Miracle-dz/UniFAR-FTUs huggingface dataset:
Feedforward mechanisms of masking in mouse V1

Sensory neurons not only encode stimuli that align with their receptive fields but are also modulated by context. For example, the responses of neurons in mouse primary visual cortex (V1) to gratings of their preferred orientation are modulated by the presence of superimposed orthogonal gratings (“plaids”). The effects of this modulation can be diverse: some neurons exhibit cross-orientation suppression while other neurons have larger responses to a plaid than its components. We investigated whether these diverse forms of masking could be explained by a unified circuit mechanism. We report that the suppression of cortical activity does not alter the effects of masking, ruling out cortical mechanisms. Instead, we demonstrate that the heterogeneity of plaid responses is explained by an interaction between stimulus geometry and orientation tuning. Highly selective neurons uniformly exhibit cross-orientation suppression, whereas in weakly-selective neurons masking depends on the spatial configuration of the stimulus, with effects transitioning systematically between suppression and facilitation. Thus, the diverse responses of mouse V1 neurons emerge as a consequence of the spatial structure of the afferent input to V1, with no need to invoke cortical interactions.
The TPLATE complex mediates membrane bending during plant clathrin–mediated endocytosis

Significance Endocytosis transports cargos inside the cell by creating spherical vesicles from the plasma membrane. This membrane remodeling requires proteins to generate force to bend the membrane inwards, overcoming the high-turgor pressure in plant cells. However, as plants create clathrin-coated vesicles without actin, the machinery to bend membranes during endocytosis is entirely unknown and appears distinct from other model systems. Here, we refine the physiological role of the plant-specific and essential endocytic TPLATE complex. We find it localizes outside of clathrin-coated vesicles and mediates membrane bending, contrasting with previous predictions. We further demonstrate that the TPLATE complex contains protein domains which have intrinsic membrane-bending activity; thus, we identify a component of the unique endocytosis membrane-bending machinery in plants. Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells.
Phenotypic diversity and sensitivity to injury of the pulmonary endothelium during a period of rapid postnatal growth

Endothelial cells (EC) sit at the forefront of dramatic physiologic changes occurring in the pulmonary circulation during late embryonic and early postnatal life. First, as the lung moves from the hypoxic fetal environment to oxygen-rich postnatal environment, marked changes in pulmonary EC structure and function facilitate a marked increase in blood flow from the placenta to the lungs. Subsequently, pulmonary angiogenesis expands the microvasculature to drive exponential distal lung growth during early postnatal life. Yet, how these marked physiologic changes alter distinct EC subtypes to facilitate the transition of the pulmonary circulation and regulate vascular growth and remodeling remains incompletely understood.In this report, we employed single cell RNA-transcriptomics and in situ RNA imaging to profile pulmonary EC in the developing mouse lung from just before birth through this period of rapid postnatal growth.Multiple, transcriptionally distinct macro- and microvascular EC were identified in the late embryonic and early postnatal lung, with gene expression profiles distinct from their adult EC counterparts. A novel arterial subtype, unique to the developing lung localized to the distal parenchyma and expressed genes that regulate vascular growth and patterning. Birth particularly heightened microvascular diversity, inducing dramatic shifts in the transcriptome of distinct microvascular subtypes in pathways related to proliferation, migration and antigen presentation. Two distinct waves of EC proliferation were identified, including one just prior to birth, and a second during early alveolarization, a time of exponential pulmonary angiogenesis. Chronic hyperoxia, an injury that impairs parenchymal and vascular growth, induced a common gene signature among all pulmonary EC, unique alterations to distinct microvascular EC subtypes, and disrupted EC-EC and EC-immune cell cross talk.Taken together, these data reveal tremendous diversity of pulmonary EC during a critical window of postnatal vascular growth, and provide a detailed molecular map that can be used to inform both normal vascular development and alterations in EC diversity upon injury. These data have important implications for lung diseases marked by dysregulated angiogenesis and pathologic pulmonary vascular remodeling.
Direct Nanopore Sequencing of Individual Full Length tRNA Strands

We describe a method for direct tRNA sequencing using the Oxford Nanopore MinION. The principal technical advance is custom adapters that facilitate end-to-end sequencing of individual tRNA molecules. A second advance is a Nanopore sequencing pipeline optimized for tRNA. We tested this method using purified E. coli tRNAfMet, tRNALys, and tRNAPhe samples. 76-to-92% of individual aligned tRNA sequence reads were full length. As proof of concept, we showed that Nanopore sequencing detected all 42 expected tRNA isoacceptors in total E. coli tRNA. Alignment-based comparison between the three purified tRNAs and their synthetic controls revealed systematic miscalls at or adjacent to the positions of known nucleotide modifications. Systematic miscalls were also observed proximal to known modifications in total E. coli tRNA alignments.
Light attention predicts protein location from the language of life

Summary Although knowing where a protein functions in a cell is important to characterize biological processes, this information remains unavailable for most known proteins. Machine learning narrows the gap through predictions from expert-designed input features leveraging information from multiple sequence alignments (MSAs) that is resource expensive to generate. Here, we showcased using embeddings from protein language models (pLMs) for competitive localization prediction without MSAs. Our lightweight deep neural network architecture used a softmax weighted aggregation mechanism with linear complexity in sequence length referred to as light attention (LA). The method significantly outperformed the state-of-the-art (SOTA) for ten localization classes by about eight percentage points (Q10). So far, this might be the highest improvement of just embeddings over MSAs. Our new test set highlighted the limits of standard static data sets: while inviting new models, they might not suffice to claim improvements over the SOTA. Availability The novel models are available as a web-service at http://embed.protein. properties. Code needed to reproduce results is provided at https://github.com/HannesStark/protein-localization. Predictions for the human proteome are available at https://zenodo.org/record/5047020.
Seed banks alter metacommunity diversity: the interactive effects of competition, germination, and survival

Dispersal and dormancy are two common strategies allowing for species persistence and the maintenance of ecological diversity in variable environments. However, theory and empirical tests of spatial diversity patterns tend to examine either mechanism in isolation. Here, we developed a stochastic, spatially explicit metacommunity model incorporating seed banks with varying germination and survival rates. We found that dormancy and dispersal had interactive, nonlinear effects on the maintenance and distribution of metacommunity diversity, where scale-dependent effects of seed banks were modified by local competitive interactions and dispersal. The interplay between seed germination and survival regulated the benefits of seed banks for diversity. Our study shows that the role of seed banks depends critically on spatial processes, and that classic predictions for how dispersal affects metacommunity diversity can be strongly influenced by dormancy. Together, these results highlight the need to consider both temporal and spatial storage when predicting multi-scale patterns of diversity.
Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores

Gene functional enrichment analysis represents one of the most popular bioinformatics methods for annotating the pathways and function categories of a given gene list. Current algorithms for enrichment computation such as Fisher’s exact test and hypergeometric test totally depend on the category count numbers of the gene list and one gene set. In this case, whatever the genes are, they were treated equally. However, actually genes show different scores in their essentiality in a gene list and in a gene set. It is thus hypothesized that the essentiality scores could be important and should be considered in gene functional analysis. For this purpose, here we proposed WEAT (https://www.cuilab.cn/weat/), a weighted gene set enrichment algorithm and online tool by weighting genes using essentiality scores. We confirmed the usefulness of WEAT using two case studies, the functional analysis of one aging-related gene list and one gene list involved in Lung Squamous Cell Carcinoma (LUSC). Finally, we believe that the WEAT method and tool could provide more possibilities for further exploring the functions of given gene lists.
Scaling between stomatal size and density in forest plants

The size and density of stomatal pores limit the maximum rate of leaf carbon gain and water loss (gmax) in land plants. The limits of gmax due to anatomy, and its constraint by the negative correlation of stomatal size and density at broad phylogenetic scales, has been unclear and controversial. The prevailing hypothesis posits that adaptation to higher gmax is typically constrained by geometry and/or an economic need to reduce the allocation of epidermal area to stomata (stomatal-area minimization), and this would require the evolution of greater numbers of smaller stomata. Another view, supported by the data, is that across plant diversity, epidermal area allocated to guard cells versus other cells can be optimized without major trade-offs, and higher gmax would typically be achieved with a higher allocation of epidermal area to stomata (stomatal-area increase). We tested these hypotheses by comparing their predictions for the structure of the covariance of stomatal size and density across species, applying macroevolutionary models and phylogenetic regression to data for 2408 species of angiosperms, gymnosperms, and ferns from forests worldwide. The observed stomatal size-density scaling and covariance supported the stomatal-area increase hypothesis for high gmax. A higher gmax involves construction costs and maintenance costs that should be considered in models assessing optimal stomatal conductance for predictions of water use, photosynthesis, and water-use efficiency as influences on crop productivity or in Earth System models.
Maintaining grass coverage increases methane uptake in Amazonian pasture soils

Cattle ranching is the largest driver of deforestation in the Brazilian Amazon. The rainforest- to-pasture conversion affects the methane cycle in upland soils, changing it from sink to source of atmospheric methane. However, it remains unknown if management practices could reduce the impact of land-use on methane cycling. In this work, we evaluated how pasture management can regulate the soil methane cycle either by maintaining continuous grass coverage on pasture soils, or by liming the soil to amend acidity. Methane fluxes from forest and pasture soils were evaluated in moisture-controlled greenhouse experiments with and without grass cover (Urochloa brizantha cv. Marandu) or liming. In parallel, we assessed changes in the soil microbial community structure of both bare pasture soil as well as rhizosphere soil through high throughput sequencing of the 16S rRNA gene, and quantified the methane cycling microbiota by their respective marker genes related to methane generation (mcrA) or oxidation (pmoA). The experiments used soils from eastern and western Amazonia, and concurrent field studies allowed us to confirm greenhouse data. The presence of a grass cover not only increased methane uptake by up to 35% in pasture soils, but also reduced the abundance of the methane-producing community. In the grass rhizosphere this reduction was up to 10-fold. Methane-producing archaea belonged to the genera Methanosarcina sp. , Methanocella sp. , Methanobacterium sp. , and Rice Cluster I. Further, we showed that liming compromised the capacity of forest and pasture soils to be a sink for methane, and instead converted formerly methane-consuming forest soils to become methane sources in only 40-80 days. Our results demonstrate that pasture management that maintains grass coverage can mitigate soil methane emissions, if compared to a bare pasture soil.
Antiviral defense via nucleotide depletion in bacteria

DNA viruses and retroviruses need to consume large quantities of deoxynucleotides (dNTPs) when replicating within infected cells. The human antiviral factor SAMHD1 takes advantage of this vulnerability in the viral life cycle, and inhibits viral replication by degrading dNTPs into their constituent deoxynucleosides and inorganic phosphate. In this study we report that bacteria employ a similar strategy to defend against phage infection. We found a family of defensive dCTP deaminase proteins that, in response to phage infection, convert dCTP into deoxy-uracil nucleotides. A second family of phage resistance genes encode dGTPase enzymes, which degrade dGTP into phosphate-free deoxy-guanosine (dG) and are distant homologs of the human SAMHD1. Our results show that the defensive proteins completely eliminate the specific deoxynucleotide (either dCTP or dGTP) from the nucleotide pool during phage infection, thus starving the phage of an essential DNA building block and halting its replication. Both defensive genes are found in a diverse set of bacterial species and are specifically enriched in Vibrio genomes. Our study demonstrates that manipulation of the deoxynucleotide pool is a potent antiviral strategy shared by both prokaryotes and eukaryotes.
Orientation and color tuning of the human visual gamma rhythm

Narrowband gamma oscillations (NBG: ∼20-60Hz) in visual cortex reflect rhythmic fluctuations in population activity generated by underlying circuits tuned for stimulus location, orientation, and color. Consequently, the amplitude and frequency of induced NBG activity is highly sensitive to these stimulus features. For example, in the non-human primate, NBG displays biases in orientation and color tuning at the population level. Such biases may relate to recent reports describing the large-scale organization of single-cell orientation and color tuning in visual cortex, thus providing a potential bridge between measurements made at different scales. Similar biases in NBG population tuning have been predicted to exist in the human visual cortex, but this has yet to be fully examined. Using intracranial recordings from human visual cortex, we investigated the tuning of NBG to orientation and color, both independently and in conjunction. NBG was shown to display a cardinal orientation bias (horizontal) and also an end- and mid-spectral color bias (red/blue and green). When jointly probed, the cardinal bias for orientation was attenuated and an end-spectral preference for red and blue predominated. These data both elaborate on the close, yet complex, link between the population dynamics driving NBG oscillations and known feature selectivity biases in visual cortex, adding to a growing set of stimulus dependencies associated with the genesis of NBG. Together, these two factors may provide a fruitful testing ground for examining multi-scale models of brain activity, and impose new constraints on the functional significance of the visual gamma rhythm. Significance Statement Oscillations in electrophysiological activity occur in visual cortex in response to stimuli that strongly drive the orientation or color selectivity of visual neurons. The significance of this induced ‘gamma rhythm’ to brain function remains unclear. Answering this question requires understanding how and why some stimuli can reliably generate gamma activity while others do not. We examined how different orientations and colors independently and jointly modulate gamma oscillations in the human brain. Our data show gamma oscillations are greatest for certain orientations and colors that reflect known biases in visual cortex. Such findings complicate the functional significance of gamma activity, but open new avenues for linking circuits to population dynamics in visual cortex. Classification Neuroscience
Comparison of the therapeutic effects of hUC-MSC intravenous delivery and intraperitoneal administration of MSCs encapsulated in alginate capsules for the treatment of rat liver cirrhosis

Mesenchymal stem cells are the most promising regenerative medicine tool for the treatment of various diseases, including liver disease, although the exact mechanism of their therapeutic action remains unclear. It was found that MSCs are captured by the lungs after systemic transplantation, quickly disappear, and are not detected at the site of injury, but at the same time exhibit an obvious therapeutic effect. Comparison of the MSC efficiency depending on the route of their administration may shed light on the mechanisms involved in the implementation of MSC therapeutic potential. In this work, we compared the therapeutic effects of human umbilical cord MSCs (hUC-MSCs) administered systemically and intraperitoneally in the form of MSCs encapsulated in alginate capsules in a CCl4-induced model of liver cirrhosis in rats. Our study showed that both treatments resulted in liver recovery. MSC transplantation by two different routes led to a decrease in collagen deposition, the disappearance of the fibrous area by the 13th week, and normalization of the morphometric parameters of liver parenchyma cells. The expression of some genes (EGF, alpha SMA, GFAP) which is activated in liver injury, decreased to the level observed in negative control animals. However, a detailed study of liver recovery in dynamics showed that encapsulated MSCs led to faster normalization in several parameters of the liver tissue. Our results showed that human umbilical cord MSCs effectively exhibit their therapeutic properties when using both methods of transplantation, however, intraperitoneal administration of encapsulated MSCs accelerated the process of liver regeneration.
Editorial: Advancing a Cross Boundary Social Science of Trust in Natural Resource Management

Managing natural resources requires coordinating across groups and individuals who often have conflicting, if not competing, interests and needs. As natural resource management (NRM) models shift from top-down to more collaborative approaches, understanding how trust among individuals and groups forms, is negotiated, and can deteriorate has become critical and a growing body of literature has much to say about the nature and dynamics of trust in this context. In general, trust influences the interpretation of information, increases support for management actions, and facilitates collective action (Vaske et al., 2007; Ostrom, 2010; Winter and Cvetkovich, 2010; Lachapelle and McCool, 2012; Brewer and Ley, 2013) but becomes especially critical under conditions of uncertainty, complexity, and controversy (Stern, 2008; Winter and Cvetkovich, 2010). Despite the clear refrain that “trust matters,” this growing body of literature has yet to be effectively integrated in a way that enables it to optimally impact the science and practice of NRM. Instead—and consistent with the wider scholarship of trust (see Hamm et al., 2016)—this work is typically conducted in relatively disconnected silos focused on issues like climate change, water quantity or quality, species ecology, and rangeland management through any number of more or less distinct disciplinary lenses. Thus, although we know much about contextualized trust, less has been done to look across these efforts to identify the core elements of the construct that are consistent and those that are more likely to change. The development of this cross-boundary social science of trust is important because of its potential to integrate existing research but also as a meaningful starting point for new research in un(der)-explored contexts. The current special issue advances the development of this cross-boundary perspective through five articles which integrate thinking across traditional disciplinary or contextual boundaries to explore the nature and dynamics of trust. Toman et al. open with a Perspective Article that explores the practical importance of trust for natural resourcemanagement efforts. Emborg et al. then harken back to a classic trust article by Lewicki et al. (1998) in a Conceptual Analysis of the interplay—and especially the potential for the coexistence—of trust and distrust. The special issue then presents two Original Research Articles that take very different approaches to exploring the likely antecedents of trust. Ford et al. employ a quantitative meta-analytic approach to synthesizing the existing research that explores the predictors of trust among a variety of stakeholders across NRM contexts. Hamm et al. report on a qualitative inquiry that evaluates the potential for trustworthiness and motivation as distinct drivers of trust in the sub-Saharan community water management context. Finally, a Hypothesis and Theory Edited and reviewed by: Tarla Rai Peterson, The University of Texas at El Paso, United States