBMSC migration, cell-material interactions, and osteoinduction were evaluated 14 days after implantation. The materials physiologically relevant for bone regeneration included a platelet gel as blood clot mimic, cartilage spheres as soft callus mimics, and a fibrin gel as control. Although the in vitro model was limited in the evaluation of immune responses, hallmarks of physiological bone regeneration were observed in vitro. These included the endothelial cell chemotaxis induced by the blood clot mimic and the mineralization of the soft callus mimic. Therefore, the present in vitro model could contribute to an improved pre-clinical evaluation of biomaterials while reducing the need for animal experiments. Graphical abstract
Transcriptomic analyses reveal neuronal specificity of Leigh syndrome associated genes

Leigh syndrome (subacute necrotising encephalomyelopathy) is a rare inherited, complex, and typically early onset mitochondrial disorder with clinical and genetic heterogeneity. It owes its heterogeneous nature to the complex nature of mitochondrial genetics and the significant interactions that occur between the mitochondrial and nuclear genomes. Stepwise developmental regression is a classical feature of patients with Leigh syndrome, but other neurological features include ataxia, tremor, seizures, and occasionally psychiatric manifestations. To date the involvement of more than 100 genes has been identified in patients with Leigh syndrome. Despite this, the pathophysiology of Leigh syndrome remains unknown, although it is thought to be due to primary mitochondrial dysfunction. Here, we sought to determine the cellular specificity of all Leigh syndrome associated genes within the brain and investigate a potential common genetic mechanism between Leigh syndrome and other disorders with overlapping clinical features. We utilized co-expression network analyses constructed using existing UK Brain Expression Consortium (UKBEC) data from 10 brain regions to identify regions of the brain where our genes of interest were enriched. Next, expression weighted cell type enrichment (EWCE) was employed to determine the cellular specificity of Leigh syndrome associated genes. Association with pre-or post-synaptic structures was identified using synaptic gene ontology (SynGO) analysis. Finally, heritability analysis was performed on the co-expression network modules demonstrating enrichment of Leigh syndrome associated genes to investigate potential genetic relationships with Parkinson disease, epilepsy, and schizophrenia. Co-expression network analyses reveal that genes encoding oxidative phosphorylation subunits and assembly factors exhibit the highest levels of expression in brain regions most affected on MRI and neuropathology in Leigh syndrome. Further, over two thirds of the genes were found to be enriched within the substantia nigra and 19 genes appeared to cluster, with selective enrichment in the putamen, substantia nigra, medulla and thalamus. EWCE analyses of single cell RNA-Seq data from mouse brain revealed significant enrichment of Leigh syndrome associated genes in hippocampal and somatosensory pyramidal neurones and interneurons of the brain. SynGO analysis demonstrated that expression of these genes is preferentially associated with pre-synaptic structures. Heritability studies suggested that some modules in which Leigh syndrome associated genes were enriched were also enriched for Parkinson disease and epilepsy. In conclusion, our findings suggest a primary mitochondrial dysfunction as the underlying basis of Leigh syndrome with causative genes primarily expressed in neuronal cells, explaining the relative sparing of glial cells observed in neuropathological studies.
AVP neurons act as the primary circadian pacesetter cells in vivo

The central circadian clock of the suprachiasmatic nucleus (SCN) is a network consisting of various neurons and glia. Individual cells have the autonomous molecular machinery of a cellular clock, but their intrinsic periods are considerably variable. Here, we show that arginine vasopressin (AVP) neurons set the ensemble period of the SCN network to control circadian behavior rhythm. Artificial lengthening of cellular periods by deleting casein kinase 1 delta (CK1δ) in the whole SCN lengthened the free-running period of behavior rhythm to an extent similar to CK1δ deletion specific to AVP neurons. In SCN slices, PER2::LUC reporter rhythms of these mice did not recapitulate the period lengthening. However, in vivo calcium rhythms of both AVP and vasoactive intestinal peptide (VIP) neurons demonstrated lengthened periods similar to the behavioral rhythm upon AVP neuron-specific CK1δ deletion. These results indicate that AVP neurons act as the primary determinant of the SCN ensemble period.
The role and mechanism of NRF2 in endothelial cells and smooth muscle cells of pulmonary artery

Pulmonary hypertension (PH) is a kind of fatal disease. There are no existing drugs that could reverse the diseas. NF-E2-related factor 2 (NRF2) is one of the most important moleculars in the range of cell protection. We examined the expression of NRF2 in PH models and explored the role of NRF2 in regulating abnormal phenotypes in pulmonary artery cells. We determined the expression level of NRF2 in lung tissues of PH model decreased significantly. We found that NRF2 was reduced in rat pulmonary artery endothelial cells (rPAEC) under hypoxia, while it was overexpressed in rat pulmonary artery smooth muscle cells (rPASMC) under hypoxia. Next, the results showed that knockdown NRF2 in rPAEC promoted endothelial-mesenchymal transformation and upregulated reactive oxygen species level. After the rPASMC was treated with siRNA or activator, we found that NRF2 could promote cell proliferation by regulating PDGFR/ERK1/2 and mTOR/P70S6K pathways, and accelerate cell migration by affecting MMP2/3/7. Therefore, the study suggests that the combination of NRF2 activators should be considered to eliminate the promoting effect of NRF2 activators on proliferation and migration of rPASMC. Summary statement Hypoxia regulates NRF2 in PAECs and PASMCs differently. We found that NRF2 could promote cell proliferation by regulating PDGFR/ERK1/2 and mTOR/P70S6K pathways, and accelerate cell migration by affecting MMP2/3/7.
TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes

Target of rapamycin complex 1 (TORC1) promotes biogenesis and inhibits degradation of ribosomes in response to nutrient availability. To ensure a basal supply of ribosomes, cells preserve a small pool of dormant ribosomes under nutrient-limited conditions. The regulation of dormant ribosomes is poorly characterized. Here, we show that upon inhibition of TORC1 by rapamycin or nitrogen starvation, Stm1 (suppressor of target of Myb protein 1) forms non-translating, dormant 80S ribosomes. Furthermore, Stm1-bound 80S ribosomes are protected from proteasomal degradation. Upon re-feeding, TORC1 directly phosphorylates and inhibits Stm1, thereby reactivating translation. Finally, SERBP1 (SERPINE1 mRNA binding protein), a mammalian ortholog of Stm1, forms dormant 80S ribosomes upon mTORC1 inhibition in mammalian cells. Thus, TORC1 regulates ribosomal dormancy in an evolutionarily conserved manner via a ribosome preservation factor.
Connexin 43 hemichannels regulate mitochondrial ATP generation, mobilization, and mitochondrial homeostasis against oxidative stress

Oxidative stress is a major risk factor that causes osteocyte cell death and bone loss. Prior studies primarily focus on the function of cell surface expressed Cx43 channels. Here, we reported a new role of mitochondrial Cx43 (mtCx43) and hemichannels (HCs) in modulating mitochondria homeostasis and function in bone osteocytes under oxidative stress. In osteocyte MLO-Y4 cells, the translocation of Cx43 to mitochondria was increased under H2O2-induced oxidative stress. H2O2 increased the mtCx43 level accompanied by elevated mitochondrial Cx43 HC activity determined by dye uptake assay. Cx43 knockdown (KD) by CRISPR-Cas9 lentivirus system resulted in impairment of mitochondrial function, primarily manifested as decreased ATP production. Cx43 KD had reduced intracellular reactive oxidative species (ROS) levels and mitochondrial membrane potential. Additionally, live-cell imaging results demonstrated that the proton flux was dependent upon mtCx43 HCs because its activity was specifically inhibited by an antibody targeting Cx43 C-terminus. The co-localization and interaction of mtCx43 and ATP synthase subunit F (ATP5J2) were confirmed by fluorescence resonance energy transfer (FRET) and a protein pull-down assay. Together, our study suggests that mtCx43 hemichannels regulate mitochondrial ATP generation by mediating K+, H+, and ATP transfer across the mitochondrial inner membrane and the interaction with mitochondrial ATP synthase, leading to enhancing the protection capacity of osteocytes against oxidative insults.
Dynamics and mechanisms of ERK activation after different protocols that induce long-term facilitation in Aplysia

The mitogen-activated protein kinase (MAPK) isoform extracellular signal–regulated kinase (ERK) is a key kinase involved in the induction of long-term synaptic facilitation (LTF) of the Aplysia sensorimotor synapse. Therefore, elucidating the dynamics of ERK activation after LTF-inducing protocols is critical for understanding the mechanisms underlying neuronal and synaptic plasticity. ERK activation has rich dynamic features. After a single stimulus, activation peaks 45-minute later and declines rapidly, but after two stimuli spaced 45 min apart, activation persists (Kopec et al. 2015). However, little is known about possible changes in ERK activation for periods beyond 3 h. Given its key role in long-term learning, understanding the dynamics of ERK at 3 h and beyond might provide insights into new protocols that could enhance memory retention. Three different protocols that induce LTF were used to probe the dynamics of ERK activation. The first, termed the Standard protocol, consists of five 5-min pulses of serotonin (5-HT) with regular interstimulus intervals (ISIs) of 20 min. The second, termed the Enhanced protocol, consists of five pulses of 5-HT with irregular ISIs identified with the use of computer simulations. This protocol induces greater and longer-lasting LTF than the Standard protocol. A third protocol, termed the two-pulse protocol, consists of just two 5-min pulses of 5-HT with an ISI of 45 min. Immunofluorescence revealed complex patterns of ERK activation up to 24 h after 5-HT treatment. The Standard and two-pulse protocols led to an immediate increase in active, phosphorylated ERK (pERK), which decayed within 5 h post treatment. A second wave of increased pERK was detected at 18 h post treatment. This late phase was blocked by RpcAMP (an inhibitor of protein kinase A), and by TrkB Fc and TGF-β RII F antagonists. The latter two are chimeras that act via receptor sequestration. These results suggest that complex interactions among kinase pathways and growth factor cascades contribute to the late increase of ERK activity after different LTF-inducing protocols. Interestingly, ERK activity returned to basal levels 24 h after the Standard or two-pulse protocol, but remained elevated 24 h after the Enhanced protocol. This finding may help explain, in part, why the Enhanced protocol is superior to the Standard protocol in inducing long-lasting LTF.
Observations on Paleospecies Determination, With Additional Data on Tyrannosaurus Including Its Highly Divergent Species Specific Supraorbital Display Ornaments That Give T. rex a New and Unique Life Appearance

Intrageneric dinosaur species have been being named for decades without either significant examination of the methods and standards used to do so, or widely publicized controversy over the results. The long standing assumption that all large known specimens of the iconic North American Tyrannosaurus consisted of just the one popular species T. rex was recently challenged with the first comprehensive test of the question. The result was the diagnosing and naming of two additional taxa, T. imperator and T. regina, based on a number of species levels characters regarding robustness and tooth proportions in the context of their stratigraphic distribution. In association a rare in-depth look was taken at the current state of naming vertebrate paleospecies, which it turns out are not highly rigorous because of inherent problems with the species concept and other matters. The results of the paper were severely criticized in in a manner never seen before for new dinosaur species even when based on less evidence. This study takes another look as the determination of paleospecies, and shows that many of the claims made in the criticisms regarding the Tyrannosaurus species work were inaccurate. New data on the proportions of strength bars in Tyrannosaurus skulls reinforces the basing of the three species in part on robustness factors, and allows all but one skull to be assigned to one of the species. These results allow the first detailed systematic examination of the supraorbital display bosses of the genus. They sort out as visually distinctive species specific ornaments based on both stratigraphic and taxonomic factors, strongly affirm that Tyrannosaurus was multispecific, and the species probably dimorphic. New skulls of T. rex show that the species sported – males probably -- striking display bosses not yet observed in other tyrannosaurids.
Selection on sperm size in response to promiscuity and variation in female sperm storage organs

Sperm cells are exceptionally morphologically diverse across taxa. However, morphology can be quite uniform within species, particularly for species where females copulate with many males per reproductive bout. Strong sexual selection in these promiscuous species is widely hypothesized to reduce intraspecific sperm variation. Conversely, we hypothesize that intraspecific sperm size variation may be maintained by high among-female variation in the size of sperm storage organs, assuming that paternity success improves when sperm are compatible in size with the sperm storage organ. We use individual-based simulations and an analytical model to evaluate how selection on sperm size depends on promiscuity level and variation in sperm storage organ size (hereafter, female preference variation). Simulated species with high promiscuity showed stabilizing selection on sperm when female preference variation was low, and disruptive selection when female preference variation was high, consistent with the analytical model results. With low promiscuity (2-3 mates per female), selection on sperm was stabilizing for all levels of female preference variation in the simulations, contrasting with the analytical model. Promiscuity level, or mate sampling, thus has a strong impact on the selection resulting from female preferences. Further, for species with low promiscuity, disruptive selection on male traits will occur under more limited circumstances than many previous models suggest. Variation in female sperm storage organs likely has strong implications for intraspecific sperm variation in highly promiscuous species, but likely does not explain differences in intraspecific sperm variation for less promiscuous taxa.
High-frequency quantitative ultrasound to assess the acoustic properties of engineered tissues in vitro

Acoustic properties of biomaterials and engineered tissues reflect their structure and cellularity. High-frequency ultrasound (US) can non-invasively characterize and monitor these properties with sub-millimetre resolution. We present an approach to estimate the acoustic properties of cell-laden hydrogels that accounts for frequency-dependent effects of attenuation in coupling media, hydrogel thickness, and interfacial transmission/reflection coefficients of US waves, all of which can bias attenuation estimates. Cell-seeded fibrin hydrogel disks were raster-scanned using a 40 MHz US transducer. Thickness, speed of sound, acoustic impedance, and acoustic attenuation coefficients were determined from the difference in the time-of-flight and ratios of the magnitudes of US signals, interfacial transmission/reflection coefficients, and acoustic properties of the coupling media. With this approach, hydrogel thickness was accurately measured by US, with excellent agreement to confocal microscopy (r2 = 0.97). Accurate thickness measurement enabled acoustic property measurements that were independent of hydrogel thickness, despite up to 60% reduction in thickness due to cell-mediated contraction. Notably, acoustic attenuation coefficients increased with increasing cell concentration (p<0.001), reflecting hydrogel cellularity independent of contracted hydrogel thickness. This approach enables accurate measurement of the intrinsic acoustic properties of biomaterials and engineered tissues to provide new insights into their structure and cellularity.
An investigation of the sex-specific genetic architecture of fitness in Drosophila melanogaster

In dioecious populations, the sexes employ divergent reproductive strategies to maximize fitness and, as a result, genetic variants can affect fitness differently in males and females. Moreover, recent studies have highlighted an important role of the mating environment in shaping the strength and direction of sex-specific selection. Here, we measure adult fitness for each sex of 357 lines from the Drosophila Synthetic Population Resource (DSPR) in two different mating environments. We analyze the data using three different approaches to gain insight into the sex-specific genetic architecture for fitness: classical quantitative genetics, genomic associations, and a mutational burden approach. The quantitative genetics analysis finds that, on average segregating genetic variation in this population has concordant fitness effects both across the sexes and across mating environments. We do not find specific genomic regions with strong associations with either sexually antagonistic (SA) or sexually concordant (SC) fitness effects, yet there is modest evidence of an excess of genomic regions with weak associations, both with SA and SC fitness effects. Our examination of mutational burden indicates stronger selection against indels and loss-of-function variants in females than males.