The authors have nothing to disclose.

understanding cerebellar pattern formation

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Understanding Cerebellar Pattern Formation

فهم مخيخي تشكيل نقش

understanding-cerebellar-pattern-formation

Research

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Biology

Video: Understanding Cerebellar Pattern Formation

Isolation and Culture of Post-Natal Mouse Cerebellar Granule Neuron Progenitor Cells and Neurons 

The cerebellar cortex is a well described structure that provides unique opportunities for studying neuronal properties and development1,2. Of the cerebellar neuronal types (granule cells, Purkinje cells and inhibitory interneurons), granule neurons are by far the most numerous and are the most abundant type of neurons in the mammalian brain. In rodents, cerebellar granule neurons are generated during the first two post-natal weeks from progenitor cells in the outermost layer of the cerebellar cortex, the external granule layer (EGL). The protocol presented here describes techniques to enrich and culture granule neurons and their progenitor cells from post-natal mouse cerebellum. We will describe procedures to obtain cultures of increasing purity3,4, which can be used to study the differentiation of proliferating progenitor cells into granule neurons5,6. Once the progenitor cells differentiate, the cultures also provide a homogenous population of granule neurons for experimental manipulation and characterization of phenomena such as synaptogenesis, glutamate receptor function7, interaction with other purified cerebellar cells8,9 or cell death7.

Isolation and Culture of Post-Natal Mouse Cerebellar Granule Neuron Progenitor Cells and Neurons

Here we present a method to isolate and culture cerebellar granule neuron progenitor cells and cerebellar granule neurons from postnatal mouse.

العزلة وثقافة ما بعد الولادة ماوس مخيخي الخلايا الحبيبية السلف الخلية العصبية والخلايا العصبية

The cerebellar cortex is a well described structure that provides unique opportunities for studying neuronal properties and development1,2. Of the ...

Fate Mapping of Human Embryonic Stem Cells by Teratoma Formation

Human embryonic stem cells (hESCs) have an unlimited capacity for self-renewal, and the ability to differentiate into cells derived from all three embryonic germ layers (1). Directed differentiation of hESCs into specific cell types has generated much interest in the field of regenerative medicine (e.g., (2-5)), and methods for determining the in vivo fate of selected or manipulated hESCs are essential to this endeavor. We have adapted a highly efficient teratoma formation assay for this purpose. A small number of specifically selected hESCs is mixed with undifferentiated wild type hESCs and Phaseolus vulgaris lectin to form a cell pellet. This is grafted beneath the kidney capsule in an immunodeficient mouse. As few as 2.5 x 105 hESCs are needed to form a 16 cm3 teratoma within 8-12 weeks. The fate of the originally selected hESCs can then be determined by immunohistochemistry. This method provides a valuable tool for characterizing tissue-specific reagents for cell-based therapy.

Directed differentiation of hESCs into specific cells has generated much interest in regenerative medicine. We provide a concise, step-by-step protocol for determining the in vivo fate of selected hESCs that provides a valuable tool for characterizing tissue-specific reagents for cell-based therapy.

رسم مصير الخلايا الجذعية الجنينية البشرية من خلال تكوين ورم مسخي

Human embryonic stem cells (hESCs) have an unlimited capacity for self-renewal, and the ability to differentiate into cells derived from all three ...

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation

Genomes are organized into three-dimensional structures, adopting higher-order conformations inside the micron-sized nuclear spaces 7, 2, 12. Such architectures are not random and involve interactions between gene promoters and regulatory elements 13. The binding of transcription factors to specific regulatory sequences brings about a network of transcription regulation and coordination 1, 14. 
Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) was developed to identify these higher-order chromatin structures 5,6. Cells are fixed and interacting loci are captured by covalent DNA-protein cross-links. To minimize non-specific noise and reduce complexity, as well as to increase the specificity of the chromatin interaction analysis, chromatin immunoprecipitation (ChIP) is used against specific protein factors to enrich chromatin fragments of interest before proximity ligation. Ligation involving half-linkers subsequently forms covalent links between pairs of DNA fragments tethered together within individual chromatin complexes. The flanking MmeI restriction enzyme sites in the half-linkers allow extraction of paired end tag-linker-tag constructs (PETs) upon MmeI digestion. As the half-linkers are biotinylated, these PET constructs are purified using streptavidin-magnetic beads. The purified PETs are ligated with next-generation sequencing adaptors and a catalog of interacting fragments is generated via next-generation sequencers such as the Illumina Genome Analyzer. Mapping and bioinformatics analysis is then performed to identify ChIP-enriched binding sites and ChIP-enriched chromatin interactions 8. 
We have produced a video to demonstrate critical aspects of the ChIA-PET protocol, especially the preparation of ChIP as the quality of ChIP plays a major role in the outcome of a ChIA-PET library. As the protocols are very long, only the critical steps are shown in the video.

Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation

Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a method for de novo detection of chromatin interactions, for better understanding of transcriptional control.

الكروماتين تحليل التفاعل مع تسلسل العلامات المقترنة النهائي (شيا-PET) لرسم خرائط التفاعلات الكروماتين وفهم تنظيم النسخ

Genomes are organized into three-dimensional structures, adopting higher-order conformations inside the micron-sized nuclear spaces 7, 2, 12. Such ...

The Soft Agar Colony Formation Assay

Anchorage-independent growth is the ability of transformed cells to grow independently of a solid surface, and is a hallmark of carcinogenesis. The soft agar colony formation assay is a well-established method for characterizing this capability in vitro and is considered to be one of the most stringent tests for malignant transformation in cells. This assay also allows for semi-quantitative evaluation of this capability in response to various treatment conditions. Here, we will demonstrate the soft agar colony formation assay using a murine lung carcinoma cell line, CMT167, to demonstrate the tumor suppressive effects of two members of the Wnt signaling pathway, Wnt7A and Frizzled-9 (Fzd-9). Concurrent overexpression of Wnt7a and Fzd-9 caused an inhibition of colony formation in CMT167 cells. This shows that expression of Wnt7a ligand and its Frizzled-9 receptor is sufficient to suppress tumor growth in a murine lung carcinoma model.

The soft agar colony formation assay is a method used to confirm cellular anchorage-independent growth in vitro. The goal of this protocol is to illustrate a stringent method for the detection of the tumorigenic potential of transformed cells and the tumor suppressive effects of proteins on transformed cells.

تشكيل مستعمرة الفحص لينة آجار

Anchorage-independent growth is the ability of transformed cells to grow independently of a solid surface, and is a hallmark of carcinogenesis. The soft ...

Visually Sexing Loggerhead Shrike (Lanius Ludovicianus) Using Plumage Coloration and Pattern

The loggerhead shrike is a small sexually monomorphic passerine bird using grassland habitats across North America. Based on Breeding Bird Survey data, the species has undergone a drastic decline since the mid-1960s. The cause of decline is unknown, and research is actively underway to address this knowledge gap. These efforts are hindered by an inability to sex the species in hand, which to date was only possible using molecular markers. Here, we present a protocol to sex loggerhead shrikes by visually analyzing the coloration and pattern in the sixth primary feather. The application of the method will facilitate our ability to identify threats on a finer scale than has been possible to date and to address various ecological and evolutionary hypotheses. The methodology is simple and results reliable&#8211;we encourage including this method for research of both in situ and ex situ populations.

Visually Sexing Loggerhead Shrike Lanius Ludovicianus Using Plumage Coloration and Pattern

We present a protocol to characterize the sex of loggerhead shrike visually based on the coloration and pattern of the sixth primary wing feather.

بصريا Sexing Loggerhead Shrike(Lanius Ludovicianus)باستخدام تلوين الريش ونمط

The loggerhead shrike is a small sexually monomorphic passerine bird using grassland habitats across North America. Based on Breeding Bird Survey data, ...

Proplatelet Formation Dynamics of Mouse Fresh Bone Marrow Explants

The last stage of megakaryopoiesis leads to cytoplasmic extensions from mature megakaryocytes, the so-called proplatelets. Much has been learned about the proplatelet formation using in vitro-differentiated megakaryocytes; however, there is an increasing evidence that conventional culture systems do not faithfully recapitulate the differentiation/maturation process that takes places inside the bone marrow. In this manuscript, we present an explant method initially described in 1956 by Thi&#233;ry and Bessis to visualize megakaryocytes which have matured in their native environment, thus circumventing potential artifacts and misinterpretations. Fresh bone marrows are collected by flushing the femurs of mice, sliced into 0.5 mm cross sections, and placed in an incubation chamber at 37 &#176;C containing a physiological buffer. Megakaryocytes become gradually visible at the explant periphery and are observed up to 6 hours under an inverted microscope coupled to a video camera. Over time, megakaryocytes change their shape, with some cells having a spherical form and others developing thick extensions or extending many thin proplatelets with extensive branching. Both qualitative and quantitative investigations are carried out. This method has the advantage of being simple, reproducible, and fast as numerous megakaryocytes are present, and classically half of them form proplatelets in 6 hours compared to 4 days for cultured mouse megakaryocytes. In addition to the study of mutant mice, an interesting application of this method is the straightforward evaluation of the pharmacological agents on the proplatelet extension process, without interfering with the differentiation process that may occur in cultures.

Here, we detail the bone marrow explant method, from sample preparation to microscopic slide analysis, to evaluate the ability of megakaryocytes which have differentiated in their physiological environment to form proplatelets.

ديناميات تشكيل الصفائح الدموية من الفأر نخاع العظم الطازج Explants

The last stage of megakaryopoiesis leads to cytoplasmic extensions from mature megakaryocytes, the so-called proplatelets. Much has been learned about the ...

Preparation of Bacterial Inoculum for Acinetobacter Biofilm Formation

Preparation of Bacterial Inoculum for Acinetobacter Biofilm Formation  

To begin the process of bacterial inoculum preparation, collect 2 to 10 microliters of the bacterial strain from the vial, using a sterile pipette tip, and inoculate a commercially-available blood agar plate with it. Using a sterile loop, streak the agar surface, thinning it out with intermittent flaming. Incubate the prepared agar plate in an upside-down position at 30 degrees Celsius for about 20 to 24 hours.Next, select a single colony of the bacterial culture with a sterile needle and inoculate five milliliters of sterile BHI broth with this culture. Incubate the inoculated broth in a shaking incubator at 30 degrees Celsius at a speed of 150 rotations per minute for about 20 to 24 hours. Then transfer one milliliter of the culture to a sterile micro-centrifuge tube and centrifuge at 6, 000 g and room temperature for 10 minutes.Following centrifugation, discard the supernatant. Add one milliliter of sterile phosphate-buffered saline, or PBS, to the pellet, and re-suspend it using a vortex. Centrifuge the re-suspended pellet at 6, 000 g for 10 minutes at room temperature and discard the supernatant.This time re-suspend the resulting pellet in sterile, tenfold-diluted BHI broth using vortex. Ensure to achieve an optical density of around 0.1 at 600 nanometers.

تحضير اللقاح البكتيري لتكوين الأغشية الحيوية الراكدة

Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics

Temperate phages are found integrated as prophages in the majority of bacterial genomes. Some prophages are cryptic and fixed in the bacterial chromosome, but others are active and can be triggered into a replicative form either spontaneously or by exposure to inducing factors. Prophages are commonly associated with the ability to confer toxin production or other virulence-associated traits on their host cell. More recent studies have shown they can play a much bigger role in altering the physiology of their hosts. The technique described here has enabled us to investigate how prophages affect gene expression in the opportunistic bacterium Pseudomonas aeruginosa.
In this work, the growth of the wild-type P. aeruginosa strain PAO1 was compared with that of isogenic lysogens carrying different combinations of prophages from the Liverpool Epidemic Strain (LES) LESB58. In a lysogen culture, a proportion of bacterial cells will be supporting lytic bacteriophage replication (spontaneous induction) with a high level of expression per cell of&#160;late phage genes, such as those associated with the assembly of phage particles,&#160;thus masking the low-level gene expression associated with lysogen-restricted gene&#160;expression. The impact of spontaneous induction can thus obscure prophage gene expression across a lysogen population.
Growth profiling experiments were used to identify spontaneous induction, which was minimal during the early exponential growth phase. This study reports how to prepare sample cultures during the early exponential growth phase and how to set up adequate controls despite low cell numbers. These protocols ensure the reliable and reproducible comparison of wild-type and lysogenic bacteria under various conditions, thus improving the transcriptomic profiling of prophage genomes and aiding in the identification of previously unrecognized prophage functions.

This protocol enables the impact of prophages on their hosts to be revealed. Bacterial cultures are synchronized using conditions that best support the lysogenic state, limiting spontaneous induction. RT-qPCR unequivocally distinguishes prophage-restricted genes and those uncoupled from phage control from those that are expressed during the lytic replication cycle.

فهم تأثير البكتيريا المعتدلة على الليزوجينات من خلال علم النسخ

Temperate phages are found integrated as prophages in the majority of bacterial genomes. Some prophages are cryptic and fixed in the bacterial chromosome, ...

MSCs Differentiation from hiPSCs via EB Formation and Monolayer Culture

To begin, culture hiPSCs in IPSC maintenance medium on a six-well tissue culture plate coated with growth factor reduced extracellular matrix gel. When the cells attain 80 to 90%v, remove the medium from the plate and wash the cells once with DPBS. Then add 700 to 800 microliters of 0.48 millimolar EDTA and incubate for one minute at room temperature.Remove the digestion solution and incubate the plate at 37 degrees Celsius for three to five minutes. When cells are digested into sheets, add two milliliters of IPSCs maintenance medium to terminate digestion. Transfer the cell suspension to a six-well low attachment plate.Incubate the cells at 37 degrees Celsius with 5%carbon dioxide and 60 RPM to form spherical embryo bodies or EBs. After 24 hours, using a past pipette, transfer the EBs to the centrifuge tube and allow it to sediment for five to 10 minutes before removing the supernatant. Add MSC differentiation medium to the tube and transfer the EBs to a six-well low attachment blade with two milliliters of MSCs differentiation medium.Culture the EBs on the shaker at 37 degrees Celsius with 5%carbon dioxide for seven days. On the eighth day, transfer the EBs to the centrifuge tube as demonstrated previously. Once the EBs are sedimented, remove the supernatant from the tube.Add MSC maintenance medium into the tube and transfer the EBs to a growth factor reduced extracellular matrix gel coated six-well plate with two milliliters of MSC maintenance medium. After cell adhesion, change the medium until the culture attains 90%confluency. Next, treat the EB derived culture with a dissociation solution at 37 degrees Celsius.When part of the cells are digested into single cells, add two milliliters of the MSC maintenance medium to terminate digestion and transfer the cell suspension to a centrifuge tube. Wash the remaining undigested cells from the wells once with DPBS. And digest again as demonstrated previously.Then centrifuge the cell suspension at 250g for five minutes. Remove the supernatant and seed the cells in a gelatin coated culture plate. Culture the cells in MSC maintenance medium to 90%confluency with regular medium change.Culture hiIPCs lines as demonstrated previously. When the cells attain 50 to 60%confluency, remove the IPSC maintenance medium from the plate. Add two milliliters of MSC maintenance medium.And culture for 14 days at 37 degrees Celsius and 5%carbon dioxide with daily medium change. For the maturation of MSCs, treat the monolayer culture with a dissociation solution at 37 degrees Celsius. When part of the cells are digested into single cells, add two milliliters of the MSC maintenance medium into the wells to terminate digestion and transfer the cell suspension to a centrifuge tube.Wash the remaining undigested cells once with DPBS and digest them as demonstrated previously. Then centrifuge the cell suspension as demonstrated previously and seed the cells on a gelatin coated culture dish. Culture the cells in MSC maintenance medium to 90%confluency with regular medium change.In the EB formation method, hiIPCs colonies exhibited a compact morphology before differentiation. After dissociation, uniform spherical EBs formed, which drew in volume over time. Subsequently, EBs transformed into adherent monolayer cells achieving 90%confluency by day 18 and acquiring a spindle shape morphology after two passages.Similarly, in the monolayer method, cells proliferated forming multilayer adherent cells. After packaging multiple times, cells matured into MSC with a typical spindle shape and swirling colony. Flow cytometry analysis revealed that hiIPCs were positive for CD90 and negative for CD34, CD45, CD105, and CD73.After differentiation, the hiIPCs driving MSCs expressed CD90, CD73, and CD105, while remaining negative for CD34 and CD45. Monolayer derived MSCs showed higher calcium deposit formation than the EB method. However, no significant differences were observed in adipogenic and chondrogenic differentiation abilities.The proliferation abilities of both methods were maintained for up to 20 passages.

تمايز MSCs عن hiPSCs عبر تكوين EB وثقافة أحادية الطبقة

Imaging Resin-Infiltrated Leaf Sections for Understanding Anatomical Differences Between Triticum aestivum and Zea mays

After staining the Triticum aestivum leaf section with toluidine blue, place the slide on the microscope stage. Using a 40x objective magnification, focus on the section and adjust the brightness to ensure all cell structures are visible. Then use the navigator function to set the sections location area to ensure the entire section is imaged, then click the stitch button.After that, click done and run to allow the microscope to image the entire section. Open the image analysis software and the tiles taken by the microscope. Using the align feature, ensure that the tiles do not overlap.After generating the image, adjust the positioning, brightness, and rotation using the adjust tab. Then print the scale on the image before saving it in TIF format. Open ImageJ software and drag the image into the window to load it.Using the line tool, draw a line over the scale bar. Choose analyze and click set scale. Change the known distance to the scale bar's length and the unit of length to the correct unit.To measure the prospective trait, select the line tool, draw a line across the area of interest and press the M key. For area measurements, use the polygon selection tool to outline the tissue of interest. Then press the M key to conclude.A pop-up window displaying the measurements will appear, which can be copied to a spreadsheet for further data analysis. Box plots illustrated significant anatomical differences between Triticum aestivum and ZMAs, particularly in interveinal distances, bundle sheath diameter, the fraction of bundle sheath cells, non-photo synthetic material, and vein frequency reflecting expected C3 and C4 leaf anatomy distinctions.