bluuebunny/crossref_metadata_2025 huggingface dataset:
Atazanavir inhibits SARS-CoV-2 replication and pro-inflammatory cytokine production
Authors: Fintelman-Rodrigues Natalia , Sacramento Carolina Q. , Lima Carlyle Ribeiro , da Silva Franklin Souza , Ferreira André C. , Mattos Mayara , de Freitas Caroline S. , Soares Vinicius Cardoso , Gomes Dias Suelen da Silva , Temerozo Jairo R. , Miranda Milene , Matos Aline R. , Bozza Fernando A. , Carels Nicolas , Alves Carlos Roberto , Siqueira Marilda M. , Bozza Patrícia T. , Souza Thiago Moreno L.
Published: April 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is already responsible for far more deaths than previous pathogenic coronaviruses (CoVs) from 2002 and 2012. The identification of clinically approved drugs to be repurposed to combat 2019 CoV disease (COVID-19) would allow the rapid implementation of potentially life-saving procedures. The major protease (Mpro) of SARS-CoV-2 is considered a promising target, based on previous results from related CoVs with lopinavir (LPV), an HIV protease inhibitor. However, limited evidence exists for other clinically approved antiretroviral protease inhibitors, such as atazanavir (ATV). ATV is of high interest because of its bioavailability within the respiratory tract. Our results show that ATV could dock in the active site of SARS-CoV-2 Mpro, with greater strength than LPV. ATV blocked Mpro activity. We confirmed that ATV inhibits SARS-CoV-2 replication, alone or in combination with ritonavir (RTV) in Vero cells, human pulmonary epithelial cell line and primary monocytes, impairing virus-induced enhancement of IL-6 and TNF-α levels. Together, our data strongly suggest that ATV and ATV/RTV should be considered among the candidate repurposed drugs undergoing clinical trials in the fight against COVID-19.
Orthogonal fluorescent chemogenetic reporters for multicolor imaging
Authors: Tebo Alison G. , Moeyaert Benjamien , Thauvin Marion , Carlon-Andres Irene , Böken Dorothea , Volovitch Michel , Padilla-Parra Sergi , Dedecker Peter , Vriz Sophie , Gautier Arnaud
Published: April 2020

Fluorescence microscopy is an indispensable tool in biological research, allowing sub-second and sub-micrometer mapping of molecules or processes inside living cells. Moreover, using spectrally separated fluorophores, one can observe multiple targets simultaneously, leading to a deeper understanding of the dynamic molecular interplays that regulate cell function and fate. Chemogenetic systems, which combine a protein tag and a synthetic fluorophore, provide certain advantages over fluorescent proteins since there is no requirement for chromophore maturation. However, the fluorophore promiscuity of chemogenetic systems renders two-color applications challenging. Here, we present the engineering of a set of spectrally orthogonal fluorogen activating tags based on the Fluorescence Activating and absorption Shifting Tag (FAST), that are compatible with two-color, live cell imaging. The resulting tags, greenFAST and redFAST, demonstrate orthogonality not only in their fluorogen recognition capabilities, but also in their one- and two-photon absorption profiles. A two-color cell cycle sensor based on greenFAST and redFAST is capable of detecting very short, early cell cycles in zebrafish development which had previously been difficult to image. Furthermore, this pair of orthogonal tags can be developed into split complementation systems that are capable of detecting multiple protein-protein interactions by live cell fluorescence microscopy.
Community assembly as a basis for tropical forest restoration in a global change scenario
Authors: Meira-Neto João Augusto Alves , de Oliveira-Júnior Neil Damas , Silva Nathália , de Oliveira-Filho Ary Teixeira , Bueno Marcelo Leandro , Pontara Vanessa , Gastauer Markus
Published: April 2020

Native tropical forests hold high levels of diversity, challenging forest restoration of large areas in a global change scenario. For a site-specific restoration is required the understanding of the main influences ruling the assemblages. We aimed to answer three questions. 1) how do environmental variables influence taxonomic, phylogenetic diversities, and the phylogenetic structure in the of Rio Doce Basin (TFRD)? 2) How do environmental variables, phylogenetic structure and the main types of seed dispersal relate to each other? 3) Which information of the TFRD assemblages can be used for ecological restoration and conservation? We used 78 sites with their checklists to calculate taxonomic, and phylogenetic diversities, phylogenetic structures, and dispersal proportions. Then, we related the diversities of the sites to their bioclimatic variables and built GLM models. Species richness was influenced negatively by water excess duration, by water deficit duration, and positively by maximum temperature, and temperature seasonality. Water regime drives diversity and phylogenetic community structure in the TFRD more than other variables. Annual precipitation and maximum temperature presented the clearer influences on diversity and phylogenetic structure. Zoochory was positively, and anemochory, autochory were negatively related to sesMPD. By choosing the lineages with high fitness for each site, the functioning and the stability of ecosystems should increase. The addition of species with anemochory and autochory increases functional and phylogenetic diversity in areas with extreme water excess or water deficit, important in a global change scenario. A high proportion of zoochory allows the communities to function conserving dispersers, biodiversity, and services.

Implications for practice

The use of objective methods based on community assembly rules enhances the choice of species, and of phylogenetic lineages better fitted to the bioclimatic profiles of the areas to be restored, improving the functioning and stability of the restored forests.

The water purification service should be improved through forest restoration as much as possible because ecosystem services and biodiversity conservation are co-benefits of restored forests.

The inclusion of species with anemochory, and autochory in forest restoration practices should become usual, as they increase functional, and phylogenetic diversities, and as a consequence, the ecosystem stability.

A large proportion of species with zoochory in restored forests co-benefits taxonomic diversity, phylogenetic diversity, and ecosystem stability.
Molecular Basis of Maintaining Circannual Rhythm in the Skin of Cashmere Goat
Authors: Wu Jianghong , li Ying , Gong Husile , Wu Dubala , li Chun , Liu Bin , Ding Lizhong
Published: April 2020

The cashmere goat (Capra hircus) is famous for the fine quality cashmere wool. The cashmere is produced by secondary hair follicle that the growth shows seasonal rhythm. Thus, in this study, the skin of cashmere goat was selected as a model to illustrate the circannual rhythm of skin. The whole length skin transcriptome mixed from selected four months was obtained by PacBio single-molecule long-read sequencing (SMRT) technology. We generated 82,382 high quality non-redundant transcripts belonging to 193,310 genes, including 4,237 novel genes. Other 39 skin transcriptomes sampled from Dec. 2014 to Dec. 2015 were sequenced by Illumina Hi-Seq2500, we found 980 genes were differentially expressed. Of these genes, 403 seasonal rhythm genes (SRGs) were expressed and exhibited a seasonal pattern in skin. The results also showed that miRNAs were differentially expressed as the daylight length changed throughout a year. Some SRG genes related to the hormone secretion and eyes morphogenesis were enriched in skin. These genes gradually increased their expression level under short light, reached the peak near the summer solstice, and then began to decline. We found that the expression of Dio1 gene may be affected by the photoperiod that induces transformation from the inactive T4 to active thyroid hormone T3 in the skin and led to the difference between the skin circannual rhythm and the core circannual rhythm. Furthermore, the skin expressed eye morphogenesis-related genes and miRNAs, which suggested some cells in the skin could have the potential of light sensitivity. These results revealed that SRGs could regulate the downstream gene expression and physiological process in the skin to adapt to the season change.
Neural circuit mechanisms for steering control in walkingDrosophila
Authors: Rayshubskiy Aleksandr , Holtz Stephen L. , Bates Alexander , Vanderbeck Quinn X. , Capdevila Laia Serratosa , Wilson Rachel I.
Published: April 2020

Orienting behaviors provide a continuous stream of information about an organism’s sensory experiences and plans. Thus, to study the links between sensation and action, it is useful to identify the neurons in the brain that control orienting behaviors. Here we describe descending neurons in theDrosophilabrain that predict and influence orientation (heading) during walking. We show that these cells have specialized functions: whereas one cell type predicts sustained low-gain steering, the other predicts transient high-gain steering. These latter cells integrate internally-directed steering signals from the head direction system with stimulus-directed steering signals from multimodal sensory pathways. The inputs to these cells are organized to produce “see-saw” steering commands, so that increasing output from one brain hemisphere is accompanied by decreasing output from the other hemisphere. Together, our results show that internal and external drives are integrated to produce descending motor commands with different timescales, for flexible and precise control of an organism’s orientation in space.
Machine Classification of Methylomes in Cancer
Authors: Newsham Isabelle , Sendera Marcin , Jammula SriGanesh , Fitzgerald Rebecca , Massie Charles , Samarajiwa Shamith A.
Published: April 2020

Cancer remains a leading cause of morbidity and mortality worldwide. Its evolutionary nature and resultant complex interactions with the tumour micro-environment and the host immune system engender heterogeneity, make developing interventions difficult. Usually detected at the advanced stages of disease, metastatic cancer accounts for 90% of cancer-associated deaths. Therefore early detection of cancer, combined with current therapies, would have a significant impact on survival and treatment of this insidious disease. Epigenetic changes such as DNA methylation are some of the early events in carcinogenesis. Here, we report on a machine learning model that can classify 13 types of cancer as well as non-cancer tissue samples using only DNA methylome data, with an accuracy of 98.2%. We utilise the features identified by this model to develop a robust deep neural network that can generalise to independent data sets. We also demonstrate that the methylation associated genomic loci detected by the classifier are associated with genes involved in cancer, providing insights into the epigenomic regulation of carcinogenesis.
ANTITUMOR SULFATED POLYSACCHARIDES FROM BROWN ALGAEDictyota caribaea
Authors: Brígido Assef Alexia Nathália , da Costa Bianca Barros , Moreira Thamyris Almeida , do Carmo Luana David , de Fátima Goebel de Souza Tamiris , Nunes Alencar Nylane Maria , Negreiros Nunes Ana Paula , Cinelli Leonardo Paes , Wilke Diego Veras
Published: April 2020

Sulfated polysaccharides (SP) are a complex group of bioactive molecules able to inhibit tumor growth. SP increase the effectiveness of chemotherapy and reduce some side effects. Brown algae produce SP with several biological activities including antitumor. This work aimed to investigate the antitumor effect of SP from the brown algaeDictyota caribaea(Dc-SP). Dc-SP were extracted with proteolytic enzyme and supernatant was precipitated with increasing concentrations of ethanol. Antiproliferative activity of Dc-SP was tested by the MTT assay against colon cancer (HCT 116) and metastatic melanoma (B16-F10) cell lines. The antitumor effect was evaluated on Swiss mice transplanted with sarcoma 180 tumor and treated i.p. during 7 days with saline or Dc-SP (25 and 50 mg/kg/animal). Dc-SP did not exhibit cytotoxicityin vitro, however the Dc-SP-treated mice depicted up to 50% tumor growth inhibition. Dc-SP treatment induced spleen weight increasing along with intense white pulp disorganization. Furthermore Dc-SP did not depict hepatic toxicity, nephrotoxicity nor leukopenia and did induce increase of platelets count. Altogether, these results represent a promising antitumor host dependent effect induced by Dc-SP.
The origin and evolution of a distinct mechanism of transcription initiation in yeasts
Authors: Lu Zhaolian , Lin Zhenguo
Published: April 2020

The molecular process of transcription by RNA Polymerase II is highly conserved among eukaryotes (“classic model”). Intriguingly, a distinct way of locating transcription start sites (TSSs) was found in a budding yeastSaccharomyces cerevisiae(“scanning model”). The origin of the “scanning model” and its underlying genetic mechanisms remain unsolved. Herein, we applied genomic approaches to address these questions. We first identified TSSs at a single-nucleotide resolution for 12 yeast species using the nAnT-iCAGE technique, which significantly improved the annotations of these genomes by providing accurate 5’boundaries of protein-coding genes. We then infer the initiation mechanism of a species based on its TSS maps and genome sequences. We found that the “scanning model” had originated after the split ofYarrowia lipolyticaand the rest of budding yeasts. An adenine-rich region immediately upstream of TSS had appeared during the evolution of the “scanning model” species, which might facilitate TSS selection in these species. Both initiation mechanisms share a strong preference for pyrimidine-purine dinucleotides surrounding the TSS. Our results suggested that the purine is required for accurately recruiting the first nucleotide, increasing the chance of being capped during mRNA maturation, which is critical for efficient translation initiation. Based on our findings, we proposed a model of TSS selection for the “scanning model” species. Besides, our study also demonstrated that the intrinsic sequence feature primarily determines the distribution of initiation activities within a core promoter (core promoter shape).
Co-stimulation with opposing macrophage polarization cues leads to orthogonal secretion programs in individual cells
Authors: Muñoz-Rojas Andrés R. , Kelsey Ilana , Pappalardo Jenna , Miller-Jensen Kathryn
Published: April 2020

Macrophages are innate immune cells that contribute to fighting infections, tissue repair, and maintaining tissue homeostasis. To enable such functional diversity, macrophages resolve potentially conflicting cues in the microenvironment via mechanisms that remain unclear. Here, we used single-cell RNA sequencing to explore how individual macrophages respond when co-stimulated with the inflammatory stimuli, LPS+IFN-γ, and the resolving cytokine, IL-4. We found that co-stimulated macrophages displayed a distinct global transcriptional program. However, variable negative cross-regulation between some LPS+IFN-γ- and IL-4-specific genes resulted in significant cell-to-cell heterogeneity in transcription. Interestingly, negative cross-regulation led to mutually exclusive expression of the T-cell-polarizing cytokinesIl6andIl12bversus the IL-4-associated factorsArg1andChil3in single co-stimulated macrophages, and single-cell secretion measurements showed that these specialized functions were maintained for at least 48 hours. Overall, our study suggests that increasing functional diversity in the population is one strategy macrophages use to respond to conflicting environmental cues.
Targeting the Src pathway enhances the efficacy of selective FGFR inhibitors in cancers with FGFR3 alterations
Authors: Lima Nadia Carvalho , Atkinson Eliza , Bunney Tom D , Katan Matilda , Huang Paul H.
Published: April 2020

Selective FGFR inhibitors such as infigratinib (BGJ398) and erdafitinib (JNJ-42756493) have been evaluated in clinical trials for cancers with FGFR3 molecular alterations, particularly in urothelial carcinoma patients. However, a substantial proportion of these patients (up to 50%) display intrinsic resistance to these drugs and receive minimal clinical benefit. There is thus an unmet need for alternative therapeutic strategies to overcome primary resistance to selective FGFR inhibitors. In this study, we demonstrate that cells expressing cancer-associated activating FGFR3 mutants and the FGFR3-TACC3 fusion showed primary resistance to infigratinib in long-term colony formation assays in both NIH-3T3 and urothelial carcinoma models. We find that expression of these FGFR3 molecular alterations resulted in elevated constitutive Src activation compared to wildtype FGFR3 and that cells co-opted this pathway as a means to achieve intrinsic resistance to infigratinib. Targeting the Src pathway with low doses of the kinase inhibitor dasatinib synergistically sensitized multiple urothelial carcinoma lines harbouring endogenous FGFR3 alterations to infigratinib. Our preclinical data provides evidence that supports the use of dasatinib in combination with selective FGFR inhibitors as a means to overcome intrinsic drug resistance in the salvage therapy setting in cancer patients with FGFR3 molecular alterations.
Using asymmetry to your advantage: learning to acquire and accept external assistance during prolonged split-belt walking
Authors: Sánchez Natalia , Simha Surabhi N. , Donelan J. Maxwell , Finley James M.
Published: April 2020

People often adapt their coordination patterns during walking to reduce energy cost by using sources of external assistance in the environment. Adaptation to walking on a split-belt treadmill, where one belt moves faster than the other, provides an opportunity for people to acquire positive work from the treadmill to reduce metabolic cost by modifying where they step on the faster belt. Though we know what people should do to acquire this assistance, this strategy is not observed during typical adaptation studies. Here, by extending the duration of adaptation, we show that people continuously optimize energetic cost by adjusting foot placement to acquire positive work from the treadmill and reduce the work performed by the legs. These results demonstrate that learning to acquire and take advantage of assistance to reduce energetic cost is central in shaping adaptive locomotion, but this process occurs over timescales longer than those used in typical studies.
The testis protein ZNF165 is a SMAD3 cofactor that coordinates oncogenic TGFβ signaling in triple-negative breast cancer
Authors: Gibbs Zane A. , Reza Luis C. , Cheng Chun-Chun , Westcott Jill M. , McGlynn Kathleen , Whitehurst Angelique W.
Published: April 2020

Cancer/testis (CT) antigens are proteins whose expression is normally restricted to germ cells yet aberrantly activated in tumors, where their functions remain relatively cryptic. Here we report that ZNF165, a CT antigen frequently expressed in triple-negative breast cancer (TNBC), associates with SMAD3 to modulate transcription of transforming growth factor β (TGFβ)-dependent genes and thereby promote growth and survival. In addition, we identify the KRAB zinc finger protein, ZNF446, and its associated tripartite motif protein, TRIM27, as obligate components of the ZNF165-SMAD3 complex that also support tumor cell viability. Importantly, we find that TRIM27 alone is necessary for ZNF165 transcriptional activity and is required for orthotopic tumor growthin vivo. Our findings indicate that aberrant expression of a testis-specific transcription factor is sufficient to co-opt somatic transcriptional machinery to drive a pro-tumorigenic gene expression program.
TagSeq for gene expression in non-model plants: a pilot study at the Santa Rita Experimental Range NEON core site
Authors: Marx Hannah E. , Scheidt Stephen , Barker Michael S. , Dlugosch Katrina M.
Published: April 2020

Premise of the study

TagSeq is a cost-effective approach for gene expression studies requiring a large number of samples. To date, TagSeq studies in plants have been limited to those with a high quality reference genome. We tested the suitability of reference transcriptomes for TagSeq in non-model plants, as part of a study of natural gene expression variation at the Santa Rita Experimental Range NEON core site.

Methods

Tissue for TagSeq was sampled from multiple individuals of four species [Bouteloua aristidoidesandEragrostis lehmanniana(Poaceae);Tidestromia lanuginosa(Amaranthaceae), andParkinsonia florida(Fabaceae)] at two locations on three dates (56 samples total). One sample per species was used to create a reference transcriptome via standard RNA-seq. TagSeq performance was assessed by recovery of reference loci, specificity of tag alignments, and variation among samples.

Results

A high fraction of tags aligned to each reference and mapped uniquely. Expression patterns were quantifiable for tens of thousands of loci, which revealed consistent spatial differentiation in expression for all species.

Discussion

TagSeq usingde novoreference transcriptomes was an effective approach to quantifying gene expression in this study. Tags were highly locus specific and generated biologically informative profiles for four non-model plant species.
On the shuttling across the blood-brain barrier via tubules formation: mechanism and cargo avidity bias
Authors: Tian Xiaohe , Leite Diana Moreira , Scarpa Edoardo , Nyberg Sophie , Fullstone Gavin , Forth Joe , Matias Diana Lourenço , Apriceno Azzurra , Poma Alessandro , Duro-Castano Aroa , Vuyyuru Manish , Harker-Kirschneck Lena , Šarić Anđela , Zhang Zhongping , Xiang Pan , Fang Bin , Tian Yupeng , Luo Lei , Rizzello Loris , Battaglia Giuseppe
Published: April 2020

The blood-brain barrier is made of polarised brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Transport across BECs is of paramount importance for nutrient uptake as well as to rid the brain of waste products. Nevertheless, currently we do not understand how large macromolecular cargo shuttles across and how BECs discriminate between the brain-bound and own nutrients. Here, we study the low-density lipoprotein receptor-related protein 1 (LRP1) an essential regulator of BEC transport, and show that it is associated with endocytic effectors, endo-lysosomal compartments as well as syndapin-2, a member of the Bin/Amphiphysin/Rvs (BAR) domain superfamily known to stabilise tubular carriers. We employed synthetic self-assembled vesicles, polymersomes, as a multivalent system with tunable avidity as a tool to investigate the mechanism of transport across BECs. We used a combination of conventional and super-resolution microscopy, bothin vivoandin vitro, accompanied with biophysical modelling of transport kinetics and membrane-bound interactions. Our results demonstrate that the avidity of the ligand-receptor interaction (the overall cargo binding energy) determines the mechanism of sorting during the early stages of endocytosis and consequent trafficking. We show that high avidity cargo biases the LRP1 towards internalisation and fast degradation in BECs, while mid avidity augments the formation of syndapin-2 stabilised tubular carriers and promotes fast shuttling across BECs. Thus, we map out a very detailed mechanism where clathrin, actin, syndapin-2, dynamin and SNARE act synergistically to enable fast shuttling across BECs.
JN403, an alpha-7-nicotine-acetylcholine-receptor agonist, reduces alpha-synuclein induced inflammatory parameters ofin vitromicroglia but fails to attenuate the reduction of TH positive nigral neurons in a focal alpha-synuclein overexpression mouse model of Parkinson’s disease
Authors: Lee Bolam , Noelker Carmen , Feuerbach Dominik , Timmermann Lars , Chiu W.-H , Oertel Wolfgang H.
Published: April 2020

Alpha-7-nicotine-acetylcholine-receptor (α7-nAChRs) agonists modulate the cholinergic antiinflammatory pathway to attenuate proinflammatory signals and reduce dopaminergic neuronal cell loss in toxin-induced experimental murine models of Parkinson’s disease (PD). The protein α-synuclein (αSyn) is considered to represent the major pathogenic component in the etiology and progression of sporadic PD. However, no research has been performed to evaluate the effect of α7-nAChR agonists in human αSyn mediated models of PD. We, therefore, investigated the effect of the compound JN403, an α7-nAChR specific agonist, in αSyn treatedin vitromicroglia culture and in a human αSyn overexpressionin vivomouse model. In primary mouse microglia cells, αSyn fragment 61-140 treatment increased the release of nitric oxide (NO), tumor necrosis factor (TNF)-α and interleukin (IL)-6, and decreased cell viability. In contrast, 100 nM or 1 μM of JN403 co-incubation significantly reduced the level of NO and TNF-α release in the microglial cells. For in-vivo testing of JN403, a recombinant adeno-associated viral vector (rAAV)-mediated unilateral intranigral overexpression of human wild-type-αSyn (WT-αSyn) or of the control protein luciferase (luc) was induced via stereotactic delivery in C57/BL6N mice. Targeted WT-αSyn overexpression reduced 20% of the number of tyrosine hydroxylase (TH) positive (+) nigral neurons after 10 weeks. Subcutaneous daily treatment of 30 mg/kg JN403 over 9 weeks starting at postoperative week 1 did not alter the decrease of TH+ neuronal numbers, and microglial density in WT-αSyn overexpression mouse model. The reduced density of TH+ striatal terminals in the WT-αSyn groups was also not recovered by the JN403 treatment. In summary, JN403, an α7-nAChR specific agonist shows a beneficial effect on ameliorating proinflammatory signals in αSyn exposed microglia cells. However, no significant in-vivo treatment effect was found in an intranigral WT-αSyn overexpression mouse model of PD.
Interpretable machine learning framework reveals novel gut microbiome features in predicting type 2 diabetes
Authors: Gou Wanglong , Ling Chu-wen , He Yan , Jiang Zengliang , Fu Yuanqing , Xu Fengzhe , Miao Zelei , Sun Ting-yu , Lin Jie-sheng , Zhu Hui-lian , Zhou Hongwei , Chen Yu-ming , Zheng Ju-Sheng
Published: April 2020

Gut microbiome targets for type 2 diabetes (T2D) prevention among human cohorts have been controversial. Using an interpretable machine learning-based analytic framework, we identified robust human gut microbiome features, with their optimal threshold, in predicting T2D. Based on the results, we constructed a microbiome risk score (MRS), which was consistently associated with T2D across 3 independent Chinese cohorts involving 9111 participants (926 T2D cases). The MRS could also predict future glucose increment, and was correlated with a variety of gut microbiota-derived blood metabolites. Faecal microbiota transplantation from humans to germ-free mice demonstrated a causal role of the identified combination of microbes in the T2D development. We further identified adiposity and dietary factors which could prospectively modulate the MRS, and found that body fat distribution may be the key factor modulating the gut microbiome-T2D relationship. Taken together, we proposed a new analytical framework for the investigation of microbiome-disease relationship. The identified microbiota may serve as potential drug targets for T2D in future.
Pyridoxal Kinase Inhibition by Artemisinins Downregulates Inhibitory Neurotransmission
Authors: Kasaragod Vikram Babu , Pacios-Michelena Anabel , Schaefer Natascha , Zheng Fang , Bader Nicole , Alzheimer Christian , Villmann Carmen , Schindelin Hermann
Published: April 2020

The anti-malarial artemisinins have also been implicated in the regulation of various other cellular pathways. Despite their widespread application, the cellular specificities and molecular mechanisms of target recognition by artemisinins remain poorly characterized. We recently demonstrated how these drugs modulate inhibitory postsynaptic signaling by direct binding to the scaffolding protein gephyrin. Here, we report the crystal structure of the central metabolic enzyme pyridoxal kinase (PDXK), which catalyzes the production of the active form of vitamin-B6 (also known as pyridoxal 5’-phosphate, PLP), in complex with artesunate at 2.4-Å resolution. Partially overlapping binding of artemisinins with the substrate pyridoxal inhibits PLP biosynthesis as demonstrated by kinetic measurements. Electrophysiological recordings from hippocampal slices and activity measurements of glutamic acid decarboxylase (GAD), a PLP-dependent enzyme synthesizing the neurotransmitter γ-aminobutyric acid (GABA), define how artemisinins interfere presynaptically with GABAergic signaling. Our data provide a comprehensive picture of artemisinin-induced effects on inhibitory signaling in the brain.
Differential regulation of the immune system in a brain-liver-fats organ network during short term fasting
Authors: Huang Susie S.Y. , Makhlouf Melanie , AbouMoussa Eman H. , Ruiz Tejada Segura Mayra L. , Mathew Lisa S. , Wang Kun , Leung Man C. , Chaussabel Damien , Logan Darren W. , Scialdone Antonio , Garand Mathieu , Saraiva Luis R.
Published: April 2020

Different fasting regimens are known to promote health, mitigate chronic immunological disorders, and improve age-related pathophysiological parameters in animals and humans. Indeed, several clinical trials are currently ongoing using fasting as a potential therapy for a wide range of conditions. Fasting alters metabolism by acting as a reset for energy homeostasis. However, the molecular mechanisms underlying the beneficial effects of short-term fasting (STF) are still not well understood, particularly at the systems or multi-organ level. Here, we investigated the dynamic gene expression patterns associated with six periods of STF in nine different mouse organs. We cataloged the transcriptional dynamics within and between organs during STF and discovered differential temporal effects of STF among organs. Using gene ontology enrichment analysis, we identified an organ network sharing 37 common biological pathways perturbed by STF. This network incorporates the brain, liver, interscapular brown adipose tissue, and posterior-subcutaneous white adipose tissue, hence we named it the brain-liver-fats organ network. Using Reactome pathways analysis, we identified the immune system, dominated by T cell regulation processes, as a central and prominent target of systemic modulations during STF in this organ network. The changes we identified in specific immune components point to the priming of adaptive immunity and parallel the fine-tuning of innate immune signaling. Our study provides a comprehensive multi-organ transcriptomic profiling of mice subjected to multiple periods of STF, and adds new insights into the molecular modulators involved in the systemic immuno-transcriptomic changes that occur during short-term energy loss.
Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish
Authors: Cayuela Hugo , Dorant Yann , Mérot Claire , Laporte Martin , Normandeau Eric , Gagnon-Harvey Stéphane , Sirois Pascal , Bernatchez Louis
Published: April 2020

Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic region and transposable elements (TEs) may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be important drivers of population genetic structure, whose study is generally restricted to the use of SNPs. Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local thermal conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1536 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene amplification. We also identified 175 CNVs associated with the divergence of three parapatric glacial lineages, of which 24% were located within protein-coding genes, which might contribute to genetic incompatibilities and ultimately, reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, that was very different from that inferred based on SNPs in a previous study. Our findings underscore the complementarity of those two types of markers in population genomics studies.
Breast cancer-associated skeletal muscle mitochondrial dysfunction and lipid accumulation is reversed by PPARG
Authors: Wilson Hannah E. , Stanton David A. , Pistilli Emidio E.
Published: April 2020

The peroxisome-proliferator activated receptors (PPARs) have been previously implicated in the pathophysiology of skeletal muscle dysfunction in women with breast cancer (BC) and in animal models of BC. Here, we sought to describe the metabolic alterations induced in skeletal muscle by BC-derived factors in anin vitroconditioned media (CM) system and hypothesized that BC cells secrete a factor that represses PPAR-gamma (PPARG) expression and its transcriptional activity, leading to downregulation of PPARG target genes involved in mitochondrial function and other metabolic pathways. We found that BC-derived factors repress PPAR-mediated transcriptional activity without altering protein expression of PPARG. Further, we show that BC-derived factors induce significant alterations in skeletal muscle mitochondrial function and lipid metabolism, which are rescued with exogenous expression of PPARG. The PPARG agonist drug rosiglitazone was able to rescue BC-induced lipid accumulation, but did not rescue effects of BC-derived factors on PPAR-mediated transcription or mitochondrial function. These data suggest that BC-derived factors induce deficits in lipid metabolism and mitochondrial function via different mechanisms that are both related to PPARG signaling, with mitochondrial dysfunction likely being altered via repression of PPAR-mediated transcription, and lipid accumulation being altered via transcription-independent functions of PPARG.
Genome-wide local ancestries discriminate homoploid hybrid speciation from secondary introgression in the red wolf (Canidae:Canis rufus)
Authors: Chafin Tyler K. , Douglas Marlis R. , Douglas Michael E.
Published: April 2020

Hybridization is well recognized as a driver of speciation, yet it often remains difficult to parse phylogenomically in that post-speciation gene flow frequently supersedes an ancestral signal. Here we examined how interactions between recombination and gene flow shaped the phylogenomic landscape of red wolf to create non-random retention of introgressed ancestry. Our re-analyses of genomic data recapitulate fossil evidence by demonstrating red wolf was indeed extant and isolated prior to more recent admixture with other North American canids. Its more ancient divergence, now sequestered within low-recombinant regions on the X-chromosome (i.e., chromosomal ‘refugia’), is effectively masked by multiple, successive waves of secondary introgression that now dominate its autosomal ancestry. These interpretations are congruent with more theoretical explanations that describe the manner by which introgression can be localized within the genome through recombination and selection. They also tacitly support the large-X effect, i.e., the manner by which loci that contribute to reproductive isolation can be enriched on the X-chromosome. By contrast, similar, high recombinant regions were also found as enriched within very shallow gene trees, thus reflecting post-speciation gene flow and a compression of divergence estimates to 1/20thof that found in recombination ‘cold spots’. Our results effectively reconcile conflicting hypotheses regarding the impact of hybridization on evolution of North American canids and support an emerging framework within which the analysis of a phylogenomic landscape structured by recombination can be used to successfully address the macroevolutionary implications of hybridization.
Shared internal models for feedforward and feedback control of arm dynamics in non-human primates
Authors: Maeda Rodrigo S. , Kersten Rhonda , Pruszynski J. Andrew
Published: April 2020

Previous work has shown that humans account for and learn novel properties or the arm’s dynamics, and that such learning causes changes in both the predictive (i.e., feedforward) control of reaching and reflex (i.e., feedback) responses to mechanical perturbations. Here we show that similar observations hold in old-world monkeys (macaca fascicularis). Two monkeys were trained to use an exoskeleton to perform a single-joint elbow reaching and to respond to mechanical perturbations that created pure elbow motion. Both of these tasks engaged robust shoulder muscle activity as required to account for the torques that typically arise at the shoulder when the forearm rotates around the elbow joint (i.e., intersegmental dynamics). We altered these intersegmental arm dynamics by having the monkeys generate the same elbow movements with the shoulder joint either free to rotate, as normal, or fixed by the robotic manipulandum, which eliminates the shoulder torques caused by forearm rotation. After fixing the shoulder joint, we found a systematic reduction in shoulder muscle activity. In addition, after releasing the shoulder joint again, we found evidence of kinematic aftereffects (i.e., reach errors) in the direction predicted if failing to compensate for normal arm dynamics. We also tested whether such learning transfers to feedback responses evoked by mechanical perturbations and found a reduction in shoulder feedback responses, as appropriate for these altered arm intersegmental dynamics. Demonstrating this learning and transfer in non-human primates will allow the investigation of the neural mechanisms involved in feedforward and feedback control of the arm’s dynamics.
A Computational Model of Levodopa-Induced Toxicity in Substantia Nigra Pars Compacta in Parkinson’s Disease
Authors: Muddapu Vignayanandam Ravindernath , Vijayakumar Karthik , Ramakrishnan Keerthiga , Chakravarthy V Srinivasa
Published: April 2020

Background

Parkinson’s disease (PD) is caused by the progressive loss of dopaminergic cells in substantia nigra pars compacta (SNc). The root cause of this cell loss in PD is still not decisively elucidated. A recent line of thinking traces the cause of PD neurodegeneration to metabolic deficiency. Due to exceptionally high energy demand, SNc neurons exhibit a higher basal metabolic rate and higher oxygen consumption rate, which results in oxidative stress. Recently, we have suggested that the excitotoxic loss of SNc cells might be due to energy deficiency occurring at different levels of neural hierarchy. Levodopa (LDOPA), a precursor of dopamine, which is used as a symptom-relieving treatment for PD, leads to outcomes that are both positive and negative. Several researchers suggested that LDOPA might be harmful to SNc cells due to oxidative stress. The role of LDOPA in the course of PD pathogenesis is still debatable.

New Method

We hypothesize that energy deficiency can lead to LDOPA-induced toxicity (LIT) in two ways: by promoting dopamine-induced oxidative stress and by exacerbating excitotoxicity in SNc. We present a multiscale computational model of SNc-striatum system, which will help us in understanding the mechanism behind neurodegeneration postulated above and provides insights for developing disease-modifying therapeutics.

Results

It was observed that SNc terminals are more vulnerable to energy deficiency than SNc somas. During LDOPA therapy, it was observed that higher LDOPA dosage results in increased loss of somas and terminals in SNc. It was also observed that co-administration of LDOPA and glutathione (antioxidant) evades LDOPA-induced toxicity in SNc neurons.

Comparison with Existing Methods

Our proposed multiscale model of SNc-striatum system is first of its kind, where SNc neuron was modelled at biophysical level, and striatal neurons were modelled at spiking level.

Conclusions

We show that our proposed model was able to capture LDOPA-induced toxicity in SNc, caused by energy deficiency.
A molecular approach to studying Hymenoptera diets using polistine wasps
Authors: Lefort M.-C. , Beggs J.R. , Glare T.R. , Doyle E.J. , Saunders T.E. , Boyer S.
Published: April 2020

The study of animal diets has benefited from the rise of high-throughput DNA sequencing applied to stomach content or faecal samples. The latter can be fresh samples used to describe recent meals, or older samples, which can inform about past feeding activities. For most invertebrates, however, it is difficult to access ‘historical’ samples, due to the small size of the animals and the absence of permanent defecation sites. Therefore, sampling must be repeated to account for seasonal variation and to capture the overall diet of a species.

This study develops a method to describe the overall diet of nest-building Hymenoptera based on a single sampling event, by analysing prey DNA from faeces accumulated in brood cells. We collected 48 nests from two species of introduced paper wasps (Polistes chinensis, andP. humilis) in the urban and peri-urban areas of Auckland, New Zealand, and selected two samples per nest. One from brood cells in the outer layer of the nest to represent the most recent diet, and one from brood cells in an inner layer to represent older diet.

Diet differed between species, although both fed mainly on Thysanoptera, Lepidoptera and Acariformes. Prey taxa identified to species level included both agricultural pests and native species. Prey communities consumed were significantly different between inner and outer nest samples suggesting seasonal variation in prey availability and/or a diversification of the wasps’ diet as the colony grows. We also show for the first time potential predation of marine organisms by Polistes wasps.

Our study provides field evidence that polistine wasps feed on agricultural pests, supporting the hypothesis that some social wasp species could have a suppressing effect on agricultural pests. The proposed methodology is readily applicable to other nest-building Hymenoptera and has the potential to provide comprehensive knowledge about their diet with minimum sampling effort. Such knowledge is Essential to measure the ecological impact of invasive Vespidae and support the conservation of native invertebrate biodiversity.
Inhibitor of Differentiation 4 (ID4) represses myoepithelial differentiation of mammary stem cells through its interaction with HEB
Authors: Holliday Holly , Roden Daniel , Junankar Simon , Wu Sunny Z. , Baker Laura A. , Krisp Christoph , Chan Chia-Ling , McFarland Andrea , Skhinas Joanna N. , Cox Thomas R. , Pal Bhupinder , Huntington Nicholas , Ormandy Christopher J. , Carroll Jason S. , Visvader Jane , Molloy Mark P. , Swarbrick Alexander
Published: April 2020

Differentiation of stem cells embedded within the mammary epithelium is orchestrated by lineage-specifying transcription factors. Unlike the well-defined luminal hierarchy, dissection of the basal lineage has been hindered by a lack of specific markers. Inhibitor of Differentiation 4 (ID4) is a basally-restricted helix-loop-helix (HLH) transcription factor essential for mammary development. Here we show that ID4 is highly expressed in basal stem cells and decreases during myoepithelial differentiation. By integrating transcriptomic, proteomic, and ChIP-sequencing data, we reveal that ID4 is required to suppress myoepithelial gene expression and cell fate. We identify the bHLH protein HEB as a direct binding partner of ID4, and describe a previously-unknown role for this regulator in mammary development. HEB binds to E-boxes in regulatory elements of developmental genes, negatively regulated by ID4, involved in extracellular matrix synthesis and cytoskeletal contraction. Together our findings support a model whereby ID4 binds to HEB and blocks it from promoting myoepithelial specialisation. These new insights expand our current understanding into control of myoepithelial differentiation and mammary gland morphogenesis.
Acute aggressive behavior perturbates the oxidative status of a wild bird independently of testosterone and progesterone
Authors: Mentesana Lucia , Adreani Nicolas M.
Published: April 2020

Aerobically demanding activities like aggression can lead to an elevated oxidative metabolism affecting the concentration of pro-oxidant and antioxidant compounds and can result in an overall perturbation of the oxidative status. Aggression may also alter the oxidative status indirectly through an increase in testosterone and progesterone concentrations. Given that changes in the oxidative status could represent a physiological cost of aggression, we tested the hypothesis that acute conspecific aggression impairs the oxidative status and evaluated the role of testosterone and progesterone as potential mediators. To achieve this, we experimentally manipulated the aggressive behavior of wild female and male birds and measured the concentrations of pro-oxidants, enzymatic- and non-enzymatic antioxidants, testosterone and progesterone in blood. After 20 minutes of conspecific aggressive behavior, both sexes had lower concentrations of non-enzymatic antioxidants than control individuals. This effect was independent of testosterone and progesterone concentrations, and much stronger in females than in males. Further, only in females (but not in males) being more aggressive came at the expense of lower antioxidant concentration. We provide the first experimental evidence that acute aggressive behavior perturbates the oxidative state of a wild vertebrate independently of testosterone and progesterone, with potential ecological and evolutionary implications given the role of the redox system in shaping life-history traits.
Hybrid genome assembly and evidence-based annotation of the egg parasitoid and biological control agentTrichogramma brassicae
Authors: Ferguson K. B. , Kursch-Metz T. , Verhulst E. C. , Pannebakker B. A.
Published: April 2020

Trichogramma brassicae(Bezdenko) are egg parasitoids that are used throughout the world as biological control agents and in laboratories as model species. Despite this ubiquity, few genetic resources exist beyond COI, ITS2, and RAPD markers. Aided by aWolbachiainfection, a wild-caught strain from Germany was reared for low heterozygosity and sequenced in a hybridde novostrategy, after which several assembling strategies were evaluated. The best assembly, derived from a DBG2OLC-based pipeline, yielded a genome of 235 Mbp made up of 1,572 contigs with an N50 of 556,663 bp. Following a rigorousab initio-, homology-, and evidence-based annotation, 16,905 genes were annotated and functionally described. As an example of the utility of the genome, a simple ortholog cluster analysis was performed with sister speciesT. pretiosum, revealing over 6000 shared clusters and under 400 clusters unique to each species. The genome and transcriptome presented here provides an essential resource for comparative genomics of the commercially relevant genusTrichogramma, but also for research into molecular evolution, ecology, and breeding ofT. brassicae.