bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two-photon patterned photostimulation with low-power, high-efficiency and reliable single-cell optogenetic control
Authors: Wang Yifan , Zheng Yao , Xu Yongxian , Li Rongrong , Zheng Yameng , Chen Jiajia , Li Xiaoming , Hu Hailan , Duan Shumin , Gong Wei , Si Ke 
Published: January 2022

ABSTRACTTwo-photon optogenetics enables selectively stimulating individual cells for manipulating neuronal ensembles. As the general photostimulation strategy, the patterned two-photon excitation has enabled millisecond-timescale activation for single or multiple neurons, but its activation efficiency is suffered from high laser power due to low beam-modulation efficiency. Here, we develop a high- efficiency beam-shaping method based on the Gerchberg-Saxton (GS) algorithm with spherical-distribution initial phase (GSSIP) to reduce the patterned two-photon excitation speckles and intensity. It can well control the phase of shaped beams to attain speckle-free accurate patterned illumination with an improvement of 44.21% in the modulation efficiency compared with that of the traditional GS algorithm. A combination of temporal focusing and the GSSIP algorithm (TF-GSSIP) achieves patterned focusing through 500-μm-thickness mouse brain slices, which is 2.5 times deeper than the penetration depth of TF-GS with the same signal-to-noise ratio (SNR). With our method, the laser power can be reduced to only 55.56% of that with traditional method (the temporal focusing with GS, TF-GS) to reliably evoke GCaMP6s response in C1V1-expressing cultured neurons with single-cell resolution. Besides, the photostimulation efficiency is remarkably increased by 80.19% at the same excitation density of 0.27 mW/μm2. This two-photon stimulation method with low-power, reliable and patterned illumination may pave the way for analyzing neural circuits and neural coding and decoding mechanism.
Validating amino acid variants in proteogenomics using sequence coverage by multiple reads
Authors: Levitsky L.I. , Kuznetsova K.G. , Kliuchnikova A.A. , Ilina I.Y. , Goncharov A.O. , Lobas A.A. , Ivanov M.V. , Lazarev V.N. , Ziganshin R.H. , Gorshkov M.V. , Moshkovskii S.A. 
Published: January 2022

AbstractMass spectrometry-based proteome analysis usually implies matching mass spectra of proteolytic peptides to amino acid sequences predicted from nucleic acid sequences. At the same time, due to the stochastic nature of the method when it comes to proteome-wide analysis, in which only a fraction of peptides are selected for sequencing, the completeness of protein sequence identification is undermined. Likewise, the reliability of peptide variant identification in proteogenomic studies is suffering. We propose a way to interpret shotgun proteomics results, specifically in data-dependent acquisition mode, as protein sequence coverage by multiple reads, just as it is done in the field of nucleic acid sequencing for the calling of single nucleotide variants. Multiple reads for each position in a sequence could be provided by overlapping distinct peptides, thus, confirming the presence of certain amino acid residues in the overlapping stretch with much lower false discovery rate than conventional 1%. The source of overlapping distinct peptides are, first, miscleaved tryptic peptides in combination with their properly cleaved counterparts, and, second, peptides generated by several proteases with different specificities after the same specimen is subject to parallel digestion and analyzed separately. We illustrate this approach using publicly available multiprotease proteomic datasets and our own data generated for HEK-293 cell line digests obtained using trypsin, LysC and GluC proteases. From 5000 to 8000 protein groups are identified for each digest corresponding to up to 30% of the whole proteome coverage. Most of this coverage was provided by a single read, while up to 7% of the observed protein sequences were covered two-fold and more. The proteogenomic analysis of HEK-293 cell line revealed 36 peptide variants associated with SNP, seven of which were supported by multiple reads. The efficiency of the multiple reads approach depends strongly on the depth of proteome analysis, the digesting features such as the level of miscleavages, and will increase with the number of different proteases used in parallel proteome digestion.Graphical abstract
RNA binding to human METTL3-METTL14 restricts N6-deoxyadenosine methylation of DNA in vitro
Authors: Qi Shan , Mota Javier , Chan Siu-Hong , Villarreal Johanna , Dai Nan , Arya Shailee , Hromas Robert A. , Rao Manjeet K. , Corrêa Ivan R. , Gupta Yogesh K. 
Published: January 2022

AbstractMethyltransferase like-3 (METTL3) and METTL14 complex transfers a methyl group from S-adenosyl-L-methionine to N6 amino group of adenosine bases in RNA (m6A) and DNA (m6dA). Emerging evidence highlights a role of METTL3-METTL14 in the chromatin context, especially in processes where DNA and RNA are held in close proximity. However, a mechanistic framework about specificity for substrate RNA/DNA and their interrelationship remain unclear. By systematically studying methylation activity and binding affinity to a number of DNA and RNA oligos with different propensities to form inter- or intra-molecular duplexes or single-stranded molecules in vitro, we uncover an inverse relationship for substrate binding and methylation and show that METTL3-METTL14 preferentially catalyzes the formation of m6dA in single-stranded DNA (ssDNA), despite weaker binding affinity to DNA. In contrast, it binds structured RNAs with high affinity, but methylates the target adenosine in RNA (m6A) much less efficiently than it does in ssDNA. We also show that METTL3-METTL14-mediated methylation of DNA is largely regulated by structured RNA elements prevalent in long noncoding and other cellular RNAs.
Characterizing the performance of a DIY air filter
Authors: Porto Rachael Dal , Kunz Monet N. , Pistochini Theresa , Corsi Richard L. , Cappa Christopher D. 
Published: January 2022

AbstractAir filtration serves to reduce concentrations of particles in indoor environments. Most standalone, also referred to as portable or in-room, air filtration systems use HEPA filters, and cost generally scales with the clean air delivery rate. A “do-it-yourself” lower-cost alternative, known as the Corsi-Rosenthal Box, that uses MERV-13 filters coupled with a box fan has been recently proposed, but lacks systematic performance characterization. We have characterized the performance of a five-panel Corsi-Rosenthal air filter. Measurements of size-resolved and overall decay rates of aerosol particles larger than 0.5 microns emitted into rooms of varying size with and without the air filter allowed for determination of the apparent clean air delivery rate—both as a function of size and integrated across particle sizes. The measurements made in the different rooms produced similar results, demonstrating the robustness of the method used. The size-integrated apparent clean air delivery rate increases with fan speed, from about 600 to 850 ft3 min−1 (1019 to 1444 m3 h−1). Overall, our results demonstrate that the Corsi-Rosenthal filter efficiently reduces suspended particle concentrations in indoor environments.One Sentence SummaryA DIY air cleaner can effectively reduce aerosols in indoor spaces.
Transient interactions drive the lateral clustering of cadherin-23 on membrane
Authors: Srinivas Cheerneni S , Singaraju Gayathri S , Kaur Veerpal , Das Sayan , Ghosh Sanat K. , Sagar Amin , Kumar Anuj , Bhatia Tripta , Rakshit Sabyasachi 
Published: January 2022

AbstractCis and trans-interactions among cadherins secure multicellularity. While the molecular structure of trans-interactions of cadherins is well understood, identifying the molecular cues that spread the cis-interactions two-dimensionally is still ongoing. Here, we report that transient, weak, multivalent, and spatially distributed hydrophobic interactions, requisite for liquid-liquid phase separations of biomolecules in solution, alone can drive the lateral-clustering of cadherin-23 on a membrane. No specific cis-dimer interactions are required for the lateral clustering. In cellulo, the cis-clustering accelerates the cell-cell adhesion and, thus, contributes in cell-adhesion kinetics along with strengthening the junction. Although the physiological connection of cis-clustering with rapid adhesion is yet to be explored, M2-macrophages that predominantly express cadherin-23 undergo fast attachments to circulatory tumor cells during metastasis.
Long-term two-photon imaging of spinal cord in freely behaving mice
Authors: Ju Furong , Jian Wenling , Han Yaning , Huang Tianwen , Ke Jin , Liu Zhiheng , Cai Shengyuan , Liu Nan , Wang Liping , Wei Pengfei 
Published: January 2022

AbstractThe spinal cord is critical to the perception of peripheral information under sensory-guided motor behaviors in health and disease. However, the cellular activity underlie spinal cord function in freely behaving animals is not clear. Here, we developed a new method for imaging the spinal cord at cellular and subcellular resolution over weeks under naturalistic conditions. The method involves an improved surgery to reduce spinal movement, and the installation of a miniaturized two-photon microscope to obtain high-resolution imaging in moving mice. In vivo calcium imaging demonstrated that dorsal horn neurons show a sensorimotor program-dependent synchronization and heterogeneity under distinct cutaneous stimuli in behaving mice. The long-term imaging of sensory neurons revealed that in the spinal cord, healthy mice demonstrated stereotyped responses. However, in a neuropathic pain model, plasticity changes and neuronal sensitization were observed. We provide a practical method to study the function of spinal cord on sensory perception and disorders in freely behaving mice.
Identification of domestic cat hepadnavirus from a cat blood sample in Japan
Authors: Takahashi Kazuki , Kaneko Yasuyuki , Shibanai Akiko , Yamamoto Shushi , Katagiri Ayana , Osuga Tatsuyuki , Inoue Yoshiyuki , Kuroda Kohei , Tanabe Mika , Okabayashi Tamaki , Naganobu Kiyokazu , Minobe Isao , Saito Akatsuki 
Published: January 2022

ABSTRACTThe hepatitis B virus (Hepadnaviridae) induces chronic hepatitis and hepatic cancer in humans. A novel domestic cat hepadnavirus (DCH) was recently identified in several countries, however, the DCH infection status of cats in Japan is unknown. Therefore, we investigated the DCH infection rate of 139 cat samples collected in Japan. We identified one positive blood sample (0.78%) from a 17-year-old female cat with chronically elevated alanine aminotransferase. Phylogenetic analysis demonstrated that the DCH strain identified in this study is genetically distinct from strains in other countries. Further investigations are required to elucidate the evolution of DCH and the impact of DCH infection on hepatic diseases in domestic cats.
Systematic comparison of ranking aggregation methods for gene lists in experimental results
Authors: Wang Bo , Law Andy , Regan Tim , Parkinson Nicholas , Cole Joby , Russell Clark D. , Dockrell David H. , Gutmann Michael U. , Baillie J. Kenneth 
Published: January 2022

AbstractA common experimental output in biomedical science is a list of genes implicated in a given biological process or disease. The results of a group of studies answering the same, or similar, questions can be combined by meta-analysis to find a consensus or a more reliable answer. Ranking aggregation methods can be used to combine gene lists from various sources in meta-analyses. Evaluating a ranking aggregation method on a specific type of dataset before using it is required to support the reliability of the result since the property of a dataset can influence the performance of an algorithm. Evaluation of aggregation methods is usually based on a simulated database especially for the algorithms designed for gene lists because of the lack of a known truth for real data. However, simulated datasets tend to be too small compared to experimental data and neglect key features, including heterogeneity of quality, relevance and the inclusion of unranked lists. In this study, a group of existing methods and their variations which are suitable for meta-analysis of gene lists are compared using simulated and real data. Simulated data was used to explore the performance of the aggregation methods as a function of emulating the common scenarios of real genomics data, with various heterogeneity of quality, noise level, and a mix of unranked and ranked data using 20000 possible entities. In addition to the evaluation with simulated data, a comparison using real genomic data on the SARS-CoV-2 virus, cancer (NSCLC), and bacteria (macrophage apoptosis) was performed. We summarise our evaluation results in terms of a simple flowchart to select a ranking aggregation method for genomics data.
Exploitation of neighbouring subsoil for nutrient acquisition under annual-perennial strip intercropping systems
Authors: Han Eusun , Czaban Weronika , Dresbøll Dorte Bodin , Thorup-Kristensen Kristian 
Published: January 2022

AbstractLittle is known of how the deep root systems of perennial crops contribute to deeper and better resource use when intercropped with annuals in arable fields. Therefore, we aimed at measuring the capacity of perennial deep roots, alfalfa (Medicago sativa L.) and curly dock (Rumex crispus L.) to access the nutrient source located under the neighboring annuals at 1.0 and 2.5 m of soil depth. Alfalfa and curly dock were able to access the tracer-labelled source placed at a distance under the annual crop strips. As a result, the reliance on deeper soil layer for nutrient uptake under intercroppings became greater compared with sole-croppings. Combination of an annual cereal (winter rye) and a perennial legume (alfalfa) with contrasting root systems exhibited higher resource complementarity compared with intercroppings having similar root systems or absence of legumes. Our results demonstrated that the deep-rooted perennials when intercropped with annuals can induce vertical niche complementarity, especially at deeper soil layers. This was assumed to be due to the vertically stratified root activity between the crop components, however, the magnitude of the effects depended on choice of crop combinations, and on types of tracers. Future studies should include estimates such as relative yield total and land equivalent ratio to quantitatively determine the effects of resource acquisition under annual-perennial intercropping in arable fields.
Distinct sub-second dopamine signaling in dorsolateral striatum measured by a genetically-encoded fluorescent sensor
Authors: Salinas Armando G. , Lee Jeong O. , Augustin Shana M. , Zhang Shiliang , Patriarchi Tommaso , Tian Lin , Morales Marisela , Mateo Yolanda , Lovinger David M. 
Published: January 2022

AbstractDopamine produces neuromodulation throughout the basal ganglia, cortex and other brain regions, and is implicated in movement control, neural mechanisms of reward and actions of misused substances. The efferent projections of dopaminergic neurons with somata in the substantia nigra pars compacta and ventral tegmental area strongly innervate different striatal subregions. While much is known about the function of these neurons, there is a relative deficiency of information aboutin vivodopamine dynamics in the nigrostriatal projections, especially those to the dorsolateral striatum (DLS). In past studies, subsecond dopamine changes were measured predominantly with fast-scan cyclic voltammetry (FSCV) both in brain slices andin vivo. However, traditional FSCV has limitations in discriminating among catecholamines, and cannot be used for simultaneous measurement of both slow and fast/phasic dopamine changes. In addition, FSCV has been most useful for measuring dopamine in the ventral striatumin vivowith less utility for measurement in dorsolateral striatum. The development of genetically encoded dopamine sensors has provided a new approach to measuring slow and fast dopamine dynamics both in brain slices andin vivo, raising the hope of more facile measurement ofin vivodopamine measurements, including in areas where measurement was previously difficult with FSCV. To this end, we first evaluated dLight photometry in brain slices with simultaneous FSCV. We found that both techniques yielded comparable findings. However, differences were noted in responses to dopamine transporter inhibitors, including cocaine. We then usedin vivofiber photometry with dLight to examine responses to cocaine in DLS and compared responses during Pavlovian conditioning in DLS to two other striatal subregions. These experiments show that dopamine increases are readily detectable in DLS and provide new information about dopamine transient kinetics and slowly developing signaling during conditioning. Overall, our findings indicate that dLight photometry is well suited to measuring dopamine dynamics in a striatal region of great interest where such measurements were difficult previously.
Identification of a phage display-derived peptide interacting with the N-terminal region of Factor VII activating protease (FSAP) enables characterization of zymogen activation
Authors: Seidl Sebastian , Nielsen Nis Valentin , Escheid Michael , Haug Bengt Erik , Stensland Maria , Thiede Bernd , Declerck Paul J. , Åge Løset Geir , Kanse Sandip M. 
Published: January 2022

ABSTRACTIncreased Factor VII activating protease (FSAP) activity has a protective effect in diverse disease conditions as inferred from studies in FSAP−/− mice and humans deficient in FSAP activity due to a single nucleotide polymorphism. The activation of FSAP zymogen in plasma is mediated by extracellular histones that are released during tissue injury or inflammation or by positively charged surfaces. However, it is not clear if this activation mechanism is specific and amenable to manipulation. Using a phage display approach we have identified a peptide, NNKC9/41, that activates pro-FSAP in plasma. Other commonly found zymogens in the plasma were not activated. Binding studies with FSAP domain deletion mutants indicate that the N-terminus of FSAP is the key interaction site of this peptide. Blocking the contact pathway of coagulation did not influence pro-FSAP activation by the peptide. In a monoclonal antibody screen, we identified MA-FSAP-38C7 that prevented the activation of pro-FSAP by the peptide. This antibody bound to the LESLDP sequence (amino acids 30-35) in the N-terminus of FSAP. The plasma clotting time was shortened by NNKC9/41 and this was reversed by MA-FSAP-38C7 demonstrating the utility of this peptide. Identification of this peptide, and the corresponding interaction site, provides proof of principle that it is possible to activate a single protease zymogen in blood in a specific manner. Peptide NNKC/41 will be useful as a tool to delineate the molecular mechanism of activation of pro-FSAP in more detail, elucidate its biological role.Graphical abstract
Universality of Form: The Case of Retinal Cone Photoreceptor Mosaics
Authors: Beygi Alireza 
Published: January 2022

AbstractCone photoreceptor cells are wavelength-sensitive neurons in the retinas of vertebrate eyes and are responsible for color vision. The spatial distribution of these nerve cells is commonly referred to as cone photoreceptor mosaic. By applying the principle of maximum entropy, we demonstrate the universality of retinal cone mosaics in vertebrate eyes by examining various species, namely, rodent, dog, monkey, human, fish, and bird. We introduce a parameter called retinal temperature, which is conserved across the retinas of vertebrates. The virial equation of state for two-dimensional cellular networks, known as Lemaître’s law, is also obtained as a special case of our formalism. We investigate the behavior of several artificially generated networks and the natural one of the retina concerning this universal, topological law.
Structural and functional analysis of the human Cone-rod homeobox transcription factor
Authors: Clanor Penelope-Marie B. , Buchholz Christine , Hayes Jonathan E. , Friedman Michael A. , White Andrew M. , Enke Ray A. , Berndsen Christopher E. 
Published: January 2022

AbstractThe cone-rod homeobox (CRX) protein is a critical K50 homeodomain transcription factor responsible for the differentiation and maintenance of photoreceptor neurons in the vertebrate retina. Mutant alleles in the human gene encoding CRX result in a variety of distinct blinding retinopathies, including retinitis pigmentosa, cone-rod dystrophy, and Leber congenital amaurosis. Despite the success of using in vitro biochemistry, animal models, and genomics approaches to study this clinically relevant transcription factor over the past 24 years since its initial characterization, there are no high-resolution structures in the published literature for the CRX protein. In this study, we use bioinformatic approaches and small-angle x-ray scattering (SAXS) structural analysis to further understand the biochemical complexity of the human CRX homeodomain (CRX-HD). We find that the CRX-HD is a compact, globular monomer in solution that can specifically bind functional cis-regulatory elements encoded upstream of retina -specific genes. This study presents the first structural analysis of CRX, paving the way for a new approach to studying the biochemistry of this protein and its disease-causing mutant protein variants.
A quantitative analysis of the similarities and differences of the HIV/FIV gag genome
Authors: Siu Charlotte , Horn Meredith , Cheng Xiao-Wen 
Published: January 2022

1.AbstractAmong viruses, human immunodeficiency virus (HIV) presents the greatest challenge to humans. Here, we retrieved genome sequences from NCBI and were then run through LALIGN bioinformatics software to compute the E value, bit score, Waterman eggert score, and percent identity, which are four important indicators of how similar the sequences are. The E value was 3.1 x 10^-9, the percent identity was 54.4 percent, and the bit score was 51.9. It was also sensed that bases 1600 to 1990 in HIV and bases 800 to 910 in FIV have a higher than normal similarity. This reflects that while the DNA sequences of the gag region of both the HIV and FIV genomes are rather similar, it is unlikely that this similarity is due to random chance; therefore, there are a noticeable number of differences. A better understanding of the level of similarity and differences in the gag region of the genome sequence would facilitate our understanding of structural and cellular behavioral differences between FIV and HIV, and in the long term, it will provide new insights into the differences observed in previous studies or even facilitate the development of an effective HIV treatment.