bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Al2O3 capping layers on the thermal properties of thin black phosphorus
Authors: Li Kuilong , Ang Kah-Wee , Lv Youming , Liu Xinke
Published: December 2016

We investigate the thermal properties of thin black phosphorus (BP) with Al2O3 capping layer using the temperature-dependent and polarized-laser power-dependent Raman spectroscopy. Compared to the BP samples without Al2O3 capping layer, the Al2O3 passivation layer significantly improves the thermal stability of BP by reducing the thermal coefficients of the Ag1, B2g, and Ag2 Raman modes from −0.0082, −0.0142, and −0.0145 cm−1/K to −0.0046, −0.0074, and −0.0088 cm−1/K, respectively, which are attributed to the compressive strain and strong Al-P and O-P bonds. Meanwhile, the thermal conductivity reaches to about 45.4 and 54.4 W/mK along the armchair and zigzag directions, greatly larger than those of the BP films without Al2O3 24.1 and 39.0 W/mK, respectively, owing to the large thermal conductivity of Al2O3 and the interface charges between Al2O3 and BP. Overall, this work will contribute to improve the BP-based device performances and extend the BP applications profoundly.
Assessing the invasion threat of non-native plant species in protected areas using Herbarium specimen and ecological survey data. A case study in two rangeland bioregions in Queensland
Authors: Ngugi Michael R. , Neldner Victor John
Published: December 2016

Naturalised non-native plants that become invasive pose a significant threat to the conservation of biodiversity in protected areas (areas dedicated and managed for long-term conservation of nature), economic productivity of agricultural businesses, and societal impacts including community, culture infrastructure and health. Quantifying the spread, potential dominance and invasion threat of these species is fundamental to effective eradication and development of threat mitigation policy. But this is often hampered by the lack of comprehensive data. This study used existing ecological survey data from 2548 sites and 64 758 Herbarium specimen records to document the status and abundance of non-native plants in two case study bioregions, Cape York Peninsula (CYP) and the Desert Uplands (DEU) in Queensland covering a total area of 186 697 km2. There were 406 non-native species in the CYP, 186 (45.6%) of which are known environmental weeds and 159 non-natives in DEU, of which 69 (43.5%) are environmental weeds. Inside the protected areas, there were 98 species of environmental weeds in CYP, 27 of which are listed as weeds of State significance (Weeds of National Significance (WONS), Queensland declared and non-declared pest plants categories). In DEU, there were 18 environmental weeds inside protected areas and none of them was listed as a weed of State significance. Non-native species that recorded foliage cover dominance in the ecological site data are generally recognised as environmental weeds in Queensland. The threat of weeds from outside of protected areas was serious, with 41 weeds of State significance found in CYP, five of which are WONS, and 25 weeds of State significance found in DEU, 10 of which are WONS.
Nrf2 mitigates LRRK2- and α-synuclein–induced neurodegeneration by modulating proteostasis
Authors: Skibinski Gaia , Hwang Vicky , Ando Dale Michael , Daub Aaron , Lee Alicia K. , Ravisankar Abinaya , Modan Sara , Finucane Mariel M. , Shaby Benjamin A. , Finkbeiner Steven
Published: December 2016

Significance

The prevailing view of nuclear factor erythroid 2-related factor (Nrf2) function in the central nervous system is that it acts by a cell-nonautonomous mechanism to activate a program of gene expression that mitigates reactive oxygen species and the damage that ensues. Our work significantly expands the biological understanding of Nrf2 by showing that Nrf2 mitigates toxicity induced by α-synuclein and leucine-rich repeat kinase 2 (LRRK2), by potently promoting neuronal protein homeostasis in a cell-autonomous and time-dependent fashion. Nrf2 accelerates the clearance of α-synuclein, shortening its half-life and leading to lower overall levels of α-synuclein. By contrast, Nrf2 promotes the aggregation of LRRK2 into inclusion bodies, leading to a significant reduction in diffuse mutant LRRK2 levels elsewhere in the neuron.
Relationship between local structure and relaxation in out-of-equilibrium glassy systems
Authors: Schoenholz Samuel S. , Cubuk Ekin D. , Kaxiras Efthimios , Liu Andrea J.
Published: December 2016

Significance

A key stumbling block in the study of out-of-equilibrium systems is that their properties depend not only on their current state but also on the manner in which the systems were prepared. Therefore, to understand generic systems out of equilibrium one must take into account the entire history of their preparation. Here we show that the history dependence of a widely studied model of a glass is captured by a quantity that depends only on the positions of the constituent particles. This quantity, called softness, is designed to be a structural order parameter for dynamics in glassy liquids. Our results suggest that a large class of out-of-equilibrium glasses can be understood by augmenting the usual state variables by the instantaneous softness distribution.
Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core
Authors: Chen Yujie , Tokuda Joshua M. , Topping Traci , Meisburger Steve P. , Pabit Suzette A. , Gloss Lisa M. , Pollack Lois
Published: December 2016

Significance

Nucleosomes are fundamental protein–DNA structures through which eukaryotes package and organize DNA inside the nucleus. Nucleosomes are disassembled to gain access to the critical information stored in DNA. Here, we describe a new experimental approach that characterizes the kinetics of nucleosome disassembly and the synergy between DNA conformation and protein components. Using NaCl to disrupt electrostatic interactions, we identify kinetic pathways and transient intermediates that reveal how DNA unwrapping and protein dissociation are linked in this macromolecular complex. These dynamic structures may provide new insight into the regulation of DNA access during transcription, replication, and repair.
Mosaic expression of claudins in thick ascending limbs of Henle results in spatial separation of paracellular Na
+
and Mg
2+
transport
Authors: Milatz Susanne , Himmerkus Nina , Wulfmeyer Vera Christine , Drewell Hoora , Mutig Kerim , Hou Jianghui , Breiderhoff Tilman , Müller Dominik , Fromm Michael , Bleich Markus , Günzel Dorothee
Published: December 2016

Significance

The thick ascending limb (TAL) of Henle’s loop is a nephron segment that reabsorbs Na
+
, Ca
2+
, and Mg
2+
via the paracellular pathway, the tight junction (TJ). TJ permeability is regulated by claudin proteins. We show that the TAL expresses claudins cldn3, cldn10b, cldn16, and cldn19 in a TJ mosaic pattern with cldn3/cldn16/cldn19 in a complex and cldn10b alone. This mutual exclusiveness is facilitated by different claudin interaction properties. TJs with cldn10b favor Na
+
over Mg
2+
, whereas TJs with cldn3/cldn16/cldn19 prefer Mg
2+
over Na
+
. Hence we conclude that mono- and divalent cations in the TAL take different paracellular routes, and their reabsorption can be regulated independently. This spatial separation is important for renal ion homeostasis and its discovery improves our understanding of paracellular transport organization.
Bax transmembrane domain interacts with prosurvival Bcl-2 proteins in biological membranes
Authors: Andreu-Fernández Vicente , Sancho Mónica , Genovés Ainhoa , Lucendo Estefanía , Todt Franziska , Lauterwasser Joachim , Funk Kathrin , Jahreis Günther , Pérez-Payá Enrique , Mingarro Ismael , Edlich Frank , Orzáez Mar
Published: December 2016

Significance

Bcl-2 (B-cell lymphoma 2) proteins are key regulators of apoptosis. The recruitment of the predominantly cytosolic Bcl-2 protein Bax (Bcl-2 associated X, apoptosis regulator) to the mitochondria is associated with mitochondrial outer membrane permeabilization and apoptosis. We report specific interactions between the transmembrane domains (TMDs) of Bax and the prosurvival Bcl-x
L
(B-cell lymphoma-extra large) and Bcl-2 proteins. Our results demonstrate that these interactions occur in nonapoptotic human cells and participate in the regulation of Bcl-2 proteins, introducing the concept of modulation mitochondrial apoptosis signaling by TMD-mediated Bcl-2 protein interactions.
High fishery catches through trophic cascades in China
Authors: Szuwalski Cody S. , Burgess Matthew G. , Costello Christopher , Gaines Steven D.
Published: December 2016

Significance

Fishing marine ecosystems indiscriminately and intensely can have negative impacts on biodiversity, but it may increase the biomass of fish available for capture in the system. We explore the possibility that China’s high fishery catches are a result of predator removal using an ecosystem model of the East China Sea (ECS). We show that China’s high fishery catches can be explained by the removal of larger predatory fish and consequent increases in the production of smaller fish. We project that single-species management would decrease catches in the ECS by reversing these ecosystem effects. Fisheries similar to those in China produce a large fraction of global catch; management reform in these areas must consider the entire ecosystem, rather than individual species.
Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics
Authors: Janouškovec Jan , Gavelis Gregory S. , Burki Fabien , Dinh Donna , Bachvaroff Tsvetan R. , Gornik Sebastian G. , Bright Kelley J. , Imanian Behzad , Strom Suzanne L. , Delwiche Charles F. , Waller Ross F. , Fensome Robert A. , Leander Brian S. , Rohwer Forest L. , Saldarriaga Juan F.
Published: December 2016

Significance

We created a dataset of dinoflagellate transcriptomes to resolve internal phylogenetic relationships of the group. We show that the dinoflagellate theca originated once, through a process that likely involved changes in the metabolism of cellulose, and suggest that a late origin of dinosterol in the group is at odds with dinoflagellates being the source of this important biomarker before the Mesozoic. We also show that nonphotosynthetic dinoflagellates have retained nonphotosynthetic plastids with vital metabolic functions, and propose that one of these may be the evolutionary source of dinoflagellate bioluminescence. Finally, we reconstruct major molecular and morphological transitions in dinoflagellates and highlight the role of horizontal gene transfer in the origin of their unique nuclear architecture.
Synthesis of arborane triterpenols by a bacterial oxidosqualene cyclase
Authors: Banta Amy B. , Wei Jeremy H. , Gill Clare C. C. , Giner José-Luis , Welander Paula V.
Published: December 2016

Significance

Polycyclic lipids produced by bacteria and eukaryotes can be preserved in sedimentary rocks for millions of years. These ancient lipids can function as “molecular fossils” or biomarkers that can inform us about the types of organisms and environments on early Earth. However, proper interpretation of these biomarkers requires a comprehensive understanding of the taxonomic distribution, biosynthesis, and physiological function of these lipids in modern organisms. In this study, we discover that a marine bacterium produces two arborinols, a class of lipids previously identified only in flowering plants. This discovery addresses a current incongruity in biomarker signatures and also provides insight into the evolution of the biosynthetic pathways of biomarker lipids.
Arginine substitution of a cysteine in transmembrane helix M8 converts Na
+
,K
+
-ATPase to an electroneutral pump similar to H
+
,K
+
-ATPase
Authors: Holm Rikke , Khandelwal Jaanki , Einholm Anja P. , Andersen Jens P. , Artigas Pablo , Vilsen Bente
Published: December 2016

Significance

This study explores the structural basis for the difference between the closely related Na
+
,K
+
-ATPase and H
+
,K
+
-ATPase with respect to ion transport stoichiometry, electrogenicity, and cation selectivity, which has long been an enigma. A cysteine in the membrane domain of Na
+
,K
+
-ATPase is substituted by arginine in H
+
,K
+
-ATPase and has been found to be replaced by phenylalanine in a patient with alternating hemiplegia of childhood. These substitutions affect the functioning of the Na
+
-specific site of Na
+
,K
+
-ATPase profoundly. The positively charged side chain of the arginine present in H
+
,K
+
-ATPase serves as an internal cation that replaces bound Na
+
, thus explaining how H
+
,K
+
-ATPase avoids binding and transporting Na
+
at this site, thereby performing electroneutral transport, despite the general structural and functional resemblance to the electrogenic Na
+
,K
+
-ATPase.
Suppression of 19S proteasome subunits marks emergence of an altered cell state in diverse cancers
Authors: Tsvetkov Peter , Sokol Ethan , Jin Dexter , Brune Zarina , Thiru Prathapan , Ghandi Mahmoud , Garraway Levi A. , Gupta Piyush B. , Santagata Sandro , Whitesell Luke , Lindquist Susan
Published: December 2016

Significance

In previous work, we used genome-wide screening to uncover a counterintuitive mechanism by which cells can acquire resistance to inhibitors of the proteasome’s catalytic core through experimentally induced imbalances in the composition of its regulatory particle. However, in many cases, mechanisms uncovered in vitro for acquired resistance often do not translate to the context of actual clinical cancers. Here, we show that this mechanism is actually deployed spontaneously and naturally in diverse human cancer lines and is associated not only with increased resistance to proteasome inhibitors both in vitro and in the clinic but also is symptomatic of a much more broadly altered state with a unique gene signature and drug targetable vulnerabilities.
Stable population coding for working memory coexists with heterogeneous neural dynamics in prefrontal cortex
Authors: Murray John D. , Bernacchia Alberto , Roy Nicholas A. , Constantinidis Christos , Romo Ranulfo , Wang Xiao-Jing
Published: December 2016

Significance

Working memory (WM) is a core cognitive function thought to rely on persistent activity patterns in populations of neurons in prefrontal cortex (PFC), yet the neural circuit mechanisms remain unknown. Single-neuron activity in PFC during WM is heterogeneous and strongly dynamic, raising questions about the stability of neural WM representations. Here, we analyzed WM activity across large populations of neurons in PFC. We found that despite strong temporal dynamics, there is a population-level representation of the remembered stimulus feature that is maintained stably in time during WM. Furthermore, these population-level analyses distinguish mechanisms proposed by theoretical models. These findings inform our fundamental understanding of circuit mechanisms underlying WM, which may guide development of treatments for WM impairment in brain disorders.
Ohr plays a central role in bacterial responses against fatty acid hydroperoxides and peroxynitrite
Authors: Alegria Thiago G. P. , Meireles Diogo A. , Cussiol José R. R. , Hugo Martín , Trujillo Madia , de Oliveira Marcos Antonio , Miyamoto Sayuri , Queiroz Raphael F. , Valadares Napoleão Fonseca , Garratt Richard C. , Radi Rafael , Di Mascio Paolo , Augusto Ohara , Netto Luis E. S.
Published: December 2016

Significance

Hydroperoxides play central roles in cell signaling. Hydroperoxides of arachidonic acid are mediators of inflammatory processes in mammals, whereas hydroperoxides of linoleic acid play equivalent roles in plants. Peroxynitrite is also involved in host–pathogen interactions, and hydroperoxide levels must therefore be strictly controlled by host-derived thiol-dependent peroxidases. Organic hydroperoxide resistance (Ohr) enzymes, which are present in many bacteria, display unique biochemical properties, reducing fatty acid hydroperoxides and peroxynitrite with extraordinary efficiency. Furthermore, Ohr (but not other thiol-dependent peroxidases) is involved in the
Pseudomonas aeruginosa
response to fatty acid hydroperoxides and to peroxynitrite, although the latter is more complex, probably depending on other enzymes. Therefore, Ohr plays central roles in the bacterial response to two hydroperoxides that are at the host–pathogen interface.
Influence of Zn coating on friction stir spot welded magnesium-aluminium joint
Authors: Xu R. Z. , Ni D. R. , Yang Q. , Liu C. Z. , Ma Z. Y.
Published: December 2016

For friction stir spot welded (FSSW) magnesium–aluminium joints, the formation of Mg–Al intermetallics in the hook region and cracking at the interface damaged seriously the strength of Mg–Al joints, resulting in lower joint load of only 0.8 ± 0.2 kN. When adding the hot-dipped Zn coating on the Al substrate surface prior to FSSW, a brazed layer, composed of Mg–Zn and Al–Zn diffusion zones at the edge of the shoulder, and a transition layer, composed of MgZn2, Zn-rich zone and residual Zn in the hook region, were formed in the FSSW Mg–Al joint, eliminating the cracking and Mg–Al intermetallics in the FSSW joint without the Zn coating. The load of the joint with the Zn coating increased to 3.7 ± 0.3 kN.
Eigenvalue bounds for matrix polynomials in generalized bases
Authors: Melman A.
Published: December 2016

We derive inclusion regions for the eigenvalues of matrix polynomials expressed in a general polynomial basis, which can lead to significantly better results than traditional bounds. We present several applications to engineering problems.
Majorization in C*-algebras
Authors: Ng Ping , Robert Leonel , Skoufranis Paul
Published: December 2016

We investigate the closed convex hull of unitary orbits of selfadjoint elements in arbitrary unital C*-algebras. Using a notion of majorization against unbounded traces, a characterization of these closed convex hulls is obtained. Furthermore, for C*-algebras satisfying Blackadar’s strict comparison of positive elements by traces or for collections of C*-algebras with a uniform bound on their nuclear dimension, an upper bound for the number of unitary conjugates in a convex combination required to approximate an element in the closed convex hull within a given error is shown to exist. This property, however, fails for certain “badly behaved” simple nuclear C*-algebras.
Bio-physical connectivity patterns of benthic marine species used in the designation of Scottish nature conservation marine protected areas
Authors: Gallego Alejandro , Gibb Fiona M. , Tullet David , Wright Peter J.
Published: December 2016

Connectivity is a key consideration in the development of networks of marine protected areas (MPAs). However, little is known about the early life history of many of the epi-benthic animals that these spatial measures try to conserve. Here, a pragmatic approach to consider connectivity in such organisms is adopted, as part of the Scottish nature conservation MPA designation process. The primary tool for the study was a basic bio-physical model, forced by a circulation climatology. In the general absence of comprehensive ecological information, the model accounted for the main biological characteristics of the benthic organisms under consideration of relevance to connectivity, namely, presence, spawning season and pelagic larval duration (PLD). The results showed that some degree of connectivity between MPAs is possible even for species with short PLD although those organisms are more likely to be vulnerable to local pressures, particularly in the case of less widely distributed species and those inhabiting less dispersive inshore locations. For MPAs further offshore and species with longer PLD, our simulations suggested large-scale advection patterns crossing large-scale environmental management boundaries. Although the study was an appropriate contribution to the MPA designation process, further refinements encompassing better basic ecological information, enhanced oceanographic resolution, more realistic representation of biological processes (e.g. spawning, larval behaviour) in the model, species presence within and outside MPAs and substrate suitability maps would provide future useful confidence boundaries around the general patterns derived from our study.
A High Prevalence Rate of a Positive Screen for Cognitive Impairment in Patients With Human Immunodeficiency Virus Attending an Irish Clinic
Authors: McNamara Patricia H. , Coen Robert , Redmond Janice , Doherty Colin P. , Bergin Colm
Published: December 2016

Background

Human immunodeficiency virus (HIV)-associated neurocognitive disorders occurs in 20%–50% of HIV-positive patients. We undertook this study to assess the prevalence of a positive screen for cognitive impairment in the clinic population at our institution and to demonstrate the feasibility of implementing a screening program in routine clinical encounters.

Methods

This was a cross-sectional study, and patients were recruited prospectively between December 2010 and February 2013. Inclusion criteria were as follows: patients were HIV positive, over the age of 18, capable of giving informed consent, and had sufficient ability to communicate in English. Patients were screened for cognitive impairment using the Brief Neurocognitive Screen.

Results

A total of 604 patients were recruited, and 51.5% had a positive screen for cognitive impairment. The majority of the study cohort were male (78.8%), mean age was 40.9 (standard deviation, 10.2) years, 70.9% were Irish, the most common mode of transmission was men who have sex with men (49.3%), 83% were on antiretroviral therapy, and 88.7% were virally suppressed. Logistic regression showed that the main factors predictive of a positive screen for cognitive impairment were the endorsement of cognitive symptoms (P = .024), being born in Africa (P < .000001), the use of benzodiazepines (P = .00341), being unemployed (P = .008), and consumption of more than 40 units of alcohol weekly (P = .035). There was a positive screen for depression in 9.1% and a positive screen for anxiety in 24.5%.

Conclusions

The study highlights the necessity for a structured, prospective, large-scale screening program for cognitive impairment across countries with limited resources and demonstrates the feasibility of easily implementing this with minimal training.
Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data
Authors: Gagnon Marie-Claude , Feau Nicolas , Dale Angela L. , Dhillon Braham , Hamelin Richard C. , Brasier Clive M. , Grünwald Niklaus J. , Brière Stephan C. , Bilodeau Guillaume J.
Published: December 2016

Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.
The food web of Potter Cove (Antarctica): complexity, structure and function
Authors: Marina Tomás I. , Salinas Vanesa , Cordone Georgina , Campana Gabriela , Moreira María Eugenia , Deregibus Dolores , Torre Luciana , Sahade Ricardo , Tatián Marcos , Oro Esteban Barrera , De Troch Marleen , Doyle Santiago , Quartino María Liliana , Saravia Leonardo A. , Momo Fernando R.
Published: December 2016

Knowledge of the food web structure and complexity are central to better understand ecosystem functioning. A food-web approach includes both species and energy flows among them, providing a natural framework for characterizing species’ ecological roles and the mechanisms through which biodiversity influences ecosystem dynamics. Here we present for the first time a high-resolution food web for a marine ecosystem at Potter Cove (northern Antarctic Peninsula). Eleven food web properties were analyzed in order to document network complexity, structure and topology. We found a low linkage density (3.4), connectance (0.04) and omnivory percentage (45), as well as a short path length (1.8) and a low clustering coefficient (0.08). Furthermore, relating the structure of the food web to its dynamics, an exponential degree distribution (in- and out-links) was found. This suggests that the Potter Cove food web may be vulnerable if the most connected species became locally extinct. For two of the three more connected functional groups, competition overlap graphs imply high trophic interaction between demersal fish and niche specialization according to feeding strategies in amphipods. On the other hand, the prey overlap graph shows also that multiple energy pathways of carbon flux exist across benthic and pelagic habitats in the Potter Cove ecosystem. Although alternative food sources might add robustness to the web, network properties (low linkage density, connectance and omnivory) suggest fragility and potential trophic cascade effects.
Rescuing Troves of Data to Tackle Emerging Mosquito-Borne Diseases
Authors: Rund Samuel S.C. , Martinez Micaela Elvira
Published: December 2016

According to the World Health Organization, every year more than a billion people are infected with vector-borne diseases worldwide. There are no vaccines for most vector-borne diseases. Vector control, therefore, is often the only way to prevent outbreaks. Despite the major impact of vectors on human health, knowledge gaps exist regarding their natural population dynamics. Even the most basic information—such as spatiotemporal abundance— is not available. Mosquitoes transmit malaria and the viruses causing Yellow Fever, West Nile, Dengue, Chikungunya, and Zika in the Americas. The Americas have a long history of mosquito control efforts, including the unsustained but successfulAedes aegyptieradication initiative. In the US, municipalities have independently created agencies for mosquito control and monitoring. We propose that the ensemble of US mosquito control agencies can, and should, be used to develop a national—and potentially international—system for Cross-Scale Vector Monitoring and Control (CSVMaC), in which local level monitoring and control efforts are cross-linked by unified real-time data streaming to build the data capital needed to gain a mechanistic understanding of vector population dynamics. Vectors, and the pathogens they transmit, know no jurisdictions. The vision of CSVMaC is, therefore, to provide data for (i) the general study of mosquito ecology and (ii) to inform vector control during epidemics/outbreaks that impact multiple jurisdictions (i.e., counties, states, etc.). We reveal >1000 mosquito control agencies in the US with enormous troves of data that are hidden among many data silos. For CSVMaC, we propose the creation of a nationally-coordinated open-access database to collate mosquito data. The database would provide scientific and public health communities with highly resolved spatiotemporal data on arboviral disease vectors, empowering new interventions and insights while leveraging pre-existing human efforts, operational infrastructure, and investments already funded by taxpayers.
AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammoxNitrospirain the environment
Authors: Pjevac Petra , Schauberger Clemens , Poghosyan Lianna , Herbold Craig W. , van Kessel Maartje A.H.J. , Daebeler Anne , Steinberger Michaela , Jetten Mike S. M. , Sebastian Lücker , Michael Wagner , Holger Daims
Published: December 2016

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers (‘comammox’), which oxidize ammonia to nitrate on their own, were identified in the bacterial genusNitrospira, previously known to contain only canonical nitrite oxidizers.Nitrospiraare widespread in nature, but for assessments of the distribution and functional importance of comammoxNitrospirain ecosystems cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizingNitrospiraare required. Here we developed new PCR primer sets that specifically target theamoAgenes coding for subunit A of the distinct ammonia monooxygenase of comammoxNitrospira. While existing primers capture only a fraction of the known comammoxamoAdiversity, the new primer sets cover as much as 95% of the comammoxamoAclade A and 92% of the clade B sequences in a reference database containing 326 comammoxamoAgenes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammoxNitrospirain all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammoxamoAwas achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammoxamoAgenes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammoxamoAgene copy numbers in environmental samples. Thus, the new comammoxamoA-targeted primers will enable more encompassing studies of nitrifying microorganisms in diverse ecosystems.
Natural Selection on MHC IIb in Parapatric Lake and Stream Stickleback: Balancing, Divergent, Both, or Neither?
Authors: E. Stutz William , Bolnick Daniel I.
Published: December 2016

Major histocompatibility (MHC) genes encode proteins that play a central role in vertebrates’ adaptive immunity to parasites. MHC loci are among the most polymorphic in vertebrates’ genomes, inspiring many studies to identify evolutionary processes driving MHC polymorphism within populations, and divergence between populations. Leading hypotheses include balancing selection favoring rare alleles within populations, and spatially divergent selection. These hypotheses do not always produce diagnosably distinct predictions, causing many studies of MHC to yield inconsistent or ambiguous results. We suggest a novel strategy to distinguish balancing versus divergent selection on MHC, taking advantage of natural admixture between parapatric populations. With divergent selection, immigrant alleles will be more infected and less fit because they are susceptible to novel parasites in their new habitat. With balancing selection, locally-rare immigrant alleles will be more fit (less infected). We tested these contrasting predictions using threespine stickleback from three replicate pairs of parapatric lake and stream habitats. We found numerous positive and negative associations between particular MHC IIβ alleles and particular parasite taxa. A few allele-parasite comparisons supported balancing selection, others supported divergent selection between habitats. But, there was no overall tendency for fish with immigrant MHC alleles to be more or less heavily infected. Instead, locally rare MHC alleles (not necessarily immigrants) were associated with heavier infections. Our results illustrate the complex relationship between MHC IIβ allelic variation and spatially varying multi-species parasite communities: different hypotheses may be concurrently true for different allele-parasite combinations.
Fenton-type chemistry by a copper enzyme: molecular mechanism of polysaccharide oxidative cleavage
Authors: Bissaro Bastien , Rohr Asmund K , Skaugen Morten , Forsberg Zarah , Horn Svein J , Vaaje-Kolstad Gustav , Eijsink Vincent
Published: December 2016

The discovery of Lytic Polysaccharide Monooxygenases (LPMOs) has been instrumental for the development of economically sustainable lignocellulose biorefineries. Despite the obvious importance of these exceptionally powerful redox enzymes, their mode of action remains enigmatic and their activity and stability under process conditions are hard to control. By using enzyme assays, mass spectrometry and experiments with labeled oxygen atoms, we show that H2O2, and not O2 as previously thought, is the co-substrate of LPMOs. By controlling H2O2 supply, stable reaction kinetics and high enzymatic rates are achieved, the LPMOs work under anaerobic conditions, and the need for adding stoichiometric amounts of reductants is alleviated. These results offer completely new perspectives regarding the mode of action of these unique mono-copper enzymes, the enzymatic conversion of biomass in Nature, and industrial biorefining.
tensorBF: an R package for Bayesian tensor factorization
Authors: Khan Suleiman A. , Ammad-ud-din Muhammad
Published: December 2016

With recent advancements in measurement technologies, many multi-way and tensor datasets have started to emerge. Exploiting the natural tensor structure in the data has been shown to be advantageous for both explorative and predictive studies in several application areas of bioinformatics and computational biology. Therefore, there has subsequently arisen a need for robust and flexible tools for effectively analyzing tensor data sets. We present the R package tensorBF, which is the first R package providing Bayesian factorization of a tensor. Our package implements a generative model that automatically identifies the number of factors needed to explain the tensor, overcoming a key limitation of traditional tensor factorizations. We also recommend best practices when using tensor factorizations for both, explorative and predictive analysis with an example application on drug response dataset. The package also implements tools related to the normalization of data, informative noise priors and visualization. Availability: The package is available athttps://cran.r-project.org/package=tensorBF.
Prestack amplitude versus angle inversion for Young's modulus and Poisson's ratio based on the exact Zoeppritz equations
Authors: Zhou Lin , Li Jingye , Chen Xiaohong , Liu Xingye , Chen Li
Published: December 2016

Elastic parameters such as Young's modulus, Poisson's ratio, and density are very important characteristic parameters that are required to properly characterise shale gas reservoir rock brittleness, evaluate gas characteristics of reservoirs, and directly interpret lithology and oil‐bearing properties. Therefore, it is significant to obtain accurate information of these elastic parameters. Conventionally, they are indirectly calculated by the rock physics method or estimated by approximate formula inversion. The cumulative errors caused by the indirect calculation and low calculation accuracy of the approximate Zoeppritz equations make accurate estimation of Young's modulus, Poisson's ratio, and density difficult in the conventional method. In this paper, based on the assumption of isotropy, we perform several substitutions to convert the Zoeppritz equations from the classical form to a new form containing the chosen elastic constants of Young's modulus, Poisson's ratio, and density. The inversion objective function is then constructed by utilising Bayesian theory. Meanwhile, the Cauchy distribution is introduced as a priori information. We then combine the idea of generalised linear inversion with an iterative reweighed least squares algorithm in order to solve the problem. Finally, we obtain the iterative updating formula of the three elastic parameters and achieve the direct inversion of these elastic parameters based on the exact Zoeppritz equations. Both synthetic and field data examples show that the new method is not only able to obtain the two elastic parameters of Young's modulus and Poisson's ratio stably and reasonably from prestack seismic data but also able to provide an accurate estimation of density information, which demonstrates the feasibility and effectiveness of the proposed method. The proposed method offers an efficient seismic method to identify a “sweet spot” within a shale gas reservoir.
Bottom‐up and trait‐mediated effects of resource quality on amphibian parasitism
Authors: Stephens Jeffrey P. , Altman Karie A. , Berven Keith A. , Tiegs Scott D. , Raffel Thomas R.
Published: December 2016

Leaf litter subsidies are important resources for aquatic consumers like tadpoles and snails, causing bottom‐up effects on wetland ecosystems. Recent studies have shown that variation in litter nutritional quality can be as important as litter quantity in driving these bottom‐up effects. Resource subsidies likely also have indirect and trait‐mediated effects on predation and parasitism, but these potential effects remain largely unexplored.

We generated predictions for differential effects of litter nutrition and secondary polyphenolic compounds on tadpole (Lithobates sylvatica) exposure and susceptibility toRibeiroia ondatrae, based on ecological stoichiometry and community‐ecology theory. We predicted direct and indirect effects on key traits of the tadpole host (rates of growth, development and survival), the trematode parasite (production of the cercaria infective stages) and the parasite's snail intermediate host (growth and reproduction).

To test these predictions, we conducted a large‐scale mesocosm experiment using a natural gradient in the concentrations of nutrients (nitrogen) and toxic secondary compounds (polyphenolics) of nine leaf litter species. To differentiate between effects on exposure vs. susceptibility to infection, we included multiple infection experiments including one with constant per capita exposure.

We found that increased litter nitrogen increased tadpole survival, and also increased cercaria production by the snail intermediate hosts, causing opposing effects on tadpole per capita exposure to trematode infection. Increased litter polyphenolics slowed tadpole development, leading to increased infection by increasing both their susceptibility to infection and the length of time they were exposed to parasites.

Based on these results, recent shifts in forest composition towards more nitrogen‐poor litter species should decrease trematode infection in tadpoles via density‐ and trait‐mediated effects on the snail intermediate hosts. However, these shifts also involve increased abundance of litter species with high polyphenolic levels, which should increase trematode infection via trait‐mediated effects on tadpoles. Future studies will be needed to determine the relative strength of these opposing effects in natural wetland communities. [Correction added after online publication on 5 January 2017: wording changed to ‘which should increase trematode infection via trait‐mediated effects on tadpoles’.]
Moving forward: insights and applications of moving‐habitat models for climate change ecology
Authors: Harsch Melanie A. , Phillips Austin , Zhou Ying , Leung Margaret‐Rose , Rinnan D. Scott , Kot Mark
Published: December 2016

Predicting and managing species’ responses to climate change is one of the most significant challenges of our time. Tools are needed to address problems associated with novel climatic conditions, biotic interactions and greater climate velocities.

We present a spatially explicit moving‐habitat model (MHM) and demonstrate its versatility in tackling critical questions in climate change research, including dispersal in multiple spatial dimensions, population stage structure, interspecific interactions, asymmetric range shifts, Allee effects and the presence of infectious diseases. The model utilizes integrodifference equations to track changes in population density over time in a habitat that is moving. The model is quite flexible and can accommodate variation in demography, dispersal patterns, biotic interaction and stochasticity in the velocity of climate change.

The methods provide a general mechanistic understanding of the underlying ecological processes that drive a system. Field data can be readily incorporated into the model to give insight into specific populations of interest and inform management decisions.

Synthesis. Moving‐habitat models unite ecological theory, data‐centred modelling and conservation decision support under a single framework. Their ability to generate testable hypotheses, incorporate data and inform best management practices proves that these models provide a valuable framework for climate change biologists.
Regulation of microvascular flow and metabolism: An overview
Authors: Keske Michelle A , Dwyer Renee M , Russell Ryan D , Blackwood Sarah J , Brown Aascha A , Hu Donghua , Premilovac Dino , Richards Stephen M , Rattigan Stephen
Published: December 2016

Skeletal muscle is an important site for insulin to regulate blood glucose levels. It is estimated that skeletal muscle is responsible for ~80% of insulin‐mediated glucose disposal in the post‐prandial period. The classical action of insulin to increase muscle glucose uptake involves insulin binding to insulin receptors on myocytes to stimulate glucose transporter 4 (GLUT 4) translocation to the cell surface membrane, enhancing glucose uptake. However, an additional role of insulin that is often under‐appreciated is its action to increase muscle perfusion thereby improving insulin and glucose delivery to myocytes. Either of these responses (myocyte and/or vascular) may be impaired in insulin resistance, and both impairments are apparent in type 2 diabetes, resulting in diminished glucose disposal by muscle. The aim of this review is to report on the growing body of literature suggesting that insulin‐mediated control of skeletal muscle perfusion is an important regulator of muscle glucose uptake and that impairment of microvascular insulin action has important physiological consequences early in the pathogenesis of insulin resistance. This work was discussed at the 2015 Australian Physiological Society Symposium “Physiological mechanisms controlling microvascular flow and muscle metabolism”.
Indole‐associated predator–prey interactions between the nematode Caenorhabditis elegans and bacteria
Authors: Lee Jin‐Hyung , Kim Yong‐Guy , Kim Minsu , Kim Eonmi , Choi Hyukjae , Kim Younghoon , Lee Jintae
Published: December 2016

Indole is an intercellular and interkingdom signalling molecule found in diverse ecological niches. Caenorhabditis elegans is a bacterivorous nematode that lives in soil and compost environments and a useful model host for studies of host–microbe interactions. Although various bacteria and some plants produce large quantities of extracellular indole, little is known about the effects of indole, its derivatives, or of indole‐producing bacteria on the behaviours of C. elegans or other animals. Here, they show that C. elegans senses and moves toward indole and several indole‐producing bacteria, but avoids non‐indole producing pathogenic bacteria. Furthermore, it was found indole‐producing and non‐indole‐producing bacteria exert divergent effects on the egg‐laying behaviour of C. elegans, and that various indole derivatives also modulate chemotaxis, egg‐laying behaviour and the survival of C. elegans. In contrast, indole at high concentration can kill C. elegans, which in turn, has the ability to detoxify indole by oxidation and glucosylation. Transcriptional analysis showed indole markedly up‐regulated the gene expressions of cytochrome P450s, UDP‐glucuronosyltransferases and glutathione S‐transferase, which well explained the modification of indole by C. elegans while indole down‐regulated the expressions of collagen and F‐box genes. Their findings suggest that indole and its derivatives are important signalling molecules during bacteria–nematode interactions.
Exploration of cultivable fungal communities in deep coal‐bearing sediments from ∼1.3 to 2.5 km below the ocean floor
Authors: Liu Chang‐Hong , Huang Xin , Xie Tian‐Ning , Duan Ning , Xue Ya‐Rong , Zhao Tan‐Xi , Lever Mark A. , Hinrichs Kai‐Uwe , Inagaki Fumio
Published: December 2016

Although subseafloor sediments are known to harbour a vast number of microbial cells, the distribution, diversity, and origins of fungal populations remain largely unexplored. In this study, we cultivated fungi from 34 of 47 deep coal‐associated sediment samples collected at depths ranging from 1289 to 2457 m below the seafloor (mbsf) off the Shimokita Peninsula, Japan (1118 m water depth). We obtained a total of 69 fungal isolates under strict contamination controls, representing 61 Ascomycota (14 genera, 23 species) and 8 Basidiomycota (4 genera, 4 species). Penicillium and Aspergillus relatives were the most dominant genera within the Ascomycetes, followed by the members of genera Cladosporium, Hamigera, Chaetomium, Eutypella, Acremonium, Aureobasidium, Candida, Eurotium, Exophiala, Nigrospora, Bionectria and Pseudocercosporella. Four Basidiomycota species were identified as genera Schizophyllum, Irpex, Bjerkandera and Termitomyces. Among these isolates, Cladosporium sphaerospermum and Aspergillus sydowii relatives were isolated from a thin lignite coal‐sandstone formation at 2457 mbsf. Our results indicate that these cultivable fungal populations are indigenous, originating from past terrigenous environments, which have persisted, possibly as spores, through ∼20 million years of depositional history.
Laribacter hongkongensis anaerobic adaptation mediated by arginine metabolism is controlled by the cooperation of FNR and ArgR
Authors: Xiong Lifeng , Yang Ying , Ye Yuan‐Nong , Teng Jade L. L. , Chan Elaine , Watt Rory M. , Guo Feng‐Biao , Lau Susanna K. P. , Woo Patrick C. Y.
Published: December 2016

Laribacter hongkongensis is a fish‐borne pathogen associated with invasive infections and gastroenteritis. Its adaptive mechanisms to oxygen‐limiting conditions in various environmental niches remain unclear. In this study, we compared the transcriptional profiles of L. hongkongensis under aerobic and anaerobic conditions using RNA‐sequencing. Expression of genes involved in arginine metabolism significantly increased under anoxic conditions. Arginine was exploited as the sole energy source in L. hongkongensis for anaerobic respiration via the arginine catabolism pathway: specifically via the arginine deiminase (ADI) pathway. A transcriptional regulator FNR was identified to coordinate anaerobic metabolism by tightly regulating the expression of arginine metabolism genes. FNR executed its regulatory function by binding to FNR boxes in arc operons promoters. Survival of isogenic fnr mutant in macrophages decreased significantly when compared with wild‐type; and expression level of fnr increased 8 h post‐infection. Remarkably, FNR directly interacted with ArgR, another regulator that influences the biological fitness and intracellular survival of L. hongkongensis by regulating arginine metabolism genes. Our results demonstrated that FNR and ArgR work in coordination to respond to oxygen changes in both extracellular and intracellular environments, by finely regulating the ADI pathway and arginine anabolism pathways, thereby optimizing bacterial fitness in various environmental niches.