Horizontal gene transfer contributes to plant evolution : the case of Agrobacterium T-DNAs

Horizontal gene transfer (HGT) can be defined as the acquisition of genetic material from another organism without being its offspring. HGT is common in the microbial world including archaea and bacteria, where HGT mechanisms are widely understood and recognized as an important force in evolution. In eukaryotes, HGT now appears to occur more frequently than originally thought. Many studies are currently detecting novel HGT events among distinct lineages using next-generation sequencing. Most examples to date include gene transfers from bacterial donors to recipient organisms including fungi, plants, and animals. In plants, one well-studied example of HGT is the transfer of the tumor-inducing genes (T-DNAs) from some Agrobacterium species into their host plant genomes. Evidence of T-DNAs from Agrobacterium spp. into plant genomes, and their subsequent maintenance in the germline, has been reported in Nicotiana, Linaria and, more recently, in Ipomoea species. The transferred genes do not produce the usual disease phenotype, and appear to have a role in evolution of these plants. In this paper, we review previous reported cases of HGT from Agrobacterium, including the transfer of T-DNA regions from Agrobacterium spp. to the sweetpotato [ Ipomoea batatas (L.) Lam.] genome which is, to date, the sole documented example of a naturally-occurring incidence of HGT from Agrobacterium to a domesticated crop plant. We also discuss the possible evolutionary impact of T-DNA acquisition on plants

Modeling the complex dynamics of enzyme-pathway coevolution.

Peer reviewedPostprin

A Genealogy of Emancipatory Values

Analytic moral philosophers have generally failed to engage in any substantial way with the cultural history of morality. This is a shame, because a genealogy of morals can help us accomplish two important tasks. First, a genealogy can form the basis of an epistemological project, one that seeks to establish the epistemic status of our beliefs or values. Second, a genealogy can provide us with functional understanding, since a history of our beliefs, values or institutions can reveal some inherent dynamic or pattern which may be problematically obscured from our view. In this paper, I try to make good on these claims by offering a sketchy genealogy of emancipatory values, or values which call for the liberation of persons from systems of dominance and oppression. The real history of these values, I argue, is both epistemologically vindicatory and functionally enlightening

Mental health clients confirm the value of occupation in building competence and self-identity

Engagement in occupation is proposed to enhance health and wellbeing. To date, few studies have demonstrated this in relation to people with mental health problems. This study aimed to evaluate occupational therapy’s beliefs in the restorative powers of occupation from the perspective of people with enduring mental health problems living in the community. Qualitative research methods were used in two mental health day service settings: a workshop, where woodwork was provided as a medium for creative therapy, and a drop-in facility. Participant observation was undertaken over 10 sessions and, during six in-depth interviews, the clients were asked about their occupational experiences and whether they had perceived any benefits from engagement in occupation. Content and inductive analysis as well as concept mapping of the data resulted in emergent themes and subthemes. Occupation was identified both as a means for building competence through the acquisition of skills, coping with challenges and achieving success and as a medium for developing self-identity through the drive to create, feelings of usefulness and engendering a sense of self. These themes help to support the need for an increase in the provision of meaningful occupation for people with enduring mental health problems. However, further research is required to develop and corroborate the findings

The physicist's guide to one of biotechnology's hottest new topics: CRISPR-Cas

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) constitute a multi-functional, constantly evolving immune system in bacteria and archaea cells. A heritable, molecular memory is generated of phage, plasmids, or other mobile genetic elements that attempt to attack the cell. This memory is used to recognize and interfere with subsequent invasions from the same genetic elements. This versatile prokaryotic tool has also been used to advance applications in biotechnology. Here we review a large body of CRISPR-Cas research to explore themes of evolution and selection, population dynamics, horizontal gene transfer, specific and cross-reactive interactions, cost and regulation, non-immunological CRISPR functions that boost host cell robustness, as well as applicable mechanisms for efficient and specific genetic engineering. We offer future directions that can be addressed by the physics community. Physical understanding of the CRISPR-Cas system will advance uses in biotechnology, such as developing cell lines and animal models, cell labeling and information storage, combatting antibiotic resistance, and human therapeutics.Comment: 75 pages, 15 figures, Physical Biology (2018

NMR quality control of fragment libraries for screening

Fragment-based screening has evolved as a remarkable approach within the drug discovery process both in the industry and academia. Fragment screening has become a more structure-based approach to inhibitor development, but also towards development of pathway-specific clinical probes. However, it is often witnessed that the availability, immediate and long-term, of a high quality fragment-screening library is still beyond the reach of most academic laboratories. Within iNEXT (Infrastructure for NMR, EM and X-rays for Translational research), a EU-funded Horizon 2020 program, a collection of 782 fragments were assembled utilizing the concept of "poised fragments" with the aim to facilitate downstream synthesis of ligands with high affinity by fragment ligation. Herein, we describe the analytical procedure to assess the quality of this purchased and assembled fragment library by NMR spectroscopy. This quality assessment requires buffer solubility screening, comparison with LC/MS quality control and is supported by state-of-the-art software for high throughput data acquisition and on-the-fly data analysis. Results from the analysis of the library are presented as a prototype of fragment progression through the quality control process