bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA barcoding in autotrophic euglenids: evaluation of COI and 18s rDNA
Authors: Łukomska‐Kowalczyk Maja , Karnkowska Anna , Krupska Małgorzata , Milanowski Rafał , Zakryś Bożena
Published: June 2016

Autotrophic euglenids (Euglenophyceae) are a common and abundant group of microbial eukaryotes in freshwater habitats. They have a limited number of features, which can be observed using light microscopy, thus species identification is often problematic. Establishing a barcode for this group is therefore an important step toward the molecular identification of autotrophic euglenids. Based on the literature, we selected verified species and used a plethora of available methods to validate two molecular markers: COI and 18S rDNA (the whole sequence and three fragments separately) as potential DNA barcodes. Analyses of the COI gene were performed based on the data set of 43 sequences (42 obtained in this study) representing 24 species and the COI gene was discarded as a DNA barcode mainly due to a lack of universal primer sites. For 18S rDNA analyses we used a data set containing 263 sequences belonging to 86 taxonomically verified species. We demonstrated that the whole 18S rDNA is too long to be a useful marker, but from the three shorter analyzed variable regions we recommend variable regions V2V3 and V4 of 18S rDNA as autotrophic euglenid barcodes due to their high efficiency (above 95% and 90%, respectively).
Microsatellite markers and cytoplasmic sequences reveal contrasting pattern of spatial genetic structure in the red algae species complex Mazzaella laminarioides
Authors: Guillemin Marie‐Laure , Valero Myriam , Morales Collio Kennia , Pinochet Sanchez Ramona , Henríquez Espinosa Miguel , Silva Andrea X.
Published: June 2016

Mazzaella laminarioides is a common haploid‐diploid red alga that forms dense beds. This alga has a wide distributional range, covering 3,500 km of the Chilean coast, but is restricted to high rocky intertidal zones. Recently, the existence of three highly divergent genetic lineages was demonstrated for this taxon, and two cytoplasmic markers were used to determine that these lineages are distributed in strict parapatry. Here, using 454 next‐generation sequencing, we developed polymorphic microsatellite loci that cross amplify in all three cytoplasmic lineages. Six sites (i.e., two sites within each lineage) were analyzed using nine microsatellite loci. Our work shows that, although substantial cytoplasmic differentiation occurs within M. laminarioides, the microsatellite loci did not retrieve three nuclear genetic clusters as expected. Indeed, while the northernmost and southernmost cytoplasmic lineages form two strongly divergent nuclear groups characterized by diagnostic alleles, the third cytoplasmic lineage did not form a third nuclear independent group. It is possible that inter‐lineage gene exchange has occurred, particularly at sites along the contact zone between the different cytoplasmic lineages. This nuclear‐cytoplasmic incongruence in M. laminarioides could be explained by incomplete lineage sorting of the nuclear genes or asymmetric introgressive hybridization between the lineages. Finally, highly significant heterozygote deficiencies (suggesting occurrence of intergametophytic selfing) were observed in the three small northernmost sites while the large southernmost sites generally approached panmixia.
Insufficient resolving power of mitogenome data in deciphering deep phylogeny of Holometabola
Authors: Song Nan , An Shi‐Heng , Yin Xin‐Ming , Zhao Te , Wang Xin‐Yu
Published: June 2016

The mitochondrial genome (mitogenome) is one of the most widely used markers for phylogenetic analysis. Compared with whole‐genome data, mitogenome data are less expensive to obtain and easier to manipulate. However, compositional bias and accelerated evolutionary rate reduce the effectiveness of the mitogenome in determining insect phylogeny. This study shows that mitogenome data are not suitable to reconstruct deep holometabolan evolution, even with a most comprehensive data coding scheme and the more realistic CAT model. For the deep levels of divergence within Holometabola, protein‐coding genes only retain weak phylogenetic signals, leading to peculiar interordinal relationships. Consensus relationships in the Holometabola phylogeny, such as the monophyly of Holometabola, the most basal position of Hymenoptera, and the sister group relationship between the Strepsiptera and Coleoptera were rarely resolved in our analyses. The relationships of the holometabolan groups as inferred by mitogenomes are highly vulnerable to gene types, data coding regimes, model choice, and optimality criteria, and no consistent alternative hypothesis of Holometabola's relationships is supported. Thus, we suggest that the slowly evolving nuclear genes or genome‐scale approaches may be better options for resolving deep‐level phylogeny of Holometabola.
Pharmacokinetics of marbofloxacin in freshwater crocodiles (Crocodylus siamensis) after intravenous and intramuscular administration
Authors: Poapolathep S. , Giorgi M. , Hantrakul S. , Klangkaew N. , Sanyathitiseree P. , Poapolathep A.
Published: June 2016

To evaluate the fate and disposition of marbofloxacin (MBF) in freshwater crocodiles (Crocodylus siamensis), MBF was administered either intravenously (i.v.) or intramuscularly (i.m.) at a dosage of 2.0 mg/kg body weight. The concentrations of MBF in plasma were measured using high‐performance liquid chromatography equipped with a fluorescence detector. The concentrations of MBF in the plasma were measurable up to 144 h after i.v. and i.m. administration. After the first 45 min, the mean pharmacokinetic profiles produced by the two administration routes were almost identical. No statistically significant differences in the pharmacokinetic parameters between the groups were observed. The half‐life was long (about 2.5 days), the volume of distribution was large (about 1.44 L/kg), λz was small (0.01 h−1), and the clearance was slow (22.6 mL/h/kg). The absolute i.m. bioavailability (F%) was 105.36%. The dose of MBF administered in this study seems to produce appropriate PK‐PD parameters that predict antibacterial success for disease caused by susceptible bacteria. More studies are warranted to evaluate the likely residues after administration of multiple doses.
Effects of Dietary Fish Oil Replacement with Palm Oil on the Growth, Feed Utilization, Biochemical Composition, and Antioxidant Status of Juvenile Chu's Croaker, Nibea coibor
Authors: Huang Yisheng , Wen Xiaobo , Li Shengkang , Li Wenjia , Zhu Dashi
Published: June 2016

A 56‐d feeding trial was conducted to evaluate the growth performance, feed utilization, biochemical composition, and antioxidant status of chu's croaker, Nibea coibor (12.6 ± 0.1 g) in net pens fed diets supplemented with various levels of crude palm oil: 0% fish oil (FO), 20% palm oil (2PO), 40% (4PO), 60% (6PO), 80% (8PO), and 100% (10PO). Weight gain and specific growth rate (SGR) were significantly lower in fish fed 8PO and 10PO diets. The increase of PO levels did not affect fish survival, feed intake, and feed conversion ratio. Feeding diet 10PO led to significantly higher lipid content in the liver, but not the whole body and dorsal muscle, than diets FO and 2PO. PO supplementation led to increased α‐tocopherol, but decreased thiobarbituric acid‐reactive substances, n‐3 highly unsaturated fatty acid (n‐3 HUFA), and n‐3/n‐6 fatty acid ratio, in both the liver and muscle. Hepatic superoxide dismutase and catalase were significantly higher in fish fed 10PO diet than FO diet. Polynomial regression analysis showed that the maximum SGR was obtained at 24.2% crude PO. Results of this study suggested that PO could replace up to 60% of FO without adverse effect on growth performance or nutritional quality of fish.
Effects of Bacillus coagulans on Growth Performance, Disease Resistance, and HSP70 Gene Expression in Juvenile Gibel Carp, Carassius auratus gibelio
Authors: Yu Yebing , Lv Fu , Wang Changhai , Wang Aimin , Zhao Weihong , Yang Wenping
Published: June 2016

We studied the effects of Bacillus coagulans on growth, nonspecific immune parameters, and disease resistance in juvenile gibel carp. The fish were randomly divided into five groups: a control group fed a basic diet and four treated groups fed the basic diet supplemented with 125, 250, 500, and 1000 mg/kg B. coagulans, respectively, for 8 wk. Growth; plasma lysozyme activity; respiratory burst activity of phagocytes (RBAP); and the activity of tumor necrosis factor‐α (TNF‐α), interleukin‐1β (IL‐1β), and antioxidant enzymes were determined. The group that received 250 mg/kg B. coagulans showed an improved protein efficiency ratio, plasma lysozyme activity, superoxide dismutase, and superoxide anion radical scavenging activity and heat shock protein (HSP70) gene expression compared with the control group. Moreover, the 250 mg/kg B. coagulans group had a reduced feeding rate, feed conversion ratio, and plasma malondialdehyde content compared with the control group. The weight gain rate, protein efficiency ratio, plasma lysozyme, RBAP, TNF‐α, and superoxide anion radical scavenging activity and HSP70 gene expression were significantly increased, whereas the feed conversion ratio was significantly reduced, in the group supplemented with 500 mg/kg B. coagulans compared with the control. Artificial infection with Aeromonas hydrophila revealed a cumulative mortality in the control group that was higher than that in the 250, 500, and 1000 mg/kg B. coagulans groups. The results suggest that feed supplementation with 250–500 mg/kg B. coagulans has the potential to stimulate immunity, increase resistance against pathogenic infection, and promote growth in gibel carp.
Evaluating the Effects of a Short‐Term Feed Restriction Period on the Behavior and Welfare of Atlantic Salmon, Salmo salar, parr Using Social Network Analysis and Fin Damage
Authors: Cañon Jones Hernán Alberto , Noble Chris , Damsgård Børge , Pearce Gareth P.
Published: June 2016

Social network analysis (SNA) was used to quantify the role of behavioral interactions on the frequency and severity of fin damage in Atlantic salmon, Salmo salar, parr subjected to a short feed restriction period of 10 d. Dorsal fin erosion was observed in both feed‐restricted (FR) and control (C) groups of fish, but was significantly more frequent and severe in FR groups. FR fish had a significantly lower weight, length, and poorer body condition in comparison to C groups. Social networks based on aggressive interactions showed significantly higher overall degree‐centrality, clustering coefficients, out and in‐degree centralities in FR groups. This led to the formation of clusters of fish into initiators and receivers of aggression. Only the receivers of aggression exhibited dorsal fin damage, while initiators did not. Initiators and receivers of aggression in FR groups retained their roles even after control conditions were restored, suggesting that short periods of feed restriction can lead to permanent modifications in aggressive behavior. This study demonstrates the applied value of using SNA to investigate the longer term effects that aggressive behavioral interactions have on fin damage and welfare in Atlantic salmon.
Radiotherapeutic strategies for hepatocellular carcinoma with portal vein tumour thrombosis in a hepatitis B endemic area
Authors: Im Jung Ho , Yoon Sang Min , Park Hee Chul , Kim Jong Hoon , Yu Jeong Il , Kim Tae Hyun , Kim Jun Won , Nam Taek‐Keun , Kim Kyubo , Jang Hong Seok , Kim Jin Hee , Kim Mi‐Sook , Yoon Won Sup , Jung Inkyung , Seong Jinsil
Published: June 2016

Background & Aims

This nationwide, multicenter study investigated treatment outcomes as well as the optimal radiotherapeutic strategy in patients with hepatocellular carcinoma (HCC) and portal vein tumour thrombosis (PVTT).

Methods

We retrospectively reviewed the records of 985 patients who received radiotherapy (RT) for PVTT. The median equivalent RT dose was 48.75 Gy. Combined treatment, defined as liver‐directed treatments performed within a month of RT, was administered to 657 patients (66.7%). The PVTT and primary tumour were irradiated in 413 patients (41.9%), and PVTT only was targeted in 572 patients (58.1%).

Results

The response rate of the PVTT was 51.8%, and RT responders had a significantly longer survival than non‐responders (15.2 vs. 6.9 months). Equivalent RT dose and combined treatment predicted response of PVTT. The median overall survival (OS) was 10.2 months. Multivariate analysis revealed the equivalent RT dose ˃45 Gy and combined treatment as significant positive factors for OS. In the propensity score matching analysis, the combined treatment group had better OS than the no combined treatment group, whereas the OS of the PVTT + primary tumour group did not differ significantly from that of the PVTT only group.

Conclusion

The equivalent RT dose ˃45 Gy, given in combination with other treatments, provided better PVTT control and OS. The optimal RT volume is suggested for either PVTT + primary or PVTT only. Taken together, multimodal treatment with equivalent RT dose higher than 45 Gy is recommended for patients with HCC and PVTT.
Contrasting support for alternative models of genomic variation based on microhabitat preference: species‐specific effects of climate change in alpine sedges
Authors: Massatti Rob , Knowles L. Lacey
Published: June 2016

Deterministic processes may uniquely affect codistributed species’ phylogeographic patterns such that discordant genetic variation among taxa is predicted. Yet, explicitly testing expectations of genomic discordance in a statistical framework remains challenging. Here, we construct spatially and temporally dynamic models to investigate the hypothesized effect of microhabitat preferences on the permeability of glaciated regions to gene flow in two closely related montane species. Utilizing environmental niche models from the Last Glacial Maximum and the present to inform demographic models of changes in habitat suitability over time, we evaluate the relative probabilities of two alternative models using approximate Bayesian computation (ABC) in which glaciated regions are either (i) permeable or (ii) a barrier to gene flow. Results based on the fit of the empirical data to data sets simulated using a spatially explicit coalescent under alternative models indicate that genomic data are consistent with predictions about the hypothesized role of microhabitat in generating discordant patterns of genetic variation among the taxa. Specifically, a model in which glaciated areas acted as a barrier was much more probable based on patterns of genomic variation in Carex nova, a wet‐adapted species. However, in the dry‐adapted Carex chalciolepis, the permeable model was more probable, although the difference in the support of the models was small. This work highlights how statistical inferences can be used to distinguish deterministic processes that are expected to result in discordant genomic patterns among species, including species‐specific responses to climate change.
Justification of full width panoramic radiography in Oral Surgery
Authors: Bell G.W. , Donaldson K.J. , Walton R.L. , Morrison J.L.
Published: June 2016

Objective

How much of a full width panoramic radiograph is required for diagnosis and treatment planning in Oral Surgery?

Study design

In this retrospective study, the panoramic radiograph was divided into five equal vertical segments and assessed as to the number of segments required for diagnosis and treatment planning in relation to their initial referral. Incidental findings outside the areas required were investigated as to whether or not they influenced treatment planning.

Results

From images of 823 patients; over half (56.5%) required only one segment of the image for diagnostic purposes in relation to their referral. The posterior mandible and temporomandibular joint areas were required least (5.3%), followed by the midline segment (10.0%). The segments required most often were the molar and premolar regions bilaterally (84.7%). In 15.8%, incidental findings were observed outside of the segments requested, but these only influenced treatment planning in 2.9% of cases.

Conclusion

In this study of patients attending an oral surgery service, a full width panoramic tomograph was not required in most instances. Referrals for segmental panoramic imaging should be regarded as regular rather than unusual practice.
Ice‐binding proteins confer freezing tolerance in transgenic Arabidopsis thaliana
Authors: Bredow Melissa , Vanderbeld Barbara , Walker Virginia K.
Published: June 2016

Lolium perenne is a freeze‐tolerant perennial ryegrass capable of withstanding temperatures below −13 °C. Ice‐binding proteins (IBPs) presumably help prevent damage associated with freezing by restricting the growth of ice crystals in the apoplast. We have investigated the expression, localization and in planta freezing protection capabilities of two L. perenne IBP isoforms, LpIRI2 and LpIRI3, as well as a processed IBP (LpAFP). One of these isoforms, LpIRI2, lacks a conventional signal peptide and was assumed to be a pseudogene. Nevertheless, both LpIRI2 and LpIRI3 transcripts were up‐regulated following cold acclimation. LpIRI2 also demonstrated ice‐binding activity when produced recombinantly in Escherichia coli. Both the LpIRI3 and LpIRI2 isoforms appeared to accumulate in the apoplast of transgenic Arabidopsis thaliana plants. In contrast, the fully processed isoform, LpAFP, remained intracellular. Transgenic plants expressing either LpIRI2 or LpIRI3 showed reduced ion leakage (12%–39%) after low‐temperature treatments, and significantly improved freezing survival, while transgenic LpAFP‐expressing lines did not confer substantial subzero protection. Freeze protection was further enhanced by with the introduction of more than one IBP isoform; ion leakage was reduced 26%–35% and 10% of plants survived temperatures as low as −8 °C. Our results demonstrate that apoplastic expression of multiple L. perenne IBP isoforms shows promise for providing protection to crops susceptible to freeze‐induced damage.
Disaster Management from a POM Perspective: Mapping a New Domain
Authors: Gupta Sushil , Starr Martin K. , Farahani Reza Zanjirani , Matinrad Niki
Published: June 2016

We have reviewed disaster management research papers published in major operations management, management science, operations research, supply chain management and transportation/logistics journals. In reviewing these studies, our objective is to assess and present the macro level “architectural blue print” of disaster management research with the hope that it will attract new researchers and motivate established researchers to contribute to this important field. The secondary objective is to bring this disaster research to the attention of disaster administrators so that disasters are managed more efficiently and more effectively. We have mapped the disaster management research on the following five attributes of a disaster: (1) Disaster Management Function (decision‐making process, prevention and mitigation, evacuation, humanitarian logistics, casualty management, and recovery and restoration), (2) Time of Disaster (before, during and after), (3) Type of Disaster (accidents, earthquakes, floods, hurricanes, landslides, terrorism and wildfires etc.), (4) Data Type (Field and Archival data, Real data and Hypothetical data), and (5) Data Analysis Technique (bidding models, decision analysis, expert systems, fuzzy system analysis, game theory, heuristics, mathematical programming, network flow models, queueing theory, simulation and statistical analysis). We have done cross tabulations of data among these five parameters to gain greater insights into disaster research. Recommendations for future research are provided.
Variation in pathotypes and virulence of Plasmodiophora brassicae populations in Germany
Authors: Zamani‐Noor N.
Published: June 2016

Between 2012 and 2015, 49 new clubroot‐infested fields were identified in 12 German federal states. Clubroot disease incidence varied within these fields from 22% to 92%. Field information revealed that in 85% of fields, oilseed rape was grown in rotation once every 2 or 3 years. Frequency of OSR in the rotation was significantly correlated with the incidence and prevalence of clubroot disease. The disease was detected in fields with soil pH ranging from 5.1 to 8.3, and a significant negative correlation was found between soil pH and the disease incidence of infested fields. Furthermore, more cases of disease and severe incidences were observed in sandy loam and loamy sand as compared with other soil types. Pathotype classification of the 49 Plasmodiophora brassicae populations was conducted on two differential sets, the European Clubroot Differential set and the set of Somé (1996). Additionally, the degree of virulence of the collected isolates was analysed on the clubroot‐resistant oilseed rape cv. Mendel. The results showed variation in pathotype distribution in different regions in Germany. The majority of isolates according to Somé were pathotypes 1 and 3, respectively, with pathotypes 2 and 5 in the minority. Detailed classification according to Buczacki showed the dominance of 16/31/31, 16/14/30 and 16/14/31 populations among 20 distinct virulence patterns of collected isolates. From all populations tested for virulence on cv. Mendel, 15 isolates were found to be moderately or highly virulent. These virulent populations were not restricted to a small geographical area in the country.
Monitoring fungi in ecological restorations of coastal Indiana, U.S.A.
Authors: Avis Peter G. , Gaswick Wyatt C. , Tonkovich Gayle S. , Leacock Patrick R.
Published: June 2016

Monitoring of ecological restorations has rarely focused on fungi. In this study, we conduct a first‐ever monitoring of macrofungi in ecological restorations of coastal Indiana (U.S.A.) and present an approach and considerations that can be followed elsewhere. Forty‐two sites were surveyed over a 2‐year period for the presence of saprotrophic, mycorrhizal, and parasitic macrofungi. Sites included those considered to be restoration, prerestoration, or reference and were in wooded, semiwooded, or grassland habitats. With 1,103 observations, 277 species of fungi were identified. Most fungi were found in wooded habitats though some were in grassland restorations. Invasive plant cover negatively impacted fungal species richness. Monitored sites were compared to a set of reference sites using two different similarity indices (overlap and Jaccard), as well as the ratios of different fungal functional guilds, revealing that choice of index can impact how restorations are perceived to match targets. Last, we present a novel, tractable, and conservative way to assess and rank sites by the functional trait guilds of fungi. We show that such an approach can provide important additional information about the success of restorations such that functional guild ratios could be used as an indicator of restoration progress early‐on while functional values are better used in later phases.
Legal instruments in private land conservation: the nature and role of conservation contracts and conservation covenants
Authors: Lindsay Bruce
Published: June 2016

Management of private land for ecological outcomes has emerged as an important facet of biodiversity management and ecological restoration in Australia. Common law conservation contracts and conservation covenants are important tools within this framework of private land conservation. They can provide legal protections to biodiversity and natural assets on private land, as well as legal frameworks, in the form of obligations, to restoration programs. They can provide distinct qualities of binding obligation: fixed term or enduring. Conservation contracts and covenants need to be recognized as possessing both transactional and relational qualities, and these qualities should be considered and reflected in the design of agreements and in practices of conservation management and agreement‐making. Two design questions are considered in this article. Conservation agreements need to contend with dynamism in ecological and social realities and this may be accommodated in mechanisms for adjustment of obligations between or within agreements. Dispute management is a second field of practice and drafting requiring attention. Constructing disputes provisions that are adapted and appropriate to long‐term conservation actions and restoration initiatives is reflective of good faith principles and can include scope for graduated, independent, corrective, and fair arrangements, informed as necessary by expert input.
Automated Geocoding of Textual Documents: A Survey of Current Approaches
Authors: Melo Fernando , Martins Bruno
Published: June 2016

This survey article describes previous research addressing text‐based document geocoding, i.e. the task of predicting the geospatial coordinates of latitude and longitude, that best correspond to an entire document, based on its textual contents. We describe (1) early document geocoding systems that use heuristics over place names mentioned in the text (e.g. names of cities and states), (2) probabilistic language modeling approaches, where generative models are built for different regions in the world (usually considering a discretization based on a rectangular grid) from the words occurring in a set of georeferenced training documents, which are then used to predict per‐region probabilities for previously unseen test documents, (3) combinations of different models and heuristics, including clustering procedures, feature selection approaches, and/or language models built from different sources, and (4) recent approaches based on discriminative classification models.
Extraocular muscle dysinnervation disorder resembling Duane retraction syndrome in a 9‐month‐old French Bulldog
Authors: Mari Lorenzo , Blacklock Benjamin T. , Stavinohova Renata , De Risio Luisa
Published: June 2016

A 9‐month‐old French Bulldog was presented with a chronic history of lateral strabismus and intermittent third eyelid protrusion in the left eye. The neuro‐ophthalmological examination revealed mild ptosis of the left upper eyelid, mild lateral strabismus, and external ophthalmoparesis of the left eye. Retraction and ventral deviation of the left eye globe with protrusion of the third eyelid and elevation of the upper eyelid were elicited on attempted voluntary adduction of the left eye. Hematology, serum biochemistry, serology for infectious diseases, magnetic resonance of the head, and cerebrospinal fluid analysis did not reveal significant abnormalities. Forced duction test did not show signs of mechanical restriction in ocular motility. A suspected congenital cranial dysinnervation disorder resembling Duane retraction syndrome in humans was diagnosed based on the typical clinical signs and exclusion of structural abnormalities. The clinical signs remained stable for 9 months until the time of writing this report.
A tool set to allow rapid screening of dog families with PRA for association with candidate genes
Authors: Winkler Paige A. , Davis Jennifer A. , Petersen‐Jones Simon M. , Venta Patrick J. , Bartoe Joshua T.
Published: June 2016

Objective

To develop a method to rapidly screen candidate genes for association with recessively inherited progressive retinal atrophy (PRA) in pedigrees of dog in which a causative mutation has not been identified.

Animal studied

Thirteen PRA‐affected dogs were used in this study.

Procedures

Two microsatellite markers (MS) were designed flanking 45 candidate genes. MS markers were analyzed for heterozygosity and allelic richness. Two dog breeds, in which the causative mutation has been identified (Entlebucher Sennenhunds [ES] and PDE6A‐mutant dogs [PDE6A]), were used to validate the MS marker panel. One breed in which the causative mutation is currently unknown (Old English Sheepdog [OES]) was investigated in this study utilizing the MS panel.

Results

Marker heterozygosity excluded 38 of 45 and 41 of 45 candidate genes (ES and PDE6A, respectively) with each true culprit gene remaining on the list of nonexcluded candidate genes. Additionally, 41 of 45 genes were excluded for OES.

Conclusions

This tool set was used quickly and efficiently to narrow down 45 candidate genes for recessively inherited PRA in two types of dogs with known mutations and one type of dog with an unknown mutation.
Edge-selenated graphene nanoplatelets as durable metal-free catalysts for iodine reduction reaction in dye-sensitized solar cells
Authors: Ju Myung Jong , Jeon In-Yup , Kim Hong Mo , Choi Ji Il , Jung Sun-Min , Seo Jeong-Min , Choi In Taek , Kang Sung Ho , Kim Han Seul , Noh Min Jong , Lee Jae-Joon , Jeong Hu Young , Kim Hwan Kyu , Kim Yong-Hoon , Baek Jong-Beom
Published: June 2016

The I
3
−
reduction mechanism on carbon-based materials is clarified by electrochemical kinetics and DFT-NEGF calculations.
Efficient and selective degradation of polyethylenes into liquid fuels and waxes under mild conditions
Authors: Jia Xiangqing , Qin Chuan , Friedberger Tobias , Guan Zhibin , Huang Zheng
Published: June 2016

A catalytic alkane metathesis provides a mild and selective degradation of polyethylene wastes into valuable fuels and waxes.
A highly shape-adaptive, stretchable design based on conductive liquid for energy harvesting and self-powered biomechanical monitoring
Authors: Yi Fang , Wang Xiaofeng , Niu Simiao , Li Shengming , Yin Yajiang , Dai Keren , Zhang Guangjie , Lin Long , Wen Zhen , Guo Hengyu , Wang Jie , Yeh Min-Hsin , Zi Yunlong , Liao Qingliang , You Zheng , Zhang Yue , Wang Zhong Lin
Published: June 2016

Researchers report a scalable approach for highly deformable and stretchable energy harvesters and self-powered sensors.
Novel multiple sclerosis susceptibility loci implicated in epigenetic regulation
Authors: Andlauer Till F. M. , Buck Dorothea , Antony Gisela , Bayas Antonios , Bechmann Lukas , Berthele Achim , Chan Andrew , Gasperi Christiane , Gold Ralf , Graetz Christiane , Haas Jürgen , Hecker Michael , Infante-Duarte Carmen , Knop Matthias , Kümpfel Tania , Limmroth Volker , Linker Ralf A. , Loleit Verena , Luessi Felix , Meuth Sven G. , Mühlau Mark , Nischwitz Sandra , Paul Friedemann , Pütz Michael , Ruck Tobias , Salmen Anke , Stangel Martin , Stellmann Jan-Patrick , Stürner Klarissa H. , Tackenberg Björn , Then Bergh Florian , Tumani Hayrettin , Warnke Clemens , Weber Frank , Wiendl Heinz , Wildemann Brigitte , Zettl Uwe K. , Ziemann Ulf , Zipp Frauke , Arloth Janine , Weber Peter , Radivojkov-Blagojevic Milena , Scheinhardt Markus O. , Dankowski Theresa , Bettecken Thomas , Lichtner Peter , Czamara Darina , Carrillo-Roa Tania , Binder Elisabeth B. , Berger Klaus , Bertram Lars , Franke Andre , Gieger Christian , Herms Stefan , Homuth Georg , Ising Marcus , Jöckel Karl-Heinz , Kacprowski Tim , Kloiber Stefan , Laudes Matthias , Lieb Wolfgang , Lill Christina M. , Lucae Susanne , Meitinger Thomas , Moebus Susanne , Müller-Nurasyid Martina , Nöthen Markus M. , Petersmann Astrid , Rawal Rajesh , Schminke Ulf , Strauch Konstantin , Völzke Henry , Waldenberger Melanie , Wellmann Jürgen , Porcu Eleonora , Mulas Antonella , Pitzalis Maristella , Sidore Carlo , Zara Ilenia , Cucca Francesco , Zoledziewska Magdalena , Ziegler Andreas , Hemmer Bernhard , Müller-Myhsok Bertram
Published: June 2016

Genome-wide study in Germans identifies four novel multiple sclerosis risk genes and confirms already known gene loci.
Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the Last Deglaciation
Authors: Metcalf Jessica L. , Turney Chris , Barnett Ross , Martin Fabiana , Bray Sarah C. , Vilstrup Julia T. , Orlando Ludovic , Salas-Gismondi Rodolfo , Loponte Daniel , Medina Matías , De Nigris Mariana , Civalero Teresa , Fernández Pablo Marcelo , Gasco Alejandra , Duran Victor , Seymour Kevin L. , Otaola Clara , Gil Adolfo , Paunero Rafael , Prevosti Francisco J. , Bradshaw Corey J. A. , Wheeler Jane C. , Borrero Luis , Austin Jeremy J. , Cooper Alan
Published: June 2016

Patagonian megafaunal extinctions reveal synergistic roles of climate change and human impacts.
Efficient solar-driven water splitting by nanocone BiVO
4
-perovskite tandem cells
Authors: Qiu Yongcai , Liu Wei , Chen Wei , Chen Wei , Zhou Guangmin , Hsu Po-Chun , Zhang Rufan , Liang Zheng , Fan Shoushan , Zhang Yuegang , Cui Yi
Published: June 2016

Efficient solar water splitting is achieved by a nanocone BiVO
4
photoelectrochemical cell in tandem with a perovskite solar cell.
The transition from linear to highly branched poly(β-amino ester)s: Branching matters for gene delivery
Authors: Zhou Dezhong , Cutlar Lara , Gao Yongsheng , Wang Wei , O’Keeffe-Ahern Jonathan , McMahon Sean , Duarte Blanca , Larcher Fernando , Rodriguez Brian J. , Greiser Udo , Wang Wenxin
Published: June 2016

Highly branched poly(β-amino ester) polymers are developed to carry a gene and to enter cells for the production of protein.
Oil droplet self-transportation on oleophobic surfaces
Authors: Li Juan , Qin Qi Hang , Shah Ali , Ras Robin H. A. , Tian Xuelin , Jokinen Ville
Published: June 2016

Oleophobic surfaces capable of power-free self-transportation of oil droplets are designed.
Tunable room-temperature spin-selective optical Stark effect in solution-processed layered halide perovskites
Authors: Giovanni David , Chong Wee Kiang , Dewi Herlina Arianita , Thirumal Krishnamoorthy , Neogi Ishita , Ramesh Ramamoorthy , Mhaisalkar Subodh , Mathews Nripan , Sum Tze Chien
Published: June 2016

A new spin on perovskites untwined: Ultrafast optical switching and tuning of spin-energy states in layered halide perovskites.
Presence and Persistence of Viable, Clinically Relevant Legionella pneumophila Bacteria in Garden Soil in the Netherlands
Authors: van Heijnsbergen E. , van Deursen A. , Bouwknegt M. , Bruin J. P. , de Roda Husman A. M. , Schalk J. A. C.
Published: June 2016

Garden soils were investigated as reservoirs and potential sources of pathogenic
Legionella
bacteria.
Legionella
bacteria were detected in 22 of 177 garden soil samples (12%) by amoebal coculture. Of these 22
Legionella
-positive soil samples, seven contained
Legionella pneumophila
. Several other species were found, including the pathogenic
Legionella longbeachae
(4 gardens) and
Legionella sainthelensi
(9 gardens). The
L. pneumophila
isolates comprised 15 different sequence types (STs), and eight of these STs were previously isolated from patients according to the European Working Group for
Legionella
Infections (EWGLI) database. Six gardens that were found to be positive for
L. pneumophila
were resampled after several months, and in three gardens,
L. pneumophila
was again isolated. One of these gardens was resampled four times throughout the year and was found to be positive for
L. pneumophila
on all occasions.

IMPORTANCE
Tracking the source of infection for sporadic cases of Legionnaires' disease (LD) has proven to be hard.
L. pneumophila
ST47, the sequence type that is most frequently isolated from LD patients in the Netherlands, is rarely found in potential environmental sources. As
L. pneumophila
ST47 was previously isolated from a garden soil sample during an outbreak investigation, garden soils were investigated as reservoirs and potential sources of pathogenic
Legionella
bacteria. The detection of viable, clinically relevant
Legionella
strains indicates that garden soil is a potential source of
Legionella
bacteria, and future research should assess the public health implication of the presence of
L. pneumophila
in garden soil.
Activating Intrinsic Carbohydrate-Active Enzymes of the Smut Fungus Ustilago maydis for the Degradation of Plant Cell Wall Components
Authors: Geiser Elena , Reindl Michèle , Blank Lars M. , Feldbrügge Michael , Wierckx Nick , Schipper Kerstin
Published: June 2016

The microbial conversion of plant biomass to valuable products in a consolidated bioprocess could greatly increase the ecologic and economic impact of a biorefinery. Current strategies for hydrolyzing plant material mostly rely on the external application of carbohydrate-active enzymes (CAZymes). Alternatively, production organisms can be engineered to secrete CAZymes to reduce the reliance on externally added enzymes. Plant-pathogenic fungi have a vast repertoire of hydrolytic enzymes to sustain their lifestyle, but expression of the corresponding genes is usually highly regulated and restricted to the pathogenic phase. Here, we present a new strategy in using the biotrophic smut fungus
Ustilago maydis
for the degradation of plant cell wall components by activating its intrinsic enzyme potential during axenic growth. This fungal model organism is fully equipped with hydrolytic enzymes, and moreover, it naturally produces value-added substances, such as organic acids and biosurfactants. To achieve the deregulated expression of hydrolytic enzymes during the industrially relevant yeast-like growth in axenic culture, the native promoters of the respective genes were replaced by constitutively active synthetic promoters. This led to an enhanced conversion of xylan, cellobiose, and carboxymethyl cellulose to fermentable sugars. Moreover, a combination of strains with activated endoglucanase and β-glucanase increased the release of glucose from carboxymethyl cellulose and regenerated amorphous cellulose, suggesting that mixed cultivations could be a means for degrading more complex substrates in the future. In summary, this proof of principle demonstrates the potential applicability of activating the expression of native CAZymes from phytopathogens in a biocatalytic process.

IMPORTANCE
This study describes basic experiments that aim at the degradation of plant cell wall components by the smut fungus
Ustilago maydis
. As a plant pathogen, this fungus contains a set of lignocellulose-degrading enzymes that may be suited for biomass degradation. However, its hydrolytic enzymes are specifically expressed only during plant infection. Here, we provide the proof of principle that these intrinsic enzymes can be synthetically activated during the industrially relevant yeast-like growth. The fungus is known to naturally synthesize valuable compounds, such as itaconate or glycolipids. Therefore, it could be suited for use in a consolidated bioprocess in which more complex and natural substrates are simultaneously converted to fermentable sugars and to value-added compounds in the future.
Listeria monocytogenes DNA Glycosylase AdlP Affects Flagellar Motility, Biofilm Formation, Virulence, and Stress Responses
Authors: Zhang Ting , Bae Dongryeoul , Wang Chinling
Published: June 2016

The temperature-dependent alteration of flagellar motility gene expression is critical for the foodborne pathogen
Listeria monocytogenes
to respond to a changing environment. In this study, a genetic determinant,
L. monocytogenes
f2365_0220
(
lmof2365_0220
), encoding a putative protein that is structurally similar to the
Bacillus cereus
alkyl base DNA glycosylase (AlkD), was identified. This determinant was involved in the transcriptional repression of flagellar motility genes and was named
adlP
(encoding an
A
lk
D
-
l
ike
p
rotein [AdlP]). Deletion of
adlP
activated the expression of flagellar motility genes at 37°C and disrupted the temperature-dependent inhibition of
L. monocytogenes
motility. The
adlP
null strains demonstrated decreased survival in murine macrophage-like RAW264.7 cells and less virulence in mice. Furthermore, the deletion of
adlP
significantly decreased biofilm formation and impaired the survival of bacteria under several stress conditions, including the presence of a DNA alkylation compound (methyl methanesulfonate), an oxidative agent (H
2
O
2
), and aminoglycoside antibiotics. Our findings strongly suggest that
adlP
may encode a bifunctional protein that transcriptionally represses the expression of flagellar motility genes and influences stress responses through its DNA glycosylase activity.

IMPORTANCE
We discovered a novel protein that we named
A
lk
D
-
l
ike
p
rotein (AdlP). This protein affected flagellar motility, biofilm formation, and virulence. Our data suggest that AdlP may be a bifunctional protein that represses flagellar motility genes and influences stress responses through its DNA glycosylase activity.
Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers
Authors: Perez Maëva , Juniper S. Kim
Published: June 2016

The symbiotic relationship between vestimentiferan tubeworms and their intracellular chemosynthetic bacteria is one of the more noteworthy examples of adaptation to deep-sea hydrothermal vent environments. The tubeworm symbionts have never been cultured in the laboratory. Nucleotide sequences from the small subunit rRNA gene suggest that the intracellular symbionts of the eastern Pacific vent tubeworms
Oasisia alvinae
,
Riftia pachyptila
,
Tevnia jerichonana
, and
Ridgeia piscesae
belong to the same phylotype of gammaproteobacteria, “
Candidatus
Endoriftia persephone.” Comparisons of symbiont genomes between the East Pacific Rise tubeworms
R. pachyptila
and
T. jerichonana
confirmed that these two hosts share the same symbionts. Two
Ridgeia
symbiont genomes were assembled from trophosome metagenomes from worms collected from the Juan de Fuca Ridge (one and five individuals, respectively). We compared these assemblies to those of the sequenced
Riftia
and
Tevnia
symbionts. Pangenome composition, genome-wide comparisons of the nucleotide sequences, and pairwise comparisons of 2,313 orthologous genes indicated that “
Ca
. Endoriftia persephone” symbionts are structured on large geographical scales but also on smaller scales and possibly through host specificity.

IMPORTANCE
Remarkably, the intracellular symbionts of four to six species of eastern Pacific vent tubeworms all belong to the same phylotype of gammaproteobacteria, “
Candidatus
Endoriftia persephone.” Understanding the structure, dynamism, and interconnectivity of “
Ca
. Endoriftia persephone” populations is important to advancing our knowledge of the ecology and evolution of their host worms, which are often keystone species in vent communities. In this paper, we present the first genomes for symbionts associated with the species
R. piscesae
, from the Juan de Fuca Ridge. We then combine these genomes with published symbiont genomes from the East Pacific Rise tubeworms
R. pachyptila
and
T. jerichonana
to develop a portrait of the “
Ca
. Endoriftia persephone” pangenome and an initial outline of symbiont population structure in the different host species. Our study is the first to apply genome-wide comparisons of “
Ca
. Endoriftia persephone” assemblies in the context of population genetics and molecular evolution.
Effects of the Nitrification Inhibitor 3,4-Dimethylpyrazole Phosphate on Nitrification and Nitrifiers in Two Contrasting Agricultural Soils
Authors: Shi Xiuzhen , Hu Hang-Wei , Müller Christoph , He Ji-Zheng , Chen Deli , Suter Helen Charlotte
Published: June 2016

The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) is a powerful tool that can be used to promote nitrogen (N) use efficiency and reduce N losses from agricultural systems by slowing nitrification. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in nitrification and N
2
O production; however, their responses to DMPP amendment and the microbial mechanisms underlying the variable efficiencies of DMPP across different soils remain largely unknown. Here we compared the impacts of DMPP on nitrification and the dynamics of ammonia oxidizers between an acidic pasture soil and an alkaline vegetable soil using a
15
N tracing and
13
CO
2
-DNA–stable-isotope probing (SIP) technique. The results showed that DMPP significantly inhibited nitrification and N
2
O production in the vegetable soil only, and the transient inhibition was coupled with a significant decrease in AOB abundance. No significant effects on the community structure of ammonia oxidizers or the abundances of total bacteria and denitrifiers were observed in either soil. The
15
N tracing experiment revealed that autotrophic nitrification was the predominant form of nitrification in both soils. The
13
CO
2
-DNA–SIP results indicated the involvement of AOB in active nitrification in both soils, but DMPP inhibited the assimilation of
13
CO
2
into AOB only in the vegetable soil. Our findings provide evidence that DMPP could effectively inhibit nitrification through impeding the abundance and metabolic activity of AOB in the alkaline vegetable soil but not in the acidic pasture soil, possibly due to the low AOB abundance or the adsorption of DMPP by organic matter.

IMPORTANCE
The combination of the
15
N tracing model and
13
CO
2
-DNA–SIP technique provides important evidence that the nitrification inhibitor DMPP could effectively inhibit nitrification and nitrous oxide emission in an alkaline soil through influencing the abundance and metabolic activity of AOB. In contrast, DMPP amendment has no significant effect on nitrification or nitrifiers in an acidic soil, potentially owing to the low abundance of AOB and the possible adsorption of DMPP by organic matter. Our findings have direct implications for improved agricultural practices through utilizing the nitrification inhibitor DMPP in appropriate situations, and they emphasize the importance of microbial communities to the efficacy of DMPP.
The
blp
Locus of Streptococcus pneumoniae Plays a Limited Role in the Selection of Strains That Can Cocolonize the Human Nasopharynx
Authors: Valente Carina , Dawid Suzanne , Pinto Francisco R. , Hinds Jason , Simões Alexandra S. , Gould Katherine A. , Mendes Luís A. , de Lencastre Hermínia , Sá-Leão Raquel
Published: June 2016

Nasopharyngeal colonization is important for
Streptococcus pneumoniae
evolution, providing the opportunity for horizontal gene transfer when multiple strains co-occur. Although colonization with more than one strain of pneumococcus is common, the factors that influence the ability of strains to coexist are not known. A highly variable
blp
(bacteriocin-like peptide) locus has been identified in all sequenced strains of
S. pneumoniae
. This locus controls the regulation and secretion of bacteriocins, small peptides that target other bacteria. In this study, we analyzed a series of cocolonizing isolates to evaluate the impact of the
blp
locus on human colonization to determine whether competitive phenotypes of bacteriocin secretion restrict cocolonization. We identified a collection of 135 nasopharyngeal samples cocolonized with two or more strains, totaling 285 isolates. The
blp
locus of all strains was characterized genetically with regard to pheromone type, bacteriocin/immunity content, and potential for locus functionality. Inhibitory phenotypes of bacteriocin secretion and locus activity were assessed through overlay assays. Isolates from single colonizations (
n
= 298) were characterized for comparison. Cocolonizing strains had a high diversity of
blp
cassettes; approximately one-third displayed an inhibitory phenotype
in vitro
. Despite
in vitro
evidence of competition, pneumococci cocolonized the subjects independently of
blp
pheromone type (
P
= 0.577), bacteriocin/immunity content,
blp
locus activity (
P
= 0.798), and inhibitory phenotype (
P
= 0.716). In addition, no significant differences were observed when single and cocolonizing strains were compared. Despite clear evidence of
blp
-mediated competition in experimental models, the results of our study suggest that the
blp
locus plays a limited role in restricting pneumococcal cocolonization in humans.

IMPORTANCE
Nasopharyngeal colonization with
Streptococcus pneumoniae
(pneumococcus) is important for pneumococcal evolution, as the nasopharynx represents the major site for horizontal gene transfer when multiple strains co-occur, a phenomenon known as cocolonization. Understanding how pneumococcal strains interact within the competitive environment of the nasopharynx is of chief importance in the context of pneumococcal ecology. In this study, we used an unbiased collection of naturally co-occurring pneumococcal strains and showed that a biological process frequently used by bacteria for competition—bacteriocin production—is not decisive in the coexistence of pneumococci in the host, in contrast to what has been shown in experimental models.