Diagnostic and public health investigation of Mycobacterium tuberculosis infection in a dog in Ontario,Canada

A 4-y-old, female mixed-breed dog was presented to the Ontario Veterinary College for further evaluation of multiple pulmonary and hepatic masses, intrathoracic lymphadenitis, and recent development of a pyogranulomatous pleural effusion. Along with other comprehensive tests, a thoracic lymph node biopsy was performed, and Mycobacterium tuberculosis complex infection was confirmed by real-time PCR. The dog’s condition declined post-operatively, and euthanasia was elected. Postmortem examination confirmed severe granulomatous pneumonia, hepatitis, intrathoracic and intraabdominal lymphadenitis, omentitis, and nephritis. Line-probe assays performed on samples collected postmortem confirmed the species as M. tuberculosis. 24-loci MIRU-VNTR genotyping, spoligotyping, and whole-genome sequencing revealed relations to known human isolates, but no epidemiologic link to these cases was investigated. Given the concern for potential human exposure during this animal’s disease course, a public health investigation was initiated; 45 individuals were tested for M. tuberculosis exposure, and no subsequent human infections related to this animal were identified. Our case highlights the need for more readily available, minimally invasive testing for the diagnosis of canine mycobacteriosis, and highlights the ability of canid species to act as potential contributors to the epidemiology of M. tuberculosis infections.     

A filter-assisted culture method for isolation of Treponema spp. from bovine digital dermatitis and their identification by MALDI-TOF MS

Digital dermatitis (DD) is a major infectious foot disease of cattle worldwide. Some DD stages are associated with lameness, and the disease has significant economic and animal welfare consequences. The pathogenesis of the disease is not yet fully understood, but Treponema spp. have been associated consistently with clinical cases. Isolation of these fastidious bacteria is difficult and cumbersome. We describe an improved method enabling the culturing of the 3 Treponema spp. (T. pedis, T. phagedenis, and T. medium) from bovine foot specimens derived from DD lesions, using a combination of membrane filtering and subsequent growth on selective agar media. The entire procedure from sampling to verification of individual Treponema spp. takes up to 24 d. In addition, we established a MALDI-TOF MS–based identification method to be applied for confirmation of the different Treponema spp. This scheme provides an unambiguous, simple, and straightforward identification procedure for DD-associated Treponema spp.     

Estimates of stem wood increments in forest resources: comparison of different approaches in forest inventory: consequences for international reporting: case studyof European forests

Key message

Quality and reliability of forest resource assessments depend on the ability of national forest inventories (NFIs) to supply necessary and high-quality data. Over the last decades and especially since the 1990s, the NFIs in European countries have been rapidly developing. Possibilities for obtaining reliable and accurate data on annual increment from different inventory types were evaluated, and sample-based inventories have been found to be superior to standwise inventories in providing reliable data. Simplified methods may be employed when increment cannot be directly estimated from inventory data.

Context

An increasing intensity of forest resource use requires more accurate, detailed and reliable information, not only on forest area and growing stock but also on forest stand productivity, wood increment and its components.

Aims

The main objectives were to assess the capacities of forest inventories, the methods used for estimation of gross increment and its components and their accuracy and to demonstrate an effective method for estimation of increment when direct inventory methods are not available.

Methods

Data about national forest inventory methods were obtained from 30 responses to a questionnaire, distributed amongst national correspondents of all European countries; reports of COST Actions E43 and FP 1001, databases of Temperate and Boreal Forest Resource Assessment (TBFRA) 2000 and State of Europe’s Forests (SoEF) 2011 were used as well. Analysis and comparison of results from different forest inventories were used for evaluation of data reliability. Relationships between growing stock and gross increment in European forests were also analysed, and corresponding models were proposed.

Results

Seventy-nine percent of European forest area is covered by national forest inventories (NFIs) based on sampling methods and the rest on stand-level inventory and other inventory methods. Data obtained by aggregating standwise data usually underestimate growing stock by 15–20 % and gross increment even more. Almost half of the European forest area (47 %) is monitored using permanent plots, measured twice or more, allowing the estimation of gross increment and its components to be made directly.

Conclusion

Implementation of NFIs based on sampling methods, especially with permanent plots, resulted in an improvement of data quality and in most cases an increase of growing stock and gross increment. The estimation of natural losses is the weakest link in today’s NFIs and in the current assessment of European forest resources. The proposed default values for gross increment and its components is an option to be used in countries not having NFI at all or those which have started it only recently.

     

Functional response of <Emphasis Type="Italic">Quercus robur</Emphasis> L. to taproot pruning: a 5-year case study

Key message

Quercus robur seedling mass was affected more by planting density than by taproot pruning. Root pruning enhanced stem biomass at the expense of roots in later growth stages. Alteration of biomass allocation due to nursery practices may result in greater susceptibility to injury and death of the seedlings under unfavorable environmental conditions.

Context

Plants adjust their growth and modulate the resource allocation in response to applied treatments and environmental conditions.

Aims

The aim was to examine how taproot pruning in seedlings grown at different densities affected long-term growth of Quercus robur.

Methods

Seedlings, sown as acorns at two planting densities, with or without pruned roots were harvested in the second, fourth, and fifth years of growth. The effect of root pruning on biomass allocation was determined by measuring leaf, stem, and root mass fractions; carbohydrate concentrations in the roots; and C/N ratios. Specific leaf area and root length were also determined to assess morphological adaptations to growth conditions.

Results

Total seedling mass was affected more by planting density than by taproot pruning. After 4 years of growth, root mass fractions were lower and stem mass fractions were greater in seedlings planted at a higher density. Five-year old root-pruned seedlings also had a lower root mass fraction and higher stem mass fractions than unpruned seedlings. Specific root length was not affected by root pruning or planting density.

Conclusion

Decrease of relative root biomass with simultaneous increase of stem biomass may be a long-term consequence of taproot pruning of Q. robur, and the effects may manifest years after the seedling stage.

     

The effect of four calcium‐based amendments on soil aggregate stability of two sandy topsoils

The structural stability of soil is a physical characteristic that affects soil degradation processes. Calcium‐based amendments, such as calcium carbonate, calcium sulfate, and calcium oxide/hydroxide, have been shown to improve the stability of soil aggregates. This study seeks to determine which calcium‐based soil amendments, and at what concentration, are the most efficient in improving aggregate stability of sandy topsoils derived from granitic and metamorphic parent materials, and to analyze the mechanisms involved. In the pot experiment, soils amended with CaCO₃, CaCl₂, and CaSO₄ did not present significant differences in aggregate stability compared to the control or among each other. In contrast, Ca(OH)₂ soil amendment brought the greatest stability to the soil aggregates. A dose of 1% Ca(OH)₂ significantly increased the stability of soil aggregates. This effect is due to the reaction of Ca(OH)₂ with atmospheric CO₂ which leads to the formation of CaCO₃, a delayed reaction not showed by the other soil amendments tested. Likewise, the greater solubility of Ca(OH)₂ compared to CaCO₃ exerts a greater aggregation effect on soil. Thus, the mechanism of action of Ca(OH)₂ is related to cementation, rather than flocculation. Future studies should be carried out to demonstrate the effectiveness of Ca(OH)₂ under field conditions.     

The practical use of semiparametric models in field trials

This article examines the practical use of semiparametric models in the analysis of field trials—that is, models with parameterized treatment effects and additive terms derived by a data-driven approach using a locally weighted running line smoother (loess). We discuss graphical methods to identify spatial structure in the data and model selection procedures to choose the degree of smoothing. Once the spatial part of the model has been chosen, hypotheses about the treatment effects may be tested. Semiparametric models are used to analyze two barley field trials exhibiting spatial trends. The first has a single experimental treatment and a row-column design. The second has a split-plot design, and we use a semiparametric model which accounts for the randomization at the different strata of this design. We compare the semiparametric analyses with classical analyses of variance and with alternative spatial models. We find that semiparametric models give a good insight into spatial variation in the field and can improve the precision of parameter estimates.     

Methanotrophy-driven accumulation of organic carbon in four paddy soils of Bangladesh

Biological methane oxidation is a crucial process in the global carbon cycle that reduces methane emissions from paddy fields and natural wetlands into the atmosphere.However,soil organic carbon accumulation associated with microbial methane oxidation is poorly understood.Therefore,to investigate methane-derived carbon incorporation into soil organic matter,paddy soils originated from different parent materials(Inceptisol,Entisol,and Alfisol) were collected after rice harvesting from four major rice-producing regions in Bangladesh.Following microcosm incubation with 5%(volume/volume)¹³ CH₄,soil¹³ C-atom abundances significantly increased from background level of 1.08% to 1.88%–2.78%,leading to a net methane-derived accumulation of soil organic carbon ranging from 120 to 307 mg kg^-1.Approximately 23.6%–60.0% of the methane consumed was converted to soil organic carbon during microbial methane oxidation.The phylogeny of¹³ C-labeled pmoA(enconding the alpha subunit of the particulate methane monooxygenase) and 16 S rRNA genes further revealed that canonical α(type II) and γ(type I) Proteobacteria were active methane oxidizers.Members within the Methylobacter-and Methylosarcina-affiliated type Ia lineages dominated active methane-oxidizing communities that were responsible for the majority of methane-derived carbon accumulation in all three paddy soils,while Methylocystis-affiliated type IIa lineage was the key contributor in one paddy soil of Inceptisol origin.These results suggest that methanotroph-mediated synthesis of biomass plays an important role in soil organic matter accumulation.This study thus supports the concept that methanotrophs not only consume the greenhouse gas methane but also serve as a key biotic factor in maintaining soil fertility.     

The source of autumn and spring downstream migrating juvenile Atlantic salmon in a small lowland river

Over 3 years, 32,444 age‐0 group Atlantic salmon (Salmo salar) parr tagged with passive integrated transponder tags throughout the River Frome catchment were assigned to one of three groups, nonmigrants, autumn migrants and spring smolts, depending on the detection and the timing of detection at downstream tag readers (situated 8.6 km above the tidal limit). We examined the effect of density at the time of tagging (n·m^?2), distance upstream from the tidal limit (km), fish length (mm), Fulton condition index, habitat type (divided into two types, main river and carrier), days after 1 September that each fish was tagged and year (replication) on the proportions of fish in each of the migration groups. Distance upstream from tidal limit was strongly negatively related to the proportion of autumn migrants and positively related to the proportion of spring smolts. Nonmigrants had a lower average body size than migrants, although there were no differences in the sizes of autumn migrants and spring smolts in September prior to migration. Fish density had no effect on migration strategy. A lower proportion of fish migrated as autumn migrants from the smaller carrier habitats than the main river channel. There is some evidence that those parr destined to become autumn migrants underwent a lower mortality rate during September before tagging than those destined to become spring migrants indicating possible physiological or behavioural differences between these two groups of fish at that time. More research into the factors responsible for initiating the autumn migration is required.     

Quantitative analysis of culture using millions of digitized books

We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of 'culturomics,' focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. Culturomics extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities.