Concept: Cauchy sequence
We report here the second complete genome sequence of Streptococcus suis serotype 3 (strain YB51). The genome is 2,043,655 bp in length, which is 14,840 bp longer than the first reported genome of the same serotype, and it covers 2,012 coding sequences, 56 tRNAs, and 4 rRNA loci.
As the cost of sequencing continues to decrease and the amount of sequence data generated grows, new paradigms for data storage and analysis are increasingly important. The relative scaling behavior of these evolving technologies will impact genomics research moving forward.
Perception is guided by the anticipation of future events. It has been hypothesized that this process may be implemented by pattern completion in early visual cortex, in which a stimulus sequence is recreated after only a subset of the visual input is provided. Here we test this hypothesis using ultra-fast functional magnetic resonance imaging to measure BOLD activity at precisely defined receptive field locations in visual cortex (V1) of human volunteers. We find that after familiarizing subjects with a spatial sequence, flashing only the starting point of the sequence triggers an activity wave in V1 that resembles the full stimulus sequence. This preplay activity is temporally compressed compared to the actual stimulus sequence and remains present even when attention is diverted from the stimulus sequence. Preplay might therefore constitute an automatic prediction mechanism for temporal sequences in V1.
Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies.
The effect of epistasis on response to selection is a highly debated topic. Here, we investigated the impact of epistasis on response to sequence-based selection via genomic best linear prediction (GBLUP) in a regime of strong non-symmetrical epistasis under divergent selection, using real Drosophila sequence data. We also explored the possible advantage of including epistasis in the evaluation model and/or of knowing the causal mutations.
Analysis of complete capsid sequences of the emerging norovirus GII.17 Kawasaki 308 from 13 countries demonstrated that they originated from a single haplotype since the initial emergence in China in late 2014. Global spread of a sublineage SL2 was identified. A new sublineage SL3 emerged in China in 2016.
The third generation PacBio SMRT long reads can effectively address the read length issue of the second generation sequencing technology, but contain approximately 15% sequencing errors. Several error correction algorithms have been designed to efficiently reduce the error rate to 1%, but they discard large amounts of uncorrected bases and thus lead to low throughput. This loss of bases could limit the completeness of downstream assemblies and the accuracy of analysis.
Here, we report the complete closed genome sequence and methylome analysis of Beggiatoa leptomitoformis strain D-401 (DSM 14945, UNIQEMU 779), which is quite different from the previously described Beggiatoa leptomitoformis neotype strain D-402T (DSM 14946, UNIQEM U 779) with regard to morphology and lithotrophic growth in the presence of thiosulfate.
Intracranial vessel wall MR imaging plays an increasing role in diagnosing intracranial vascular diseases. For a complete assessment, pre- and postcontrast sequences are required, and including other sequences, these result in a long scan duration. Ideally, the scan time of the vessel wall sequence should be reduced. The purpose of this study was to evaluate different intracranial vessel wall sequence variants to reduce scan duration, provided an acceptable image quality can be maintained.
The emergence of nosocomial infections by multidrug-resistantStaphylococcus haemolyticusisolates has been reported in several European countries. Here, we report the first two complete genome sequences ofS. haemolyticussequence type 25 (ST25) isolates 83131A and 83131B. Both isolates were isolated from the same clinical sample and were first identified through shotgun metagenomics.