bluuebunny/crossref_metadata_2025 huggingface dataset:
Adaptation by copy number variation increases insecticide resistance in fall armyworms
Authors: Nam Kiwoong , Gimenez Sylvie , Hilliou Frederique , Blanco Carlos A. , Hänniger Sabine , Bretaudeau Anthony , Legeai Fabrice , Nègre Nicolas , d’Alençon Emmanuelle
Published: October 2019

Insecticide resistance is a major main challenge in pest control, and understanding its genetic basis is a key topic in agricultural ecology. Detoxification genes are well-known genetic elements that play a key role in adaptation to xenobiotics. The adaptive evolution of detoxification genes by copy number variations has been interpreted as a cause of insecticide resistance. However, the same pattern can be generated by the adaptation to host-plant defense toxins as well. In this study, we tested in fall armyworms (Lepidoptera Spodoptera frugiperda) if adaptation by copy number variation is the cause of the increased level of insecticide resistance from two geographic populations with different levels of resistance and two strains with different host plants. Following the generation of an assembly with chromosome-sized scaffolds (N50 = 13.2Mb), we observed that these two populations show a significant allelic differentiation of copy number variations, which is not observed between strains. In particular, a locus with almost complete allelic differentiation (Fst > 0.8) includes a cluster of P450 genes, which are well-known key players in detoxification. Detoxification genes are overrepresented in the genes with copy number variations, and the observed copy number variation appears to have beneficial effects in general. From this result, we concluded that copy number variation of detoxification genes in fall armyworms plays a key role in the insecticide resistance but not in the adaptation to host-plants, suggesting that the evolution of insecticide resistance may occur independently from host-plant adaptation.
mTORC1-Plin3 pathway is essential to activate lipophagy and protects against hepatosteatosis
Authors: Garcia-Macia Marina , Santos-Ledo Adrián , Leslie Jack , Paish Hanna , Watson Abigail , Borthwick Lee , Mann Jelena , Oakley Fiona , Korolchuk Viktor I. , Mann Derek A.
Published: October 2019

During postprandial state, the liver is exposed to high levels of dietary fatty acids (FAs) and carbohydrates. FAs are re-esterified into triglycerides, which can be stored in lipid droplets (LDs) in the liver. Aberrant accumulation of LDs can lead to diseases such as alcoholic liver disease and non-alcoholic fatty liver disease, the latter being the most common liver pathology in western countries. Improved understanding of LD biology has potential to unlock new treatments for these liver diseases. The Perilipin (Plin) family is the group of proteins that coat LDs, controlling their biogenesis, stabilization, and preventing their degradation. Recent studies have revealed that autophagy is involved in LD degradation and, therefore, may be crucial to avoid lipid accumulation. Here, we show that a phosphorylated form of Plin3 is required for selective degradation of LDs in fibroblasts, primary hepatocytes and human liver slices. We demonstrate that oleic acid treatment induces the recruitment of the autophagy machinery to the surface of LDs. When Plin3 is silenced, this recruitment is suppressed resulting in accumulation of lipid. Plin3 pulldowns revealed interactions with the autophagy initiator proteins Fip200 and Atg16L indicating that Plin3 may function as a docking protein involved in lipophagy activation. Of particular importance, we define Plin3 as a substrate for mTORC1-dependent phosphorylation and show that this event is decisive for lipophagy. Our study therefore reveals that Plin3, and its phosphorylation by mTORC1, is crucial for degradation of LDs by autophagy. We propose that stimulating this pathway to enhance LD autophagy in hepatocytes will help protect the liver from lipid-mediated toxicity thus offering new therapeutic opportunities in human steatotic liver diseases.
Distinct CASK domains control cardiac sodium channel membrane expression and focal adhesion anchoring
Authors: Beuriot Adeline , Eichel Catherine A. , Dilanian Gilles , Louault Florent , Melgari Dario , Doisne Nicolas , Coulombe Alain , Hatem Stéphane N. , Balse Elise
Published: October 2019

Membrane-associated guanylate kinase (MAGUK) proteins function as adaptor proteins to mediate the recruitment and scaffolding of ion channels in the plasma membrane in various cell types. In the heart, the protein CASK (Calcium/CAlmodulin-dependent Serine protein Kinase) negatively regulates the main cardiac sodium channel, NaV1.5, which carries the sodium current (INa) by preventing its anterograde trafficking. CASK is also a new member of the dystrophin-glycoprotein complex, and like syntrophin, binds to the C-terminal domain of the channel. Here we show that both L27B and GUK domains are required for the negative regulatory effect of CASK on INa and NaV1.5 surface expression and that the HOOK domain is essential for interaction with the cell adhesion dystrophin-glycoprotein complex. Thus, the multi-modular structure of CASK potentially provides the ability to control channel delivery at adhesion points in cardiomyocyte.

Sequential functional domain deletion approach identifies three critical domains of CASK in cardiomyocytes. CASK binds the cell adhesion dystrophin-glycoprotein complex through HOOK domain and inhibits NaV1.5 channel membrane expression by impeding trafficking through L27B and GUK domains.
Parkinson’s disease phenotypes in patient specific brain organoids are improved by HP-β-CD treatment
Authors: Jarazo Javier , Barmpa Kyriaki , Rosety Isabel , Smits Lisa M. , Arias-Fuenzalida Jonathan , Walter Jonas , Gomez-Giro Gemma , Monzel Anna S. , Qing Xiaobing , Cruciani Gerald , Boussaad Ibrahim , Jäger Christian , Rakovic Aleksandar , Berger Emanuel , Bolognin Silvia , Antony Paul M. A. , Klein Christine , Krüger Rejko , Seibler Philip , Schwamborn Jens C.
Published: October 2019

The etiology of Parkinson’s disease (PD) is only partially understood despite the fact that environmental causes, risk factors, and specific gene mutations are contributors to the disease. Biallelic mutations in the PTEN-induced putative kinase 1 (PINK1) gene involved in mitochondrial homeostasis, vesicle trafficking, and autophagy, are sufficient to cause PD. By comparing PD patient-derived cells, we show differences in their energetic profile, imbalanced proliferation, apoptosis, mitophagy, and a reduced differentiation efficiency to dopaminergic neurons compared to control cells. Using CRISPR/Cas9 gene editing, correction of a patient’s point mutation ameliorated the metabolic properties and neuronal firing rates but without reversing the differentiation phenotype. However, treatment with 2-Hydroxypropyl-β-Cyclodextrin (HP-β-CD) increased the mitophagy capacity of neurons leading to an improved dopaminergic differentiation of patient specific neurons in midbrain organoids. In conclusion, we show that treatment with a repurposed compound is sufficient for restoring dopaminergic differentiation of PD patient-derived cells.
High-depth resequencing reveals hybrid population and insecticide resistance characteristics of fall armyworm (Spodoptera frugiperda) invading China
Authors: Zhang Lei , Liu Bo , Zheng Weigang , Liu Conghui , Zhang Dandan , Zhao Shengyuan , Xu Pengjun , Wilson Kenneth , Withers Amy , Jones Christopher M. , Smith Judith A. , Chipabika Gilson , Kachigamba Donald L. , Nam Kiwoong , d’Alençon Emmanuelle , Liu Bei , Liang Xinyue , Jin Minghui , Wu Chao , Chakrabarty Swapan , Yang Xianming , Jiang Yuying , Liu Jie , Liu Xiaolin , Quan Weipeng , Wang Guirong , Fan Wei , Qian Wanqiang , Wu Kongming , Xiao Yutao
Published: October 2019

The rapid wide-scale spread of fall armyworm (Spodoptera frugiperda) has caused serious crop losses globally. However, differences in the genetic background of subpopulations and the mechanisms of rapid adaptation behind the invasion are still not well understood. Here we report a 393.25-M chromosome-level genome assembly of fall armyworm with scaffold N50 of 13.3 M consisting of 23281 annotated protein-coding genes. Genome-wide resequencing of 105 samples from 16 provinces in China revealed that the fall armyworm population comprises a complex inter-strain hybrid, mainly with the corn-strain genetic background and less of the rice-strain genetic background, which highlights the inaccuracy of strain identification using mitochondrial or Tpi genes. An analysis of genes related to pesticide- and Bt-resistance showed that the risk of fall armyworm developing resistance to conventional pesticides is very high, while remaining currently susceptible to Bt toxins. Laboratory bioassay results showed that insects invading China carry resistance to organophosphate and pyrethroid pesticides, but are sensitive to genetically modified maize expressing Cry1Ab in field experiments. Additionally, we found that two mitochondrial fragments are inserted into the nuclear genome, and the insertion event occurred after the differentiation of the two strains. This study represents a valuable advancement toward the analysis of genetic differences among subpopulations and improving management strategies for fall armyworm.
Interplay between axonal Wnt5-Vang and dendritic Wnt5-Drl/Ryk signaling controls glomerular patterning in the Drosophila antennal lobe
Authors: Hing Huey , Snyder Jennifer , Reger Noah , Fradkin Lee G.
Published: October 2019

Despite the importance of dendritic targeting in neural circuit assembly, the mechanisms by which it is controlled still remain incompletely understood. We previously showed that in the developing Drosophila antennal lobe, the Wnt5 protein forms a gradient that directs the ~45° rotation of a cluster of projection neuron (PN) dendrites, including the adjacent DA1 and VA1d dendrites. We report here that the Van Gogh (Vang) transmembrane planar cell polarity (PCP) protein is required for the rotation of the DA1/VA1d dendritic pair. Cell type-specific rescue and mosaic analyses showed that Vang functions in the olfactory receptor neurons (ORNs), suggesting a codependence of ORN axonal and PN dendritic targeting. Loss of Vang suppressed the repulsion of the VA1d dendrites by Wnt5, indicating that Wnt5 signals through Vang to direct the rotation of the DA1 and VA1d glomeruli. We observed that the Derailed (Drl)/Ryk atypical receptor tyrosine kinase is also required for the rotation of the DA1/VA1d dendritic pair. Antibody staining showed that Drl/Ryk is much more highly expressed by the DA1 dendrites than the adjacent VA1d dendrites. Mosaic and epistatic analyses showed that Drl/Ryk specifically functions in the DA1 dendrites in which it antagonizes the Wnt5-Vang repulsion and mediates the migration of the DA1 glomerulus towards Wnt5. Thus, the nascent DA1 and VA1d glomeruli appear to exhibit Drl/Ryk-dependent biphasic responses to Wnt5. Our work shows that the final patterning of the fly olfactory map is the result of an interplay between ORN axons and PN dendrites, wherein converging pre- and postsynaptic processes contribute key Wnt5 signaling components, allowing Wnt5 to orient the rotation of nascent synapses through a PCP mechanism.
Pinealectomy increases thermogenesis and decreases lipogenesis
Authors: Kim Mikyung , Lee So Min , Jung Jeeyoun , Kim Yun Jin , Moon Kyo Chul , Seo Ji Hae , Ha Eunyoung
Published: October 2019

This study was designed to determine the effects of pineal gland-derived melatonin on obesity by employing rat pinealectomy (Pnx) model. After 10 weeks of high-fat diet (HFD) feeding, rats received sham or Pnx surgery followed by 10 weeks normal chow diet (NCD) feeding. Pnx decreased expressions of melatonin receptors, MTNR1A and MTNR1B, in brown (BAT) and white adipose tissues (WAT). Pnx rats showed increased insulin sensitivity compared with those that received sham surgery. Leptin levels were significantly decreased in the serum of Pnx group. In addition, Pnx stimulated thermogenic genes in BAT whereas attenuated lipogenic genes in WAT and the liver. Histologic analyses revealed marked decreased in the size of lipid droplets and increased expressions of UCP1 in BAT and attenuated lipid droplets in the sized and the number in the liver of Pnx group. In conclusion, these results in the current study suggest that Pnx increases thermogenesis in BAT and decreases lipogenesis in WAT and the liver.
The role of swnR gene on the biosynthesis pathway of the swainsonine in Metarhizium anisopliae
Authors: Sun Lu , Song Runjie , Wang Jinglong , Liu Yiling , Zhang Yu , Zhu Yanli , Guo Qingyun , Mo Chonghui , Wang Baohai , Zhao Baoyu , Lu Hao
Published: October 2019

Swainsonine (SW) is the principal toxic ingredient of locoweeds, and is produced by fungi including Metarhizium anisopliae, Slafractonia leguminicola, and Alternaria oxytropis. Studies of the SW biosynthesis pathway in these fungi have demonstrated the requirement for a swnK gene and the presence of a variety of other SWN cluster genes, but have not determined a precise role for the swnR gene, which encodes a NADB Rossmann-fold reductase, nor if it is necessary for the biosynthesis of SW. In this study, we used homologous recombination (HR) to knock out the swnR gene of M. anisopliae to determine its effect on the SW biosynthesis pathway. The concentration of SW was measured in the fermentation broth of M. anisopliae at 1 d, 3 d, 5 d and 7 d using a Q Exactive Mass Spectrometer. The gene for swnR was detected by RT-qPCR. To determine the role of the swnR gene in the SW biosynthesis pathway of M. anisopliae, we used PEG-mediated homologous recombination (HR) to transform a wild-type strain (WT) with a Benomyl (ben)-resistant fragment to knock out the swnR gene producing a mutant-type strain (MT). A complemented-type (CT) strain was produced by adding a complementation vector that contains the glufosinate (herbicide) resistance (bar) gene as a marker. The content of SW decreased, but was not eliminated in the fermentation broth of the MT strain, and returned to the original level in the CT strain. These results indicate that the swnR gene plays a crucial role in the SW biosynthesis pathway of M. anisopliae, but suggests that another gene in the fungus may share the function of swnR.
The Elephant in the room: What can we learn from California regarding the use of sport hunting of pumas (Puma concolor) as a management tool?
Authors: Laundré John W. , Papouchis Christopher
Published: October 2019

Pumas (Puma concolor) in 10 western states of the U.S. have been managed through the use of a sport hunt. The rational for this management technique is that puma populations needed to be hunted to reduce threats to human safety, their livestock, and wild ungulate populations. We evaluated these claims with the state of California as a control, which has prohibited sport hunting since 1972. We tested four hypotheses: 1) Sport hunting reduces puma density, 2) Sport hunting reduces problematic puma-human encounters, 3) Sport hunting reduces puma predation on livestock, and 4) Sport hunting reduces the impact of puma predation on wild ungulate numbers. Results indicated: 1) Puma densities did not differ between California and sport hunting states, 2) California was the 3rdlowest in per capita puma-human incidents. 3) The per capita loss of sheep was significantly lower (t= 5.7, P < 0.001) and the per capita loss of cattle in California did not differ significantly, from the other 10 states (P = 0.13). 4). Changes in annual deer populations in California correlated with changes in other states (F = 95.4, P < 0.001, R2= 0.68) and average deer densities in California did not differ significantly from the other states. We concluded that sport hunting of pumas as a management tool has not produced the outcomes sought by wildlife managers and may even exacerbate conflicts between pumas and humans. It is suggested that state agencies re-assess the use of sport hunting as a management tool for pumas.
Robust, automated sleep scoring by a compact neural network with distributional shift correction
Authors: Barger Zeke , Frye Charles G. , Liu Danqian , Dan Yang , Bouchard Kristofer E.
Published: October 2019

Studying the biology of sleep requires the accurate assessment of the state of experimental subjects, and manual analysis of relevant data is a major bottleneck. Recently, deep learning applied to electroencephalogram and electromyogram data has shown great promise as a sleep scoring method, approaching the limits of inter-rater reliability. As with any machine learning algorithm, the inputs to a sleep scoring classifier are typically standardized in order to remove distributional shift caused by variability in the signal collection process. However, in scientific data, experimental manipulations introduce variability that should not be removed. For example, in sleep scoring, the fraction of time spent in each arousal state can vary between control and experimental subjects. We introduce a standardization method, mixture z-scoring, that preserves this crucial form of distributional shift. Using both a simulated experiment and mouse in vivo data, we demonstrate that a common standardization method used by state-of-the-art sleep scoring algorithms introduces systematic bias, but that mixture z-scoring does not. We present a free, open-source user interface that uses a compact neural network and mixture z-scoring to allow for rapid sleep scoring with accuracy that compares well to contemporary methods. This work provides a set of computational tools for the robust automation of sleep scoring.
Rapidly cycling stem cells regenerate the intestine independent ofLgr5highcells
Authors: Sheng Xiaole , Lin Ziguang , Lv Cong , Shao Chunlei , Bi Xueyun , Deng Min , Xu Jiuzhi , Guerrero-Juarez Christian F. , Li Mengzhen , Wu Xi , Zhao Ran , Liu Xiaowei , Wang Qingyu , Nie Qing , Cui Wei , Gao Shan , Zhang Hongquan , Liu Zhihua , Cong Yingzi , Plikus Maksim V. , Lengner Christopher J. , Andersen Bogi , Ren Fazheng , Yu Zhengquan
Published: October 2019

The +4 cells in intestinal crypts are DNA damage-resistant and contribute to regeneration. However, their exact identity and the mechanism underlying +4 cell-mediated regeneration remain unclear. Using lineage tracing, we show that cells marked by anMsi1reporter (Msi1+) are enriched at the +4 position in intestinal crypts and exhibit DNA damage resistance. Single-cell RNA sequencing reveals that theMsi1+cells are heterogeneous with the majority being intestinal stem cells (ISCs). The DNA damage-resistant subpopulation ofMsi1+cells is characterized by low-to-negativeLgr5expression and is more rapidly cycling thanLgr5highradio-sensitive crypt base columnar stem cells (CBCs); they enable fast repopulation of the intestinal epithelium independent of CBCs that are largely depleted after irradiation. Furthermore, relative to CBCs,Msi1+cells preferentially produce Paneth cells during homeostasis and upon radiation repair. Together, we demonstrate that the DNA damage-resistantMsi1+cells are rapidly cycling ISCs that maintain and regenerate the intestinal epithelium.
Gene copy normalization of the 16S rRNA gene cannot outweigh the methodological biases of sequencing
Authors: Starke Robert , Morais Daniel
Published: October 2019

The 16S rRNA gene is the golden standard target of sequencing to uncover the composition of bacterial communities but the presence of multiple copies of the gene makes gene copy normalization (GCN) inevitable. Even though GCN resulted in abundances closer to the metagenome, it should be validated by communities with known composition as both amplicon and shotgun sequencing are prone to methodological biases. Here we compared the composition of three mock communities to the composition derived from 16S sequencing without and with GCN. In all of them, the 16S composition was different from the mock community and GCN improved the picture only in the community with the lowest Shannon diversity. Albeit with low abundance, half of the identified genera were not present in the mock communities. Our approach provides empirical evidence to the methodological biases introduced by sequencing that was only counteracted by GCN in the case of low α-diversity, potentially due to the small number of bacterial taxa with known gene copy numbers. We thus cannot recommend the use of GCN moving forward and it is questionable whether a complete catalogue of 16S rRNA copy numbers can outweigh the methodological biases of sequencing.
Tumors attenuating the mitochondrial activity in T cells escape from PD-1 blockade therapy
Authors: Kumar Alok , Chamoto Kenji , Chowdhury Partha S. , Honjo Tasuku
Published: October 2019

PD-1 blockade therapy has revolutionized cancer treatments. However, a substantial population of patients is unresponsive. To rescue unresponsive patients, the mechanism of unresponsiveness to PD-1 blockade therapy must be elucidated. Using a ‘bilateral tumor model’ where responsive and unresponsive tumors were inoculated into different sides of the mouse belly, we demonstrated that unresponsive tumors can be categorized into two groups: with and without systemic immunosuppressive property (SIP). The SIP-positive tumors released uncharacterized, non-proteinaceous small molecules which inhibited T cell proliferation and mitochondrial activation. By contrast, the SIP-negative B16 tumor, escaped from immunity by losing MHC class I expression. Unresponsiveness of SIP-positive tumors was partially overcome by improving the mitochondrial function with a mitochondrial activator; this was not successful to B16, which employs immune ignorance. These results demonstrated that our ‘bilateral tumor model’ was useful for stratifying tumors to investigate the mechanism of unresponsiveness and develop strategy for proper combination therapy.
Rapid assessment of the suitability of multi-species citizen science datasets for occupancy trend analysis
Authors: Pocock Michael J.O. , Logie Mark W. , Isaac Nick J.B. , Outhwaite Charlotte L. , August Tom
Published: October 2019

Species records from volunteers are a vast and valuable source of information on biodiversity for a wide range of taxonomic groups. Although these citizen science data are opportunistic and unstructured, occupancy analysis can be used to quantify trends in distribution. However, occupancy analysis of unstructured data can be resource-intensive and requires substantial expertise. It is valuable to have simple ‘rules of thumb’ to efficiently assess the suitability of a dataset for occupancy analysis prior to analysis.

Our analysis was possible due to the production of trends, from our Bayesian occupancy analysis, for 10 967 species from 34 multi-species recording schemes in Great Britain. These schemes had an average of 500 visits to sites per year, and an average of 20% of visited sites received a revisit in a year. Occupancy trend outputs varied in their precision and we used expert elicitation on a subset of outputs to determine a precision threshold above which trends were suitable for further consideration. We then used classification trees with seven metrics to define simple rules explaining when the data would result in outputs that met the precision threshold.

We found that the suitability of a species’ data was best described by (i) the number of records of the focal species in the 10% best-recorded years, and (ii) the proportion of recording visits for that taxonomic group with non-detections of the focal species. Surprisingly few data were required to be predicted to meet the precision threshold. Specifically, for 98% confidence that our Bayesian occupancy models would produce outputs meeting the precision threshold, there needed to be ≥29 records of the focal species in the 10% best-recorded years (equivalent to an average of 12.5 records per year in our dataset), although only ≥10 records (equivalent to 4.5 records per year) were required for species recorded in less than 1 in 25 visits.

We applied these rules to regional species data for Great Britain. Data from 32% of the species:region combinations met the precision threshold with 80% confidence, and 14% with 98% confidence. There was great variation between taxonomic groups (e.g. butterflies, moths and dragonflies were well recorded) and region (e.g. south-east England was best recorded).

These simple criteria provide no indication of the accuracy or representativeness of the trend outputs: this is vital, but needs to be assessed individually. However our criteria do provide a rapid, quantitative assessment of the predicted suitability of existing data for occupancy analysis and could be used to inform the design and implementation of multi-species citizen science recording projects elsewhere in the world.
A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2’-deoxynucleotides
Authors: Kim Seohyun Chris , Zhou Lijun , Zhang Wen , O’Flaherty Derek K. , Rondo-Brovetto Valeria , Szostak Jack W.
Published: October 2019

The abiotic synthesis of ribonucleotides is thought to have been an essential step towards the emergence of the RNA world. However, it is likely that the prebiotic synthesis of ribonucleotides was accompanied by the simultaneous synthesis of arabinonucleotides, 2′-deoxyribonucleotides, and other variations on the canonical nucleotides. In order to understand how relatively homogeneous RNA could have emerged from such complex mixtures, we have examined the properties of arabinonucleotides and 2′-deoxyribonucleotides in nonenzymatic template-directed primer extension reactions. We show that nonenzymatic primer extension with activated arabinonucleotides is much less efficient than with activated ribonucleotides, and furthermore that once an arabinonucleotide is incorporated, continued primer extension is strongly inhibited. As previously shown, 2′-deoxyribonucleotides are also less efficiently incorporated in primer extension reactions, but the difference is more modest. Experiments with mixtures of nucleotides suggest that the coexistence of ribo- and arabino-nucleotides does not impede the copying of RNA templates. Moreover, chimeric oligoribonucleotides containing 2′-deoxy- or arabino-nucleotides are effective templates for RNA synthesis. We propose that the initial genetic polymers were random sequence chimeric oligonucleotides formed by untemplated polymerization, but that template copying chemistry favored RNA synthesis; multiple rounds of replication may have led to pools of oligomers composed mainly of RNA.
Exploring the relationship between polymorphisms of leptin and IGF-1 genes with milk yield in indicine and taurine crossbred cows
Authors: Dar Mohammad Rayees , Singh Mahendra , Thakur Sunita , Verma Archana
Published: October 2019

Leptin and IGF-1 plays a significant role in milk production and lactation in bovines. The present investigation was carried out to identify the novel polymorphisms in exon 3 region of leptin gene and exon 3 + partial intron 3 of IGF-1 gene and to analyze their association with the milk production performance in indicine and taurine crossbred (Karan Fries) cows. Blood samples were collected from 160 apparently healthy Karan Fries cows. Four SNPs at positions rs29004508 (C>T), rs29004509 (C>T), rs29004510 (T>C), rs29004511 (T>C) in Leptin gene and two SNPs at positions rs133251968 (C>A), rs137289661(C>T) in IGF-1 gene were found in Karan Fries cows, however rs29004509 (C>T) had positive correlation (p<0.05) with milk yield. The genetic variants observed in exon 3 region of leptin gene and their association with milk yield traits revealed the importance of CT genotype, which had been useful for genetic improvement of Karan Fries cow for milk production traits and can also be utilized as a potential genetic marker to select appropriate animals.
Synaptonemal complex-deficientDrosophila melanogasterfemales exhibit rare DSB repair events, recurrent copy number variation, and an increased rate ofde novotransposable element movement
Authors: Miller Danny E.
Published: October 2019

Genetic stability depends on the maintenance of a variety of chromosome structures and the precise repair of DNA breaks. During meiosis, programmed double-strand breaks (DSBs) made in prophase I are normally repaired as gene conversions or crossovers. Additionally, DSBs are made by the movement of transposable elements (TEs), which must also be resolved. Incorrect repair of these DNA lesions can lead to mutations, copy number variations, translocations, and/or aneuploid gametes. InDrosophila melanogaster, as in most organisms, meiotic DSB repair occurs in the presence of a rapidly evolving multiprotein structure called the synaptonemal complex (SC). Here, whole-genome sequencing is used to investigate the fate of meiotic DSBs inD. melanogastermutant females lacking functional SC, to assay for de novo CNV formation, and to examine the role of the SC in transposable element movement in flies. The data indicate that, in the absence of SC, copy number variation still occurs but meiotic DSB repair by gene conversion may occur only rarely. Remarkably, an 856-kilobase de novo CNV was observed in two unrelated individuals of different genetic backgrounds and was identical to a CNV recovered in a previous wild-type study, suggesting that recurrent formation of large CNVs occurs in Drosophila. In addition, the rate of novel TE insertion was markedly higher than wild type in one of two SC mutants tested, suggesting that SC proteins may contribute to the regulation of TE movement and insertion in the genome. Overall, this study provides novel insight into the role that the SC plays in genome stability and provides clues as to why SC proteins are among the most rapidly evolving in any organism.
Manumycin Polyketides Act as Molecular Glues Between UBR7 and P53 to Impair Breast Cancer Pathogenicity
Authors: Isobe Yosuke , Okumura Mikiko , White Ross , McGregor Lynn M. , McKenna Jeffrey M. , Tallarico John A. , Schirle Markus , Maimone Thomas J. , Nomura Daniel K.
Published: October 2019

Molecular glues are an intriguing therapeutic modality that harness small-molecules to induce interactions between proteins that typically do not interact, thus enabling the creation of novel protein functions not naturally encoded in biology. While molecular glues such as thalidomide and rapamycin have catalyzed drug discovery efforts, such molecules are rare and have often been discovered fortuitously, thus limiting their potential as a general strategy for therapeutic intervention of disease. Historically, natural products have proven to be important sources of molecular glues and we postulated that natural products bearing multiple electrophilic sites may be an unexplored source of such molecules, potentially through multi-covalent attachment. Using activity-based protein profiling (ABPP)-based chemoproteomic platforms, we show that members of the manumycin family of polyketides, which bear multiple potentially reactive sites, target C374 of the putative E3 ligase UBR7 in breast cancer cells to impair breast cancer pathogenicity through engaging in molecular glue interactions with the neo-substrate tumor-suppressor TP53, leading to the activation of p53 transcriptional activity and cell death. Our results reveal a previously undiscovered anti-cancer mechanism of this natural product family and highlight the potential for combining chemoproteomics and multi-covalent natural products for the discovery and characterization of new molecular glues.
A requirement for Potassium and Calcium Channels during the Endosomal Trafficking of Polyomavirus Virions
Authors: Dobson Samuel J. , Mankouri Jamel , Whitehouse Adrian
Published: October 2019

Following internalisation viruses have to escape the endocytic pathway and deliver their genomes to initiate replication. Members of thePolyomaviridaetransit through the endolysosomal network and through the endoplasmic reticulum (ER), from which heavily degraded capsids escape into the cytoplasm prior to nuclear entry. Acidification of endosomes and ER entry are essential in the lifecycle of polyomaviruses, however many mechanistic requirements are yet to be elucidated. Alteration of endocytic pH relies upon the activity of ion channels. Using two polyomaviruses with differing capsid architecture, namely Simian virus 40 (SV40) and Merkel cell polyomavirus (MCPyV), we firstly describe methods to rapidly quantify infection using an IncuCyte ZOOM instrument, prior to investigating the role of K+and Ca2+channels during early stages of infection. Broad spectrum inhibitors identified that MCPyV, but not SV40, is sensitive to K+channel modulation. In contrast, both viruses are restricted by the broad spectrum Ca2+channel inhibitor verapamil, however specific targeting of transient or long lasting Ca2+channel subfamilies had no detrimental effect. Further investigation revealed that tetrandrine blockage of two-pore channels (TPCs), the activity of which is essential for endolysosomal-ER fusion, ablates infectivity of both MCPyV and SV40 by preventing disassembly of the capsid, which is required for the exposure of minor capsid protein nuclear signals necessary for nuclear transport. This study therefore identifies a novel target to restrict the entry of polyomaviruses.

IMPORTANCE

Polyomaviruses establish ubiquitous, asymptomatic infection in their host. However, in the immunocompromised these viruses can cause a range of potentially fatal diseases. Through the use of SV40 and MCPyV, two polyomaviruses with different capsid organisation, we have investigated the role of ion channels during infection. Here, we show that Ca2+channel activity is essential for both polyomaviruses and that MCPyV is also sensitive to K+channel blockage, highlighting new mechanistic requirements of ion channels during polyomavirus infection. In particular, tetrandrine blockage of endolysosomal-ER fusion is highlighted as an essential modulator of both SV40 and MCPyV. Given that the role of ion channels in disease have been well characterised, there is a large panel of clinically available therapeutics that could be repurposed to restrict persistent polyomavirus infection and may ultimately prevent polyomavirus-associated disease.
Genetic engineering of hoxb8 immortalized hematopoietic progenitors: a potent tool to study macrophage tissue migration
Authors: Accarias Solene , Sanchez Thibaut , Labrousse Arnaud , Ben-Neji Myriam , Boyance Aurélien , Poincloux Renaud , Maridonneau-Parini Isabelle , Le Cabec Véronique
Published: October 2019

Tumor-associated macrophages (TAM) are detrimental in most cancers. Controlling their recruitment is thus potentially therapeutic. We showed that TAM perform the protease-dependent mesenchymal migration in cancer, while macrophages perform amoeboid migration in other tissues. Inhibition of mesenchymal migration correlates with decreased TAM infiltration and tumor growth, providing rationale for a new cancer immunotherapy specifically targeting TAM motility. To identify new effectors of mesenchymal migration, we produced ER-Hoxb8-immortalized hematopoietic progenitors with unlimited proliferative ability. The functionality of macrophages differentiated from ER-Hoxb8 progenitors was compared to bone marrow-derived macrophages (BMDM). They polarized into M1- and M2-orientated macrophages, generated ROS, ingested particles, formed podosomes, degraded the extracellular matrix, adopted amoeboid and mesenchymal migration in 3D, and infiltrated tumor explantsex vivousing mesenchymal migration. We also used the CRISPR/Cas9 system to disrupt gene expression of a known effector of mesenchymal migration, WASP, to provide a proof of concept. We observed impaired podosome formation and mesenchymal migration capacity, thus recapitulating the phenotype of BMDM isolated fromWasp-KO mice. Thus, we validate the use of Hoxb8-macrophages as a potent tool to investigate macrophage functionalities.

Summary statement

We validate the use of ER-Hoxb8-immortalized hematopoietic progenitors combined to CRISPR/Cas9 technology as a potent tool to investigate macrophage functionalities with a large scale of applications.
FXD-CSD-GUI: a graphical user interface for the X-ray-diffraction-based determination of crystallite size distributions
Authors: Neher Sigmund H. , Klein Helmut , Kuhs Werner F.
Published: October 2019

Bragg intensities can be used to analyse crystal size distributions in a method called FXD-CSD, which is based on the fast measurement of many Bragg spots using two-dimensional detectors. This work presents the Python-based software and its graphical user interface FXD-CSD-GUI. The GUI enables user-friendly data handling and processing and provides both graphical and numerical crystal size distribution results.
The dynamical theory of diffraction in a crystal modulated by a surface acoustic wave in the case of spatially restricted X-ray beams
Authors: Punegov Vasily I.
Published: October 2019

The dynamical theory of X-ray diffraction in a crystal modulated by a surface acoustic wave (SAW) is developed for spatially restricted beams. It is shown that this approach is applicable to X-ray reciprocal space mapping. Rayleigh's surface-wave model is used to describe ultrasonic excitation. Based on the recurrent relations, a numerical simulation of the dynamical diffraction in a crystal modulated by a SAW is performed. Within the framework of the triple-axis diffraction scheme, the effect of the instrumental function on X-ray diffraction data is studied.
Full-field neutron microscopy based on refractive optics
Authors: Leemreize Hanna , Knudsen Erik B. , Birk Jonas O. , Strobl Markus , Detlefs Carsten , Poulsen Henning F.
Published: October 2019

Placing a compound refractive lens (CRL) as an objective in a neutron beam generates new possibilities for 2D and 3D nondestructive mapping of the structure, strain and magnetic domains within extended objects. A condenser setup is introduced that allows correction for the lateral chromatic aberration. More generally, for full-field microscopy the loss in performance caused by the chromatic aberration can be more than offset by introducing arrays of CRLs and exploiting the fact that the field of view can be much larger than the physical aperture of the CRL. Comments are made on the manufacture of such devices. The potential use is illustrated by comparisons between state-of-the-art instrumentation and suggested approaches for bright-field microscopy, small-angle neutron scattering microscopy, grain mapping and mapping of stresses. Options are discussed for depth-resolved imaging inspired by confocal light microscopy. Finally, experimental demonstrations are given of some of the basic properties of neutron full-field imaging for a single CRL.
Upgrade of laser pump time-resolved X-ray probes in Beijing synchrotron
Authors: Yu Can , Zhang Yan , Lei Ge , Wang Hao , Wang Yu-hang , Zhang Bing-Bing , Sun Da-Rui , Zhao Jia-Li , Zhou Yang-Fan , Li Qiu-Ju , Gao Zhen-hua , Zhan Fei , Tao Ye
Published: October 2019

The upgrade of the laser pump time-resolved X-ray probes, namely time-resolved X-ray absorption spectroscopy (TR-XAS) and X-ray diffraction (TR-XRD), implemented at the Beijing Synchrotron Radiation Facility, is described. The improvements include a superbunch fill, a high-efficiency fluorescence collection, an efficient spatial overlap protocol and a new data-acquisition scheme. After upgrade, the adequate TR-XAS signal is now obtained in a 0.3 mM solution, compared with a 6 mM solution in our previous report. Furthermore, to extend application in photophysics, the TR-XAS probe is applied on SrCoO2.5 thin film. And for the first time, TR-XAS is combined with TR-XRD to simultaneously detect the kinetic trace of structural changes in thin film.
Multi-element effects on arsenate accumulation in a geochemical matrix determined using µ-XRF, µ-XANES and spatial statistics
Authors: Sharma Aakriti , Muyskens Amanda , Guinness Joseph , Polizzotto Matthew L. , Fuentes Montserrat , Tappero Ryan V. , Chen-Wiegart Yu-chen K. , Thieme Juergen , Williams Garth J. , Acerbo Alvin S. , Hesterberg Dean
Published: October 2019

Soils regulate the environmental impacts of trace elements, but direct measurements of reaction mechanisms in these complex, multi-component systems can be challenging. The objective of this work was to develop approaches for assessing effects of co-localized geochemical matrix elements on the accumulation and chemical speciation of arsenate applied to a soil matrix. Synchrotron X-ray fluorescence microprobe (µ-XRF) images collected across 100 µm × 100 µm and 10 µm × 10 µm regions of a naturally weathered soil sand-grain coating before and after treatment with As(V) solution showed strong positive partial correlations (r′ = 0.77 and 0.64, respectively) between accumulated As and soil Fe, with weaker partial correlations (r′ > 0.1) between As and Ca, and As and Zn in the larger image. Spatial and non-spatial regression models revealed a dominant contribution of Fe and minor contributions of Ca and Ti in predicting accumulated As, depending on the size of the sample area analyzed. Time-of-flight secondary ion mass spectrometry analysis of an area of the sand grain showed a significant correlation (r = 0.51) between Fe and Al, so effects of Fe versus Al (hydr)oxides on accumulated As could not be separated. Fitting results from 25 As K-edge microscale X-ray absorption near-edge structure (µ-XANES) spectra collected across a separate 10 µm × 10 µm region showed ∼60% variation in proportions of Fe(III) and Al(III)-bound As(V) standards, and fits to µ-XANES spectra collected across the 100 µm × 100 µm region were more variable. Consistent with insights from studies on model systems, the results obtained here indicate a dominance of Fe and possibly Al (hydr)oxides in controlling As(V) accumulation within microsites of the soil matrix analyzed, but the analyses inferred minor augmentation from co-localized Ti, Ca and possibly Zn.
Crystal structure and luminescence properties of 2-[(2′,6′-dimethoxy-2,3′-bipyridin-6-yl)oxy]-9-(pyridin-2-yl)-9H-carbazole
Authors: Moon Suk-Hee , Park Ki-Min , Kim Jinho , Kang Youngjin
Published: October 2019

In the title compound, C29H22N4O3, the carbazole system forms a dihedral angle of 68.45 (3)° with the mean plane of the bipyridine ring system. The bipyridine ring system, with two methoxy substituents, is approximately planar (r.m.s. deviation = 0.0670 Å), with a dihedral angle of 7.91 (13)° between the planes of the two pyridine rings. Intramolecular C—H...O/N hydrogen bonds may promote the planarity of the bipyridyl ring system. In the pyridyl-substituted carbazole fragment, the pyridine ring is tilted by 56.65 (4)° with respect to the mean plane of the carbazole system (r.m.s. deviation = 0.0191 Å). In the crystal, adjacent molecules are connected via C—H...O/N hydrogen bonds and C—H...π interactions, resulting in the formation of a three-dimensional (3D) supramolecular network. In addition, the 3D structure contains intermolecular π–π stacking interactions, with centroid–centroid distances of 3.5634 (12) Å between pyridine rings. The title compound exhibits a high energy gap (3.48 eV) and triplet energy (2.64 eV), indicating that it could be a suitable host material in organic light-emitting diode (OLED) applications.
High-pressure synthesis and crystal structure of SrGa4As4
Authors: Weippert Valentin , Johrendt Dirk
Published: October 2019

Strontium tetragallate(II,III) tetraarsenide, SrGa4As4, was synthesized in a Walker-type multianvil apparatus under high-pressure/high-temperature conditions of 8 GPa and 1573 K. The compound crystallizes in a new structure type (P3221, Z = 3) as a three-dimensional (3D) framework of corner-sharing SrAs8 quadratic antiprisms with strontium situated on a twofold rotation axis (Wyckoff position 3b). This arrangement is surrounded by a 3D framework which can be described as alternately stacked layers of either condensed GaIIIAs4 tetrahedra or honeycomb-like layers built up from distorted ethane-like GaII
2As6 units comprising Ga—Ga bonds.
Unexpected reactions of NHC*—CuI and —AgI bromides with potassium thio- or selenocyanate
Authors: Tacke Matthias , Marhöfer Daniel , Althani Hessah , Müller-Bunz Helge
Published: October 2019

The reactions of N-heterocyclic carbene CuI and AgI halides with potassium thio- or selenocyanate gave unexpected products. The attempted substitution reaction of bromido(1,3-dibenzyl-4,5-diphenylimidazol-2-ylidene)silver (NHC*—Ag—Br) with KSCN yielded bis[bis(1,3-dibenzyl-4,5-diphenylimidazol-2-ylidene)silver(I)] tris(thiocyanato)argentate(I) diethyl ether disolvate, [Ag(C29H24N2)2][Ag(NCS)3]·2C4H10O or [NHC*2Ag]2[Ag(SCN)3]·2Et2O, (1), while reaction with KSeCN led to bis(μ-1,3-dibenzyl-4,5-diphenyl-2-selenoimidazole-κ2
Se:Se)bis[bromido(1,3-dibenzyl-4,5-diphenyl-2-selenoimidazole-κSe)silver(I)] dichloromethane hexasolvate, [Ag2Br2(C29H24N2Se)4]·6CH2Cl2 or (NHC*Se)4Ag2Br2·6CH2Cl2, (2), via oxidation of the NHC* fragment to 2-selenoimidazole. This oxidation was observed again in the reaction of NHC*—Cu—Br with KSeCN, yielding catena-poly[[[(1,3-dibenzyl-4,5-diphenyl-2-selenoimidazole-κSe)copper(I)]-μ-cyanido-κ2
C:N] acetonitrile monosolvate], {[Cu(CN)(C29H24N2Se)]·C2H3N}
n
or NHC*Se—CuCN·CH3CN, (3). Compound (1) represents an organic/inorganic salt with AgI in a linear coordination in each of the two cations and in a trigonal coordination in the anion, accompanied by diethyl ether solvent molecules. The tri-blade boomerang-shaped complex anion [Ag(SCN)3]2− present in (1) is characterized by X-ray diffraction for the first time. Compound (2) comprises an isolated centrosymmetric molecule with AgI in a distorted tetrahedral BrSe3 coordination, together with dichloromethane solvent molecules. Compound (3) exhibits a linear polymeric 1
∞[Cu—C[triple-bond]N—Cu—] chain structure with a selenoimidazole moiety additionally coordinating to each CuI atom, and completed by acetonitrile solvent molecules. Electron densities associated with an additional ether solvent molecule in (1) and two additional dichloromethane solvent molecules in (2) were removed with the SQUEEZE procedure [Spek (2015). Acta Cryst. C71, 9–18] in PLATON.
The first structural characterization of the protonated azacyclam ligand incatena-poly[[[(perchlorato)copper(II)]-μ-3-(3-carboxypropyl)-1,5,8,12-tetraaza-3-azoniacyclotetradecane] bis(perchlorate)]
Authors: Tsymbal Liudmyla V. , Arion Vladimir B. , Lampeka Yaroslaw D.
Published: October 2019

The asymmetric unit of the title compound,catena-poly[[[(perchlorato-κO)copper(II)]-μ-3-(3-carboxypropyl)-1,5,8,12-tetraaza-3-azoniacyclotetradecane-κ4N1,N5,N8,N12] bis(perchlorate)], {[Cu(C13H30N5O2)(ClO4)](ClO4)2}n, (I), consists of a macrocyclic cation, one coordinated perchlorate anion and two perchlorate ions as counter-anions. The metal ion is coordinated in a tetragonally distorted octahedral geometry by the four secondary N atoms of the macrocyclic ligand, the mutuallytransO atoms of the perchlorate anion and the carbonyl O atom of the protonated carboxylic acid group of a neighbouring cation. The average equatorial Cu—N bond lengths [2.01 (6) Å] are significantly shorter than the axial Cu—O bond lengths [2.379 (8) Å for carboxylate and average 2.62 (7) Å for disordered perchlorate]. The coordinated macrocyclic ligand in (I) adopts the most energetically favourabletrans-III conformation with an equatorial orientation of the substituent at the protonated distal 3-position N atom in a six-membered chelate ring. The coordination of the carboxylic acid group of the cation to a neighbouring complex unit results in the formation of infinite chains running along theb-axis direction, which are crosslinked by N—H...O hydrogen bonds between the secondary amine groups of the macrocycle and O atoms of the perchlorate counter-anions to form sheets lying parallel to the (001) plane. Additionally, the extended structure of (I) is consolidated by numerous intra- and interchain C—H...O contacts.