Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance

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Structure of the connector of bacteriophage T7 at 8A resolution: structural homologies of a basic component of a DNA translocating machinery

The three-dimensional structure of the bacteriophage T7 head-to-tail connector has been obtained at 8A resolution using cryo-electron microscopy and single-particle analysis from purified recombinant connectors. The general morphology of the T7 connector is that of a 12-folded toroidal homopolymer with a channel that runs along the longitudinal axis of the particle. The structure of the T7 connector reveals many structural similarities with the connectors from other bacteriophages. Docking of the atomic structure of the varphi29 connector into the three-dimensional reconstruction of T7 connector reveals that the narrow, distal region of the two oligomers are almost identical. This region of the varphi29 connector has been suggested to be involved in DNA translocation, and is composed of an alpha-beta-alpha-beta-beta-alpha motif. A search for alpha-helices in the same region of the T7 three-dimensional map has located three alpha-helices in approximately the same position as those of the varphi29 connector. A comparison of the predicted secondary structure of several bacteriophage connectors, including among others T7, varphi29, P22 and SPP1, reveals that, despite the lack of sequence homology, they seem to contain the same alpha-beta-alpha-beta-beta-alpha motif as that present in the varphi29 connector. These results allow us to suggest a common architecture related to a basic component of the DNA translocating machinery for several viruses.     

Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area

Current methods for monitoring marine fish (including bony fishes and elasmobranchs) diversity mostly rely on trawling surveys, which are invasive, costly, and time‐consuming. Moreover, these methods are selective, targeting a subset of species at the time, and can be inaccessible to certain areas. Here, we used environmental DNA (eDNA), the DNA present in the water column as part of shed cells, tissues, or mucus, to provide comprehensive information about fish diversity in a large marine area. Further, eDNA results were compared to the fish diversity obtained in pelagic trawls. A total of 44 5 L‐water samples were collected onboard a wide‐scale oceanographic survey covering about 120,000 square kilometers in Northeast Atlantic Ocean. A short region of the 12S rRNA gene was amplified and sequenced through metabarcoding generating almost 3.5 million quality‐filtered reads. Trawl and eDNA samples resulted in the same most abundant species (European anchovy, European pilchard, Atlantic mackerel, and blue whiting), but eDNA metabarcoding resulted in more detected bony fish and elasmobranch species (116) than trawling (16). Although an overall correlation between fishes biomass and number of reads was observed, some species deviated from the common trend, which could be explained by inherent biases of each of the methods. Species distribution patterns inferred from eDNA metabarcoding data coincided with current ecological knowledge of the species, suggesting that eDNA has the potential to draw sound ecological conclusions that can contribute to fish surveillance programs. Our results support eDNA metabarcoding for broad‐scale marine fish diversity monitoring in the context of Directives such as the Common Fisheries Policy or the Marine Strategy Framework Directive.     

Bird and Mammal Footprints From the Tertiary of Navarre (Western Pyrenees)

A rich variety of vertebrate footprints is known from a number of Upper Eocene to Lower Miocene localities of Navarre (western Pyrenees). The sediments were deposited in a wide range of depositional environments, from marginal marine to diversified terrestrial. Abundant bird tracks have been found in the coastal deposits of the Upper Eocene Liedena Sandstone of the Yesa and Itzagaondoa areas. Ciconiiformes-like (Leptoptilostipus pyrenaicus) and Charadriiformes-like (Charadriipeda ichnospp.) footprints have been recognized. Mammal ichnites have been discovered in the Oligocene and Lower Miocene deposits of Navarre. Equoid perissodactyl ichnites similar to those of Plagiolophustipus occur in the Oligocene fluviatile rocks of the Mués Sandstone of Olexoa and the Rocaforte Sandstone near Oibar and Sada. Trackways of entelodontids (Entelodontipus) are known in fluviatile-palustrine beds of the Oligocene Mués Sandstone of Olkotz. Additionally, bird (Charadriiformes-like) tracks are known in fluviatile-palustrine floodplain deposits of the Lower Miocene Ujué Formation of Los Arcos. In the same area, the Desoio and Los Arcos outcrops have also yielded perissodactyl trackways of possible Equoidea. Trackways of rhinocerotids (?) and artiodactyls (possibly Pecoripeda) are described from the Lower Miocene (Ramblian) palustrine limestones marginal to the Lerín Formation of Kaparroso and from alluvial fan deposits of the Uncastillo-Perdón Formation of Altzorritz, respectively.     

Maturation of phage T7 involves structural modification of both shell and inner core components

The double-stranded DNA bacteriophages are good model systems to understand basic biological processes such as the macromolecular interactions that take place during the virus assembly and maturation, or the behavior of molecular motors that function during the DNA packaging process. Using cryoelectron microscopy and single-particle methodology, we have determined the structures of two phage T7 assemblies produced during its morphogenetic process, the DNA-free prohead and the mature virion. The first structure reveals a complex assembly in the interior of the capsid, which involves the scaffolding, and the core complex, which plays an important role in DNA packaging and is located in one of the phage vertices. The reconstruction of the mature virion reveals important changes in the shell, now much larger and thinner, the disappearance of the scaffolding structure, and important rearrangements of the core complex, which now protrudes the shell and interacts with the tail. Some of these changes must originate by the pressure exerted by the DNA in the interior of the head.     

Physiology and population structure of Calanus finmarchicus (Copepoda: Calanoida) during a Lagrangian tracer release experiment in the North Atlantic

A population of Calanus finmarchicus was followed in the opensea for a period of 10 days at the end of June 1996 using atracer release method. Gut fluorescence, egg production, carboncontent and stage specific abundance, together with phytoplanktonconcentration and composition, were measured during this period.Chlorophyll levels were less than 1 µg l^–1 and thephytoplankton population was dominated by coccolithophorids.Gut fluorescence decreased during a period with strong winds,whereas egg production remained constant. Estimated phytoplanktoningestion was too low to cover egg production requirements.However, the microzooplankton concentration seemed to be highenough to complement phytoplankton ingestion, enabling egg productioncarbon requirements to be covered. C/N ratios of adult femalesand stage CV were low, indicating low levels of lipid storage.The population was dominated by stage CIV, but shifted to adominance of younger stages during the study. Mortality calculatedfrom population structure indicates that higher death ratesoccurred at stage CV.     

Microarray time course experiments: finding profiles

Time course studies with microarray techniques and experimental replicates are very useful in biomedical research. We present, in replicate experiments, an alternative approach to select and cluster genes according to a new measure for association between genes. First, the procedure normalizes and standardizes the expression profile of each gene, and then, identifies scaling parameters that will further minimize the distance between replicates of the same gene. Then, the procedure filters out genes with a flat profile, detects differences between replicates, and separates genes without significant differences from the rest. For this last group of genes, we define a mean profile for each gene and use it to compute the distance between two genes. Next, a hierarchical clustering procedure is proposed, a statistic is computed for each cluster to determine its compactness, and the total number of classes is determined. For the rest of the genes, those with significant differences between replicates, the procedure detects where the differences between replicates lie, and assigns each gene to the best fitting previously identified profile or defines a new profile. We illustrate this new procedure using simulated data and a representative data set arising from a microarray experiment with replication, and report interesting results.     

Feeding rates and productivity of the copepod Acartia bifilosa in a highly turbid estuary; the Gironde (SW France)

Acartia spp. are the dominant copepod species in the Gironde estuary, seaward of the turbidity maximum area. Acartia bifilosa develop a large population in spring and early summer whereas Acartia tonsa appear in late summer. High values and high variability of chlorophyll a/suspended particulate matter ratio are found seaward of the turbidity maximum area. Feeding rates of A. bifilosa were measured by fluorometry. Phytoplankton ingestion was found to be highly variable, between 8 to 80% of copepod carbon body weight. Except for adult females, copepods were heavier in summer than in winter. PB ratios, estimated by the instantaneous growth rate method, varied from 0.03 d^–1 to 0.14 d^–1. The gut contents and P/B ratios of Acartia bifilosa were related to chl a/SPM ratio. From those data, and a few obtained for A. tonsa, it is concluded that only in summer months phytoplankton ingestion is enough to maintain secondary production.