bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of mosquito gene drive on malaria elimination in a computational model with explicit spatial and temporal dynamics
Authors: Eckhoff Philip A. , Wenger Edward A. , Godfray H. Charles J. , Burt Austin
Published: December 2016

Significance

Gene drive mosquitoes have tremendous potential to help eliminate malaria, and multiple gene drive approaches have recently shown promise in laboratory settings. These approaches include population suppression through fertility disruption, driving-Y chromosomes, and population replacement with genes that limit malaria transmission. Mathematical modeling is used to evaluate these approaches by simulating realistic field settings with seasonality to determine constraints on construct parameters and release strategies. Parameter variation from simulation baselines captures much of sub-Saharan African epidemiology and shows high potential for gene drive constructs to provide transformational tools to facilitate elimination of malaria, even in the most challenging settings. This analysis provides insights into performance characteristics necessary for each approach to succeed that can inform their further development.
The global decline of cheetah
Acinonyx jubatus
and what it means for conservation
Authors: Durant Sarah M. , Mitchell Nicholas , Groom Rosemary , Pettorelli Nathalie , Ipavec Audrey , Jacobson Andrew P. , Woodroffe Rosie , Böhm Monika , Hunter Luke T. B. , Becker Matthew S. , Broekhuis Femke , Bashir Sultana , Andresen Leah , Aschenborn Ortwin , Beddiaf Mohammed , Belbachir Farid , Belbachir-Bazi Amel , Berbash Ali , Brandao de Matos Machado Iracelma , Breitenmoser Christine , Chege Monica , Cilliers Deon , Davies-Mostert Harriet , Dickman Amy J. , Ezekiel Fabiano , Farhadinia Mohammad S. , Funston Paul , Henschel Philipp , Horgan Jane , de Iongh Hans H. , Jowkar Houman , Klein Rebecca , Lindsey Peter Andrew , Marker Laurie , Marnewick Kelly , Melzheimer Joerg , Merkle Johnathan , M'soka Jassiel , Msuha Maurus , O'Neill Helen , Parker Megan , Purchase Gianetta , Sahailou Samaila , Saidu Yohanna , Samna Abdoulkarim , Schmidt-Küntzel Anne , Selebatso Eda , Sogbohossou Etotépé A. , Soultan Alaaeldin , Stone Emma , van der Meer Esther , van Vuuren Rudie , Wykstra Mary , Young-Overton Kim
Published: December 2016

Significance

Here, we compile and present the most comprehensive data available on cheetah distribution and status. Our analysis shows dramatic declines of cheetah across its distributional range. Most cheetah occur outside protected areas, where they are exposed to multiple threats, but there is little information on population status. Simulation modeling shows that, where cheetah population growth rates are suppressed outside protected areas, extinction risk increases markedly. This result can be generalized to other “protection-reliant” species, and a decision tree is provided to improve their extinction risk estimation. Ultimately, the persistence of protection-reliant species depends on their survival outside and inside protected areas and requires a holistic approach to conservation that engages rather than alienates local communities.
Programming function into mechanical forms by directed assembly of silk bulk materials
Authors: Marelli Benedetto , Patel Nereus , Duggan Thomas , Perotto Giovanni , Shirman Elijah , Li Chunmei , Kaplan David L. , Omenetto Fiorenzo G.
Published: December 2016

Significance

Engineering multiple functions in a single material format is a key design parameter to fabricate devices that can perform at the confluence between biology and technology. This can be achieved by designing materials with hierarchical structures across several scales or by embedding active molecules at the point of material formation. These approaches have been successfully pursued to engineer 2D materials formats. However, current technologies have limited the formation of 3D constructs with orthogonal functions. In this study, we demonstrate an entirely water-based sol–gel–solid process to generate 3D mechanical forms that embed biological (and other) functions. This approach is a step toward the development of multifunctional devices that may liaise between the biotic and abiotic worlds.
In operando
evidence of deoxygenation in ionic liquid gating of YBa
2
Cu
3
O
7-X
Authors: Perez-Muñoz Ana M. , Schio Pedro , Poloni Roberta , Fernandez-Martinez Alejandro , Rivera-Calzada Alberto , Cezar Julio C. , Salas-Colera Eduardo , Castro German R. , Kinney Joseph , Leon Carlos , Santamaria Jacobo , Garcia-Barriocanal Javier , Goldman Allen M.
Published: December 2016

Significance

In this work, we investigate the origin of the charge induced in a high-temperature superconducting cuprate film, incorporated in an electric double-layer transistor. Using X-ray spectroscopic measurements made while operating the transistor, together with simulations based on density functional theory, we find that the accumulated charge in the cuprate is due to the depletion of oxygen from specific sites in its unit cell. These results constitute direct evidence of the microscopic mechanism of charge modification. The systematic control of the oxygen content in complex oxides such as the cuprates allows for the study of complex phase diagrams and opens up a route for the design of new complex oxide compounds and devices with improved functionalities.
Abscisic acid signaling is controlled by a
BRANCHED1/HD-ZIP I
cascade in
Arabidopsis
axillary buds
Authors: González-Grandío Eduardo , Pajoro Alice , Franco-Zorrilla José M. , Tarancón Carlos , Immink Richard G. H. , Cubas Pilar
Published: December 2016

Significance

Shoot-branching patterns affect key aspects of plant life and are important targets for crop breeding. However, we are still ignorant of the genetic mechanisms controlling locally an important decision during branch development: whether the axillary bud grows out to give a lateral shoot or remains dormant. Here we show that the TEOSINTE BRANCHED1, CYCLOIDEA, PCF (TCP) transcriptional regulator BRANCHED1 (BRC1), which acts inside axillary buds, binds and activates three genes encoding Homeodomain leucine zipper (HD-ZIP) transcription factors. These factors, together with BRC1, trigger a cascade leading to local abscisic acid (ABA) accumulation and response, essential for bud dormancy under light-limiting conditions. This finding demonstrates a direct relationship between
BRC1
and
ABA
signaling and places ABA downstream of BRC1 in the control of axillary bud dormancy.
Spatiotemporal dynamics of similarity-based neural representations of facial identity
Authors: Vida Mark D. , Nestor Adrian , Plaut David C. , Behrmann Marlene
Published: December 2016

Significance

Humans can rapidly discriminate among many highly similar facial identities across identity-preserving image transformations (e.g., changes in facial expression), an ability that requires the system to rapidly transform image-based inputs into a more abstract, identity-based representation. We used magnetoencephalography to provide a temporally precise description of this transformation within human face-selective cortical regions. We observed a transition from an image-based representation toward an identity-based representation after ∼200 ms, a result suggesting that, rather than computing a single representation, a given face-selective region may represent multiple distinct types of information about face identity at different times. Our results advance our understanding of the microgenesis of fine-grained, high-level neural representations of object identity, a process critical to human visual expertise.
Wireless physical layer security
Authors: Poor H. Vincent , Schaefer Rafael F.
Published: December 2016

Significance

Security is a very important issue in the design and use of wireless networks. Traditional methods of providing security in such networks are impractical for some emerging types of wireless networks due to the light computational abilities of some wireless devices [such as radio-frequency identification (RFID) tags, certain sensors, etc.] or to the very large scale or loose organizational structure of some networks. Physical layer security has the potential to address these concerns by taking advantage of the fundamental ability of the physics of radio propagation to provide certain types of security. This paper provides a review of recent research in this field.
Aberrantly expressed LGR4 empowers Wnt signaling in multiple myeloma by hijacking osteoblast-derived R-spondins
Authors: van Andel Harmen , Ren Zemin , Koopmans Iris , Joosten Sander P. J. , Kocemba Kinga A. , de Lau Wim , Kersten Marie José , de Bruin Alexander M. , Guikema Jeroen E. J. , Clevers Hans , Spaargaren Marcel , Pals Steven T.
Published: December 2016

Significance

Multiple myeloma (MM) cells are highly dependent on signals provided by the bone marrow (BM) niche for growth and survival. Most MMs display hallmarks of active Wnt signaling, but lack activating Wnt-pathway mutations, suggesting activation by autocrine Wnt ligands and/or paracrine Wnts emanating from the BM niche. In this study we uncover a pivotal role for the leucine-rich repeat-containing G protein-coupled receptor 4 (LGR4)/R-spondin axis in facilitating activation of Wnt signaling in MM. LGR4 is expressed by most MMs, but not by healthy plasma cells, and is regulated by STAT3 signaling. LGR4 expression allows MMs to respond to (pre)osteoblast–derived R-spondins, resulting in stabilization of Wnt receptors and greatly enhanced sensitivity to auto- and paracrine Wnt ligands. These results advocate targeting of proximal Wnt signaling in MM.
Single-pixel interior filling function approach for detecting and correcting errors in particle tracking
Authors: Burov Stanislav , Figliozzi Patrick , Lin Binhua , Rice Stuart A. , Scherer Norbert F. , Dinner Aaron R.
Published: December 2016

Significance

Researchers in many areas of science and engineering gather imaging data consisting of a set of pixel intensities. Quantitative analyses of such data often rely on estimating the positions of objects (e.g., single-particle tracking), and many of the algorithms used promise subpixel precision and accuracy. Here, we introduce a method that can reveal biases in such tracking algorithms and correct the associated errors. An advantage of the method is that it uses only the output of the tracking algorithm without needing knowledge of how it works. We illustrate how the method can solve common problems in single-particle tracking. Under some circumstances the method can even outperform the precision limit to which most algorithms are compared.
Hot-rolled and continuously cooled bainitic steel with good strength–elongation combination
Authors: Das S. , Sinha S. , Lodh A. , Chintha A. R. , Krugla M. , Haldar A.
Published: December 2016

The current work demonstrates the microstructural evolution and mechanical property evaluation of a newly designed steel composition after hot rolling in laboratory-scale rolling mill, followed by continuous cooling. The steel thus developed has typically about 80% carbide-free bainite; about 20% retained austenite and can deliver ∼1400 MPa ultimate tensile strength along with more than 20% total elongation. The presence of ultra-fine bainite plates (∼100–130 nm thick) with high dislocation density was thought to be responsible for ultra-high strength. Excellent ductility at such strength level could be due to the presence of sufficient amount of retained austenite (∼20%) thermally stable at room temperature but starts transforming to martensite during deformation exhibiting transformation-induced plasticity effect.
CD70/CD27 signaling promotes blast stemness and is a viable therapeutic target in acute myeloid leukemia
Authors: Riether Carsten , Schürch Christian M. , Bührer Elias D. , Hinterbrandner Magdalena , Huguenin Anne-Laure , Hoepner Sabine , Zlobec Inti , Pabst Thomas , Radpour Ramin , Ochsenbein Adrian F.
Published: December 2016

Aberrant proliferation, symmetric self-renewal, increased survival, and defective differentiation of malignant blasts are key oncogenic drivers in acute myeloid leukemia (AML). Stem cell gene signatures predict poor prognosis in AML patients; however, with few exceptions, these deregulated molecular pathways cannot be targeted therapeutically. In this study, we demonstrate that the TNF superfamily ligand–receptor pair CD70/CD27 is expressed on AML blasts and AML stem/progenitor cells. CD70/CD27 signaling in AML cells activates stem cell gene expression programs, including the Wnt pathway, and promotes symmetric cell divisions and proliferation. Soluble CD27, reflecting the extent of CD70/CD27 interactions in vivo, was significantly elevated in the sera of newly diagnosed AML patients and is a strong independent negative prognostic biomarker for overall survival. Blocking the CD70/CD27 interaction by mAb induced asymmetric cell divisions and differentiation in AML blasts and AML stem/progenitor cells, inhibited cell growth and colony formation, and significantly prolonged survival in murine AML xenografts. Importantly, hematopoietic stem/progenitor cells from healthy BM donors express neither CD70 nor CD27 and were unaffected by blocking mAb treatment. Therefore, targeting CD70/CD27 signaling represents a promising therapeutic strategy for AML.
Peptidylarginine deiminase 4 promotes age-related organ fibrosis
Authors: Martinod Kimberly , Witsch Thilo , Erpenbeck Luise , Savchenko Alexander , Hayashi Hideki , Cherpokova Deya , Gallant Maureen , Mauler Maximilian , Cifuni Stephen M. , Wagner Denisa D.
Published: December 2016

Aging promotes inflammation, a process contributing to fibrosis and decline in organ function. The release of neutrophil extracellular traps (NETs [NETosis]), orchestrated by peptidylarginine deiminase 4 (PAD4), damages organs in acute inflammatory models. We determined that NETosis is more prevalent in aged mice and investigated the role of PAD4/NETs in age-related organ fibrosis. Reduction in fibrosis was seen in the hearts and lungs of aged PAD4−/− mice compared with wild-type (WT) mice. An increase in left ventricular interstitial collagen deposition and a decline in systolic and diastolic function were present only in WT mice, and not in PAD4−/− mice. In an experimental model of cardiac fibrosis, cardiac pressure overload induced NETosis and significant platelet recruitment in WT but not PAD4−/− myocardium. DNase 1 was given to assess the effects of extracellular chromatin. PAD4 deficiency or DNase 1 similarly protected hearts from fibrosis. We propose a role for NETs in cardiac fibrosis and conclude that PAD4 regulates age-related organ fibrosis and dysfunction.
TRIM65-catalized ubiquitination is essential for MDA5-mediated antiviral innate immunity
Authors: Lang Xueting , Tang Tiantian , Jin Tengchuan , Ding Chen , Zhou Rongbin , Jiang Wei
Published: December 2016

MDA5 plays a critical role in antiviral innate immunity by functioning as a cytoplasmic double-stranded RNA sensor that can activate type I interferon signaling pathways, but the mechanism for the activation of MDA5 is poorly understood. Here, we show that TRIM65 specifically interacts with MDA5 and promotes K63-linked ubiquitination of MDA5 at lysine 743, which is critical for MDA5 oligomerization and activation. Trim65 deficiency abolishes MDA5 agonist or encephalomyocarditis virus (EMCV)–induced interferon regulatory factor 3 (IRF3) activation and type I interferon production but has no effect on retinoic acid–inducible I (RIG-I), Toll-like receptor 3 (TLR3), or cyclic GMP-AMP synthase signaling pathways. Importantly, Trim65−/− mice are more susceptible to EMCV infection than controls and cannot produce type I interferon in vivo. Collectively, our results identify TRIM65 as an essential component for the MDA5 signaling pathway and provide physiological evidence showing that ubiquitination is important for MDA5 oligomerization and activation.
Lipin-2 regulates NLRP3 inflammasome by affecting P2X7 receptor activation
Authors: Lordén Gema , Sanjuán-García Itziar , de Pablo Nagore , Meana Clara , Alvarez-Miguel Inés , Pérez-García M. Teresa , Pelegrín Pablo , Balsinde Jesús , Balboa María A.
Published: December 2016

Mutations in human LPIN2 produce a disease known as Majeed syndrome, the clinical manifestations of which are ameliorated by strategies that block IL-1β or its receptor. However the role of lipin-2 during IL-1β production remains elusive. We show here that lipin-2 controls excessive IL-1β formation in primary human and mouse macrophages by several mechanisms, including activation of the inflammasome NLRP3. Lipin-2 regulates MAPK activation, which mediates synthesis of pro–IL-1β during inflammasome priming. Lipin-2 also inhibits the activation and sensitization of the purinergic receptor P2X7 and K+ efflux, apoptosis-associated speck-like protein with a CARD domain oligomerization, and caspase-1 processing, key events during inflammasome activation. Reduced levels of lipin-2 in macrophages lead to a decrease in cellular cholesterol levels. In fact, restoration of cholesterol concentrations in cells lacking lipin-2 decreases ion currents through the P2X7 receptor, and downstream events that drive IL-1β production. Furthermore, lipin-2–deficient mice exhibit increased sensitivity to high lipopolysaccharide doses. Collectively, our results unveil lipin-2 as a critical player in the negative regulation of NLRP3 inflammasome.
Metric mean dimension for algebraic actions of Sofic groups
Authors: Hayes Ben
Published: December 2016

We prove that if

Γ
\Gamma

is a sofic group and

A
A

is a finitely generated

Z

(
Γ
)

\mathbb {Z}(\Gamma )

-module, then the metric mean dimension of

Γ
↷

A
^

,

\Gamma \curvearrowright \widehat {A},

in the sense of Hanfeng Li, is equal to the von Neumann-Lück rank of

A
.

A.

This partially extends the results of Hanfeng Li and Bingbing Liang from the case of amenable groups to the case of sofic groups. Additionally we show that the mean dimension of

Γ
↷

A
^

\Gamma \curvearrowright \widehat {A}

is the von Neumann-Lück rank of

A
A

if

A
A

is finitely presented and

Γ
\Gamma

is residually finite. It turns out that our approach naturally leads to a notion of

p
p

-metric mean dimension, which is in between mean dimension and the usual metric mean dimension. This can be seen as an obstruction to the equality of mean dimension and metric mean dimension. While we cannot decide if mean dimension is the same as metric mean dimension for algebraic actions, we show in the metric case that for all

p
p

the

p
p

-metric mean dimension coincides with the von Neumann-Lück rank of the dual module.
A Case Report of Pediatric Brucellosis in an Algerian Immigrant
Authors: Kitt Eimear , Brannock Kristina R. , VonHolz Lauren A. , Planet Paul J. , Graf Erin , Pillai Vinodh
Published: December 2016

An 8-year old girl presented to our facility with a 10-day history of fever, fatigue, abdominal pain and refusal to walk. She recently travelled from her native Algeria where she first developed symptoms. On evaluation, she was ill-appearing, febrile and tachycardic with hepatosplenomegaly and lymphadenopathy noted on examination. A strong musty odor was also noted from the child. Laboratory evaluation revealed pancytopenia, hyponatremia, and an elevated AST, ALT, and LDH. Malaria testing was negative, as was a PPD. On further questioning, the family reported multiple sick contacts in Algeria with similar symptoms. After discussion with Oncology and Infectious Diseases, she underwent a bone marrow biopsy that was significant for multiple non-caseating ring granulomas. She was started on combination therapy of doxycycline and for presumed brucellosis infection with improvement in her symptoms and resolution of fever. Bone marrow culture returned several days later positive for Brucella melitensis.
Cost Effectiveness and Cost Containment in the Era of Interferon-Free Therapies to Treat Hepatitis C Virus Genotype 1
Authors: Linas Benjamin P. , Morgan Jake R. , Pho Mai T. , Leff Jared A. , Schackman Bruce R. , Horsburgh C. Robert , Assoumou Sabrina A. , Salomon Joshua A. , Weinstein Milton C. , Freedberg Kenneth A. , Kim Arthur Y.
Published: December 2016

Background

Interferon-free regimens to treat hepatitis C virus (HCV) genotype 1 are effective but costly. At this time, payers in the United States use strategies to control costs including (1) limiting treatment to those with advanced disease and (2) negotiating price discounts in exchange for exclusivity.

Methods

We used Monte Carlo simulation to investigate budgetary impact and cost effectiveness of these treatment policies and to identify strategies that balance access with cost control. Outcomes included nondiscounted 5-year payer cost per 10000 HCV-infected patients and incremental cost-effectiveness ratios.

Results

We found that the budgetary impact of HCV treatment is high, with 5-year undiscounted costs of $1.0 billion to 2.3 billion per 10000 HCV-infected patients depending on regimen choices. Among noncirrhotic patients, using the least costly interferon-free regimen leads to the lowest payer costs with negligible difference in clinical outcomes, even when the lower cost regimen is less convenient and/or effective. Among cirrhotic patients, more effective but costly regimens remain cost effective. Controlling costs by restricting treatment to those with fibrosis stage 2 or greater disease was cost ineffective for any patient type compared with treating all patients.

Conclusions

Treatment strategies using interferon-free therapies to treat all HCV-infected persons are cost effective, but short-term cost is high. Among noncirrhotic patients, using the least costly interferon-free regimen, even if it is not single tablet or once daily, is the cost-control strategy that results in best outcomes. Restricting treatment to patients with more advanced disease often results in worse outcomes than treating all patients, and it is not preferred.
Relative Abundance of Potato Psyllid Haplotypes in Southern Idaho Potato Fields During 2012 to 2015, and Incidence of ‘Candidatus Liberibacter solanacearum’ Causing Zebra Chip Disease
Authors: Dahan Jennifer , Wenninger Erik J. , Thompson Brandon , Eid Sahar , Olsen Nora , Karasev Alexander V.
Published: December 2016

Zebra chip (ZC) disease, a serious threat to the potato industry, is caused by the bacterium ‘Candidatus Liberibacter solanacearum’ (Lso). Five haplotypes (hapA to hapE) of this pathogen have been described so far in different crops, with only hapA and hapB being associated with ZC in potato. Both haplotypes are vectored and transmitted to a variety of solanaceaeous plants by the tomato/potato psyllid, Bactericera cockerelli (Šulc). Psyllids are native to North America, and four haplotypes have been identified and named based on their predominant geographic association: Northwestern, Central, Western, and Southwestern. Although all psyllid haplotypes have been found in southern Idaho potato fields, data on relative haplotype abundances and dynamic changes in the fields over time have not previously been reported. Here, psyllid samples collected in Idaho potato fields from 2012 to 2015 were used to clarify spatial and temporal patterns in distribution and abundance of psyllid and Lso haplotypes. A shift from hapA toward hapB population of Lso was revealed during these four seasons, indicating possible evolution of Lso in Idaho fields. Although we confirmed that Western psyllids were the most abundant by far during the four seasons of observation, we also observed changes in abundance of other haplotypes, including increased diversity of psyllid haplotypes during 2015. Seasonal changes observed for the Northwestern and Central haplotypes could potentially be linked to psyllid migration and/or habitat changes. South-central Idaho exhibited more diversity in psyllid haplotypes than southwestern Idaho.
A Threshold-Based Weather Model for Predicting Stripe Rust Infection in Winter Wheat
Authors: El Jarroudi Moussa , Kouadio Louis , Bock Clive H. , El Jarroudi Mustapha , Junk Jürgen , Pasquali Matias , Maraite Henri , Delfosse Philippe
Published: December 2016

Wheat stripe rust (caused by Puccinia striiformis f. sp. tritici) is a major threat in most wheat growing regions worldwide, which potentially causes substantial yield losses when environmental conditions are favorable. Data from 1999 to 2015 for three representative wheat-growing sites in Luxembourg were used to develop a threshold-based weather model for predicting wheat stripe rust. First, the range of favorable weather conditions using a Monte Carlo simulation method based on the Dennis model were characterized. Then, the optimum combined favorable weather variables (air temperature, relative humidity, and rainfall) during the most critical infection period (May-June) was identified and was used to develop the model. Uninterrupted hours with such favorable weather conditions over each dekad (i.e., 10-day period) during May-June were also considered when building the model. Results showed that a combination of relative humidity >92% and 4°C < temperature < 16°C for a minimum of 4 continuous hours, associated with rainfall ≤0.1 mm (with the dekad having these conditions for 5 to 20% of the time), were optimum to the development of a wheat stripe rust epidemic. The model accurately predicted infection events: probabilities of detection were ≥0.90 and false alarm ratios were ≤0.38 on average, and critical success indexes ranged from 0.63 to 1. The method is potentially applicable to studies of other economically important fungal diseases of other crops or in different geographical locations. If weather forecasts are available, the threshold-based weather model can be integrated into an operational warning system to guide fungicide applications.
Environment determines evolutionary trajectory in a constrained phenotypic space
Authors: Fraebel David T. , Mickalide Harry , Schnitkey Diane , Merritt Jason , Kuhlman Thomas E , Kuehn Seppe
Published: December 2016

Constraints on phenotypic variation limit the capacity of organisms to adapt to the multiple selection pressures encountered in natural environments. To better understand evolutionary dynamics in this context, we selectEscherichia colifor faster migration through a porous environment, a process which depends on both motility and growth. We find that a trade-off between swimming speed and growth rate constrains the evolution of faster migration. Evolving faster migration in rich medium results in slow growth and fast swimming, while evolution in minimal medium results in fast growth and slow swimming. In each condition parallel genomic evolution drives adaptation through different mutations. We show that the trade-off is mediated by antagonistic pleiotropy through mutations that affect negative regulation. A model of the evolutionary process shows that the genetic capacity of an organism to vary traits can qualitatively alter the evolutionary trajectory when selection pressures are complex.
Canonical and cross-reactive binding of NK cell inhibitory receptors to HLA-C allotypes is dictated by peptides bound to HLA-C
Authors: Sim Malcolm J. W. , Malaker Stacy A. , Khan Ayesha , Stowell Janet M. , Shabanowitz Jeffrey , Peterson Mary E. , Rajagopalan Sumati , Hunt Donald F. , Altmann Daniel M. , Long Eric O. , Boyton Rosemary J.
Published: December 2016

Background

Human natural killer (NK) cell activity is regulated by a family of killer-cell Ig-like receptors (KIR) that bind human leucocyte antigen (HLA) class I. Combinations of KIR and HLA genotypes are associated with disease, including susceptibility to viral infection and disorders of pregnancy. KIR2DL1 binds HLA-C alleles of group C2 (Lys80) and KIR2DL2 and KIR2DL3 bind HLA-C alleles of group C1 (Asn80). However, this model does not capture allelic diversity in HLA-C or the impact of HLA-bound peptides. The goal of this study was to determine the extent to which the endogenous HLA-C peptide repertoire can influence the specific binding of inhibitory KIR to HLA-C allotypes.

Results

The impact of HLA-C bound peptide on inhibitory KIR binding was investigated taking advantage of the fact that HLA-C*05:01 (HLA-C group 2, C2) and HLA-C*08:02 (HLA-C group 1, C1) have identical sequences apart from the key KIR specificity determining epitope at residues 77 and 80. Endogenous peptides were eluted from HLA-C*05:01 and used to test the peptide dependence of KIR2DL1 and KIR2DL2/3 binding to HLA-C*05:01 and HLA-C*08:02 and subsequent impact on NK cell function. Specific binding of KIR2DL1 to the C2 allotype occurred with the majority of peptides tested. In contrast, KIR2DL2/3 binding to the C1 allotype occurred with only a subset of peptides. Cross-reactive binding of KIR2DL2/3 with the C2 allotype was restricted to even fewer peptides. Unexpectedly, two peptides promoted binding of the C2 allotype-specific KIR2DL1 to the C1 allotype. We showed that presentation of endogenous peptides, or predicted HIV Gag peptides, by HLA-C can promote KIR cross-reactive binding.

Conclusions

KIR2DL2/3 binding to C1 is more peptide selective than that of KIR2DL1 binding to C2, which provides an explanation for why KIR2DL3–C1 interactions appear weaker than KIR2DL1–C2. In addition, cross-reactive binding of KIR is characterized by even higher peptide selectivity. We demonstrate a hierarchy of functional peptide selectivity of KIR–HLA-C interactions with relevance to NK cell biology and human disease associations. This selective peptide sequence-driven binding of KIR provides a potential mechanism for pathogen as well as self-peptide to modulate NK cell activation through altering levels of inhibition.
Model-based analysis of DNA replication profiles: predicting replication fork velocity and initiation rate by profiling free-cycling cells
Authors: Gispan Ariel , Carmi Miri , Barkai Naama
Published: December 2016

Eukaryotic cells initiate DNA synthesis by sequential firing of hundreds of origins. This ordered replication is described by replication profiles, which measure the DNA content within a cell population. Here, we show that replication dynamics can be deduced from replication profiles of free-cycling cells. While such profiles lack explicit temporal information, they are sensitive to fork velocity and initiation capacity through the passive replication pattern, namely the replication of origins by forks emanating elsewhere. We apply our model-based approach to a compendium of profiles that include most viable budding yeast mutants implicated in replication. Predicted changes in fork velocity or initiation capacity are verified by profiling synchronously replicating cells. Notably, most mutants implicated in late (or early) origin effects are explained by global modulation of fork velocity or initiation capacity. Our approach provides a rigorous framework for analyzing DNA replication profiles of free-cycling cells.
Anisotropy parameter inversion in vertical axis of symmetry media using diffractions
Authors: bin Waheed Umair , Stovas Alexey , Alkhalifah Tariq
Published: December 2016

Diffractions play a vital role in seismic processing as they can be utilized for high‐resolution imaging applications and analysis of subsurface medium properties like velocity. They are particularly valuable for anisotropic media as they inherently possess a wide range of dips necessary to resolve the angular dependence of velocity. However, until recently, the focus of diffraction imaging or inversion algorithms have been only on the isotropic approximation of the subsurface. Using diffracted waves, we develop a framework to invert for the effective η model. This effective model is obtained through scanning over possible effective η values and selecting the one that best fits the observed moveout curve for each diffractor location. The obtained effective η model is then converted to an interval η model using a Dix‐type inversion formula. The inversion methodology holds the potential to reconstruct the true η model with sufficiently high accuracy and resolution properties. However, it relies on an accurate estimation of diffractor locations, which in turn requires good knowledge of the background velocity model. We test the effectiveness and applicability of our method on the vertical transverse isotropic Marmousi model. The inversion results yield a reasonable match even for the complex Marmousi model.
The first post‐injection seismic monitor survey at the Ketzin pilot CO2 storage site: results from time‐lapse analysis
Authors: Huang Fei , Bergmann Peter , Juhlin Christopher , Ivandic Monika , Lüth Stefan , Ivanova Alexandra , Kempka Thomas , Henninges Jan , Sopher Daniel , Zhang Fengjiao
Published: December 2016

The injection of CO2 at the Ketzin pilot CO2 storage site started in June 2008 and ended in August 2013. During the 62 months of injection, a total amount of about 67 kt of CO2 was injected into a saline aquifer. A third repeat three‐dimensional seismic survey, serving as the first post‐injection survey, was acquired in 2015, aiming to investigate the recent movement of the injected CO2. Consistent with the previous two time‐lapse surveys, a predominantly west–northwest migration of the gaseous CO2 plume in the up‐dip direction within the reservoir is inferred in this first post‐injection survey. No systematic anomalies are detected through the reservoir overburden. The extent of the CO2 plume west of the injection site is almost identical to that found in the 2012 second repeat survey (after injection of 61 kt); however, there is a significant decrease in its size east of the injection site. Assessment of the CO2 plume distribution suggests that the decrease in the size of the anomaly may be due to multiple factors, such as limited vertical resolution, CO2 dissolution, and CO2 migration into thin layers, in addition to the effects of ambient noise. Four‐dimensional seismic modelling based on dynamic flow simulations indicates that a dynamic balance between the newly injected CO2 after the second repeat survey and the CO2 migrating into thin layers and being dissolved was reached by the time of the first post‐injection survey. In view of the significant uncertainties in CO2 mass estimation, both patchy and non‐patchy saturation models for the Ketzin site were taken into consideration.
Meta‐corridor solutions for climate‐vulnerable plant species groups in South Korea
Authors: Choe Hyeyeong , Thorne James H. , Hijmans Robert , Kim Jiyoen , Kwon Hyuksoo , Seo Changwan
Published: December 2016

Vulnerability assessments can provide useful information for the establishment of climate change adaptation strategies. We performed spatial vulnerability assessments for multiple plant species that incorporate potential range shifts to areas of future suitable climate. We conducted the assessments at a national level for plant species organized into vulnerable species groups. We then identified a climate meta‐corridor for each vulnerable group that could potentially be a pathway for multiple species.

We estimated climate suitability for 2297 South Korean terrestrial plant species under current climate conditions and climate projections for 2050 using the Multivariate Adaptive Regression Splines multiresponse species distribution model. We classified the plants into five groups based on their current spatial distribution patterns: centrally located species, wide‐range species, coastal mountain species, montane species, and lowland species. Three vulnerability assessment components — exposure, spatial disruption, and dispersal pressure — were used to calculate the spatial vulnerability of each species. Vulnerability values were averaged by group. We identified climate meta‐corridors that would link current suitable areas to future climatically suitable areas, and tested the corridors for multi‐species accessibility.

The vulnerability assessment indicates that coastal mountain, montane, and lowland species groups, comprising 37% of all modelled species, are the most vulnerable to climate change. The climate meta‐corridor for each group overlaps at least some portion of 83% or more of its species' current modelled ranges. The current and future climate‐suitable areas for the lowland species group have very little spatial overlap, suggesting a high priority should be placed on the corridor identified for these species. We found that the destinations of the climate corridors converge, raising questions about large numbers of species moving to limited areas, and that transboundary corridor modelling is needed on the Korean Peninsula.

Policy implications. Each of the three meta‐corridors has unique policy implications: assisted migration for the highest elevation species for the montane; significant conservation and restoration work for the lowland; and perhaps no direct intervention but monitoring to evaluate effectiveness of the relatively intact habitats of the coastal mountain meta‐corridor. Overall, implementation policies for climate connectivity will be context‐dependent, requiring different approaches dependent on local and regional conditions and the species targeted.
Predicting the global incidence of seed desiccation sensitivity
Authors: Wyse Sarah V. , Dickie John B.
Published: December 2016

The ability of seeds to tolerate desiccation plays an important role in plant regeneration ecology. Globally, the majority of species produce desiccation‐tolerant (orthodox) seeds, while comparatively few produce desiccation‐sensitive (recalcitrant) seeds that are unable to survive dehydration. The trait has important implications for species conservation, as desiccation‐sensitive species cannot be conserved using traditional seed banking techniques. In addition, these species may be less resilient to the increases in droughts predicted for some regions under climate change scenarios.

The best available resource on seed desiccation tolerance is the Royal Botanic Gardens, Kew's Seed Information Database. This database contains seed desiccation‐sensitivity data for over 18 000 taxa, approximately 3% of which have desiccation‐sensitive seeds. However, this database is likely biased towards desiccation‐tolerant species. Previous attempts to estimate the proportion of seed plants with desiccation‐sensitive seeds have ranged from 7% to 50%. Here, we aimed to overcome sampling bias to derive a best estimate for the proportion of seed plants with desiccation‐sensitive seeds, based on current data.

We used a recently developed method, based on taxonomic relatedness, to account for sampling bias and estimate the proportion of seed plants with desiccation‐sensitive seeds. As a comparison, given that seed desiccation sensitivity is strongly related to habitat, we repeated our analyses using habitat as a basis.

The predictions from our taxonomy‐based models ranged between estimates of 7·5% and 19·6% of the world's seed‐plant species with desiccation‐sensitive seeds, depending on model type, while the habitat‐based models suggested a value of approximately 8%. Our evidence suggests that, based on current data, the best estimate of the proportion of species with desiccation‐sensitive seeds is likely to be approximately 8%. Tropical and subtropical moist broadleaf forests had the highest incidence of seed desiccation sensitivity, where an estimated 18·5% of the seed‐plant flora possessed the trait.

Synthesis. Alongside our estimation of the numbers of species with desiccation‐sensitive seeds, we provide data on taxa and habitats where this trait may be most prevalent. These findings can be used to support conservation planning, particularly with respect to providing decision support for in and ex situ conservation techniques.
Contrasting mass‐ratio vs. niche complementarity effects on litter C and N loss during decomposition along a regional climatic gradient
Authors: García‐Palacios Pablo , Shaw E. Ashley , Wall Diana H. , Hättenschwiler Stephan
Published: December 2016

The mass‐ratio and niche complementarity mechanisms drive the influence of litter trait diversity on decomposition. However, the implications of these mechanisms remain poorly understood, as few studies have evaluated their importance relative to environmental conditions and soil decomposers when assessing different processes during decomposition (e.g. C dynamics and N transformations).

We measured litter C and N losses during decomposition in 10 litter mixtures and calculated community‐weighted means (CWM) and dissimilarity (Rao's Q) of 13 litter traits as metrics of the mass‐ratio and niche complementarity mechanisms respectively. The 10 litter mixtures were incubated along a regional gradient (10 sites) in southern France over a year, where local environmental conditions (climate and soil parameters), and soil decomposers (microbes, nematodes, and macrofauna) were considered as drivers of decomposition.

Sites and litter mixtures represented a wide range of environmental conditions, decomposers, and litter diversity. Litter mixture was the major factor affecting litter C and N loss. N was immobilized during the early decomposition stages (up to c. 40% mass loss), especially in mixtures of low N concentrations. Litter CWM traits were the key drivers of litter C and N loss, but litter trait dissimilarity emerged as a major driver of litter N loss. Macrofauna played a significant role on C and N loss, but environmental conditions exerted a minor influence.

Our results highlight that distinct aspects of trait diversity in mixed species litter can play a more important role than environmental conditions and decomposers, which can affect the cycling of litter C and N at regional scales. Rather than opposing mass‐ratio and niche complementarity mechanisms, our study shows that both can play a critical role simultaneously in litter decomposition.

Synthesis. Our study emphasizes that, in the current context of global biodiversity decline, the mass‐ratio and niche complementarity mechanisms should be considered to assess litter decomposition dynamics under global change. As litter diversity mechanisms distinctly affected the cycling of C and N, we recommend taking into account such element‐specific effects to improve the prediction of the impacts of biodiversity change on biogeochemical cycles.
Population dynamics of Eichhornia crassipes (C. Mart.) Solms in the Nile Delta, Egypt
Authors: Eid Ebrahem M. , Shaltout Kamal H.
Published: December 2016

The present study aims to evaluate the growth and seasonal allocation of the biomass of water hyacinth (Eichhornia crassipes) under natural conditions in the south Mediterranean region (the Nile Delta, Egypt). In this study, the population characteristics (density, morphology and primary production) over a one‐growing‐season cycle were described. In the Nile Delta, the biomass of the shoot and root systems of E.crassipes was sampled monthly along three water courses from April 2014 to November 2014 using five quadrats (each of 0.5 m × 0.5 m) at each water course. The shoot system started to grow in April (121 g/DM/m2), reached a maximum biomass of 887 g/DM/m2 in July, and then decreased until reaching a minimum of 299 g/DM/m2 in November. The biomass of the root system increased from 75 g/DM/m2 in April to a maximum of 235 g/DM/m2 in August and decreased to a minimum of 100 g/DM/m2 in November. Water hyacinth allocated ca. 2% of its total biomass to stolons, 22% to laminae, 24% to roots and 52% to petioles. Peak density as high as 144 individual/m2 occurred in May, but it reduced to 33–50 individual/m2 during July to November. The average rate of change of biomass was maximum (17.3 g/DM/m2/day) during April and May and minimum (−8.9 g/DM/m2/day) during October and November. Relative growth rates were found to be lowest during the cooler months, October and November (−0.017 g/DM/g /day), whereas highest yields were recorded during the spring months, April and May (up to 0.044 g/DM/g/day). The correlation coefficients between the water characteristics and the first two canonical correspondence analysis axes indicated that the separation of the population parameters of water hyacinth along the first axis was negatively influenced by Zn. On the other hand, the second axis was positively correlated with electric conductivity, total N, total P, Mg, Na, K and Mn and negatively with pH.
Development and characterization of EST‐SSR markers for the genus Rhododendron section Brachycalyx (Ericaceae)
Authors: Yoichi Watanabe , Sakaguchi Shota , Ueno Saneyoshi , Tomaru Nobuhiro , Uehara Koichi
Published: December 2016

Simple sequence repeat (SSR) markers were developed from expressed sequence tags (ESTs) for Rhododendron section Brachycalyx in order to elucidate its evolutionary processes and reproductive ecology. Nineteen polymorphic EST‐SSR markers were developed from EST libraries of R. amagianum and R. hyugaense. Polymorphisms for these markers were assessed using four species of section Brachycalyx. The number of alleles ranged from 1 to 14, and the observed and expected heterozygosity ranged from 0.000 to 0.931 and 0.000 to 0.904, respectively. The EST‐SSR markers developed in this study will be useful for elucidating population genetic structure and breeding systems in section Brachycalyx.
The microtubule end‐binding protein FgEB1 regulates polar growth and fungicide sensitivity via different interactors in Fusarium graminearum
Authors: Liu Zunyong , Wu Sisi , Chen Yun , Han Xinyue , Gu Qin , Yin Yanni , Ma Zhonghua
Published: December 2016

In yeasts, the end‐binding protein 1 (EB1) homologs regulate microtubule dynamics, cell polarization, and chromosome stability. However, functions of EB1 orthologs in plant pathogenic fungi have not been characterized yet. Here, we observed that the FgEB1 deletion mutant (ΔFgEB1) of Fusarium graminearum exhibits twisted hyphae, increased hyphal branching and curved conidia, indicating that FgEB1 is involved in the regulation of cellular polarity. Microscopic examination further showed that the microtubules of ΔFgEB1 exhibited less organized in comparison with those of the wild type. In addition, the lack of FgEB1 also altered the distribution of polarity‐related class I myosin via the interaction with the actin. On the other hand, we identified four core septins as FgEB1‐interacting proteins, and found that FgEB1 and septins regulated conidial polar growth in the opposite orientation. Interestingly, FgEB1 and FgKar9 constituted another complex that modulated the response to carbendazim, a microtubule‐damaging agent specifically. In addition, the deletion of FgEB1 led to dramatically decreased deoxynivalenol (DON) biosynthesis. Taken together, results of this study indicate that FgEB1 regulates cellular polarity, fungicide sensitivity and DON biosynthesis via different interactors in F. graminarum, which provides a novel insight into understanding of the biological functions of EB1 in filamentous fungi.