https://archive-ouverte.unige.ch/unige:26185/ATTACHMENT01

Cortical oscillations and sensory predictions

http://www.f.waseda.jp/fukuzawa/eeg/Bendixen2012.pdf

Early electrophysiological indicators for predictive processing in audition: a review.

Rhythmic facilitation of sensory processing: A critical review.

Human milk contains a diverse population of bacteria that likely influences colonization of the infant gastrointestinal tract. Recent studies, however, have been limited to characterization of this microbial community by 16S rRNA analysis. In the present study, a metagenomic approach using Illumina sequencing of a pooled milk sample (ten donors) was employed to determine the genera of bacteria and the types of bacterial open reading frames in human milk that may influence bacterial establishment and stability in this primal food matrix. The human milk metagenome was also compared to that of breast-fed and formula-fed infants’ feces (n = 5, each) and mothers’ feces (n = 3) at the phylum level and at a functional level using open reading frame abundance. Additionally, immune-modulatory bacterial-DNA motifs were also searched for within human milk. The bacterial community in human milk contained over 360 prokaryotic genera, with sequences aligning predominantly to the phyla of Proteobacteria (65%) and Firmicutes (34%), and the genera of Pseudomonas (61.1%), Staphylococcus (33.4%) and Streptococcus (0.5%). From assembled human milk-derived contigs, 30,128 open reading frames were annotated and assigned to functional categories. When compared to the metagenome of infants’ and mothers’ feces, the human milk metagenome was less diverse at the phylum level, and contained more open reading frames associated with nitrogen metabolism, membrane transport and stress response (P < 0.05). The human milk metagenome also contained a similar occurrence of immune-modulatory DNA motifs to that of infants’ and mothers’ fecal metagenomes. Our results further expand the complexity of the human milk metagenome and enforce the benefits of human milk ingestion on the microbial colonization of the infant gut and immunity. Discovery of immune-modulatory motifs in the metagenome of human milk indicates more exhaustive analyses of the functionality of the human milk metagenome are warranted.

/pdf/human-milk-metagenome-a-functional-capacity-analysis-3hpmn31m35.pdf

Human milk metagenome: a functional capacity analysis

Strains of Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from nitrogen-fixing nodules of the native legumes Listia angolensis (from Zambia) and Lupinus texensis (from Texas, USA). Phylogenetic analysis of the 16S rRNA gene showed that the novel strains belong to the genus Microvirga, with 96.1 % or greater sequence similarity with type strains of this genus. The closest relative of the representative strains Lut6T and WSM3557T was M. flocculans TFBT, with 97.6-98.0 % similarity, while WSM3693T was most closely related to M. aerilata 5420S-16T, with 98.8 % similarity. Analysis of the concatenated sequences of four housekeeping gene loci (dnaK, gyrB, recA, rpoB) and cellular fatty acid profiles confirmed the placement of Lut6T, WSM3557T and WSM3693T within Microvirga. DNA:DNA relatedness values and physiological and biochemical tests allowed genotypic and phenotypic differentiation of Lut6T, WSM3557T and WSM3693T from each other and from other validly published Microvirga species. The nodA sequence of Lut6T was placed in a clade that contained strains of Rhizobium, Mesorhizobium and Sinorhizobium, while the 100 % identical nodA sequences of WSM3557T and WSM3693T clustered with Bradyrhizobium, Burkholderia and Methylobacterium strains. Concatenated sequences for nifD and nifH show that Lut6T, WSM3557T and WSM3693T were most closely related to Rhizobium etli CFN42T nifDH. On the basis of genotypic, phenotypic and DNA relatedness data, three novel species of Microvirga are proposed: Microvirga lupini (Lut6T = LMG26460T, = HAMBI 3236) Microvirga lotononidis (WSM3557T = LMG26455T, = HAMBI 3237) and Microvirga zambiensis (WSM3693T = LMG26454T, = HAMBI 3238).

/pdf/microvirga-lupini-sp-nov-microvirga-lotononidis-sp-nov-and-1mhc834606.pdf

Microvirga lupini sp. nov., Microvirga lotononidis sp. nov. and Microvirga zambiensis sp. nov. are alphaproteobacterial root-nodule bacteria that specifically nodulate and fix nitrogen with geographically and taxonomically separate legume hosts

The purpose of this protocol is the isolation of bulk cellular DNA from bacteria (alternatively see Preparation of genomic DNA from Saccharomyces cerevisiae or Isolation of Genomic DNA from Mammalian Cells protocols).

Preparation of genomic DNA from bacteria.

The role of temporal regularity in auditory segregation

https://eprints.ncl.ac.uk/file_store/production/222364/1B6D0C8F-7A29-43A6-AC4D-5D54EFF6B44A.pdf

Sensitivity to the temporal structure of rapid sound sequences - An MEG study.

The purpose of this protocol is to detect specific DNA sequences in a complex sample by hybridization to a labeled probe.

Analysis of DNA by Southern blotting.

The purpose of this protocol is the isolation of plasmid DNA from bacteria The boiling method for isolating plasmids by Holmes and Quigley (1981) is presented here This method is rapid and simple and it allows for a large number of samples to be processed simultaneously (up to 40 samples) Thus, it is appropriate for the preparation of bacterial plasmids in order to screen a large number of colonies or small cultures for the presence of recombinant DNA inserts The protocol can be effectively scaled up for the preparation of plasmids from liter cultures

Lefkothea-Vasiliki Andreou

Papers

Preparation of genomic DNA from bacteria.

The role of temporal regularity in auditory segregation

Sensitivity to the temporal structure of rapid sound sequences - An MEG study.

Analysis of DNA by Southern blotting.

Isolation of plasmid DNA from bacteria