bluuebunny/crossref_metadata_2025 huggingface dataset:
KLF6 Promotes Pyroptosis of Renal Tubular Epithelial Cells in Septic Acute Kidney Injury
Authors: Gao Min , Li Hongbin , Liu Qilong , Ma Ning , Zi Panpan , Shi Huijuan , Du Yuming
Published: October 2021

Septic acute kidney injury (SAKI) represents a clinical challenge with high morbidity and mortality. The current study aimed to analyze the effects and molecular mechanism of Krüppel-like factor 6 (KLF6) on SAKI. First, SAKI mouse models were established by cecum ligation and puncture, while in vivo cell models were established using lipopolysaccharide (LPS). RT-qPCR assay was subsequently performed to detect the levels of KLF6 mRNA. SAKI mice and LPS-treated TCMK-1 cells were further treated with KLF6 siRNA. Afterward, HE staining, PAS staining, Western blot assay, and ELISA were adopted to ascertain the effects of KLF6 in pyroptosis. The binding relationships between KLF6 and miR-223-3p promoter /miR-223-3p and NLRP3 were analyzed with the help of CHIP and dual-luciferase reporter assays. RT-qPCR was adopted to determine the expression patterns of miR-223-3p and NLRP3. Lastly, a rescue experiment was designed to confirm the role of miR-223-3p. It was found that KLF6 was highly expressed in SAKI, whereas knockdown of KLF6 alleviated oxidative stress (OS) and pyroptosis in SAKI mice and LPS-treated TCMK-1 cells. Mechanistic results confirmed that KLF6 inhibited miR-223-3p via binding to the miR-223-3p promoter and promoted NLRP3. On the other hand, downregulation of miR-223-3p activated the NLRP3/Caspase-1/IL-1β pathway and aggravated OS and pyroptosis. Overall, our findings indicated that KLF6 inhibited miR-223-3p via binding to the miR-223-3p promoter and promoted NLRP3, and activated the NLRP3/Caspase-1/IL-1β pathway, thereby aggravating pyroptosis and SAKI.
Different Tendencies in Muscle Ultrasound Characteristic in Amyotrophic Lateral Sclerosis and Chronic Inflammatory Demyelinating Polyradiculoneuropathy
Authors: Hokkoku Keiichi , Tsukamoto Hiroshi , Uchida Yudai , Gatto Dario M. , Sonoo Masahiro
Published: October 2021

Introduction:

The difference in muscle ultrasound (MUS) characteristics in primary axonal degeneration and demyelination has not been well established. The authors aimed to investigate the subject based on the correlation between MUS findings (echo intensity and muscle thickness) and compound muscle action potential (CMAP) amplitude in amyotrophic lateral sclerosis (ALS) and chronic inflammatory demyelinating polyradiculoneuropathy.

Methods:

Fifteen patients with ALS and 16 patients with chronic inflammatory demyelinating polyradiculoneuropathy were examined. For each patient, echo intensity and muscle thickness of the abductor pollicis brevis, abductor digiti minimi, and first dorsal interosseous muscles were investigated. Compound muscle action potential amplitudes were measured by median and ulnar nerve conduction studies.

Results:

In total, 45 muscles were evaluated in each group. The ALS group showed a linear correlation between the MUS finding and CMAP amplitude (rs = −0.70 and 0.59 for echo intensity and muscle thickness, respectively), whereas the chronic inflammatory demyelinating polyradiculoneuropathy group showed a weaker correlation than the ALS group (rs = −0.32 for echo intensity and rs = 0.34 for muscle thickness).

Conclusions:

The relationship between MUS abnormalities and CMAP amplitude showed different tendencies in ALS and chronic inflammatory demyelinating polyradiculoneuropathy. The results suggested that MUS abnormalities substantially reflect the muscle function in primary axonal degeneration, whereas a discrepancy between MUS findings and muscle function can be frequently seen in demyelination; specifically, MUS findings tend to be normal even though CMAP showed a reduction. These tendencies originating from underlying pathophysiology should be considered when MUS findings are used as biomarkers of disease severity.
TIME-Seq Enables Scalable and Inexpensive Epigenetic Age Predictions
Authors: Griffin Patrick T , Kane Alice E , Trapp Alexandre , Li Jien , Arnold Matthew , Poganik Jesse R , McNamara Maeve S , Meer Margarita V , Hoffman Noah , Amorim João , Tian Xiao , MacArthur Michael R , Mitchell Sarah J , Mueller Amber L , Carmody Colleen , Vera Daniel L , Kerepesi Csaba , Hooten Nicole Noren , Mitchell James R , Evans Michele K , Gladyshev Vadim N , Sinclair David A
Published: October 2021

Epigenetic “clocks” based on DNA methylation (DNAme) have emerged as the most robust and widely employed aging biomarkers, but conventional methods for applying them are expensive and laborious. Here, we developTagmentation-based Indexing forMethylationSequencing (TIME-Seq), a highly multiplexed and scalable method for low-cost epigenetic clocks. Using TIME-Seq, we applied multi-tissue and tissue-specific epigenetic clocks to over 1,600 mouse DNA samples. We also discovered a novel approach for age prediction from shallow sequencing (e.g., 10,000 reads) by adaptingscAgefor bulk measurements. In benchmarking experiments, TIME-Seq performed favorably against prevailing methods and could quantify the effects of interventions thought to accelerate, slow, and reverse aging in mice. Finally, we built and validated a highly accurate human blood clock from 1,056 demographically representative individuals. Our methods increase the scalability and reduce the cost of epigenetic age predictions by more than 100-fold, enabling accurate aging biomarkers to be applied in more large-scale animal and human studies.
European Vintage tomatoes galore: a result of farmers combinatorial assorting/swapping of a few diversity rich loci
Authors: Blanca Jose , Pons Clara , Montero-Pau Javier , Sanchez-Matarredona David , Ziarsolo Peio , Fontanet Lilian , Fisher Josef , Plazas Mariola , Casals Joan , Rambla Jose Luis , Riccini Alessandro , Pombarelli Samuela , Ruggiero Alessandra , Sulli Maria , Grillo Stephania , Kanellis Angelos , Giuliano Giovanni , Finkers Richard , Cammareri Maria , Grandillo Silvana , Mazzucato Andrea , Causse Mathilde , Díez Maria José , Prohens Jaime , Zamir Dani , Cañizares Joaquin , Monforte Antonio Jose , Granell Antonio
Published: October 2021

A comprehensive collection of 1,254 tomato accessions corresponding to European heirlooms and landraces, together with modern varieties, early domesticates and wild relatives, were analyzed by genotyping by sequencing. A continuous genetic gradient between the vintage and modern varieties was observed. European vintage tomatoes displayed very low genetic diversity, with only 298 loci out of 64,943 variants being polymorphic at the 95% threshold. European vintage tomatoes could be classified in several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed a higher genetic diversity than the rest varieties, suggesting that these regions might be independent secondary centers of diversity and with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a GWAS with fruit morphological traits in the European vintage collection, and the corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise diversity-poor genome suggests a history of balancing selection, in which tomato farmers maintained the morphological variation by applying a high selective pressure within different varietal types.

Highlight

The high phenotypic diversity observed among European vintage varieties was created by traditional farmers by combining very few polymorphic loci subjected to balancing selection.
Cognitive and affective Theory of Mind double dissociation after parietal and temporal lobe tumors
Authors: Campanella Fabio , West Thomas , Corradi Dell’Acqua Corrado , Skrap Miran
Published: October 2021

Extensive neuroimaging literature suggests that understanding others’ thoughts and emotions engages a wide network encompassing parietal, temporal and medial frontal brain areas. However, the causal role played by these regions in social inferential abilities is still unclear. Moreover very little is known about ToM deficits in brain tumours and whether potential anatomical substrates are comparable to those identified in fMRI literature. This study evaluated the performance of 105 tumour patients, before and immediately after brain surgery, on a cartoon-based non-verbal task evaluating Cognitive (Intention Attribution) and Affective (Emotion Attribution) ToM, as well as a non-social control condition (Causal Inference). Across multiple analyses, we found converging evidence of a double dissociation between patients with right superior parietal damage, selectively impaired in Intention Attribution, and those with right antero-medial temporal lesion, exhibiting deficits only in Emotion attribution. Instead, patients with damage to the frontal cortex were impaired in all kinds of inferential processes, including those from the non-social control conditions. Overall, our data provides novel reliable causal evidence of segregation between different aspects of the ToM network from both the cognitive and also the anatomical point of view.
High spatial resolution analysis using indentation mapping differentiates biomechanical properties of normal vs. degenerated mouse articular cartilage
Authors: Masson Anand O. , Besler Bryce A. , Edwards W. Brent , Krawetz Roman J
Published: October 2021

Characterizing the biomechanical properties of articular cartilage is crucial to understanding processes of tissue homeostasis vs. degeneration. In mouse models, however, limitations are imposed by their small joint size and thin cartilage surfaces. Here we present a 3D automated surface mapping system and methodology that allows for mechanical characterization of mouse cartilage with high spatial resolution. We performed repeated indentation mappings, followed by cartilage thickness measurement via needle probing, at 31 predefined positions distributed over the medial and lateral femoral condyles of healthy mice. High-resolution 3D x-ray microscopy (XRM) imaging was used to validate tissue thickness measurements. The automated indentation mapping was reproducible, and needle probing yielded cartilage thicknesses comparable to XRM imaging. When comparing healthy vs. degenerated cartilage, topographical variations in biomechanics were identified, with altered thickness and stiffness (instantaneous modulus) across condyles and within anteroposterior sub-regions. This quantitative technique comprehensively characterized cartilage function in mice femoral condyle cartilage. Hence, it has the potential to improve our understanding of tissue structure-function interplay in mouse models of repair and disease.
Relative importance of region, seasonality and weed management practices effects on the functional structure of weed communities in French vineyards
Authors: Bopp Marie-Charlotte , Kazakou Elena , Metay Aurélie , Fried Guillaume
Published: October 2021

Winegrowers have diversified their weed management practices over the last two decades changing the structure and the composition of weed communities. Complementary to taxonomic studies, trait-based approaches are promising ways for a better understanding of weed communities’ responses to environmental and agronomic filters. In the present study, the impact of climate, soil characteristics, seasons and weed management practices (chemical weeding, tillage and mowing) were assessed on weed communities in three French wine-growing regions (Champagne, Languedoc and Rhône valley). These agro-environmental gradients structuring weed communities according to their combination of traits were highlighted using multivariate analysis (RLQ). The impacts of these filters on Community Weighted Means (CWM) and the Community Weighted Variance (CWV) of weed communities were analysed using mixed and null modelling. Our results showed that spatio-temporal and weed management practices variables explained from 13% to 48% of the total variance of CWM (specific leaf area, maximum height, seed mass, flowering onset and duration and lateral spread). Region, seasonality and management practices explained 53%, 28% and 19% of CWM marginal variance, respectively. Weed management impacted CWM and CWV through two main gradients: (i) a soil disturbance gradient with high mechanical disturbance of soil in tilled plots and low mechanical disturbance in chemically weeded plots and (ii) a vegetation cover gradient with high vegetation abundance in mowed plots compared to more bare soils in tilled and chemically weeded plots. Chemically weeded communities showed trait values of ruderal strategies (low seed mass, small-stature) in Languedoc. Mowed plots were associated with more competitive strategies (higher seed mass, higher stature and lower SLA) in Languedoc. Tillage favoured communities with high seed mass that increases the viability of buried seeds and high lateral spread values associated to the ability to resprout after tillage in Languedoc and Champagne. This study demonstrated that trait-based approach can be successfully applied to perennial cropping systems such as vineyards, in order to understand community assembly to better guide weed management practices.
Effects of perfluoroalkyl and polyfluoroalkyl substances on soil structure and function
Authors: Xu Baile , Yang Gaowen , Lehmann Anika , Riedel Sebastian , Rillig Matthias C.
Published: October 2021

Soils are impacted at a global scale by several anthropogenic factors, including chemical pollutants. Among those, perfluoroalkyl and polyfluoroalkyl substances (PFAS) are of concern due to their high environmental persistence, and as they might affect soil health and functions. However, data on impacts of PFASs on soil structure and microbially-driven processes are currently lacking. This study explored the effects of perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA) and perfluorobutanesulfonic acid (PFBS) at environmental-relevant nominal concentrations (1 ~ 1000 ng g−1) on soil functions, using a 6-week microcosm experiment. We measured soil respiration, litter decomposition, enzyme and microbial activities, soil aggregates, and bacterial abundance. PFAS (even at 1 ng g−1 for PFBS) significantly increased litter decomposition, associated with positive effects on bacterial abundance, and β-glucosidase activities. This effect increased with PFAS concentrations. Soil respiration was significantly inhibited by PFAS in the 3rd week, while this effect was more variable in week 6. Water-stable aggregates were negatively affected by PFOS and PFOA, possibly related to microbial shifts. The general microbial activities and β-D-cellobiosidase and phosphatase activities were barely affected by PFAS treatments. Our work highlights the potential effects of PFAS on soil health, and we argue that this substance class could be a factor of environmental change of potentially broad relevance in terrestrial ecosystem functioning.

Synopsis

PFAS are likely to affect soil health.

Abstract Art
Functional and historical drivers of leaf shape evolution in Palms (Arecaceae)
Authors: Jimenez Maria Fernanda Torres , Chazot Nicolas , Emilio Thaise , Fredin Johan Uddling , Antonelli Alexandre , Faurby Soren , Bacon Christine D
Published: October 2021

Aim

Leaves display a remarkable variety of shapes, each with potential ecological advantages in specific climates. While relations between leaf shape and either climate or height has been relatively well studied in eudicots, the macroecological drivers of shape remain poorly known in monocots. Here, we investigated associations between climate and plant height with the evolution of leaf shape in a clade with high species and morphological diversity.

Location

Global.

Time period

Cretaceous to contemporary.

Major taxa studied

Palms (Arecaceae).

Methods

We apply a Bayesian phylogenetic mixed model to test for associations between climate and leaf shape (all entire-leaved, pinnate-dissected, palmate-dissected, and costapalmate). We further reconstruct the ancestral leaf shape using multistate speciation and extinction models and compare the frequency of shapes with global temperatures through time.

Results

We find that plant height associates with dissected leaves and that annual precipitation associates with pinnate shapes. The ancestral leaf shape is unclear but early diversification was dominated by pinnate-dissected palms, which has remained the most species-rich form of leaves throughout palm history.

Main conclusions

Palms that are tall and live in humid regions are more likely to have pinnate leaves. Through geological time scales, temperature did not play an obvious role in determining leaf shapes. This study contributes to our understanding of how the diversity of leaf shapes is linked to biological and climatic factors.
Actinosomes: condensate-templated proteinaceous containers for engineering synthetic cells
Authors: Ganar Ketan A. , Leijten Liza , Deshpande Siddharth
Published: October 2021

Engineering synthetic cells has a broad appeal, from understanding living cells to designing novel biomaterials for therapeutics, biosensing, and hybrid interfaces. A key prerequisite to creating synthetic cells is a functional three-dimensional container capable of orchestrating biochemical reactions. In this study, we present an easy and effective technique to make cell-sized porous containers crafted using the interactions between biomolecular condensates and actin cytoskeleton - we coin them actinosomes. This approach uses polypeptide/nucleoside triphosphate condensates and localizes actin monomers on their surface. By triggering actin polymerization at the expense of sequestered ATP and using osmotic gradients, the condensates are structurally transformed into containers with the boundary made up of actin filaments and polylysine polymers. We show that the GTP-to-ATP ratio is a crucial parameter for forming actinosomes: insufficient ATP prevents condensate dissolution while excess ATP leads to undesired crumpling. The surface of actinosomes lacks any structural order and is porous. We show the functionality of the actinosomes by using them as bioreactors capable of protein synthesis. Actinosomes are a handy addition to the synthetic cell platform, with appealing properties like ease-of-production, inherent encapsulation capacity, and an active surface which holds the potential to trigger signaling cascades and form multicellular assemblies, with potential for medical and biotechnological applications.
Unravelling complex molecular mechanisms in pine with genome-wide association analysis and gene co-expression networks
Authors: Bajay Stephanie Karenina , Aono Alexandre Hild , Kirst Matias , de Souza Anete Pereira
Published: October 2021

The authors have withdrawn this manuscript because they decided to change the phenotypic characteristics to be evaluated, considering the more significant contribution to the field. Therefore, the authors do not want this work to be cited as a reference for the project. If you have any questions, please contact the corresponding author.
Whole-genome sequencing of Vero E6 (C1008) and comparative analysis of four Vero cell sublines
Authors: Konishi Kazuhiro , Yamaji Toshiyuki , Sakuma Chisato , Kasai Fumio , Endo Toshinori , Kohara Arihiro , Hanada Kentaro , Osada Naoki
Published: October 2021

The Vero cell line is an immortalized cell line established from kidney epithelial cells of the African green monkey. A variety of sublines have been established from the original cell line, which display different characteristics. In this study, we determined the whole-genome sequence of Vero E6 (C1008) and performed comparative analysis among Vero JCRB 0111, Vero CCL-81, Vero 76 and Vero E6. Analysis of the copy number changes and loss of heterozygosity revealed that all sublines share a large deletion and loss of heterozygosity on chromosome 12, which harbors type I interferon and CDKN2 gene clusters. We identified a substantial number of genetic differences among the sublines including single nucleotide variants, indels, and copy number variations. The spectrum of single nucleotide variants indicated a close genetic relationship between Vero JCRB0111 and Vero CCL-81, and between Vero 76 and Vero E6, and a considerable genetic gap between the former two and the latter two lines. In contrast, we confirmed the pattern of genomic integration sites of simian endogenous retroviral sequences, which was consistent among the sublines. We identified subline-specific/enriched loss of function and missense variants, which potentially contribute to the differences in response to viral infection among the Vero sublines. In particular, we focused on Vero E6-specific/enriched variants and identified four genes (IL1RAP, TRIM25, RB1CC1, and ATG2A) that contained missense variants specific or enriched in Vero E6. In addition, we found that V739I variants of ACE2, which functions as the receptor for SARS-CoV-2, were heterozygous in Vero JCRB0111, Vero CCL-81, and Vero 76; however, Vero E6 contained the allele with isoleucine, resulting from the loss of one of the X chromosomes.
Kinetics of immune responses to the AZD1222/Covishield vaccine with varying dose intervals in Sri Lankan individuals
Authors: Jeewandara Chandima , Aberathna Inoka Sepali , Gomes Laksiri , Pushpakumara Pradeep Darshana , Danasekara Saubhagya , Guruge Dinuka , Ranasinghe Thushali , Gunasekera Banuri , Kamaladasa Achala , Kuruppu Heshan , Somathilake Gayasha , Dissanayake Osanda , Gamalath Nayanathara , Ekanayake Dinithi , Jayamali Jeewantha , Jayathilaka Deshni , Mudunkotuwa Anushika , Harvie Michael , Nimasha Thashmi , Wijayamuni Ruwan , Schimanski Lisa , Rijal Pramila , Tan Tiong K. , Dong Tao , Townsend Alain , Ogg Graham S. , Malavige Gathsaurie Neelika
Published: October 2021

Background

To understand the kinetics of immune responses with different dosing gaps of the AZD1222 vaccine, we compared antibody and T cell responses in two cohorts with two different dosing gaps.

Methods

Antibodies to the SARS-CoV-2 virus were assessed in 297 individuals with a dosing gap of 12 weeks, sampled at 12 weeks post second dose (cohort 1) and in 77 individuals with a median dosing gap of 21.4 weeks (cohort 2) sampled 6 weeks post second dose. ACE2 receptor blocking antibodies (ACE2R-Abs), antibodies to the receptor binding domain (RBD) of the virus and variants of concern (VOC) and ex vivo T cell responses were assessed in a sub cohort.

Results

All individuals (100%) had SARS-CoV-2 specific total antibodies and 94.2% of cohort 1 and 97.1% of cohort 2 had ACE2R-blocking Abs. There was no difference in antibody titres or positivity rates in different age groups in both cohorts. The ACE2R-blocking Abs (p<0.0001) and antibodies to the RBD of the VOCs were significantly higher in cohort 2, compared to cohort 1. 41.2% to 65.8% of different age groups gave a positive response by the haemagglutination assay to the RBD of the ancestral virus and VOCs in cohort 1, while 53.6% to 90% gave a positive response in cohort 2. 17/57 (29.8%) of cohort 1 and 17/29 (58.6%) of cohort 2 had ex vivo IFNγ ELISpot responses above the positive threshold. The ACE2R-blocking antibodies and ex vivo IFNγ ELISpot responses at 12 weeks post-first dose, significantly correlated with levels 12 weeks post second dose (Spearman’s r=0.46, p=0.008) and (Spearman’s r=0.71, p<0.0001) respectively.

Conclusions

Both dosing schedules resulted in high levels of antibody and T cell responses post vaccination, although those with a longer dosing gap had a higher magnitude of responses, possibly as immune responses were measured 6 weeks post second dose compared to 12 weeks post second dose.
Computational analysis reveals similarities and differences between SCLC subtypes
Authors: Singh Abhay , Desai Parth , Pillai Maalavika , Agarwal Nilay , Takahashi Nobuyuki , Thomas Anish , Jolly Mohit Kumar
Published: October 2021

Small cell lung cancer (SCLC) is a neuroendocrine malignancy with dismal survival rates. Previous studies have revealed inter and intra tumoral heterogeneity of SCLC driven by neuroendocrine differentiation and multiple gene expression signatures have been proposed to classify the distinct SCLC molecular subtypes However, few questions remain unanswered: a) how many SCLC subtypes exist? b) how similar or different are these subtypes?, c) which gene list(s) can be used to identify those specific subtypes? Here, we show that irrespective of the three gene sets (33 genes, 50 genes, 105 genes) proposed in different studies to classify SCLC into different subtypes, the markers of phenotypic heterogeneity in SCLC form a “teams” like pattern of co-expressed modules. Moreover, the 105 geneset could classify SCLC cell lines into five clusters, three of which can be distinctly mapped to the SCLC-A, SCLC-N and SCLC-Y subtypes. Intriguingly, we noticed a high degree of similarity in the transcriptional landscape of two non-neuroendocrine subtypes: SCLC-Y and SCLC-I*, as well as in their enrichment of EMT. Thus, our analysis elucidates the landscape of phenotypic heterogeneity enabling diverse SCLC subtypes.
On the dynamics of spatial updating
Authors: Blouin Jean , Pialasse Jean-Philippe , Mouchnino Laurence , Simoneau Martin
Published: October 2021

Most of our knowledge on the human neural bases of spatial updating comes from fMRI studies in which recumbent participants moved in virtual environments. As a result, little is known about the dynamic of spatial updating during real body motion. Here, we exploited the high temporal resolution of electroencephalography (EEG) to investigate the dynamics of cortical activation in a spatial updating task where participants had to remember their initial orientation while they were passively rotated about their vertical axis in the dark. After the rotations, the participants pointed towards their initial orientation. We contrasted the EEG signals with those recorded in a control condition in which participants had no cognitive task to perform during body rotations. We found that the amplitude of the P1N1 complex of the rotation-evoked potential (RotEPs) (recorded over the vertex) was significantly greater in the Updating task. The analyses of the cortical current in the source space revealed that the main significant task-related cortical activities started during the N1P2 interval (136-303 ms after rotation onset). They were essentially localised in the temporal and frontal (supplementary motor complex, dorsolateral prefrontal cortex, anterior prefrontal cortex) regions. During this time-window, the right superior posterior parietal cortex (PPC) also showed significant task-related activities. The increased activation of the PPC became bilateral over the P2N2 component (303-470 ms after rotation onset). In this late interval, the cuneus and precuneus started to show significant task-related activities. Together, the present results are consistent with the general scheme that the first task-related cortical activities during spatial updating are related to the encoding of spatial goals and to the storing of spatial information in working memory. These activities would precede those involved in higher order processes also relevant for updating body orientation during rotations linked to the egocentric and visual representations of the environment.
Virally Encoded Connectivity Transgenic Overlay RNA sequencing (VECTORseq) defines projection neurons involved in sensorimotor integration
Authors: Cheung Victoria , Chung Philip , Bjorni Max , Shvareva Varvara A. , Lopez Yesenia C. , Feinberg Evan H.
Published: October 2021

Behavior arises from concerted activity throughout the brain. Consequently, a major focus of modern neuroscience is defining the physiology and behavioral roles of projection neurons linking different brain areas. Single-cell RNA sequencing has facilitated these efforts by revealing molecular determinants of cellular physiology and markers that enable genetically targeted perturbations such as optogenetics, but existing methods for sequencing of defined projection populations are low-throughput, painstaking, and costly. We developed a straightforward, multiplexed approach, Virally Encoded Connectivity Transgenic Overlay RNA sequencing (VECTORseq). VECTORseq repurposes commercial retrogradely infecting viruses typically used to express functional transgenes, e.g., recombinases and fluorescent proteins, by treating viral transgene mRNA as barcodes within single-cell datasets. VECTORseq is compatible with different viral families, resolves multiple populations with different projection targets in one sequencing run, and identifies cortical and subcortical excitatory and inhibitory projection populations. Our study provides a roadmap for high-throughput identification of neuronal subtypes based on connectivity.
Comparative analysis of zooplankton diversity in freshwaters: What can we gain from metagenomic analysis?
Authors: Monchamp Marie-Ève , Walsh David A. , Garner Rebecca E. , Kraemer Susanne A. , Beisner Beatrix E. , Cristescu Melania E. , Gregory-Eaves Irene
Published: October 2021

Molecular genetic approaches applied to environmental DNA have great potential for biodiversity research and ecosystem monitoring. A metagenome contains genetic information from all organisms captured in an environmental sample. It has been primarily used to study bacteria and archaea, but promising reports focusing on metazoan diversity are emerging. However, methodological uncertainties remain, and studies are required to validate the power and the limitations of such an approach when applied to macro-eukaryotes. Here, we analyzed water sample metagenomes to estimate zooplankton diversity in 22 freshwater lakes across Eastern Canada. We tested the coherence of data based on morphologically identified zooplankton taxa and molecular genetic data derived from shotgun sequencing of environmental DNA collected at the same time. RV coefficients showed a significant correlation between the relative abundance of zooplankton families derived from small subunit rRNA genes extracted from the metagenomes and morphologically identified zooplankton. However, differences in congruence with morphological counts were detected when varied bioinformatic approaches were applied to presence-absence data. This study presents one of the first diversity assessments of a group of aquatic metazoans using metagenomes and validates the coherence of the community composition derived from genetic and classical species surveys. Overall, our results suggest that metagenomics has the potential to be further developed to describe metazoan biodiversity in aquatic ecosystems, and to advance this area we provide key recommendations for workflow improvement.
Phylogeography of Lanius senator reveals conflicts between alpha taxonomy, subspecies ranges and genetics
Authors: Nasuelli Martina , Ilahiane Luca , Boano Giovanni , Cucco Marco , Galimberti Andrea , Pavia Marco , Pioltelli Emiliano , Shafaeipour Arya , Voelker Gary , Pellegrino Irene
Published: October 2021

Implementing the effort in understanding biogeographic distribution patterns and taxonomic limits within animal groups is crucial for addressing several challenges of modern zoology. Although avian phylogeography has been deeply investigated within Western Palearctic, several families, such as shrikes, still display complicated or neglected biogeographic patterns both between and within species, thus requiring further investigations. The Woodchat Shrike (Lanius senator) is a long-distance migratory species that exhibits three morphologically well-recognizable subspecies, whose boundaries have never been molecularly investigated. Here, we aimed to define the phylogeographic structure of Lanius senator throughout its breeding range and assess the genetic coherence with the phenotypically described subspecies. We assembled a collection of 34 samples mainly from breeding populations of each subspecies and analyzed them at four mtDNA and two nuDNA markers. We did not find a clear phylogenetic structure with nuclear Ornithine Decarboxylase (ODC) and myoglobin intron 2 (MYO), while all the four mtDNA loci (i.e., ND2, COI, cytb and Control Region) highlighted two main haplogroups, one including both the nominate subspecies L. s. senator and L. s. badius and the second consistent with L. s. niloticus only from the easternmost part of the range. Surprisingly, individuals phenotypically assigned to L. s. niloticus from Israel were genetically assigned to the senator/badius haplogroup. Moreover, genetic distances showed intermediate values between inter-intraspecies diversity usually found in Passerines. We estimated a divergence time among the two haplogroups around 800 kya (549 - 1.259 kya HPD). Our findings showed a mismatch in subspecies assignment using morphology and genetic information and a marked differentiation between the eastern L.s. niloticus and all the other L. senator populations.
Spontaneous emergence of music detectors in a deep neural network
Authors: Kim Gwangsu , Kim Dong-Kyum , Jeong Hawoong
Published: October 2021

Music exists in almost every society, has universal acoustic features, and is processed by distinct neural circuits in humans even with no experience of musical training. These characteristics suggest an innateness of the sense of music in our brain, but it is unclear how this innateness emerges and what functions it has. Here, using an artificial deep neural network that models the auditory information processing of the brain, we show that units tuned to music can spontaneously emerge by learning natural sound detection, even without learning music. By simulating the responses of network units to 35,487 natural sounds in 527 categories, we found that various subclasses of music are strongly clustered in the embedding space, and that this clustering arises from the music-selective response of the network units. The music-selective units encoded the temporal structure of music in multiple timescales, following the population-level response characteristics observed in the brain. We confirmed that the process of generalization is critical for the emergence of music-selectivity and that music-selectivity can work as a functional basis for the generalization of natural sound, thereby elucidating its origin. These findings suggest that our sense of music can be innate, universally shaped by evolutionary adaptation to process natural sound.

One-sentence summary

Music-selectivity can arise spontaneously in deep neural networks trained for natural sound detection without learning music.
Benchmarking phasing software with a whole-genome sequenced cattle pedigree
Authors: Oget-Ebrad Claire , Kadri Naveen Kumar , Moreira Gabriel Costa Monteiro , Karim Latifa , Coppieters Wouter , Georges Michel , Druet Tom
Published: October 2021

Background

Accurate haplotype reconstruction is required in many applications in quantitative and population genomics. Different phasing methods are available but their accuracy must be evaluated for samples with different properties (population structure, marker density, etc.). We herein took advantage of whole-genome sequence data available for a Holstein cattle pedigree containing 264 individuals, including 98 trios, to evaluate several population-based phasing methods. This data represents a typical example of a livestock population, with low effective population size, high levels of relatedness and long-range linkage disequilibrium.

Results

After stringent filtering of our sequence data, we evaluated several population-based phasing programs including one or more versions of AlphaPhase, ShapeIT, Beagle, Eagle and FImpute. To that end we used 98 individuals having both parents sequenced for validation. Their haplotypes reconstructed based on Mendelian segregation rules were considered the gold standard to assess the performance of population-based methods in two scenarios. In the first one, only these 98 individuals were phased, while in the second one, all the 264 sequenced individuals were phased simultaneously, ignoring the pedigree relationships. We assessed phasing accuracy based on switch error counts (SEC) and rates (SER), lengths of correctly phased haplotypes and pairwise SNP phasing accuracies (the probability that a pair of SNPs is correctly phased as a function of their distance). For most evaluated metrics or scenarios, the best software was either ShapeIT4.1 or Beagle5.2, both methods resulting in particularly high phasing accuracies. For instance, ShapeIT4.1 achieved a median SEC of 50 per individual and a mean haplotype block length of 24.1 Mb in the second scenario. These statistics are remarkable since the methods were evaluated with a map of 8,400,000 SNPs, and this corresponds to only one switch error every 40,000 phased informative markers. When more relatives were included in the data, FImpute3.0 reconstructed extremely long segments without errors.

Conclusions

We report extremely high phasing accuracies in a typical livestock sample of 100 sequenced individuals. ShapeIT4.1 and Beagle5.2 proved to be the most accurate, particularly for phasing long segments. Nevertheless, most tools achieved high accuracy at short distances and would be suitable for applications requiring only local haplotypes.
Automated hyperspectral vegetation index derivation using a hyperparameter optimization framework for high-throughput plant phenotyping
Authors: Koh Joshua C.O. , Banerjee Bikram P. , Spangenberg German , Kant Surya
Published: October 2021

Hyperspectral vegetation indices (VIs) are widely deployed in agriculture remote sensing and plant phenotyping to estimate plant biophysical and biochemical traits. However, existing VIs consist mainly of simple 2-band indices which limits the net performance and often do not generalize well for other traits than they were originally designed for.

We present an automated hyperspectral vegetation index (AutoVI) system for the rapid generation of novel 2- to 6-band trait-specific indices in a streamlined process covering model selection, optimization and evaluation driven by the tree parzen estimator algorithm. Its performance was tested in generating novel indices to estimate chlorophyll and sugar contents in wheat.

Results show that AutoVI can rapidly generate complex novel VIs (≥4-band index) which correlated strongly (R2 > 0.8) with measured chlorophyll and sugar contents in wheat. AutoVI-derived indices were used as features in simple and stepwise multiple linear regression for chlorophyll and sugar content estimation, and outperformed results achieved with existing 47 VIs and those provided by partial least squares regression.

The AutoVI system can deliver novel trait-specific VIs readily adoptable in high-throughput plant phenotyping platforms and should appeal to plant scientists and breeders. A graphical user interface of AutoVI is herein provided.
TET2-mediated epigenetic reprogramming of breast cancer cells impairs lysosome biogenesis
Authors: Laurent Audrey , Madigou Thierry , Bizot Maud , Turpin Marion , Palierne Gaëlle , Mahé Elise , Guimard Sarah , Métivier Raphaël , Avner Stéphane , Le Péron Christine , Salbert Gilles
Published: October 2021

Methylation and demethylation of cytosines in DNA are believed to act as keystones of cell-specific gene expression through controlling chromatin structure and accessibility to transcription factors. Cancer cells have their own transcriptional programs and we sought to alter such a cancer-specific program by enforcing expression of the catalytic domain (CD) of the methylcytosine dioxygenase TET2 in breast cancer cells. TET2 CD decreased the tumorigenic potential of cancer cells through both activation and repression of a repertoire of genes that, interestingly, differed in part from the one observed upon treatment with the hypomethylating agent decitabine. In addition to promoting the establishment of an antiviral state, TET2 activated 5mC turnover at thousands of MYC binding motifs and down-regulated a panel of known MYC-repressed genes involved in lysosome biogenesis and function. Thus, an extensive cross-talk between TET2 and the oncogenic transcription factor MYC establishes a lysosomal storage disease-like state that contributes to an exacerbated sensitivity to autophagy inducers.
Specific ATPases drive compartmentalized glycogen utilization in rat skeletal muscle
Authors: Nielsen Joachim , Dubillot Peter , Stausholm Marie-Louise H. , Ørtenblad Niels
Published: October 2021

Glycogen is a key energy substrate in excitable tissue and especially in skeletal muscle fibers it contributes with a substantial, but also local energy production. A heterogenic subcellular distribution of three distinct glycogen pools in skeletal muscle is proved by transmission electron microscopy (TEM), which is thought to represent the requirements for local energy stores at the subcellular level. Here, we show that the three main energy-consuming ATPases in skeletal muscles (Ca2+-, Na+,K+-, and myosin ATPases) utilize different local pools of glycogen. These results clearly demonstrate compartmentalized glycogen metabolism and emphasize that spatially distinct pools of glycogen particles act as energy substrate for separated energy requiring processes, suggesting a new paradigm for understanding glycogen metabolism in working muscles, muscle fatigue and metabolic disorders.
Implementation of a novel optogenetic tool in mammalian cells based on a split T7 RNA polymerase
Authors: Dionisi Sara , Piera Karol , Baumschlager Armin , Khammash Mustafa
Published: October 2021

Optogenetic tools are widely used to control gene expression dynamics both in prokaryotic and eukaryotic cells. These tools are used in a variety of biological applications from stem cell differentiation to metabolic engineering. Despite some tools already available in bacteria, no light-inducible system currently exists to orthogonally control gene expression in mammalian cells. Such a tool would be particularly important in synthetic biology, where orthogonality is advantageous to achieve robust activation of synthetic networks. Here we implement, characterize and optimize a new orthogonal optogenetic tool in mammalian cells based on a previously published system in bacteria called Opto-T7RNAPs. The tool consists of a split T7 RNA polymerase coupled with the blue light-inducible magnets system (mammalian OptoT7 – mOptoT7). In our study we exploited the T7 polymerase’s viral origins to tune our system’s expression level, reaching up to 20-fold change activation over the dark control. mOptoT7 is used here to generate mRNA for protein expression, shRNA for protein inhibition and Pepper aptamer for RNA visualization. Moreover, we show that mOptoT7 can mitigate gene expression burden when compared to other optogenetic constructs. These properties make mOptoT7 a new powerful tool to use when orthogonality and viral-like RNA species are desired in both synthetic biology and basic science applications.
Weakly migratory metastatic breast cancer cells activate fibroblasts via microvesicle-Tg2 to facilitate dissemination and metastasis
Authors: Schwager Samantha C. , Hapach Lauren A. , Carlson Caroline M. , Mosier Jenna A. , McArdle Tanner J. , Wang Wenjun , Jayathilake Anissa L. , Bordeleau Francois , Antonyak Marc A. , Cerione Richard A. , Reinhart-King Cynthia A.
Published: October 2021

Cancer cell migration is highly heterogeneous, and the migratory capability of cancer cells is thought to be an indicator of metastatic potential. It is becoming clear that a cancer cell does not have to be inherently migratory to metastasize, with weakly migratory cancer cells often found to be highly metastatic. However, the mechanism through which weakly migratory cells escape from the primary tumor remains unclear. Here, utilizing phenotypically sorted highly and weakly migratory breast cancer cells, we demonstrate that weakly migratory metastatic cells disseminate from the primary tumor via communication with stromal cells. While highly migratory cells are capable of single cell migration, weakly migratory cells rely on cell-cell signaling with fibroblasts to escape the primary tumor. Weakly migratory cells release microvesicles rich in tissue transglutaminase 2 (Tg2) which activate fibroblasts and lead weakly migratory cancer cell migration in vitro. These microvesicles also induce tumor stiffening and fibroblast activation in vivo and enhance the metastasis of weakly migratory cells. Our results identify microvesicles and Tg2 as potential therapeutic targets for metastasis and reveal a novel aspect of the metastatic cascade in which weakly migratory cells release microvesicles which activate fibroblasts to enhance cancer cell dissemination.
Eicosanoids in the pancreatic tumor microenvironment – a multicellular, multifaceted progression
Authors: Gubbala Vikas B. , Jytosana Nidhi , Trinh Vincent Q. , Maurer H. Carlo , Naeem Razia F. , Lytle Nikki K. , Ma Zhibo , Zhao Steven , Lin Wei , Han Haiyong , Shi Yu , Hunter Tony , Singh Pankaj K. , Olive Kenneth P. , Tan Marcus C.B. , Kaech Susan M. , Wahl Geoffrey M. , DelGiorno Kathleen E.
Published: October 2021

Eicosanoids, oxidized fatty acids that serve as cell-signaling molecules, have been broadly implicated in tumorigenesis. To identify eicosanoids relevant to pancreatic tumorigenesis, we profiled normal pancreas and pancreatic ductal adenocarcinoma (PDAC) in mouse models and patient samples using mass spectrometry. We interrogated RNA sequencing datasets for eicosanoid synthase or receptor expression. Findings were confirmed by immunostaining. In murine models, we identified elevated levels of PGD2, prostacyclin, and thromboxanes in neoplasia while PGE2, 12-HHTre, HETEs, and HDoHEs are elevated specifically in tumors. Analysis of scRNA-seq datasets suggests that PGE2and prostacyclins are derived from fibroblasts, PGD2and thromboxanes from myeloid cells, and PGD2and 5-HETE from tuft cells. In patient samples, we identified a transition from PGD2to PGE2-producing enzymes in the epithelium during the transition to PDAC, fibroblast/tumor expression of PTGIS, and myeloid/tumor cell expression of TBXAS1. Altogether, our analyses identify key changes in eicosanoid species during pancreatic tumorigenesis and the cell types responsible for their synthesis.
A Locus Coeruleus- dorsal CA1 dopaminergic circuit modulates memory linking
Authors: Chowdhury Ananya , Luchetti Alessandro , Fernandes Giselle , Filho Daniel Almeida , Kastellakis George , Tzilivaki Alexandra , Ramirez Erica M , Tran Mary Y , Poirazi Panayiota , Silva Alcino J
Published: October 2021

Individual memories are often linked so that the recall of one triggers the recall of another. For example, contextual memories acquired close in time can be linked, and this is known to depend on temporary increase in excitability that drive the overlap between dorsal CA1 (dCA1) hippocampal ensembles encoding the linked memories. Here, we show that the Locus Coeruleus (LC) cells projecting to dCA1 have a key permissive role in contextual memory linking, without affecting contextual memory formation, and that this effect is mediated by dopamine and not by noradrenaline. Additionally, we found that LC to dCA1 projecting neurons modulate the excitability of dCA1 neurons, and the extent of overlap between dCA1 memory ensembles, as well as the stability of coactivity patterns within these ensembles. This discovery of a neuromodulatory system that specifically affects memory linking without affecting memory formation, reveals a fundamental separation between the brain mechanisms that modulate these two distinct processes.