Correction of the Caulobacter Crescentus NA1000 Genome Annotation

Bacterial genome annotations are accumulating rapidly in the GenBank database and the use of automated annotation technologies to create these annotations has become the norm. However, these automated methods commonly result in a small, but significant percentage of genome annotation errors. To improve accuracy and reliability, we analyzed the Caulobacter crescentus NA1000 genome utilizing computer programs Artemis and MICheck to manually examine the third codon position GC content, alignment to a third codon position GC frame plot peak, and matches in the GenBank database. We identified 11 new genes, modified the start site of 113 genes, and changed the reading frame of 38 genes that had been incorrectly annotated. Furthermore, our manual method of identifying protein-coding genes allowed us to remove 112 non-coding regions that had been designated as coding regions. The improved NA1000 genome annotation resulted in a reduction in the use of rare codons since noncoding regions with atypical codon usage were removed from the annotation and 49 new coding regions were added to the annotation. Thus, a more accurate codon usage table was generated as well. These results demonstrate that a comparison of the location of peaks third codon position GC content to the location of protein coding regions could be used to verify the annotation of any genome that has a GC content that is greater than 60%

A comparison of the Caulobacter NA1000 and K31 genomes reveals extensive genome rearrangements and differences in metabolic potential

The genus Caulobacter is found in a variety of habitats and is known for its abilityto thrive in low-nutrient conditions. K31 is a novel Caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 48Cwith a doubling time of 40 h. K31 contains a 5.5 Mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) thatcode for 438 additional proteins. A comparison of the K31 and the Caulobactercrescentus NA1000 genomes revealed extensive rearrangements of gene order,suggesting that the genomes had been randomly scrambled. However, a careful analysis revealed that the distance from the origin of replication was conserved for the majority of the genes and that many of the rearrangements involved inversions that included the origin of replication. On a finer scale, numerous small indels were observed. K31 proteins involved in essential functions shared 80-95% amino acid sequence identity with their C. crescentus homologues,while other homologue pairs tended to have lower levels of identity.In addition, the K31 chromosome contains more than 1600 genes with nohomologue in NA1000

Testing the gravitational redshift with an inner Solar System probe: the VERITAS case

The NASA Discovery-class mission VERITAS, selected in June 2021, will be launched towards Venus after 2027. In addition to the science instrumentation that will build global foundational geophysical datasets, VERITAS proposed to conduct a technology demonstration for the Deep Space Atomic Clock (DSAC-2). A first DSAC successfully operated in low-Earth orbit for more than two years, demonstrated the trapped ion atomic clock technology, and established a new level of performance for clocks in space. DSAC-2 would have further improvements in size, power, and performance. It would host a $1\times{10}^{-13}$ grade USO to produce a frequency output with short-term stability of less than $2\times{10}^{-13}/\sqrt\tau$ (where $\tau$ is the averaging time). However, due to funding shortfalls, DSAC-2, had to be canceled. The initially foreseen presence of an atomic clock on board the probe, however, raised the question whether this kind of instrumentation could be useful not only for navigation and time transfer but also for fundamental physics tests. In this work, we consider the DSAC-2 atomic clock and VERITAS mission as a specific example to measure possible discrepancies in the redshift predicted by General Relativity by using an atomic clock onboard an interplanetary spacecraft. In particular we investigate the possibility of measuring possible violations of the Local Lorentz Invariance and Local Position Invariance principles. We perform accurate simulations of the experiment during the VERITAS cruise phase. We consider different parametrizations of the possible violations of the General Relativity, different operational conditions, and several different assumptions on the expected measurement performance. Our analysis shows the scientific value of atomic clocks like DSAC-2 hosted onboard interplanetary spacecraft.Comment: 15 pages, 9 figure

Testbeam studies of pre-prototype silicon strip sensors for the LHCb UT upgrade project

The LHCb experiment is preparing for a major upgrade in 2018-2019. One of the key components in the upgrade is a new silicon tracker situated upstream of the analysis magnet of the experiment. The Upstream Tracker (UT) will consist of four planes of silicon strip detectors, with each plane covering an area of about 2 m$^2$. An important consideration of these detectors is their performance after they have been exposed to a large radiation dose. In this article we present test beam results of pre-prototype n-in-p and p-in-n sensors that have been irradiated with fluences up to $4.0\times10^{14}$ $n_{\rm eq}$ cm$^{-2}$.Comment: 25 pages, 20 figure

Alanine scan mutagenesis of the switch I domain of the Caulobacter crescentus CgtA protein reveals critical amino acids required for in vivo function

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75411/1/j.1365-2958.2001.02285.x.pd

Geographical origin of dabbling ducks wintering in Iberia: Sex differences and implications for pair formation

Los humedales ibéricos naturales y antropógenos del sur de Europa son bien conocidos por sustentar a un gran número de aves migratorias acuáticas del Palaearctico en cada invierno. Sin embargo, la información sobre el origen geográfico de los patos de humedal que pasan el invierno en estos espacios es escasa y se limita principalmente a datos de sonar. Aquí, hemos utilizado marcadores isotópicos para determinar el origen geográfico de machos y hembras de Pintails septentrional, Anas acuta y Anas crecca euroasiática en Extremadura, en el interior de la península Ibérica, sitio clave para invernar los patos de humedal. Además, hemos instalado seis etiquetas GPSGSM en Pintails septentrional para complementar los datos derivados del análisis de isótopos estables. La mayoría (> 70%) de los Pintails septentrional, dentro del primer año calendario, fueron asignados a regiones situadas por encima de los 55° N, volando 2600-5600 km desde sus regiones de procedencia a Extremadura. Los valores promedio de δ2Hf variaron significativamente entre macho y hembra de Pintails septentrional, sugiriendo que los sexos tienen diferentes orígenes geográficos. Los datos de los adultos etiquetados Pintails septentrional apoyan los datos isotópicos, un macho volando más de 5000 km de la costa de la mar Pechora (Rusia). La mayoría (> 70%) de los Teal euroasiáticos, dentro del primer año calendario, fueron asignados a la región situada entre 48° y 60° N y viajaron 1500-4500 km para llegar en Extremadura. Los machos y hembras de Cerceta euroasiáticos mostraron diferencias marginales en valores promedio de δ2Hf. En patos de humedal migratorios, el emparejamiento se produce normalmente en las zonas de invernada, y los patos en su primer invierno pueden reproducirse en la primavera siguiente. Para Pintails septentrional, la formación de parejas en Extremadura podría suceder entre individuos con diferentes orígenes geográficos, lo que podría contribuir a la variabilidad genética de su descendencia.Natural and anthropogenic Iberian wetlands in southern Europe are well known for supporting large numbers of migratory Palaearctic waterbirds each winter. However, information on the geographical origin of dabbling ducks overwintering in these wetlands is scarce and mostly limited to data from ringing recoveries. Here, we used intrinsic isotopic markers to determine the geographical origin of male and female Northern Pintails Anas acuta and Eurasian Teal Anas crecca in Extremadura, inland Iberia, a key site for overwintering dabbling ducks. Additionally, we fitted six Northern Pintails with GPSGSM tags to complement the data derived from stable isotope analysis. Most (> 70%) first calendar-year Northern Pintails were assigned to regions above 55°N, flying 2600–5600 km from their main natal regions to Extremadura. Mean values of δ2Hf varied significantly between male and female Northern Pintails, suggesting that the sexes had different geographical origins. Data from tagged adult Northern Pintails supported the isotopic data, one male flying more than 5000 km to the coast of the Pechora Sea (Russia). Most (> 70%) first calendar-year Eurasian Teal were assigned to the region between 48° and 60°N, travelling 1500–4500 km to arrive in Extremadura. Male and female Eurasian Teal showed marginal differences in mean values of δ2Hf. In migratory dabbling ducks, pairing typically occurs on the wintering grounds, and ducks in their first winter can breed the following spring. For Northern Pintails, pair formation in Extremadura could occur between individuals with different geographical origins, which could contribute to the genetic variability of their offspring.Trabajo patrocinado por: Junta de Extremadura. Proyecto PRI 09C128 Gobierno de Extremadura y Fondos FEDER. Ayuda GR10174 Confederación Hidrográfica del Guadiana (Ministerio de Medio Ambiente). Ayuda financierapeerReviewe

CDK Inhibitor p18INK4c Is Required for the Generation of Functional Plasma Cells

B cell terminal differentiation is associated with the onset of high-level antibody secretion and cell cycle arrest. Here the cyclin-dependent kinase (CDK) inhibitor p18INK4c is shown to be required within B cells for both terminating cell proliferation and differentiation of functional plasma cells. In its absence, B cells hyperproliferate in germinal centers and extrafollicular foci in response to T-dependent antigens but serum antibody titers are severely reduced, despite unimpaired germinal center formation, class switch recombination, variable region-directed hypermutation, and differentiation to antibody-containing plasmacytoid cells. The novel link between cell cycle control and plasma cell differentiation may, at least in part, relate to p18INK4c inhibition of CDK6. Cell cycle arrest mediated by p18INK4C is therefore requisite for the generation of functional plasma cells

CDK Inhibitor p18INK4c Is Required for the Generation of Functional Plasma Cells

AbstractB cell terminal differentiation is associated with the onset of high-level antibody secretion and cell cycle arrest. Here the cyclin-dependent kinase (CDK) inhibitor p18INK4c is shown to be required within B cells for both terminating cell proliferation and differentiation of functional plasma cells. In its absence, B cells hyperproliferate in germinal centers and extrafollicular foci in response to T-dependent antigens but serum antibody titers are severely reduced, despite unimpaired germinal center formation, class switch recombination, variable region-directed hypermutation, and differentiation to antibody-containing plasmacytoid cells. The novel link between cell cycle control and plasma cell differentiation may, at least in part, relate to p18INK4c inhibition of CDK6. Cell cycle arrest mediated by p18INK4C is therefore requisite for the generation of functional plasma cells

The evolution of the cosmic molecular gas density

One of the last missing pieces in the puzzle of galaxy formation and evolution through cosmic history is a detailed picture of the role of the cold gas supply in the star-formation process. Cold gas is the fuel for star formation, and thus regulates the buildup of stellar mass, both through the amount of material present through a galaxy's gas mass fraction, and through the efficiency at which it is converted to stars. Over the last decade, important progress has been made in understanding the relative importance of these two factors along with the role of feedback, and the first measurements of the volume density of cold gas out to redshift 4, (the "cold gas history of the Universe") has been obtained. To match the precision of measurements of the star formation and black-hole accretion histories over the coming decades, a two orders of magnitude improvement in molecular line survey speeds is required compared to what is possible with current facilities. Possible pathways towards such large gains include significant upgrades to current facilities like ALMA by 2030 (and beyond), and eventually the construction of a new generation of radio-to-millimeter wavelength facilities, such as the next generation Very Large Array (ngVLA) concept.Comment: 7 pages, 2 figures, Science White paper submitted to Astro2020 Decadal Surve

Unprecedented generation of 3D heterostructures by mechanochemical disassembly and re-ordering of incommensurate metal chalcogenides

Three-dimensional heterostructures are usually created either by assembling two-dimensional building blocks into hierarchical architectures or using stepwise chemical processes that sequentially deposit individual monolayers. Both approaches suffer from a number of issues, including lack of suitable precursors, limited reproducibility, and poor scalability of the preparation protocols. Therefore, development of alternative methods that enable preparation of heterostructured materials is desired. We create heterostructures with incommensurate arrangements of well-defined building blocks using a synthetic approach that comprises mechanical disassembly and simultaneous reordering of layered transition-metal dichalcogenides, MX2, and non-layered monochalcogenides, REX, where M = Ta, Nb, RE = Sm, La, and X = S, Se. We show that the discovered solid-state processes are rooted in stochastic mechanochemical transformations directed by electronic interaction between chemically and structurally dissimilar solids toward atomic-scale ordering, and offer an alternative to conventional heterostructuring. Details of composition–structure–properties relationships in the studied materials are also highlighted