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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 1,315 records · Page 73Linked to original sources

bioRxiv2018

Double-digest RAD-sequencing: do wet and dry protocol parameters impact biological results?

O_LINext-generation sequencing technologies have opened a new era of research in genomics. Among these, restriction enzyme-based techniques such as restriction-site associated DNA sequencing (RADseq) or double-digest RAD-sequencing (ddRADseq) are now widely used in many population genomics fields. From DNA sampling to SNP calling, both wet and dry protocols have been discussed in the literature to identify key parameters for an optimal loci reconstruction.\nC_LIO_LIThe impact of these parameters on downstream analyses and biological results drawn from RADseq or ddRADseq data has however not been fully explored yet. In this study, we tackled this issue by investigating the effects of ddRADseq laboratory (i.e. wet protocol) and bioinformatics (i.e. dry protocol) settings on loci reconstruction and inferred biological signal at two evolutionary scale using two systems: a complex of butterfly species (Coenonympha sp.) and populations of Common beech (Fagus sylvatica).\nC_LIO_LIResults suggest an impact of wet protocol parameters (DNA quantity, number of PCR cycles during library preparation) on the number of recovered reads and SNPs, the number of unique alleles and individual heterozygosity. We also found that bioinformatic settings (i.e. clustering and minimum coverage thresholds) impact loci reconstruction (e.g. number of loci, mean coverage) and SNP calling (e.g. number of SNPs, heterozygosity). We however do not detect an impact of parameter settings on three types of analysis performed with ddRADseq data: measure of genetic differentiation, estimation of individual admixture, and demographic inferences. In addition, our work demonstrates the high reproducibility and low rate of genotyping inconsistencies of the ddRADseq protocol.\nC_LIO_LIThus, our study highlights the impact of wet parameters on ddRADseq protocol with strong consequences on experimental success and biological conclusions. Dry parameters affects loci reconstruction and descriptive statistics but not biological conclusion for the two studied systems. Overall, this study illustrates, with others, the relevance of ddRADseq for population and evolutionary genomics at the inter- or intraspecific scales.\nC_LI

molecular biology↗

bioRxiv2018

Insulin Receptor Deletion in S100a4-lineage cells accelerates age-related bone loss

Type I and Type II Diabetes dramatically impair skeletal health. Altered Insulin Receptor (IR) signaling is a common feature of both diseases, and insulin has potent bone anabolic functions. Several previous studies have demonstrated that loss of IR in bone cells results in disrupted bone homeostasis during early post-natal growth. Here we have deleted IR in S100a4-lineage cells (IRcKOS100a4) and assessed the effects on bone homeostasis at both young (15 weeks) and older adult (48 weeks) mice. S100a4-cre has previously been shown to target the perichondrium during bone development, and here we show that S100a4 is expressed by adult trabecular and cortical bone cells, and that S100a4-Cre effectively targets adult bone, resulting in efficient deletion of IR. Deletion of IR in S100a4-lineage cells does effect initial bone acquisition or homeostasis with no changes in cortical, trabecular or mechanical properties at 15-weeks of age, relative to wild type (WT) littermates. However, by 48-weeks of age, IRcKOS100a4 mice display substantial declines in trabecular bone volume, bone volume fraction and torsional rigidity, relative to age-matched WT controls. This work establishes the utility of using S100a4-cre to target bone and demonstrates that IR in S100a4-lineage cells is required for maintenance of bone homeostasis in adult mice.

cell biology↗

bioRxiv2018

ahr2, but not ahr1a or ahr1b, is required for craniofacial and fin development and TCDD-dependent cardiotoxicity in zebrafish

The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that binds environmental toxins and regulates gene expression. AHR also regulates developmental processes, like craniofacial development and hematopoiesis, in the absence of environmental exposures. Zebrafish have three paralogues of AHR: ahr1a, ahr1b and ahr2. Adult zebrafish with mutations in ahr2 exhibited craniofacial and fin defects. However, the degree to which ahr1a and ahr1b influence ahr2 signaling and contribute to fin and craniofacial development are not known. We compared morphology of adult ahr2 mutants and ahr1a/ahr1b single and double mutant zebrafish. We found that ahr1a/ahr1b single and double mutants were morphologically normal while ahr2 mutant zebrafish demonstrated fin and craniofacial malformations. At 5 days post fertilization, both ahr1a/ahr1b and ahr2 mutant larvae were normal, suggesting that adult phenotypes are due to defects in maturation or maintenance. AHR was shown to interact with estrogen receptor alpha, yet it is not known whether these interactions are constitutive or dependent on ahr1 genes. To determine whether estrogen receptors are constitutive cofactors for AHR signaling, we used genetic and pharmacologic techniques to analyze TCDD-dependent toxicity in estrogen receptor and ahr mutant embryos. We found that embryos with mutations in ahr1a/ahr1b or estrogen receptor genes are susceptible to TCDD toxicity while ahr2 mutant embryos are TCDD-resistant. Moreover, pharmacologic blockade of nuclear estrogen receptors failed to prevent TCDD toxicity. These findings suggest that ahr1 genes do not have overlapping functions with ahr2 in fin and craniofacial development or TCDD-dependent toxicity, and that estrogen receptors are not constitutive partners of ahr2.

developmental biology↗

bioRxiv2018

Cellular labeling of endogenous virus replication (CLEVR) reveals de novo insertions of the gypsy endogenous retrovirus in cell culture and in both neurons and glial cells of aging fruit flies

Evidence is rapidly mounting that transposable element expression and replication may impact biology more widely than previously thought. This includes potential effects on normal physiology of somatic tissues and dysfunctional impacts in diseases associated with aging such as cancer and neurodegeneration. Investigation of the biological impact of mobile elements in somatic cells will be greatly facilitated by use of donor elements that are engineered to report de novo events in vivo. In multicellular organisms, successful reporters of LINE element mobilization have been in use for some time, but similar strategies have not been developed to report Long Terminal Repeat (LTR) retrotransposons and endogenous retroviruses. We describe Cellular Labeling of Endogenous Virus Replication (CLEVR), which reports replication of the gypsy element in Drosophila. The gypsy-CLEVR reporter reveals gypsy replication both in cell culture and in individual neurons and glial cells of the aging adult fly. We also demonstrate that the gypsy-CLEVR replication rate is increased when the short interfering RNA silencing system is genetically disrupted. This CLEVR strategy makes use of universally conserved features of retroviruses and should be widely applicable to other LTR-retrotransposons, endogenous retroviruses and exogenous retroviruses.

genetics↗

bioRxiv2018

Development of a robust automated tool for the annotation of embryo morphokinetic parameters

Study QuestionIs it possible to automatically annotate human embryo development in time-lapse devices, with results comparable to manual annotation?\n\nSummary AnswerWe developed an automated tool for the annotation of embryo morphokinetic parameters having a high concordance with expert manual annotation in a large scale-study.\n\nWhat is Known AlreadyMorphokinetic parameters obtained with time-lapse devices are increasingly used for human embryo quality assessment. However, their annotation is timeconsuming and can be operator-dependent, highlighting the need of developing automated approaches.\n\nStudy Design, Size, DurationThis monocentric pilot study was conducted using 701 blastocysts originating from 584 couples undergoing IVF with embryo culture in a time-lapse device and on 4 mouse embryos.\n\nParticipants/Materials, Setting, MethodsAn automated annotation tool was developed based on grey level coefficient of variation and detection of the thickness of the zona pellucida. The timings of cellular events obtained with the automated tool were compared with those obtained manually by 2 expert embryologists. The same procedure was applied on 4 mouse preimplantation embryos obtained with a different device in a different setting.\n\nMain Results and the Role of ChanceAlthough some differences were found when embryos were considered individually, we found an overall excellent concordance between automated and manual annotation of human embryo morphokinetics from fertilization to expanded blastocyst stage (r2=0.94). Moreover, the automated annotation tool gave promising results across species (human, mice).\n\nLimitations, Reasons for CautionThese results should undergo multi-centric external evaluation in order to test the overall performance of the annotation tool.\n\nWider Implications of the FindingsOur system performs significantly better than the ones reported in the literature and on a bigger cohort, paving the way for high-throughput analysis of multicentric morphokinetic databases, providing new insights into the clinical value of morphokinetics as predictor of embryo quality and implantation.\n\nStudy Funding/Competing Interest(s)This study was partly funded by Finox Forward Grant 2016.\n\nTrial Registration NumberNA

developmental biology↗

bioRxiv2018

An organoleptic survey of meads made with lactic acid-producing yeasts

We previously reported the isolation a suite of wild lactic acid-producing yeasts (LAYs) that enable "primary souring" during beer fermentation without the use of lactic acid bacteria. With sour meads gaining popularity in modern mead making, we were interested in exploring the same primary souring approach to traditional semi-sweet meads. In this study, we utilized 13 LAY strains to produce semi-sweet meads using a standardized batch of honey must to ensure consistent starting conditions. Thirteen 11-L batches of mead were prepared, and each was inoculated with one of the LAY strains, along with two control batches inoculated with champagne yeast. The initial pH and specific gravity were measured for each batch before inoculation. Traditional organic staggered nutrient addition was utilized for the first 72 h of fermentation with specific gravities being taken throughout the mead making process. Meads were racked, tasted, stabilized, cold crashed, bottled, and transported to the American Mead Makers Association 2018 Conference in Broomfield, Colorado. There, organoleptic surveys were conducted on these meads utilizing an array of tasters with varying levels of mead sensory analysis experience. The results of the sensory analysis, focusing on aroma and flavor, are discussed.

microbiology↗

bioRxiv2018

Sparse additive interaction learning

A conceptual paradigm for onset of a new disease is often considered to be the result of changes in entire biological networks whose states are affected by a complex interaction of genetic and environmental factors. However, when modelling a relevant phenotype as a function of high dimensional measurements, power to estimate interactions is low, the number of possible interactions could be enormous and their effects may be non-linear. In this work, we introduce a method called sail for detecting non-linear interactions with a key environmental or exposure variable in high-dimensional settings which respects the strong or weak heredity constraints. We prove that asymptotically, our method possesses the oracle property, i.e., it performs as well as if the true model were known in advance. We develop a computationally efficient fitting algorithm with automatic tuning parameter selection, which scales to high-dimensional datasets. Through an extensive simulation study, we show that sail outperforms existing penalized regression methods in terms of prediction accuracy and support recovery when there are non-linear interactions with an exposure variable. We apply sail to detect non-linear interactions between genes and a prenatal psychosocial intervention program on cognitive performance in children at 4 years of age. Results show that individuals who are genetically predisposed to lower educational attainment are those who stand to benefit the most from the intervention. Our algorithms are implemented in an R package available on CRAN (https://cran.r-project.org/package=sail).

bioinformatics↗

bioRxiv2018

Connectional architecture of a mouse hypothalamic circuit node controlling social behavior

Type 1 Estrogen receptor-expressing neurons in the ventrolateral subdivision of the ventromedial hypothalamus (VMHvlEsr1) play a causal role in the control of social behaviors including aggression. Here we use six different viral-genetic tracing methods to map the connectional architecture of VMHvlEsr1 neurons. These data reveal a high level of input convergence and output divergence (\"fan-in/fan-out\") from and to over 30 distinct brain regions, with a high degree (~90%) of recurrence. Unlike GABAergic populations in other hypothalamic nuclei controlling feeding and parenting behavior, VMHvlEsr1 glutamatergic neurons collateralize to multiple targets. However, we identify two anatomically distinct subpopulations with anterior vs. posterior biases in their collateralization patterns. Surprisingly, these two subpopulations receive indistinguishable inputs. These studies suggest an overall system architecture in which an anatomically feed-forward sensory-to-motor processing stream is integrated with a dense, highly recurrent central processing circuit. This architecture differs from the \"brain-inspired\" feed-forward circuits used in certain types of artificial intelligence networks.\n\nSIGNIFICANCEHow the cellular heterogeneity of brain nuclei maps onto circuit connectivity, the relationship of this anatomical mapping to behavioral function, and whether there are general principles underlying this relationship, remains poorly understood. Here we systematically map the connectivity of estrogen receptor-1-expressing neurons in the ventromedial hypothalamus (VMHvlEsr1), which control aggression and other social behaviors. We find that a relatively sparse, anatomically feed-forward sensory-to-motor processing stream is integrated with a dense, highly recurrent central processing circuit. Further, the VMHvl contains at least two subpopulations of Esr1+ neurons with different cell body characteristics and locations, with distinct patterns of collateralization to downstream targets. Nevertheless, these projection-defined subpopulations receive similar inputs. This input-output organization appears distinct from those described in other hypothalamic nuclei.

neuroscience↗

bioRxiv2018

Probe Sensitivity to Cortical versus Intracellular Cytoskeletal Network Stiffness

In development, wound healing, and pathology, cell biomechanical properties are increasingly recognized as being of central importance. To measure these properties, experimental probes of various types have been developed, but how each probe reflects the properties of heterogeneous cell regions has remained obscure. To better understand differences attributable to the probe technology, as well as to define the relative sensitivity of each probe to different cellular structures, here we took a comprehensive approach. We studied two cell types --Schlemms canal (SC) endothelial cells and mouse embryonic fibroblasts (MEFs) - using four different probe technologies: 1) atomic force microscopy (AFM) with sharp-tip; 2) AFM with round-tip; 3) optical magnetic twisting cytometry (OMTC); and 4) traction microscopy (TM). Perturbation of SC cells with dexamethasone treatment, a-actinin overexpression, or Rho-A overexpression caused increases in traction reported by TM and stiffness reported by sharp-tip AFM, as compared to corresponding controls. By contrast, under these same experimental conditions, stiffness reported by round-tip AFM and by OMTC indicated little change. Knock out (KO) of vimentin in MEFs caused a diminution of traction reported by TM, as well as stiffness reported by sharp-tip and round-tip AFM. However, stiffness reported by OMTC in vimentin KO MEFs was greater than in wild-type. Finite element analysis demonstrated that this paradoxical OMTC result in vimentin KO MEFs could be attributed to reduced cell thickness. Our results also suggest that vimentin contributes not only to intracellular network stiffness but also cortex stiffness. Taken together, this evidence suggests that AFM sharp-tip and TM emphasize properties of the actin-rich shell of the cell whereas round-tip AFM and OMTC emphasize those of the non-cortical intracellular network.

biophysics↗

bioRxiv2018

Deliberation and enaction during adaptive economic choice

Economic decisions can adapt to contexts. Choices can be quick and impulsive or slow and more deliberative, depending on the temporal context. Choices can also depend on how we enact the choice, in an action context. Where we decide to go for dinner may change if we can take a taxi or need to walk.\n\nWe hypothesized that frontal action circuits could contribute to adapting economic choices to context because of their privileged position over actions as endpoints of decisions.\n\nTo test this, we performed an unbiased survey of neuronal population activity across motor, premotor and prefrontal cortices as animals expressed context-dependent economic preferences. Activity in distributed action circuits tracked the animals evolving preferences in real-time and integrated them with a signal for their enaction. We propose that frontal action circuits form a neural substrate that supports an adaptive control over economic choice by flexibly translating real-time preferences into actions.

neuroscience↗

bioRxiv2018

Baseline human gut microbiota profile in healthy people and standard reporting template

A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with clinical applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individuals microbiome to the growing knowledgebase of \"normal\" microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and abundances the study also generated a list of contigs of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBIs Short Read Archive.

microbiology↗

bioRxiv2018

Exploratory and prospective model of stent restenosis after Percutaneous Coronary Intervention using MultivariateGaussian Subspatial Regression

A new statistical analysis methodology, "Multivariate Gaussian Subspatial Regression" (MGSR), has been applied to randomized clinical trial data collected from percutaneous coronary intervention (PCI) patients, which combines the descriptive quality of Factorial Techniques and the predictive power of Gaussian Processes. This model has been built from 3 different quantitative coronary angiographic core-lab measures of the same lesion from 2 separate angiograms (at baseline before PCI, at baseline immediately after PCI and at 12 months follow-up). Measurements of the pre-PCI variables of a patient are mapped to the factorial plane and predictions are visualized as regions of interest in this plane. MGSR makes it possible to detect patients at risk of coronary stent restenosis or patients in whom ruling out the disease, in a graphical way; avoiding unnecessary, costly and possibly risky treatments for patients with no complications predicted; and advising to closely follow patients at risk. In addition, the model recovers missing values regardless of the variables, and once fitted, it corrects itself when more dependent variables are included. MGSR software is freely available online at https://github.com/victorvicpal/MGSR.

bioinformatics↗

bioRxiv2018

Detection of multiple circulating Leishmania species in Lutzomyia longipalpis in the city of Governador Valadares, southeastern Brazil

BackgroundLeishmaniasis encompasses a group of diverse clinical diseases caused by protozoan parasites of the Leishmania genus. This disease is a major public health problem in the New World affecting people exposed in endemic regions. The city of Governador Valadares (Minas Gerais/Brazil) is a re-emerging area for visceral leishmaniasis, with 191 human cases reported from 2008 to 2017 and a lethality rate of 14.7%. The transmission of the parasite occurs intensely in this region with up to 22% of domestic dogs with positive serology for the visceral form. Lu. longipalpis is one of the most abundant sand fly species in this area. Despite this scenario, so far there is no information regarding the circulating Leishmania species in the insect vector Lutzomyia longipalpis in this focus.\n\nMethodology/Principal FindingsWe collected 616 female Lutzomyia longipalpis sand flies between January and September 2015 in the Vila Parque Ibituruna neighborhood (Governador Valadares/MG), which is located on a transitional area between the sylvatic and urban environments with residences built near a preserved area. After DNA extraction of individual sand flies, the natural Leishmania infections in Lu. longipalpis were detected by end-point PCR, using primers derived from kDNA sequences, specific for L. (Leishmania) or L. (Viannia) subgenus. The sensitivity of these PCR reactions was 0.1 pg of DNA for each Leishmania subgenus and the total infection rate of 16.2% (100 positive specimens). Species-specific PCR detected the presence of multiple Leishmania species in infected Lu. longipalpis specimens in Governador Valadares, including L. amazonensis (n=3), L. infantum (n=28), L. (Viannia) spp. (n=20), coinfections with L. infantum and L. (Viannia) spp. (n=5), and L. (Leishmania) spp (n=44).\n\nConclusionsOur results demonstrate that multiple Leishmania species circulate in Lu. longipalpis in Governador Valadares and reveal a potential increasing risk of transmission of the different circulating parasite species. This information is a key factor for planning surveillance and effective control strategies against leishmaniasis in this endemic focus.\n\nAuthor summaryLeishmaniasis is a neglected tropical disease transmitted to mammals by the bite of sand flies infected with parasites of the Leishmania genus. This disease affects millions of people in various regions of the world, including Brazil. The municipality of Governador Valadares (Minas Gerais/Brazil) is a re-emergent focus of intense transmission of leishmaniasis, with a high number of human cases and a high prevalence of infected domestic dogs. To develop better leishmaniasis control strategies for the region, we performed a surveillance study of Lu. longipalpis, the main vector of visceral leishmaniasis in Brazil, and identified circulating species of Leishmania in this insect vector. We estimate that the natural infection rate of Lu. longipalpis for these parasites was of 16.2% in the study area. We also detected the presence of multiple circulating Leishmania species (L. amazonensis, L. infantum and Viannia subgenus) in Lu. longipalpis in Governador Valadares city, including 5 sand flies coinfected with L. infantum and L. (Viannia). Thus, our results reinforce the need for a rigid and systematic control of the sand flies monitoring in this area, due to the potential risk of transmission of different species of the Leishmania parasites.

epidemiology↗

bioRxiv2018

Pixel Quantum Efficiency Differences and Variance Stabilization for sCMOS Single Molecule Localization Microscopy Data Analysis

Optimal analysis of single molecule localization microscopy (SMLM) data acquired with a CMOS camera requires compensation for single pixel differences in gain, offset and readout noise. For some CMOS cameras we found that it is also necessary to compensate for pixel differences in sensitivity or relative quantum efficiency (RQE). We present the modifications to the original sCMOS analysis algorithm necessary to correct for these RQE differences. We also discuss the use of the Anscombe transform (AT) for variance stabilization. Removing the variance dependence on the mean allows simpler least squares fitting approaches to achieve the Cramer-Rao bound on the mixed Poisson and Gaussian distributed data typically acquired with an sCMOS camera.

biophysics↗

bioRxiv2018

Synergistic interactions between confinement and macromolecular crowding spatially order transcription and translation in cell-free expression

Synergistic interactions between macromolecular crowding and confinement spatially organize transcription and translation in cells. Yet, reproducing such spatial ordering in cell-free expression platforms has proven to be elusive. Here we report crowding- and confinement-driven spatial self-organization of cell-free expression that mimics expression behavior within and around the nucleoid of prokaryotes. These experiments use Ficoll-70 to approximate cellular macromolecular crowding conditions within cell-size lipid vesicles. Intriguingly, there was an abrupt change in transcriptional dynamics when crowding reached physiologically relevant levels. Imaging experiments revealed that this change in transcriptional dynamics was coincident with localization of plasmid DNA and mRNA at the vesicle wall. Computer simulations demonstrated that crowding leads to an entropically induced attraction between plasmid DNA and the wall, causing localization of DNA near the wall at sufficiently high crowding levels. The experiments demonstrate cell-like spatial organization of translation, where translational activity is controlled by chromosomally-templated positioning of mRNA. This cell-free system provides a flexible experimental platform to probe the underlying mechanisms of self-organization of membrane-less structures in cells and the spatial control of gene expression.

synthetic biology↗

bioRxiv2018

GAL4 drivers specific for Type Ib and Type Is motor neurons in Drosophila

The Drosophila larval neuromuscular system is extensively used by researchers to study neuronal cell biology, and Drosophila glutamatergic motor neurons (MNs) have become a major model system. There are two main Types of glutamatergic MNs, Ib and Is, with different structural and physiological properties at synaptic level at the neuromuscular junction. To generate genetic tools to identify and manipulate MNs of each Type, we screened for GAL4 driver lines for this purpose. Here we describe GAL4 drivers specific for examples of neurons within each Type, Ib or Is. These drivers showed high expression levels and were expressed in only few MNs, making them amenable tools for specific studies of both axonal and synapse biology in identified Type I MNs.

neuroscience↗

bioRxiv2018

TADs pair homologous chromosomes to promote interchromosomal gene regulation

Homologous chromosomes colocalize to regulate gene expression in processes including genomic imprinting and X-inactivation, but the mechanisms driving these interactions are poorly understood. In Drosophila, homologous chromosomes pair throughout development, promoting an interchromosomal gene regulatory mechanism called transvection. Despite over a century of study, the molecular features that facilitate chromosome-wide pairing are unknown. The \"button\" model of pairing proposes that specific regions along chromosomes pair with a higher affinity than their surrounding regions, but only a handful of DNA elements that drive homologous pairing between chromosomes have been described. Here, we identify button loci interspersed across the fly genome that have the ability to pair with their homologous sequences. Buttons are characterized by topologically associated domains (TADs), which drive pairing with their endogenous loci from multiple locations in the genome. Fragments of TADs do not pair, suggesting a model in which combinations of elements interspersed along the full length of a TAD are required for pairing. Though DNA-binding insulator proteins are not associated with pairing, buttons are enriched for insulator cofactors, suggesting that these proteins may mediate higher order interactions between homologous TADs. Using a TAD spanning the spinelessd gene as a paradigm, we find that pairing is necessary but not sufficient for transvection. spineless pairing and transvection are cell-type-specific, suggesting that local buttoning and unbuttoning regulates transvection efficiency between cell types. Together, our data support a model in which specialized TADs button homologous chromosomes together to facilitate cell-type-specific interchromosomal gene regulation.

molecular biology↗

bioRxiv2018

Quantitative Analysis of Interactive Behavior of Mitochondria and Lysosomes Using Structured Illumination Microscopy

Super-resolution optical microscopy has extended the spatial resolution of cell biology from the cellular level to the nanoscale, enabling the observation of the interactive behavior of single mitochondria and lysosomes. Quantitative parametrization of interaction between mitochondria and lysosomes under super-resolution optical microscopy, however, is currently unavailable, which has severely limited our understanding of the molecular machinery underlying mitochondrial functionality. Here, we introduce an M-value to quantitatively investigate mitochondria and lysosome contact (MLC) and mitophagy under structured illumination microscopy. We found that the M-value for an MLC is typically less than 0.4, whereas in mitophagy it ranges from 0.5 to 1.0. This system permits further investigation of the detailed molecular mechanism governing the interactive behavior of mitochondria and lysosomes.

cell biology↗