bluuebunny/crossref_metadata_2025_split huggingface dataset:
m6A and YTHDF proteins contribute to the localization of select neuronal mRNAs
Authors: Flamand Mathieu N , Meyer Kate D 
Published: April 2022

Abstract
The transport of mRNAs to distal subcellular compartments is an important component of spatial gene expression control in neurons. However, the mechanisms that control mRNA localization in neurons are not completely understood. Here, we identify the abundant base modification, m6A, as a novel regulator of this process. Transcriptome-wide analysis following genetic loss of m6A reveals hundreds of transcripts that exhibit altered subcellular localization in hippocampal neurons. Additionally, using a reporter system, we show that mutation of specific m6A sites in select neuronal transcripts diminishes their localization to neurites. Single molecule fluorescent in situ hybridization experiments further confirm our findings and identify the m6A reader proteins YTHDF2 and YTHDF3 as mediators of this effect. Our findings reveal a novel function for m6A in controlling mRNA localization in neurons and enable a better understanding of the mechanisms through which m6A influences gene expression in the brain.
patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures
Authors: Schmitz Mirko , Schultze Anne , Vanags Raimonds , Voigt Karsten , Di Ventura Barbara , Öztürk Mehmet Ali 
Published: April 2022

Abstract
pH regulates protein function and interactions by altering the charge of individual residues causing loss or gain of intramolecular noncovalent bonds, which may lead to structural rearrangements. While tools to analyze residue-specific charge distribution of proteins at a given pH exist, currently no tool is available to investigate noncovalent bond changes at two different pH values. To make protein pH sensitivity analysis more accessible, we developed patcHwork, a web server that combines the identification of amino acids undergoing a charge shift with the determination of affected noncovalent bonds at two user-defined pH values. At the sequence-only level, patcHwork applies the Henderson–Hasselbalch equation to determine pH-sensitive residues. When the 3D protein structure is available, patcHwork can be employed to gain mechanistic understanding of the effect of pH. This is achieved using the PDB2PQR and PROPKA tools and noncovalent bond determination algorithms. A user-friendly interface allows visualizing pH-sensitive residues, affected salt bridges, hydrogen bonds and aromatic (pi–pi and cation–pi) interactions. patcHwork can be used to identify patches, a new concept we propose of pH-sensitive residues in close proximity on the protein, which may have a major impact on function. We demonstrate the attractiveness of patcHwork studying experimentally investigated pH-sensitive proteins (https://patchwork.biologie.uni-freiburg.de/).
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs
Authors: Boytsov Alexandr , Abramov Sergey , Aiusheeva Ariuna Z , Kasianova Alexandra M , Baulin Eugene , Kuznetsov Ivan A , Aulchenko Yurii S , Kolmykov Semyon , Yevshin Ivan , Kolpakov Fedor , Vorontsov Ilya E , Makeev Vsevolod J , Kulakovskiy Ivan V 
Published: April 2022

AbstractWe present ANANASTRA, https://ananastra.autosome.org, a web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with allele-specific binding events. ANANASTRA accepts a list of dbSNP IDs or a VCF file and reports allele-specific binding (ASB) sites of particular transcription factors or in specific cell types, highlighting those with ASBs significantly enriched at SNPs in the query list. ANANASTRA is built on top of a systematic analysis of allelic imbalance in ChIP-Seq experiments and performs the ASB enrichment test against background sets of SNPs found in the same source experiments as ASB sites but not displaying significant allelic imbalance. We illustrate ANANASTRA usage with selected case studies and expect that ANANASTRA will help to conduct the follow-up of GWAS in terms of establishing functional hypotheses and designing experimental verification.
DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes
Authors: Mohammadi-Arani Razieh , Javadi-Zarnaghi Fatemeh , Boccaletto Pietro , Bujnicki Janusz M , Ponce-Salvatierra Almudena 
Published: April 2022

Abstract
Nucleic acid cleaving DNAzymes are versatile and robust catalysts that outcompete ribozymes and protein enzymes in terms of chemical stability, affordability and ease to synthesize. In spite of their attractiveness, the choice of which DNAzyme should be used to cleave a given substrate is far from obvious, and requires expert knowledge as well as in-depth literature scrutiny. DNAzymeBuilder enables fast and automatic assembly of DNAzymes for the first time, superseding the manual design of DNAzymes. DNAzymeBuilder relies on an internal database with information on RNA and DNA cleaving DNAzymes, including the reaction conditions under which they best operate, their kinetic parameters, the type of cleavage reaction that is catalyzed, the specific sequence that is recognized by the DNAzyme, the cleavage site within this sequence, and special design features that might be necessary for optimal activity of the DNAzyme. Based on this information and the input sequence provided by the user, DNAzymeBuilder provides a list of DNAzymes to carry out the cleavage reaction and detailed information for each of them, including the expected yield, reaction products and optimal reaction conditions. DNAzymeBuilder is a resource to help researchers introduce DNAzymes in their day-to-day research, and is publicly available at https://iimcb.genesilico.pl/DNAzymeBuilder.
Riboswitch-inspired toehold riboregulators for gene regulation in Escherichia coli
Authors: Wang Tianhe , Simmel Friedrich C 
Published: April 2022

Abstract
Regulatory RNA molecules have been widely investigated as components for synthetic gene circuits, complementing the use of protein-based transcription factors. Among the potential advantages of RNA-based gene regulators are their comparatively simple design, sequence-programmability, orthogonality, and their relatively low metabolic burden. In this work, we developed a set of riboswitch-inspired riboregulators in Escherichia coli that combine the concept of toehold-mediated strand displacement (TMSD) with the switching principles of naturally occurring transcriptional and translational riboswitches. Specifically, for translational activation and repression, we sequestered anti-anti-RBS or anti-RBS sequences, respectively, inside the loop of a stable hairpin domain, which is equipped with a single-stranded toehold region at its 5′ end and is followed by regulated sequences on its 3′ side. A trigger RNA binding to the toehold region can invade the hairpin, inducing a structural rearrangement that results in translational activation or deactivation. We also demonstrate that TMSD can be applied in the context of transcriptional regulation by switching RNA secondary structure involved in Rho-dependent termination. Our designs expand the repertoire of available synthetic riboregulators by a set of RNA switches with no sequence limitation, which should prove useful for the development of robust genetic sensors and circuits.
GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents
Authors: Kuechler Erich R , Jacobson Matthew , Mayor Thibault , Gsponer Jörg 
Published: April 2022

AbstractPhase separation-based condensate formation is a novel working paradigm in biology, helping to rationalize many important cellular phenomena including the assembly of membraneless organelles. Uncovering the functional impact of cellular condensates requires a better knowledge of these condensates’ constituents. Herein, we introduce the webserver GraPES (Granule Protein Enrichment Server), a user-friendly online interface containing the MaGS and MaGSeq predictors, which provide propensity scores for proteins’ localization into cellular condensates. Our webpage contains models trained on human (Homo sapiens) and yeast (Saccharomyces cerevisiae) stress granule proteins. MaGS utilizes experimentally-based protein features for prediction, whereas MaGSeq is an entirely protein sequence-based implementation. GraPES is implemented in HTML/CSS and Javascript and is freely available for public use at https://grapes.msl.ubc.ca/. Documentation for using the provided webtools, descriptions of their methodology, and implementation notes can be found on the webpage.
P-TEFb is degraded by Siah1/2 in quiescent cells
Authors: Huang Fang , Feng Yongmei , Peterlin B Matija , Fujinaga Koh 
Published: April 2022

Abstract
P-TEFb, composed of CycT1 and CDK9, regulates the elongation of transcription by RNA polymerase II. In proliferating cells, it is regulated by 7SK snRNA in the 7SK snRNP complex. In resting cells, P-TEFb is absent, because CycT1 is dephosphorylated, released from CDK9 and rapidly degraded. In this study, we identified the mechanism of this degradation. We mapped the ubiquitination and degradation of free CycT1 to its N-terminal region from positions 1 to 280. This region is ubiquitinated at six lysines, where E3 ligases Siah1 and Siah2 bind and degrade these sequences. Importantly, the inhibition of Siah1/2 rescued the expression of free CycT1 in proliferating as well as resting primary cells. We conclude that Siah1/2 are the E3 ligases that bind and degrade the dissociated CycT1 in resting, terminally differentiated, anergic and/or exhausted cells.
The flexible N-terminal motif of uL11 unique to eukaryotic ribosomes interacts with P-complex and facilitates protein translation
Authors: Yang Lei , Lee Ka-Ming , Yu Conny Wing-Heng , Imai Hirotatsu , Choi Andrew Kwok-Ho , Banfield David K , Ito Kosuke , Uchiumi Toshio , Wong Kam-Bo 
Published: April 2022

Abstract
Eukaryotic uL11 contains a conserved MPPKFDP motif at the N-terminus that is not found in archaeal and bacterial homologs. Here, we determined the solution structure of human uL11 by NMR spectroscopy and characterized its backbone dynamics by 15N–1H relaxation experiments. We showed that these N-terminal residues are unstructured and flexible. Structural comparison with ribosome-bound uL11 suggests that the linker region between the N-terminal domain and C-terminal domain of human uL11 is intrinsically disordered and only becomes structured when bound to the ribosomes. Mutagenesis studies show that the N-terminal conserved MPPKFDP motif is involved in interacting with the P-complex and its extended protuberant domain of uL10 in vitro. Truncation of the MPPKFDP motif also reduced the poly-phenylalanine synthesis in both hybrid ribosome and yeast mutagenesis studies. In addition, G→A/P substitutions to the conserved GPLG motif of helix-1 reduced poly-phenylalanine synthesis to 9–32% in yeast ribosomes. We propose that the flexible N-terminal residues of uL11, which could extend up to ∼25 Å from the N-terminal domain of uL11, can form transient interactions with the uL10 that help to fetch and fix it into a position ready for recruiting the incoming translation factors and facilitate protein synthesis.
Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome
Authors: Herzel Lydia , Stanley Julian A , Yao Chun-Chen , Li Gene-Wei 
Published: April 2022

Abstract
Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3’ status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median&gt;60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total cellular RNA, these intermediates are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications and differential expression analyses for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs.
SuperPred 3.0: drug classification and target prediction—a machine learning approach
Authors: Gallo Kathleen , Goede Andrean , Preissner Robert , Gohlke Bjoern-Oliver 
Published: April 2022

Abstract
Since the last published update in 2014, the SuperPred webserver has been continuously developed to offer state-of-the-art models for drug classification according to ATC classes and target prediction. For the first time, a thoroughly filtered ATC dataset, that is suitable for accurate predictions, is provided along with detailed information on the achieved predictions. This aims to overcome the challenges in comparing different published prediction methods, since performance can vary greatly depending on the training dataset used. Additionally, both ATC and target prediction have been reworked and are now based on machine learning models instead of overall structural similarity, stressing the importance of functional groups for the mechanism of action of small molecule substances. Additionally, the dataset for the target prediction has been extensively filtered and is no longer only based on confirmed binders but also includes non-binding substances to reduce false positives. Using these methods, accuracy for the ATC prediction could be increased by almost 5% to 80.5% compared to the previous version, and additionally the scoring function now offers values which are easily assessable at first glance. SuperPred 3.0 is publicly available without the need for registration at: https://prediction.charite.de/index.php.
“Pseudo-pseudogenes” in bacterial genomes: Proteogenomics reveals a wide but low protein expression of pseudogenes in Salmonella enterica
Authors: Feng Ye , Wang Zeyu , Chien Kun-Yi , Chen Hsiu-Ling , Liang Yi-Hua , Hua Xiaoting , Chiu Cheng-Hsun 
Published: April 2022

Abstract
Pseudogenes (genes disrupted by frameshift or in-frame stop codons) are ubiquitously present in the bacterial genome and considered as nonfunctional fossil. Here, we used RNA-seq and mass-spectrometry technologies to measure the transcriptomes and proteomes of Salmonella enterica serovars Paratyphi A and Typhi. All pseudogenes’ mRNA sequences remained disrupted, and were present at comparable levels to their intact homologs. At the protein level, however, 101 out of 161 pseudogenes suggested successful translation, with their low expression regardless of growth conditions, genetic background and pseudogenization causes. The majority of frameshifting detected was compensatory for -1 frameshift mutations. Readthrough of in-frame stop codons primarily involved UAG; and cytosine was the most frequent base adjacent to the codon. Using a fluorescence reporter system, fifteen pseudogenes were confirmed to express successfully in vivo in Escherichia coli. Expression of the intact copy of the fifteen pseudogenes in S. Typhi affected bacterial pathogenesis as revealed in human macrophage and epithelial cell infection models. The above findings suggest the need to revisit the nonstandard translation mechanism as well as the biological role of pseudogenes in the bacterial genome.
Novel intraoperative strategies for enhancing tumor control: Future directions
Authors: Haddad Alexander F , Aghi Manish K , Butowski Nicholas 
Published: April 2022

AbstractMaximal safe surgical resection plays a key role in the care of patients with gliomas. A range of technologies have been developed to aid surgeons in distinguishing tumor from normal tissue, with the goal of increasing tumor resection and limiting postoperative neurological deficits. Technologies that are currently being investigated to aid in improving tumor control include intraoperative imaging modalities, fluorescent tumor makers, intraoperative cell and molecular profiling of tumors, improved microscopic imaging, intraoperative mapping, augmented and virtual reality, intraoperative drug and radiation delivery, and ablative technologies. In this review, we summarize the aforementioned advancements in neurosurgical oncology and implications for improving patient outcomes.
Spinal brachytherapy
Authors: Mao Gordon , Theodore Nicholas 
Published: April 2022

Abstract
Brachytherapy remains an underrecognized and underutilized radiation therapy modality for the treatment of spinal tumors. This article summarizes the existing body of medical literature on the usage, indications, techniques, and outcomes of brachytherapy for the treatment of spine tumors. The disease pathology most commonly treated with brachytherapy is metastatic spine cancer, rather than primary bone tumors of the spine. Brachytherapy can be used alone, as percutaneous needle injections; however, it is more often used in conjunction with open surgery or cement vertebral body augmentation. Although the data are still relatively sparse, studies show consistent benefit from brachytherapy in terms of improvements in pain, function, local recurrence rate, and overall survival. Brachytherapy is also associated with a favorable complication profile.
Evaluation of magnetic resonance imaging-based radiomics characteristics for differentiation of benign and malignant peripheral nerve sheath tumors in neurofibromatosis type 1
Authors: Ristow Inka , Madesta Frederic , Well Lennart , Shenas Farzad , Wright Felicia , Molwitz Isabel , Farschtschi Said , Bannas Peter , Adam Gerhard , Mautner Victor F , Werner René , Salamon Johannes 
Published: April 2022

Abstract

Background
Patients with neurofibromatosis type 1 (NF1) develop benign (BPNST), premalignant atypical (ANF), and malignant (MPNST) peripheral nerve sheath tumors. Radiological differentiation of these entities is challenging. Therefore, we aimed to evaluate the value of a magnetic resonance imaging (MRI)-based radiomics machine-learning (ML) classifier for differentiation of these three entities of internal peripheral nerve sheath tumors in NF1 patients.

Methods
MRI was performed at 3T in 36 NF1 patients (20 male; age: 31 ± 11 years). Segmentation of 117 BPNSTs, 17 MPNSTs, and 8 ANFs was manually performed using T2w spectral attenuated inversion recovery sequences. One hundred seven features per lesion were extracted using PyRadiomics and applied for BPNST versus MPNST differentiation. A 5-feature radiomics signature was defined based on the most important features and tested for signature-based BPNST versus MPNST classification (random forest [RF] classification, leave-one-patient-out evaluation). In a second step, signature feature expressions for BPNSTs, ANFs, and MPNSTs were evaluated for radiomics-based classification for these three entities.

Results
The mean area under the receiver operator characteristic curve (AUC) for the radiomics-based BPNST versus MPNST differentiation was 0.94, corresponding to correct classification of on average 16/17 MPNSTs and 114/117 BPNSTs (sensitivity: 94%, specificity: 97%). Exploratory analysis with the eight ANFs revealed intermediate radiomic feature characteristics in-between BPNST and MPNST tumor feature expression.

Conclusion
In this proof-of-principle study, ML using MRI-based radiomics characteristics allows sensitive and specific differentiation of BPNSTs and MPNSTs in NF1 patients. Feature expression of premalignant atypical tumors was distributed in-between benign and malignant tumor feature expressions, which illustrates biological plausibility of the considered radiomics characteristics.
Tobacco Use Among Gender-Varying and Gender-Stable Adolescents and Adults Living in the United States
Authors: Kcomt Luisa , Evans-Polce Rebecca J , Engstrom Curtiss W , Boyd Carol J , Veliz Philip T , West Brady T , McCabe Sean Esteban 
Published: April 2022

Abstract

Introduction
This study examines the proportion of the United States adolescents and adults who are variable (ie, at least one change in gender identity) versus stable in their gender identities over time, and whether they differ significantly in their nicotine/tobacco use after adjusting for key covariates.

Methods
We fit multivariable logistic regression models to data from Waves 2–4 (2014/15–2016/18) of the Population Assessment of Tobacco and Health (PATH), a nationally representative study (n = 33 197 U.S. adolescents and adults aged ≥14 years). We examined associations of gender stability/variability over three waves with tobacco use at wave 4 (2016–2018). Differences in any past 30-day tobacco, cigarette, e-cigarette, other tobacco, and poly-tobacco use were assessed among cisgender-stable, transgender-stable, and gender-varying respondents.

Results
An estimated 1.0% of adolescents and adults were classified as gender-varying. Prevalence of any past 30-day tobacco use was higher among gender-varying individuals (42.7%) than among gender-stable individuals (transgender-stable, 37.8% and cisgender-stable, 26.7%). There were no significant differences in the odds of nicotine/tobacco use between the two gender-stable groups. However, gender-varying respondents had significant increased odds of any past 30-day tobacco use (adjusted odds ratio [AOR] = 2.0, 95% confidence interval [CI] = 1.3 to 3.0), cigarette use (AOR = 1.7, 95% CI = 1.1 to 2.5), e-cigarette use (AOR = 2.2, 95% CI = 1.4-3.5), other tobacco use (AOR = 2.2, 95% CI = 1.4 to 3.4), and poly-tobacco use (AOR = 2.0, 95% CI = 1.3 to 3.1) compared with cisgender-stable individuals.

Conclusions
Gender-varying individuals are at higher risk for nicotine/tobacco use, placing them at greater risk for tobacco-related health consequences.

Implications
Despite increased knowledge about transgender health in recent years, there remains a paucity of research about gender-varying individuals. This study is the first to examine the proportion of gender-varying individuals in the United States using a longitudinal, nationally representative sample and to explore differences in nicotine/tobacco use among gender-varying and gender-stable individuals. Our findings suggest that gender-varying people have an increased risk for nicotine/tobacco use, placing them at higher risk for tobacco-related health consequences. This study increases knowledge about nicotine/tobacco use among this under-represented population in research and underscores the importance of developing an awareness of gender diversity.