An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM

C-Phycoerythrin (PE) from Phormidium sp. A09DM has been crystallized using different conditions and its structure determined to atomic resolution (1.14 Å). In order for the pigment present, phycoerythrobilin (PEB), to function as an efficient light-harvesting molecule it must be held rigidly (Kupka and Scheer in Biochim Biophys Acta 1777:94–103, 2008) and, moreover, the different PEB molecules in PE must be arranged, relative to each other, so as to promote efficient energy transfer between them. This improved structure has allowed us to define in great detail the structure of the PEBs and their binding sites. These precise structural details will facilitate theoretical calculations of each PEB’s spectroscopic properties. It was possible, however, to suggest a model for which chromophores contribute to the different regions of absorption spectrum and propose a tentative scheme for energy transfer. We show that some subtle differences in one of these PEB binding sites in two of the 12 subunits are caused by crystal contacts between neighboring hexamers in the crystal lattice. This explains some of the differences seen in previous lower resolution structures determined at two different pH values (Kumar et al. in Photosyn Res 129:17–28, 2016)

On the Munn-Silbey approach to polaron transport with off-diagonal coupling

Improved results using a method similar to the Munn-Silbey approach have been obtained on the temperature dependence of transport properties of an extended Holstein model incorporating simultaneous diagonal and off-diagonal exciton-phonon coupling. The Hamiltonian is partially diagonalized by a canonical transformation, and optimal transformation coefficients are determined in a self-consistent manner. Calculated transport properties exhibit substantial corrections on those obtained previously by Munn and Silbey for a wide range of temperatures thanks to a numerically exact evaluation and an added momentum-dependence of the transformation matrix. Results on the diffusion coefficient in the moderate and weak coupling regime show distinct band-like and hopping-like transport features as a function of temperature.Comment: 12 pages, 6 figures, accpeted in Journal of Physical Chemistry B: Shaul Mukamel Festschrift (2011

Characterisation of a pucBA deletion mutant from Rhodopseudomonas palustris lacking all but the pucBAd genes

Rhodopseudomonas palustris is a species of purple photosynthetic bacteria that has a multigene family of puc genes that encode the alpha and beta apoproteins, which form the LH2 complexes. A genetic dissection strategy has been adopted in order to try and understand which spectroscopic form of LH2 these different genes produce. This paper presents a characterisation of one of the deletion mutants generated in this program, the pucBAd only mutant. This mutant produces an unusual spectroscopic form of LH2 that only has a single large NIR absorption band at 800 nm. Spectroscopic and pigment analyses on this complex suggest that it has basically a similar overall structure as that of the wild-type HL LH2 complex. The mutant has the unique phenotype where the mutant LH2 complex is only produced when cells are grown at LL. At HL the mutant only produces the LH1-RC core complex

Public Health Ethics: Cases Spanning the Globe

Public health ethics can be seen both as the application of principles and norms to guide the practice of public health and as a process for identifying, analyzing, and resolving ethical issues inherent in the practice of public health. Public health ethics helps us decide what we should do and why. Although the practice of public health has always considered ethical issues, the emergence of public health ethics as a discipline is relatively new. Although rooted in bioethics and clinical and research ethics, public health ethics has many characteristics that set it apart. The defining characteristics are its focus on achieving social goods for populations while respecting individual rights and recognizing the interdependence of people. Currently there are few practical training resources for public health practitioners that consider ethical issues and dilemmas likely to arise in the practice of public health. In public health ethics training, we have found it advantageous to use cases to illustrate how ethical principles can be applied in practical ways to decision making. The use of cases encourages reflection and discussion of ethics, reinforces basic ethical concepts through application to concrete examples, highlights practical decision making, allows learners to consider different perspectives, and sensitizes learners to the complex, multidimensional context of issues in public health practice. The case-based approach (known as casuistry) contrasts with the theoretical approach to considering moral principles, rules, and theories. By describing scenarios, cases allow the learner to use ethical principles in the context of a realistic situation that sheds light on ethical challenges and illustrates how ethical principles can help in making practical decisions. This casebook comprises a broad range of cases from around the globe to highlight the ethical challenges of public health. For those new to public health ethics, Section I introduces public health ethics. Chapter 1, “Public Health Ethics: Global Cases, Practice, and Context” by Ortmann and colleagues, summarizes basic concepts and describes how public health ethics differ from bioethics, clinical ethics, and research ethics. The chapter also includes an approach for conducting an ethical analysis in public health. In Chap. 2, “Essential Cases in the Development of Public Health Ethics,” Lee, Spector-Bagdady, and Sakhuja highlight important events that shaped the practice of public health and explain how practitioners address and prevent ethical challenges. Section II is organized into chapters that discuss the following public health topics: • Resource allocation and priority setting • Disease prevention and control • Chronic disease prevention and health promotion • Environmental and occupational public health • Vulnerability and marginalized populations • International collaboration for global public health • Public health research We have invited some of the leading writers and thinkers in public health ethics to provide an overview of the major ethical considerations associated with each topic. The topic overviews offer the authors’ perspectives about applicable ethical theories, frameworks, and tools and draw attention to the cases that follow. The cases are meant to highlight the ethical issues in practice. Each represents the work of authors from around the globe who responded to a solicitation from the U.S. Centers for Disease Control and Prevention. We worked with the authors to ensure that each case included a concise articulation of a public health situation that raises ethical tensions, challenges, or concerns that require decisions or recommendations from public health officials or practitioners. The cases are presented in a standard format that includes a background, case description, discussion questions, and references. However, we also allowed for variation in the amount of detail provided in each section and the approach used to set up the case. Our goal was to include just enough contextual information to orient the reader who is not an expert in the case topic. We include the case setting, population, or intervention in question, legal or regulatory landscape, and questions to stimulate discussion on core ethical issues. Each case—although fictionalized—is as realistic as possible to reflect the ethical challenges that public health practitioners face daily. Sometimes the cases were based on actual or composite events. In these instances, the case details were modified to exclude identifying information that could be considered private, sensitive, or disputable by others involved in the case. We deliberately did not attempt to provide a resolution or solution for the cases. Often in public health practice, there is no single correct answer. Instead, ethical analysis in public health is a process to identify the ethical dimensions of the options available and to arrive at a decision that is ethically justifiable, through deliberation and consideration of relevant facts, values, and contexts. The cases and other writings in this book represent the opinions, findings, and conclusions of the authors and do not necessarily reflect the official position, views, or policies of the editors, the editors’ host institutions, or the authors’ host institutions. We decided which topic category to place the case in to best distribute the cases across chapters. However, you may note that some cases cross topic areas and could just as easily have been included in another chapter. This casebook is written for public health practitioners, including frontline workers, field epidemiology trainers and trainees, and managers, planners, and decision makers with an interest in learning about how to integrate ethical analysis in their day-to-day public health practice. However, the casebook will also be useful to instructors in schools of public health and public health students as well as to academic ethicists who can use the book to teach public health ethics and distinguish it from clinical and research ethics. Our hope is that the casebook will increase awareness and understanding of public health ethics and the value of ethical analysis in public health practice in all of its forms. This includes applied public health research; public health policy development, implementation, and evaluation; and public health decision making in national and international field settings and training programs. By emphasizing prospective practical decision making, rather than just presenting a theoretical academic discussion of ethical principles, we hope this casebook will serve as a useful tool to support instruction, debate, and dialogue about the nature of ethical challenges encountered in public health practice and how to resolve these challenges. We recommend discussing the cases in small groups and using the discussion questions, the ethical framework described in Chap. 1, and the information provided in the topic area overview sections as a starting place for exploring the ethical issues reflected in the cases. The ultimate goal of case-based learning is to develop skills in ethical analysis and decision making in daily public health practice. The ethical framework provides a convenient tool for putting our ideas into practice

Key ethical issues discussed at CDC-sponsored international, regional meetings to explore cultural perspectives and contexts on pandemic influenza preparedness and response

Background: Recognizing the importance of having a broad exploration of how cultural perspectives may shape thinking about ethical considerations, the Centers for Disease Control and Prevention (CDC) funded four regional meetings in Africa, Asia, Latin America, and the Eastern Mediterranean to explore these perspectives relevant to pandemic influenza preparedness and response. The meetings were attended by 168 health professionals, scientists, academics, ethicists, religious leaders, and other community members representing 40 countries in these regions. Methods: We reviewed the meeting reports, notes and stories and mapped outcomes to the key ethical challenges for pandemic influenza response described in the World Health Organization’s (WHO’s) guidance, Ethical Considerations in Developing a Public Health Response to Pandemic Influenza: transparency and public engagement, allocation of resources, social distancing, obligations to and of healthcare workers, and international collaboration. Results: The important role of transparency and public engagement were widely accepted among participants. However, there was general agreement that no “one size fits all” approach to allocating resources can address the variety of economic, cultural and other contextual factors that must be taken into account. The importance of social distancing as a tool to limit disease transmission was also recognized, but the difficulties associated with this measure were acknowledged. There was agreement that healthcare workers often have competing obligations and that government has a responsibility to assist healthcare workers in doing their job by providing appropriate training and equipment. Finally, there was agreement about the importance of international collaboration for combating global health threats. Conclusion: Although some cultural differences in the values that frame pandemic preparedness and response efforts were observed, participants generally agreed on the key ethical principles discussed in the WHO’s guidance. Most significantly the input gathered from these regional meetings pointed to the important role that procedural ethics can play in bringing people and countries together to respond to the shared health threat posed by a pandemic influenza despite the existence of cultural differences

Finite size effects on transport coefficients for models of atomic wires coupled to phonons

We consider models of quasi-1-d, planar atomic wires consisting of several, laterally coupled rows of atoms, with mutually non-interacting electrons. This electronic wire system is coupled to phonons, corresponding, e.g., to some substrate. We aim at computing diffusion coefficients in dependence on the wire widths and the lateral coupling. To this end we firstly construct a numerically manageable linear collision term for the dynamics of the electronic occupation numbers by following a certain projection operator approach. By means of this collision term we set up a linear Boltzmann equation. A formula for extracting diffusion coefficients from such Boltzmann equations is given. We find in the regime of a few atomic rows and intermediate lateral coupling a significant and non-trivial dependence of the diffusion coefficient on both, the width and the lateral coupling. These results, in principle, suggest the possible applicability of such atomic wires as electronic devices, such as, e.g., switches.Comment: 9 pages, 5 figures, accepted for publication in Eur. Phys. J.

The complete mitochondrial genome of the burrowing ghost shrimp, Nihonotrypaea harmandi (Bouvier, 1901), (Crustacea, Decapoda, Axiidea, Callianassidae) - a validation of the genus and species classifications

The complete mitochondrial genome of the burrowing ghost shrimp Nihonotrypaea harmandi wasreconstructed using the Illumina HiSeq platform. The genome was 15,272 bp in length made up of 37 mitochondrial genes (13 CDSs, 22 tRNAs, and 2 rRNAs) in the same order as other Nihonotrypaea species.Phylogenetic analyses suggested that Nihonotrypaea is a valid genus, and that N. harmandi can be phylogenetically marginally separated from N. japonica, though some authors considered the former as a synonym of the latte