jueves, 3 de diciembre de 2015

Complete nitrification by a single microorganism (Comammox)

Nitrification is a two-step process where ammonia is first oxidized to nitrite by ammonia-oxidizing bacteria and/or archaea, and subsequently to nitrate by nitrite-oxidizing bacteria. Already described by Winogradsky in 1890, this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle. Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible, and it was postulated that this process could occur under conditions selecting for species with lower growth rates but higher growth yields than canonical ammonia-oxidizing microorganisms. Still, organisms catalysing this process have not yet been discovered. Here we report the enrichment and initial characterization of two Nitrospira species that encode all the enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel amoA sequence group will lead to an improved understanding of the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle.

In situ detection of Nitrospira and their ammonia-oxidizing capacity.

a, Co-aggregation of Nitrospira and Brocadia in the enrichment. Cells are stained by FISH with probes for all bacteria (EUB338mix, blue), and specific for Nitrospira (Ntspa712, green, resulting in cyan) and anammox bacteria (Amx820, red, resulting in magenta). b, AMO labelling by FTCP (green). Nitrospira was counterstained by FISH (probes Ntspa662 (blue) and Ntspa476 (red), resulting in white). c, Ammonium-dependent CO2 fixation by Nitrospira shown by FISH-MAR. Silver grain deposition (black) above cell clusters indicates 14CO2 incorporation. Nitrospira was stained by FISH (probes Ntspa476 (red) and Ntspa662 (blue), resulting in magenta). Images in b and c are representative of two individual experiments, with three (b) or two (c) technical replicates each. Scale bars in all panels represent 10 μm.

Enlace al trabajo original

jueves, 26 de noviembre de 2015

¿Cómo cultivar microorganismos no cultivables?

Many microorganisms are "unculturable," or at least not able to grow in known media. Now, a new tool enables researchers to predict what nutrients organisms need to thrive in the lab, eliminating most of the guesswork involved in setting up new cultures. Read more...
Studying microbes has provided unparalleled insights into the molecular mechanisms governing cell functions, but expanding on such studies with new microbes depends on finding the right media for culturing the bacteria. Now, Matthew Oberhardt, a postdoctoral fellow at the Center for Bioinformatics and Computational Biology at the University of Maryland, and his colleagues present a new way to approach these “unculturables” in the journal Nature Communications.
“We had a very simple question in mind. Could we try to predict the minimal media needed to actually grow organisms?” he said. To find the answer, Oberhardt and his fellow researchers turned to the Leibniz Institute German Collection of Microorganisms and Cell Cultures, which hosts a repository of around 1300 media recipes for 23,000 microbes. “We thought that we might be able to extract a lot of information and create a new paradigm where we could do some predictive modeling.”
The team combed through recipe files and extracted details such as ingredient lists and salt concentrations to create a Known Media Database (KOMODO) that includes more than 18,000 strain-media combinations as well as more than 3000 media variants and compound concentrations.
Oberhardt and his colleagues then leveraged the database to predict which organisms would grow well in which media. By looking at media that support multiple microbes and applying the transitive property and a phylogeny-based filter, they were able to predict which microbes would grow in new in vitro experiments with approximately 83% accuracy.
“No one has really looked at this problem this way before, and we’ve been able to set a new framework,” Oberhardt said. “We’re not done yet. We’re going to improve the database by including more biogenetic data and ecological data. But we think this is a really good starting point, and we can use more sophisticated machine learning methods to help us create good metabolic models in the future.”

Oberhardt MA, Zarecki R, Gronow S, Lang E, Klenk HP, Gophna U, Ruppin E. Harnessing the landscape of microbial culture media to predict new organism-media pairings. Nat Commun. 2015 Oct 13;6:8493. doi: 10.1038/ncomms9493.  

jueves, 5 de noviembre de 2015

Novel antibody–antibiotic conjugate eliminates intracellular S. aureus

Staphylococcus aureus is considered to be an extracellular pathogen. However, survival of S. aureus within host cells may provide a reservoir relatively protected from antibiotics, thus enabling long-term colonization of the host and explaining clinical failures and relapses after antibiotic therapy. Here we confirm that intracellular reservoirs of S. aureus in mice comprise a virulent subset of bacteria that can establish infection even in the presence of vancomycin, and we introduce a novel therapeutic that effectively kills intracellular S. aureus. This antibody–antibiotic conjugate consists of an anti-S. aureus antibody conjugated to a highly efficacious antibiotic that is activated only after it is released in the proteolytic environment of the phagolysosome. The antibody–antibiotic conjugate is superior to vancomycin for treatment of bacteraemia and provides direct evidence that intracellular S. aureus represents an important component of invasive infections.

AAC design.

a, Model of AAC (not drawn to scale). b, Mechanism of AAC action. c, Binding of Alexa-488 anti-β-GlcNAC WTA monoclonal antibody (mAb) or anti-α-GlcNAC WTA monoclonal antibody, or isotype control antibody, anti-cytomegalovirus glycoprotein-D (gD) to USA300 isolated from infected kidneys (n = 3). MFI, mean fluorescence intensity. d, Binding of anti-GlcNAC WTA antibodies (red) or isotype control (grey) to protein-A-deficient USA300 lacking tarM or tarS (n = 3). WT, wild type. e, Crystal structure of anti-β-GlcNAc WTA Fab bound to a synthetic minimal β-WTA unit. Antibody light chain (pink) and heavy chain (blue) are shown. f, MIC determination for rifampicin and rifalogue on USA300 (n = 5). g, Survival of stationary phase USA300 incubated with 1 × 10−6 M rifampicin or rifalogue (n = 4). h, USA300 bacteria were incubated without antibiotic (black) or with 3 μg ml−1 ciprofloxacin (Cipro; green, red and grey). 1 μg ml−1 of rifalogue (red) or rifampicin (grey) was added as indicated (n = 3). i, Intact AAC does not kill planktonic bacteria but does after pre-treatment with cathepsin-B (n = 3). g–i, Error bars show s.d. for triplicate samples (n = biological repeats).

Enlace al trabajo

miércoles, 7 de octubre de 2015

Premio Nobel de Química 2015 para los padres de los mecanismos de reparación del ADN

La Real Academia de las Ciencias Sueca ha galardonado con el Nobel de Química 2015 a Tomas Lindahl, Paul Modrich y Aziz Sancarr, considerados los padres de los mecanismos de reparación del ADN, cuyo conocimiento ha permitido, por ejemplo, desarrollar tratamientos para enfermedades como el cáncer.
Tomas Lindahl

Tomas Lindahl

Prize share: 1/3
Paul Modrich

Paul Modrich

Prize share: 1/3
Aziz Sancar

Aziz Sancar

Prize share: 1/3
El jurado ha considerado que los trabajos de los tres investigadores han sido clave para aprender cómo reparan las células su ADN y cómo salvaguardan su material genético.
Lindahl (Estocolmo, 1938) trabaja en el Instituto Francis Crick del Reino Unido, Modrich (1946) es investigador de la Universidad de Duke (EEUU) mientras que Sancar (de origen turco, aunque con pasaporte estadounidense) es investigador de la Universidad de Carolina del Norte. Como ha explicado el jurado, nuestras células sufren cada día cientos de alteraciones provocadas por agentes como el tabaco, las radiaciones solares o los radicales libres; "incluso sin esos ataques, el ADN es altamente inestable". Lo que los nuevos Nobel de Química descubrieron en sus laboratorios desde los años 70 es que existe todo un complejo sistema de reparación del material genético de las células para impedir que estos cambios se traduzcan en un completo "caos celular".

lunes, 5 de octubre de 2015

El Nobel de Medicina premia nuevos tratamientos contra infecciones de parásitos y malaria

De izquierda a derecha: William C. Campbell, Satoshi Omura y Yoyou Tu
De izquierda a derecha: William C. Campbell, Satoshi Omura y Yoyou Tu

El Nobel de Medicina y Fisiología ha premiado este año avances cruciales contra enfermedades provocadas por parásitos que durante milenios han asolado a la Humanidad y hoy siguen constituyendo uno de los problemas sanitarios más graves del mundo actual, sobre todo en los países más pobres. El Instituto Karolinska ha anunciado en Estocolmo el galardón, que comparten William C. Campbell y Satoshi Omura por descubrir una nueva terapia contra infecciones de lombrices redondas (nemátodos) y Youyou Tu por desarrollar un tratamiento novedoso contra la malaria. Los galardonados compartirán un premio económico de ocho millones de coronas suecas (855.000 euros, 954.000 dólares).
Según informó el comité al dar a conocer el nombre de los galardonados, los tres premiados este año "han desarrollado terapias que han revolucionado el tratamiento de algunas de las más devastadoras enfermedades parasitarias".
El irlandés Campbell y el japonés Omura descubrieron un nuevo fármaco, la Ivermectina, que ha logrado reducir de forma radical la incidencia de la oncocercosis o ceguera de los ríos y la filariasis linfática o elefantiasis, además de mostrar una eficacia parcial contra otras enfermedades parasitarias. La científica china Youyou Tu, por su parte, descubrió la Artemisina, una droga que ha reducido de manera muy significativa la mortalidad por malaria.

Un fármaco 'revolucionario'

El primer compuesto se desarrolló en los años '80 y, según los expertos, rompió todos los esquemas, primero en el mercado veterinario. Mataba parásitos de dos tipos, los que viven en la piel y los que proceden del intestino. Al poco tiempo, este fármaco demostró eficacia contra un parásito 'primo hermano' del que causa la oncocercosis en caballos. Dados los resultados y teniendo en cuenta el grave problema que había en África y Latinoamérica con la ceguera de los ríos en humanos, se pusieron en marcha ensayos clínicos. Se comprobó que en personas, la Ivermectina "no era capaz de matar al parásito (Onchocerca volvulus), pero sí lo dejaba estéril, es decir, conseguía prevenir la enfermedad durante un periodo de tiempo", expone a EL MUNDO Carlos Chaccour, médico e investigador de la Universidad de Navarra.
Desde entonces, como medida de prevención, argumenta Chaccour, "en estas zonas de riesgo, donde la oncocercosis causaba estragos y dejaba a poblaciones enteras ciegas, se toma este fármaco aproximadamente una vez al año. En el Amazonas incluso hasta cuatro veces al año". Tales eran los efectos que la farmacéutica Merck & Co., la empresa que descubrió y fabrica el fármaco, decidió donarlo a los países donde la oncocercosis es endémica. Gracias a ello, se han tratado anualmente a unos 60-80 millones de personas.
La Ivermectina no sólo previene la ceguera de los ríos, también está autorizada en Francia, por ejemplo, para la sarna complicada y actúa frente a otros parásitos como la filariasis linfática o elefantiasis (una enfermedad tropical que puede producir alteraciones del sistema linfático e hipertrofia anormal de algunas partes del cuerpo, causando dolor, discapacidad grave y estigma social), entre otras enfermedades parasitarias.

Tomado de "El Mundo"

jueves, 24 de septiembre de 2015

Los virus se defienden de nuevo

The battle for survival between bacteria and the viruses that infect them (phages) has led to the evolution of many bacterial defence systems and phage-encoded antagonists of these systems. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated (cas) genes comprise an adaptive immune system that is one of the most widespread means by which bacteria defend themselves against phages. We identified the first examples of proteins produced by phages that inhibit a CRISPR–Cas system. Here we performed biochemical and in vivo investigations of three of these anti-CRISPR proteins, and show that each inhibits CRISPR–Cas activity through a distinct mechanism. Two block the DNA-binding activity of the CRISPR–Cas complex, yet do this by interacting with different protein subunits, and using steric or non-steric modes of inhibition. The third anti-CRISPR protein operates by binding to the Cas3 helicase–nuclease and preventing its recruitment to the DNA-bound CRISPR–Cas complex. In vivo, this anti-CRISPR can convert the CRISPR–Cas system into a transcriptional repressor, providing the first example—to our knowledge—of modulation of CRISPR–Cas activity by a protein interactor. The diverse sequences and mechanisms of action of these anti-CRISPR proteins imply an independent evolution, and foreshadow the existence of other means by which proteins may alter CRISPR–Cas function.

Tomado de: 

Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR protein

Published online

jueves, 2 de julio de 2015

Eye-like ocelloids are built from different endosymbiotically acquired components