bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trait stacking via targeted genome editing
Authors: Ainley William M. , Sastry‐Dent Lakshmi , Welter Mary E. , Murray Michael G. , Zeitler Bryan , Amora Rainier , Corbin David R. , Miles Rebecca R. , Arnold Nicole L. , Strange Tonya L. , Simpson Matthew A. , Cao Zehui , Carroll Carley , Pawelczak Katherine S. , Blue Ryan , West Kim , Rowland Lynn M. , Perkins Douglas , Samuel Pon , Dewes Cristie M. , Shen Liu , Sriram Shreedharan , Evans Steven L. , Rebar Edward J. , Zhang Lei , Gregory Phillip D. , Urnov Fyodor D. , Webb Steven R. , Petolino Joseph F. 
Published: August 2013

SummaryModern agriculture demands crops carrying multiple traits. The current paradigm of randomly integrating and sorting independently segregating transgenes creates severe downstream breeding challenges. A versatile, generally applicable solution is hereby provided: the combination of high‐efficiency targeted genome editing driven by engineered zinc finger nucleases (ZFNs) with modular ‘trait landing pads’ (TLPs) that allow ‘mix‐and‐match’, on‐demand transgene integration and trait stacking in crop plants. We illustrate the utility of nuclease‐driven TLP technology by applying it to the stacking of herbicide resistance traits. We first integrated into the maize genome an herbicide resistance gene, pat, flanked with a TLP (ZFN target sites and sequences homologous to incoming DNA) using WHISKERS™‐mediated transformation of embryogenic suspension cultures. We established a method for targeted transgene integration based on microparticle bombardment of immature embryos and used it to deliver a second trait precisely into the TLP via cotransformation with a donor DNA containing a second herbicide resistance gene, aad1, flanked by sequences homologous to the integrated TLP along with a corresponding ZFN expression construct. Remarkably, up to 5% of the embryo‐derived transgenic events integrated the aad1 transgene precisely at the TLP, that is, directly adjacent to the pat transgene. Importantly and consistent with the juxtaposition achieved via nuclease‐driven TLP technology, both herbicide resistance traits cosegregated in subsequent generations, thereby demonstrating linkage of the two independently transformed transgenes. Because ZFN‐mediated targeted transgene integration is becoming applicable across an increasing number of crop species, this work exemplifies a simple, facile and rapid approach to trait stacking.
Development of AS‐PCR marker based on a key mutation confirmed by resequencing of Wx‐mp in Milky Princess and its application in japonica soft rice (Oryza sativa L.) breeding
Authors: Yang Jie , Wang Jun , Fan Fang‐Jun , Zhu Jin‐Yan , Chen Tao , Wang Cai‐Lin , Zheng Tian‐Qing , Zhang Jian , Zhong Wei‐Gong , Xu Jian‐Long 
Published: August 2013

AbstractSoft rice with low amylose content (AC) ranging by 5–15% is a unique type with special eating and appearance quality and has become popular in the rice market. We resequenced the Wx‐mp, a key allele from Milky Princess, a Japanese low AC variety, and found that the +473 mutation in exon 4 is the key mutation in both Wx‐mp and its ancestor allele, Wx‐mq from Milky Queen. Based on this functional mutation, an allele‐specific PCR (AS‐PCR) marker was developed and proven in a breeding population derived from a cross between a Chinese late variety Nan Keng 46 (Wx‐mp/Wx‐mp) and an early line Ning 63121(Wx‐b/Wx‐b). Based on the marker‐aided selection by our newly developed AS‐PCR marker for Wx‐mp and the known ST10 marker for Stvb‐i, a total of 12 Wx‐mp homozygotes were selected from 198 F2 progenies, and four of them were immune to rice stripe virus (RSV) with averagely 11.3 days earlier heading than Nan Keng 46 without significant change in grain yield.
Identification of glycogen synthase kinase 3α as a therapeutic target in melanoma
Authors: Madhunapantula SubbaRao V. , Sharma Arati , Gowda Raghavendra , Robertson Gavin P. 
Published: August 2013

SummaryDeregulated expression or activity of kinases can lead to melanomas, but often the particular kinase isoform causing the effect is not well established, making identification and validation of different isoforms regulating disease development especially important. To accomplish this objective, an siRNA screen was undertaken that which identified glycogen synthase kinase 3α (GSK3α) as an important melanoma growth regulator. Melanocytes and melanoma cell lines representing various stages of melanoma tumor progression expressed both GSK3α and GSK3β, but analysis of tumors in patients with melanoma showed elevated expression of GSK3α in 72% of samples, which was not observed for GSK3β. Furthermore, 80% of tumors in patients with melanoma expressed elevated levels of catalytically active phosphorylated GSK3α (pGSK3αY279), but not phosphorylated GSK3β (pGSK3βY216). siRNA‐mediated reduction in GSK3α protein levels reduced melanoma cell survival and proliferation, sensitized cells to apoptosis‐inducing agents and decreased xenografted tumor development by up to 56%. Mechanistically, inhibiting GSK3α expression using siRNA or the pharmacological agent AR‐A014418 arrested melanoma cells in the G0/G1 phase of the cell cycle and induced apoptotic death to retard tumorigenesis. Therefore, GSK3α is a key therapeutic target in melanoma.
Reproductive ecology and genetic variability in natural populations of the wild potato, Solanum kurtzianum
Authors: Marfil C. F. , Masuelli R. W. 
Published: August 2013

AbstractThe cultivated potato (Solanum tuberosum ssp. tuberosum) has more than 200 related wild species distributed along the Andes, adapted to a wide range of geographical and ecological areas. Since the last century, several collection expeditions were carried out to incorporate genetic variability into the potato germplasm around the world. However, little is known about the reproductive ecology and genetic population structure of natural potato population from field studies. The aim of this work is to study, in the field, the genetic variability and reproductive strategies of populations of one of the most widely distributed potato species in Argentina, Solanum kurtzianum, growing in Mendoza province. AFLP markers showed that the genetic variability is mainly present among plants within populations, indicating that in the sampled populations, sexual reproduction is more relevant than clonal multiplication (by tubers). Additional evidence was obtained evaluating the genetic diversity in populations with a distribution in patches, where several genotypes were always detected. From a field study performed in the Villavicencio Natural Reserve, we found that the average number of plump seeds per fruit was 94.3, identified and calculated the foraging distance of four insect pollinators, and demonstrated the seed dispersal by storm water channels. We argue that the breeding system, the two modes of reproduction and the ecological interaction described here may have a prominent role in determining the genetic structure of S. kurtzianum populations, and discuss the importance of field studies on population genetics, reproductive biology and ecology to design collections and conservation strategies.
The comparative reproductive biology of a tetraploid species,Hedychium villosum, and its diploid progenitorH. tenuiflorum(Zingiberaceae)
Authors: Gao J. Y. , Liu Q. , Li Q. J. 
Published: August 2013

AbstractThe evolutionary advantages of polyploidy may result from a number of changes in floral traits and breeding system, which may enable polyploids to exploit new habitats and become widespread. In this study, we comparatively investigated the floral biology of the tetraploid speciesHedychium villosumand its diploid progenitorH. tenuiflorum, to assess reproductive divergence between the two species. The results showed that flowers of the tetraploid species last longer and produce more nectar than did diploid species. The flowering times of the two species did not overlap at all. Observations of floral visitors in natural populations demonstrated that butterflies and hawkmoths were effective pollinators of both species, but there was a significant difference in butterfly and hawkmoth assemblages between the two species. The hand‐pollination experiments and pollen tube growth experiments suggested that diploidH. tenuiflorumwas self‐incompatible, while tetraploidH. villosumwas completely self‐compatible.H. villosumhas a much wider distribution range and occupies more diverse habitats thanH.tenuiflorum. Polyploidisation may enable tetraploidH. villosumto exploit new habitats previously unavailable to diploidH.tenuiflorum.
Identification, characterisation and molecular modelling of two AP endonucleases from base excision repair pathway in sugarcane provide insights on the early evolution of green plants
Authors: Maira N. , Torres T. M. , de Oliveira A. L. , de Medeiros S. R. B. , Agnez‐Lima L. F. , Lima J. P. M. S. , Scortecci K. C. 
Published: August 2013

AbstractUnlike bacteria and mammals, plant DNA repair pathways are not well characterised, especially in monocots. The understanding of these processes in the plant cell is of major importance, since they may be directly involved in plant acclimation and adaptation to stressful environments. Hence, two sugarcane ESTs were identified as homologues of AP endonuclease from the base‐excision repair pathway: ScARP1 and ScARP3. In order to understand their probable function and evolutionary origin, structural and phylogenetic studies were performed using bioinformatics approaches. The two predicted proteins present a considerable amino acid sequence similarity, and molecular modelling procedures indicate that both are functional, since the main structural motifs remain conserved. However, inspection of the sort signal regions on the full‐length cDNAs indicated that these proteins have a distinct organelle target. Furthermore, variances in their promoter cis‐element motifs were also found. Although the mRNA expression pattern was similar, there were significant differences in their expression levels. Taken together, these data raise the hypothesis that the ScARP is an example of a probable gene duplication event that occurred before monocotyledon/dicotyledon segregation, followed by a sub‐functionalisation event in the Poaceae, leading to new intracellular targeting and different expression levels.
Root antioxidant responses of two Pisum sativum cultivars to direct and induced Fe deficiency
Authors: Jelali N. , Donnini S. , Dell'Orto M. , Abdelly C. , Gharsalli M. , Zocchi G. 
Published: August 2013

AbstractThe contribution of antioxidant defence systems in different tolerance to direct and bicarbonate‐induced Fe deficiency was evaluated in two pea cultivars (Kelvedon, tolerant and Lincoln, susceptible). Fe deficiency enhanced lipid peroxidation and H2O2 concentration in roots of both cultivars, particularly in the sensitive one grown under bicarbonate supply. The results obtained on antioxidant activities (SOD, CAT, POD) suggest that H2O2 accumulation could be due to an overproduction of this ROS and, at the same time, to a poor capacity to detoxify it. Moreover, under bicarbonate supply the activity of POD isoforms was reduced only in the sensitive cultivar, while in the tolerant one a new isoform was detected, suggesting that POD activity might be an important contributor to pea tolerance to Fe deficiency. The presence of bicarbonate also resulted in stimulation of GR, MDHAR and DHAR activities, part of the ASC‐GSH pathway, which was higher in the tolerant cultivar than in the sensitive one. Overall, while in the absence of Fe only slight differences were reported between the two cultivars, the adaptation of Kelvedon to the presence of bicarbonate seems to be related to its greater ability to enhance the antioxidant response at the root level.
Association of CXCL12 and CXCR4 gene polymorphisms with the susceptibility and prognosis of renal cell carcinoma
Authors: Cai C. , Wang L.‐H. , Dong Q. , Wu Z.‐J. , Li M.‐Y. , Sun Y.‐H. 
Published: August 2013

AbstractCXCL12 and its unique receptor CXCR4, play important roles in inflammation and cancer metastasis. This study was undertaken to investigate the association of CXCL12 and CXCR4 polymorphisms with risk and prognosis of renal cell carcinoma (RCC) in the Chinese population. Blood was collected from 322 RCC patients and 402 healthy controls. The CXCL12 rs1801157G/A polymorphism and CXCR4 rs2228014C/T polymorphism were genotyped by polymerase chain reaction‐restriction fragment length polymorphism. Results showed that prevalence of CXCL12 rs1801157AA genotype was significantly increased in RCC cases than in controls [odds ratio (OR) = 3.07, 95% confidence interval (CI), 1.98–5.46, P = 6.1 × 10−6; data were adjusted for age and sex]. Similarly, subjects carrying CXCR4 rs2228014CT or TT genotypes showed significantly high risk of RCC (OR = 1.77, 95% CI, 1.28–2.71, P = 0.0003; OR = 4.01, 95% CI, 1.87–9.12, P = 7.8 × 10−4, respectively; data were adjusted for age and sex). When analyzing the survival time of RCC, patients with CXCL12 rs1801157AA genotype revealed significantly shorter survival time compared to cases with CXCL12 rs1801157GG and GA genotypes (P = 0.001), whereas RCC patients carrying CXCR4 rs2228014CT and TT genotypes showed shorter survival time than the wild type (P = 0.002). These data indicated that CXCL12 and CXCR4 may be new risk factors for RCC and could be used as prognostic markers for this malignancy.
Distribution patterns of variability for 18 immune system genes in Amerindians – relationship with history and epidemiology
Authors: Lindenau J. D. , Salzano F. M. , Guimarães L. S. P. , Callegari‐Jacques S. M. , Hurtado A. M. , Hill K. R. , Petzl‐Erler M. L. , Tsuneto L. T. , Hutz M. H. 
Published: August 2013

AbstractNative American populations generally have a higher prevalence of infectious diseases than non‐Native populations and this fact can induce different pressures in their immune system. We investigated the patterns of population differentiation (FST) of 32 polymorphisms related to adaptive immune response in four Native American populations (Aché, Guarani‐Kaiowá, Guarani‐Ñandeva and Kaingang), and the results were compared with the three major world population data [Yoruba of Ibadan, Nigeria (YRI), Utah residents with northern and Western Europe ancestry (CEU) and Han Chinese of Beijing, China (CHB)] available in the HapMap database. The Aché clearly differentiated from the other Amerindians, but when all Native Americans were compared with the samples of other ethnic groups the lowest difference (0.08) was found with CHB (Asians), the second lowest (0.15) with YRI (Africans) and the most marked with CEU (European‐derived). The considerable intra and interethnic differences found can be explained both in terms of diverse evolutionary distances and more recent environmental pathogen exposures; and they should be appropriately considered prior to any specific public health action.
Algorithm for the diagnosis of smear‐negative pulmonary tuberculosis in high‐incidence resource‐constrained settings
Authors: Soto Alonso , Solari Lely , Agapito Juan , Gotuzzo Eduardo , Accinelli Roberto , Vargas Dante , Acurio Vilma , Matthys Francine , Van der Stuyft Patrick 
Published: August 2013

AbstractObjectivesDiagnosis of smear‐negative pulmonary tuberculosis (SNPT) remains a challenge, particularly in resource‐constrained settings. We evaluated a diagnostic algorithm that combines affordable laboratory tools and a clinical prediction rule (CPR).MethodsWe derived, based on published evidence, a diagnostic algorithm for SNPT. Sputum concentration constitutes its first step. In suspects with negative results, SNPT probability is classified with a CPR as low (excluded), high (confirmed) or intermediate. For intermediate patients, sputum Middlebrook 7H9 liquid culture is performed, and they are assessed after 2 weeks. If clinically deteriorated, with still negative liquid culture, bronchoscopy is offered. Otherwise, results of Middlebrook 7H9 culture are awaited. We prospectively evaluated this algorithm against a reference standard of solid and liquid cultures in two reference hospitals in Lima, Peru.Results670 SNPT suspects were included from September 2005 to March 2008. The prevalence of SNPT was 27% according to the reference standard. The algorithm's overall accuracy was 0.94 (95% CI 0.91–0.95), its sensitivity was 0.88 (95% CI 0.82–0.92) and its specificity, 0.96 (95% CI 0.94–0.98). Sputum concentration, the CPR, Middlebrook 7H9 sputum culture and bronchoscopic samples defined a diagnosis of SNPT according to the algorithm in 57 (37%), 25 (16%), 63 (41%) and 8(5%) of patients, respectively. 65% of patients were diagnosed within 3 weeks.ConclusionsThe algorithm was accurate for SNPT diagnosis. Sputum concentration, CPR and selective Middlebrook 7H9 culture are essential components.
Studies on the inactivation of human parvovirus 4
Authors: Baylis Sally A. , Tuke Philip W. , Miyagawa Eiji , Blümel Johannes 
Published: August 2013

BackgroundHuman parvovirus 4 (PARV4) is a novel parvovirus, which like parvovirus B19 (B19V) can be a contaminant of plasma pools used to prepare plasma‐derived medicinal products. Inactivation studies ofB19Vhave shown that it is more sensitive to virus inactivation strategies than animal parvoviruses. However, inactivation ofPARV4 has not yet been specifically addressed.Study Design and MethodsTreatment of parvoviruses by heat or low‐pHconditions causes externalization of the virus genome. Using nuclease treatment combined with real‐time polymerase chain reaction, the extent of virusDNAexternalization was used as an indirect measure of the inactivation ofPARV4, B19V, and minute virus of mice (MVM) by pasteurization of albumin and by low‐pHtreatment. Infectivity studies were performed in parallel forB19VandMVM.ResultsPARV4 showed greater resistance to pasteurization and low‐pHtreatment thanB19V, althoughPARV4 was not as resistant asMVM. There was a 2‐ to 3‐log reduction of encapsidatedPARV4DNAafter pasteurization and low‐pHtreatment. In contrast,B19Vwas effectively inactivated whileMVMwas stable under these conditions. Divalent cations were found to have a stabilizing effect onPARV4 capsids. In the absence of divalent cations, even at neutralpH, there was a reduction ofPARV4 titer, an effect not observed forB19VorMVM.ConclusionIn the case of heat treatment and incubation at lowpH, PARV4 shows intermediate resistance when compared toB19VandMVM. Divalent cations seem important for stabilizingPARV4 virus particles.
Effects of Inoculum Additions in the Presence of a Preestablished Arbuscular Mycorrhizal Fungal Community
Authors: Janoušková Martina , Krak Karol , Wagg Cameron , Štorchová Helena , Caklová Petra , Vosátka Miroslav 
Published: August 2013

ABSTRACT
Communities of arbuscular mycorrhizal fungi (AMF) are crucial for promoting plant productivity in most terrestrial systems, including anthropogenically managed ecosystems. Application of AMF inocula has therefore become a widespread practice. It is, however, pertinent to understand the mechanisms that govern AMF community composition and their performance in order to design successful manipulations. Here we assess whether the composition and plant growth-promotional effects of a synthetic AMF community can be altered by inoculum additions of the isolates forming the community. This was determined by following the effects of three AMF isolates, each inoculated in two propagule densities into a preestablished AMF community. Fungal abundance in roots and plant growth were evaluated in three sequential harvests. We found a transient positive response in AMF abundance to the intraspecific inoculation only in the competitively weakest isolate. The other two isolates responded negatively to intra- and interspecific inoculations, and in some cases plant growth was also reduced. Our results suggest that increasing the AMF density may lead to increased competition among fungi and a trade-off with their ability to promote plant productivity. This is a key ecological aspect to consider when introducing AMF into soils.
The D3 Bacteriophage α-Polymerase Inhibitor (Iap) Peptide Disrupts O-Antigen Biosynthesis through Mimicry of the Chain Length Regulator Wzz in Pseudomonas aeruginosa
Authors: Taylor Véronique L. , Udaskin Molly L. , Islam Salim T. , Lam Joseph S. 
Published: August 2013

ABSTRACT

Lysogenic bacteriophage D3 causes seroconversion of
Pseudomonas aeruginosa
PAO1 from serotype O5 to O16 by inverting the linkage between O-specific antigen (OSA) repeat units from α to β. The OSA units are polymerized by Wzy to modal lengths regulated by Wzz
1
and Wzz
2
. A key component of the D3 seroconversion machinery is the
i
nhibitor of
α
-
p
olymerase (Iap) peptide, which is able to solely suppress α-linked long-chain OSA production in
P. aeruginosa
PAO1. To establish the target specificity of Iap for Wzy
α
, changes in OSA phenotypes were examined via Western immunoblotting for
wzz
1
and
wzz
2
single-knockout strains, as well as a
wzz
1
wzz
2
double knockout, following the expression of
iap
from a tuneable vector. Increased induction of Iap expression completely abrogated OSA production in the
wzz
1
wzz
2
double mutant, while background levels of OSA production were still observed in either of the single mutants. Therefore, Iap inhibition of OSA biosynthesis was most effective in the absence of both Wzz proteins. Sequence alignment analyses revealed a high degree of similarity between Iap and the first transmembrane segment (TMS) of either Wzz
1
or Wzz
2
. Various topology prediction analyses of the Iap sequence consistently predicted the presence of a single TMS, suggesting a propensity for Iap to insert itself into the inner membrane (IM). The compromised ability of Iap to abrogate Wzy
α
function in the presence of Wzz
1
or Wzz
2
provides compelling evidence that inhibition occurs after Wzy
α
inserts itself into the IM and is achieved through mimicry of the first TMS from the Wzz proteins of
P. aeruginosa
PAO1.
Causes and Predictability of the 2012 Great Plains Drought
Authors: Hoerling M. , Eischeid J. , Kumar A. , Leung R. , Mariotti A. , Mo K. , Schubert S. , Seager R. 
Published: August 2013

Central Great Plains precipitation deficits during May–August 2012 were the most severe since at least 1895, eclipsing the Dust Bowl summers of 1934 and 1936. Drought developed suddenly in May, following near-normal precipitation during winter and early spring. Its proximate causes were a reduction in atmospheric moisture transport into the Great Plains from the Gulf of Mexico. Processes that generally provide air mass lift and condensation were mostly absent, including a lack of frontal cyclones in late spring followed by suppressed deep convection in the summer owing to large-scale subsidence and atmospheric stabilization.Seasonal forecasts did not predict the summer 2012 central Great Plains drought development, which therefore arrived without early warning. Climate simulations and empirical analysis suggest that ocean surface temperatures together with changes in greenhouse gases did not induce a substantial reduction in sum mertime precipitation over the central Great Plains during 2012. Yet, diagnosis of the retrospective climate simulations also reveals a regime shift toward warmer and drier summertime Great Plains conditions during the recent decade, most probably due to natural decadal variability. As a consequence, the probability of the severe summer Great Plains drought occurring may have increased in the last decade compared to the 1980s and 1990s, and the so-called tail risk for severe drought may have been heightened in summer 2012. Such an extreme drought event was nonetheless still found to be a rare occurrence within the spread of 2012 climate model simulations. The implications of this study's findings for U.S. seasonal drought forecasting are discussed.