bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective targeting of the conserved active site cysteine of Mycobacterium tuberculosis methionine aminopeptidase with electrophilic reagents
Authors: Reddi Ravikumar , Arya Tarun , Kishor Chandan , Gumpena Rajesh , Ganji Roopa J. , Bhukya Supriya , Addlagatta Anthony 
Published: May 2014

Methionine aminopeptidases (MetAPs) cleave initiator methionine from ~ 70% of the newly synthesized proteins in every living cell, and specific inhibition or knockdown of this function is detrimental. MetAPs are metalloenzymes, and are broadly classified into two subtypes, type I and type II. Bacteria contain only type I MetAPs, and the active site of these enzymes contains a conserved cysteine. By contrast, in type II enzymes the analogous position is occupied by a conserved glycine. Here, we report the reactivity of the active site cysteine in a type I MetAP, MetAP1c, of Mycobacterium tuberculosis (MtMetAP1c) towards highly selective cysteine‐specific reagents. The authenticity of selective modification of Cys105 of MtMetAP1c was established by using site‐directed mutagenesis and crystal structure determination of covalent and noncovalent complexes. On the basis of these observations, we propose that metal ions in the active site assist in the covalent modification of Cys105 by orienting the reagents appropriately for a successful reaction. These studies establish, for the first time, that the conserved cysteine of type I MetAPs can be targeted for selective inhibition, and we believe that this chemistry can be exploited for further drug discovery efforts regarding microbial MetAPs.
Activity of the upstream TATA‐less promoter of the p21Waf1/Cip1 gene depends on transcription factor IIA (TFIIA) in addition to TFIIA‐reactive TBP‐like protein
Authors: Suzuki Hidefumi , Maeda Ryo , Nakadai Tomoyoshi , Tamura Taka‐aki 
Published: May 2014

TATA‐binding protein‐like protein (TLP) binds to transcription factor IIA (TFIIA) with high affinity, although the significance of this binding is poorly understood. In this study, we investigated the role of TFIIA in transcriptional regulation of the p21Waf1/Cip1 (p21) gene. It has been shown that TLP is indispensable for p53‐activated transcription from an upstream TATA‐less promoter of the p21 gene. We found that mutant TLPs having decreased TFIIA‐binding ability exhibited weakened transcriptional activation function for the upstream promoter. Activity of the upstream promoter was enhanced considerably by an increased amount of TFIIA in a p53‐dependent manner, whereas activity of the TATA‐containing downstream promoter was enhanced only slightly. TFIIA potentiated the upstream promoter additively with TLP. Although TFIIA is recruited to both promoters, activity of the upstream promoter was much more dependent on TFIIA. Recruitment of TFIIA and TLP to the upstream promoter was augmented in etoposide‐treated cells, in which the amount of TFIIA–TLP complex is increased, and TFIIA‐reactive TLP was required for the recruitment of both factors. It was confirmed that etoposide‐stimulated transcription depends on TLP. We also found that TFIIA‐reactive TLP acts to decrease cell growth rate, which can be explained by interaction of the p21 promoter with the transcription factors that we examined. The results of the present study suggest that the upstream TATA‐less promoter of p21 needs TFIIA and TFIIA‐reactive TLP for p53‐dependent transcriptional enhancement.Structured digital abstract

TLP physically interacts with TFIIA beta and TFIIA alpha by anti tag coimmunoprecipitation (View interaction)

TFIIA alpha/beta physically interacts with TLP by anti bait coip (View interaction)
A computational tool for estimating stress fields along a surface crack front
Authors: Chernyatin A. S. , Matvienko Y. G. , Razumovsky I. A. 
Published: May 2014

AbstractA combined experimental and computational method for determination of the singular and non‐singular stress terms along the front of the 3D surface crack is proposed. It is suggested to evaluate the terms by means of comprehensive comparison between deformation responses on the structure surface in the vicinity of the crack obtained experimentally and from numerical solutions of the corresponding boundary problem of solid mechanics. As the deformation response, a local displacement field caused by the formation of a small hole at the tip of the crack recorded by digital speckle pattern interferometry may be considered. The proposed approach allows defining such real parameters of the structure as the active load conditions in the crack region and crack sizes. These parameters are used to solve the direct problem and to determine the stress intensity factor KI and Txx‐, Tzz‐stresses along the surface crack front by means of an improved technique of their calculation.The approach accuracy and stability at different conditions have been proved by means of numerical simulation that examined half‐space with planar semi‐elliptical surface crack under biaxial loading. So, the potential applicability of the proposed method is demonstrated. The biaxiality effect on KI and Txx, Tzz is discussed.
Horizon scanning for invasive alien species with the potential to threaten biodiversity in Great Britain
Authors: Roy Helen E. , Peyton Jodey , Aldridge David C. , Bantock Tristan , Blackburn Tim M. , Britton Robert , Clark Paul , Cook Elizabeth , Dehnen‐Schmutz Katharina , Dines Trevor , Dobson Michael , Edwards François , Harrower Colin , Harvey Martin C. , Minchin Dan , Noble David G. , Parrott Dave , Pocock Michael J. O. , Preston Chris D. , Roy Sugoto , Salisbury Andrew , Schönrogge Karsten , Sewell Jack , Shaw Richard H. , Stebbing Paul , Stewart Alan J. A. , Walker Kevin J. 
Published: May 2014

AbstractInvasive alien species (IAS) are considered one of the greatest threats to biodiversity, particularly through their interactions with other drivers of change. Horizon scanning, the systematic examination of future potential threats and opportunities, leading to prioritization of IAS threats is seen as an essential component of IAS management. Our aim was to consider IAS that were likely to impact on native biodiversity but were not yet established in the wild in Great Britain. To achieve this, we developed an approach which coupled consensus methods (which have previously been used for collaboratively identifying priorities in other contexts) with rapid risk assessment. The process involved two distinct phases:

Preliminary consultation with experts within five groups (plants, terrestrial invertebrates, freshwater invertebrates, vertebrates and marine species) to derive ranked lists of potential IAS.

Consensus‐building across expert groups to compile and rank the entire list of potential IAS.

Five hundred and ninety‐one species not native to Great Britain were considered. Ninety‐three of these species were agreed to constitute at least a medium risk (based on score and consensus) with respect to them arriving, establishing and posing a threat to native biodiversity. The quagga mussel, Dreissena rostriformis bugensis, received maximum scores for risk of arrival, establishment and impact; following discussions the unanimous consensus was to rank it in the top position. A further 29 species were considered to constitute a high risk and were grouped according to their ranked risk. The remaining 63 species were considered as medium risk, and included in an unranked long list. The information collated through this novel extension of the consensus method for horizon scanning provides evidence for underpinning and prioritizing management both for the species and, perhaps more importantly, their pathways of arrival. Although our study focused on Great Britain, we suggest that the methods adopted are applicable globally.
Patterns of drought tolerance in major European temperate forest trees: climatic drivers and levels of variability
Authors: Zang Christian , Hartl‐Meier Claudia , Dittmar Christoph , Rothe Andreas , Menzel Annette 
Published: May 2014

AbstractThe future performance of native tree species under climate change conditions is frequently discussed, since increasingly severe and more frequent drought events are expected to become a major risk for forest ecosystems. To improve our understanding of the drought tolerance of the three common European temperate forest tree species Norway spruce, silver fir and common beech, we tested the influence of climate and tree‐specific traits on the inter and intrasite variability in drought responses of these species. Basal area increment data from a large tree‐ring network in Southern Germany and Alpine Austria along a climatic cline from warm‐dry to cool‐wet conditions were used to calculate indices of tolerance to drought events and their variability at the level of individual trees and populations. General patterns of tolerance indicated a high vulnerability of Norway spruce in comparison to fir and beech and a strong influence of bioclimatic conditions on drought response for all species. On the level of individual trees, low‐growth rates prior to drought events, high competitive status and low age favored resilience in growth response to drought. Consequently, drought events led to heterogeneous and variable response patterns in forests stands. These findings may support the idea of deliberately using spontaneous selection and adaption effects as a passive strategy of forest management under climate change conditions, especially a strong directional selection for more tolerant individuals when frequency and intensity of summer droughts will increase in the course of global climate change.
Predicting Aquifer Response Time for Application in Catchment Modeling
Authors: Walker Glen R. , Gilfedder Mat , Dawes Warrick R. , Rassam David W. 
Published: May 2014

AbstractIt is well established that changes in catchment land use can lead to significant impacts on water resources. Where land‐use changes increase evapotranspiration there is a resultant decrease in groundwater recharge, which in turn decreases groundwater discharge to streams. The response time of changes in groundwater discharge to a change in recharge is a key aspect of predicting impacts of land‐use change on catchment water yield. Predicting these impacts across the large catchments relevant to water resource planning can require the estimation of groundwater response times from hundreds of aquifers. At this scale, detailed site‐specific measured data are often absent, and available spatial data are limited. While numerical models can be applied, there is little advantage if there are no detailed data to parameterize them. Simple analytical methods are useful in this situation, as they allow the variability in groundwater response to be incorporated into catchment hydrological models, with minimal modeling overhead. This paper describes an analytical model which has been developed to capture some of the features of real, sloping aquifer systems. The derived groundwater response timescale can be used to parameterize a groundwater discharge function, allowing groundwater response to be predicted in relation to different broad catchment characteristics at a level of complexity which matches the available data. The results from the analytical model are compared to published field data and numerical model results, and provide an approach with broad application to inform water resource planning in other large, data‐scarce catchments.
Unsaturated Hydraulic Conductivity Models Based on Truncated Lognormal Pore‐Size Distributions
Authors: Malama Bwalya , Kuhlman Kristopher L. 
Published: May 2014

AbstractWe develop a closed‐form three‐parameter model for unsaturated hydraulic conductivity associated with the Kosugi three‐parameter lognormal moisture retention model. The model derivation uses a slight modification to Mualem's theory, which is nearly exact for nonclay soils. Kosugi's three‐parameter lognormal moisture retention model uses physically meaningful parameters, but a corresponding closed‐form relative hydraulic conductivity model has never been developed. The model is further extended to a four‐parameter model by truncating the underlying pore‐size distribution at physically permissible minimum and maximum pore radii. The proposed closed‐form models are fitted to well‐known experimental data to illustrate their utility. They have the same physical basis as Kosugi's two‐parameter model, but are more general.
Arthroscopically Assisted Treatment of Injury to the Lateral Glenohumeral Ligament in Dogs
Authors: Ridge Patrick A. , Cook James L. , Cook Cristi R. 
Published: May 2014

ObjectiveTo report short and medium term outcomes, and complications, in dogs treated for rupture of the lateral glenohumeral ligament (LGHL) with a novel, arthroscopically assisted technique.Study DesignRetrospective case series.AnimalsDogs (n = 10) with LGHL injury.MethodsDogs were included after arthroscopic confirmation of rupture of the LGHL and treatment using an arthroscopically assisted suture anchor technique with informed owner consent. Outcomes were assessed by the authors and owners and complications arising from treatment recorded.ResultsAfter 6 months, 7 dogs were assessed as having full function, 2 as having acceptable function, and 1 had poor function. There was 1 minor intra‐operative and 1 minor post‐operative complication. There were no major complications encountered 6 months after treatment.ConclusionsDogs with LGHL injury can be treated using this novel technique with low complication rates and good outcomes after 6 months.
A Short Overview of Measures for Securing Water Resources for Irrigated Crop Production
Authors: Jensen C. R. , Ørum J. E. , Pedersen S. M. , Andersen M. N. , Plauborg F. , Liu F. , Jacobsen S.‐E. 
Published: May 2014

AbstractAgriculture is the main user of limited fresh water resources in the world. Optimisation of agricultural water resources and their use can be obtained by both agronomical and political incentives. Important options are: reduction of the loss of irrigation water in conveyance before it reaches the farm; selection of water‐efficient irrigation methods such as drip and micro‐irrigation saving 30–40 % water compared to furrow irrigation; improvement of irrigation scheduling using plant and soil sensors and remote sensing‐based models; deficit irrigation (DI) raising the water productivity in the range of 10–50 %; use of saline and wastewater for which modelling tools lately have been developed; introduction of drought and salt‐tolerant crops eases the use of DI and use of saline water; improvement of cropping systems with development of conservation agriculture. Further options are: use of the ‘virtual water’ principles so that water‐rich regions secure food supply to dry regions; reduction in waste of food, feed and biofuel from post‐harvest to the end consumer; changing of food composition to less water‐consuming products; regulating amount of irrigation water by rationing, subsidies or water pricing to support water‐saving measures such as use of drip, irrigation scheduling and DI. The potential for water saving for different measures is discussed and estimated. Reduction in waste of food and loss of irrigation water from conveyance source to farm both has a great potential for water saving compared to other measures. How to choose the measures will depend on the local situation, which is ultimately a political choice.
Commentary: From noise to insight? Reaction time variability in ADHD and autism spectrum disorders – a commentary on Karalunas et al. (2014)
Authors: Kuntsi Jonna 
Published: May 2014

Increased reaction time variability (RTV) emerged, for many of us in the field, initially as more of an ‘irritant’: a strong correlate of ADHD in particular that persisted when our pet hypotheses on other cognitive constructs withered. But the persistence of this now widespread observation – with high RTV reported across many disorders – has led to investigators paying increasingly more attention to this initially uncool concept. Time is ripe, it seems, for listening to what the ‘noise’ in our reaction time (RT) data may tell us. It is against this background that the accompanying Annual Research Review by Karalunas and colleagues captures the current enthusiasm in trying to elucidate whether RTV reflects ‘a trans‐diagnostic phenotype that is associated with shared risk for several disorders or with symptom domains that cut across several disorder categories’ or whether RTV could be ‘decomposed into distinct processes that differ among psychiatric conditions’. Focusing on two neurodevelopmental disorders, ADHD and autism spectrum disorders (ASD), Karalunas et al. performed two new meta‐analyses and provide an additional review of the literature, which lead to helpful interim conclusions and open a discussion (which this Commentary preludes) on the next steps in our attempts to make sense of the RT ‘noise’.
Niche evolution and thermal adaptation in the temperate species Drosophila americana
Authors: Sillero N. , Reis M. , Vieira C. P. , Vieira J. , Morales‐Hojas R. 
Published: May 2014

AbstractThe study of ecological niche evolution is fundamental for understanding how the environment influences species' geographical distributions and their adaptation to divergent environments. Here, we present a study of the ecological niche, demographic history and thermal performance (locomotor activity, developmental time and fertility/viability) of the temperate species Drosophila americana and its two chromosomal forms. Temperature is the environmental factor that contributes most to the species' and chromosomal forms' ecological niches, although precipitation is also important in the model of the southern populations. The past distribution model of the species predicts a drastic reduction in the suitable area for the distribution of the species during the last glacial maximum (LGM), suggesting a strong bottleneck. However, DNA analyses did not detect a bottleneck signature during the LGM. These contrasting results could indicate that D. americana niche preference evolves with environmental change, and thus, there is no evidence to support niche conservatism in this species. Thermal performance experiments show no difference in the locomotor activity across a temperature range of 15 to 38 °C between flies from the north and the south of its distribution. However, we found significant differences in developmental time and fertility/viability between the two chromosomal forms at the model's optimal temperatures for the two forms. However, results do not indicate that they perform better for the traits studied here in their respective optimal niche temperatures. This suggests that behaviour plays an important role in thermoregulation, supporting the capacity of this species to adapt to different climatic conditions across its latitudinal distribution.
Sex‐ratio meiotic drive and interspecific competition
Authors: Unckless R. L. , Clark A. G. 
Published: May 2014

AbstractIt has long been known that processes occurring within a species may impact the interactions between species. For example, as competitive ability is sensitive to parameters including reproductive rate, carrying capacity and competition efficiency, the outcome of interspecific competition may be influenced by any process that alters these attributes. Although several such scenarios have been discussed, the influence of selfish genetic elements within one species on competition between species has not received theoretical treatment. We show that, with strong competition, sex‐ratio meiotic drive systems can result in a significant shift in community composition because the effective birth rate in the population may be increased by a female‐biased sex ratio. Using empirical data, we attempt to estimate the magnitude of this effect in several Drosophila species. We infer that meiotic drive elements, selfish genetic elements within species, can provide a substantial competitive advantage to that species within a community.
Effects of genetic similarity on the life‐history strategy of co‐infecting trematodes: are parasites capable of intrahost kin recognition?
Authors: Joannes A. , Lagrue C. , Poulin R. , Beltran‐Bech S. 
Published: May 2014

AbstractFor conspecific parasites sharing the same host, kin recognition can be advantageous when the fitness of one individual depends on what another does; yet, evidence of kin recognition among parasites remains limited. Some trematodes, like Coitocaecum parvum, have plastic life cycles including two alternative life‐history strategies. The parasite can wait for its intermediate host to be eaten by a fish definitive host, thus completing the classical three‐host life cycle, or mature precociously and produce eggs while still inside its intermediate host as a facultative shortcut. Two different amphipod species are used as intermediate hosts by C. parvum, one small and highly mobile and the other larger, sedentary, and burrow dwelling. Amphipods often harbour two or more C. parvum individuals, all capable of using one or the other developmental strategy, thus creating potential conflicts or cooperation opportunities over transmission routes. This model was used to test the kin recognition hypothesis according to which cooperation between two conspecific individuals relies on the individuals' ability to evaluate their degree of genetic similarity. First, data showed that levels of intrahost genetic similarity between co‐infecting C. parvum individuals differed between host species. Second, genetic similarity between parasites sharing the same host was strongly linked to their likelihood of adopting identical developmental strategies. Two nonexclusive hypotheses that could explain this pattern are discussed: kin recognition and cooperation between genetically similar parasites and/or matching genotypes involving parasite genotype–host compatibility filters.
Sexually selected dichromatism in the hihiNotiomystis cincta: multiple colours for multiple receivers
Authors: Walker L. K. , Ewen J. G. , Brekke P. , Kilner R. M. 
Published: May 2014

AbstractWhy do some bird species show dramatic sexual dichromatism in their plumage? Sexual selection is the most common answer to this question. However, other competing explanations mean it is unwise to assume that all sexual dichromatism has evolved by this mechanism. Even if sexual selection is involved, further work is necessary to determine whether dichromatism results from competition amongst rival males, or by female choice for attractive traits, or both. Here, we test whether sexually dichromatic hihi (Notiomystis cincta) plumage is currently under sexual selection, with detailed behavioural and genetic analyses of a free‐living island population. Bateman gradients measured for males and females reveal the potential for sexual selection, whilst selection gradients, relating reproductive success to specific colourful traits, show that there is stabilizing selection on white ear tuft length in males. By correlating colourful male plumage with different components of reproductive success, we show that properties of yellow plumage are most likely a product of male–male competition, whilst properties of the black and white plumage are an outcome of both male–male competition and female choice. Male plumage therefore potentially signals to multiple receivers (rival males and potential mates), and this may explain the multicoloured appearance of one of the most strikingly dichromatic species inNewZealand.