scholarly journals The Geometry of Masking in Neural Populations

2019 ◽  
Author(s):  
Dario L. Ringach

We introduce a geometric approach to study the representation of orientation by populations of neurons in primary visual cortex in the presence and absence of an additive mask. Despite heterogeneous effects at the single cell level, a simple geometric model explains how population responses are transformed by the mask and reveals how changes in discriminability and bias relate to each other. We propose that studying the geometry of neural populations can yield insights into the role of contextual modulation in the processing of sensory signals.

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Dario L. Ringach

Abstract The normalization model provides an elegant account of contextual modulation in individual neurons of primary visual cortex. Understanding the implications of normalization at the population level is hindered by the heterogeneity of cortical neurons, which differ in the composition of their normalization pools and semi-saturation constants. Here we introduce a geometric approach to investigate contextual modulation in neural populations and study how the representation of stimulus orientation is transformed by the presence of a mask. We find that population responses can be embedded in a low-dimensional space and that an affine transform can account for the effects of masking. The geometric analysis further reveals a link between changes in discriminability and bias induced by the mask. We propose the geometric approach can yield new insights into the image processing computations taking place in early visual cortex at the population level while coping with the heterogeneity of single cell behavior.


2014 ◽  
Vol 115 (suppl_1) ◽  
Author(s):  
Konstantina Ioanna Sereti ◽  
Paniz Kamran Rashani ◽  
Peng Zhao ◽  
Reza Ardehali

It has been proposed that cardiac development in lower vertebrates is driven by the proliferation of cardiomyocytes. Similarly, cycling myocytes have been suggested to direct cardiac regeneration in neonatal mice after injury. Although, the role of cardiomyocyte proliferation in cardiac tissue generation during development has been well documented, the extent of this contribution as well as the role of other cell types, such as progenitor cells, still remains controversial. Here we used a novel stochastic four-color Cre-dependent reporter system (Rainbow) that allows labeling at a single cell level and retrospective analysis of the progeny. Cardiac progenitors expressing Mesp1 or Nkx2.5 were shown to be a source of cardiomyocytes during embryonic development while the onset of αMHC expression marked the developmental stage where the capacity of cardiac cells to proliferate diminishes significantly. Through direct clonal analysis we provide strong evidence supporting that cardiac progenitors, as opposed to mature cardiomyocytes, are the main source of cardiomyocytes during cardiac development. Moreover, we have identified quadri-, tri-, bi, and uni-potent progenitors that at a single cell level can generate cardiomyocytes, fibroblasts, endothelial and smooth muscle cells. Although existing cardiomyocytes undergo limited proliferation, our data indicates that it is mainly the progenitors that contribute to heart development. Furthermore, we show that the limited proliferation capacity of cardiomyocytes observed during normal development was enhanced following neonatal cardiac injury allowing almost complete regeneration of the scared tissue. However, this ability was largely absent in adult injured hearts. Detailed characterization of dividing cardiomyocytes and proliferating progenitors would greatly benefit the development of novel therapeutic options for cardiovascular diseases.


2020 ◽  
Author(s):  
Cuifen Gan ◽  
Rongrong Wu ◽  
Yeshen Luo ◽  
Jianhua Song ◽  
Dizhou Luo ◽  
...  

AbstractIron-reducing microorganisms (FeRM) play key roles in many natural and engineering processes. Visualizing and isolating FeRM from multispecies samples are essential to understand the in-situ location and geochemical role of FeRM. Here, we visualized FeRM by a “turn-on” Fe2+-specific fluorescent chemodosimeter (FSFC) with high sensitivity, selectivity and stability. This FSFC could selectively identify and locate active FeRM from either pure culture, co-culture of different bacteria or sediment-containing samples. Fluorescent intensity of the FSFC could be used as an indicator of Fe2+ concentration in bacterial cultures. By integrating FSFC with a single cell sorter, we obtained three FSFC-labeled cells from an enriched consortia and all of them were subsequently evidenced to be capable of iron-reduction and two unlabeled cells were evidenced to have no iron-reducing capability, further confirming the feasibility of the FSFC.ImportanceVisualization and isolation of FeRM from samples containing multispecies are commonly needed by researchers from different disciplines, such as environmental microbiology, environmental sciences and geochemistry. However, no available method has been reported. In this study, we provid a solution to visualize FeRM and evaluate their activity even at single cell level. Integrating with single cell sorter, FeRM can also be isolated from samples containing multispecies. This method can be used as a powerful tool to uncover the in-situ or ex-situ role of FeRM and their interactions with ambient microbes or chemicals.


2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi248-vi248
Author(s):  
Aaron Mochizuki ◽  
Alexander Lee ◽  
Joey Orpilla ◽  
Jenny Kienzler ◽  
Mildred Galvez ◽  
...  

Abstract INTRODUCTION Glioblastoma (GBM) is the most common malignant brain tumor in adults and is associated with a dismal prognosis. Neoadjuvant anti-PD-1 blockade has demonstrated efficacy in melanoma, non-small cell lung cancer and recurrent GBM; however, responses vary. While T cells have garnered considerable attention in the context of immunotherapy, the role of myeloid cells in the GBM microenvironment remains controversial. METHODS We isolated CD45+ immune populations from patients who underwent brain tumor resection at UCLA. We hypothesized that myeloid cells in glioblastoma contribute to T cell dysfunction; however, this immune suppression can be mitigated by neoadjuvant PD-1 inhibition. To test this, we utilized mass cytometry and single-cell RNA sequencing to characterize these immune populations. RESULTS Mass cytometry profiling of tumor infiltrating lymphocytes from patients with GBM demonstrated a preponderance of CD11b+ myeloid populations (75% versus 25% CD3+). At the transcriptomic level, myeloid cells in newly diagnosed GBMs exhibited decreased expression of CCL4 (loge fold change -1.18, Bonferroni-adjusted P = 1.62x10-254) and its ligands compared to anaplastic astrocytoma. In ranked gene set enrichment analysis, patients who received neoadjuvant pembrolizumab demonstrated enrichment in TNFα-, NFκB- and lipid metabolism-related gene sets by bootstrapped Kolmogorov-Smirnov test (Benjamini-Hochberg adjusted P = 4.74x10-3, 1.45x10-2 and 2.48x10-3, respectively) in tumor-associated myeloid populations. Additionally, single-cell trajectory analysis demonstrated increased CCL4 and decreased ISG15 with neoadjuvant checkpoint inhibition. CONCLUSIONS Here, we utilize mass cytometry and single-cell RNA sequencing to demonstrate the predominance and transcriptomic features of myeloid populations in GBM. Myeloid cells in patients who receive neoadjuvant PD-1 blockade re-express increased levels NFκB, TNFα and CCL4, a cytokine crucial for the recruitment of dendritic cells to the tumor for antigen-specific T cell activation. By delving into the GBM microenvironment at the single-cell level, we hope to better delineate the role of myeloid populations in this uniformly fatal tumor.


Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1151-1151
Author(s):  
Juleta H. Sepulveda-Yanez ◽  
Diego Alvarez-Saravia ◽  
Edwin Quinten ◽  
Roberta Menafra ◽  
Susan L. Kloet ◽  
...  

Abstract Introduction Follicular Lymphoma (FL) is one of the most prevalent B-cell neoplasms and despite recent advances remains incurable in most cases. FL cells are malignant counterparts of normal germinal center B-cells. At molecular level FL are characterized by the t(14;18) which results in the overexpression of the BCL-2. These apoptosis resistant cells accumulate somatic mutations associated with tumorigenesis and progression. Whereas several mutagenic mechanisms shape the FL genomic landscape, up to 22% of the mutations may be attributed to activation-induced cytidine deaminase (AID) activity. Under physiological conditions AID is responsible for somatic hypermutation (SHM) in immunoglobulin genes (IG) of germinal center B-cells. In fact, it is accepted that ongoing SHM still occurs at relatively high rates in FL cells as compared with other germinal center lymphoid neoplasms. Moreover, we recently demonstrated the direct effect of AID overexpression inducing somatic mutations driving murine and human B-cell neoplasm progression in vivo. Therefore, unveiling the molecular basis of AID activity in lymphoma cells remains essential to understand lymphomagenesis and to develop novel targeted therapies. The advent of single-cell high-throughput sequencing has enabled the analysis of molecular events at an unprecedented resolution. Therefore, we designed a study to capture AID-induced somatic hypermutation at the single cell level in FL. Methods Tumor samples derived from 14 FL patients were analyzed, as controls, we chose a B-cell malignancy with lower SHM rates and included 5 samples derived from chronic lymphocytic leukemia (CLL) and 2 from monoclonal B lymphocytosis (MBL). Single cell whole cDNA libraries were obtained by 10X Genomics. Immunoglobulin gene single cell libraries were prepared by enrichment with seminested amplification using 3 ′ constant domain primers followed by 10X Genomics prep. Both single-cell libraries were sequenced in paired-end mode (2 × 150 bp) on an Illumina Hiseq platform. We developed an immunoglobulin alignment tool to enable the analysis of highly mutated IG sequences derived from FL. A consensus sequence was obtained by transcript associated with a unique molecular identifier (UMI) for every cell. Then, the presence of variants in the IG by position in a particular cell was annotated. These observations were filtered using quality parameters (read depth => 25 , frequency of the event => 20%, UMIs supporting every variant => 5). Results We analyzed an average of 926 cells per case. Our data confirms at the single cell level previous reports on high clonal heterogeneity and hypermutation rate (mean 18.7%) in FL. When analyzing intracellular heterogeneity we observed single FL cells expressing simultaneously transcripts derived from the same immunoglobulin VDJ rearrangement but displaying high confidence single nucleotide variants. After applying strict filtering strategies to account for potential technical issues we defined the occurrence of "SHM snapshot events'' when a single cell displayed a set of transcripts from a particular VDJ rearrangement with and without the occurring single nucleotide variant. Such events were detected in 8 of the 14 FL analyzed samples. In those 8 samples, 114 events were observed in which two different transcripts of one specific IG were found within a single cell. AID-related motifs (WRCY, WA and RCG) were found in 45% of the SHM snapshot events. SHM snapshot events were undetectable in CLL (5 samples) and 3 SHM snapshot events were detected in MBL (2 samples). In addition, the occurrence of SHM snapshot events was significantly associated with AID expression (Fisher exact test, p-value < 0.001). On the other hand, AID expression was not detectable on CLL and MBL samples. Conclusion Here we report for the first time the occurrence of ongoing somatic hypermutation at a single cell level in FL. The simultaneous detection of both the pre and post mutation IG mRNA transcripts within a single cell may be indicative of SHM occurring more recently than the lifespan of mRNA transcript. The detection of this phenomenon in 57% of FL samples and its association with AID expression suggests that AID-induced mutagenesis may be acting at a much higher rate than expected. This work highlights the role of AID in shaping the tumor heterogeneity in FL and the need to further understand the role of this enzyme in lymphomagenesis and tumor progression. Disclosures No relevant conflicts of interest to declare.


Blood ◽  
1997 ◽  
Vol 90 (6) ◽  
pp. 2282-2292 ◽  
Author(s):  
Ole J. Borge ◽  
Veslemøy Ramsfjell ◽  
Li Cui ◽  
Sten E.W. Jacobsen

Purified primitive progenitor/stem cells from bone marrow represent likely target populations for ex vivo expansion of stem cells to be used in high-dose chemotherapy or gene therapy. Whereas such primitive progenitor cells require combined stimulation by multiple cytokines for growth, some cytokines selectively promote viability rather than growth when acting individually. We investigated here for the first time the direct effects of cytokines on survival of primitive CD34+CD38− human bone marrow progenitor cells at the single-cell level. Interleukin-3 (IL-3) and the ligands for c-kit (KL) and flt3 (FL) had direct and selective viability-promoting effects on a small fraction of CD34+CD38− but not CD34+CD38+ progenitor cells. Interestingly, the recently cloned thrombopoietin (Tpo), although stimulating little growth, kept most CD34+CD38− progenitors viable after prolonged culture, maintaining twofold and fourfold more progenitors viable than KL and IL-3, respectively. A high fraction of these progenitors had a combined myeloid and erythroid differentiation potential, as well as capacity for prolonged production of progenitor cells under stroma-independent conditions. In addition, Tpo promoted viability of CD34+CD38− long-term culture-initiating cells, further supporting the idea that Tpo promotes viability of primitive human progenitor cells. Finally, Tpo suppressed apoptosis of CD34+CD38− cells in culture. Thus, the present studies show a novel effect of Tpo, implicating a potential role of this cytokine in maintaining quiescent primitive human progenitor cells viable.


Author(s):  
Cuifen Gan ◽  
Rongrong Wu ◽  
Yeshen Luo ◽  
Jianhua Song ◽  
Dizhou Luo ◽  
...  

Iron-reducing microorganisms (FeRM) play key roles in many natural and engineering processes. Visualizing and isolating FeRM from multispecies samples are essential to understand the in-situ location and geochemical role of FeRM. Here, we visualized FeRM by a “turn-on” Fe2+-specific fluorescent chemodosimeter (FSFC) with high sensitivity, selectivity and stability. This FSFC could selectively identify and locate active FeRM from either pure culture, co-culture of different bacteria or sediment-containing samples. Fluorescent intensity of the FSFC could be used as an indicator of Fe2+ concentration in bacterial cultures. By integrating FSFC with a single cell sorter, we obtained three FSFC-labeled cells from an enriched consortia and all of them were subsequently evidenced to be capable of iron-reduction and two unlabeled cells were evidenced to have no iron-reducing capability, further confirming the feasibility of the FSFC. IMPORTANCE Visualization and isolation of FeRM from samples containing multispecies are commonly needed by researchers from different disciplines, such as environmental microbiology, environmental sciences and geochemistry. However, no available method has been reported. In this study, we provide a solution to visualize FeRM and evaluate their activity even at single cell level. Integrating with single cell sorter, FeRM can also be isolated from samples containing multispecies. This method can be used as a powerful tool to uncover the in-situ or ex-situ role of FeRM and their interactions with ambient microbes or chemicals.


Blood ◽  
1997 ◽  
Vol 90 (6) ◽  
pp. 2282-2292 ◽  
Author(s):  
Ole J. Borge ◽  
Veslemøy Ramsfjell ◽  
Li Cui ◽  
Sten E.W. Jacobsen

Abstract Purified primitive progenitor/stem cells from bone marrow represent likely target populations for ex vivo expansion of stem cells to be used in high-dose chemotherapy or gene therapy. Whereas such primitive progenitor cells require combined stimulation by multiple cytokines for growth, some cytokines selectively promote viability rather than growth when acting individually. We investigated here for the first time the direct effects of cytokines on survival of primitive CD34+CD38− human bone marrow progenitor cells at the single-cell level. Interleukin-3 (IL-3) and the ligands for c-kit (KL) and flt3 (FL) had direct and selective viability-promoting effects on a small fraction of CD34+CD38− but not CD34+CD38+ progenitor cells. Interestingly, the recently cloned thrombopoietin (Tpo), although stimulating little growth, kept most CD34+CD38− progenitors viable after prolonged culture, maintaining twofold and fourfold more progenitors viable than KL and IL-3, respectively. A high fraction of these progenitors had a combined myeloid and erythroid differentiation potential, as well as capacity for prolonged production of progenitor cells under stroma-independent conditions. In addition, Tpo promoted viability of CD34+CD38− long-term culture-initiating cells, further supporting the idea that Tpo promotes viability of primitive human progenitor cells. Finally, Tpo suppressed apoptosis of CD34+CD38− cells in culture. Thus, the present studies show a novel effect of Tpo, implicating a potential role of this cytokine in maintaining quiescent primitive human progenitor cells viable.


2021 ◽  
Vol 754 ◽  
pp. 142076
Author(s):  
Peng Yan ◽  
Jin-song Guo ◽  
Ping Zhang ◽  
Yan Xiao ◽  
Zhe Li ◽  
...  

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