Science Verification Results from PMAS

PMAS, the Potsdam Multi-Aperture Spectrophotometer, is a new integral field instrument which was commissioned at the Calar Alto 3.5m Telescope in May 2001. We report on results obtained from a science verification run in October 2001. We present observations of the low-metallicity blue compact dwarf galaxy SBS0335-052, the ultra-luminous X-ray Source X-1 in the Holmberg II galaxy, the quadruple gravitational lens system Q2237+0305 (the "Einstein Cross"), the Galactic planetary nebula NGC7027, and extragalactic planetary nebulae in M31. PMAS is now available as a common user instrument at Calar Alto Observatory.Comment: 4 pages, 9 figures (attached in JPEG format), Euro3D Science Workshop Proceedings, held in Cambridge May 21-23, 2003, to appear in AN (accepted

Bacteriophage and their potential roles in the human oral cavity.

The human oral cavity provides the perfect portal of entry for viruses and bacteria in the environment to access new hosts. Hence, the oral cavity is one of the most densely populated habitats of the human body containing some 6 billion bacteria and potentially 35 times that many viruses. The role of these viral communities remains unclear; however, many are bacteriophage that may have active roles in shaping the ecology of oral bacterial communities. Other implications for the presence of such vast oral phage communities include accelerating the molecular diversity of their bacterial hosts as both host and phage mutate to gain evolutionary advantages. Additional roles include the acquisitions of new gene functions through lysogenic conversions that may provide selective advantages to host bacteria in response to antibiotics or other types of disturbances, and protection of the human host from invading pathogens by binding to and preventing pathogens from crossing oral mucosal barriers. Recent evidence suggests that phage may be more involved in periodontal diseases than were previously thought, as their compositions in the subgingival crevice in moderate to severe periodontitis are known to be significantly altered. However, it is unclear to what extent they contribute to dysbiosis or the transition of the microbial community into a state promoting oral disease. Bacteriophage communities are distinct in saliva compared to sub- and supragingival areas, suggesting that different oral biogeographic niches have unique phage ecology shaping their bacterial biota. In this review, we summarize what is known about phage communities in the oral cavity, the possible contributions of phage in shaping oral bacterial ecology, and the risks to public health oral phage may pose through their potential to spread antibiotic resistance gene functions to close contacts

Anisotropic superexchange of a 90 degree Cu-O-Cu bond

The magnetic anisotropy af a rectangular Cu-O-Cu bond is investigated in second order of the spin-orbit interaction. Such a bond is characteristic for cuprates having edge sharing CuO_2 chains, and exists also in the Cu_3O_4 plane or in ladder compounds. For a ferromagnetic coupling between the copper spins an easy axis is found perpendicular to the copper oxygen plaquettes in agreement with the experimental spin structure of Li_2CuO_2. In addition, a pseudo-dipolar interaction is derived. Its estimation in the case of the Cu_3O_4 plane (which is present for instance in Ba_2Cu_3O_4Cl_2 or Sr_2Cu_3O_4Cl_2) gives a value which is however two orders of magnitude smaller than the usual dipole-dipole interaction.Comment: 6 pages, 2 figures, improved referenc

Genomic donor cassette sharing during VLRA and VLRC assembly in jawless vertebrates

Lampreys possess two T-like lymphocyte lineages that express either variable lymphocyte receptor (VLR) A or VLRC antigen receptors. VLRA+ and VLRC+ lymphocytes share many similarities with the two principal T-cell lineages of jawed vertebrates expressing the αβ and γδ T-cell receptors (TCRs). During the assembly of VLR genes, several types of genomic cassettes are inserted, in step-wise fashion, into incomplete germ-line genes to generate the mature forms of antigen receptor genes. Unexpectedly, the structurally variable components of VLRA and VLRC receptors often possess partially identical sequences; this phenomenon of module sharing between these two VLR isotypes occurs in both lampreys and hagfishes. By contrast, VLRA and VLRC molecules typically do not share their building blocks with the structurally analogous VLRB receptors that are expressed by B-like lymphocytes. Our studies reveal that VLRA and VLRC germ-line genes are situated in close proximity to each other in the lamprey genome and indicate the interspersed arrangement of isotype-specific and shared genomic donor cassettes; these features may facilitate the shared cassette use. The genomic structure of the VLRA/VLRC locus in lampreys is reminiscent of the interspersed nature of the TCRA/TCRD locus in jawed vertebrates that also allows the sharing of some variable gene segments during the recombinatorial assembly of TCR genes

Co-evolution of mutagenic genome deditors and vertebrate adaptive immunity

The adaptive immune systems of all vertebrates rely on self-DNA mutating enzymes to assemble their antigen receptors in lymphocytes of their two principal lineages. In jawed vertebrates, the RAG1/2 recombinase directs V(D)J recombination of B cell and T cell receptor genes, whereas the activation-induced cytidine deaminase AID engages in their secondary modification. The recombination activating genes (RAG) 1 and 2 evolved from an ancient transposon-encoded genome modifier into a self-DNA mutator serving adaptive immunity; this was possible as a result of domestication, involving several changes in RAG1 and RAG2 proteins suppressing transposition and instead facilitating-coupled cleavage and recombination. By contrast, recent evidence supports the notion that the antigen receptors of T-like and B-like cells of jawless vertebrates, designated variable lymphocyte receptors (VLRs), are somatically assembled through a process akin to gene conversion that is believed to be dependent on the activities of distant relatives of AID, the cytidine deaminases CDA1 and CDA2, respectively. It appears, therefore, that the precursors of AID and CDAs underwent a domestication process that changed their target range from foreign nucleic acids to self-DNA; this multi-step evolutionary process ensured that the threat to host genome integrity was minimized. Here, we review recent findings illuminating the evolutionary steps associated with the domestication of the two groups of genome editors, RAG1/2 and cytidine deaminases, indicating how they became the driving forces underlying the emergence of vertebrate adaptive immune systems

Fruits of our labour: Work and organisation in the global food system

This is the author accepted manuscript. The final version is available from SAGE Publications via the DOI in this record.This is the first special issue of any organisation studies journal on food labour. Why is this a big deal? In this Introduction, we argue that the field should pay much more attention to the agri-food system and the work that goes into producing, distributing and consuming foodstuff. Food is such an all-important, basic ingredient to human existence, incorporating a vast web of organisational processes that are constantly changing, being contested at all scales. Whether subsistence peasants, new-age community foodies, massive food logistics companies, Deliveroo dark kitchens or Uber Eats cyclists – there is a huge amount of labour everywhere in the agri-food system. Food labour is so vast, this special issue can only begin lifting the lid. In this Introduction, we provide an overview of the current scholarly work on food labour. We identify some of the historical contexts and struggles that have led to the agri-food system in existence today. We identify food labour types, particularly focusing on those that are vanishing or emerging, crucially asking why these transitions are taking place. We also engage with the various resistances expressed by people against the ever globalising agri-food system, outlining logics for the emergence of alternative food movements. Finally, we introduce each of the seven papers collated in this Special Issue, all of which, we hope, will provide food for thought to all of us who tend to have three meals a day without thinking too much about the labour that goes into our grub.Economic and Social Research Counci

Selection of the lamprey VLRC antigen receptor repertoire

The alternative adaptive immune system of jawless vertebrates is based on different isotypes of variable lymphocyte receptors (VLRs) that are composed of leucine-rich repeats (LRRs) and expressed by distinct B- and T-like lymphocyte lineages. VLRB is expressed by B-like cells, whereas VLRA and VLRC are expressed by two T-like lineages that develop in the thymoid, a thymus-like structure in lamprey larvae. In each case, stepwise combinatorial insertions of different types of short donor LRR cassettes into incomplete germ-line genes are required to generate functional VLR gene assemblies. It is unknown, however, whether the diverse repertoires of VLRs that are expressed by peripheral blood lymphocytes are shaped by selection after their assembly. Here, we identify signatures of selection in the peripheral repertoire of VLRC antigen receptors that are clonally expressed by one of the T-like cell types in lampreys. Selection strongly favors VLRC molecules containing four internal variable leucine-rich repeat (LRRV) modules, although VLRC assemblies encoding five internal modules are initially equally frequent. In addition to the length selection, VLRC molecules in VLRC+ peripheral lymphocytes exhibit a distinct pattern of high entropy sites in the N-terminal LRR1 module, which is inserted next to the germ-line–encoded LRRNT module. This is evident in comparisons to VLRC gene assemblies found in the thymoid and to VLRC gene assemblies found in some VLRA+ cells. Our findings are the first indication to our knowledge that selection operates on a VLR repertoire and provide a framework to establish the mechanism by which this selection occurs during development of the VLRC+ lymphocyte lineage

Kinematics of disk galaxies in (proto-)clusters at z=1.5

We observed star-forming galaxies at z~1.5 selected from the HyperSuprimeCam Subaru Strategic Program. The galaxies are part of two significant overdensities of [OII] emitters identified via narrow-band imaging and photometric redshifts from grizy photometry. We used VLT/KMOS to carry out Halpha integral field spectroscopy of 46 galaxies in total. Ionized gas maps, star formation rates and velocity fields were derived from the Halpha emission line. We quantified morphological and kinematical asymmetries to test for potential gravitational (e.g. galaxy-galaxy) or hydrodynamical (e.g. ram-pressure) interactions. Halpha emission was detected in 36 targets. 34 of the galaxies are members of two (proto-)clusters at z=1.47, confirming our selection strategy to be highly efficient. By fitting model velocity fields to the observed ones, we determined the intrinsic maximum rotation velocity Vmax of 14 galaxies. Utilizing the luminosity-velocity (Tully-Fisher) relation, we find that these galaxies are more luminous than their local counterparts of similar mass by up to ~4 mag in the rest-frame B-band. In contrast to field galaxies at z<1, the offsets of the z~1.5 (proto-)cluster galaxies from the local Tully-Fisher relation are not correlated with their star formation rates but with the ratio between Vmax and gas velocity dispersion sigma_g. This probably reflects that, as is observed in the field at similar redshifts, fewer disks have settled to purely rotational kinematics and high Vmax/sigma_g ratios. Due to relatively low galaxy velocity dispersions (sigma_v < 400 km/s) of the (proto-)clusters, gravitational interactions likely are more efficient, resulting in higher kinematical asymmetries, than in present-day clusters. (abbr.)Comment: Accepted for publication in A&A. 11 pages, 8 figures, 1 tabl

On Evidence-based Risk Management in Requirements Engineering

Background: The sensitivity of Requirements Engineering (RE) to the context makes it difficult to efficiently control problems therein, thus, hampering an effective risk management devoted to allow for early corrective or even preventive measures. Problem: There is still little empirical knowledge about context-specific RE phenomena which would be necessary for an effective context- sensitive risk management in RE. Goal: We propose and validate an evidence-based approach to assess risks in RE using cross-company data about problems, causes and effects. Research Method: We use survey data from 228 companies and build a probabilistic network that supports the forecast of context-specific RE phenomena. We implement this approach using spreadsheets to support a light-weight risk assessment. Results: Our results from an initial validation in 6 companies strengthen our confidence that the approach increases the awareness for individual risk factors in RE, and the feedback further allows for disseminating our approach into practice.Comment: 20 pages, submitted to 10th Software Quality Days conference, 201

Transcriptome analysis of bacteriophage communities in periodontal health and disease.

BackgroundThe role of viruses as members of the human microbiome has gained broader attention with the discovery that human body surfaces are inhabited by sizeable viral communities. The majority of the viruses identified in these communities have been bacteriophages that predate upon cellular microbiota rather than the human host. Phages have the capacity to lyse their hosts or provide them with selective advantages through lysogenic conversion, which could help determine the structure of co-existing bacterial communities. Because conditions such as periodontitis are associated with altered bacterial biota, phage mediated perturbations of bacterial communities have been hypothesized to play a role in promoting periodontal disease. Oral phage communities also differ significantly between periodontal health and disease, but the gene expression of oral phage communities has not been previously examined.ResultsHere, we provide the first report of gene expression profiles from the oral bacteriophage community using RNA sequencing, and find that oral phages are more highly expressed in subjects with relative periodontal health. While lysins were highly expressed, the high proportion of integrases expressed suggests that prophages may account for a considerable proportion of oral phage gene expression. Many of the transcriptome reads matched phages found in the oral cavities of the subjects studied, indicating that phages may account for a substantial proportion of oral gene expression. Reads homologous to siphoviruses that infect Firmicutes were amongst the most prevalent transcriptome reads identified in both periodontal health and disease. Some genes from the phage lytic module were significantly more highly expressed in subjects with periodontal disease, suggesting that periodontitis may favor the expression of some lytic phages.ConclusionsAs we explore the contributions of viruses to the human microbiome, the data presented here suggest varying expression of bacteriophage communities in oral health and disease