bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes of porcine pancreas α‐amylase in activity and secondary conformations under inhibition of tea polyphenols
Authors: Liu Shumin , Ou Shiyi , Huang Huihua
Published: May 2016

To investigate two‐sided functions of tea polyphenols (TP) in antinutrition and energy balance modulation, TP were extracted from Chinese green tea and used to complex porcine pancreas α‐amylase (PPA). Changes of PPA in activity and secondary conformations were analysed. Porcine pancreas α‐amylase was found sensitive to TP treatment. Tea polyphenols exhibited IC50 at 0.41 mg mL−1 against PPA and maximum inhibitory rate (98.17%) at 3.0 mg mL−1. Tea polyphenols inhibition was concluded as noncompetitive pattern based on its unchanged Km value (0.98 mg mL−1) for soluble starch substrate. Tea polyphenols inhibition arose from pH 1.5 to 10.14, covering gastric and intestinal environments inside body. Circular dichroism spectra analysis revealed regular changes of PPA in secondary conformations (increased proportions of α‐helix and β‐sheet) prior to its inactivation at low TP concentrations. Tea polyphenols‐inhibited PPA had distinct double‐negative peaks at 204 nm and 208 nm. Porcine pancreas α‐amylase was inactivated by TP in ways of complexation and modification of secondary conformations.
A Digital Approach to Improved Overdentures for the Adolescent Oligodontia Patient
Authors: Cooper Lyndon F. , Culp Lee , Luedin Nicole
Published: May 2016

Objective

The use of overdentures for treatment of oligodontia in adolescent patients using conventional techniques has described limitations. The aim of the case report is to demonstrate the use of CAD (Computer Aided Design) CAM (Computer Aided Manufacture) technology to produce an esthetic monolithic polymethylmethacrylate prosthesis that is retentive and stable on insertion.

Clinical Considerations

Adolescent oligodontia patients are typically not suitable candidates for dental implant therapy. Overdentures provide interim or definitive restorative advantages. Given the important esthetic, psychological, and social functions of the prosthesis, an important therapeutic goal for the overdenture prosthesis is esthetics. A CAD‐CAM approach to overdenture manufacture can provide a highly esthetic, strong, and retentive prosthesis.

Conclusions

CAD‐CAM manufacture of monolithic acrylic overdentures offer several advantages that include (1) improved planning and clinical communication, (2) high fidelity manufacture, (3) improved flexural strength, impact strength, and porosity, (4) improved prosthesis integrity and durability (due to the monolithic design), (5) CNC control of occlusal contacts, (6) high esthetic potential due to quality of bulk material and iterative design, and (7) archival nature of the digital prosthesis. CAD‐CAM manufacture of monolithic overdentures is a viable approach to completing high value esthetic management of the adolescent oligodontia patient.

Clinical Significance

This case report identifies a new way to utilize CAD CAM technology to produce an improved overdenture for the oligodontia patient. It will be of interest to many and underscores the fundamental principles of smile design transfer to the digital environment. (J Esthet Restor Dent, 2016)
Food Regime Analysis in a Post‐Neoliberal Era: Argentina and the Expansion of Transgenic Soybeans
Authors: Torrado Marla
Published: May 2016

This paper uses the food regime literature to analyse the political and economic relations promoting the expansion of soybeans in Argentina following the post‐neoliberal turn in the early 2000s. Continuities of the agrarian expansion from the neoliberal to post‐neoliberal model highlight the state's role in supporting a neoliberal food regime. Neoregulation in the post‐neoliberal agenda continues to favour increased production of transgenic food over ecological and human‐health considerations. Moreover, the emergence of new corporate and transnational actors has contributed to a new form of corporate‐agrarian governance premised on biotechnology. First, a food regime lens is used to describe the expansion of transgenic soybeans in Argentina, followed by an analysis of planning documents to show the state's position in reproducing neoliberal discourses and policies favouring the expansion of agriculture. The conclusion discusses the utility of food regime analysis for explaining the new forms of agricultural governance in Argentina.
A Honey‐Sealed Alliance: Mayan Beekeepers in the Yucatan Peninsula versus Transgenic Soybeans in Mexico's Last Tropical Forest
Authors: Gómez González Irma
Published: May 2016

The peasant economy of the Yucatan Peninsula is sustained by agriculture and beekeeping. Honey production has great economic importance, given that it represents the main source of income for Mayan rural families. Furthermore, Mexico is the world's fourth‐largest exporter of honey. The honey comes from jungle that covers the peninsular territory and forms part of a production system that broadly utilizes forestry resources. Two new situations emerged in 2011 that detonated social mobilization to defend beekeeping: the Mexican government authorized the planting of transgenic soybeans, while the European Union announced that honey that originated from transgenic pollen would have to be labelled (‘contains transgenics’), whereas honey importers demand transgenic‐free honey. The introduction of transgenic soybeans in the Yucatan Peninsula is part of the modern, industrial agricultural impetus in the region, which is entering into conflict with the Mayan peasant agriculture and threatens the survival of the most important Mexican tropical forest. A movement alliance was built among different social actors, including Mayan communities, beekeeper and civil‐society organizations, universities and honey‐exporting entrepreneurs, who developed an opposition and a resistance strategy to the cultivation of transgenic soybeans. Their repertoire has included collective legal, educational and organizational action, scientific research, mobilization, information, a media presence and lobbying. This mobilization has yielded results, as in 2015 the judiciary power invalidated the authorization of the cultivation of transgenic soybeans.
The Red de Semillas Libres: Contesting Biohegemony in Colombia
Authors: Gutiérrez Escobar Laura , Fitting Elizabeth
Published: May 2016

The Red de Semillas Libres (Network of Free Seeds) in Colombia contests the expansion of, and dominant narratives on, agricultural biotechnology and intellectual property rights (IPRs) protections on seed – or what has been called ‘biohegemony’. We argue that despite its challenges, the Network contests ‘biohegemony’ through lawsuits, supporting ‘seed sovereignty’, and reframing the often taken‐for‐granted discourse on local seed varieties as raw material and a resource to be ‘discovered’, ‘invented’ and commodified by industry and Western‐based technoscience. Based on ethnographic research, we extend the concept of biohegemony to include struggle and contestation by examining how the Network pursues seed sovereignty.
Hegemony, Technological Innovation and Corporate Identities: 50 Years of Agricultural Revolutions in Argentina
Authors: Gras Carla , Hernández Valeria
Published: May 2016

The technological changes that have occurred since the mid‐1960s in Argentine agriculture – first the Green Revolution and then the Agribusiness Paradigm – have been conceptualized as revolutionary not only with regard to their productivity improvements but also because they brought with them a change of mentality. Based on two different business conceptions, during each period an agrarian elite led the ‘revolutionary’ process, offering a technological response as the means of guaranteeing agriculture's ‘survival’ after various crises. For each period, we can identify a correspondence between the status given to technology, the conception of business and the type of government regulation. This paper analyses how the proposition of a ‘technological revolution’ corresponds to the construction of the ideological leadership through which the agrarian bourgeoisie managed to orientate agrarian development.
Environmental Injustice in Argentina: Struggles against Genetically Modified Soy
Authors: Leguizamón Amalia
Published: May 2016

This paper explores the unequal distribution of the environmental and social costs and benefits of the genetically modified (GM) soy model in Argentina and its impact on grievance formation and the emergence of contestation. In the 1990s, Argentina transitioned into a neoliberal agro‐industrial model based on producing GM soy for export. Though celebrated as a success, the expansion of GM soy monocultures has brought widespread socio‐ecological disruption. Various social actors have started to mobilize against the resulting environmental injustice. I focus on the peasant–indigenous movement in the north of the country, which is struggling for land rights, and the movements against agrochemical spraying in the central Pampas region. These groups, which are relatively powerless to control resources where they live, and that experience little or no benefit from GM soy production, nevertheless bear most of its social and ecological costs. These struggles link environmental and social well‐being, becoming struggles for ecological sustainability as well as social justice and equity.
Global Capitalism and the Nation State in the Struggles over GM Crops in Brazil
Authors: Motta Renata
Published: May 2016

The introduction of biotechnology is part of a global process of structural change in agriculture characterized by an increased integration of world agriculture with high corporate control. However, as the legal competence to allow the planting and trade of genetically modified (GM) crops commonly lies at the level of the nation state, this remains strategic in the politics of GM crops, both for actors promoting the technology and for social movements struggling against it. This paper illustrates this argument with an analysis of the struggles over GM crops in Brazil. It shows how the implementation of a food regime based on biotechnology, corporate control and neoliberal globalism depended on the state and was a contested process.
Serum Cystatin C Concentrations in Cats with Hyperthyroidism and Chronic Kidney Disease
Authors: Williams T.L. , Dillon H. , Elliott J. , Syme H.M. , Archer J.
Published: May 2016

Background

Currently, no test can accurately predict the development of azotemia after treatment of hyperthyroidism. Serum cystatin C concentrations (sCysC) might be less influenced by changes in body muscle mass and so better indicate the presence of concurrent chronic kidney disease (CKD) in hyperthyroidism.

Hypotheses

sCysC will be higher in hyperthyroid cats that develop azotemia compared with hyperthyroid cats that remain nonazotemic after treatment;sCysC will be higher in nonhyperthyroid cats with azotemicCKDthan healthy older cats and,sCysC will decrease after treatment of hyperthyroidism.

Animals

Ninety‐one cats treated in first opinion practice.

Methods

Case–control study.sCysC were compared between hyperthyroid cats which developed azotemia within 4 months of successful treatment of hyperthyroidism (pre‐azotemic group) and hyperthyroid cats which remained nonazotemic after treatment (nonazotemic group), and between nonhyperthyroid cats with azotemicCKDand healthy older cats.sCysC were also compared between hyperthyroid cats before treatment and at time of establishment of euthyroidism. Data are presented as median [25th, 75th percentile].

Results

BaselinesCysC were not different between the pre‐azotemic and nonazotemic groups (1.9 [1.4, 2.3] mg/L versus 1.5 [1.1, 2.2] mg/L, respectively;P= .22).sCysC in nonhyperthyroid cats with azotemicCKDand healthy older cats were not significantly different (1.5 [1.0, 1.9] mg/L versus 1.2 [0.8, 1.4] mg/L, respectively;P= .16).sCysC did not change significantly after treatment of hyperthyroidism (pretreatment 1.8 [1.2, 2.3] mg/L, after treatment 1.6 [1.1, 2.4] mg/L;P= .82).

Conclusions and Clinical Importance

sCysC do not appear to be a reliable marker of renal function in hyperthyroid cats.
Cerebrospinal Nematodiasis in 20 Camelids
Authors: Bertin F.R. , Taylor S.D.
Published: May 2016

Background

Information about the clinical and clinicopathologic aspects of cerebrospinal nematodiasis (CN) in camelids is limited.

Hypothesis

Clinical and therapeutic variables will be identified as factors predictive of survival.

Animals

Client‐owned camelids suspected of having CN admitted to Purdue University between 1995 and 2015.

Methods

A retrospective study was performed. A diagnosis of CN was based on cerebrospinal fluid (CSF) eosinophilic pleocytosis or postmortem findings.

Results

Eleven alpacas and 9 llamas met the inclusion criteria. Seventy‐five percent of the camelids were male (27% castrated and 73% intact). Common clinical abnormalities included proprioceptive deficits (100% of animals), recumbency (55%), tachypnea (55%), and ataxia (40%). Among the 85% of treated animals, 100% received PO fenbendazole, and 88% received a nonsteroidal anti‐inflammatory drug. The survival rate to discharge was 45%. Plasma fibrinogen concentration, creatine kinase activity, and serum creatinine concentration were significantly higher in nonsurvivors. Blood eosinophil count, platelet count, and total CO2 were significantly lower in nonsurvivors. Factors associated with survival were species, sex, absence of treatment with corticosteroids, and clinical improvement. There was no association between recumbency at admission and survival. A plasma fibrinogen concentration above >266 mg/dL was an excellent diagnostic test to predict survival in the presence of neurological signs or CSF eosinophilia.

Conclusions

Although prognosis for CN in camelids is guarded, presence of recumbency at admission is not predictive of nonsurvival. Male camelids and llamas appear more likely to die from CN. Corticosteroid treatment is contraindicated in animals diagnosed with CN.
Diagnostic disagreement between tests of evacuatory function: a prospective study of 100 constipated patients
Authors: Palit S. , Thin N. , Knowles C. H. , Lunniss P. J. , Bharucha A. E. , Scott S. M.
Published: May 2016

Background

Evacuatory dysfunction (ED) is a common cause of constipation and may be sub‐classified on the basis of specialist tests. Such tests may guide treatment e.g., biofeedback therapy for ‘functional’ defecatory disorders (FDD). However, there is no gold standard, and prior studies have not prospectively and systematically compared all tests that are used to diagnose forms of ED.

Methods

One hundred consecutive patients fulfilling Rome III criteria for functional constipation underwent four tests: expulsion of a rectal balloon distended to 50 mL (BE50) or until patients experienced the desire to defecate (BEDDV), evacuation proctography (EP) and anorectal manometry. Yields and agreements between tests for the diagnosis of ED and FDD were assessed.

Key Results

Positive diagnostic yields for ED were: BEDDV 18%, BE50 31%, EP 38% and anorectal manometry (ARM) 68%. Agreement was substantial between the two balloon tests (k = 0.66), only fair between proctography and BE50 (k = 0.27), poor between manometry and proctography (k = 0.01), and there was no agreement between the balloon tests and manometry (k = −0.07 for both BE50 and BEDDV). For the diagnosis of FDD, there was only fair agreement between ARM and EP (k = 0.23), ARM ± BE50 and EP (k = 0.18), ARM and EP ± BE50 (k = 0.30) and ARM ± BE50 and EP ± BE50 (k = 0.23).

Conclusions & Inferences

There is considerable disagreement between the results of various tests used to diagnose ED and FDD. This highlights the need for a reappraisal of both diagnostic criteria, and what represents the ‘gold standard’ investigation.
On the existence of non‐microbiotherian Australidelphian marsupials (Diprotodontia) in the Eocene of Patagonia
Authors: Lorente Malena , Chornogubsky Laura , Goin Francisco J.
Published: May 2016

A diverse assemblage of extinct mammals of early–middle Eocene age (Ypresian–Lutetian boundary) come from the Patagonian localities of La Barda and Laguna Fría around Paso del Sapo in northwestern Chubut Province (Argentina). Metatherians are well represented, mostly by dental remains of ‘Didelphimorphia’, Paucituberculata, Sparassodonta, Microbiotheria, and Polydolopimorphia. Here we analyse three calcanea and one astragalus referable to the same, indeterminate taxon, from La Barda, showing the fusion of their ectal and sustentacular facets. This facet arrangement characterizes the Australidelphia, a marsupial clade represented by Microbiotheria from South America and Antarctica, plus all Australasian lineages. Other australidelphian features shown by these tarsals include: in the calcanea, a reduced peroneal process and a tripartite cuboid facet; in the astragalus, a round, very small astragalar head in relation to the body; a convex trochlea with a half for the tibia and half, in slightly lower position, for the fibula. Their size and other anatomical features suggest that the new tarsals cannot be referred to the Microbiotheria. Phylogenetic analysis suggests that the La Barda taxon lies within the Australidelphia, and that it is either closely related or belongs to, the Diprotodontia. The existence of advanced australidelphians in Patagonia adds further evidence of the close relationship between Patagonia, Antarctica, and Australia during the Late Cretaceous – early Palaeogene.
Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy
Authors: Campbell Bradley C. , Gilding Edward K. , Mace Emma S. , Tai Shuaishuai , Tao Yongfu , Prentis Peter J. , Thomelin Pauline , Jordan David R. , Godwin Ian D.
Published: May 2016

Next‐generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP‐glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well‐characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.
Seasonal dynamics of δ13C of C‐rich fractions fromPicea abies(Norway spruce) andFagus sylvatica(European beech) fine roots
Authors: Paya Alex M. , Grams Thorsten E. E. , Bauerle Taryn L.
Published: May 2016

The13/12C ratio in plant roots is likely dynamic depending on root function (storage versus uptake), but to date, little is known about the effect of season and root order (an indicator of root function) on the isotopic composition of C‐rich fractions in roots. To address this, we monitored the stable isotopic composition of one evergreen (Picea abies) and one deciduous (Fagus sylvatica), tree species' roots by measuring δ13C of bulk, respired and labile C, and starch from first/second and third/fourth order roots during spring and fall root production periods. In both species, root order differences in δ13C were observed in bulk organic matter, labile, and respired C fractions. Beech exhibited distinct seasonal trends in δ13C of respired C, while spruce did not. In fall, first/second order beech roots were significantly depleted in13C, whereas spruce roots were enriched compared to higher order roots. Species variation in δ13C of respired C may be partially explained by seasonal shifts from enriched to depleted C substrates in deciduous beech roots. Regardless of species identity, differences in stable C isotopic composition of at least two root order groupings (first/second, third/fourth) were apparent, and should hereafter be separated in belowground C‐supply‐chain inquiry.
Multiple roles of NF1 in the melanocyte lineage
Authors: Larribère Lionel , Utikal Jochen
Published: May 2016

NF1 is a tumour suppressor gene, germline mutations of which lead to neurofibromatosis type 1 syndrome. Patients develop benign tumours from several types of cells including neural crest‐derived cells. NF1 somatic mutations also occur in 15% of sporadic melanoma, a cancer originating from melanocytes. Evidence now suggests the involvement of NF1 mutations in melanoma resistance to targeted therapies. Although NF1 is ubiquitously expressed, genetic links between NF1 and genes involved in melanocyte biology have been described, implying the lineage‐specific mechanisms. In this review, we summarize and discuss the latest advances related to the roles of NF1 in melanocyte biology and in cutaneous melanoma.
Comparative genomics‐informed design of two LAMP assays for detection of the kiwifruit pathogenPseudomonas syringaepv.actinidiaeand discrimination of isolates belonging to the pandemic biovar 3
Authors: Ruinelli M. , Schneeberger P. H. H. , Ferrante P. , Bühlmann A. , Scortichini M. , Vanneste J. L. , Duffy B. , Pothier J. F.
Published: May 2016

The aim of this study was to develop a rapid, sensitive and reliable field‐based assay for detection of the quarantine pathogenPseudomonas syringaepv.actinidiae(Psa), the causal agent of the most destructive and economically important bacterial disease of kiwifruit. A comparative genomic approach was used on the publicly available Psa genomic data to select unique target regions for the development of two loop‐mediated isothermal amplification (LAMP) assays able to detect Psa and to discriminate strains belonging to the highly virulent and globally spreading Psa biovar 3. BothLAMPassays showed specificity in accordance with their target and were able to detect reliably 125CFUper reaction in less than 30 min. The developed assays were able to detect the presence of Psa in naturally infected kiwifruit material with and without symptoms, thus increasing the potential of theLAMPassays for phytosanitary use.
International Lifestyle Migration in the Andes of Ecuador: How Migrants from the USA Perform Privilege, Import Rurality and Evaluate Their Impact on Local Community
Authors: Kordel Stefan , Pohle Perdita
Published: May 2016

Using the example of Vilcabamba in Ecuador, this article explores the ways that migrants from the USA materialise their quest for better lives by relocating to small communities in the Global South. Taking a lifestyle migration approach, we explore the ways migrants interpret and perform rurality in their post‐migration lives according to their economic and symbolically privileged status. Empirical data gathered from biographical narrative interviews with immigrants and guideline‐based interviews with experts show that migrants construct their own, mostly idealised, meanings of rurality; for instance, through the enactment of a healthy way of life close to nature, and social community spirit. Performing their privileged status through everyday practices, lifestyle migrants transfer their mostly Western understandings of rurality, derived from notions of the rural idyll, to other socio‐cultural settings. Consequently, they foster various transformations of local society, economy and public space. At the same time, however, via critical self‐reflection, they exhibit an ambivalent attitude to these transformations.
Proteomics and metabolomics analyses reveal the cucurbit sieve tube system as a complex metabolic space
Authors: Hu Chaoyang , Ham Byung‐Kook , El‐shabrawi Hattem M. , Alexander Danny , Zhang Dabing , Ryals John , Lucas William J.
Published: May 2016

The plant vascular system, and specifically the phloem, plays a pivotal role in allocation of fixed carbon to developing sink organs. Although the processes involved in loading and unloading of sugars and amino acids are well characterized, little information is available regarding the nature of other metabolites in the sieve tube system (STS) at specific sites along the pathway. Here, we elucidate spatial features of metabolite composition mapped with phloem enzymes along the cucurbit STS. Phloem sap (PS) was collected from the loading (source), unloading (apical sink region) and shoot–root junction regions of cucumber, watermelon and pumpkin. Our PS analyses revealed significant differences in the metabolic and proteomic profiles both along the source–sink pathway and between the STSs of these three cucurbits. In addition, metabolite profiles established for PS and vascular tissue indicated the presence of distinct compositions, consistent with the operation of the STS as a unique symplasmic domain. In this regard, at various locations along the STS we could map metabolites and their related enzymes to specific metabolic pathways. These findings are discussed with regard to the function of the STS as a unique and highly complex metabolic space within the plant vascular system.
Identification of line‐specific strategies for improving carotenoid production in synthetic maize through data‐driven mathematical modeling
Authors: Comas Jorge , Benfeitas Rui , Vilaprinyo Ester , Sorribas Albert , Solsona Francesc , Farré Gemma , Berman Judit , Zorrilla Uxue , Capell Teresa , Sandmann Gerhard , Zhu Changfu , Christou Paul , Alves Rui
Published: May 2016

Plant synthetic biology is still in its infancy. However, synthetic biology approaches have been used to manipulate and improve the nutritional and health value of staple food crops such as rice, potato and maize. With current technologies, production yields of the synthetic nutrients are a result of trial and error, and systematic rational strategies to optimize those yields are still lacking. Here, we present a workflow that combines gene expression and quantitative metabolomics with mathematical modeling to identify strategies for increasing production yields of nutritionally important carotenoids in the seed endosperm synthesized through alternative biosynthetic pathways in synthetic lines of white maize, which is normally devoid of carotenoids. Quantitative metabolomics and gene expression data are used to create and fit parameters of mathematical models that are specific to four independent maize lines. Sensitivity analysis and simulation of each model is used to predict which gene activities should be further engineered in order to increase production yields for carotenoid accumulation in each line. Some of these predictions (e.g. increasing Zmlycb/Gllycb will increase accumulated β‐carotenes) are valid across the four maize lines and consistent with experimental observations in other systems. Other predictions are line specific. The workflow is adaptable to any other biological system for which appropriate quantitative information is available. Furthermore, we validate some of the predictions using experimental data from additional synthetic maize lines for which no models were developed.
Monitoring southwest Greenland’s ice sheet melt with ambient seismic noise
Authors: Mordret Aurélien , Mikesell T. Dylan , Harig Christopher , Lipovsky Bradley P. , Prieto Germán A.
Published: May 2016

Researchers monitor southwest Greenland’s ice sheet mass changes by measuring seismic velocity variations in Greenland’s crust.
Dehydration of chlorite explains anomalously high electrical conductivity in the mantle wedges
Authors: Manthilake Geeth , Bolfan-Casanova Nathalie , Novella Davide , Mookherjee Mainak , Andrault Denis
Published: May 2016

Development of interconnected magnetite during chlorite dehydration explains anomalous high conductivity at shallow mantle wedges.
Dynamics of Biofilm Regrowth in Drinking Water Distribution Systems
Authors: Douterelo I. , Husband S. , Loza V. , Boxall J.
Published: May 2016

The majority of biomass within water distribution systems is in the form of attached biofilm. This is known to be central to drinking water quality degradation following treatment, yet little understanding of the dynamics of these highly heterogeneous communities exists. This paper presents original information on such dynamics, with findings demonstrating patterns of material accumulation, seasonality, and influential factors. Rigorous flushing operations repeated over a 1-year period on an operational chlorinated system in the United Kingdom are presented here. Intensive monitoring and sampling were undertaken, including time-series turbidity and detailed microbial analysis using 16S rRNA Illumina MiSeq sequencing. The results show that bacterial dynamics were influenced by differences in the supplied water and by the material remaining attached to the pipe wall following flushing. Turbidity, metals, and phosphate were the main factors correlated with the distribution of bacteria in the samples. Coupled with the lack of inhibition of biofilm development due to residual chlorine, this suggests that limiting inorganic nutrients, rather than organic carbon, might be a viable component in treatment strategies to manage biofilms. The research also showed that repeat flushing exerted beneficial selective pressure, giving another reason for flushing being a viable advantageous biofilm management option. This work advances our understanding of microbiological processes in drinking water distribution systems and helps inform strategies to optimize asset performance.

IMPORTANCE
This research provides novel information regarding the dynamics of biofilm formation in real drinking water distribution systems made of different materials. This new knowledge on microbiological process in water supply systems can be used to optimize the performance of the distribution network and to guarantee safe and good-quality drinking water to consumers.
Cardiolipins Act as a Selective Barrier to Toll-Like Receptor 4 Activation in the Intestine
Authors: Coats Stephen R. , Hashim Ahmed , Paramonov Nikolay A. , To Thao T. , Curtis Michael A. , Darveau Richard P.
Published: May 2016

Intestinal homeostasis mechanisms must protect the host intestinal tissue from endogenous lipopolysaccharides (LPSs) produced by the intestinal microbiota. In this report, we demonstrate that murine intestinal fecal lipids effectively block Toll-like receptor 4 (TLR4) responses to naturally occurring
Bacteroidetes
sp. LPS. Cardiolipin (CL) represents a significant proportion of the total intestinal and fecal lipids and, furthermore, potently antagonizes TLR4 activation by reducing LPS binding at the lipopolysaccharide binding protein (LBP), CD14, and MD-2 steps of the TLR4 signaling pathway. It is further demonstrated that intestinal lipids and CL are less effective at neutralizing more potent
Enterobacteriaceae
-type LPS, which is enriched in feces obtained from mice with dextran sodium sulfate (DSS)-treated inflammatory bowel disease. The selective inhibition of naturally occurring LPS structures by intestinal lipids may represent a novel homeostasis mechanism that blocks LPS activation in response to symbiotic but not dysbiotic microbial communities.

IMPORTANCE
The guts of animals harbor a variety of Gram-negative bacteria associated with both states of intestinal health and states of disease. Environmental factors, such as dietary habits, can drive the microbial composition of the host animal's intestinal bacterial community toward a more pathogenic state. Both beneficial and harmful Gram-negative bacteria are capable of eliciting potentially damaging inflammatory responses from the host intestinal tissues via a lipopolysaccharide (LPS)-dependent pathway. Physical mucosal barriers and antibodies produced by the intestinal immune system protect against the undesired inflammatory effects of LPS, although it is unknown why some bacteria are more effective at overcoming the protective barriers than others. This report describes the discovery of a lipid-type protective barrier in the intestine that reduces the deleterious effects of LPSs from beneficial bacteria but is less effective in dampening the inflammatory effects of LPSs from harmful bacteria, providing a novel mechanistic insight into inflammatory intestinal disorders.
In Vivo
Application of Bacteriophage as a Potential Therapeutic Agent To Control OXA-66-Like Carbapenemase-Producing Acinetobacter baumannii Strains Belonging to Sequence Type 357
Authors: Jeon Jongsoo , Ryu Choong-Min , Lee Jun-Young , Park Jong-Hwan , Yong Dongeun , Lee Kyungwon
Published: May 2016

The increasing prevalence of carbapenem-resistant
Acinetobacter baumannii
(CRAB) strains in intensive care units has caused major problems in public health worldwide. Our aim was to determine whether this phage could be used as an alternative therapeutic agent against multidrug-resistant bacterial strains, specifically CRAB clinical isolates, using a mouse model. Ten bacteriophages that caused lysis in CRAB strains, including
bla
OXA-66-like
genes, were isolated. YMC13/01/C62 ABA BP (phage Bϕ-C62), which showed the strongest lysis activity, was chosen for further study by transmission electron microscopy (TEM), host range test, one-step growth and phage adsorption rate, thermal and pH stability, bacteriolytic activity test, genome sequencing and bioinformatics analysis, and therapeutic effect of phage using a mouse intranasal infection model. The phage Bϕ-C62 displayed high stability at various temperatures and pH values and strong cell lysis activity
in vitro
. The phage Bϕ-C62 genome has a double-stranded linear DNA with a length of 44,844 bp, and known virulence genes were not identified
in silico. In vivo
study showed that all mice treated with phage Bϕ-C62 survived after intranasal bacterial challenge. Bacterial clearance in the lung was observed within 3 days after bacterial challenge, and histologic damage also improved significantly; moreover, no side effects were observed.

IMPORTANCE
In our study, the novel
A. baumannii
phage Bϕ-C62 was characterized and evaluated
in vitro
,
in silico
, and
in vivo
. These results, including strong lytic activities and the improvement of survival rates, showed the therapeutic potential of the phage Bϕ-C62 as an antimicrobial agent. This study reports the potential of a novel phage as a therapeutic candidate or nontoxic disinfectant against CRAB clinical isolates
in vitro
and
in vivo
.
Degradation Pathways of 2- and 4-Nitrobenzoates in Cupriavidus sp. Strain ST-14 and Construction of a Recombinant Strain, ST-14::3NBA, Capable of Degrading 3-Nitrobenzoate
Authors: Basu Soumik , Pal Chowdhury Piyali , Deb Satamita , Dutta Tapan K.
Published: May 2016

Strain ST-14, characterized as a member of the genus
Cupriavidus
, was capable of utilizing 2- and 4-nitrobenzoates individually as sole sources of carbon and energy. Biochemical studies revealed the assimilation of 2- and 4-nitrobenzoates via 3-hydroxyanthranilate and protocatechuate, respectively. Screening of a genomic fosmid library of strain ST-14 constructed in
Escherichia coli
identified two gene clusters,
onb
and
pob-pca
, to be responsible for the complete degradation of 2-nitrobenzoate and protocatechuate, respectively. Additionally, a gene segment (
pnb
) harboring the genes for the conversion of 4-nitrobenzoate to protocatechuate was unveiled by transposome mutagenesis. Reverse transcription-PCR analysis showed the polycistronic nature of the gene clusters, and their importance in the degradation of 2- and 4-nitrobenzoates was ascertained by gene knockout analysis. Cloning and expression of the relevant pathway genes revealed the transformation of 2-nitrobenzoate to 3-hydroxyanthranilate and of 4-nitrobenzoate to protocatechuate. Finally, incorporation of functional 3-nitrobenzoate dioxygenase into strain ST-14 allowed the recombinant strain to utilize 3-nitrobenzoate via the existing protocatechuate metabolic pathway, thereby allowing the degradation of all three isomers of mononitrobenzoate by a single bacterial strain.

IMPORTANCE
Mononitrobenzoates are toxic chemicals largely used for the production of various value-added products and enter the ecosystem through industrial wastes. Bacteria capable of degrading mononitrobenzoates are relatively limited. Unlike other contaminants, these man-made chemicals have entered the environment since the last century, and it is believed that bacteria in nature evolved not quite efficiently to assimilate these compounds; as a consequence, to date, there are only a few reports on the bacterial degradation of one or more isomers of mononitrobenzoate. In the present study, fortunately, we have been able to isolate a
Cupriavidus
sp. strain capable of assimilating both 2- and 4-nitrobenzoates as the sole carbon source. Results of the biochemical and molecular characterization of catabolic genes responsible for the degradation of mononitrobenzoates led us to manipulate a single enzymatic step, allowing the recombinant host organism to expand its catabolic potential to assimilate 3-nitrobenzoate.
Fast, Continuous, and High-Throughput (Bio)Chemical Activity Assay forN-Acyl-l-Homoserine Lactone Quorum-Quenching Enzymes
Authors: Last Daniel , Krüger Georg H. E. , Dörr Mark , Bornscheuer Uwe T.
Published: May 2016

Quorum sensing, the bacterial cell-cell communication by small molecules, controls important processes such as infection and biofilm formation. Therefore, it is a promising target with several therapeutic and technical applications besides its significant ecological relevance. Enzymes inactivatingN-acyl-l-homoserine lactones, the most common class of communication molecules among Gram-negative proteobacteria, mainly belong to the groups of quorum-quenching lactonases or quorum-quenching acylases. However, identification, characterization, and optimization of these valuable biocatalysts are based on a very limited number of fundamentally different methods with their respective strengths and weaknesses. Here, a (bio)chemical activity assay is described, which perfectly complements the other methods in this field. It enables continuous and high-throughput activity measurements of purified and unpurified quorum-quenching enzymes within several minutes. For this, the reaction products released by quorum-quenching lactonases and quorum-quenching acylases are converted either by a secondary enzyme or by autohydrolysis tol-homoserine. In turn,l-homoserine is detected by the previously described calcein assay, which is sensitive to α-amino acids with free N and C termini. Besides its establishment, the method was applied to the characterization of three previously undescribed quorum-quenching lactonases and variants thereof and to the identification of quorum-quenching acylase-expressingEscherichia coliclones in an artificial library. Furthermore, this study indicates that porcine aminoacylase 1 is not active towardN-acyl-l-homoserine lactones as published previously but instead converts the autohydrolysis productN-acyl-l-homoserine.

IMPORTANCEIn this study, a novel method is presented for the identification, characterization, and optimization of quorum-quenching enzymes that are active towardN-acyl-l-homoserine lactones. These are the most common communication molecules among Gram-negative proteobacteria. The activity assay is a highly valuable complement to the available analytical tools in this field. It will facilitate studies on the environmental impact of quorum-quenching enzymes and contribute to the development of therapeutic and technical applications of this promising enzyme class.
Thermal Stability of Hepatitis E Virus as Estimated by a Cell Culture Method
Authors: Johne Reimar , Trojnar Eva , Filter Matthias , Hofmann Jörg
Published: May 2016

Hepatitis E virus (HEV) is an increasingly recognized zoonotic pathogen. Transmission is suspected to occur from infected pigs or wild boars to humans through direct contact, environmental pathways, or contaminated food. However, the physical and chemical stability of HEV is largely unknown, because suitable cell culture methods for infectivity measurement are missing. Here, we developed a titration method using infection of the cell line A549/D3 with HEV genotype 3 strain 47832c and subsequent counting of focus-forming units by immunofluorescence, which allowed HEV infectivity measurements within a 4-log-dilution range. Long-term storage of HEV in cell culture medium at different temperatures indicated a phase of rapid virus inactivation, followed by a slower progression of virus inactivation. Infective HEV was detected up to 21 days at 37°C, up to 28 days at room temperature, and until the end of the experiment (56 days) with a 2.7-log decrease of infectious virus at 4°C. Heat treatment for 1 min resulted in moderate decreases of infectivity up to 60°C, 2- to 3.5-log decreases between 65°C and 75°C, and no remaining virus was detected at temperatures of ≥80°C. Heating for 70°C resulted in a 3.6-log decrease after 1.5 min and the absence of detectable virus (>3.9-log decrease) after 2 min. The data were used to calculate predictive heat inactivation models for HEV. The results may help estimate HEV stability in the environment or food. The established method may be used to study other aspects of HEV stability in the future.

IMPORTANCE
In this study, a cell culture method was developed which allows the measurement of hepatitis E virus (HEV) infectivity. Using this system, the stability of HEV at different time-temperature combinations was assessed, and a predictive model was established. The obtained data may help estimate HEV stability in the environment or food, thus enabling an assessment of the relative risks of HEV infection through distinct routes and by distinct types of food in the future.
Isolation of Nontuberculous Mycobacteria from the Environment of Ghanian Communities Where Buruli Ulcer Is Endemic
Authors: Aboagye Samuel Yaw , Danso Emelia , Ampah Kobina Assan , Nakobu Zuliehatu , Asare Prince , Otchere Isaac Darko , Röltgen Katharina , Yirenya-Tawiah Dzidzo , Yeboah-Manu Dorothy
Published: May 2016

This study aimed to isolate nontuberculous mycobacterial species from environmental samples obtained from some selected communities in Ghana. To optimize decontamination, spiked environmental samples were used to evaluate four decontamination solutions and supplemented media, after which the best decontamination solution and media were used for the actual analysis. The isolates obtained were identified on the basis of specific genetic sequences, including heat shock protein 65, IS
2404
, IS
2606
,
rpoB
, and the ketoreductase gene, as needed. Among the methods evaluated, decontamination with 1 M NaOH followed by 5% oxalic acid gave the highest rate of recovery of mycobacteria (50.0%) and the lowest rate of contamination (15.6%). The cultivation medium that supported the highest rate of recovery of mycobacteria was polymyxin B-amphotericin B-nalidixic acid-trimethoprim-azlocillin–supplemented medium (34.4%), followed by isoniazid-supplemented medium (28.1%). Among the 139 samples cultivated in the main analysis, 58 (41.7%) yielded mycobacterial growth, 70 (50.4%) had no growth, and 11 (7.9%) had all inoculated tubes contaminated. A total of 25 different mycobacterial species were identified. Fifteen species (60%) were slowly growing (e.g.,
Mycobacterium ulcerans
,
Mycobacterium avium
,
Mycobacterium mantenii
, and
Mycobacterium malmoense
), and 10 (40%) were rapidly growing (e.g.,
Mycobacterium chelonae
,
Mycobacterium fortuitum
, and
Mycobacterium abscessus
). The occurrence of mycobacterial species in the various environmental samples analyzed was as follows: soil, 16 species (43.2%); vegetation, 14 species (38.0%); water, 3 species (8.0%); moss, 2 species (5.4%); snail, 1 species (2.7%); fungi, 1 species (2.7%). This study is the first to report on the isolation of
M. ulcerans
and other medically relevant nontuberculous mycobacteria from different environmental sources in Ghana.

IMPORTANCE
Diseases caused by mycobacterial species other than those that cause tuberculosis and leprosy are increasing. Control is difficult because the current understanding of how the organisms are spread and where they live in the environment is limited, although this information is needed to design preventive measures. Growing these organisms from the environment is also difficult, because the culture medium becomes overgrown with other bacteria that also live in the environment, such as in soil and water. We aimed to improve the methods for growing these organisms from environmental sources, such as soil and water samples, for better understanding of important mycobacterial ecology.
Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments
Authors: Tully Benjamin J. , Heidelberg John F.
Published: May 2016

The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching
Alphaproteobacteria
, two novel organisms within the
Proteobacteria
, and new members of the
Nitrospirae
,
Nitrospinae
, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry.

IMPORTANCE
This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1
Thaumarchaeota
,
Nitrospinae
, and
Nitrospirae
and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium.