bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS
Authors: Ilter Metehan , Kaşmer Ramazan , Jalalypour Farzaneh , Atilgan Canan , Topcu Ozan , Karakaş Nihal , Sensoy Ozge 
Published: May 2022

AbstractUndruggability of RAS proteins has necessitated alternative strategies for the development of effective inhibitors. In this respect, phosphorylation has recently come into prominence as this reversible post-translational modification attenuates sensitivity of RAS towards RAF. As such, in this study, we set out to unveil the impact of phosphorylation on dynamics of HRASWT and aim to invoke similar behavior in HRASG12D mutant by means of small therapeutic molecules. To this end, we performed molecular dynamics (MD) simulations using phosphorylated HRAS and showed that phosphorylation of Y32 distorted Switch I, hence the RAS/RAF interface. Consequently, we targeted Switch I in HRASG12D by means of approved therapeutic molecules and showed that the ligands enabled detachment of Switch I from the nucleotide-binding pocket. Moreover, we demonstrated that displacement of Switch I from the nucleotide-binding pocket was energetically more favorable in the presence of the ligand. Importantly, we verified computational findings in vitro where HRASG12D/RAF interaction was prevented by the ligand in HEK293T cells that expressed HRASG12D mutant protein. Therefore, these findings suggest that targeting Switch I, hence making Y32 accessible might open up new avenues in future drug discovery strategies that target mutant RAS proteins.
FBXW7β isoform drives transcriptional activation of a proinflammatory TNF cluster in normal and malignant pro-B cells
Authors: Yang Scarlett Y. , Hayer Katharina E. , Fazelinia Hossein , Spruce Lynn A. , Asnani Mukta , Black Kathryn L. , Naqvi Ammar S. , Pillai Vinodh , Barash Yoseph , Elenitoba-Johnson Kojo S. J. , Thomas-Tikhonenko Andrei 
Published: May 2022

AbstractNon-canonical exon usage plays many important roles in cellular phenotypes, but its contribution to human B-cell development remains sketchily understood. To fill this gap, we collected various B-cell fractions from bone marrow and tonsil donors, performed RNA-seq, and examined transcript variants. We identified 150 genes that harbor local splicing variations in all pairwise comparisons. One of them encodes FBXW7, an E3 ubiquitin ligase implicated as a cancer driver in several blood cancers. Surprisingly, we discovered that in normal human pro-B cells, the predominant transcript utilized an alternative first exon to produce the poorly characterized FBXW7β isoform, previously thought to be restricted to neural tissues. The FBXW7β transcript was also abundant in cell lines and primary samples of pediatric B-cell acute lymphoblastic leukemia (B-ALL), which originates in the bone marrow. When overexpressed in a heterologous cell system, this transcript yielded the expected protein product, as judged by anti-FLAG immunoblotting and mass spectrometry. Furthermore, in REH B-ALL cells, FBXW7β mRNA was the only FBXW7 isoform enriched in the polyribosome fraction. To shed light on possible functions of FBXW7β, we utilized gain- and loss-of-function approaches and identified an FBXW7β-dependent inflammatory gene signature, apparent in a subset of B-ALL with high FBXW7β expression. This signature contained several members of the TNF superfamily, including those comprising the HLA Class III cluster (LTB, LST1, NCR3, LTA, and NFKBIL1). Our findings suggest that FBXW7β expression drives proinflammatory responses, which could contribute to normal B-cell development, leukemogenesis and responses to anti-cancer therapies.Key pointsPreviously thought to be restricted to neural tissues, FBXW7β is the predominant FBXW7 isoform in normal and malignant human pro-B cells.FBXW7β promotes transcriptional activation of a proinflammatory gene cluster that contains TNF superfamily members.
The language network reliably ‘tracks’ naturalistic meaningful non-verbal stimuli
Authors: Sueoka Yotaro , Paunov Alexander , Ivanova Anna , Tanner Alyx , Blank Idan A. , Fedorenko Evelina 
Published: May 2022

AbstractThe language network, comprised of brain regions in the left frontal and temporal cortex, responds robustly and reliably during language comprehension but shows little or no response during many non-linguistic cognitive tasks (e.g., Fedorenko & Blank, 2020). However, one domain whose relationship with language remains debated is semantics—our conceptual knowledge of the world. Given that the language network responds strongly to meaningful linguistic stimuli, could some of this response be driven by the presence of rich conceptual representations encoded in linguistic inputs? In this study, we used a naturalistic cognition paradigm to test whether the cognitive and neural resources that are responsible for language processing are also recruited for processing semantically rich non-verbal stimuli. To do so, we measured BOLD responses to a set of ∼5-minute-long video and audio clips that consisted of meaningful event sequences but did not contain any linguistic content. We then used the inter-subject correlation (ISC) approach (Hasson et al., 2004) to examine the extent to which the language network ‘tracks’ these stimuli, i.e. exhibits stimulus-related variation. Across all the regions of the language network, non-verbal meaningful stimuli elicited reliable ISCs. These ISCs were higher than the ISCs elicited by semantically impoverished non-verbal stimuli (e.g., a music clip), but substantially lower than the ISCs elicited by linguistic stimuli. Our results complement earlier findings from controlled experiments (e.g., Ivanova et al., 2021) in providing further evidence that the language network shows some sensitivity to semantic content in non-verbal stimuli.
Direct N-Me Aziridination Reaction Enables Pinpointing C=C Bonds in Lipids with Mass Spectrometry
Authors: Feng Guifang , Gao Ming , Fu Rongrong , Wan Qiongqiong , Wang Tianze , Zhang Zhourui , Chen Suming 
Published: May 2022

AbstractThe biological functions of lipids largely depend on their chemical structures. The position of C=C bonds is an essential attribute that determines the structures of unsaturated lipids. Here, we developed a new type of chemical derivatization method for C=C bond using aziridination reaction. This new cyclization method for the C=C bonds in lipids based on the direct N-Me aziridination reaction of olefins using N-methyl-O-tosylhydroxylamine (TsONHCH3) as the aminating reagent. When combined with the tandem MS analysis, this novel activation approach for C=C bonds enables the accurate identification their positions in different kinds of unsaturated lipids. Furthermore, an integrated workflow has been established for comprehensively identifying the C=C bond positional isomers of lipids in complicated biological sample. This work provided a new chemical approach for the structural lipidomics.
Small-amplitude head oscillations result from a multimodal head stabilization reflex in hawkmoths
Authors: Chatterjee Payel , Mohan Umesh , Sane Sanjay P. 
Published: May 2022

AbstractIn flying insects, head stabilization is an important reflex which helps to reduce motion blur during fast aerial maneuvers. This reflex is multimodal and requires the integration of visual and antennal mechanosensory feedback, each operating as a negative-feedback control loop. As in any negative-feedback system, the head stabilization system possesses inherent oscillatory dynamics that depends on the rates and latencies of the sensorimotor components constituting the reflex. Consistent with this expectation, we observed small amplitude oscillations in the head motion (or head wobble) of the Oleander hawkmoth Daphnis nerii. We show here that these oscillations emerge from the inherent dynamics of the multimodal reflex that underlies gaze stabilization, and the amplitude of the head wobble is a function of both the visual feedback and antennal mechanosensory feedback from the Johnston’s organs. The head wobble is thus an outcome of a multimodal, dynamically-stabilized head positioning reflex.
Mircubactin B rescues the lethal effect of cell wall biosynthesis mutations in Bacillus subtilis
Authors: Kepplinger Bernhard , Wen Xin , Tyler Andrew Robert , Kim Byung-Yong , Brown James , Banks Peter , Dashti Yousef , Mackenzie Eilidh Sohini , Wills Corinne , Kawai Yoshikazu , Waldron Kevin John , Allenby Ellis Nicholas Edward , Wu Ling Juan , Hall Michael John , Errington Jeff 
Published: May 2022

AbstractGrowth of most rod-shaped bacteria is accompanied by the insertion of new peptidoglycan into the cylindrical cell wall. This insertion, which helps maintain and determine the shape of the cell, is guided by a complex protein machinery called the rod complex or elongasome. Although most of the proteins in this complex are essential under normal growth conditions, cell viability can be rescued, for reasons that are not understood, by the presence of a high (mM) Mg2+ concentration. We screened for natural product compounds that could rescue the growth of mutants affected in rod-complex function. By screening >2,000 extracts from a diverse collection of actinobacteria, we identified a new compound, mirubactin B, related to the known iron siderophore mirubactin A, which rescued growth in the low micromolar range, and this activity was confirmed by synthesising mirubactin B. The compound also displayed toxicity at higher concentrations, and this effect appears related to iron homeostasis. However, several lines of evidence suggest that the mirubactin B rescuing activity is not due simply to iron sequestration. The results demonstrate a novel antibacterial compound and add to growing evidence that bacterial siderophores have a range of activities beyond simple iron sequestration.
Mechanisms and functions of respiration-driven gamma oscillations in the primary olfactory cortex
Authors: González Joaquín , Torterolo Pablo , Tort Adriano BL 
Published: May 2022

AbstractGamma oscillations are believed to underlie cognitive processes by shaping the formation of transient neuronal partnerships on a millisecond scale. These oscillations are coupled to the phase of breathing cycles in several brain areas, possibly reflecting local computations driven by sensory inputs sampled at each breath. Here, we investigated the mechanisms and functions of gamma oscillations in the piriform (olfactory) cortex of awake mice to understand their dependence on breathing and how they relate to local spiking activity. Mechanistically, we find that respiration drives gamma oscillations in the piriform cortex, which correlate with local feedback inhibition and result from recurrent connections between local excitatory and inhibitory neuronal populations. Moreover, respiration-driven gamma oscillations are triggered by the activation of mitral/tufted cells in the olfactory bulb and are abolished during ketamine/xylazine anesthesia. Functionally, we demonstrate that they locally segregate neuronal assemblies through a winner-take-all computation leading to sparse odor coding during each breathing cycle. Our results shed new light on the mechanisms of gamma oscillations, bridging computation, cognition and physiology.
LRRK2 Phosphorylates Neuronal Elav RNA-Binding Proteins to Regulate Phenotypes Relevant to Parkinson’s Disease
Authors: Pastic Alyssa , Negeri Olanta , Ravel-Chapuis Aymeric , Savard Alexandre , Trung My Tran , Palidwor Gareth , Guo Huishan , Marcogliese Paul , Taylor James A. , Okano Hideyuki , Trinkle-Mulcahy Laura , Jasmin Bernard J. , Park David , Gibbings Derrick 
Published: May 2022

AbstractParkinson’s disease (PD) is characterized by accumulation of α-synuclein and the loss of dopaminergic neurons. Mutations which cause an increase in the kinase activity of Leucine-Rich-Repeat Kinase-2 (LRRK2) are a major inherited cause of PD. Research continues to determine which targets LRRK2 phosphorylates to cause disease. Polymorphisms in the locus of ELAVL4, an RNA-binding protein are a risk-factor for Parkinson’s disease and an ELAV family member was identified in Drosophila as required for pathology instigated by human mutant LRRK2. We discovered that three neuronal ELAVs including ELAVL4 (also known as HuD) are phosphorylated by LRRK2. This controls binding of neuronal ELAVs to mRNA and their post- transcriptional regulation of mRNA abundance and splicing in neuronal cell lines and the mouse midbrain. LRRK2 G2019S functionally inhibits neuronal ELAVs effects on mRNA abundance, while enhancing their effects on mRNA splicing. The combination of LRRK2 G2019S and ELAVL4-/- causes accumulation of LRRK2 and α-synuclein, loss of dopaminergic neurons and motor deficits. Targets of neuronal ELAVs are also selectively misregulated in cells and tissues of PD patients. Together, this suggests that misregulation of neuronal ELAVs, triggered by LRRK2 mutations may contribute to the characteristic pathology of Parkinson’s disease.Brief SummaryLRRK2, a kinase linked to Parkinson’s disease, phosphorylates the neuronal ELAV RNA-binding proteins to aggravate key hallmarks of Parkinson’s disease including accumulation of α-synuclein and motor deficits in mice.
The bHLH transcription factor MpHYPNOS regulates gemma dormancy in the liverwort Marchantia polymorpha
Authors: Kato Hirotaka , Yoshimura Nami , Yoshikawa Mikako , Matsuura Hideyuki , Takahashi Kosaku , Takezawa Daisuke , Furuya Tomoyuki , Kondo Yuki , Fukaki Hidehiro , Mimura Tetsuro , Ishizaki Kimitsune 
Published: May 2022

SummaryDormancy is a key process employed by land plants to adapt to harsh terrestrial environments. The liverwort Marchantia polymorpha produces dormant propagules called gemmae for asexual reproduction. The plant hormone abscisic acid (ABA) plays important roles in regulating dormancy in both the seeds of flowering plants and the gemmae of M. polymorpha.Based on previous transcriptome analysis, we identified the basic helix-loop-helix transcription factor MpHYPNOS (MpHYP) as a key regulator of gemma dormancy.Knock-out mutants of MpHYP showed much higher germination rates of gemmae in gemma cups than ABA-related mutants, while the growth and development of these mutants resembled that of the wild type. Transient induction of MpHYP caused irreversible growth arrest of gemmae and thalli. Transcriptome and RT-qPCR analyses revealed that MpHYP represses the expression of cell cycle–related genes and induces ABA biosynthesis and ABA-responsive genes. Indeed, ABA levels increased in MpHYP overexpression lines and decreased in Mphyp knock-out lines. However, the growth arrest caused by MpHYP overexpression was not suppressed by a mutation in an ABA receptor gene.These findings suggest that MpHYP regulates gemma dormancy and thallus growth mainly through the ABA-independent pathway, providing clues about ABA-dependent and independent regulation of dormancy in land plants.
Exploiting threonine sidechains as molecular switches to modulate the fluorescence of genetically encoded biosensors
Authors: Leong Lee Min , Shin Sang Chul , Rhee Jun Kyu , Kim Heejung , Seong Jihye , Woo Junhyuk , Han Kyungreem , Storace Douglas , Baker Bradley J. 
Published: May 2022

AbstractRapid and reproducible optical transitions of a fluorescent protein (FP) can be achieved with a Genetically Encoded Voltage Indicator (GEVI) via manipulation of the membrane potential. These transitions revealed novel effects of internal mutations near the chromophore that would not be detected under steady state conditions. Mutating an internal threonine (T203) affected the speed of the voltage-dependent fluorescence transition suggesting a conformational change inside the protein. These optical transitions also demonstrated interplay between internal and externally oriented sidechains of the β-can structure. Replacing the steric hindrance of a phenylalanine near the chromophore with threonine (F165T) did not alter the resting fluorescence but resulted in a more complex fluorescent transition providing evidence for a flexible chromophore undergoing conformational changes. F165T orientation was influenced by the flanking external amino acids at positions 164 and 166 with 164F/165T/166T exacerbating the complexity of the voltage-dependent transition while 164T/165T/166F reduced the flexibility of the chromophore resembling the transition pattern of the original F165 version. Alphafold predictions reveal a threonine switch with different orientations of the F165T internal side chain depending on the direction of the offset in polarity at external positions 164 and 166. The crystal structures of the pH-sensitive FP, Super Ecliptic pHluorin and two derivatives solved in varying pH conditions also indicate interactions between the external protein surface and the internal environment providing another example of a threonine switch near the chromophore at T203. This ability to orient internal sidechains has led to the development of a novel GEVI that gets brighter upon depolarization of the plasma membrane, works at low light levels, is less susceptible to physiological pH, and provides in vivo signals. These observations affecting fluorescent transitions should also prove valuable to the development of any FP-based biosensor.
Flavivirus prM interacts with MDA5 and MAVS to inhibit RLR antiviral signaling
Authors: Sui Liyan , Zhao Yinghua , Wang Wenfang , Chi Hongmiao , Tian Tian , Wu Ping , Zhang Jinlong , Zhao Yicheng , Wei Zheng-Kai , Hou Zhijun , Zhou Guoqiang , Wang Guoqing , Wang Zedong , Liu Quan 
Published: May 2022

AbstractVector-borne flaviviruses, including tick-borne encephalitis virus (TBEV), Zika virus (ZIKA), West Nile virus (WNV), yellow fever virus (YFV), dengue virus (DENV), and Japanese encephalitis virus (JEV), pose a growing threat to public health worldwide, and have evolved complex mechanisms to overcome host antiviral innate immunity. However, the underlying mechanisms of flavivirus structural proteins to evade host immune response remain elusive. Here we show that TBEV structural proteins, including pre-membrane (prM), envelope, and capsid proteins, could inhibit type I interferon (IFN-I) production. Mechanically, TBEV prM interacted with both MDA5 and MAVS and interfered with the formation of MDA5-MAVS complex, thereby impeded the nuclear translocation and dimerization of IRF3 to inhibit RLR antiviral signaling. ZIKA and WNV prM was also demonstrated to interact with both MDA5 and MAVS, while dengue virus serotype 2 (DENV2) and YFV prM associated only with MDA5 or MAVS to suppress IFN-I production. In contrast, JEV prM could not suppress IFN-I production. Overexpression of TBEV and ZIKA prM significantly promoted the replication of Sendai virus. Our findings reveal the immune evasion mechanisms of flavivirus prM, which may contribute to understanding flavivirus pathogenicity, therapeutic intervention and vaccine development.Author SummaryAll flaviviruses must overcome the antiviral innate immunity to infect vertebrate host. The non-structural proteins of flaviviruses are mainly responsible for viral replication and host innate immune escape, and the structural proteins are involved in the virus assembly, which are potential targets for prevention and treatment of flaviviral infections. Whether flavivirus structural proteins participate in host innate immune escape remains to be determined. Here, we found that tick-borne encephalitis virus structural proteins precursor membrane (prM), capsid, and envelope proteins can antagonize type I interferon production, in which prM interacts with both MDA5 and MAVS to inhibit RLR antiviral signaling. Additionally, Zika virus and West Nile virus prMs also interact with both MDA5 and MAVS, while dengue virus serotype 2 and yellow fever virus prMs associate only with MDA5 or MAVS to suppress type I interferon production. In contrast, Japanese encephalitis virus prM cannot antagonize type I interferon production. Our findings reveal that flavivirus prM inhibits type I interferon production via interacting with MDA5 and/or MAVS in a species-dependent manner, which may contribute to understanding flavivirus pathogenicity, therapeutic intervention, and vaccine development.
CircEML1 facilitates the steroid synthesis in follicular granulosa cells of chicken through sponging gga-miR-449a to release IGF2BP3 expression
Authors: Li Jing , Si Sujin , Wu Xing , Zhang Zihao , Li Chong , Tao Yiqing , Yang Pengkun , Li Donghua , Li Guoxi , Liu Xiaojun , Tian Yadong , Kang Xiangtao 
Published: May 2022

AbstractNon-coding RNAs (ncRNAs) induced competing endogenous RNAs (ceRNA) play crucial roles in various biological process by regulating target gene expression. However, the studies of ceRNA networks in the regulation of ovarian ovulation process of chicken remains deficient compared to that in mammals. In the present study, it was revealed that circEML1 was differential expressed in hen’s ovarian tissue at different ages (15W, 20W, 30W and 68W) and identified as a loop structure from EML1 pre-mRNA, which promoted the expressions of CYP19A1 and StAR and the production of E2 and P4 in follicular granulosa cells (GCs) using qRT-PCR and ELISA. Furthermore, circEML1 was proved to serve as a sponge of gga-miR-449a to participate in the steroidogenesis using the dual luciferase reporter, RNA FISH assays, qRT-PCR and ELISA assays. In addition, we evaluated several potential target genes of gga-miR-449a and found that IGF2BP3 was targeted by gga-miR-449a and promoted steroidogenesis and E2/P4 secretions in GCs, which may act the regulatory role via mTOR/p38MAPK pathways. Meanwhile, we implemented a rescue experiment and demonstrated that gga-miR-449a reversed the promoting role of circEML1 on IGF2BP3 expression and steroidogenesis. Eventually, this study suggested that circEML1/gga-miR-449a/IGF2BP3 axis exerted an important role in the regulation of steroidogenesis and steroid hormones’ production possibly through mTOR/p38MAPK pathways in follicular GCs of chicken and may contribute a better understanding of ceRNA network in the modulatory mechanism of hen’s ovarian development and ovulation cycle.
Sequences and proteins that influence mRNA processing in Trypanosoma brucei: evolutionary conservation of SR-domain and PTB protein functions
Authors: Waithaka Albina , Maiakovska Olena , Grimm Dirk , Melo do Nascimento Larissa , Clayton Christine 
Published: May 2022

AbstractSpliced leader trans splicing is the addition of a short, capped sequence to the 5’ end of mRNAs. It is widespread in eukaryotic evolution, but factors that influence trans splicing acceptor site choice have been little investigated. In Kinetoplastids, all protein-coding mRNAs are 5’ trans spliced. A polypyrimidine tract is usually found upstream of the AG splice acceptor, but there is no branch point consensus; moreover, splicing dictates polyadenylation of the preceding mRNA. We here describe a trans splicing reporter system that can be used for studies and screens concerning the roles of sequences and proteins in processing site choice and efficiency. Splicing was poor with poly(U) tracts less than 9 nt long, and was influenced by nearby secondary structures. A screen for signals resulted in selection of sequences that were on average 45% U and 35% C. Tethering of either the splicing factor SF1, or the cleavage and polyadenylation factor CPSF3 within the intron stimulated processing in the correct positions, while tethering of two possible homologues of Opisthokont PTB inhibited processing. In contrast, tethering of SR-domain proteins RBSR1, RBSR2, or TSR1 or its interaction partner TSR1IP, promoted use of alternative signals upstream of the tethering sites. RBSR1 interacts predominantly with proteins implicated in splicing, whereas the interactome of RBSR2 is more diverse. These results suggest that the functions of PTB and SR-domain proteins in splice site definition were already present in the last eukaryotic common ancestor.