Miracle-dz/UniFAR-FTUs huggingface dataset:
Human melanocyte development and melanoma dedifferentiation at single cell resolution

In humans, epidermal melanocytes are responsible for skin pigmentation, defense against ultraviolet radiation, and the deadliest common skin cancer, melanoma. While there is substantial overlap in melanocyte development pathways between different model organisms, species dependent differences are frequent and the conservation of these processes in human skin remains unresolved1–3. Thus, the biology of developing and adult human melanocytes remains largely uncharacterized. Here, we used a single-cell enrichment and RNA-sequencing pipeline to study human epidermal melanocytes derived directly from skin, capturing transcriptomes across different anatomic sites, developmental age, sexes, and multiple skin tones. Using donor-matched skin from distinct volar and non-volar anatomic locations, we uncovered subpopulations of melanocytes exhibiting site-specific enrichment that occurs during gestation and persists through adulthood. In addition, we identified human melanocyte differentiation transcriptional programs that are distinct from gene signatures generated from model systems. Finally, we use these programs to define patterns of dedifferentiation that are predictive of melanoma prognosis. Overall, the characterization of human melanocytes fresh from skin revealed new subpopulations, human-specific transcriptional programs, and valuable insights into melanoma dedifferentiation.
Population structure and transmission of Mycobacterium bovis in Ethiopia

Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis (M. bovis), which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole genome sequencing (WGS) to examine the population structure of M. bovis in Ethiopia. A total of 134 M. bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis, based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.
Sensory-based quantification of male colour patterns in Trinidadian guppies reveals nonparallel phenotypic evolution across an ecological transition in multivariate trait space

Parallel evolution, in which independent populations evolve along similar phenotypic trajectories, offers insights into the repeatability of adaptive evolution. Here, we revisit a classic example of parallelism, that of repeated evolution of brighter males in the Trinidadian guppy. In guppies, colonisation of low predation habitats is associated with emergence of ‘more colourful’ phenotypes since predator-induced viability selection for crypsis weakens while sexual selection by female preference for conspicuity remains strong. Our study differs from previous investigations in three respects. First, we adopt a multivariate phenotyping approach to characterise parallelism in multi-trait space. Second, we use ecologically-relevant colour traits defined by the visual systems of the two selective agents (i.e. guppy, predatory cichlid). Third, we estimate population genetic structure to test for adaptive (parallel) evolution against a model of neutral phenotypyc divergence. We find strong phenotypic differentiation that is inconsistent with a neutral model, but only limited support for the predicted pattern of greater conspicuity at low predation. Effects of predation regime on each trait were in the expected direction, but weak, largely non-significant, and explained little among-population variation. In multi-trait space, phenotypic trajectories of lineages colonising low from high predation regimes were not parallel. Our results are consistent with reduced predation risk facilitating adaptive differentiation by female choice, but suggest that this proceeds in (effectively) independent directions of multi-trait space across lineages. Pool-sequencing data also revealed SNPs showing greater differentiation than expected under neutrality and/or associations with known colour genes in other species, presenting opportunities for future genetic study.
Pupil dilation predicts individual success in emotion regulation and dietary self-control

Multiple theories have proposed that increasing central arousal through the brain’s locus coeruleus – norepinephrine system may facilitate cognitive control and memory. However, for emotion research this hypothesis poses a puzzle, because conventionally, successful emotion regulation is associated with a decrease in arousal. Pupil diameter is a proxy to infer upon the central arousal state. We employed an emotion regulation paradigm with a combination of design features that allowed us to dissociate regulation- from stimulus-associated arousal in the pupil diameter time course of healthy adults. A pupil diameter increase during regulation predicted individual differences in emotion regulation success beyond task difficulty. Moreover, the extent of this individual arousal boost predicted performance in another self-control task, dietary health challenges. Participants who harnessed more regulation-associated arousal during emotion regulation were also more successful in choosing healthier foods. These results suggest that a common arousal-based facilitation mechanism may support an individual’s self-control across domains.
Oxytocin receptors in the nucleus accumbens shell are necessary for the onset of maternal behavior in post-parturient mice

Oxytocin (Oxt) signaling via its receptor, the Oxt receptor (Oxtr), is important to the onset of mammalian maternal care. Specifically, evidence suggests that Oxt signaling around the time of parturition underlies the critical shift in how pups are perceived, i.e. from aversive stimuli to rewarding stimuli. Previous work from our lab has found that both Oxtr knockout (−/−) mice and forebrain-specific Oxtr knockout (FB/FB) are more likely than controls to abandon their first litters. Based on these data, we hypothesized that this observed pup abandonment phenotype was due to a failure of the brain to “switch” to a more maternal state. In order to identify where in the brain Oxt signaling contributes to the onset of maternal care we performed three experiments. In Experiment 1, virgin Oxtr FB/FB females were assessed for genotypic differences in maternal behavior and c-Fos expression following maternal sensitization was quantified. In Experiment 2, c-Fos expression was quantified in Oxtr −/− and Oxtr FB/FB females following parturition. In Experiment 3, based on our findings from Experiment 2, the Oxtr in the nucleus accumbens shell (NAcc) was genetically deleted in female Oxtr floxed mice (Oxtr Flox/Flox) mice using a Cre recombinase expressing adeno-associated virus. In Experiment 1, sensitized virgin Oxtr FB/FB females had significantly lower retrieval latencies on the first day of testing and reduced c-Fos expression in the dorsal lateral septum compared to controls. In Experiment 2, increased c-Fos expression was observed in the NAcc shell of both Oxtr −/− and Oxtr FB/FB dams as compared to controls. In Experiment 3, virally mediated knockout of the Oxtr in the NAcc shell completely disrupted the onset of maternal care. Thus, by genetically deleting Oxtr expression in the NAcc the pup abandonment phenotype previously observed in Oxtr −/− and Oxtr FB/FB dams was recreated. Taken together, these data suggest that in post-parturient mice, Oxtr expression in the NAcc shell is critical to the onset of maternal behavior.
GEMC1-MCIDAS transcriptional program regulates multiciliogenesis in the choroid plexus and acts as a barrier to tumorigenesis

Multiciliated cells (MCCs) in the brain include the ependymal cells and choroid plexus (CP) epithelial cells. The CP secretes cerebrospinal fluid that circulates within the ventricular system, driven by ependymal cilia movement. However, the mechanisms and functional significance of multiciliogenesis in the CP remain unknown. Deregulated oncogenic signals cause CP carcinoma (CPC), a rare but aggressive pediatric brain cancer. Here we show that aberrant NOTCH and Sonic Hedgehog signaling in mice drive tumors that resemble CPC in humans. NOTCH-driven CP tumors were monociliated, whereas disruption of the NOTCH complex restored multiciliation and decreased tumor growth. NOTCH suppressed multiciliation in tumor cells by inhibiting the expression of GEMC1 and MCIDAS, early regulators of multiciliogenesis. Consistently, GEMC1-MCIDAS function is essential for multiciliation in the CP, and is critical for correcting multiciliation defect in tumor cells by a NOTCH inhibitor. Disturbances to the GEMC1 program are commonly observed in human CPCs characterized by solitary cilia. Consistently, CPC driven by deletion of Trp53 and Rb1 in mice exhibits a cilia deficit consequent to loss of Gemc1-Mcidas expression. Taken together, these findings reveal a GEMC1-MCIDAS multiciliation program in the CP critical for inhibiting tumorigenesis, and it may have therapeutic implications for the treatment of CPC.
Metformin prevented high glucose-induced endothelial reactive oxygen species via OGG1 in an AMPKα-Lin-28 dependent pathway

Metformin improved vascular function in obese type 2 diabetic patients. 8-oxoguanine glycosylase (OGG1), a main DNA glycosylase, was involved in vascular complications in diverse diseases. However, whether metformin suppressed endothelial ROS via OGG1 pathway was unclear. Human umbilical vein endothelial cells (HUVECs) were exposed to HG (high glucose) or HG with metformin. OGG1 and AMPfα levels were measured after metformin treatment while HG-caused ROS was measured by DHE prober. Diabetic mice were induced by daily intraperitoneal injections of streptozotocin (STZ). Metformin reduced Endothelial ROS caused by HG via upregulating OGG1. Additionally, OGG1 protein expression was dependent on its mRNA stability, which was reversed by genetic inhibition of AMPKα and Lin-28. The role of OGG1 on ROS stimulated by HG was partially dependent on NFKB/NOX4 pathway in HUVECs. These results suggested that metformin contacted HG-induced endothelial ROS via AMPKα/Lin-28/OGG1 pathway.
Supporting Student Learning and Experiences in the Lab: (How) Should We Design Their Groups?

Undergraduate science students spend a substantial amount of time working in their laboratory groups, and instructors want to make evidence-based decisions on how to best set up these groups. Despite several studies on group composition, the evidence appears to be quite context-specific, and very little has been published about lab groups. Further, many studies focus solely on conceptual learning; however, the lab is an important venue for also supporting non-content outcomes such as confidence, process skills, team skills, and attitudes. Thus, in our introductory course on molecules, cells, and physiology we were interested in the impact of group composition, on a spread of student outcomes. Students were either placed into groups by the instructor, or self-selected into groups. To assess the impact of group composition on student outcome, we collected pre/post data from >500 students over 2 semesters. Our measures assess conceptual knowledge, confidence in lab skills, attitudes toward group learning, lab grades, gender, year of study, and (via open-ended questions) student perspectives. Using a multiple regression approach, we established models that predict student outcomes based on their individual attributes and on their lab group attributes. Surprisingly, the hetero/homogeneity of the initial group, and whether the groups were student- or instructor-selected, did not affect student outcomes in these models. Further MANCOVA analysis demonstrated that student interaction outside of the lab time was the strongest predictor of positive student attitudes toward group learning. Student perspectives on group formation are mixed, and suggest that a simple and flexible choice approach may best support our students. Overall, these findings have clear implications for our course design and instructional choices: we should focus our efforts to promote positive student interactions, rather than worrying about initial composition.
Co-existence of prediction and error signals in electrophysiological responses to natural speech

Prior knowledge facilitates perception and allows us to interpret our sensory environment. However, the neural mechanisms underlying this process remain unclear. Theories of predictive coding propose that feedback connections between cortical levels carry predictions about upcoming sensory events whereas feedforward connections carry the error between the prediction and the sensory input. Although predictive coding has gained much ground as a viable mechanism for perception, in the context spoken language comprehension it lacks empirical support using more naturalistic stimuli. In this study, we investigated theories of predictive coding using continuous, everyday speech. EEG recordings from human participants listening to an audiobook were analysed using a 2-stage regression framework. This tested the effect of top-down linguistic information, estimated using computational language models, on the bottom-up encoding of acoustic and phonetic speech features. Our results show enhanced encoding of both semantic predictions and surprising words, based on preceding context. This suggests that signals pertaining to prediction and error units can be observed in the same electrophysiological responses to natural speech. In addition, temporal analysis of these signals reveals support for theories of predictive coding that propose that perception is first biased towards what is expected followed by what is informative. Significance Statement Over the past two decades, predictive coding has grown in popularity as an explanatory mechanism for perception. However, there has been lack of empirical support for this theory in research studying natural speech comprehension. We address this issue by developing an analysis framework that tests the effects of top-down linguistic information on the auditory encoding of continuous speech. Our results provide evidence for the co-existence of prediction and error signals and support theories of predictive coding using more naturalistic stimuli.
“Multiplex” rheostat positions cluster around allosterically critical regions of the lactose repressor protein

Amino acid variation at “rheostat” positions provides opportunity to modulate various aspects of protein function – such as binding affinity or allosteric coupling – across a wide range. Previously a subclass of “multiplex” rheostat positions was identified at which substitutions simultaneously modulated more than one functional parameter. Using the Miller laboratory’s dataset of ∼4000 variants of lactose repressor protein (LacI), we compared the structural properties of multiplex rheostat positions with (i) “single” rheostat positions that modulate only one functional parameter, (ii) “toggle” positions that follow textbook substitution rules, and (iii) “neutral” positions that tolerate any substitution without changing function. The combined rheostat classes comprised >40% of LacI positions, more than either toggle or neutral positions. Single rheostat positions were broadly distributed over the structure. Multiplex rheostat positions structurally overlapped with positions involved in allosteric regulation. When their phenotypic outcomes were interpreted within a thermodynamic framework, functional changes at multiplex positions were uncorrelated. This suggests that substitutions lead to complex changes in the underlying molecular biophysics. Bivariable and multivariable analyses of evolutionary signals within multiple sequence alignments could not differentiate single and multiplex rheostat positions. Phylogenetic analyses – such as ConSurf – could distinguish rheostats from toggle and neutral positions. Multivariable analyses could also identify a subset of neutral positions with high probability. Taken together, these results suggest that detailed understanding of the underlying molecular biophysics, likely including protein dynamics, will be required to discriminate single and multiplex rheostat positions from each other and to predict substitution outcomes at these sites.
Optimal density of bacterial cells

A substantial fraction of the bacterial cytosol is occupied by catalysts and their substrates. While a higher volume density of catalysts and substrates might boost biochemical fluxes, the resulting molecular crowding can slow down diffusion, perturb the reactions’ Gibbs free energies, and reduce the catalytic efficiency of proteins. Due to these tradeoffs, dry mass density likely possesses an optimum that facilitates maximal cellular growth and that is interdependent on the cytosolic molecule size distribution. Here, we analyze the balanced growth of a model cell, accounting systematically for crowding effects on reaction kinetics. Its optimal cytosolic volume occupancy depends on the nutrient-dependent resource allocation into large ribosomal vs. small metabolic macromolecules, reflecting a tradeoff between the saturation of metabolic enzymes, favoring larger occupancies with higher encounter rates, and the inhibition of the ribosomes, favoring lower occupancies with unhindered diffusion of tRNAs. Our predictions across growth rates are quantitatively consistent with the experimentally observed reduction in volume occupancy on rich media compared to minimal media in E. coli. Strong deviations from optimal cytosolic occupancy only lead to minute reductions in growth rate, which are nevertheless evolutionarily relevant due to large bacterial population sizes. In sum, cytosolic density variation in bacterial cells appears to be consistent with an optimality principle of cellular efficiency.
Functional traits predict species responses to environmental variation in a California grassland annual plant community

Turnover in species composition and community-wide functional traits across environmental gradients is a ubiquitous pattern in ecology, and is generally assumed to reflect shifts in trait optima across these gradients. However, the demographic processes that give rise to these trait turnover patterns at the community level remain unclear. We asked whether shifts in the community-weighted means of three key functional traits across an environmental gradient in a southern California grassland reflect variation in the trait-performance relationship across the landscape. We planted seeds of 17 annual plant species in cleared patches with no competitors, and quantified the lifetime seed production of 1360 individuals. We then asked whether models that included trait-environment interactions help explain interspecific variation in demographic responses to the environment. This allowed us to evaluate whether observed shifts in community-weighted mean traits matched the direction of any trait-environment interactions detected in the plant performance experiment. Our results indicate that commonly-measured plant functional traits help explain variation in species responses to the environment – for example, high-SLA species had a demographic advantage in soils with high soil Ca:Mg levels, while low-SLA species had an advantage in low Ca:Mg soils. We also found that shifts in community-weighted mean traits often reflect the direction of these trait-environment interactions, though not all trait-environment relationships at the community level reflect interactive effects of traits and environment on species performance. Our results support the value of plant functional traits for predicting species responses to environmental variation, and highlight a need for more detailed evaluation of how trait-performance relationships change across environments to improve such predictions.
Cellulosic wall thickenings restrict cell expansion to shape the 3D puzzle sclereids of the walnut shell

Walnut (Juglans regia) kernels are protected by a tough shell consisting of polylobate sclereids that interlock into a 3D puzzle. The shape transformations from isodiametric to lobed cells is well documented for 2D pavement cells, but not for 3D puzzle sclereids. Here, we tackle the morphogenesis of these cells by using a combination of different imaging techniques. Serial face-microtomy enabled us to reconstruct tissue growth of whole walnut fruits in 3D and serial block face-scanning electron microscopy exposed cell shapes and their transformation in 3D during shell tissue development. In combination with Raman and fluorescence microscopy we revealed multiple loops of cellulosic thickenings in cell walls, acting as stiff restrictions during cell expansion and leading to the lobed cell shape. Our findings contribute to a better understanding of the 3D shape transformation of polylobate sclereids and the role of pectin and cellulose within this process.
A neural turning point - the EEG P3 component tracks unfolding changes of mind

The ability to change one’s mind is a key feature of human cognition. Yet, the neural mechanisms underpinning our capacity to change our minds remain poorly understood. Here, we investigated the neural correlates of evidence accumulation and changes of mind in a two-step sequential sampling task. Participants provided a first, quick guess regarding the relative frequencies of target letters in a visual stream, followed by a slower, more deliberate decision. We found that the P3 amplitude evoked by successive target letters tracks an internal signed decision variable and predicts choices on a single-trial level. Moreover, this neural decision variable offers new insights into the dynamics of changes of mind. In particular, we show that the start of evidence accumulation after the early decision constitutes a neural turning point: the P3 evoked by the first letter contrary to the initial decision can be used to predict subsequent changes of mind. Our results highlight a critical interaction between the processing of external evidence and endogenous modulations of decisional parameters that facilitate reversing an original decision.