bluuebunny/crossref_metadata_2025 huggingface dataset:
Faunal remains from the Upper Paleolithic site of Nahal Rahaf 2 in the southern Judean Desert, Israel
Authors: Marom Nimrod , Gnezdilov Dariya Lokshin , Shafir Roee , Barzilai Omry , Shemer Maayan
Published: May 2022

Abstract

Nahal Rahaf 2 (NR2) is an Early Upper Paleolithic (ca. 35 kya) rock shelter in the southern Judean Desert in Israel. Two excavation seasons in 2019 and 2020 revealed a stratigraphical sequence composed of intact archaeological surfaces attributed to the ‘Arkov-Divshon’ cultural entity of the arid southern Levant. We present the faunal assemblages from the site, which are rare among the desert sites due to preservation problems. Our results suggest that the residents of the site exploited prime adult caprines (Capra cf. Capra ibex), but were also engaged in hunting of gazelles (Gazella cf. Gazella gazella), whose carcasses were selectively transported to the site and processed for within-bone nutrients. Long-range hunting trips are suggested by the body-part selection in relatively small bovids, and by the presence of species representing wetter habitat patches 20-30 km north of the site. The bi-focal emphasis on generalized gazelle and age-specific caprine hunting, is unique among Late Pleistocene sites from the Levant. The proportion of caprines increases through the stratigraphic sequence, suggesting more specialized economy through time and in inverse relations to site use intensity.
A new paradigm for personal protection against ticks: efficacy of spatial repellents to reduce host seeking activities in three major tick species of medical importance
Authors: Siegel Eric L. , Olivera Marcos , Roig Esteban Martinez , Perry Melynda , Li Andrew Y. , D’hers Sebastián , Elman Noel M. , Rich Stephen M.
Published: May 2022

Addressing the prevalence of tick-borne disease requires robust chemical options as an integral component of Integrative Vector Management (IVM) program. Spatial repellency is a novel concept in tick bite prevention. To date, there is no standard for the evaluation of spatial repellency against ticks, despite the speculated value of volatilized chemicals in control systems. This study reports a novel vertical climb assay that was specifically created for the quantitative evaluation of spatial repellency in ticks. Controlled release devices (CRDs) were used to control the dispersion of multiple Active Ingredients (AIs) transfluthrin, metofluthrin, nootkatone, and DEET against adult females of three medically important tick species: Dermacentor variabilis, Amblyomma americanum, and Ixodes scapularis. Results of our study indicate significant associations between AI exposure and changing in tick climbing behavior when compared controls in the absence of the AI, from several perspectives, including changes in tick movement velocity, displacement, detachment, and rate of successful vertical climbing. Metofluthrin and transfluthrin caused strong reductions in host seeking activities against D. variabilis and A. americanum, while both demonstrated slightly weaker effects against I. scapularis. Further work is planned to evaluate spatial repellency in ticks in more natural environments and assess their potential in future tick control programs.
Comprehensive benchmark and architectural analysis of deep learning models for Nanopore sequencing basecalling
Authors: Pagès-Gallego Marc , de Ridder Jeroen
Published: May 2022

Abstract

Nanopore-based DNA sequencing relies on basecalling the electric current signal. Basecalling requires neural networks to achieve competitive accuracies. To improve sequencing accuracy further, new models are continuously proposed. However, benchmarking is currently not standardized, and evaluation metrics and datasets used are defined on a per publication basis, impeding progress in the field. To standardize the process of benchmarking, we unified existing benchmarking datasets and defined a rigorous set of evaluation metrics. We benchmarked the latest seven basecaller models and analyzed their deep learning architectures. Our results show that overall Bonito has the best architecture for basecalling. We find, however, that species bias in training can have a large impact on performance. Our comprehensive evaluation of 90 novel architecture demonstrates that different models excel at reducing different types of errors and using RNNs (LSTM) and a CRF decoder are the main drivers of high performing models.
Pig manure treatment strategies for mitigating the spread of antibiotic resistance
Authors: Zalewska Magdalena , Błażejewska Aleksandra , Czapko Agnieszka , Popowska Magdalena
Published: May 2022

One of the most important public health challenges facing the world today is that posed by antibiotic resistance. Many pathogenic antibiotic-resistant bacteria and their antibiotic resistance genes, usually located on mobile genetic elements, are frequently present in the faeces of farm animals. To prevent the possibility of antimicrobial resistance transfer to the environment, these faeces should undergo treatment before being used as natural fertilizer. The two strategies for processing pig manure proposed in this study, viz. storage (most commonly used for livestock manure today) and composting, are cheap and do not require special tools or technologies. The present study examines the changes in the physicochemical properties of treated manure, in the microbiome, through metagenomic sequencing, and in the resistome, using the SmartChip Real-time PCR system compared to raw manure. This is the first such comprehensive analysis performed on the same batch of manure. Our results suggest that while none of the processes completely eliminates the environmental risk, composting results in a faster and more pronounced reduction of mobile genetic elements harbouring antibiotic resistance genes, including those responsible for multi-drug resistance. The physicochemical parameters of the treated manure are comparable after both processes; however, composting resulted in significantly higher organic matter. Overall, it appears that the composting process can be an efficient strategy for mitigating the spread of antibiotic resistance in the environment and reducing the risk of its transfer to agricultural crops and hence, the food chain. It also provides the organic matter necessary for humus formation, and increases the sorption properties of the soil and the micro and macro elements necessary for plant growth, which in turn translates into increased soil productivity.

Highlights

The changes in microbial population composition correlate with changes in specific antibiotic-resistance genes and mobile genetic elements in the studied populations.

Positive correlations have been demonstrated between microbial phyla and genes coding the multi-drug resistance mechanism

Co-occurrence networks showed positive correlations between antibiotic-resistance genes and mobile genetic elements

The composting strategy was most efficient at reducing microbial loads, antibiotic resistance genes and mobile genetic elements.

Composted manure can be part of a natural, safe soil fertilization strategy.
Nature-Inspired Chemical Probes for in-cell Labeling of Lipidized RNA and Identification of New Regulatory Enzymes
Authors: Zhou Hongling , Li Yuanyuan , Zhang Jingwen , Wang Li , Zheng Ya Ying , Begley Thomas J. , Sheng Jia , Wang Rui
Published: May 2022

RNA modifications play pivotal roles in numerous cellular processes and human diseases. In addition to well-studied methyl-based modifications, hydrophobic prenyl-modifications have also been found in many RNA species. Here we report two chemical labeling strategies for tagging lipid-modified RNAs by taking advantage of a natural SelU-mediated tRNA geranylation process and the special reactivity of prenyl-groups. We synthesized a series of ‘clickable’ geranyl-pyrophosphate analogs and identified two candidates for indirect RNA labeling using a two-step process,azidation-and-click-tagging offluorescent dyes, namely ACT-Flu. We also developed a directmetabolicincorporation andbiorthogonal tagging (MIBT-Tag) method based on the Ene-ligation of prenyl-groups. Both methods have been successfully applied to in-cell RNA labeling and the identification of new proteins associated with the geranylation process through proteomic and bioinformatic studies. These biochemical toolsets enable furtherin vivoapplications to study prenylation pathways and monitor their status in both healthy and diseased cells.
Rtapas: An R package to assess cophylogenetic signal between two evolutionary histories
Authors: Llaberia-Robledillo Mar , Lucas-Lledó J. Ignacio , Pérez-Escobar Oscar Alejandro , Krasnov Boris R. , Balbuena Juan Antonio
Published: May 2022

Cophylogeny represents a framework to understand how ecological and evolutionary process influence lineage diversification. However, linking patterns to mechanisms remains a major challenge. The recently developed Random Tanglegram Partitions provides a directly interpretable statistic to quantify the strength of cophylogenetic signal, maps onto a tanglegram the contribution to phylogenetic signal of individual host-symbiont associations, and can incorporate phylogenetic uncertainty into estimation of cophylogenetic signal. We introduce Rtapas (v1.2), an R package to perform Random Tanglegram Partitions. Rtapas applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals, and nodes that maximize phylogenetic congruence. Rtapas extends the original implementation with a new algorithm that tests phylogenetic incongruence and adds ParaFit, a method designed to test for topological congruence between two phylogenies using patristic distances, to the list of global-fit methods than can be applied. Rtapas can particularly cater for the need for causal inference in cophylogeny as demonstrated herein using to two real-world systems. One involves assessing topological (in)congruence between phylogenies produced with different DNA markers and identifying the particular associations that contribute most to topological incongruence, whereas the other implies analyzing the evolutionary histories of symbiont partners in a large dataset. Rtapas facilitates and speeds up cophylogenetic analysis, as it can handle large phylogenies reducing computational time, and is directly applicable to any scenario that may show phylogenetic congruence (or incongruence).
Simulating structurally variable Nuclear Pore Complexes for Microscopy
Authors: Theiss Maria , Hériché Jean-Karim , Russell Craig , Helekal David , Soppitt Alisdair , Ries Jonas , Ellenberg Jan , Brazma Alvis , Uhlmann Virginie
Published: May 2022

Motivation

The Nuclear Pore Complex (NPC) is the only passageway for macromolecules between nucleus and cytoplasm, and one of localization microscopy’s most important reference standards: it is massive and stereotypically arranged. The average architecture of NPC proteins has been resolved with pseudo-atomic precision, however observed NPC heterogeneities evidence a high degree of divergence from this average. Single Molecule Localization Microscopy (SMLM) images NPCs at protein-level resolution, whereupon image analysis software studies NPC variability. However the true picture of NPC variability is unknown. In quantitative image analysis experiments, it is thus difficult to distinguish intrinsically high SMLM noise from true variability of the underlying structure.

Results

We introduce CIR4MICS (“ceramics”, Configurable, Irregular Rings FOR MICroscopy Simulations), a pipeline that creates artificial datasets of structurally variable synthetic NPCs based on architectural models of the true NPC. Users can select one or more N- or C-terminally tagged NPC proteins, and simulate a wide range of geometric variations. We also represent the NPC as a spring-model such that arbitrary deforming forces, of user-defined magnitudes, simulate irregularly shaped variations. We provide an open-source simulation pipeline, as well as reference datasets of simulated human NPCs. Accompanying ground truth annotations allow to test the capabilities of image analysis software and facilitate a side-by-side comparison with real data. We demonstrate this by synthetically replicating a geometric analysis of real NPC radii and reveal that a wide range of simulated variability parameters can lead to observed results. Our simulator is therefore valuable to benchmark and develop image analysis methods, as well as to inform experimentalists about the requirements of hypothesis-driven imaging studies.

Availability

Code:https://github.com/uhlmanngroup/cir4mics. Simulated data is available at BioStudies (Accession number S-BSST1058).

Contact

theiss@ebi.ac.uk

Supplementary information

Supplementary data are available at
Structure Activity Relationship of the Stem Peptide in Sortase A mediated Ligation from Staphylococcus aureus
Authors: Apostolos Alexis J. , Kelly Joey J. , Ongwae George G. , Pires Marcos M.
Published: May 2022

The surfaces of most Gram-positive bacterial cells, including that of Staphylococcus aureus (S. aureus), are heavily decorated with proteins that coordinate cellular interactions with the extracellular space. In S. aureus, sortase A is the principal enzyme responsible for covalently anchoring proteins, which display the sorting signal LPXTG, onto the peptidoglycan (PG) matrix. Considerable efforts have been made to understand the role of this signal peptide in the sortase-mediated reaction. In contrast, much less is known about how the primary structure of the other substrate involved in the reaction (PG stem peptide) could impact sortase activity. To assess the sortase activity, a library of synthetic analogs of the stem peptide that mimic naturally existing variations found in the S. aureus PG primary sequence were evaluated. Using a combination of two unique assays, we showed that there is broad tolerability of substrate variations that are effectively processed by sortase A. While some of these stem peptide derivatives are naturally found in mature PG, they are not known to be present in the PG precursor, lipid II. These results suggest that sortase A could process both lipid II and mature PG as acyl-acceptor strands, which has not been previously described.
CRISPR/Cas9-Mediated Excision of ALS/FTD-Causing Hexanucleotide Repeat Expansion in C9ORF72 rescues major disease mechanisms in vivo and in vitro
Authors: Meijboom Katharina E. , Abdallah Abbas , Fordham Nicholas P. , Nagase Hiroko , Rodriguez Tomás , Kraus Carolyn , Gendron Tania F. , Krishnan Gopinath , Esanov Rustam , Andrade Nadja S. , Rybin Matthew J. , Ramic Melina , Stephens Zachary D. , Edraki Alireza , Blackwood Meghan T. , Kahriman Aydan , Henninger Nils , Kocher Jean-Pierre A. , Benatar Michael , Brodsky Michael H. , Petrucelli Leonard , Gao Fen-Biao , Sontheimer Erik J. , Brown Robert H. , Zeier Zane , Mueller Christian
Published: May 2022

A hexanucleotide repeat expansion (HRE) consisting of GGGGCC24+ in the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Both are fatal neurodegenerative diseases with no current approved treatments that significantly slow disease progression or extend life expectancy. Several hypotheses have emerged to explain how this HRE causes neuronal death, including C9ORF72 haploinsufficiency, sequestration of RNA-binding proteins in the nucleus, and production of dipeptide repeat proteins. In the present study we used a CRISPR/Cas9 gene-editing approach to remove the HRE from the C9ORF72 genomic locus, designing guide RNAs (gRNAs) flanking the HRE, and delivered Cas9 and gRNAs using adeno-associated virus serotype 9 (AAV9) vectors. Here, we demonstrate successful excision of the HRE in C9ORF72 in primary cortical neurons and brains of three mouse models containing the C9ORF72 expanded HRE (ranging from 500-600 repeats) as well as in patient-derived iPSC motor neurons and brain organoids (450 repeats). This resulted in a reduction of RNA foci, poly-dipeptides and haploinsufficiency, the major hallmarks of C9-ALS/FTD, making this an extremely attractive therapeutic approach to these diseases.
INSISTC: Incorporating Network Structure Information for Single-Cell Type Classification
Authors: Zheng Hansi , Wang Saidi , Li Xiaoman , Hu Haiyan
Published: May 2022

Motivation

Uncovering gene regulatory mechanisms in individual cells can provide insight into cell heterogeneity and function. Recent accumulated single-cell RNA sequencing data have made it possible to analyze gene regulation at single-cell resolution. On the other hand, understanding cell-type-specific gene regulation can also assist in more accurate cell type and state identification. Computational approaches utilizing gene regulatory relationships for single-cell type classification are under development. Methods pioneering in integrating gene regulatory mechanism discovery with cell-type classification encounter challenges such as how to accurately determine gene regulatory relation-ships and how to incorporate gene regulatory network structure into consideration.

Results

We developed a computational method to incorporate gene regulatory network structure information for single-cell type classification (INSISTC). INSISTC is capable of identifying cell-type-specific gene regulatory mechanisms while performing single cell type classification. Tested on three mouse scRNA-Seq datasets, including thousands of single-cell samples, INSISTC demonstrated its accuracy in cell type classification and its potential for providing insight into molecular mechanisms specific to individual cells. In comparison with the alternative methods, INSISTC demonstrated its complementary performance for gene regulation interpretation.

Availability

https://hulab.ucf.edu/research/projects/INSISTC/

Contact

haihu@cs.ucf.eduorxiaoman@mail.ucf.edu

Supplementary information

Supplementary data are available at xxxxxx online.
Adaptation-proof SARS-CoV-2 vaccine design
Authors: Vishweshwaraiah Yashavantha L. , Hnath Brianna , Rackley Brendan , Wang Jian , Gontu Abhinay , Chandler Morgan , Afonin Kirill A. , Kuchipudi Suresh V. , Christensen Neil , Yennawar Neela H. , Dokholyan Nikolay V.
Published: May 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface spike glycoprotein - a major antibody target - is critical for virus entry via engagement of human angiotensin-converting enzyme 2 (ACE2) receptor. Despite successes with existing vaccines and therapies that primarily target the receptor binding domain (RBD) of the spike protein, the susceptibility of RBD to mutations provides escape routes for the SARS-CoV-2 from neutralizing antibodies. On the other hand, structural conservation in the spike protein can be targeted to reduce escape mutations and achieve broad protection. Here, we designed candidate stable immunogens that mimic surface features of selected conserved regions of spike protein through ‘epitope grafting,’ in which we present the target epitope topology on diverse heterologous scaffolds that can structurally accommodate the spike epitopes. Structural characterization of the epitope-scaffolds showed stark agreement with our computational models and target epitopes. The sera from mice immunized with engineered designs display epitope-scaffolds and spike binding activity. We also demonstrated the utility of the designed epitope-scaffolds in diagnostic applications. Taken all together, our study provides important methodology for targeting the conserved, non-RBD structural motifs of spike protein for SARS-CoV-2 epitope vaccine design and demonstrates the potential utility of ‘epitope grafting’ in rational vaccine design.
Bayesian statistics improves biological interpretability of metabolomics data from human cohorts
Authors: Brydges Christopher , Che Xiaoyu , Lipkin W. Ian , Fiehn Oliver
Published: May 2022

Background

Univariate analyses of metabolomics data currently follow a frequentist approach, using p-values to reject a null-hypothesis. However, the usability ofp-values is plagued by many misconceptions and inherent pitfalls. We here propose the use of Bayesian statistics to quantify evidence supporting different hypotheses and discriminate between the null hypothesis versus lack of statistical power.

Methods

We use metabolomics data from three independent human cohorts that studied plasma signatures of subjects with myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS). Data are publicly available, covering 84-197 subjects in each study with 562-888 identified metabolites of which 777 were common between two studies, and 93 compounds reported in all three studies. By comparing results from classic multiple regression against Bayesian multiple regression we show how Bayesian statistics incorporates results from one study as ‘prior information’ into the next study, thereby improving the overall assessment of the likelihood of finding specific differences between plasma metabolite levels and disease outcomes in ME/CFS.

Results

Whereas using classic statistics and Benjamini-Hochberg FDR-corrections, study 1 detected 18 metabolic differences, study 2 detected no differences. Using Bayesian statistics on the same data, we found a high likelihood that 97 compounds were altered in concentration in study 2, after using the results of study 1 as prior distributions. These findings included lower levels of peroxisome-produced ether-lipids, higher levels of long chain, unsaturated triacylglycerides, and the presence of exposome compounds that are explained by difference in diet and medication between healthy subjects and ME/CFS patients. Although study 3 reported only 92 reported compounds in common with the other two studies, these major differences were confirmed. We also found that prostaglandin F2alpha, a lipid mediator of physiological relevance, was significantly reduced in ME/CFS patients across all three studies.

Conclusions

The use of Bayesian statistics led to biological conclusions from metabolomic data that were not found through the frequentist analytical approaches more commonly employed. We propose that Bayesian statistics to be highly useful for studies with similar research designs if similar metabolomic assays are used.
EDGE2: advancing the prioritisation of threatened evolutionary history for conservation action
Authors: Gumbs Rikki , Gray Claudia L. , Böhm Monika , Burfield Ian J. , Couchman Olivia R. , Faith Daniel P. , Forest Félix , Hoffmann Michael , Isaac Nick J. B. , Jetz Walter , Mace Georgina M. , Mooers Arne O. , Safi Kamran , Scott Oenone , Steel Mike , Tucker Caroline M. , Pearse William D. , Owen Nisha R. , Rosindell James
Published: May 2022

The global biodiversity crisis threatens the natural world and its capacity to provide benefits to humans into the future. The conservation of evolutionary history, captured by the measure phylogenetic diversity (PD), is linked to the maintenance of these benefits and future options. The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to identify species for conservation action that embody large amounts of threatened evolutionary history. In 2017, we convened a workshop to update the EDGE metric to incorporate advances in the field of phylogenetically-informed conservation. Building on that workshop, we devised the metric ‘EDGE2’, which we present here. EDGE2 uses a modular, tiered approach to provide priority rankings—and associated measures of uncertainty in both phylogenetic and extinction risk data—for all species in a clade. EDGE2 takes into account the extinction risk of closely-related species to better reflect the contribution a species is expected to make to overall PD in the future. We applied EDGE2 to the world’s mammals to identify an updated list of priority EDGE species and compare the results with the original EDGE approach. Despite similarity in the priority lists produced between EDGE and EDGE2, EDGE2 places greater priority on species with fewer close relatives on the Tree of Life. As we approach a crossroads for global biodiversity policy, EDGE2 exemplifies how academic and applied conservation biologists can collaborate to guide effective priority-setting to conserve the most irreplaceable components of biodiversity upon which humanity depends.
An automated high-content synaptic phenotyping platform in human neurons and astrocytes reveals a role for BET proteins in synapse assembly
Authors: Berryer Martin H. , Rizki Gizem , Susco Sara G. , Lam Daisy , Messana Angelica , Trendafilova Darina , Nathanson Anna , Karhohs Kyle W. , Cimini Beth A. , Pfaff Kathleen , Carpenter Anne E. , Rubin Lee L. , Barrett Lindy E.
Published: May 2022

Resolving fundamental molecular and functional processes underlying human synaptic development is crucial for understanding normal brain function as well as dysfunction in disease. Based upon increasing evidence of species divergent features of brain cell types, coupled with emerging studies of complex human disease genetics, we developed the first automated and quantitative high-content synaptic phenotyping platform using human neurons and astrocytes. To establish the robustness of our platform, we screened the effects of 376 small molecules on presynaptic density, neurite outgrowth and cell viability, validating six small molecules which specifically enhanced human presynaptic density in vitro. Astrocytes were essential for mediating the effects of all six small molecules, underscoring the relevance of non-cell autonomous factors in synapse assembly and their importance in synaptic screening applications. Bromodomain and extraterminal (BET) inhibitors emerged as the most prominent hit class and global transcriptional analyses using multiple BET inhibitors confirmed upregulation of synaptic gene expression programs. Through these analyses, we demonstrate the robustness of our automated screening platform for identifying potent synaptic modulators, which can be further leveraged for scaled analyses of human synaptic mechanisms and drug discovery efforts.
Integrative analysis ofHydrahead regeneration reveals actions of conserved signaling pathways and transposable elements
Authors: Macias-Muñoz Aide , Mesrop Lisa Y. , Liang Heidi Yahan , Mortazavi Ali
Published: May 2022

The extent to which animals can regenerate cells, tissues, or body parts varies largely.Hydrahas a remarkable ability to undergo full body regeneration. Bisected polyps can regenerate the head and foot, and whole polyps can form from aggregates of cells. This capability is made possible by a cluster of cells known as the head organizer. Previous studies have foundWnt3and other developmental genes associated with head organizer function. Yet, the genetic and molecular mechanisms of regeneratingHydraheads remain unresolved. In this study, we used bulk RNA-seq, bulk ATAC-seq, and single-cell RNA-seq from a regeneration time course to characterize the gene expression, gene regulation, molecular, and cellular features ofHydrahead regeneration. WGCNA modules andcis-regulation of candidate head organizer genes identified genes co-expressed withWnt3and transcription factors important for regeneration. At the single-cell level, we identified at least six distinct cell types in the regenerating head tissue and characterized the expression of candidate genes. With these combined data sets, we identify and clarify some of the interactions between JNK, Wnt3, and EGRF signaling duringHydrahead regeneration. Our study reveals coordination of early wound response, developmental transcription factors, and transposable elements duringHydratissue regeneration and provides insight into the evolution of regeneration programs.
Rab10 inactivation promotes AMPAR trafficking and spine enlargement during long-term potentiation
Authors: Wang Jie , Nishiyama Jun , Parra-Bueno Paula , Okaz Elwy , Oz Goksu , Liu Xiaodan , Watabe Tetsuya , Suponitsky-Kroyter Irena , McGraw Timothy E , Szatmari Erzsebet M. , Yasuda Ryohei
Published: May 2022

Rab-dependent membrane trafficking is critical for changing the structure and function of dendritic spines during synaptic plasticity. Here, we developed highly sensitive sensors to monitor Rab protein activity in single dendritic spines undergoing structural long-term potentiation (sLTP) in rodent organotypic hippocampal slices. During sLTP, Rab10 was persistently inactivated (>30 min) in the stimulated spines, whereas Rab4 was transiently activated over ∼5 min. Inhibiting or deleting Rab10 enhanced sLTP, electrophysiological LTP and AMPA receptor (AMPAR) trafficking during sLTP. In contrast, disrupting Rab4 impaired sLTP only in the first few minutes, and decreased AMPAR trafficking during sLTP. Thus, our results suggest that Rab10 and Rab4 oppositely regulate AMPAR trafficking during sLTP, and inactivation of Rab10 signaling facilitates the induction of LTP and associated spine structural plasticity.
The circadian clock mediates daily bursts of cell differentiation by periodically restricting cell differentiation commitment
Authors: Zhang Zhi-Bo , Sinha Joydeb , Bahrami-Nejad Zahra , Teruel Mary N.
Published: May 2022

Most mammalian cells have an intrinsic circadian clock that coordinates their metabolic activity with the daily rest and wake cycle. In addition, the circadian clock is known to regulate cell differentiation, but how continuous daily oscillations of the internal clock control a much longer, multi-day differentiation process is not known. Here we simultaneously monitor the circadian clock and progression of adipocyte differentiation live in single cells. Strikingly, we find a bursting behavior in the cell population whereby individual preadipocytes commit to differentiate primarily during a 12-hour window each day corresponding to the time of rest. Daily gating of differentiation occurs because cells can irreversibly commit to differentiate within a few hours, which is faster than the rest phase and much faster than the overall multi-day differentiation process. We show that the daily bursts in differentiation are driven by a variable and slow increase in expression of PPARG, the master regulator of adipogenesis, combined with rapid, clock-driven expression of CEBPA, which is in a fast positive feedback relationship with PPARG. During each rest cycle, the increase in CEBPA causes a brief step increase in PPARG so that some cells can reach the threshold to irreversibly commit to differentiate, causing the consecutive daily bursts in cell differentiation at the population level. Our findings are broadly relevant given that most differentiating somatic cells are regulated by the circadian clock. Having a restricted time each day when differentiation occurs may open therapeutic strategies to use timed treatment relative to the clock to promote tissue regeneration.

Significance Statement

Cells rely on a circadian clock that coordinates cellular activities with the day-night cycle. Defects in circadian clock genes dysregulate cell differentiation processes in immune, muscle, skin and fat cells. However, how a perpetual daily clock can regulate a multi-day long cell differentiation process was not understood. Here we show that the circadian clock controls a fast upregulation of the transcription factor CEBPA during each daily rest phase which in turn controls a fast irreversible step during the overall slow multi-day differentiation of fat cells, causing daily bursts of cell differentiation. Our finding opens potential therapeutic strategies to enhance tissue regeneration by timing when during the day drugs are administered.
X-ray imaging of 30 year old wine grape wood reveals cumulative impacts of rootstocks on scion secondary growth and harvest index
Authors: Migicovsky Zoë , Quigley Michelle Y. , Mullins Joey , Ali Tahira , Swift Joel F. , Agasaveeran Anita Rose , Dougherty Joseph D. , Grant Brendan Michael , Korkmaz Ilayda , Malpeddi Maneesh Reddy , McNichol Emily L. , Sharp Andrew W. , Harris Jackie L. , Hopkins Danielle R. , Jordan Lindsay M. , Kwasniewski Misha T. , Striegler R. Keith , Dowtin Asia L. , Stotts Stephanie , Cousins Peter , Chitwood Daniel H.
Published: May 2022

Annual rings from 30 year old vines in a California rootstock trial were measured to determine the effects of 15 different rootstocks on Chardonnay and Cabernet Sauvignon scions. Viticultural traits measuring vegetative growth, yield, berry quality, and nutrient uptake were collected at the beginning and end of the lifetime of the vineyard.

X-ray Computed Tomography (CT) was used to measure ring widths in 103 vines. Ring width was modeled as a function of ring number using a negative exponential model. Early and late wood ring widths, cambium width, and scion trunk radius were correlated with 27 traits.

Modeling of annual ring width shows that scions alter the width of the first rings but that rootstocks alter the decay thereafter, consistently shortening ring width throughout the lifetime of the vine. The ratio of yield to vegetative growth, juice pH, photosynthetic assimilation and transpiration rates, and stomatal conductance are correlated with scion trunk radius.

Rootstocks modulate secondary growth over years, altering hydraulic conductance, physiology, and agronomic traits. Rootstocks act in similar but distinct ways from climate to modulate ring width, which borrowing techniques from dendrochronology, can be used to monitor both genetic and environmental effects in woody perennial crop species.
Impact of genus (Geotrigona,Melipona,Scaptotrigona) in the1H-NMR organic profile and authenticity test of honey processed in cerumen pots by stingless bees in Ecuador
Authors: Vit Patricia , van der Meulen Jane , Pedro Silvia RM , Esperança Isabelle , Zakaria Rahimah , Beckh Gudrun , Maza Favian
Published: May 2022

The biodiversity of Ecuadorian stingless bees is almost 200 species. Traditional pot-honey harvest in Ecuador is mostly done from nests of the three genera selected hereGeotrigonaMoure, 1942,Melipona, Illiger, 1806 andScaptotrigona, Moure 1943. The 20 pot-honey samples collected from cerumen pots and three ethnic honeys “abeja de tierra”, “bermejo”, and “cushillomishki” were analyzed for qualitative and quantitative1H-NMR honey profiling and for the Honey Authenticity Test by Interphase Emulsion (HATIE). Extensive data of targeted organic compounds (41 parameters) was identified, quantified and described. The three honey types were compared by ANOVA. Amino acids, ethanol, hydroxymethylfurfural, aliphatic organic acids, sugars, and markers of botanical or entomological origin. The number of phases observed with the HATIE was one inScaptotrigonaand three inGeotrigonaandMeliponahoneys. Acetic acid (19.60 ± 1.45 g/kg) and lactic acid (24.30 ± 1.65 g/kg) were particularly high inGeotrigonahoney (in contrast to 1.3 g/kg acetic acid and 1.6 g/kg lactic acid inMeliponaandScaptotrigona), with the lowest fructose + glucose (18.39 ± 1.68) g/100g honey compared toMelipona(52.87 ± 1.75) andScaptotrigona(52.17 ± 0.60). Three local honeys were tested using PCA (Principal Component Analysis), two were assigned with a correct declared bee origin, but “bermejo” was not aMeliponaand grouped with theScaptotrigonacluster. However, after HCA (Hierarchical Cluster Analysis), the three kinds of honey were positioned in theMelipona-Scaptotrigonacluster. This research supports the targeted NMR-based profiling in pot-honey metabolomics approach for multi-parameter visualization of organic compounds, descriptive and pertained multivariate statistics (Hierarchical Cluster Analysis HCA, and Principal Component Analysis PCA) to discriminate the stingless bee genus in a set ofGeotrigona,MeliponaandScaptotrigonahoney types. The NMR characterization of Ecuadorian honey produced by stingless bees is a contribution to the needed regulatory norms. A final note on searching stingless bee markers in pot-honey metabolites that may become nutritional trait candidates for phylogeny.Scaptotrigonahoney revealed biosurfactant activity in the HATIE, originating a fingerprint Honey Biosurfactant Test (HBT) for the genus in this set of pot-honeys.
Longitudinal white matter alterations in SIVmac239 infected rhesus monkeys with and without regular cART treatment
Authors: Liu Jiaojiao , Nguchu Benedictor Alexander , Liu Dan , Qi Yu , Alixire  , Han Shuai , Gao Yuxun , Wang Xiaoxiao , Qiao Hongwei , Cai Chao , Huang Xiaojie , Li Hongjun
Published: May 2022

Objective

We use the SIV-mac239 infected Chinese rhesus monkeys to longitudinally investigate white matters alterations with and without regular combined antiretroviral therapy (cART) treatment, and its relationship with clinical tests.

Material and methods

Diffusion tensor imaging (DTI), CD4 T cell counts, and CD4/CD8 were obtained at baseline, 10 days, 4th week,12th week, 24th week, and 36th week post virus inoculation. postinfection (wpi). Microstructural properties were examined within 76 white matter defined by DTI-WM atlas for rhesus macaques. Corrections for multiple comparisons were performed using a false discovery rate (p < 0.05, FDR). Correlation analyses between imaging markers and clinical measures (CD4 T-cell counts, CD4/CD8 ratio) were determined using Pearson’s correlations.

Results

In our model, White matter alterations in SIV-infected macaques can be detected as soon as 4 weeks post inoculation in several brain regions. And with time proceeding, the cART can reverse, relieve, or even progressive effects. CD4 T-cell count is mainly associated with DTI metrics before the cART, whereas CD4/CD8 ratio was associated with white matter alteration with and without cART.

Conclusion

SIV-mac239 infection can be an idol modal to explore HIV induced HIV associated brain alterations, and the first group of white matter alterations was as soon as 4 weeks post inoculation in structure next to the periventricular area. As the time progressed, cART can bring different effect to each region, including reversed, relieved, and even progressive effects. In addition, these changes are closely linked to CD4/CD8 ratio even after cART.

Importance
Phenol Sensing in Nature Modulated via a Conformational Switch Governed by Dynamic Allostery
Authors: Singh Jayanti , Sahil Mohammad , Ray Shamayeeta , Dcosta Criss , Panjikar Santosh , Krishnamoorthy G. , Mondal Jagannath , Anand Ruchi
Published: May 2022

NtrC family of proteins sense external stimuli and accordingly stimulate stress and virulence pathways via activation of associated σ54-dependent RNA polymerases. Here, we establish that MopR, an NtrC protein, harbors a dynamic bi-directional electrostatic network that connects the phenol pocket to two distal regions, namely the “G-hinge” and the “allo-steric-linker”. While G-hinge influences the entry of phenol, the allosteric-linker passes the signal to the downstream ATPase domain. Phenol binding induces a rewiring of the electrostatic connections by eliciting dynamic allostery, and it was demonstrated that perturbation of the core relay residues results in a complete loss of ATPase stimulation. A mutation of the G-hinge,∼20Å from the phenol pocket, demonstrated altered flexibility by shifting the pattern of conformational states accessed, leading to a protein with 7-fold enhanced phenol binding ability and enhanced transcriptional activation. A global analysis illustrates that dynamic allostery-driven conserved community networks are universal and evolutionarily conserved across species.
Increased CaMKK2 expression is an adaptive response that maintains the fitness of tumor-infiltrating natural killer cells
Authors: Juras Patrick K. , Racioppi Luigi , Mukherjee Debarati , Artham Sandeep , Gao Xia , D’Agostino Laura Akullian , Chang Ching-Yi , McDonnell Donald P.
Published: May 2022

Calcium/calmodulin-dependent protein kinase kinase 2 (CaMKK2) is a key regulator of energy homeostasis in several cell types. Expression of this enzyme in tumor cells promotes proliferation and migration, and expression in tumor-associated immune cells facilitates M2 macrophage polarization and the development of myeloid-derived suppressor cells. Thus, there has been considerable interest in developing CaMKK2 inhibitors as potential cancer therapeutics. However, the roles of CaMKK2 in other cellular compartments within the tumor immune environment remain to be established, an impediment to the clinical development of these agents. We report that CaMKK2 is expressed at low basal levels in natural killer (NK) cells but is significantly upregulated in tumor-infiltrating NK cells where it suppresses apoptosis and promotes proliferation. It was further demonstrated that NK cell-intrinsic deletion of CaMKK2 increased metastatic progression across several murine models, establishing a critical role for this enzyme in NK cell tumor immunity. Interestingly, ablation of the CaMKK2 protein, but not inhibition of its kinase activity, resulted in decreased NK cell survival. These results indicate an important scaffold function for CaMKK2 in NK cells and suggest that competitive CaMKK2 inhibitors and ligand-directed degraders (LDDs) are likely to have distinct therapeutic utilities. Finally, we determined that intracellular lactic acid is a key driver of CaMKK2 expression, suggesting that upregulated expression of this enzyme is an adaptive mechanism by which tumor-infiltrating NK cells mitigate the deleterious effects of a lactate-rich tumor environment. The findings of this study should inform strategies to manipulate the CaMKK2 signaling axis as a therapeutic approach in cancer.
Midbrain-Hippocampus Structural Connectivity Selectively Predicts Motivated Memory Encoding
Authors: Elliott Blake L. , D’Ardenne Kimberlee , Murty Vishnu P. , Brewer Gene A. , McClure Samuel M.
Published: May 2022

Motivation is a powerful driver of learning and memory. Functional MRI studies show that interactions between the dopaminergic midbrain (SN/VTA), hippocampus, and nucleus accumbens (NAc) are critical for motivated memory encoding. However, it is not known if these effects are transient and purely functional, or if individual differences in the structure of this circuit underlie motivated memory encoding. To quantify individual differences in structure, diffusion-weighted MRI and probabilistic tractography were used to quantify SN/VTA-striatum and SN/VTA-hippocampus pathways associated with motivated memory encoding in humans.

Participants completed a motivated source memory paradigm. During encoding, words were randomly assigned to one of three conditions: reward ($1.00), control ($0.00), or punishment (-$1.00). During retrieval, participants were asked to retrieve item and source information of the previously studied words and were rewarded or penalized according to their performance. Source memory for words assigned to both reward and punishment conditions was greater than control words, while there were no differences in item memory based on value. Anatomically, probabilistic tractography results revealed a heterogeneous, topological arrangement of the SN/VTA. Tract density measures of SN/VTA-hippocampus pathways were positively correlated with individual differences in reward and punishment modulated memory performance, while density of SN/VTA-striatum pathways showed no association. This novel finding suggests that pathways emerging from the human SV/VTA are anatomically separable and functionally heterogeneous. Individual differences in structural connectivity of the dopaminergic hippocampus-VTA loop are selectively associated with motivated memory encoding.

Significance Statement

Functional MRI studies show that interactions between the dopaminergic midbrain (SN/VTA), hippocampus, and nucleus accumbens (NAc) are critical for motivated memory encoding. This has led to competing theories that posit either SN/VTA-NAc reward prediction errors or SN/VTA-hippocampus signals underlie motivated memory encoding. Additionally, it is not known if these effects are transient and purely functional, or if individual differences in the structure of these circuits underlie motivated memory encoding. Using diffusion-weighted MRI and probabilistic tractography, we show that tract density measures of SN/VTA-hippocampus pathways are positively correlated with motivated memory performance, while density of SN/VTA-striatum pathways show no association. This finding suggests that anatomical individual differences of the dopaminergic hippocampus-VTA loop are selectively associated with motivated memory encoding.
Disruption of Smarce1, a component of the SWI/SNF chromatin remodeling complex, decreases nucleosome stability in mouse embryonic stem cells and impairs differentiation
Authors: Kashiwagi Katsunobu , Yoshida Junko , Kimura Hiroshi , Horie Kyoji
Published: May 2022

The SWI/SNF chromatin remodeling complex consists of more than 10 component proteins that form a large protein complex of > 1 MDa. The catalytic proteins Smarca4 or Smarca2 work in concert with the component proteins to form a chromatin platform suitable for transcriptional regulation. However, the mechanism by which each component protein works synergistically with the catalytic proteins remains largely unknown. Here, we report on the function of Smarce1, a component of the SWI/SNF complex, through the phenotypic analysis of homozygous mutant embryonic stem (ES) cells. Disruption of Smarce1 induced the dissociation of other complex components from the SWI/SNF complex. Histone binding to DNA was loosened in homozygous mutant ES cells, indicating that disruption of Smarce1 decreased nucleosome stability. Sucrose gradient sedimentation analysis suggested an ectopic genomic distribution of the SWI/SNF complex, accounting for the misregulation of chromatin conformations. Unstable nucleosomes remained during ES cell differentiation, impairing the heterochromatin formation that is characteristic of the differentiation process. These results suggest that Smarce1 guides the SWI/SNF complex to the appropriate genomic regions to generate chromatin structures adequate for transcriptional regulation.