bluuebunny/crossref_metadata_2025_split huggingface dataset:
CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators
Authors: Fang Liang , Wang Wen , Li Guipeng , Zhang Li , Li Jun , Gan Diwen , Yang Jiao , Tang Yisen , Ding Zewen , Zhang Min , Zhang Wenhao , Deng Daqi , Song Zhengyu , Zhu Qionghua , Cui Huanhuan , Hu Yuhui , Chen Wei 
Published: October 2020

AbstractCellular RNA is decorated with over 170 types of chemical modifications. Many modifications in mRNA, including m6A and m5C, have been associated with critical cellular functions under physiological and/or pathological conditions. To understand the biological functions of these modifications, it is vital to identify the regulators that modulate the modification rate. However, a high-throughput method for unbiased screening of these regulators is so far lacking. Here, we report such a method combining pooled CRISPR screen and reporters with RNA modification readout, termedCRISPRintegratedgRNAandreporter sequencing (CIGAR-seq). Using CIGAR-seq, we discovered NSUN6 as a novel mRNA m5C methyltransferase. Subsequent mRNA bisulfite sequencing in HAP1 cells without or with NSUN6 and/or NSUN2 knockout showed that NSUN6 and NSUN2 worked on non-overlapping subsets of mRNA m5C sites, and together contributed to almost all the m5C modification in mRNA. Finally, using m1A as an example, we demonstrated that CIGAR-seq can be easily adapted for identifying regulators of other mRNA modification.
A transposon surveillance mechanism that safeguards plant male fertility during stress
Authors: Lee Yang-Seok , Maple Robert , Dürr Julius , Dawson Alexander , Tamim Saleh , Genio Charo del , Papareddy Ranjith , Luo Anding , Lamb Jonathan C. , Sylvester Anne W. , Birchler James A. , Meyers Blake C. , Nodine Michael D. , Rouster Jacques , Gutierrez-Marcos Jose 
Published: October 2020

ABSTRACTAlthough plants are able to withstand a range of environmental conditions, spikes in ambient temperature can impact plant fertility causing reductions in seed yield and significant economic losses1,2. Therefore, understanding the precise molecular mechanisms that underpin plant fertility under environmental constraints is critical to safeguard future food production3. Here, we identified two Argonaute-like proteins whose activities are required to sustain male fertility in maize plants under high temperatures. We found that MALE-ASSOCIATED ARGONAUTE 1 and 2 (MAGO1 and MAGO2) associate with temperature-induced phased secondary small RNAs in pre-meiotic anthers and are essential to control the activity of retrotransposons in male meiocyte initials. Biochemical and structural analyses revealed how MAGO2 activity and its interaction with retrotransposon RNA targets are modulated through the dynamic phosphorylation of a set of highly conserved surface-located serine residues. Our results demonstrate that an Argonaute-dependent RNA-guided surveillance mechanism is critical in plants to sustain male fertility under environmentally constrained conditions by controlling the mutagenic activity of transposons in male germ cells.
Comprehensive Comparative Genomics Reveals Over 50 Phyla of Free-living and Pathogenic Bacteria are Associated with Diverse Members of the Amoebozoa
Authors: Tekle Yonas I. , Lyttle Janae M. , Blasingame Maya G. 
Published: October 2020

AbstractThe association of bacteria with microbial eukaryotes has been extensively studied. Among these the supergroup Amoebozoa containing predominantly amoeboid unicellular protists has been shown to play an important ecological role in controlling environmental bacteria. Amoebozoans not only graze bacteria but also serve as a safe niche for bacterial replication and harbor endosymbiotic bacteria including dangerous human pathogens. Despite their importance, only a few lineages of Amoebozoa have been studied in this regard. Amoebozoa encompasses lineages of extreme diversity in ecology, morphology and evolutionary history. The limited amoebozoans studied are not representative of the high diversity known in the supergroup, and could undermine our understanding of their role as key players in environmental ecosystems and as emerging public health threats. In this research, we conducted a comprehensive genomic and transcriptomic study with expansive taxon sampling by including representatives from the three known clades of the Amoebozoa. We used culture independent whole culture and single cell genomics maintained in our laboratory cultures, and additionally published RNA-Seq data to investigate the association of bacteria with diverse amoebozoans. Relative to current published evidence, we recovered the largest number of bacterial phyla (57) and pathogen genera (49) associated with the Amoebozoa. Using single cell genomics we were able to determine up to 24 potential endobiotic bacterial phyla, some potentially endosymbionts. This includes the majority of multidrug-resistant pathogens designated as major public health threats. Our study demonstrates amoebozoans are associated with many more phylogenetically diverse bacterial phyla than previously recognized. It also shows that all amoebozoans are capable of harboring far more dangerous human pathogens than presently documented, making them of primal public health concern.
A potent neutralizing mouse monoclonal antibody specific to dengue virus type 1 Mochizuki strain recognized a novel epitope around the N-67 glycan on the E protein: a possible explanation of dengue virus evolution regarding the acquisition of N-67 glycan
Authors: Kotaki Tomohiro , Yamanaka Atsushi , Konishi Eiji , Kameoka Masanori 
Published: October 2020

AbstractAnalysis of the neutralizing epitope of dengue virus (DENV) is important for the development of an effective dengue vaccine. A potent neutralizing mouse monoclonal antibody named 7F4 was previously reported and, here, we further analyze the detailed epitope of this antibody. 7F4 recognized a novel conformational epitope close to the N-67 glycan on the E protein. This antibody was specific to the DENV that lacks N-67 glycan, including the Mochizuki strain. Interestingly, the Mochizuki strain acquired N-67 glycan by 7F4 selective pressure. DENVs might have evolved to escape from this antibody considering that most of currently circulating DENVs possess N-67 glycan. However, this suggests that 7F4 epitope might be useless as a vaccine target. Nevertheless, this study demonstrated the existence of epitopes competing for 7F4 epitope, which are involved in neutralization. This study describes the importance of antibodies recognizing epitopes near the N-67 glycan for future dengue vaccine development.
A Universal Stress Protein upregulated by hypoxia may contribute to chronic lung colonisation and intramacrophage survival in cystic fibrosis
Authors: O’Connor Andrew , Berisio Rita , Lucey Mary , Schaffer Kirsten , McClean Siobhán 
Published: October 2020

SummaryUniversal stress proteins (USPs) are ubiquitously expressed in bacteria, plants and eukaryotes and play a lead role in adaptation to environmental conditions. In Gram negative bacteria they enable adaption of bacterial pathogens to the conditions encountered in the human niche, including hypoxia, oxidative stress, osmotic stress, nutrient deficiency or acid stress, thereby facilitating colonisation. We previously reported that all six USP proteins encoded within a low-oxygen responsive locus inBurkholderia cenocepaciashowed increased abundance during chronic colonisation of the CF lung. However, the role of USPs in chronic infection is not known. Using mutants derived fromB. cenocepaciastrain, K56-2, we show that USP76 is required for growth and survival in many conditions associated with the CF lung including, hypoxia, acidic conditions, oxidative stress. Moreover, it is involved in attachment to host epithelial cells, but not virulence. It also has a role in survival in macrophages isolated from people with CF. In contrast, another USP encoded in the same locus, USP92 had no effect on host cell attachment or oxidative stress, but was responsible for a 3-fold increase in virulence. Overall this shows that these USPs, both upregulated during chronic infection, have distinct roles inBurkholderiapathogenesis and may support the survival ofB. cenocepaciain the CF lung. Specifically, USP76 is involved in its survival within CF macrophages, a hallmark ofBurkholderiainfection.
Spectrin Interactome under normal and HbE-disease conditions
Authors: Bose Dipayan , Islam Sk Ramiz , Saha Sutapa , Chakrabarti Abhijit 
Published: October 2020

ABSTRACTSpectrin, the major component of the erythrocyte membrane skeleton is a key player in red cell biology. It has a significant role in signalling pathways and as such knowledge of spectrin interactors becomes crucial. Here we report the cytosolic interactome of human erythroid spectrin (ProteomeXchange id: PXD021525). This is to the best of our knowledge the first report of the interactome of human erythroid spectrin. We have further investigated the spectrin interactome under HbE disease conditions. Our findings indicate that there is no difference in the identity of the proteins interacting with spectrin between normal and disease conditions. However relative abundance of the interacting partners is seen to change. Very interestingly the interacting chaperone proteins, heme-containing proteins and redox active proteins are seen to be up-regulated in HbE disease state. This is consistent with our previous observation that presence of oxidation prone hemoglobin variants leads to an increase of redox regulators and chaperones in the red cell proteome. Spectrin can also interact with horse radish peroxidase and oxidatively crosslink hemoglobin, which has possible implications in oxidative stress management. Since a large fraction of spectrin interacting proteins are chaperones and redox active proteins, it is possible that spectrin may have a broader role in redox regulation, especially in cases where there are unstable hemoglobin variants present.
Spatial modulation of hippocampal activity in freely moving macaques
Authors: Mao D. , Avila E. , Caziot B. , Laurens J. , Dickman J.D. , Angelaki D.E. 
Published: October 2020

SummaryThe hippocampal formation is linked to spatial navigation, but there is little corroboration from freely-moving primates with concurrent monitoring of three-dimensional head and gaze stances. We recorded neurons and local field potentials across hippocampal regions in rhesus macaques during free foraging in an open environment while tracking their head and eye. Theta band activity was intermittently present at movement onset and modulated by saccades. Many cells were phase-locked to theta, with few showing theta phase precession. Most hippocampal neurons encoded a mixture of spatial variables beyond place fields and a negligible number showed prominent grid tuning. Spatial representations were dominated by facing location and allocentric direction, mostly in head, rather than gaze, coordinates. Importantly, eye movements strongly modulated neural activity in all regions. These findings reveal that the macaque hippocampal formation represents three-dimensional space using a multiplexed code, with head orientation and eye movement properties dominating over simple place and grid coding during free exploration.
Individual differences in proprioception predict the extent of implicit sensorimotor adaptation
Authors: Tsay Jonathan S. , Kim Hyosub E. , Parvin Darius E. , Stover Alissa R. , Ivry Richard B. 
Published: October 2020

ABSTRACTRecent studies have revealed an upper bound in motor adaptation, beyond which other learning systems may be recruited. The factors determining this upper bound are poorly understood. The multisensory integration hypothesis states that this limit arises from opposing responses to visual and proprioceptive feedback. As individuals adapt to a visual perturbation, they experience an increasing proprioceptive error in the opposite direction, and the upper bound is the point where these two error signals reach an equilibrium. Assuming that visual and proprioceptive feedback are weighted according to their variability, there should be a correlation between proprioceptive variability and the limits of adaptation. Alternatively, the proprioceptive realignment hypothesis states that the upper bound arises when the (biased) sensed hand position realigns with the target. When a visuo-proprioceptive discrepancy is introduced, the sensed hand position is biased towards the visual cursor and the adaptive system nullifies this discrepancy by driving the hand away from the target. This hypothesis predicts a correlation between the size of the proprioceptive shift and the upper bound of adaptation. We tested these two hypotheses by considering natural variation in proprioception and motor adaptation across individuals. We observed a modest, yet reliable correlation between the upper bound of adaptation withbothproprioceptive measures (variability and shift). While these results do not favor one hypothesis over the other, they underscore the critical role of proprioception in sensorimotor adaptation, and moreover, motivate a novel perspective on how these proprioceptive constraints drive implicit changes in motor behavior.SIGNIFICANCE STATEMENTWhile the sensorimotor system uses sensory feedback to remain properly calibrated, this learning process is constrained, limited in the maximum degree of plasticity. The factors determining this limit remain elusive. Guided by two hypotheses concerning how visual and proprioceptive information are integrated, we show that individual differences in the upper bound of adaptation in response to a visual perturbation can be predicted by the bias and variability in proprioception. These results underscore the critical, but often neglected role of proprioception in human motor learning.
Leptin-receptor neurons in the dorsomedial hypothalamus regulate the timing of circadian rhythms in feeding and metabolism in mice
Authors: Faber Chelsea L. , Deem Jennifer D. , Phan Bao Anh , Doan Tammy P. , Ogimoto Kayoko , Mirzadeh Zaman , Schwartz Michael W. , Morton Gregory J. 
Published: October 2020

AbstractAnimal behavior and metabolism are tightly coordinated with sleep-wake cycles governed by the brain in harmony with environmental light:dark cycles. Within the brain, the dorsomedial hypothalamic nucleus (DMH) has been implicated in the integrative control of feeding, energy homeostasis, and circadian rhythms [1], but the underlying cell types are unknown. Here, we identify a role for DMH leptin receptor-expressing neurons (DMHLepR) in these effects. Using a viral approach, we show that silencing DMHLepRneurons in adult mice not only increases body weight and adiposity, but also shifts circadian rhythms in feeding and metabolism into the light-cycle. Moreover, DMHLepRsilencing abolishes the normal increase in dark-cycle locomotor activity characteristic of nocturnal rodents. Furthermore, DMHLepR-silenced mice fail to entrain to a restrictive change in food availability. Together, these findings identify DMHLepRneurons as critical determinants of the daily time of feeding and associated metabolic rhythms.
Sucrose transport and metabolism control carbon partitioning between stem and grain in rice
Authors: Mathan Jyotirmaya , Singh Anuradha , Ranjan Aashish 
Published: October 2020

AbstractThe source-sink relationship is key to overall crop performance. Detailed understanding of the factors that determine source-sink dynamics is imperative for the balance of biomass and grain yield in crop plants. We investigated the differences in the source-sink relationship between a cultivated riceOryza sativacv. Nipponbare and a wild riceOryza australiensisthat show striking differences in biomass and grain yield.Oryza australiensis, accumulating higher biomass, not only showed higher photosynthesis per unit leaf area but also exported more sucrose from leaves than Nipponbare. However, grain features and sugar levels suggested limited sucrose mobilization to the grains in the wild rice due to vasculature and sucrose transporter functions. Low cell wall invertase activity and high sucrose synthase cleavage activity followed by higher expression of cellulose synthase genes inOryza australiensisstem utilized photosynthates preferentially for the synthesis of structural carbohydrates, resulting in high biomass. In contrast, the source-sink relationship favored high grain yield in Nipponbare via accumulation of transitory starch in the stem, due to higher expression of starch biosynthetic genes, which is mobilized to panicles at the grain filling stage. Thus, vascular features, sucrose transport, and functions of sugar metabolic enzymes explained the differences in the source-sink relationship between Nipponbare andOryza australiensis.HighlightVascular features, sucrose transport, and sugar metabolic enzyme activity contribute to the differential source-sink relationship between the selected cultivated and wild rice that differ in biomass and grain yield.
In silicocharacterization and expression profiles of zinc transporter-like (LOC100037509) gene of tomato
Authors: Kabir Ahmad Humayan 
Published: October 2020

ABSTRACTZinc (Zn) is an essential microelement for plants. ZIP transporters play a critical role in Zn homeostasis in plants. Thisin silicostudy characterizes different features of putative Zn transporter of tomato (Solyc07g065380) and its homologs. A total of 10 ZIP protein homologs were identified across nine plant species by protein BLAST. All these ZIP protein homologs located at chromosome 7 showed 305-350 amino acid residues, 7-8 transmembrane helices, and stable instability index. Further, these ZIP protein homologs are localized in the plasma membrane at the subcellular level corresponding to the ZIP zinc transporter (PF02535) domain. Gene organization analysis reveals the presence of 3 exon along with the position of the promoter, TATA-box, transcriptional start site, and splice sites in these ZIP transporter homologs, in which tomato ZIP transporter (NM_001247420.1) contains a promoter, TATA-box, transcriptional start site at 500, 911 and 946 bp, respectively along with several splice sites, which may be useful for targeting binding sites and transcription factor analysis. Further, the cutting sites and restriction enzymes of each ZIP gene homologs might be helpful for future transgenic studies underlying Zn homeostasis. MEMO displayed five conserved motifs associated with the ZIP zinc transporter, N-glycosylation site, and phosphorylation site. Phylogenetic studies reveal a close relationship of Solyc07g065380 withSolanum pennelliihomolog, while ZIP transporter ofNicotiana sylvestrisandNicotiana tabacumpredicted to be in close connection. The Solyc07g065380 transporter is predominantly linked to several uncharacterized zinc metal ion transporters and expressed in diverse anatomical part, developmental stage, and subjected to pathogen and heat stress. The secondary structural prediction reveals unique signal peptide in the ZIP protein homologs ofS. lycopersicumandS. pennelliialong with extended alpha-helix. These bioinformatics analyses might provide essential background to perform wet-lab experiments and to understand Zn homeostasis for the development of Zn-biofortified crops.Key message♦ ZIP protein homologs are localized in the plasma membrane and are linked to ZIP zinc transporter (PF02535) domain at chromosome 7.♦ ZIP protein motifs are associated with the ZIP zinc transporter, N-glycosylation site, and phosphorylation site.♦ Phylogenetic studies reveal a closet relationship of Solyc07g065380 withSolanum pennelliihomolog.♦ ZIP protein homologs ofS. lycopersicumandS. pennelliishow unique signal peptide along with extended alpha-helix.
Generating new FANCA-deficient HNSCC cell lines by genomic editing recapitulate the cellular phenotypes of Fanconi anemia
Authors: Errazquin Ricardo , Sieiro Esther , Moreno Pilar , Ramirez María José , Lorz Corina , Peral Jorge , Casado José Antonio , Roman-Rodriguez Francisco J. , Hanenberg Helmut , Río Paula , Surralles Jordi , Segrelles Carmen , Garcia-Escudero Ramon 
Published: October 2020

AbstractFanconi anemia (FA) patients have an exacerbated risk of head and neck squamous cell carcinoma (HNSCC). Treatment is challenging as FA patients display enhanced toxicity to standard treatments, including radio/chemotherapy. Therefore better therapies as well as new disease models are urgently needed. We have used CRISPR/Cas9 editing tools in order to interrupt the humanFANCAgene by the generation of insertions/deletions (indels) in exon 4 in two cancer cell lines from sporadic HNSCC having no mutation in FA-genes: CAL27 and CAL33 cells. Our approach allowed efficient editing, subsequent purification of single-cell clones, and Sanger sequencing validation at the edited locus. Clones having frameshift indels in homozygosis did not express FANCA protein and were selected for further analysis. When compared with parental CAL27 and CAL33,FANCA-mutant cell clones displayed a FA-phenotype as they i) are highly sensitive to DNA interstrand crosslink (ICL) agents such as mitomycin C (MMC) or cisplatin, ii) do not monoubiquitinate FANCD2 upon MMC treatment and therefore iii) do not formFANCD2nuclear foci, and iv) they display increased chromosome fragility and G2 arrest after diepoxybutane (DEB) treatment. TheseFANCA-mutant clones display similar growth rates as their parental cells. Interestingly, mutant cells acquire phenotypes associated with more aggressive disease, such as increased migration in wound healing assays. Therefore, CAL27 and CAL33 cells withFANCAmutations are phenocopies of FA-HNSCC cells.