Biology subjects

Xie, D.

Publications and source records attributed to Xie, D..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

High activity and high functional connectivity are mutually exclusive in resting state zebrafish and human brains

Active neurons impact cell types with which they are functionally connected. Both activity and functional connectivity are heterogeneous across the brain, but the nature of their relationship is not known. Here we employ brain-wide calcium imaging at cellular resolution in larval zebrafish to record spontaneous activity of >12,000 neurons in the forebrain. By classifying their activity and functional connectivity into three levels (high, medium, low), we find that highly active neurons have low functional connections and highly connected neurons are of low activity. Intriguingly, deploying the same analytical methods on functional magnetic resonance imaging (fMRI) data from the resting state human brain, we uncover a similar relationship between activity and functional connectivity, that is, regions of high activity are non-overlapping with those of high connectivity. These findings reveal a previously unknown and evolutionarily conserved brain organizational principle that have implications for understanding disease states and designing artificial neuronal networks.

neuroscience↗

bioRxiv2021

MicroRNA-202 safeguards meiotic progression by preventing premature degradation of REC8 mediated by separase

MicroRNAs (miRNAs) are believed to play important roles in mammalian spermatogenesis but the in vivo functions of single miRNAs in this highly complex developmental process remain unclear. Here, we reported that miR-202, a member of the let-7 family, played an important role in mouse spermatogenesis by phenotypic evaluation of miR-202 knockout (KO) mice. In miR-202 KO mice, germ cells underwent apoptosis. Multiple processes in meiosis I including synapsis and crossover formation were disrupted, and inter-sister chromatid synapses were detected. More importantly, we found that upon miR-202 KO, meiotic-specific cohesin protein REC8 was prematurely cleaved by precociously activated separase, whose mRNA was a direct target of miR-202-3p. Our findings identify miR-202 as a novel regulator of meiosis and contribute to the list of miRNAs that play specific and important roles in developmental processes.

developmental biology↗

bioRxiv2021

YAP1 induces invadopodia formation by transcriptionally activating TIAM1 through its enhancer in breast cancer

Yes-associated protein 1 (YAP1), a central component of the Hippo pathway, plays an important role in tumor metastasis; however, the mechanism remains to be elucidated. Here, we reported that YAP1 could induce invadopodia formation and promote tumor metastasis in breast cancer cells. We identified that TIAM1, the guanine nucleotide exchange factor, is a target of YAP1-TEAD4 complex. YAP1 promotes TEAD4 binding to the enhancer region of TIAM1, which activates TIAM1 expression and subsequently increases RAC1 activity. These findings reveal the functional role of Hippo signaling in invadopodia, and provide potential molecular targets for preventing tumor metastasis in breast cancer. SignificanceThrough regulating the enhancer region of TIAM1, YAP1 induces invadopodia formation and promotes tumor metastasis in breast cancer.

cancer biology↗

bioRxiv2021

Genomic architecture of 5S rDNA cluster and its variations within and between species

Ribosomal genes (rDNAs) are arranged in purely tandem repeats, preventing them from being reliably assembled onto chromosome. The uncertainty of rDNA genomic structure presents a significant barrier for studying their function and evolution. Here, we generate ultra-long Nanopore and short NGS reads to delineate the architecture and variation of the 5S rDNA cluster in the different strains of C. elegans and C. briggsae. We classify the individual rDNA units into 25 types based on the unique sequence variations in each unit of C. elegans (N2). We next perform manual assembly of the cluster using the long reads that carry these units, which led to an assembly of rDNA cluster consisting of up to 167 5S rDNA units. The ordering and copy number of various rDNA units are indicative of separation time between strains. Surprisingly, we observed a drastically lower level of variation in the 5S rDNA cluster in the C. elegans CB4856 and C. briggsae AF16 strains than C. elegans N2 strain, suggesting a unique mechanism in maintaining the rDNA cluster stability in the N2. Single-copy transgenes landed into the rDNA cluster shows the expected expression in the soma, supporting that rDNA genomic environment is transcriptionally compatible with RNA polymerase II. Delineating the structure and variation of rDNA cluster paves the way for its functional and evolutionary studies.

genomics↗

bioRxiv2021

MMP12 Knockout Prevent Weight and Muscle Loss Induced by Cancer Cachexia

Weight loss and muscle wasting can have devastating impacts on survival and quality of life of patients with cancer cachexia. Here, we have established a hybrid mouse of ApcMin/+ mice and MMP12 knockout mice (ApcMin/+; MMP12-/-) and found that knockout MMP12 can suppress the weight and muscle loss of ApcMin/+ mice. In detail, we found that interleukin 6 was highly upregulated in the serum of cancer patients and MMP12 was increased in muscle of tumor-bearing mice. Interestingly, the interleukin 6 secreted by tumor cells led to MMP12 overexpression in the macrophages, which further resulted in degradation of insulin and insulin-like growth factor 1 and interruption of glycolipid metabolism. Notably, depletion of MMP12 prevented weight loss of ApcMin/+ mice. Our study uncovers the critical role of MMP12 in controlling weight and highlights the great potential of MMP12 in the treatment of cancer cachexia.

cancer biology↗

bioRxiv2021

In vivo structure and dynamics of the RNA genome of SARS-Cov-2

The SARS-CoV-2 coronavirus, which causes the COVID-19 pandemic, is one of the largest positive strand RNA viruses. Here we developed a simplified SPLASH assay and comprehensively mapped the in vivo RNA-RNA interactome of SARS-CoV-2 RNA during the viral life cycle. We observed canonical and alternative structures including 3-UTR and 5-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in cells and in virions. We provide direct evidence of interactions between Transcription Regulating Sequences (TRS-L and TRS-Bs), which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE, forming a "high-order pseudoknot" embedding FSE, which might help ribosome stalling at frameshift sites. More importantly, we found that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome cyclization is weakened and genome domains remain stable. Our data provides a structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, describes dynamics of RNA structures during life cycle of SARS-CoV-2, and will help to develop antiviral strategies.

genomics↗

bioRxiv2020

Correlation and co-localization of QTL for stomatal density and canopy temperature under drought stress in Setaria

Mechanistic modeling indicates that stomatal conductance could be reduced to improve water use efficiency (WUE) in C4 crops. Genetic variation in stomatal density and canopy temperature was evaluated in the model C4 genus, Setaria. Recombinant inbred lines (RIL) derived from a Setaria italica x Setaria viridis cross were grown with ample or limiting water supply under field conditions in Illinois. An optical profilometer was used to rapidly assess stomatal patterning and canopy temperature was measured using infrared imaging. Stomatal density and canopy temperature were positively correlated but both were negatively correlated with total above-ground biomass. These trait relationships suggest a likely interaction between stomatal density and the other drivers of water use such as stomatal size and aperture. Multiple QTLs were identified for stomatal density and canopy temperature, including co-located QTLs on chromosomes 5 and 9. The direction of the additive effect of these QTLs on chromosome 5 and 9 were in accordance with the positive phenotypic relationship between these two traits. This suggests a common genetic architecture between stomatal patterning in the greenhouse and canopy transpiration in the field, while highlighting the potential of setaria as a model to understand the physiology and genetics of WUE in C4 species. HighlightThis article reports a phenotypic and genetic relationship between two water use related traits operating at leaf level and canopy level in a C4 model crop species.

plant biology↗

bioRxiv2019

Decorin inhibits glucose-induced lens epithelial cell apoptosis via suppressing p22phox-p38 MAPK signaling pathway

PurposeTo determine the effect of decorin on oxidative stress and apoptosis of human lens epithelial (HLE) cells under high glucose condition.\n\nMethodsHLE cell line (HLEB3) was incubated in normal glucose (5.5 mM) or high glucose (60 mM) medium. Decorin (50 nM) was applied 2 hours before high glucose medium was added. Apoptosis detection was executed by flow cytometry and western blotting (analysis of bcl-2 and bax). Oxidative stress level was measured by the generation of reactive oxygen species (ROS), glutathione peroxidase (GSH) and superoxide dismutase (SOD). P38 mitogen-activated protein kinase (MAPK) phosphorylation, the expression of p22phox of HLE cells and human lens anterior capsules were detected by western blotting. Small interfering RNA transfection to p22phox and p38 MAPK was also carried out on HLEB3.\n\nResultsHigh glucose caused HLE cells oxidative stress and apoptosis exhibiting the increase of apoptotic cells and ROS production and decrease of bcl-2/bax ratio, GSH/GSSG ration and SOD activity. P22phox and phospho-p38 MAPK were upregulated in high glucose treated HLEB3 cells. Knocking down p22phox or p38 by siRNAs can reduce high glucose induced cell apoptosis and oxidative stress level. Silencing p22phox by siRNA can downregulate p38 MAPK activation. Decorin can inhibit the apoptosis, oxidative stress level and the induction of p22phox and p-p38 of HLEB3 induced by high glucose. Furthermore, the expression of p22phox and p38 were found significantly increased in lens anterior capsules of diabetic cataract patients compared to that of normal age-related cataract patients.\n\nConclusionsResults showed that p22phox-p38 pathway may be particepated in high glucose induced lens epithelial cell injury, decorin may inhibit the high glucose induced apoptosis and oxidative stress injury by suppressing this pathway in part.

cell biology↗

bioRxiv2019

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

Cactus, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequence. We describe progressive extensions to Cactus that enable reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We show that Cactus is capable of scaling to hundreds of genomes and beyond by describing results from an alignment of over 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment yet created. Further, we show improvements in orthology resolution leading to downstream improvements in annotation.

genomics↗

bioRxiv2019

Highly efficient transgenesis with miniMos in Caenorhabditis briggsae

C. briggsae as a companion species for C. elegans has played an increasingly important role in study of evolution of development, gene regulation and genome. Aided by the isolation of its sister spices, it has recently been established as a model for speciation study. To take full advantage of the species for comparative study, an effective transgenesis method especially those with single copy insertion is important for functional comparison. Here we modified a transposon-based transgenesis methodology that had been originally developed in C. elegans but worked marginally in C. briggsae. By incorporation of a heat shock step, the transgenesis efficiency in C. briggsae with single copy insertion is comparable to that in C. elegans. We used the method to generate 54 independent insertions mostly consisting of a mCherry tag over the C. briggsae genome. We demonstrated the use of the tags in identifying interacting loci responsible for hybrid male sterility between C. briggsae and C. nigoni when combined with the GFP tags we generated previously. Finally, we demonstrated that C. briggsae has developed native immunity against the C. elegans toxin, PEEL-1, but not SUP-35, making the latter a potential negative selection marker against extrachromosomal array.\n\nSummaryNematode C. briggsae has been used for comparative study against C. elegans over decades. Importantly, a sister species has recently been identified, with which C. briggsae is able to mate and produce viable hybrid progeny. This opens the possibility of using nematode species as a model for speciation study for the first time. To take full advantage of C. briggsae for comparative study, an effective transgenesis method to generate single copy insertion is important especially for functional comparison. An attempt was made previously to generate single copy insertion with transposon-based transgenesis methodology, which had been originally developed in C. elegans but with limited success in C. briggsae. Here we modified the transposon-based methodology by incorporation of a heat shock step, which allows us to achieve a much higher transgenesis efficiency in C. briggsae with single copy insertion. We used the method to generate 54 independent insertions mostly consisting of a mCherry tag over the C. briggsae genome. We demonstrated the use of the tags in identifying interacting loci responsible for hybrid male sterility between C. briggsae and C. nigoni when combined with the GFP tags we generated previously. Finally, we demonstrated that C. briggsae has developed native immunity against the C. elegans toxin, PEEL-1, but not SUP-35, making the latter a potential negative selection marker against extrachromosomal array. Taken together, the modified transgenesis methodology and the transgenic strains generated in this study are expected to further facilitate C. briggsae as a model for comparative study or speciation study.

genetics↗

bioRxiv2018

Genome wide screen reveals a specific interaction between autosome and X that is essential for hybrid male sterility

Hybrid male progeny from interspecies cross are more prone to sterility or inviability than hybrid female progeny, and the male sterility and inviability often demonstrate a parent-of-origin asymmetry. However, the underlying mechanism of asymmetric sterility or inviability remains elusive. We previously established a genome-wide hybrid incompatibility (HI) landscape between Caenorhabditis briggsae and C. nigoni by phenotyping a large collection of C. nigoni strains each carrying a C. briggsae introgression. In this study, we investigate the genetic mechanism of asymmetric sterility and inviability in both hybrid male and female progeny between the two species. Specifically, we performed reciprocal crosses between C. briggsae and different C. nigoni strains that each carries a GFP-labeled C. briggsae genomic fragment referred to as introgression, and scored the HI phenotypes in the F1 progeny. The aggregated introgressions cover 94.6% of the C. briggsae genome, including 100% of the X chromosome. Surprisingly, we observed that two C. briggsae X fragments that produce C. nigoni male sterility as an introgression rescued hybrid F1 sterility in males fathered by C. briggsae, indicating that at least two separate X-autosome interactions are involved in the hybrid male sterility. In addition, we identified another two C. briggsae genomic intervals on the Chromosome II or IV, respectively, which can rescue the inviability, but not the sterility, of hybrid F1 males fathered by C. nigoni, suggesting the involvement of differential epistatic interactions in the asymmetric hybrid male fertility and inviability. Importantly, backcrossing of the rescued sterile males with C. nigoni led to isolation of a 1.1-Mb genomic interval that specifically interacts with an X-linked introgression, which is essential for hybrid male fertility. We further identified three C. briggsae genomic intervals on the Chromosome I, II and III, respectively that produce inviability in all F1 progeny dependent or independent of the parent-of-origin. Taken together, we identified multiple independent interacting loci that are responsible for asymmetric hybrid male and female sterility and inviability, which provides important insights into the asymmetric HI and lays a foundation for their molecular characterization.\n\nAuthor summaryIt is common that closely related species can mate with each other, but their hybrid progeny are often sterile or inviable, especially in the male progeny. The mechanism underlying the asymmetric sterility or inviability remains poorly understood. We previously addressed this question between two nematodes, Caenorhabditis briggsae and C. nigoni, by systematic substitution of various parts of the C. nigoni genome with its C. briggsaes equivalent followed by phenotypic examination. Here we investigate the genetic mechanism of the asymmetric sterility and inviability in the hybrid F1 male and female progeny between the two species. We achieved this through crossing a cohort of C. nigoni strains each carrying a substitution with C. briggsae, which led to differential homozygosity of the C. briggsae substitution in the hybrid progeny. The aggregated substitutions cover 94.6% of the C. briggsae genome, including 100% of the X chromosome. Surprisingly, we identified two C. briggsae X fragments that produced C. nigoni male sterility as a substitution but rescued hybrid F1 sterility in males fathered by C. briggsae, indicating that at least two separate X-autosome interactions are involved in the hybrid male sterility. In addition, we identified multiple genomic intervals on C. briggsae autosomes that can rescue the inviability, but not the sterility, of hybrid F1 males fathered by C. nigoni. Importantly, we isolated a 1.1-Mb genomic interval that specifically interacts with an X-linked introgression, which is essential for hybrid male fertility. We further identified three C. briggsae genomic intervals on the Chromosome I, II and III, respectively that produce inviability in all F1 progeny dependent or independent of the parent-of-origin. The identified interacting loci lays a foundation for their molecular characterization.

evolutionary biology↗

bioRxiv2018

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments.\n\nDeveloping such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.\n\nAuthor summaryBayesian phylogenetic inference methods have undergone considerable development in recent years, and joint modelling of rich evolutionary data, including genomes, phenotypes and fossil occurrences is increasingly common. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing scientific software is increasingly crucial to advancement in many fields of biology. The challenges range from practical software development and engineering, distributed team coordination, conceptual development and statistical modelling, to validation and testing. BEAST 2 is one such computational software platform for phylogenetics, population genetics and phylodynamics, and was first announced over 4 years ago. Here we describe the full range of new tools and models available on the BEAST 2.5 platform, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics.

evolutionary biology↗

bioRxiv2018

A GYS2/p53 negative feedback loop restricts tumor growth in HBV-related hepatocellular carcinoma

Hepatocarcinogenesis is attributed to the reprogramming of cellular metabolism as consequence of the alteration in metabolite-related gene regulation. Identifying the mechanism of aberrant metabolism is of great potential to provide novel targets for the treatment of hepatocellular carcinoma (HCC). Here, we demonstrated that glycogen synthase 2 (GYS2) restricted tumor growth in HBV-related HCC via a negative feedback loop with p53. Expression of GYS2 was significantly downregulated in HCC and correlated with decreased glycogen content and unfavorable patient outcomes. GYS2 overexpression suppressed, whereas GYS2 knockdown facilitated cell proliferation in vitro and tumor growth in vivo via modulating p53 expression. GYS2 competitively bound to MDM2 to prevent p53 from MDM2-mediated ubiquitination and degradation. Furthermore, GYS2 enhanced the p300-induced acetylation of p53 at K373/382, which in turn inhibited the transcription of GYS2 in the support of HBx/HDAC1 complex. In summary, our findings suggest that GYS2 serves as a prognostic factor and functions as a tumor suppressor in HCC. The newly identified HBx/GYS2/p53 axis is responsible for the deregulation of glycogen metabolism and represents a promising therapeutic target for the clinical management of HCC.\n\nSynopsisThis study elucidate the role of GYS2 in glycogen metabolism and the progression of HCC. The newly identified HBx/GYS2/p53 axis is responsible for the deregulation of glycogen metabolism and represents a promising therapeutic target for the clinical management of HCC.\n\nO_LIDecrease of GYS2 was significantly correlated with decreased glycogen content and unfavorable patient outcomes in a large cohort containing 768 patients with HCC.\nC_LIO_LIGYS2 overexpression suppressed, whereas GYS2 knockdown facilitated cell proliferation in vitro and tumor growth in vivo via modulating p53 signaling pathway.\nC_LIO_LIGYS2 competitively bound to MDM2 to prevent p53 from MDM2-mediated ubiquitination and degradation.\nC_LIO_LIGYS2 enhanced the p300-induced acetylation of p53 at Lys373/382, which in turn inhibited the transcription of GYS2 in the support of HBx/HDAC1 complex.\nC_LI

pathology↗

bioRxiv2018

Effect of eco-remediation and microbial community using multilayer solar planted floating island (MS-PFI) in the drainage channel

A multilayer solar planted floating island (MS-PFI) planted with Eichhornia crassipes are potential alternatives to traditional PFI. The highest removal rates of suspended solids, total nitrogen, total phosphorus, ammonia nitrogen and chemical oxygen demand was 86%, 75%, 80%, 95% and 84%, respectively. Proteobacteria (average 43.4% of total sequences) and Actinobacteria (19.9%) were the dominant phyla. Numerous genus had obvious differences between influent and effluent water, for instance, 13, 12 and 7 % in effluent water were assigned to the hgcl_clade, Norank_c_Cyanobacteria, and Rhizorhapis, while their relative abundances were decreased to 5, 3 and 0 %. In contrast, a distinct increase among Flavobacterium (10%), Limnohabitans (7%), Alpinimonas (4%), norank_p_Saccharibacteria (4%), Erwinia (3%) after MS-PFI treatment. MS-PFI brings various bacteria involved in contaminant degradation and nutrient removal in biological wastewater treatment systems. An amount of {yen} 1,843 was totally inputted to construct floating bed, which was rarely needed operation and maintenance costs.\n\nImportanceIn-situ micro-polluted water ecological remediation, microorganisms and plants are effective to improve environmental quality and provide essential ecosystem services. Recently, we invent a new multilayer solar with an excellent pollutant removal efficiency. Microbes can decompose or mineralize organic matter effectively, also provide food for aquatic animals and increase nutrients or substances for plants, it is an important part of biogeochemical cycles and energy flows in aquatic ecological systems. However, few study explain the bacteria diversity and its responses between influent and effluent water in a planted floating island. The significance of our study is in identifying-in greater detail-the responses of bacteria in the new MS-PFI. This will greatly enhance our knowledge of bacteria communities, and can be widely used in micro-polluted water remediation.

bioengineering↗

bioRxiv2017

A new sequence logo plot to highlight enrichment and depletion

BackgroundSequence logo plots have become a standard graphical tool for visualizing sequence motifs in DNA, RNA or protein sequences. However standard logo plots primarily highlight enrichment of symbols, and may fail to highlight interesting depletions. Current alternatives that try to highlight depletion often produce visually cluttered logos.\n\nResultsWe introduce a new sequence logo plot, the EDLogo plot, that highlights both enrichment and depletion, while minimizing visual clutter. We provide an easy-to-use and highly customizable R package Logolas to produce a range of logo plots, including EDLogo plots. This software also allows elements in the logo plot to be strings of characters, rather than a single character, extending the range of applications beyond the usual DNA, RNA or protein sequences. We illustrate our methods and software on applications to transcription factor binding site motifs, protein sequence alignments and cancer mutation signature profiles.\n\nConclusionOur new EDLogo plots, and flexible software implementation, can help data analysts visualize both enrichment and depletion of characters (DNA sequence bases, amino acids, etc) across a wide range of applications.

genetics↗

bioRxiv2017

Chemical genomic guided engineering of gamma-valerolactone tolerant yeast

BackgroundGamma valerolactone (GVL) is a promising technology for degradation of biomass for biofuel production; however, GVL has adverse toxicity effects on fermentative microbes. Using a combination of chemical genomics and chemical proteomics we sought to understand the mechanism toxicity and resistance to GVL with the goal of engineering a GVL-tolerant, xylose-fermenting yeast.\n\nResultsChemical genomic profiling of GVL predicted that this chemical affects membranes and membrane-bound processes. We show that GVL causes rapid, dose-dependent cell permeability, and is synergistic with ethanol. Chemical genomic profiling of GVL revealed that deletion of the functionally related enzymes Pad1p and Fdc1p, which act together to decarboxylate phenolic acids to vinyl derivatives, increases yeast tolerance to GVL. Further, overexpression of Pad1p sensitizes cells to GVL toxicity. To improve GVL tolerance, we deleted PAD1 and FDC1 in a xylose-fermenting yeast strain. The modified strain exhibited increased anaerobic growth, sugar utilization, and ethanol production in synthetic hydrolysate with 1.5% GVL, and under other conditions. Chemical proteomic profiling of the engineered strain revealed that enzymes involved in ergosterol biosynthesis were more abundant in the presence of GVL compared to the background strain. The engineered GVL strain contained greater amounts of ergosterol than the background strain.\n\nConclusionsWe found that GVL exerts toxicity to yeast by compromising cellular membranes, and that this toxicity is synergistic with ethanol. Deletion of PAD1 and FDC1 conferred GVL resistance to a xylose-fermenting yeast strain by increasing ergosterol content in cells. The GVL-tolerant strain fermented sugars in the presence of GVL levels that were inhibitory to the unmodified strain. This strain represents a xylose fermenting yeast specifically tailored to GVL produced hydrolysates

bioengineering↗

bioRxiv2017

5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages

5-Hydroxymethylcytosine (5hmC) is an important mammalian DNA epigenetic modification that has been linked to gene regulation and cancer pathogenesis. Here we explored the diagnostic potential of 5hmC in circulating cell-free DNA (cfDNA) using a sensitive chemical labeling-based low-input shotgun sequencing approach. We sequenced cell-free 5hmC from 49 patients of seven different cancer types and found distinct features that could be used to predict cancer types and stages with high accuracy. Specifically, we discovered that lung cancer leads to a progressive global loss of 5hmC in cfDNA, whereas hepatocellular carcinoma and pancreatic cancer lead to disease-specific changes in the cell-free hydroxymethylome. Our proof of principle results suggest that cell-free 5hmC signatures may potentially be used not only to identify cancer types but also to track tumor stage in some cancers.\n\nOne Sentence SummaryAnalyzing the epigenetic modification 5-hydroxymethylcysoine in circulating cell-free DNA reveals tumor tissue of origin and stages for cancer diagnostics.

genomics↗

bioRxiv2017

Aberration-corrected high-NA open-top selective-plane illumination microscopy for biological imaging

AbstractSelective-plane illumination microscopy (SPIM) provides unparalleled advantages for volumetric imaging of living organisms over extended times. However, the spatial configuration of a SPIM system often limits its compatibility with many widely used biological sample holders such as multi-well chambers and plates. To solve this problem, we developed a high numerical aperture (NA) open-top configuration that places both the excitation and detection objectives on the opposite of the sample coverglass. We carried out a theoretical calculation to analyze the structure of the system-induced aberrations. We then experimentally compensated the system aberrations using adaptive optics combined with static optical components, demonstrating near-diffraction-limited performance in imaging fluorescently labeled cells.\n\n(C) 2017 Optical Society of America\n\nOCIS codes: (080.080) Geometric Optics; (110.0110) Imaging systems; (110.0180) Microscopy.

bioengineering↗