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1.
Nature ; 566(7743): E6, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30670873

RESUMEN

In this Article, the top label in Fig. 5d should read 'DISH 3/16' instead of 'DISH 3/17'. This error has been corrected online.

2.
Nucleic Acids Res ; 51(9): 4178-4190, 2023 05 22.
Artículo en Inglés | MEDLINE | ID: mdl-37070603

RESUMEN

The human gut microbiome has been linked to health and disease. Investigation of the human microbiome has largely employed 16S amplicon sequencing, with limited ability to distinguish microbes at the species level. Herein, we describe the development of Reference-based Exact Mapping (RExMap) of microbial amplicon variants that enables mapping of microbial species from standard 16S sequencing data. RExMap analysis of 16S data captures ∼75% of microbial species identified by whole-genome shotgun sequencing, despite hundreds-fold less sequencing depth. RExMap re-analysis of existing 16S data from 29,349 individuals across 16 regions from around the world reveals a detailed landscape of gut microbial species across populations and geography. Moreover, RExMap identifies a core set of fifteen gut microbes shared by humans. Core microbes are established soon after birth and closely associate with BMI across multiple independent studies. RExMap and the human microbiome dataset are presented as resources with which to explore the role of the human microbiome.


Asunto(s)
Microbioma Gastrointestinal , Microbiota , Humanos , Bacterias/clasificación , Microbioma Gastrointestinal/genética , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN
3.
Nature ; 563(7733): 639-645, 2018 11.
Artículo en Inglés | MEDLINE | ID: mdl-30464338

RESUMEN

The diversity and complexity of the human brain are widely assumed to be encoded within a constant genome. Somatic gene recombination, which changes germline DNA sequences to increase molecular diversity, could theoretically alter this code but has not been documented in the brain, to our knowledge. Here we describe recombination of the Alzheimer's disease-related gene APP, which encodes amyloid precursor protein, in human neurons, occurring mosaically as thousands of variant 'genomic cDNAs' (gencDNAs). gencDNAs lacked introns and ranged from full-length cDNA copies of expressed, brain-specific RNA splice variants to myriad smaller forms that contained intra-exonic junctions, insertions, deletions, and/or single nucleotide variations. DNA in situ hybridization identified gencDNAs within single neurons that were distinct from wild-type loci and absent from non-neuronal cells. Mechanistic studies supported neuronal 'retro-insertion' of RNA to produce gencDNAs; this process involved transcription, DNA breaks, reverse transcriptase activity, and age. Neurons from individuals with sporadic Alzheimer's disease showed increased gencDNA diversity, including eleven mutations known to be associated with familial Alzheimer's disease that were absent from healthy neurons. Neuronal gene recombination may allow 'recording' of neural activity for selective 'playback' of preferred gene variants whose expression bypasses splicing; this has implications for cellular diversity, learning and memory, plasticity, and diseases of the human brain.


Asunto(s)
Enfermedad de Alzheimer/genética , Enfermedad de Alzheimer/patología , Precursor de Proteína beta-Amiloide/genética , Variación Genética/genética , Neuronas/citología , Neuronas/patología , Recombinación Genética , Empalme Alternativo/genética , Animales , ADN Complementario/análisis , ADN Complementario/genética , ADN Polimerasa Dirigida por ADN/metabolismo , Exones/genética , Femenino , Humanos , Intrones/genética , Masculino , Ratones , Ratones Transgénicos , Neuronas/metabolismo , Especificidad de Órganos , Mutación Puntual/genética , ARN Mensajero/análisis , ARN Mensajero/genética , Análisis de Secuencia de ADN , Eliminación de Secuencia/genética
4.
Phys Biol ; 19(2)2022 01 31.
Artículo en Inglés | MEDLINE | ID: mdl-34942613

RESUMEN

In studies of the unicellular eukaryoteDictyostelium discoideum, many have anecdotally observed that cell dilution below a certain 'threshold density' causes cells to undergo a period of slow growth (lag). However, little is documented about the slow growth phase and the reason for different growth dynamics below and above this threshold density. In this paper, we extend and correct our earlier work to report an extensive set of experiments, including the use of new cell counting technology, that set this slow-to-fast growth transition on a much firmer biological basis. We show that dilution below a certain density (around 104cells ml-1) causes cells to grow slower on average and exhibit a large degree of variability: sometimes a sample does not lag at all, while sometimes it takes many moderate density cell cycle times to recover back to fast growth. We perform conditioned media experiments to demonstrate that a chemical signal mediates this endogenous phenomenon. Finally, we argue that while simple models involving fluid transport of signal molecules or cluster-based signaling explain typical behavior, they do not capture the high degree of variability between samples but nevertheless favor an intra-cluster mechanism.


Asunto(s)
Modelos Biológicos , Transducción de Señal , Ciclo Celular , Densidad de Población , Dinámica Poblacional
5.
Proc Natl Acad Sci U S A ; 113(41): 11414-11419, 2016 10 11.
Artículo en Inglés | MEDLINE | ID: mdl-27681630

RESUMEN

The ecology of microbes in the gut has been shown to play important roles in the health of the host. To better understand microbial growth and population dynamics in the proximal colon, the primary region of bacterial growth in the gut, we built and applied a fluidic channel that we call the "minigut." This is a channel with an array of membrane valves along its length, which allows mimicking active contractions of the colonic wall. Repeated contraction is shown to be crucial in maintaining a steady-state bacterial population in the device despite strong flow along the channel that would otherwise cause bacterial washout. Depending on the flow rate and the frequency of contractions, the bacterial density profile exhibits varying spatial dependencies. For a synthetic cross-feeding community, the species abundance ratio is also strongly affected by mixing and flow along the length of the device. Complex mixing dynamics due to contractions is described well by an effective diffusion term. Bacterial dynamics is captured by a simple reaction-diffusion model without adjustable parameters. Our results suggest that flow and mixing play a major role in shaping the microbiota of the colon.


Asunto(s)
Bacterias/crecimiento & desarrollo , Tracto Gastrointestinal/microbiología , Peristaltismo , Reología , Recuento de Colonia Microbiana , Difusión , Modelos Biológicos
6.
Phys Rev Lett ; 119(24): 248101, 2017 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-29286727

RESUMEN

Eukaryotic cells sense molecular gradients by measuring spatial concentration variation through the difference in the number of occupied receptors to which molecules can bind. They also secrete enzymes that degrade these molecules, and it is presently not well understood how this affects the local gradient perceived by cells. Numerical and analytical results show that these enzymes can substantially increase the signal-to-noise ratio of the receptor difference and allow cells to respond to a much broader range of molecular concentrations and gradients than they would without these enzymes.


Asunto(s)
AMP Cíclico/metabolismo , Células Eucariotas/metabolismo , Modelos Biológicos , Hidrolasas Diéster Fosfóricas/metabolismo , Ácido Aspártico Endopeptidasas/metabolismo , Quimiotaxis , Dictyostelium/enzimología , Dictyostelium/metabolismo , Difusión , Células Eucariotas/citología , Células Eucariotas/enzimología , Saccharomyces cerevisiae/enzimología , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo
7.
Phys Biol ; 11(3): 036001, 2014 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-24732749

RESUMEN

Unicellular eukaryotic amoebae Dictyostelium discoideum are generally believed to grow in their vegetative state as single cells until starvation, when their collective aspect emerges and they differentiate to form a multicellular slime mold. While major efforts continue to be aimed at their starvation-induced social aspect, our understanding of population dynamics and cell cycle in the vegetative growth phase has remained incomplete. Here we show that cell populations grown on a substrate spontaneously synchronize their cell cycles within several hours. These collective population-wide cell cycle oscillations span millimeter length scales and can be completely suppressed by washing away putative cell-secreted signals, implying signaling by means of a diffusible growth factor or mitogen. These observations give strong evidence for collective proliferation behavior in the vegetative state.


Asunto(s)
Dictyostelium/citología , Dictyostelium/crecimiento & desarrollo , Ciclo Celular , Proliferación Celular , Modelos Biológicos , Periodicidad
8.
Science ; 378(6624): eabk2066, 2022 12 09.
Artículo en Inglés | MEDLINE | ID: mdl-36480614

RESUMEN

Protein concentrations are set by a complex interplay between gene-specific regulatory processes and systemic factors, including cell volume and shared gene expression machineries. Elucidating this interplay is crucial for discerning and designing gene regulatory systems. We quantitatively characterized gene-specific and systemic factors that affect transcription and translation genome-wide for Escherichia coli across many conditions. The results revealed two design principles that make regulation of gene expression insulated from concentrations of shared machineries: RNA polymerase activity is fine-tuned to match translational output, and translational characteristics are similar across most messenger RNAs (mRNAs). Consequently, in bacteria, protein concentration is set primarily at the promoter level. A simple mathematical formula relates promoter activities and protein concentrations across growth conditions, enabling quantitative inference of gene regulation from omics data.


Asunto(s)
Escherichia coli , Regulación Bacteriana de la Expresión Génica , Biosíntesis de Proteínas , ARN Mensajero , Biosíntesis de Proteínas/genética , ARN Bacteriano/genética , ADN Bacteriano/genética , Escherichia coli/genética , Regiones Promotoras Genéticas , ARN Mensajero/genética , ARN Mensajero/metabolismo , Transcripción Genética
9.
Nucleic Acids Res ; 36(Web Server issue): W332-5, 2008 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-18480121

RESUMEN

MADNet is a user-friendly data mining and visualization tool for rapid analysis of diverse high-throughput biological data such as microarray, phage display or even metagenome experiments. It presents biological information in the context of metabolic and signalling pathways, transcription factors and drug targets through minimal user input, consisting only of the file with the experimental data. These data are integrated with information stored in various biological databases such as NCBI nucleotide and protein databases, metabolic and signalling pathway databases (KEGG), transcription regulation (TRANSFAC(c)) and drug target database (DrugBank). MADNet is freely available for academic use at http://www.bioinfo.hr/madnet.


Asunto(s)
Perfilación de la Expresión Génica/métodos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Programas Informáticos , Gráficos por Computador , Bases de Datos Genéticas , Internet , Redes y Vías Metabólicas/genética , Transducción de Señal/genética , Integración de Sistemas , Interfaz Usuario-Computador
10.
Cell Rep ; 30(6): 1753-1766.e6, 2020 02 11.
Artículo en Inglés | MEDLINE | ID: mdl-32049008

RESUMEN

Growing evidence supports the importance of gut microbiota in the control of tumor growth and response to therapy. Here, we select prebiotics that can enrich bacterial taxa that promote anti-tumor immunity. Addition of the prebiotics inulin or mucin to the diet of C57BL/6 mice induces anti-tumor immune responses and inhibition of BRAF mutant melanoma growth in a subcutaneously implanted syngeneic mouse model. Mucin fails to inhibit tumor growth in germ-free mice, indicating that the gut microbiota is required for the activation of the anti-tumor immune response. Inulin and mucin drive distinct changes in the microbiota, as inulin, but not mucin, limits tumor growth in syngeneic mouse models of colon cancer and NRAS mutant melanoma and enhances the efficacy of a MEK inhibitor against melanoma while delaying the emergence of drug resistance. We highlight the importance of gut microbiota in anti-tumor immunity and the potential therapeutic role for prebiotics in this process.


Asunto(s)
Microbioma Gastrointestinal/efectos de los fármacos , Inulina/uso terapéutico , Melanoma/tratamiento farmacológico , Mucinas/uso terapéutico , Prebióticos/análisis , Animales , Inulina/farmacología , Melanoma/patología , Ratones , Mucinas/farmacología
11.
Nat Commun ; 10(1): 1492, 2019 04 02.
Artículo en Inglés | MEDLINE | ID: mdl-30940817

RESUMEN

Accumulating evidence points to an important role for the gut microbiome in anti-tumor immunity. Here, we show that altered intestinal microbiota contributes to anti-tumor immunity, limiting tumor expansion. Mice lacking the ubiquitin ligase RNF5 exhibit attenuated activation of the unfolded protein response (UPR) components, which coincides with increased expression of inflammasome components, recruitment and activation of dendritic cells and reduced expression of antimicrobial peptides in intestinal epithelial cells. Reduced UPR expression is also seen in murine and human melanoma tumor specimens that responded to immune checkpoint therapy. Co-housing of Rnf5-/- and WT mice abolishes the anti-tumor immunity and tumor inhibition phenotype, whereas transfer of 11 bacterial strains, including B. rodentium, enriched in Rnf5-/- mice, establishes anti-tumor immunity and restricts melanoma growth in germ-free WT mice. Altered UPR signaling, exemplified in Rnf5-/- mice, coincides with altered gut microbiota composition and anti-tumor immunity to control melanoma growth.


Asunto(s)
Proliferación Celular , Microbioma Gastrointestinal , Melanoma/inmunología , Melanoma/microbiología , Proteínas de la Membrana/deficiencia , Ubiquitina-Proteína Ligasas/deficiencia , Animales , Péptidos Catiónicos Antimicrobianos/inmunología , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Humanos , Intestinos/inmunología , Intestinos/microbiología , Melanoma/enzimología , Melanoma/fisiopatología , Proteínas de la Membrana/genética , Proteínas de la Membrana/inmunología , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Ubiquitina-Proteína Ligasas/genética , Ubiquitina-Proteína Ligasas/inmunología , Respuesta de Proteína Desplegada
12.
J R Soc Interface ; 10(88): 20130606, 2013 Nov 06.
Artículo en Inglés | MEDLINE | ID: mdl-24026470

RESUMEN

Living cells depend upon the detection of chemical signals for their existence. Eukaryotic cells can sense a concentration difference as low as a few per cent across their bodies. This process was previously suggested to be limited by the receptor-ligand binding fluctuations. Here, we first determine the chemotaxis response of Dictyostelium cells to static folic acid gradients and show that they can significantly exceed this sensitivity, responding to gradients as shallow as 0.2% across the cell body. Second, using a previously developed information theory framework, we compare the total information gained about the gradient (based on the cell response) to its upper limit: the information gained at the receptor-ligand binding step. We find that the model originally applied to cAMP sensing fails as demonstrated by the violation of the data processing inequality, i.e. the total information exceeds the information at the receptor-ligand binding step. We propose an extended model with multiple known receptor types and with cells allowed to perform several independent measurements of receptor occupancy. This does not violate the data processing inequality and implies the receptor-ligand binding noise dominates both for low- and high-chemoattractant concentrations. We also speculate that the interplay between exploration and exploitation is used as a strategy for accurate sensing of otherwise unmeasurable levels of a chemoattractant.


Asunto(s)
Quimiotaxis/fisiología , Dictyostelium/fisiología , Ácido Fólico/metabolismo , Modelos Biológicos , Transducción de Señal/fisiología , AMP Cíclico/metabolismo
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