Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and biophysical characterization of GSU0105, a triheme c-type cytochrome from Geobacter sulfurreducens

C-type cytochromes play an important role in respiration of dissimilatory metal-reducing bacteria. They form extended conduits for charge transfer between the cellular metabolism and external electron acceptors such as particles of iron oxide, metal ions, and humic substances. Out of more than a hundred c-type cytochromes in Geobacter sulfurreducens, only a small fraction has been previously characterized. Here we present our results on expression and biophysical characterization of GSU0105, a novel 3-heme cytochrome, important for Fe(III) respiration in G. sulfurreducens. We successfully cloned the gene and achieved ~3 mg/L of culture GSU0105 expression in E.coli. Despite a similar size (71 amino acids) and the same number of c-type hemes to the members of the cytochrome (cyt) c7 family, multiple sequence alignment suggests that GSU0105 does not belong to the cyt c7 family. UV-Vis spectroscopy revealed typical c-type cytochrome spectral features, including a weak iron-sulfur charge transfer band suggesting that at least one heme is ligated with a methionine residue. Far UV circular dichroism studies demonstrate approximately 35% content of α-helices and β-sheets, each, as well as thermal aggregation occurring above 60 °C. A combination of SAXS and analytical size exclusion chromatography data shows that GSU0105 is monomeric in solution. Finally, affinity pull-down assays demonstrate high binding affinity to PpcD and weaker binding to the other members of the cyt c7 family.
Genomic Insights into the Demographic History of Southern Chinese

Southern China is the birthplace of rice-cultivating agriculture, different language families, and human migrations that facilitated these cultural diffusions. The fine-scale demographic history in situ, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with more than 1,200 ancient and modern genomes. We discover that the previously described ‘Southern East Asian’ or ‘Yangtze River Farmer’ lineage is monophyletic but not homogeneous, comprising four regionally differentiated sub-ancestries. These ancestries are respectively responsible for the transmission of Austronesian, Kra-Dai, Hmong-Mien, and Austroasiatic languages and their original homelands successively distributed from East to West in Southern China. Multiple phylogenetic analyses support that the earliest living branching among East Asian-related populations is First Americans (∼27,700 BP), followed by the pre-LGM differentiation between Northern and Southern East Asians (∼23,400 BP) and the pre-Neolithic split between Coastal and Inland Southern East Asians (∼16,400 BP). In North China, distinct coastal and inland routes of south-to-north gene flow had established by the Holocene, and further migration and admixture formed the genetic profile of Sinitic speakers by ∼4,000 BP. Four subsequent massive migrations finalized the complete genetic structure of present-day Southern Chinese. First, a southward Sinitic migration and the admixture with Kra-Dai speakers formed the ‘Sinitic Cline’. Second, a bi-directional admixture between Hmong-Mien and Kra-Dai speakers gave rise to the ‘Hmong-Mien Cline’ in the interior of South China between ∼2,000 and ∼1,000 BP. Third, a southwestward migration of Kra-Dai speakers in recent ∼2,000 years impacted the genetic profile for the majority of Mainland Southeast Asians. Finally, an admixture between Tibeto-Burman incomers and indigenous Austroasiatic speakers formed the Tibeto-Burman speakers in Southeast Asia by ∼2,000 BP.
Annual and 16-day rangeland production estimates for the western United States

Rangeland production is a foundational ecosystem service and resource upon which livestock, wildlife, and people depend. Capitalizing on recent advancements in the use of remote sensing data across rangelands we provide estimates of herbaceous rangeland production from 1986-2019 at 16-day and annual time steps and 30m resolution across the western United States. Herbaceous aboveground biomass at this scale and resolution provide critical information applicable for management and decision-making, particularly in the face of annual grass invasion and woody encroachment of rangeland systems. These readily available data remove analytical and technological barriers allowing immediate utilization for monitoring and management.
Single Cell Transcriptomic Re-analysis of Immune Cells in Bronchoalveolar Lavage Fluids Reveals the Correlation of B Cell Characteristics and Disease Severity of Patients with SARS-CoV-2 Infection

The COVID-19 pandemic (SARS-CoV-2) is a global infectious disease with rapid spread. Some patients have severe symptoms and clinical signs caused by an excessive inflammatory response, which increases the risk of mortality. In this study, we reanalyzed scRNA-seq data of cells from bronchoalveolar lavage fluids of patients with COVID-19 with mild and severe symptoms, focusing on antibody-producing cells. In patients with severe disease, B cells seemed to be more activated and expressed more immunoglobulin genes compared with cells from patients with mild disease, and macrophages expressed higher levels of the TNF superfamily member B-cell activating factor but not of APRIL (a proliferation-inducing ligand). In addition, macrophages from patients with severe disease had increased pro-inflammatory features and pathways associated with Fc receptor-mediated signaling, compared with patients with mild disease. CCR2-positive plasma cells accumulated in patients with severe disease, probably because of increased CCL2 expression on macrophages from patients with severe disease. Together, these results support that different characteristics of B cells might affect the severity of COVID-19 infection.
Bioarchaeological sex prediction from central Italy using generalized low rank imputation for cross-validated metric craniodental supervised ensemble machine learning with missing data

I use a novel supervised ensemble machine learning approach to verify sex estimation of known males and females from central Italian bioarchaeological contexts with large amounts of missing data present. Eighteen cranial interlandmark distances and five maxillary metric distances were recorded from n = 240 males and n = 180 females from four locations at Alfedena (600-400 BCE) and two locations at Campovalano (750-200 BCE and 9-11th Century CE). A generalized low rank model (GLRM) was used to impute missing data and 20-fold external stratified cross-validation was used to fit an ensemble of eight machine learning algorithms to six different subsets of the data: 1) the face, 2) vault, 3) cranial base, 4) combined face/vault/base, 5) dentition, and 6) combined cranianiodental. Area under the receiver operator characteristic curve (AUC) was used to evaluate the predictive performance of six constituent algorithms, the discrete algorithmic winner(s), and the SuperLearner weighted ensemble’s classification of males and females from these six bony regions. This approach is useful for predicting male/female sex from central Italy. AUC for the combined craniodental data was the highest (0.9722), followed by the combined cranial data (0.9644), the face (0.9426), vault (0.9116), base (0.9060), and dentition (0.7421). Cross-validated ensemble machine learning of cranial and dental data shows strong potential for estimating sex in the bioarchaeological record and can contribute additional perspectives to help refine our understanding of human sex estimation. Additionally, GLRMs have the potential to handle missing data in ways previously unexplored in the discipline. The main limitation is that the biological sexes of the individuals estimated in this study are not known, and were instead estimated macroscopically using common bioarchaeological methods. However, these methods show great promise for estimation of sex in bioarchaeological and forensic contexts, and should be investigated on known-sex reference samples for confirmation.
Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot Systems

Background Within an individual plant, different compartments (e.g. roots, leaves, fruits) host distinct communities of microorganisms due to variation in structural characteristics and resource availability. Grafting, which joins the root system of one individual with the shoot system of a second genetically distinct individual, has the potential to bring the microbial communities of different genotypes together. An important question is the extent to which unique root system and shoot system genotypes, when grafted together, influence the microbiota of the graft partner. Our study sought to answer this question by utilizing an experimental vineyard composed of ‘Chambourcin’ vines growing ungrafted and grafted to three different rootstocks, replicated across three irrigation treatments. We characterized bacterial and fungal communities in roots, leaves, and berries, as well as surrounding soil. Our objectives were to (1) characterize the microbiota of compartments within the root system (roots and adjacent soil) and the shoot system (leaves and berries), (2) determine the influence of rootstock genotypes, irrigation, and their interaction on the microbiota of aboveground and belowground compartments, and (3) investigate the distribution of microorganisms implicated in the late-season grapevine bunch rot disease sour rot (Acetobacterales and Saccharomycetes). Results Compartments were significantly differentiated in bacterial and fungal richness and composition. Abundance-based machine learning accurately predicted the compartment and differential abundance analysis showed a large portion of taxa differed significantly across compartments. Rootstock genotypes did not differ significantly in microbial community richness or composition; however, individual microbial taxa exhibited significant differences in abundance based on rootstock and irrigation treatment. The relative abundance of Acetobacterales and Saccharomycetes in the berry was influenced by complex interactions among rootstock genotype and irrigation. Conclusion Our results indicate that grapevine compartments retain distinct core microbiota regardless of the rootstock to which they are grafted. While rootstock genotype generally had a subtle impact on global patterns of microbial diversity, we found associations between rootstock genotypes and specific groups of microorganisms. Further experimental validation is needed in order to understand how associations with these microorganisms impacts a vine’s susceptibility to sour rot upon damage and whether the characteristics of wine are impacted.
Vasopressin acts as a synapse organizer in limbic regions by boosting PSD95 and GluA1 expression

Hypothalamic arginine vasopressin (AVP)-containing magnocellular neurosecretory neurons (AVPMNN) emit collaterals to synaptically innervate limbic regions influencing learning, motivational behaviour, and fear responses. Here, we characterize the dynamics of expression changes of two key determinants for synaptic strength, the postsynaptic density (PSD) proteins AMPAR subunit GluA1 and PSD scaffolding protein 95 (PSD95), in response to in vivo manipulations of AVPMNN neuronal activation state, or exposure to exogenous AVP ex vivo. Both long term water deprivation in vivo, which powerfully upregulates AVPMNN metabolic activity, and exogenous AVP application ex vivo, in brain slices, significantly increased GluA1 and PSD95 expression measured by western blot, in brain regions reportedly receiving direct ascending innervations from AVPMNN (i.e., ventral hippocampus, amygdala and lateral habenula). In contrast, the visual cortex, a region not observed to receive AVPMNN projections, showed no such changes. Ex vivo application of V1a and V1b antagonists to ventral hippocampal slices ablated the AVP stimulated increase in postsynaptic protein expression measured by western blot. Using a modified expansion microscopy technique, we were able to quantitatively assess the significant augmentation of PSD95 and GLUA1 densities in subcellular compartments in locus coeruleus’ tyrosine hydroxylase immunopositive fibres, adjacent to AVP axon terminals. Our data strongly suggest that the AVPMNN ascending system plays a role in the regulation of the excitability of targeted neuronal circuits through upregulation of key post-synaptic density proteins corresponding to excitatory synapse. Supported by grants UNAM-DGAPA-PAPIIT-IN200121 & CONACYT-CB-238744 (LZ); CONACYT A1-S-8731 (LIE); MH002386, NIMH, NIH, USA (LEE)
iDamage: a method to integrate modified DNA into the yeast genome

In order to explore the mechanisms employed by living cells to deal with DNA alterations, we have developed a method by which we insert a modified DNA into a specific site of the yeast genome. This is achieved by the site-specific integration of a modified plasmid at a chosen locus of the genome of Saccharomyces cerevisiae, through the use of the Cre/lox recombination system. In the present work, we have used our method to insert a single UV lesion into the yeast genome, and studied how the balance between error-free and error-prone lesion bypass is regulated. We show that the inhibition of homologous recombination, either directly (by the inactivation of Rad51 recombinase) or through its control by prevenAng the poly-ubiquitination of PCNA (ubc13 mutant), leads to a strong increase in the use of TLS. Such regulatory aspects of the DNA damage tolerance could not have been observed with previous strategies using plasmid or randomly distributed DNA lesions, which shows the advantage of our new method. The very robust and precise integration of any modified DNA at any chosen locus of the yeast genome that we describe here is a powerful tool that will enable the exploration of many biological processes related to replication and repair of modified DNA.
Reciprocal social ties drive stability within a social network

Social reciprocity is thought to be the most important driver of cooperation among non-kin, but its effects within complex social networks where individuals choose their partners have not been studied. Here, we test whether reciprocation can explain social dynamics in a bird species where males form coalitions to court females, the wire-tailed manakin (Pipra filicauda). In our study population, approximately a third of male-male social interactions involve one male leaving his territory to interact and display with the owner of another territory; this directional behaviour provides benefits to the recipient at a cost to the visiting male. We characterize social ties among pairs of territory holders according to the directionality of their interactions, and show here that territory holding males engaged in far more reciprocated (bidirectional) partnerships with other territory holders than expected by chance. Reciprocated partnerships were also stronger (i.e., the partners interacted more frequently) than non-reciprocated partnerships, controlling for spatial proximity of the territories. An individual-level analysis revealed that a male’s social contribution to a given partner was predictive of the number of social interactions he received from that same partner. Finally, we show that reciprocation predicted the long-term stability of social partnerships one year later. Together, these results demonstrate that reciprocity is associated with stability in complex social networks where partner choice is flexible. LAY SUMMARY When animals are free to choose their partners, how does reciprocity influence social dynamics? In the wire-tailed manakin, males form coalitions with other males to help attract mates. We tracked male social networks and found that some males form reciprocal partnerships where each male leaves its territory to display at the other’s territory. These bidirectional partnerships are particularly strong and stable, indicating that reciprocity is associated with stability in complex social networks.
Paraspeckles are constructed as block copolymer micelles through microphase separation

Paraspeckles are constructed by NEAT1_2 architectural long noncoding RNAs and possess characteristic cylindrical shapes with highly ordered internal organization, distinct from typical liquid–liquid phase-separated condensates. We experimentally and theoretically investigated how the shape and organization of paraspeckles are determined. We identified the NEAT1_2 RNA domains responsible for shell localization of the NEAT1_2 ends, which determine the characteristic internal organization. We then applied a theoretical framework using soft matter physics to understand the principles that determine the NEAT1_2 organization, shape, number, and size of paraspeckles. By treating paraspeckles as amphipathic block copolymer micelles, we could explain and predict the experimentally observed behaviors of paraspeckles upon NEAT1_2 domain deletions or transcriptional modulation. Thus, we propose that paraspeckles are block copolymer micelles assembled through microphase separation. This work provides an experimentally-based theoretical framework for the concept that ribonucleoprotein complexes (RNPs) can act as block copolymers to form RNA-scaffolding microphase-separated condensates in cells.
Role of Inferior Frontal Junction (IFJ) in the Control of Feature vs Spatial Attention

Feature-based attention refers to preferential selection and processing of items and objects based on their non-spatial attributes such as color or shape. While it is intuitively an easier form of attention to relate to in our day to day lives, the neural mechanisms of feature-based attention are not well understood. Studies have long implicated the dorsal attention network as a key control system for voluntary spatial, feature and object-based attention. Recent studies have expanded on this model by focusing on the inferior frontal junction (IFJ), a region in the pre-frontal cortex to be the source of feature attention control, but not spatial attention control. However, the extent to which IFJ contributes to spatial attention remains a topic of debate. We investigated the role of IFJ in the control of feature versus spatial attention in a cued visual spatial (attend left or right) and feature attention (attend red or green) task using fMRI. Analyzing single-trial cue-evoked fMRI responses using univariate GLM and multi-voxel pattern analysis (MVPA), we observed the following. First, the univariate BOLD activation responses yielded no significant differences between feature and spatial cues. Second, MVPA analysis showed above chance level decoding in classifying feature attention (attend-red vs. attend-green) in both the left and right IFJ, whereas during spatial attention (attend-left vs. attend-right) decoding was at chance. Third, while the cue-evoked decoding accuracy was significant for both left and right IFJ during feature attention, target stimulus-evoked neural responses were not different. Importantly, only the connectivity patterns from the right IFJ was predictive of target-evoked activity in visual cortex (V4); this was true for both left and right V4. Finally, the strength of this connectivity between right IFJ and V4 (bilaterally) was found to be predictive of behavioral performance. These results support a model where the right IFJ plays a crucial role in top down control of feature but not spatial attention.
Comparative genomic analyses provide clues to capsule switch in Streptococcus suis

Streptococcus suis (S. suis) is a major bacterial pathogen in swine industry and also an emerging zoonotic agent. S. suis produces an important extracellular component, capsular polysaccharides (CPS). Based on which, dozens of serotypes have been identified. Through virulence genotyping, we uncovered the relatedness between proportions of SS2, SS3 and SS7 strains despite their differences in serotypes. Multi-locus sequence typing (MLST) was used to characterize whole S. suis population, revealing that there is capsule switch between S. suis strains. Importantly, capsule switch occurred in SS2, 3 and 7 strains belonging to CC28 and CC29, which is phylogenetically distinct from the main CC1 SS2 lineage. To further explore capsule switch in S. suis, comparative genomic analyses were performed using available S. suis complete genomes. Phylogenetic analyses suggested that SS2 strains can be divided into two clades (1 and 2), and those classified into clade 2 are colocalized with SS3 and SS7 strains, which is in accordance with above virulence genotyping and MLST analyses. Clade 2 SS2 strains presented high genetic similarity with SS3 and SS7 and shared common competence and defensive elements, but are significantly different from Clade 1 SS2 strains. Notably, although the cps locus shared by Clade 1 and 2 SS2 strains is almost the same, a specific region in cps locus of strain NSUI002 (Clade 2 SS2) can be found in SS3 cps locus, but not in Clade 1 SS2 strain. These data indicated that SS2 strains appeared in CC28 and CC29 might acquire cps locus through capsule switch, which could well explain the distinction of genetic lineages within SS2 population.
Time-dependent spatial specificity of high-resolution fMRI: insights into mesoscopic neurovascular coupling

High-resolution functional magnetic resonance imaging (fMRI) is becoming increasingly popular because of the growing availability of ultra-high magnetic fields which are capable of improving sensitivity and spatial resolution. However, it is debatable whether increased spatial resolutions for haemodynamic-based techniques, like fMRI, can accurately detect the true location of neuronal activity. We have addressed this issue in functional columns and layers of animals with haemoglobin-based optical imaging and different fMRI contrasts, such as blood oxygenation level-dependent, cerebral blood flow and cerebral blood volume fMRI. In this review, we describe empirical evidence primarily from our own studies on how well these fMRI signals are spatially specific to the neuronally active site and discuss insights into neurovascular coupling at the mesoscale. This article is part of the theme issue ‘Key relationships between non-invasive functional neuroimaging and the underlying neuronal activity’.