Wood construction more strongly shapes deadwood microbial communities than spatial location over 5 years of decay

Diverse communities of fungi and bacteria in deadwood mediate wood decay. While rates of decomposition vary greatly among woody species and spatially distinct habitats, the relative importance of these factors in structuring microbial communities and whether these shift over time remains largely unknown. We characterized fungal and bacterial diversity within pieces of deadwood that experienced 6.3–98.8% mass loss while decaying in common garden ‘rotplots’ in a temperate oak-hickory forest in the Ozark Highlands, MO, USA. Communities were isolated from 21 woody species that had been decomposing for 1–5 years in spatially distinct habitats at the landscape scale (top and bottom of watersheds) and within stems (top and bottom of stems). Microbial community structure varied more strongly with wood traits than with spatial locations, mirroring the relative role of these factors on decay rates on the same pieces of wood even after 5 years. Co-occurring fungal and bacterial communities persistently influenced one another independently from their shared environmental conditions. However, the relative influence of wood construction versus spatial locations differed between fungi and bacteria, suggesting that life history characteristics of these clades structure diversity differently across space and time in decomposing wood.     

Genetic diversity of Trypanosoma cruzi parasites infecting dogs in southern Louisiana sheds light on parasite transmission cycles and serological diagnostic performance

BackgroundChagas disease is a neglected zoonosis of growing concern in the southern US, caused by the parasite Trypanosoma cruzi. We genotyped parasites in a large cohort of PCR positive dogs to shed light on parasite transmission cycles and assess potential relationships between parasite diversity and serological test performance.Methodology/principal findingsWe used a metabarcoding approach based on deep sequencing of T. cruzi mini-exon marker to assess parasite diversity. Phylogenetic analysis of 178 sequences from 40 dogs confirmed the presence of T. cruzi discrete typing unit (DTU) TcI and TcIV, as well as TcII, TcV and TcVI for the first time in US dogs. Infections with multiple DTUs occurred in 38% of the dogs. These data indicate a greater genetic diversity of T. cruzi than previously detected in the US. Comparison of T. cruzi sequence diversity indicated that highly similar T. cruzi strains from these DTUs circulate in hosts and vectors in Louisiana, indicating that they are involved in a shared T. cruzi parasite transmission cycle. However, TcIV and TcV were sampled more frequently in vectors, while TcII and TcVI were sampled more frequently in dogs.Conclusions/significanceThese observations point to ecological host-fitting being a dominant mechanism involved in the diversification of T. cruzi-host associations. Dogs with negative, discordant or confirmed positive T. cruzi serology harbored TcI parasites with different mini-exon sequences, which strongly supports the hypothesis that parasite genetic diversity is a key factor affecting serological test performance. Thus, the identification of conserved parasite antigens should be a high priority for the improvement of current serological tests.     

Insufficient potassium and sulfur supply threaten the productivity of perennial forage grasses in smallholder farms on tropical sandy soils

Plant and Soil - Perennial forage grass production has the potential to improve smallholder livelihoods in the tropics. However, nutrient management is often challenging, especially on infertile...     

Knockout of a highly GC-rich gene in Burkholderia pyrrocinia by recombineering with freeze-thawing transformation

Genetic transformation is a valuable and essential method that provides powerful insights into the gene function of microorganisms and contributes to the construction of engineered bacteria. Here, we developed a novel genetic transformation system to easily knock out a highly GC-rich gene (74.71% GC) from Burkholderia pyrrocinia JK-SH007, a biocontrol strain of poplar canker disease. This system revealed a reliable selectable marker (trimethoprim resistance gene, Tmp) and a simplified, efficient transformation method (6,363.64 CFU/μg, pHKT2) that was developed via freeze-thawing. The knockout recombineering of B. pyrrocinia JK-SH007 was achieved through a suicide plasmid with a three-fragment mutagenesis construct. The three-fragment cassette for mutagenesis was generated by overlap extension and touchdown PCRs and composed of Tmp flanked by GC-rich upstream and downstream fragments from B. pyrrocinia JK-SH007. The mutant strain (ΔBpEG), which was verified by PCR, lost 93.3% of its ability to degrade carboxymethyl cellulose over 40 days. Overall, this system may contribute to future research on B. pyrrocinia traits.     

Urban development and sustainability challenges chronicled by a century of construction material flows and stocks in Tiexi,China

Construction materials are considerable forces of global environmental impacts, but their dynamics vis‐à‐vis urban development are poorly documented, in part because their long lifespans require elusive and sometimes nonexistent decade‐long high‐resolution data. This study analyzes the construction material flow and stock trends that shaped and were shaped by the development, decline, and renewal of the Tiexi district of Shenyang, a microcosm of China's urban transformations since the early 20th century. Chronicling building‐by‐building the material flows and stock accumulations involved in the buildup of this area, we shed light on the physical resource context of its socioeconomic history. We find that 42 million tonnes of construction materials were needed to develop the Tiexi district from 1910 to 2018, and 18 million tonnes of material outflows were generated by end‐of‐life building demolition. However, over 55% of inflows and 93% of outflows occurred since 2002 during a complete redevelopment of the district. Only small portions of end‐of‐life materials could have been reused or recycled because of temporal and typological mismatches of supply and demand and technical limitations. Our analysis reveals a dramatic decrease in median building lifetimes to as low as 6 years in the early 21st century. These findings contribute to the discussion of long‐term environmental efficiency and sustainability of societal development through construction and reflect on the challenges of urban renewal processes not only in China but also in other developing and developed countries that lost (or may lose) their traditional economic base and restructure their urban forms. This article met the requirements for a Silver/Silver JIE data openness badge described at http://jie.click/badges .     

Doctors on Status and Respect: A Qualitative Study

While doctors generally enjoy considerable status, some believe that this is increasingly threatened by consumerism, managerialism, and competition from other health professions. Research into doctors’ perceptions of the changes occurring in medicine has provided some insights into how they perceive and respond to these changes but has generally failed to distinguish clearly between concerns about “status,” related to the entitlements associated with one’s position in a social hierarchy, and concerns about “respect,” related to being held in high regard for one’s moral qualities. In this article we explore doctors’ perceptions of the degree to which they are respected and their explanations for, and responses to, instances of perceived lack of respect. We conclude that doctors’ concerns about loss of respect need to be clearly distinguished from concerns about loss of status and that medical students need to be prepared for a changing social field in which others’ respect cannot be taken for granted.     

How Pharmaceutical Industry Employees Manage Competing Commitments in the Face of Public Criticism

The pharmaceutical industry has been criticised for pervasive misconduct. These concerns have generally resulted in increasing regulation. While such regulation is no doubt necessary, it tends to assume that everyone working for pharmaceutical companies is equally motivated by commerce, without much understanding of the specific views and experiences of those who work in different parts of the industry. In order to gain a more nuanced picture of the work that goes on in the “medical affairs” departments of pharmaceutical companies, we conducted 15 semi-structured interviews with professionals working in medical departments of companies in Sydney, Australia. We show that this group of pharmaceutical professionals are committed to their responsibilities both to patients, research participants, and the public and to their companies. Despite the discrepancies between these commitments, our participants did not express much cognitive dissonance, and this appeared to stem from their use of two dialectically related strategies, one of which embraces commerce and the other of which resists the commercial imperative. We interpret these findings through the lens of institutional theory and consider their implications for pharmaceutical ethics and governance.     

Isolation and characterisation of human pulmonary microvascular endothelial cells from patients with severe emphysema

Background

Loss of the pulmonary microvasculature in the pathogenesis of emphysema has been put forward as a credible alternative to the classical inflammatory cell driven proteolysis hypothesis. Mechanistic studies in this area have to date employed animal models, immortalised cell lines, primary endothelial cells isolated from large pulmonary arteries and non-pulmonary tissues and normal human pulmonary microvascular endothelial cells. Although these studies have increased our understanding of endothelial cell function, their relevance to mechanisms in emphysema is questionable. Here we report a successful technique to isolate and characterise primary cultures of pulmonary microvascular endothelial cells from individuals with severe emphysema.

Methods

A lobe of emphysematous lung tissue removed at the time of lung transplantation surgery was obtained from 14 patients with severe end-stage disease. The pleura, large airways and large blood vessels were excised and contaminating macrophages and neutrophils flushed from the peripheral lung tissue before digestion with collagenase. Endothelial cells were purified from the cell mixture via selection with CD31 and UEA-1 magnetic beads and characterised by confocal microscopy and flow cytometry.

Results

Successful isolation was achieved from 10 (71%) of 14 emphysematous lungs. Endothelial cells exhibited a classical cobblestone morphology with high expression of endothelial cell markers (CD31) and low expression of mesenchymal markers (CD90, αSMA and fibronectin). E-selectin (CD62E) was inducible in a proportion of the endothelial cells following stimulation with TNFα, confirming that these cells were of microvascular origin.

Conclusions

Emphysematous lungs removed at the time of transplantation can yield large numbers of pulmonary microvasculature endothelial cells of high purity. These cells provide a valuable research tool to investigate cellular mechanisms in the pulmonary microvasculature relevant to the pathogenesis of emphysema.