bluuebunny/crossref_metadata_2025_split huggingface dataset:
Essential role for TrpC5-containing extracellular vesicles in breast cancer with chemotherapeutic resistance
Authors: Ma Xin , Chen Zhen , Hua Dong , He Dongxu , Wang Linjun , Zhang Peng , Wang Junqi , Cai Yanfei , Gao Caiji , Zhang Xiaodong , Zhang Fangfang , Wang Teng , Hong Tingting , Jin Linfang , Qi Xiaowei , Chen Shuxian , Gu Xiaoting , Yang Dangtong , Pan Qiongxi , Zhu Yifei , Chen Yun , Chen Daozhen , Jiang Liwen , Han Xiaofeng , Zhang Yanyun , Jin Jian , Yao Xiaoqiang 
Published: April 2014

Significance
A critical challenge for chemotherapy is development of chemoresistance, but underlying molecular mechanisms remain unclear. In this study, we found that drug-resistant adriamycin-resistant human breast cancer cells possessed numerous transient receptor potential channel 5 (TrpC5) -containing extracellular vesicles (EVs) on the cell surface. Suppressing TrpC5 expression diminished the formation of EVs. Incubation of drug-sensitive recipient cells with EVs endowed recipients with drug-resistant properties. In both human samples and a mouse model of breast cancer, the expression of TrpC5 proteins was high in the tumor, and the levels of TrpC5-positive EVs were high in the circulation. These data suggest a critical role of TrpC5-containing EVs in the transfer of drug resistance. In the future, monitoring TrpC5-containing EVs in the circulation could potentially be used to predict the clinical outcome of chemotherapy.
Measurement of histidine pKavalues and tautomer populations in invisible protein states
Authors: Hansen Alexandar L. , Kay Lewis E. 
Published: April 2014

SignificanceElectrostatic interactions in proteins play significant roles in conferring stability and in dictating function. Histidine residues are particularly important because their side chains can serve as both acids and bases over the physiological pH range and as both hydrogen bond donors and acceptors. Solution NMR spectroscopy is a powerful method for studying these residues in highly populated ground-state conformers. Here we develop a strategy for extending such studies to sparsely populated, short-lived protein states that can also play a significant role in defining protein function. An application to an invisible folding intermediate of the Im7 protein is provided, where site-specific pKavalues of histidine residues have been determined that explain the strong pH-dependent stability differences between native and intermediate states.
Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR
Authors: Lee Soon Goo , Krishnan Hari B. , Jez Joseph M. 
Published: April 2014

Significance
Nitrogen nodules formed by the symbiosis of rhizobial microbes and legume roots are essential for fixation of nitrogen in the environment. As part of the symbiosis that leads to nodule formation, a series of changes in gene expression of the Rhizobium must occur. The protein NolR is a global regulator of rhizobial genes for symbiosis and nodulation. Here, we describe the three-dimensional structure of this transcription factor in unliganded and DNA bound forms. These structures show how NolR recognizes asymmetric DNA binding sites and reveal a previously unknown mechanism for conformational switching that alters the energetics of interaction to accommodate variable DNA sequences. Two models for the role of NolR in the regulation of nodulation and symbiosis genes are also proposed.
Cellular heterogeneity profiling by hyaluronan probes reveals an invasive but slow-growing breast tumor subset
Authors: Veiseh Mandana , Kwon Daniel H. , Borowsky Alexander D. , Tolg Cornelia , Leong Hon S. , Lewis John D. , Turley Eva A. , Bissell Mina J. 
Published: April 2014

Significance
Tumor heterogeneity is a poorly understood phenomenon. We lack biomarkers for identifying aggressive primary tumor subsets that give rise to metastases and impact early cancer detection and treatment. Many solid tumors are known to accumulate hyaluronan (HA), a glycosaminoglycan, which is also produced by the tumor cells themselves. We report a quantitative approach for uncovering breast cancer heterogeneity using fluorescent HA to detect differential binding patterns to CD44 and RHAMM/HMMR receptors. This approach permits identification of tumor-cell subsets that bind high levels of HA, and may be applicable to other ligands/receptors and disease models. Despite representing the invasive/metastatic subset of parental tumors, unexpectedly, the high HA-binding subset was slow-growing, and is thus likely to be a source of dormancy and relapse.
(Finite) statistical size effects on compressive strength
Authors: Weiss Jérôme , Girard Lucas , Gimbert Florent , Amitrano David , Vandembroucq Damien 
Published: April 2014

SignificanceLarge structures generally fail under stresses significantly lower than those of small ones. This is the size effect on strength, one of the oldest problems of engineering, already discussed by Leonardo da Vinci and Edmé Mariotte centuries ago. One classical explanation is the weakest-link hypothesis: The larger the “chain” is, the larger the probability to find a weak link whose breaking will set the failure of the whole chain. We show, however, that it is irrelevant in the case of compressive loading, a situation particularly crucial for, e.g., geotechnical problems. Interpreting compressive failure as a critical transition between an “intact” and a “failed” state, we quantitatively explain the size effects on compressive strength of materials such as concrete, rocks, coal, ice, or granular materials.
Prevention of influenza by targeting host receptors using engineered proteins
Authors: Connaris Helen , Govorkova Elena A. , Ligertwood Yvonne , Dutia Bernadette M. , Yang Lei , Tauber Sandra , Taylor Margaret A. , Alias Nadiawati , Hagan Robert , Nash Anthony A. , Webster Robert G. , Taylor Garry L. 
Published: April 2014

Significance
We have developed a new class of host-targeted biologics to prevent influenza by engineering multivalent carbohydrate-binding modules that bind with high affinity to sialic acid, the critical component of the influenza virus cell surface receptor. Mouse studies reveal a remarkable efficacy: a single 1-μg dose of the lead biologic given 7 d before a lethal challenge with 2009 pandemic H1N1 influenza virus provides complete protection. This new approach has the potential to be a front-line defense against any current and future influenza virus, overcoming viral escape to vaccines and antivirals. In addition, the biologics may have broader application against other respiratory pathogens.
Training-free atomistic prediction of nucleosome occupancy
Authors: Minary Peter , Levitt Michael 
Published: April 2014

Significance
Nucleosomes alter gene expression by preventing transcription factors from occupying binding sites along DNA. Conventional methods to predict nucleosome occupancy are trained on observed DNA sequence patterns. The method presented here uses physical principles and all-atom force fields to predict both nucleosome occupancy along genomic sequences as well as binding to known positioning sequences. Our method calculates the energy of both nucleosomal and linear DNA of the given sequence. Based on the DNA deformation energy, we accurately predict the in vitro occupancy profile observed experimentally for a 20,000-bp genomic region. DNA with all C bases methylated at the 5 position shows less variation of nucleosome binding: Strong binding is weakened and weak binding is strengthened compared with normal DNA.
Methylation protects microRNAs from an AGO1-associated activity that uridylates 5′ RNA fragments generated by AGO1 cleavage
Authors: Ren Guodong , Xie Meng , Zhang Shuxin , Vinovskis Carissa , Chen Xuemei , Yu Bin 
Published: April 2014

Significance
This study, for the first time to the authors' knowledge, establishes HUA1 enhancer 1 (HEN1) suppressor 1 as a 5′ fragment uridyl transferase and shows that uridylation triggers the degradation of 5′ fragments. This study also demonstrates that HEN1 suppressor 1 interacts with Argonaute (AGO1) and is able to act on microRNA substrates in the AGO1 complex. Furthermore, this study reveals that methylation protects microRNAs from AGO1-associated uridylation activity in plants. Because methylation and uridylation are conserved processes in small RNA pathways in plants and animals, this study may have a broad effect in related fields.
Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms
Authors: Schweikhard Volker , Meng Cong , Murakami Kenji , Kaplan Craig D. , Kornberg Roger D. , Block Steven M. 
Published: April 2014

Significance
In higher organisms, DNA is bound to proteins and tightly packed within the nucleus, leaving only certain regions accessible for gene expression. As the enzyme RNA polymerase II (RNAPII) travels along the DNA template synthesizing RNA, it must contend with forces generated by various obstacles, and some of these forces are known to produce transient pausing and even transcriptional arrest. How do organisms deal with such problems? Using optical-trapping technology, we performed a single-molecule study of RNAPII interactions with transcription factors TFIIS and TFIIF, which are involved in modulating and regulating transcriptional elongation. By applying controlled loads to RNAPII and combinations of these factors, we learned about the mechanisms by which pausing and arrest are overcome.
Conserved electron donor complex Dre2–Tah18 is required for ribonucleotide reductase metallocofactor assembly and DNA synthesis
Authors: Zhang Yan , Li Haoran , Zhang Caiguo , An Xiuxiang , Liu Lili , Stubbe JoAnne , Huang Mingxia 
Published: April 2014

Significance
Ribonucleotide reductases (RNR) play a critical role in supplying cellular deoxynucleotide pools. Nucleotide reduction by class Ia RNR requires a diferric-tyrosyl radical cofactor, which is a target of anticancer agents. How this essential cofactor is assembled in vivo is not well understood. We show here that a conserved protein complex composed of the Fe-S–requiring Dre2 and the diflavin-requiring Tah18, previously shown to donate electrons for Fe-S cluster assembly for proteins found in the cytosol and nucleus, also is required for RNR cofactor assembly. Deficiency in this complex leads to activation of both the DNA-damage checkpoint and the iron regulon, linking iron homeostasis to maintenance of genome stability. These findings may provide new insights into development of RNR-targeted therapeutics.
Consequences of Air Exposure on the Physiology and Behavior of Caught-and-Released Common Carp in the Laboratory and under Natural Conditions
Authors: Rapp Tobias , Hallermann Jan , Cooke Steven J. , Hetz Stefan K. , Wuertz Sven , Arlinghaus Robert 
Published: April 2014

Abstract
Specialized anglers of Common Carp Cyprinus carpio in Europe and increasingly in North America usually release trophy-sized fish, often following retention in carp sacks, to facilitate photographic memories. This practice is associated with extended air exposure. We assessed the impact of air exposure for a period of 10 min after capture and after an additional 9 h of retention in carp sacks on the physiology of small carp at two water temperatures (12°C and 22°C) under laboratory conditions. In a complementary field experiment with large carp, we also assessed the effects of air exposure on their physiology and additionally assessed the effects on tissue damage, postrelease behavior (i.e., movement and time rested), and survival. In the laboratory, plasma lactate increased by 24% during air exposure following simulated capture, and blood pH dropped by 0.16 units relative to a capture-only situation. Other physiological variables were unaffected by the treatment. In the field, air exposure after capture did not affect any physiological variables or indicators of tissue damage. During retention in carp sacks, fish recovered from capture, but subsequent air exposure caused a plasma lactate rise of 358% in the laboratory and 89% in the field experiment, and blood pH dropped by 0.38 units in the laboratory relative to that for the retained fish. In the field experiment, postrelease movement was significantly reduced in air-exposed fish, but normalized within 12 h. No mortalities occurred within 2 months postrelease. From a fish welfare perspective, our results suggest that photography should be conducted directly following capture without further retention in carp sacks as this approach is less deleterious to the fish. However, there is no benefit in doing so for maintaining carp populations because no substantial mortalities are to be expected. Overall, Common Carp are highly resilient to even extended air exposure.
Received April 26, 2013; accepted October 8, 2013
Black Bass and Crappie Use of Installed Habitat Structures in Table Rock Lake, Missouri
Authors: Allen Michael J. , Bush Shane C. , Vining Ivan , Siepker Michael J. 
Published: April 2014

Abstract
Reservoirs are important resources utilized by millions of freshwater anglers annually, but as reservoirs age the quality of the habitat that they provide for fish deteriorates. In 2007, a large-scale habitat improvement project began on Table Rock Lake, Missouri, with the goal of supplementing existing fish habitat in this large reservoir. Over 2,000 habitat structures composed of cedar, pine, hardwoods, stumps, and rocks were installed between 2007 and 2013. By means of scuba surveys, we evaluated the use of these structures by black bass Micropterus spp. and crappies Pomoxis spp. to determine whether it varied among fish species, fish sizes, and structure types. Black bass were observed utilizing all structure types but appeared to utilize hardwoods most. Covariates such as water depth and visibility at the structure confounded our analysis of black bass use, however, limiting our ability to clearly document differences in use. Crappies never used rock structures, and more crappies were observed on cedar structures than any other type. In Table Rock Lake, black bass were attracted to all structure types and crappies were attracted to all structure types except rock. Since fish use is similar across nearly all habitat types, other factors such as cost and installation times should be considered when planning habitat enhancement projects on large reservoirs.
Received August 12, 2013; accepted October 30, 2013
Changes to a Brown Trout Population after Introducing Steelhead in a Michigan Stream
Authors: Nuhfer Andrew J. , Wills Todd C. , Zorn Troy G. 
Published: April 2014

Abstract
We evaluated the effects of steelhead Oncorhynchus mykiss (migratory Rainbow Trout) introduction on the population dynamics of resident Brown Trout Salmo trutta from 1995 to 2008 in a small, low-gradient trout stream. Data on Brown Trout population density, survival, and growth were collected from the treatment section in Hunt Creek, Michigan, where adult steelhead were stocked each spring during 1998–2003, as well as from two reference stream reaches. The presence of steelhead had no apparent effect on the density of age-0 Brown Trout, but the mean density of all age-1 and older (age-1+) Brown Trout year-classes that interacted with juvenile steelhead of the same age was 46% lower than the density of age-1+ year-classes that did not interact with juvenile steelhead of the same age. No differences in density of age-1+ Brown Trout were detected in reference sections between the periods of steelhead presence or absence in the treatment section. Lower annual survival rates for year-classes of age-0 Brown Trout that interacted with steelhead in the Hunt Creek treatment section were the primary reason that density of age-1+ Brown Trout fell to nearly half the levels that existed before steelhead were introduced or after most steelhead had emigrated from the stream. Although our case study showed that the introduction of steelhead into a small, low-gradient stream resulted in lower densities of resident Brown Trout, upstream passage of steelhead into streams with high-quality habitat also offers tremendous potential to increase wild production of juvenile steelhead, thereby reducing fisheries managers’ reliance on hatchery-reared fish for stocking the Great Lakes.
Received August 16, 2013; accepted January 2, 2014
Spawning Dynamics and Associated Management Implications for Atlantic Cod
Authors: Zemeckis Douglas R. , Dean Micah J. , Cadrin Steven X. 
Published: April 2014

Abstract
Many stocks of Atlantic Cod Gadus morhua have been depleted due to interactions between overfishing and environmental variation. Stock declines were often accompanied by reductions in spawning diversity and collapses of population structure. Studying Atlantic Cod spawning activity can provide insights into the mechanisms involved in rebuilding. This paper reviews the existing literature on Atlantic Cod spawning dynamics, including habitat, timing, behavior, gamete production, larval survivorship, and fishery impacts. The associated implications for fisheries management are discussed, and critical information gaps are identified for inclusion in future research. Of primary importance for consideration by fisheries managers are the spatial and temporal extent of spawning, the behavior of spawners, and the reproductive contributions of older age-classes. The application of spawning closures as part of a multidisciplinary approach to fisheries management is advocated to prevent the disruption of spawning activity and the extirpation of semidiscrete spawning components. Integrating information on Atlantic Cod spawning dynamics into fisheries management plans will better account for reproductive processes, which is expected to promote rebuilding and decrease the risk of further collapses of population structure.
Received August 22, 2013; accepted December 17, 2013
Analysis of a putative auxin biosynthesis inhibitor, indole-3-oxoethylphosphonic acid, in Arabidopsis
Authors: Ishida Yosuke , Hayashi Ken-ichiro , Soeno Kazuo , Asami Tadao , Nakamura Shouichi , Suzuki Masashi , Nakamura Ayako , Shimada Yukihisa 
Published: April 2014

Abstract
Previously we identified indole-3-acetic acid (IAA) biosynthesis inhibitors that act on the conversion of l-tryptophan to indole-3-pyruvic acid in the IAA biosynthesis of Arabidopsis. In the present study, we synthesized a new compound, indole-3-oxoethylphosphonic acid (IOEP), and found that IOEP had an inhibitory effect on IAA biosynthesis in Arabidopsis. The results suggest that IOEP is a novel inhibitor of auxin biosynthesis in Arabidopsis.
Development of Captive Breeding and Seed Production Techniques for Giant River Catfish Sperata seenghala
Authors: Rahman M Aminur , Arshad A , Yusoff Fatimah Md , Amin S M N , Marimuthu K , Ara R 
Published: April 2014

Abstract
The Giant River Catfish Sperata seenghala, locally known as “Guizza Air” (and hereafter referred to as just Guizza), has significant aquacultural and conservational values, but closer monitoring of the fish is now badly needed. To protect the species from extinction, an experiment was undertaken to breed and produce seed of Guizza in a captive-rearing system. In our study, Guizza were successfully bred and the naturally produced fry were reared at different stocking densities in nine earthen nursery ponds having an area of 0.012 ha each with an average depth of 0.8 m. Three stocking densities were evaluated in three replicates each. Fry produced from natural propagation that were stocked at 100,000/ha were defined as treatment 1 (T1), those stocked at 150,000/ha as treatment 2 (T2), and those stocked at 200,000/ha as treatment 3 (T3). At stocking, all reared fry were of the same age-group with a mean±SD length and weight of 1.74±0.27 cm and 0.20±0.03 g, respectively. Fry in all the experimental ponds were reared with commercial Saudi Bangla (SABINCO) nursery feed (32.06% crude protein) for the first 14 d and starter-I (31.53% crude protein) for days 15–56. Growth (final weight, final length, weight gain, length gain, and specific growth rate) and survival of the fingerlings were significantly higher in T1 than in T2 and T3. Feed conversion rate was significantly lower in T1 than in T2 and T3. Moreover, the physicochemical measurements and plankton population of the pond water were within the optimal level for fish culture, with plankton abundance being higher in T1 than in T2 and T3. Consistently higher net benefits were obtained from T1 than from T2 and T3. Hence, of the three stocking densities, 100,000 fry/ha was the most suitable density for rearing Guizza fingerlings in nursery ponds.
The Influence of Dietary Lysine on Yellow Perch Maturation and the Quality of Sperm
Authors: Kwasek Karolina , Dabrowski Konrad , Nynca Joanna , Wojno Michal , Wick Macdonald 
Published: April 2014

Abstract
The objective of the present study was to determine whether lysine (Lys) supplementation influences the maturation and sperm quality of Yellow Perch Perca flavescens. Juveniles raised on a formulated commercial diet and weighing approximately 75 g each were randomly distributed into six 400-L tanks. This experiment included two wheat-gluten-based diets in triplicate: (−) Lys (Lys-deficient) and (+) Lys (Lys-supplemented; 2.23% in dry feed) diets. In addition, 16 control fish were kept under identical conditions and fed a commercial diet. The weight of males was larger in the control group than in the (+) Lys and (−) Lys groups. The sperm concentration was significantly higher in the control and (+) Lys groups than in the (−) Lys group. Sperm motility was lower in the (−) Lys group than in the control and (+) Lys groups. The control group had significantly higher protein concentration in its seminal plasma than did the (+) Lys and (−) Lys groups. The seminal plasma trypsin inhibitor activity showed the same trend. The seminal plasma free amino acid concentrations of arginine, methionine, threonine, glutamine, alanine, and glycine differed significantly among treatments. This is the first report demonstrating the negative effect of dietary lysine level in plant-protein-based diets on reproduction in fish.
Critical Thermal Maxima of Two Geographic Strains of Channel and Hybrid Catfish
Authors: Stewart Heather A , Allen Peter J 
Published: April 2014

Abstract
Critical thermal maxima have been used extensively to provide physiologically and ecologically valuable reference points that identify early signs of thermal stress. In catfish pond culture, daily temperature maxima up to 36°C and daily fluctuations of as much as 6°C are observed. These extreme conditions will probably be exacerbated by the effects of global climate change. Channel Catfish Ictalurus punctatus have a broad natural distribution from southern Canada to northern Mexico. If regional genetic differences could cause strains with a southern distribution to have greater thermal tolerance than strains with a northern distribution, and consequently a greater critical thermal maximum, then hybrid catfish (Channel Catfish × Blue Catfish I. furcatus) strains might be expected to have greater critical thermal maxima than their respective Channel Catfish strains because Blue Catfish have a more southern range of distribution. To examine this, we quantified differences of acute thermal tolerance in two geographically distinct strains of Channel Catfish and their hybrid crosses with an industry standard strain of Blue Catfish. The catfish were subjected to water temperature increases of 2.0 ± 0.1°C · h−1 until they lost equilibrium. Standard length, which ranged from 162 to 320 mm, had a significant effect on survival, survival being greater in larger fish. The critical thermal maximum ranged from 38.6°C to 40.3°C. Southern Channel Catfish tolerated higher temperatures than northern Channel Catfish did, and both strains of Channel Catfish tolerated higher temperatures than their hybrid catfish strains did. This study indicates that geographically distinct catfish strains differ in acute thermal tolerance and suggests heritability for this trait, as evidenced by similar responses in Channel Catfish and their corresponding hybrid crosses with Blue Catfish.