bluuebunny/crossref_metadata_2025_split huggingface dataset:
Manganese homeostasis and utilization in pathogenic bacteria
Authors: Juttukonda Lillian J. , Skaar Eric P. 
Published: April 2015

SummaryManganese (Mn) is a required cofactor for all forms of life. Given the importance of Mn to bacteria, the host has devised strategies to sequester Mn from invaders. In the macrophage phagosome, NRAMP1 removes Mn and other essential metals to starve intracellular pathogens; in the extracellular space, calprotectin chelates Mn and Zn. Calprotectin‐mediated Mn sequestration is a newly appreciated host defense mechanism, and recent findings are highlighted herein. In order to acquire Mn when extracellular concentrations are low, bacteria have evolved efficient Mn acquisition systems that are under elegant transcriptional control. To counteract Mn overload, some bacteria possess Mn‐specific export systems that are important in vivo, presumably for control of intracellular Mn levels. Mn transporters, their transcriptional regulators and some Mn‐requiring enzymes are necessary for virulence of certain bacterial pathogens, as revealed by animal models of infection. Furthermore, Mn is an important facet of the cellular response to oxidative stress, a host antibacterial strategy. The battle for Mn between host and pathogen is now appreciated to be a major determinant of the outcome of infection. In this MicroReview, the contribution of Mn to the host–pathogen interaction is reviewed, and key questions are proposed for future study.
Balancing drug resistance and growth rates via compensatory mutations in the Plasmodium falciparum chloroquine resistance transporter
Authors: Petersen Ines , Gabryszewski Stanislaw J. , Johnston Geoffrey L. , Dhingra Satish K. , Ecker Andrea , Lewis Rebecca E. , de Almeida Mariana Justino , Straimer Judith , Henrich Philipp P. , Palatulan Eugene , Johnson David J. , Coburn‐Flynn Olivia , Sanchez Cecilia , Lehane Adele M. , Lanzer Michael , Fidock David A. 
Published: April 2015

SummaryThe widespread use of chloroquine to treat Plasmodium falciparum infections has resulted in the selection and dissemination of variant haplotypes of the primary resistance determinant PfCRT. These haplotypes have encountered drug pressure and within‐host competition with wild‐type drug‐sensitive parasites. To examine these selective forces in vitro, we genetically engineered P. falciparum to express geographically diverse PfCRT haplotypes. Variant alleles from the Philippines (PH1 and PH2, which differ solely by the C72S mutation) both conferred a moderate gain of chloroquine resistance and a reduction in growth rates in vitro. Of the two, PH2 showed higher IC50 values, contrasting with reduced growth. Furthermore, a highly mutated pfcrt allele from Cambodia (Cam734) conferred moderate chloroquine resistance and enhanced growth rates, when tested against wild‐type pfcrt in co‐culture competition assays. These three alleles mediated cross‐resistance to amodiaquine, an antimalarial drug widely used in Africa. Each allele, along with the globally prevalent Dd2 and 7G8 alleles, rendered parasites more susceptible to lumefantrine, the partner drug used in the leading first‐line artemisinin‐based combination therapy. These data reveal ongoing region‐specific evolution of PfCRT that impacts drug susceptibility and relative fitness in settings of mixed infections, and raise important considerations about optimal agents to treat chloroquine‐resistant malaria.
ComGA‐RelA interaction and persistence in the Bacillus subtilis K‐state
Authors: Hahn Jeanette , Tanner Andrew W. , Carabetta Valerie J. , Cristea Ileana M. , Dubnau David 
Published: April 2015

SummaryThe bistably expressed K‐state of Bacillus subtilis is characterized by two distinct features; transformability and arrested growth when K‐state cells are exposed to fresh medium. The arrest is manifested by a failure to assemble replisomes and by decreased rates of cell growth and rRNA synthesis. These phenotypes are all partially explained by the presence of the AAA+ protein ComGA, which is also required for the binding of transforming DNA to the cell surface and for the assembly of the transformation pilus that mediates DNA transport. We have discovered that ComGA interacts with RelA and that the ComGA‐dependent inhibition of rRNA synthesis is largely bypassed in strains that cannot synthesize the alarmone (p)ppGpp. We propose that the interaction of ComGA with RelA prevents the hydrolysis of (p)ppGpp in K‐state cells, which are thus trapped in a non‐growing state until ComGA is degraded. We show that some K‐state cells exhibit tolerance to antibiotics, a form of type 1 persistence, and we propose that the bistable expression of both transformability and the growth arrest are bet‐hedging adaptations that improve fitness in the face of varying environments, such as those presumably encountered by B. subtilis in the soil.
Early Pennsylvanian (Langsettian) fish assemblages from the Joggins Formation, Canada, and their implications for palaeoecology and palaeogeography
Authors: Carpenter David K. , Falcon‐Lang Howard J. , Benton Michael J. , Grey Melissa 
Published: April 2015

AbstractA review of all available specimens of fossil fishes from the classic Pennsylvanian Joggins locality of Nova Scotia, Canada, reveals the existence of a diverse community of chondrichthyans (xenacanthids, ctenacanthids and the enigmaticAgeleodus), acanthodians (gyracanthids), sarcopterygians (rhizodontids, megalichthyids, rhizodopsids and dipnoans) and actinopterygians (haplolepids). Reassessment of supposed endemic species (Ctenoptychius cristatus,Sagenodus plicatus,Gyracanthus duplicatus) indicates they are invalid, and overall, the assemblage comprises cosmopolitan taxa that were widespread around the coasts of tropical Pangaea. Strontium isotope analysis of fish remains and a critical study of their facies context suggest that these fish communities occupied bodies of water with salinities across the marine–freshwater spectrum. This preponderance of euryhaline forms implies a community structure quite distinct from that of today and might represent a transitory phase prior to the establishment of fully freshwater fish communities. Interpretation of fish ecology provides further evidence that the Joggins Formation was deposited in a paralic setting, and the recognition of one previously undetected brackish incursion strengthens the link between sedimentary cycles at Joggins and Milankovitch‐induced glacio‐eustatic change. Furthermore, interregional correlation of these marine transgressions supports palynostratigraphical arguments for an early Langsettian age for the Joggins Formation. This places tighter constraints on the age of the earliest known crown amniote,Hylonomus lyelli, an important calibration point used in phylogenomic studies.
Transcript profiling of jasmonate‐elicited Taxus cells reveals a β‐phenylalanine‐CoA ligase
Authors: Ramírez‐Estrada Karla , Altabella Teresa , Onrubia Miriam , Moyano Elisabeth , Notredame Cedric , Osuna Lidia , Vanden Bossche Robin , Goossens Alain , Cusido Rosa M. , Palazon Javier 
Published: April 2015

SummaryPlant cell cultures constitute eco‐friendly biotechnological platforms for the production of plant secondary metabolites with pharmacological activities, as well as a suitable system for extending our knowledge of secondary metabolism. Despite the high added value of taxol and the importance of taxanes as anticancer compounds, several aspects of their biosynthesis remain unknown. In this work, a genomewide expression analysis of jasmonate‐elicited Taxus baccata cell cultures by complementary DNA‐amplified fragment length polymorphism (cDNA‐AFLP) indicated a correlation between an extensive elicitor‐induced genetic reprogramming and increased taxane production in the targeted cultures. Subsequent in silico analysis allowed us to identify 15 genes with a jasmonate‐induced differential expression as putative candidates for genes encoding enzymes involved in five unknown steps of taxane biosynthesis. Among them, the TB768 gene showed a strong homology, including a very similar predicted 3D structure, with other genes previously reported to encode acyl‐CoA ligases, thus suggesting a role in the formation of the taxol lateral chain. Functional analysis confirmed that the TB768 gene encodes an acyl‐CoA ligase that localizes to the cytoplasm and is able to convert β‐phenylalanine, as well as coumaric acid, into their respective derivative CoA esters. β‐phenylalanyl‐CoA is attached to baccatin III in one of the last steps of the taxol biosynthetic pathway. The identification of this gene will contribute to the establishment of sustainable taxol production systems through metabolic engineering or synthetic biology approaches.
Breeding and characterization of soybean Triple Null; a stack of recessive alleles of Kunitz Trypsin Inhibitor, Soybean Agglutinin, and P34 allergen nulls
Authors: Schmidt Monica A. , Hymowitz Theodore , Herman Eliot M. 
Published: April 2015

AbstractSoybean (Glycine max) seeds contain bioactive proteins with antinutritional and immunological properties that affect metabolism and assimilation of nutrients. The presence of antinutritional proteins requires soybeans to be heat‐treated resulting in input energy costs. Nulls for bioactive seed proteins have been previously isolated from the USDA soybean collection, including Kunitz trypsin inhibitor (TI), soybean agglutinin (LE) and immunodominant soybean allergen P34 protein. Each of these nulls has the potential to partially address the concerns of soybean feed/food consumption. A stack of recessive nulls of TI, LE and P34 was created in a cv ‘Williams 82’ background termed ‘Triple Null’. Triple Null has a slight reduction of total protein compared with ‘Williams 82’ corresponding to aggregate contribution of TI, LE and P34 in the seed proteome. Triple Null's proteome analysis revealed P34 and TI nulls are frame‐shift mutants able to accumulate small amounts of authentic P34 and TI proteins. Triple Null has possible application as a conventional feed/food source and for immunotherapy to mitigate soybean allergenic response.
EST‐SSR analysis provides insights about genetic relatedness, population structure and gene flow in grass pea (Lathyrus sativus)
Authors: Soren Khela R. , Yadav Ashutosh , Pandey Gaurav , Gangwar Priyanka , Parihar Ashok K. , Bohra Abhishek , Dixit Girish P. , Datta Subhojit , Singh Narendra Pratap 
Published: April 2015

AbstractGrass pea (Lathyrus sativus) is an important food‐legume crop for resource‐poor farmers in the developing world. However, given its cultivation in the most underprivileged regions, the crop has not received appropriate scientific attention particularly from the genomic perspective, thereby giving it a status of genomic orphan. Nevertheless, some recent studies have attempted to develop modern molecular tools to strengthen the genetic and genomic research. In the present investigation, a comprehensive collection comprising 176 accessions was analysed using EST‐simple sequence repeats (SSRs). The SSR analysis revealed existence of a total of 51 alleles with an average polymorphic information content value of 0.35. A moderate level of gene diversity was noticed that ranged from 0.04 to 0.73 with an average of 0.43. Noticeably, two distinct subpopulations were recovered using cluster analysis. In addition, the presence of admixtures in population reflected the strong possibilities of gene flow between the accessions across the geographical boundary. In summary, we provide additional insights about the informativeness of available EST‐SSR markers along with an extended understanding of relatedness, genetic structure and gene flow in an under‐researched legume crop.
Genetic characterization of group A acetylsaponin‐deficient mutants from wild soybean (Glycine soja Sieb. and Zucc.)
Authors: Krishnamurthy Panneerselvam , Lee Jeong‐Dong , Ha Bo‐Keun , Chae Jong‐Hyun , Song Jong Tae , Tsukamoto Chigen , Singh Ram J. , Chung Gyuhwa 
Published: April 2015

AbstractGroup A acetylsaponins are the main causative components for bitter and astringent tastes of soybean (Glycine max). In this study, we examined the genetic nature of the absence of group A acetylsaponins in 12 Korean wild soybean (Glycine soja) accessions. In all 12 accessions, the coding region (1431‐bp) of Sg‐1 locus was identical with Sg‐1a, which adds the xylose sugar moiety at the terminal position of the C‐22 sugar chain of SS‐A, except one nucleotide (G→A change) at +948th position. This point mutation results in change of one amino acid from tryptophan (TGG) to stop codon (TGA). We observed that the mutated Sg‐1 was controlled by a single recessive gene (sg‐10‐a1). This gene was mapped between BARCSOYSSR_07_1561 and BARCSOYSSR_07_1598 on soybean chromosome 7. Our study demonstrated that the mutated Sg‐1 gene in Korean wild soybeans is genetically different from those identified in Japanese soybean cultivar ‘Kinusayaka’ and wild soybean JP‐36121. We believe that the new Sg‐1 mutants can also be utilized to produce a new soybean variety without bitter and astringent properties.
Mind as an Intrinsic Property of Matter
Authors: Jylkkä Jussi 
Published: April 2015

AbstractThis paper argues that the epistemic gap in philosophy of mind stems from the fact that our awareness of our subjective experiences is categorically different from our knowledge of external phenomena. Our knowledge of external objects is always mediated through empirical observation or theoretical descriptions, and does not afford us knowledge of the intrinsic nature of the thing referred to, whereas our awareness of our experiences is immediate and affords us knowledge of the intrinsic nature of our experiences. Finally, it is argued that the thing itself referred to as “neural correlate of consciousness” is constituted by consciousness.
The Strategic Use of Noise in Pragmatic Reasoning
Authors: Bergen Leon , Goodman Noah D. 
Published: April 2015

AbstractWe combine two recent probabilistic approaches to natural language understanding, exploring the formal pragmatics of communication on a noisy channel. We first extend a model of rational communication between a speaker and listener, to allow for the possibility that messages are corrupted by noise. In this model, common knowledge of a noisy channel leads to the use and correct understanding of sentence fragments. A further extension of the model, which allows the speaker to intentionally reduce the noise rate on a word, is used to model prosodic emphasis. We show that the model derives several well‐known changes in meaning associated with prosodic emphasis. Our results show that nominal amounts of actual noise can be leveraged for communicative purposes.
Uncertainty and Exploration in a Restless Bandit Problem
Authors: Speekenbrink Maarten , Konstantinidis Emmanouil 
Published: April 2015

AbstractDecision making in noisy and changing environments requires a fine balance between exploiting knowledge about good courses of action and exploring the environment in order to improve upon this knowledge. We present an experiment on a restless bandit task in which participants made repeated choices between options for which the average rewards changed over time. Comparing a number of computational models of participants’ behavior in this task, we find evidence that a substantial number of them balanced exploration and exploitation by considering the probability that an option offers the maximum reward out of all the available options.
Two Chlamydomonas OPR proteins stabilize chloroplast mRNAs encoding small subunits of photosystem II and cytochrome b6f
Authors: Wang Fei , Johnson Xenie , Cavaiuolo Marina , Bohne Alexandra‐Viola , Nickelsen Joerg , Vallon Olivier 
Published: April 2015

SummaryIn plants and algae, chloroplast gene expression is controlled by nucleus‐encoded proteins that bind to mRNAs in a specific manner, stabilizing mRNAs or promoting their splicing, editing, or translation. Here, we present the characterization of two mRNA stabilization factors of the green alga Chlamydomonas reinhardtii, which both belong to the OctotricoPeptide Repeat (OPR) family. MCG1 is necessary to stabilize the petG mRNA, encoding a small subunit of the cytochrome b6f complex, while MBI1 stabilizes the psbI mRNA, coding for a small subunit of photosystem II. In the mcg1 mutant, the small RNA footprint corresponding to the 5′‐end of the petG transcript is reduced in abundance. In both cases, the absence of the small subunit perturbs assembly of the cognate complex. Whereas PetG is essential for formation of a functional cytochrome b6f dimer, PsbI appears partly dispensable as a low level of PSII activity can still be measured in its absence. Thus, nuclear control of chloroplast gene expression is not only exerted on the major core subunits of the complexes, but also on small subunits with a single transmembrane helix. While OPR proteins have thus far been involved in translation or trans‐splicing of plastid mRNAs, our results expand the potential roles of this repeat family to their stabilization.
A two‐component enzyme complex is required for dolichol biosynthesis in tomato
Authors: Brasher Megan I. , Surmacz Liliana , Leong Bryan , Pitcher Jocelyn , Swiezewska Ewa , Pichersky Eran , Akhtar Tariq A. 
Published: April 2015

SummaryDolichol plays an indispensable role in the N‐glycosylation of eukaryotic proteins. As proteins enter the secretory pathway they are decorated by a ‘glycan’, which is preassembled onto a membrane‐anchored dolichol molecule embedded within the endoplasmic reticulum (ER). Genetic and biochemical evidence in yeast and animals indicate that a cis‐prenyltransferase (CPT) is required for dolichol synthesis, but also point to other factor(s) that could be involved. In this study, RNAi‐mediated suppression of one member of the tomato CPT family (SlCPT3) resulted in a ~60% decrease in dolichol content. We further show that the involvement of SlCPT3 in dolichol biosynthesis requires the participation of a distantly related partner protein, designated as CPT‐binding protein (SlCPTBP), which is a close homolog of the human Nogo‐B receptor. Yeast two‐hybrid and co‐immunoprecipitation assays demonstrate that SlCPT3 and its partner protein interact in vivo and that both SlCPT3 and SlCPTBP are required to complement the growth defects and dolichol deficiency of the yeast dolichol mutant, rer2∆. Co‐expression of SlCPT3 and SlCPTBP in yeast and in E. coli confirmed that dolichol synthase activity strictly requires both proteins. Finally, organelle isolation and in vivo localization of fluorescent protein fusions showed that both SlCPT3 and SlCPTBP localize to the ER, the site of dolichol accumulation and synthesis in eukaryotes.
The dynamic loss and gain of introns during the evolution of the Brassicaceae
Authors: Milia Giampiera , Camiolo Salvatore , Avesani Linda , Porceddu Andrea 
Published: April 2015

SummarySequence comparison allows the detailed analysis of evolution at the nucleotide and amino acid levels, but much less information is known about the structural evolution of genes, i.e. how the number, length and distribution of introns change over time. We constructed a parsimonious model for the evolutionary rate of intron loss (IL) and intron gain (IG) within the Brassicaceae and found that IL/IG has been highly dynamic, with substantial differences between and even within lineages. The divergence of the Brassicaceae lineages I and II marked a dramatic change in the IL rate, with the common ancestor of lineage I losing introns three times more rapidly than the common ancestor of lineage II. Our data also indicate a subsequent declining trend in the rate of IL, although in Arabidopsis thaliana introns continue to be lost at approximately the ancestral rate. Variations in the rate of IL/IG within lineage II have been even more remarkable. Brassica rapa appears to have lost introns approximately 15 times more rapidly than the common ancestor of B. rapa and Schenkiella parvula, and approximately 25 times more rapidly than its sister species Eutrema salsugineum. Microhomology was detected at the splice sites of several dynamic introns suggesting that the non‐homologous end‐joining and double‐strand break repair is a common pathway underlying IL/IG in these species. We also detected molecular signatures typical of mRNA‐mediated IL, but only in B. rapa.
The hotter the weather, the greater the infestation of Portulaca oleracea: opportunistic life‐history traits in a serious weed
Authors: Feng L , Chen G‐Q , Tian X‐S , Yang H‐M , Yue M‐F , Yang C‐H 
Published: April 2015

SummaryPortulaca oleracea, an r‐strategist, is one of the world's most troublesome weeds. During hot seasons, P. oleracea frequently becomes monodominant in choy sum (Brassica parachinensis) fields in Guangzhou city, southern China. Here, we studied the seasonal dynamics of P. oleracea's germinable soil seedbank, population density and above‐ground biomass in choy sum fields that had been cultivated continuously for several years. Using P. oleracea seeds collected from these fields, we tested seed dormancy, survival and germination, seedling growth and generation time. Portulaca oleracea occurred at high levels during the hot season, but its occurrence was low, and the germinable soil seedbank was much greater during the cold season. The weed's opportunistic characteristics allowed it to avoid freezing and to proliferate during optimal conditions. Portulaca oleracea's generation time was very flexible, as short as 31 days during the hot season, but longer than 100 days during the colder season. Seed dormancy tended to be shorter when the seeds were stored at a higher temperature. At a temperature of 35°C, both seed germination and seedling growth showed advantages over those of choy sum. Storage for one year at a temperature of −20°C or burial in a paddy field did not significantly reduce P. oleracea seed germination. Nevertheless, seed storage at a temperature of 15°C and soil coverage of 0.5 cm on top of the seeds significantly constrained seed germination. ‘Stale seedbed’ and/or coverage of the surface with soil are recommended during the hot season. However, rotation of rice and upland crops is not an efficient method for managing Portulaca oleracea infestation.