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Tan, Z.

Publications and source records attributed to Tan, Z..

At least 37 records · Page 2Linked to original sources

Targeted stimulation of motor cortex neural ensembles drives learned movements

During the execution of learned motor skills, the neural population in the layer 2/3 (L2/3) of the primary motor cortex (M1) expresses a reproducible spatiotemporal activity pattern. It is debated whether M1 actively participates in generating this activity pattern and whether this learned pattern causally drives the learned movement. To address these questions, we utilized in vivo two-photon calcium imaging combined with holographic optogenetic stimulation of functionally defined M1 L2/3 neuronal ensembles in mice performing a skilled lever-pressing task. A brief and synchronous stimulation of [~]20 neurons whose activity onset in voluntary trials precedes movement onsets induced movements that resembled the learned movement, while producing spatiotemporal activity patterns in other M1 neurons that resembled those during the voluntary learned movement. Moreover, trial-by-trial variability of optogenetically triggered population activity correlated with the variability in the induced movements. These trial-by-trial variabilities were predicted by the initial state of M1 population activity immediately preceding the stimulation. In some trials, the stimulation induced the learned activity without inducing overt movements, indicating that the learned activity is not simply a reflection of movements and instead can be induced internally. The stimulation failed to generate movements or learned activity when mice were disengaged from the task. Stimulation of the neurons whose activity followed voluntary movement onsets failed to induce the learned movement in task-engaged mice. Taken together, the learned activity pattern in M1 L2/3 can be generated when the M1 network is prepared at the optimal initial state and receives precise triggering inputs, supporting the active role of M1 in the generation of learned activity and learned movements.

neuroscience↗

G-Quadruplex-Protein Interactome at Human Gene Promoters

DNA-protein interactions at gene promoters play a critical role in gene expression. The promoters of human cells are highly enriched in guanine-rich sequences, which can form four-stranded G-quadruplex (G4) structures. G4s are emerging as a distinct class of structure-based regulatory elements in gene regulation, and their interaction with proteins is essential for the role G4s play. Currently, our understanding of G4-protein interaction is mainly on a case-by-case basis, without systematic information. In this work, we examined the spatial occupancy of 1,183 human DNA-binding proteins, including transcription factors, histones and their modifying enzymes, around the consensus G4-forming region, G4(+), using data from the ENCODE project. We found that the G4(+), its immediate proximal side, and its distal side serve as three primary protein binding sites. Nearly all proteins are either enriched or depleted at these sites, likely due to competition, or in a spatiotemporal transition between the sites, resulting in different degrees of variation or persistence within or across cell/tissue types. Notably, histones were excluded from the proximal side of G4(+), and their binding to G4(+) was turned on and off by acetylation and methylation, respectively. Furthermore, the distal side is preferentially enriched for H3K23me2 and H3K4me2. Our experiments also revealed corresponding patterns of G4-protein interaction. Taken together, our results suggest a general role for G4s in dynamically defining and coordinating chromatin architecture and DNA-protein interactions at gene promoters for transcriptional regulation, a task that is unlikely to be accomplished by sequence-based DNA recognition. O_FIG O_LINKSMALLFIG WIDTH=175 HEIGHT=200 SRC="FIGDIR/small/630896v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1eb0b6eorg.highwire.dtl.DTLVardef@3b7d63org.highwire.dtl.DTLVardef@1a4f4dborg.highwire.dtl.DTLVardef@c760f7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO A protein can be either enriched or suppressed at G-quadruplexes (G4s), at the proximal side of G4s, or enriched at the distal side of G4s in a 2 kb neighborhood. Regulatory roles of proteins may result from spatial transitions between the different binding regions. C_FIG

genomics↗

Dominant Formation of DNA:RNA Hybrid G-Quadruplexes in the Genomes of Living Human and Mouse Cells

Guanine-rich nucleic acids can form four-stranded structures known as G-quadruplexes (G4s), which play critical roles in essential cellular activities. Putative G-quadruplex-forming sequences (PQSs) are abundant in the genomes of animal cells. To date, research on G4s has focused primarily on intramolecular G4s formed by four contiguous G-tracts from the same nucleic acid strand. However, our recent study indicates that a hybrid type of G4s, DNA:RNA hybrid G4s (hG4s), comprising G-tracts from both DNA and RNA, is, in fact, the most abundant G4 species found in the genomes of living yeast cells. Here, we demonstrate that hG4s also readily form and predominate in the genomes of living human and mouse cells, with an abundance several orders of magnitude greater than that of intramolecular DNA G4s (dG4s). Furthermore, each individual G-tract in a PQS tends to form an hG4 independent of adjacent G-tracts. This independence of DNA G-tracts is maintained even in PQSs containing four G-tracts, despite their potential to form intramolecular DNA G4s only by themselves. Collectively, our studies demonstrate that hG4s are the predominant physiological G4 structures in the genomes of eukaryotic organisms. Given that hG4s differ significantly from intramolecular dG4s in terms of structural form, formation mechanism, abundance, and association with transcription, there is a clear need for a comprehensive revision of our current understanding of genomic G4s and their functional roles. We hypothesize that hG4 formation may serve as a global sensing mechanism to monitor RNA levels in cells to maintain transcriptional homeostasis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/630557v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@6a9f0org.highwire.dtl.DTLVardef@17f02f8org.highwire.dtl.DTLVardef@19bfd10org.highwire.dtl.DTLVardef@34f4b_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Time-resolved fluorescent proteins towards fluorescence microscopy in the temporal and spectral domains

Fluorescence microscopy has been widely applied in life sciences. While steady-state fluorescence intensity is mostly used, the time-resolved detection mode relying on fluorescence lifetime remains underexplored. Herein, we present a family of time-resolved fluorescent proteins (TRFP). Using a strategy that regulates lifetime without affecting spectra of FPs, we have developed different TRFPs that cover the visible spectrum and a wide range of lifetime. TRFPs are employed in the temporal-spectral resolved microscopy, allowing the simultaneous imaging of 9 different proteins in live cells and correlation of multiple activities to cell cycles. Finally, TRFPs are integrated into multiplexing super-resolution microscopy to concurrently visualize 4 proteins in live cells, acquiring a remarkable 50 nm spatial resolution using lifetime as signal. TRFPs represent a transformative toolset towards fluorescence microscopy in both the temporal and spectral domains. Beyond the multiplexing imaging, TRFPs could introduce unprecedented opportunities of system complexity and quantitative accuracy into biological research.

biochemistry↗

DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences

MotivationRNA structure is essential for the function of many non-coding RNAs. Using multiple homologous sequences, which share structure and function, secondary structure can be predicted with much higher accuracy than with a single sequence. It can be difficult, however, to establish a set of homologous sequences when their structure is not yet known. We developed a method to identify sequences in a set of putative homologs that are in fact non-homologs. ResultsPreviously, we developed TurboFold to estimate conserved structure using multiple, unaligned RNA homologs. Here, we report that the positive predictive value of TurboFold is significantly reduced by the presence of contamination by non-homologous sequences, although the reduction is less than 1%. We developed a method called DecoyFinder, which applies machine learning trained with features determined by TurboFold, to detect sequences that are not homologous with the other sequences in the set. This method can identify approximately 45% of non-homologous sequences, at a rate of 5% misidentification of true homologous sequences. AvailabilityDecoyFinder and TurboFold are incorporated in RNAstructure, which is provided for free and open source under the GPL V2 license. It can be downloaded at http://rna.urmc.rochester.edu/RNAstructure.html

bioinformatics↗

BDNF augmentation reverses cranial radiation therapy-induced cognitive decline and neurodegenerative consequences

Cranial radiation therapy (RT) for brain cancers is often associated with the development of radiation-induced cognitive dysfunction (RICD). RICD significantly impacts the quality of life for cancer survivors, highlighting an unmet medical need. Previous human studies revealed a marked reduction in plasma brain-derived neurotrophic factor (BDNF) post-chronic chemotherapy, linking this decline to a substantial cognitive dysfunction among cancer survivors. Moreover, riluzole (RZ)-mediated increased BDNF in vivo in the chemotherapy-exposed mice reversed cognitive decline. RZ is an FDA-approved medication for ALS known to increase BDNF in vivo. In an effort to mitigate the detrimental effects of RT-induced BDNF decline in RICD, we tested the efficacy of RZ in a cranially irradiated (9 Gy) adult mouse model. Notably, RT-exposed mice exhibited significantly reduced hippocampal BDNF, accompanied by increased neuroinflammation, loss of neuronal plasticity-related immediate early gene product, cFos, and synaptic density. Spatial transcriptomic profiling comparing the RT+Veh with the RT+RZ group showed gene expression signatures of neuroprotection of hippocampal excitatory neurons post-RZ. RT-exposed mice performed poorly on learning and memory, and memory consolidation tasks. However, irradiated mice receiving RZ (13 mg/kg, drinking water) for 6-7 weeks showed a significant improvement in cognitive function compared to RT-exposed mice receiving vehicle. Dual-immunofluorescence staining, spatial transcriptomics, and biochemical assessment of RZ-treated irradiated brains demonstrated preservation of synaptic integrity and neuronal plasticity but not neurogenesis and reduced neuroinflammation concurrent with elevated BDNF levels and transcripts compared to vehicle-treated irradiated brains. In summary, oral administration of RZ represents a viable and translationally feasible neuroprotective approach against RICD.

neuroscience↗

Spatiotemporal Patterns of Gene Expression During Development of a Complex Colony Morphology

Clonal communities of single celled organisms, such as bacterial or fungal colonies and biofilms, are spatially structured, with subdomains of cells experiencing differing environmental conditions. In the development of such communities, cell specialization is not only important to respond and adapt to the local environment but has the potential to increase the fitness of the clonal community through division of labor. Here, we examine colony development in a yeast strain (F13) that produces colonies with a highly structured "ruffled" phenotype in the colony periphery and an unstructured "smooth" phenotype in the colony center. We demonstrate that in the F13 genetic background deletions of transcription factors can either increase (dig1{Delta}, sfl1{Delta}) or decrease (tec1{Delta}) the degree of colony structure. To investigate the development of colony structure, we carried out gene expression analysis on F13 and the three deletion strains using RNA-seq. Samples were taken early in colony growth (day2), which precedes ruffled phenotype development in F13, and from the peripheral and central regions of colonies later in development (day5), at which time these regions are structured and unstructured (respectively) in F13. We identify genes responding additively and non-additively to the genotype and spatiotemporal factors and cluster these genes into a number of different expression patterns. We identify clusters whose expression correlates closely with the degree of colony structure in each sample and include genes with known roles in the development of colony structure. Individual deletion of 26 genes sampled from different clusters identified 5 with strong effects on colony morphology (BUD8, CIS3, FLO11, MSB2 and SFG1), all of which eliminated or greatly reduced the structure of the F13 outer region.

genetics↗

Inhibition of Inflammatory Osteoclasts Enhances CGRP+TrkA+ Signaling and Accelerates Callus Remodeling in Osteoporotic Fractures

Impaired callus remodeling significantly contributes to the delayed healing of osteoporotic fractures; however, the underlying mechanisms remain unclear. Sensory neuronal signaling plays a crucial role in bone repair. In this study, we demonstrate that in ovariectomized (OVX) mice, the loss of CGRP+TrkA+ sensory neuronal signaling during callus remodeling correlates with increased Cx3cr1+iOCs expression within the bone callus. Conditional knockout of Cx3cr1+iOCs restored CGRP+TrkA+ sensory neuronal, enabling normal callus remodeling progression. Mechanistically, we further demonstrate that Cx3cr1+iOCs secrete seme3A in the osteoporotic fracture repair microenvironment, inhibiting CGRP+TrkA+ sensory neurons axonal regeneration and suppressing nerve-bone signaling exchange, thus hindering bone remodeling. Lastly, in human samples, we observed an association between the loss of CGRP+TrkA+ sensory neuronal signaling and increased expression of Cx3cr1+iOCs. In conclusion, enhancing CGRP+TrkA+ sensory nerve signaling by inhibiting Cx3cr1+iOCs activity presents a potential strategy for treating delayed healing in osteoporotic fractures.

pathology↗

scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution

Single-cell RNA-seq (scRNA-seq) is a powerful technique for decoding the complex cellular compositions in the tumor microenvironment (TME). As previous studies have defined many meaningful cell subtypes in several tumor types, there is a great need to computationally transfer these labels to new datasets. Also, different studies used different approaches or criteria to define the cell subtypes for the same major cell lineages. The relationships between the cell subtypes defined in different studies should be carefully evaluated. In this updated package scCancer2, designed for integrative tumor scRNA-seq data analysis, we developed a supervised machine learning framework to annotate TME cells with annotated cell subtypes from 15 scRNA datasets with 594 samples in total. Based on the trained classifiers, we quantitatively constructed the similarity maps between the cell subtypes defined in different references by testing on all the 15 datasets. Secondly, to improve the identification of malignant cells, we designed a classifier by integrating large-scale pan-cancer TCGA bulk gene expression datasets and scRNA-seq datasets (10 cancer types, 159 samples, 652,160 cells). This classifier shows robust performances when no internal confidential reference cells are available. Thirdly, this package also integrated a module to process the seq-based spatial transcriptomic data and analyze the spatial features of TME. Software availability: http://lifeome.net/software/sccancer2/.

bioinformatics↗

Gut microbiota-derived gamma-aminobutyric acid from metformin treatment reduces hepatic ischemia/reperfusion injury through inhibiting ferroptosis.

Hepatic ischemia/reperfusion injury (HIRI) is a common and inevitable factor leading to poor prognosis in various liver diseases, making the outcomes of current treatments in clinic unsatisfactory. Metformin has been demonstrated to be beneficial to alleviate HIRI in recent studies, however, the underpinning mechanism remains unclear. In this study, we found metformin mitigates HIRI-induced ferroptosis through reshaped gut microbiota in mice, which was confirmed by the results of fecal microbiota transplantation (FMT) treatment but showed the elimination of the beneficial effects when gut bacteria were depleted using antibiotics. Detailedly, through 16S rRNA and metagenomic sequencing, we identified that the metformin-reshaped microbiota was characterized by the increase of gamma-aminobutyric acid (GABA) producing bacteria. This increase was further confirmed by the elevation of GABA synthesis key enzymes, glutamic acid decarboxylase (GAD) and putrescine aminotransferase (PAT), in gut microbes of metformin-treated mice and healthy volunteers. Furthermore, the benefit of GABA against HIRI-induced ferroptosis was demonstrated in GABA-treated mice. Collectively, our data indicate that metformin can mitigate HIRI-induced ferroptosis by reshaped gut microbiota, with GABA identified as a key metabolite.

microbiology↗

Discovery and Engineering of the L-Threonine Aldolase from Neptunomonas Marine for Efficient Synthesis of β-Hydroxy-α-Amino Acids via C-C Formation

O_SCPLOWLC_SCPLOW-Threonine aldolases (LTAs) are attractive biocatalysts for synthesizing {beta}-hydroxy--amino acids (HAAs) via C-C bond formation in pharmaceuticals, although their industrial applications suffer from low activity and diastereoselectivity. Herein, we describe the discovery of a new LTA from Neptunomonas marine (NmLTA) that displays both ideal enzymatic activity (64.8 U/mg) and diastereoselectivity (89.5% diastereomeric excess; de) for the desired product O_SCPLOWLC_SCPLOW-threo-4-methylsulfonylphenylserine (O_SCPLOWLC_SCPLOW-threo-MPTS). Using X-ray crystallography, site-directed mutagenesis, and computational modeling, we propose a "dual-conformation" mechanism for the diastereoselectivity control of NmLTA, whereby the incoming 4-methylsulfonylbenzaldehyde (4-MTB) could potentially bind at the NmLTA active site in two distinct orientations, potentially forming two diastereoisomers (threo- or erythro-form products). Importantly, two key NmLTA residues H140 and Y319 play critical roles in fine-tuning the binding mode of 4-MTB, supported by our site-mutagenesis assays. Uncovering of the catalytic mechanism in NmLTA guides us to further improve the diastereoselectivity of this enzyme. A triple variant of NmLTA (N18S/Q39R/Y319L; SRL) exhibited both improved diastereoselectivity (de value > 99%) and enzymatic activity (95.7 U/mg) for the synthesis of O_SCPLOWLC_SCPLOW-threo-MPTS compared with that of wild type. The preparative gram-scale synthesis for O_SCPLOWLC_SCPLOW-threo-MPTS with the SRL variant produced a space-time yield of up to 9.0 g L-1h-1, suggesting a potential role as a robust C-C bond synthetic tool for industrial synthesis of HAAs at a preparative scale. Finally, the SRL variant accepted a wider range of aromatic aldehyde derivatives as substrates and exhibited improved diastereoselectivity toward para-site substituents. This work provides deep structural insights into the molecular mechanism underlying the catalysis in NmLTA and pinpoints the key structural motifs responsible for regulating the diastereoselectivity control, thereby guiding future attempts for protein engineering of various LTAs from different sources.

biochemistry↗

Cationic Polymers Enable Internalization of Negatively Charged Chemical Probe into Bacteria

The bacterial cell envelope provides a protective barrier that is challenging for small molecules and biomolecules to cross. Given the anionic nature of both Gram-positive and Gramnegative bacterial cell envelopes, negatively charged molecules are particularly difficult to deliver into these organisms. Many strategies have been employed to penetrate bacteria ranging from reagents such as cell-penetrating peptides, enzymes, and metal-chelating compounds, to physical perturbations. While cationic polymers are known antimicrobial agents, their ability to permeabilize bacterial cells without causing high levels of toxicity and cell lysis has not been demonstrated. Here, we evaluate the ability of four cationic polymers, two linear and two micellar (from self-assembled amphiphilic block copolymers), to facilitate the internalization of an anionic ATP-based chemical probe into Escherichia coli and Bacillus subtilis. Not only did we observe the permeabilization of these organisms, but also found that labeled cells were able to continue to grow and divide. In particular, the micelle-based polymers yielded effective internalization of the negatively charged chemical probe better than their linear analogues.

microbiology↗

Genome-Wide Formation of DNA:RNA Hybrid G-Quadruplexes in Live Yeast Cells

Guanine-rich nucleic acids form G-quadruplex (G4) structures that play a critical role in cellular processes. Previous studies have mostly focused on monomeric intramolecular G4s with four consecutive guanine tracts (G-tracts) from a single strand. However, this structural form has never been confirmed in eukaryotic cells. Here, we report the formation of hybrid G4s (hG4s), consisting of G-tracts from both DNA and RNA, in the genome of living yeast cells. Analysis of Okazaki fragment syntheses and G4-specific probing reveals that hG4s can efficiently form with as few as a single DNA guanine-guanine (GG) tract due to the participation of G-tracts from RNA. This finding increases the number of G4-forming sites in the yeast genome from 38 to 587,694, a more than 15,000-fold increase. Interestingly, hG4s still form and even dominate at genomic G4 sites that are theoretically capable of forming the monomeric intramolecular DNA G4s by themselves. Compared to DNA G4s (dG4s), hG4s exhibit a wider range of kinetics, higher prevalence, and greater structural diversity and stability. Most importantly, hG4 formation is tightly coupled to transcription through the involvement of RNA, allowing hG4s to function in a transcription-dependent manner. Overall, our study establishes hG4s as the overwhelmingly dominant G4 species in the yeast genome and emphasizes a renewal of the current perception of the structural form, formation mechanism, prevalence, and functional role of G4s in eukaryotic genomes. It also provides a sensitive and currently the only method for detecting the structural form of G4s in living cells. SignificanceThe identification of hybrid G-quadruplexes (hG4s) has disclosed a previously unrecognized structural form of G4s as the most common and abundant G4 species in the yeast genome. It reveals not only a dominant rule governing the formation of G4s in eukaryotic genomes, but also a unique genotype that allows G4-mediated transcriptional regulation to take feedback from the output as input, thus allowing the creation of feedback loops at the transcriptome scale.

biochemistry↗

Autoinhibited kinesin-1 adopts a hierarchical folding pattern

Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 remains unknown. Here, we combine cross-linking mass spectrometry (XL-MS), electron microscopy (EM), and AlphaFold structure prediction to determine the architecture of the full-length autoinhibited kinesin-1 homodimer [kinesin-1 heavy chain (KHC)] and kinesin-1 heterotetramer [KHC bound to kinesin light chain 1 (KLC1)]. Our integrative analysis shows that kinesin-1 forms a compact, bent conformation through a break in coiled coil 3. Moreover, our XL-MS analysis demonstrates that kinesin light chains stabilize the folded inhibited state rather than inducing a new structural state. Using our structural model, we show that disruption of multiple interactions between the motor, stalk, and tail domains is required to activate the full-length kinesin-1. Our work offers a conceptual framework for understanding how cargo adaptors and microtubule-associated proteins relieve autoinhibition to promote activation.

biophysics↗

Comparison of DNA targeting CRISPR editors in human cells

Profiling and comparing the performance of current widely used DNA targeting CRISPR systems provide the basic information for the gene-editing toolkit and can be a useful resource for this field. Herein we made a parallel comparison between the recently reported miniature Cas12f1 and the widely used Cas12a and Cas9 nucleases in mammalian cells. The results revealed that as a CRISPRa activator, Un1Cas12f1 could induce gene expression with a comparable level to these of Cas12a and Cas9, while as a cleaving editor, Cas12f1 exhibited similar properties to Cas12a, like high specificity and dominantly induced deletions over insertions, but with less activity. In contrast, wild-type SpCas9 showed the highest activity, lowest specificity, and induced balanced deletions over insertions. Thus, Cas12f1 is recommended for gene-activation-based applications, Cas12a is for therapy applications, and wild-type Cas9 is for in vitro and animal investigations. The comparison provided the editing properties of current widely used DNA-targeting CRISPR systems for the gene-editing field.

synthetic biology↗

MMP14 cleaves PTH1R in the chondrocyte derived osteoblast lineage, curbing signaling intensity for proper bone anabolism

Bone homeostasis is regulated by hormones such as parathyroid hormone (PTH). While PTH can stimulate osteo-progenitor expansion and bone synthesis, how PTH-signaling intensity in progenitors is controlled is unclear. Endochondral bone osteoblasts arise from perichondrium-derived osteoprogenitors and hypertrophic chondrocytes (HC). We found, via single-cell transcriptomics, HC descendent cells activate membrane-type 1 metalloproteinase 14 (MMP14) and the PTH pathway as they transition to osteoblasts in neonatal and adult mice. Unlike Mmp14 global knockouts, HC lineage-specific Mmp14 null mutants (Mmp14{Delta}HC) produce more bone. Mechanistically, MMP14 cleaves the extracellular domain of PTH1R, dampening PTH signaling and PTH signaling is enhanced in Mmp14{Delta}HC mutants. We found HC-derived osteoblasts contribute [~]50% of osteogenesis promoted by treatment with PTH 1-34 and this response was amplified in Mmp14{Delta}HC. MMP14 control of PTH signaling likely applies also to both HC- and non- HC-derived osteoblasts because their transcriptomes are highly similar. Our study identifies a novel paradigm of MMP14 activity-mediated titration of PTH signaling in the osteoblast lineage, contributing new insights into bone metabolism with therapeutic significance for bone-wasting diseases.

developmental biology↗

Maps of high density microsatellites accumulation in human genome

BackgroundMicrosatellites are increasingly realized to have biological significance in human genome and health in past decades, the assembled complete reference sequence of human genome T2T-CHM13 brought great help for a comprehensive study of short tandem repeats in the human genome. ResultsMicrosatellites density landscapes of all 24 chromosomes were built here for the first complete reference sequence of human genome T2T-CHM13. These landscapes showed that short tandem repeats (STRs) are prone to aggregate characteristically to form a large number of STRs density peaks. We classified 8,823 High Microsatellites Density Peaks (HMDPs), 35,257 Middle Microsatellites Density Peaks (MMDPs) and 199, 649 Low Microsatellites Density Peaks (LMDPs) on the 24 chromosomes; and also classified the motif types of every microsatellites density peak. These STRs density aggregation peaks are mainly composing of a single motif, and AT is the most dominant motif, followed by AATGG and CCATT motifs. And 514 genomic regions were characterized by microsatellite density feature in the full T2T-CHM13 genome. ConclusionsThese landscape maps exhibited that microsatellites aggregate in many genomic positions to form a large number of microsatellite density peaks with composing of mainly single motif type in the complete reference genome, indicating that the local microsatellites density varies enormously along the every chromosome of T2T-CHM13.

bioinformatics↗

Sequential increase of PHGDH expression with Alzheimer's pathology and symptoms

We report consistent increases in phosphoglycerate dehydrogenase (PHGDH) expression in mouse models of Alzheimers disease (AD) (3xTg-AD) and related tauopathy (PS19), particularly in hippocampal astrocytes. Human single-cell RNA-sequencing data reveal a sequential increase of PHGDH expression in people with no, early, and late AD pathology, which is corroborated by protein mass spectrometry and immunohistochemical analyses of three independent cohorts. A sequential increase of PHGDH expression also correlates with increasing clinical AD symptoms and worsening cognitive decline in patients. The consistent increase of PHGDH expression in six AD cohorts (Mayo, ROSMAP, Mount Sinai, Baltimore, Amsterdam, and UCSD/UCI) corroborates with the recent report of PHGDH extracellular RNA in blood plasma as a candidate biomarker for early diagnosis of AD and offers a caution to the suggested use of L-serine as a potential therapy of AD.

neuroscience↗