Identification of the Genes Required for the Culture of Liberibacter crescens, the Closest Cultured Relative of the Liberibacter Plant Pathogens

Here Tn5 random transposon mutagenesis was used to identify the essential elements for culturing Liberibacter crescens BT-1 that can serve as antimicrobial targets for the closely related pathogens of citrus, Candidatus Liberibacter asiaticus (Las) and tomato and potato, Candidatus Liberibacter solanacearum (Lso). In order to gain insight on the virulence, metabolism, and culturability of the pathogens within the genus Liberibacter, a mini-Tn5 transposon derivative system consisting of a gene specifying resistance to kanamycin, flanked by a 19-base-pair terminal repeat sequence of Tn5, was used for the genome-wide mutagenesis of L. crescens BT-1 and created an insertion mutant library. By analyzing the location of insertions using Sanger and Illumina Mi-Seq sequencing, 314 genes are proposed as essential for the culture of L. crescens BT-1 on BM-7 medium. Of those genes, 76 are not present in the uncultured Liberibacter pathogens and, as a result, suggest molecules necessary for the culturing these pathogens. Those molecules include the aromatic amino acids, several vitamins, histidine, cysteine, lipopolysaccharides, and fatty acids. In addition, the 238 essential genes of L. crescens in common with L. asiaticus are potential targets for the development of therapeutics against the disease

Complete genome sequence of Liberibacter crescens BT-1

Liberibacter crescens BT-1, a Gram-negative, rod-shaped bacterial isolate, was previously recovered from mountain papaya to gain insight on Huanglongbing (HLB) and Zebra Chip (ZC) diseases. The genome of BT-1 was sequenced at the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida. A finished assembly and annotation yielded one chromosome with a length of 1,504,659 bp and a G+C content of 35.4%. Comparison to other species in the Liberibacter genus, L. crescens has many more genes in thiamine and essential amino acid biosynthesis. This likely explains why L. crescens BT-1 is culturable while the known Liberibacter strains have not yet been cultured. Similar to Candidatus L. asiaticus psy62, the L. crescens BT-1 genome contains two prophage regions

Gut Microbiome Metagenomics Analysis Suggests a Functional Model for the Development of Autoimmunity for Type 1 Diabetes

Peer reviewe

The methylome of the gut microbiome : disparate Dam methylation patterns in intestinal Bacteroides dorei

Peer reviewe

Bacteroides dorei dominates gut microbiome prior to autoimnnunity in Finnish children at high risk for type 1 diabetes

Peer reviewe

LIGO’s quantum response to squeezed states

Gravitational Wave interferometers achieve their profound sensitivity by combining a Michelson interferometer with optical cavities, suspended masses, and now, squeezed quantum states of light. These states modify the measurement process of the LIGO, VIRGO and GEO600 interferometers to reduce the quantum noise that masks astrophysical signals; thus, improvements to squeezing are essential to further expand our gravitational view of the universe. Further reducing quantum noise will require both lowering decoherence from losses as well more sophisticated manipulations to counter the quantum back-action from radiation pressure. Both tasks require fully understanding the physical interactions between squeezed light and the many components of km-scale interferometers. To this end, data from both LIGO observatories in observing run three are expressed using frequency-dependent metrics to analyze each detector's quantum response to squeezed states. The response metrics are derived and used to concisely describe physical mechanisms behind squeezing's simultaneous interaction with transverse-mode selective optical cavities and the quantum radiation pressure noise of suspended mirrors. These metrics and related analysis are broadly applicable for cavity-enhanced optomechanics experiments that incorporate external squeezing, and -- for the first time -- give physical descriptions of every feature so far observed in the quantum noise of the LIGO detectors

Point absorbers in Advanced LIGO

Small, highly absorbing points are randomly present on the surfaces of the main interferometer optics in Advanced LIGO. The resulting nano-meter scale thermo-elastic deformations and substrate lenses from these micron-scale absorbers significantly reduces the sensitivity of the interferometer directly though a reduction in the power-recycling gain and indirect interactions with the feedback control system. We review the expected surface deformation from point absorbers and provide a pedagogical description of the impact on power build-up in second generation gravitational wave detectors (dual-recycled Fabry-Perot Michelson interferometers). This analysis predicts that the power-dependent reduction in interferometer performance will significantly degrade maximum stored power by up to 50% and hence, limit GW sensitivity, but suggests system wide corrections that can be implemented in current and future GW detectors. This is particularly pressing given that future GW detectors call for an order of magnitude more stored power than currently used in Advanced LIGO in Observing Run 3. We briefly review strategies to mitigate the effects of point absorbers in current and future GW wave detectors to maximize the success of these enterprises