bluuebunny/crossref_metadata_2025 huggingface dataset:
87 IS HOXA10 EXPRESSION REGULATED THROUGH PROMOTER DNA METHYLATION IN THE PIG?
Authors: Pistek V. L. , Fürst R. W. , Bauersachs S. , Kliem H. S. , Meyer H. H. D. , Ulbrich S. E.
Published: December 2012

In utero and early postnatal exposure to exogenous oestrogens may alter the epigenome, possibly influencing health later in life. The reproductive organs are the main target of oestrogens. Uterine HOXA10 expression and promoter DNA methylation have been shown to be sensitive to endocrine disruptors in rodents. In the endometrium of pigs, in vitro exposure to estradiol-17β resulted in an increase of HOXA10 mRNA and protein expression, and a regulation for HOXA10 has also been shown during early pregnancy. However, it is unclear whether modification in promoter DNA methylation was involved herein. In the present study, we investigated the effect of oral estradiol-17β supplementation to pregnant pigs from Day 0 until delivery (0, 0.05, 10, and 1000 µg kg–1 per day; n = 8–12/group) on HOXA10 expression and promoter DNA methylation in the uterus of prepubertal and the endometrium of postpubertal porcine offspring. In addition, endometrial samples from 2 physiological situations were analyzed, namely the oestrous cycle at Day 0, 3, 6, 12, and 18 (n = 6/day), and early pregnancy at Day 10, 12, and 14 (n = 4/day). Furthermore, different reproductive and nonreproductive tissues from pre- and postpubertal untreated animals were investigated (n = 2/tissue). Gene expression was measured using RT-qPCR. The DNA was first bisulfite converted, amplified by using methylation-sensitive high-resolution melting qPCR, followed by pyrosequencing. Statistical analyses were conducted using one-way ANOVA. In utero estradiol-17β exposure did neither alter HOXA10 expression compared to the control group nor HOXA10 promoter DNA methylation in pre- and postpubertal porcine offspring, respectively. Because the prepubertal group displayed higher HOXA10 mRNA expression than did postpubertal animals, while DNA methylation was lower in the younger animals, a potential role of DNA methylation may be assumed. During the oestrous cycle, HOXA10 expression was significantly regulated (P < 0.001); it was highest at oestrous (Day 0), decreased 2.5-fold by Day 3, and increased again 1.5-fold by Day 6. In early pregnant sows, endometrial HOXA10 transcripts were significantly higher at Day 14 (P = 0.031) compared with nonpregnant controls. In both settings promoter DNA methylation did not change. Regarding HOXA10 expression between different tissues, the DNA methylation at one CpG site was significantly correlated with mRNA expression in prepubertal animals (R2 = 0.582) but not in the adult (R2 = 0.004). We conclude that HOXA10 expression is regulated through other mechanisms than is promoter DNA methylation in adult sows. Still, in prepubertal pigs promoter DNA methylation may influence HOXA10 expression. In utero estradiol-17β exposure did not affect HOXA10 expression and promoter DNA methylation.
96 EXPRESSION OF THE LONG FORM OF THE LEPTIN RECEPTOR IN BOVINE OVIDUCT EPITHELIAL, UTERINE EPITHELIAL, AND BLASTOCYST-STAGE EMBRYOS
Authors: Gentry G. T. , Gentry L. R. , Lynn J. W. , Godke R. A.
Published: December 2012

Critical reproductive events of animals are affected via metabolic cues that directly modulate the hypothalamic-pituitary-gonadal axis. The adipose-derived 146-amino-acid protein-hormone leptin has been associated with puberty and reproduction in many mammals and may be of critical importance in the regulation of reproduction. Leptin receptors are expressed in the brain, pituitary, and gonads, and there is growing evidence that leptin may be required for normal embryonic implantation and development in some animals. To date 6 isoforms of the leptin receptor have been identified; the long form (Ob-Rb) is the only isoform to be associated with signal transduction. The objective of this experiment was to test the hypothesis that the Ob-Rb isoform is expressed in cultured bovine oviduct and uterine epithelial cells, in vivo-derived mid-luteal uterine biopsies, and expanded bovine blastocyst-stage embryos. For cells, cell lines from mid-luteal abattoir-derived reproductive tracts (n = 5) were used; for uterine biopsies (n = 20), biopsies were collected from both uterine horns at the greater curvature from mature beef cows (n = 4) in mid-luteal phase; expanded IVP blastocyst-stage embryos (n = 40) were produced from abattoir-derived ovaries. For fluorescence microscopy samples were incubated in rabbit anti-human leptin receptor (#4781-L, Linco Research, St. Charles, MO) followed by Alexa Fluor 488 anti-rabbit IgG (#A-11008, Molecular Probes, Carlsbad, CA). We confirmed that the Ob-Rb isoform is expressed in both oviductal and uterine in vitro-cultured epithelial cells and uterine biopsies. All oviduct but not all uterine-cultured epithelial cells were immunopositive for the Ob-Rb isoform. All uterine biopsies were positive for the Ob-Rb isoform along the luminal side of the uterine endometrium with an apparent lack of staining occurring in myometrial tissue. Moreover, we demonstrated that all bovine blastocysts were immunopositive with staining occurring within the trophoblast cell type but not the inner cell mass. These results show for the first time that bovine oviduct and uterine epithelial cells express the long form of the leptin receptor and support earlier findings that blastocyst-stage embryos contain Ob-Rb isoforms. This suggests that the Ob-Rb isoform is a component of the bovine maternal-embryonic complex; however, its function in pre-implantation embryo development remains to be clarified.
97 THE REGULATION OF UTERINE CONTRACTION BY ENDOCRINE-DISRUPTING CHEMICALS IN RATS
Authors: An B. S. , Jeung E. B.
Published: December 2012

Environmental oestrogens, class of endocrine-disrupting chemicals, are defined as compounds that bind the oestrogen receptors and elicit or modulate an ER-mediated response. Examples of suspected environmental oestrogenic chemicals include plastic components such as bisphenol A (BPA) and some components of detergents and their biodegradation products, 4-octylphenol (OP). The uterus frequently contracts throughout the entire menstrual cycle, and these contractions have been termed endometrial waves or contractile waves. The balanced contractile waves play an important role in regulating oestrus or menstrual cycles, implantation, maintaining pregnancy, and parturition. The uterine contraction has been known to be regulated by contraction-associated proteins such as oxytocin, oxytocin receptor (OTR), connexin 43, prostaglandin F2 alpha receptor (FP), and 15-hydroxy prostaglandin dehydrogenase (PDGH). Endogenous steroid hormones including oestrogen and progesterone have been shown to regulate contraction-associated proteins and, thereby, modify uterine contraction. Forty female immature rats were divided into 8 groups, each group composed of 5 rats. They were injected subcutaneously daily for 3 days with BPA and OP at doses of 20, 100, and 500 mg kg–1 of BW per day; 17β-estradiol (E2, 40 µg kg–1 per day) was a positive control. After 24 h of the final treatment, the rats were euthanized and the uteri were collected for further experiments. Total RNA and protein were extracted from uteri. The mRNA expressions for CaBP-9k, oxytocin, OTR, FP, and PDGH were determined by real-time PCR with specific primers, and the protein levels were examined by Western blot assay. The data were analyzed using a one-way ANOVA. The P-values <0.05 were considered statistically significant. The treatment of oestrogenic compounds significantly regulated the contraction-associated proteins. First, the mRNA levels of CaBP-9k that is a biomarker for evaluating oestrogenicity in the rats were significantly induced by positive control, E2. Chemicals OP and BPA at doses of 100 and 500 mg kg–1 also induced the gene expression of CaBP-9k. Oxytocin and OTR were highly augmented by OP (40 fold) and BPA (6-fold) at a dose of 500 mg kg–1 compared with control, whereas PDGH was moderately upregulated by the chemicals. Interestingly, FP was decreased by E2 and high doses of OP and BPA. These results showed that exposure of immature rats to BPA and OP regulated expression of oxytocin, OTR, PDGH, and FP genes in the rat uterus. Taken together, uterine contraction and physiological conformational change of the uterus were affected by exposure to oestrogenic endocrine-disrupting chemicals. Because balanced contractile activity of the uterus maintains regular menstrual cycles, pregnancy, and labor, alteration of the contractility raised by oestrogenic compounds may cause severe adverse effects on the female reproductive system.
How national context, project design, and local community characteristics influence success in community-based conservation projects
Authors: Brooks Jeremy S. , Waylen Kerry A. , Borgerhoff Mulder Monique
Published: December 2012

Community-based conservation (CBC) promotes the idea that conservation success requires engaging with, and providing benefits for, local communities. However, CBC projects are neither consistently successful nor free of controversy. Innovative recent studies evaluating the factors associated with success and failure typically examine only a single resource domain, have limited geographic scope, consider only one outcome, or ignore the nested nature of socioecological systems. To remedy these issues, we use a global comparative database of CBC projects identified by systematic review to evaluate success in four outcome domains (attitudes, behaviors, ecological, economic) and explore synergies and trade-offs among these outcomes. We test hypotheses about how features of the national context, project design, and local community characteristics affect these measures of success. Using bivariate analyses and multivariate proportional odds logistic regressions within a multilevel analysis and model-fitting framework, we show that project design, particularly capacity-building in local communities, is associated with success across all outcomes. In addition, some characteristics of the local community in which projects are conducted, such as tenure regimes and supportive cultural beliefs and institutions, are important for project success. Surprisingly, there is little evidence that national context systematically influences project outcomes. We also find evidence of synergies between pairs of outcomes, particularly between ecological and economic success. We suggest that well-designed and implemented projects can overcome many of the obstacles imposed by local and national conditions to succeed in multiple domains.
Peripheral selection rather than thymic involution explains sudden contraction in naive CD4 T-cell diversity with age
Authors: Johnson Philip L. F. , Yates Andrew J. , Goronzy Jörg J. , Antia Rustom
Published: December 2012

A diverse array of T cells is required for defense against pathogens. The naive CD4 T-cell repertoire reaches its peak diversity by early human adulthood and is maintained until older age. Surprisingly, around age 70, this diversity appears to plummet abruptly. A similar qualitative pattern holds for the CD4 T memory-cell population. We used mathematical models to explore different hypotheses for how such a loss of diversity might occur. The prevailing hypotheses suggest that the loss of diversity is due to a decline in emigration of cells from the thymus or a contraction in total number of cells. Our models reject these mechanisms because they yield only a gradual and minimal decline in the repertoire instead of the observed sudden and profound decrease later in life. We propose that an abrupt decline in the repertoire could be caused by the accumulation of mutations (defined here as any cell-intrinsic heritable event) that provide a short-term fitness advantage to a small number of T-cell clones (e.g., by an increased division rate or decreased death rate), with the person as a whole incurring the long-term cost of a decreased ability to fight infections.
Noninvasive in vivo model demonstrating the effects of autonomic innervation on pancreatic islet function
Authors: Rodriguez-Diaz Rayner , Speier Stephan , Molano Ruth Damaris , Formoso Alexander , Gans Itai , Abdulreda Midhat H. , Cabrera Over , Molina Judith , Fachado Alberto , Ricordi Camillo , Leibiger Ingo , Pileggi Antonello , Berggren Per-Olof , Caicedo Alejandro
Published: December 2012

The autonomic nervous system is thought to modulate blood glucose homeostasis by regulating endocrine cell activity in the pancreatic islets of Langerhans. The role of islet innervation, however, has remained elusive because the direct effects of autonomic nervous input on islet cell physiology cannot be studied in the pancreas. Here, we used an in vivo model to study the role of islet nervous input in glucose homeostasis. We transplanted islets into the anterior chamber of the eye and found that islet grafts became densely innervated by the rich parasympathetic and sympathetic nervous supply of the iris. Parasympathetic innervation was imaged intravitally by using transgenic mice expressing GFP in cholinergic axons. To manipulate selectively the islet nervous input, we increased the ambient illumination to increase the parasympathetic input to the islet grafts via the pupillary light reflex. This reduced fasting glycemia and improved glucose tolerance. These effects could be blocked by topical application of the muscarinic antagonist atropine to the eye, indicating that local cholinergic innervation had a direct effect on islet function in vivo. By using this approach, we found that parasympathetic innervation influences islet function in C57BL/6 mice but not in 129X1 mice, which reflected differences in innervation densities and may explain major strain differences in glucose homeostasis. This study directly demonstrates that autonomic axons innervating the islet modulate glucose homeostasis.
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
Authors: Fierer Noah , Leff Jonathan W. , Adams Byron J. , Nielsen Uffe N. , Bates Scott Thomas , Lauber Christian L. , Owens Sarah , Gilbert Jack A. , Wall Diana H. , Caporaso J. Gregory
Published: December 2012

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.
Detecting intraannual dietary variability in wild mountain gorillas by stable isotope analysis of feces
Authors: Blumenthal Scott A. , Chritz Kendra L. , Rothman Jessica M. , Cerling Thure E.
Published: December 2012

We use stable isotope ratios in feces of wild mountain gorillas (
Gorilla beringei
) to test the hypothesis that diet shifts within a single year, as measured by dry mass intake, can be recovered. Isotopic separation of staple foods indicates that intraannual changes in the isotopic composition of feces reflect shifts in diet. Fruits are isotopically distinct compared with other staple foods, and peaks in fecal δ
13
C values are interpreted as periods of increased fruit feeding. Bayesian mixing model results demonstrate that, although the timing of these diet shifts match observational data, the modeled increase in proportional fruit feeding does not capture the full shift. Variation in the isotopic and nutritional composition of gorilla foods is largely independent, highlighting the difficulty for estimating nutritional intake with stable isotopes. Our results demonstrate the potential value of fecal sampling for quantifying short-term, intraindividual dietary variability in primates and other animals with high temporal resolution even when the diet is composed of C
3
plants.
Targeting the ERAD pathway via inhibition of signal peptide peptidase for antiparasitic therapeutic design
Authors: Harbut Michael B. , Patel Bhumit A. , Yeung Bryan K. S. , McNamara Case W. , Bright A. Taylor , Ballard Jaime , Supek Frantisek , Golde Todd E. , Winzeler Elizabeth A. , Diagana Thierry T. , Greenbaum Doron C.
Published: December 2012

Early secretory and endoplasmic reticulum (ER)-localized proteins that are terminally misfolded or misassembled are degraded by a ubiquitin- and proteasome-mediated process known as ER-associated degradation (ERAD). Protozoan pathogens, including the causative agents of malaria, toxoplasmosis, trypanosomiasis, and leishmaniasis, contain a minimal ERAD network relative to higher eukaryotic cells, and, because of this, we observe that the malaria parasite
Plasmodium falciparum
is highly sensitive to the inhibition of components of this protein quality control system. Inhibitors that specifically target a putative protease component of ERAD, signal peptide peptidase (SPP), have high selectivity and potency for
P. falciparum
. By using a variety of methodologies, we validate that SPP inhibitors target
P. falciparum
SPP in parasites, disrupt the protein’s ability to facilitate degradation of unstable proteins, and inhibit its proteolytic activity. These compounds also show low nanomolar activity against liver-stage malaria parasites and are also equipotent against a panel of pathogenic protozoan parasites. Collectively, these data suggest ER quality control as a vulnerability of protozoan parasites, and that SPP inhibition may represent a suitable transmission blocking antimalarial strategy and potential pan-protozoan drug target.
Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems
Authors: Morse Robert P. , Nikolakakis Kiel C. , Willett Julia L. E. , Gerrick Elias , Low David A. , Hayes Christopher S. , Goulding Celia W.
Published: December 2012

Contact-dependent growth inhibition (CDI) systems encode polymorphic toxin/immunity proteins that mediate competition between neighboring bacterial cells. We present crystal structures of CDI toxin/immunity complexes from
Escherichia coli
EC869 and
Burkholderia pseudomallei
1026b. Despite sharing little sequence identity, the toxin domains are structurally similar and have homology to endonucleases. The EC869 toxin is a Zn
2+
-dependent DNase capable of completely degrading the genomes of target cells, whereas the Bp1026b toxin cleaves the aminoacyl acceptor stems of tRNA molecules. Each immunity protein binds and inactivates its cognate toxin in a unique manner. The EC869 toxin/immunity complex is stabilized through an unusual β-augmentation interaction. In contrast, the Bp1026b immunity protein exploits shape and charge complementarity to occlude the toxin active site. These structures represent the initial glimpse into the CDI toxin/immunity network, illustrating how sequence-diverse toxins adopt convergent folds yet retain distinct binding interactions with cognate immunity proteins. Moreover, we present visual demonstration of CDI toxin delivery into a target cell.
Microstructured barbs on the North American porcupine quill enable easy tissue penetration and difficult removal
Authors: Cho Woo Kyung , Ankrum James A. , Guo Dagang , Chester Shawn A. , Yang Seung Yun , Kashyap Anurag , Campbell Georgina A. , Wood Robert J. , Rijal Ram K. , Karnik Rohit , Langer Robert , Karp Jeffrey M.
Published: December 2012

North American porcupines are well known for their specialized hairs, or quills that feature microscopic backward-facing deployable barbs that are used in self-defense. Herein we show that the natural quill’s geometry enables easy penetration and high tissue adhesion where the barbs specifically contribute to adhesion and unexpectedly, dramatically reduce the force required to penetrate tissue. Reduced penetration force is achieved by topography that appears to create stress concentrations along regions of the quill where the cross sectional diameter grows rapidly, facilitating cutting of the tissue. Barbs located near the first geometrical transition zone exhibit the most substantial impact on minimizing the force required for penetration. Barbs at the tip of the quill independently exhibit the greatest impact on tissue adhesion force and the cooperation between barbs in the 0–2 mm and 2–4 mm regions appears critical to enhance tissue adhesion force. The dual functions of barbs were reproduced with replica molded synthetic polyurethane quills. These findings should serve as the basis for the development of bio-inspired devices such as tissue adhesives or needles, trocars, and vascular tunnelers where minimizing the penetration force is important to prevent collateral damage.
G-protein signaling modulator 1 deficiency accelerates cystic disease in an orthologous mouse model of autosomal dominant polycystic kidney disease
Authors: Kwon Michelle , Pavlov Tengis S. , Nozu Kandai , Rasmussen Shauna A. , Ilatovskaya Daria V. , Lerch-Gaggl Alexandra , North Lauren M. , Kim Hyunho , Qian Feng , Sweeney William E. , Avner Ellis D. , Blumer Joe B. , Staruschenko Alexander , Park Frank
Published: December 2012

Polycystic kidney diseases are the most common genetic diseases that affect the kidney. There remains a paucity of information regarding mechanisms by which G proteins are regulated in the context of polycystic kidney disease to promote abnormal epithelial cell expansion and cystogenesis. In this study, we describe a functional role for the accessory protein, G-protein signaling modulator 1 (GPSM1), also known as activator of G-protein signaling 3, to act as a modulator of cyst progression in an orthologous mouse model of autosomal dominant polycystic kidney disease (ADPKD). A complete loss of
Gpsm1
in the
Pkd1
V/V
mouse model of ADPKD, which displays a hypomorphic phenotype of polycystin-1, demonstrated increased cyst progression and reduced renal function compared with age-matched cystic
Gpsm1
+/+
and
Gpsm1
+/−
mice. Electrophysiological studies identified a role by which GPSM1 increased heteromeric polycystin-1/polycystin-2 ion channel activity via Gβγ subunits. In summary, the present study demonstrates an important role for GPSM1 in controlling the dynamics of cyst progression in an orthologous mouse model of ADPKD and presents a therapeutic target for drug development in the treatment of this costly disease.
Extracellular superoxide dismutase is important for hippocampal neurogenesis and preservation of cognitive functions after irradiation
Authors: Zou Yani , Corniola Rikki , Leu David , Khan Aslam , Sahbaie Peyman , Chakraborti Ayanabha , Clark David J. , Fike John R. , Huang Ting-Ting
Published: December 2012

Cranial irradiation is widely used in cancer therapy, but it often causes cognitive defects in cancer survivors. Oxidative stress is considered a major cause of tissue injury from irradiation. However, in an earlier study mice deficient in the antioxidant enzyme extracellular superoxide dismutase (EC-SOD KO) showed reduced sensitivity to radiation-induced defects in hippocampal functions. To further dissect the role of EC-SOD in neurogenesis and in response to irradiation, we generated a bigenic EC-SOD mouse model (OE mice) that expressed high levels of EC-SOD in mature neurons in an otherwise EC-SOD–deficient environment. EC-SOD deficiency was associated with reduced progenitor cell proliferation in the subgranular zone of dentate gyrus in KO and OE mice. However, high levels of EC-SOD in the granule cell layer supported normal maturation of newborn neurons in OE mice. Following irradiation, wild-type mice showed reduced hippocampal neurogenesis, reduced dendritic spine densities, and defects in cognitive functions. OE and KO mice, on the other hand, were largely unaffected, and the mice performed normally in neurocognitive tests. Although the resulting hippocampal-related functions were similar in OE and KO mice following cranial irradiation, molecular analyses suggested that they may be governed by different mechanisms: whereas neurotrophic factors may influence radiation responses in OE mice, dendritic maintenance may be important in the KO environment. Taken together, our data suggest that EC-SOD plays an important role in all stages of hippocampal neurogenesis and its associated cognitive functions, and that high-level EC-SOD may provide protection against irradiation-related defects in hippocampal functions.
Shape change in the receptor for gliding motility in
Plasmodium
sporozoites
Authors: Song Gaojie , Koksal Adem C. , Lu Chafen , Springer Timothy A.
Published: December 2012

Sporozoite gliding motility and invasion of mosquito and vertebrate host cells in malaria is mediated by thrombospondin repeat anonymous protein (TRAP). Tandem von Willebrand factor A (VWA) and thrombospondin type I repeat (TSR) domains in TRAP connect through proline-rich stalk, transmembrane, and cytoplasmic domains to the parasite actin-dependent motility apparatus. We crystallized fragments containing the VWA and TSR domains from
Plasmodium vivax
and
Plasmodium falciparum
in different crystal lattices. TRAP VWA domains adopt closed and open conformations, and bind a Mg
2+
ion at a metal ion–dependent adhesion site implicated in ligand binding. Metal ion coordination in the open state is identical to that seen in the open high-affinity state of integrin I domains. The closed VWA conformation associates with a disordered TSR domain. In contrast, the open VWA conformation crystallizes with an extensible β ribbon and ordered TSR domain. The extensible β ribbon is composed of disulfide-bonded segments N- and C-terminal to the VWA domain that are largely drawn out of the closed VWA domain in a 15 Å movement to the open conformation. The extensible β ribbon and TSR domain overlap at a conserved interface. The VWA, extensible β ribbon, and TSR domains adopt a highly elongated overall orientation that would be stabilized by tensile force exerted across a ligand-receptor complex by the actin motility apparatus of the sporozoite. Our results provide insights into regulation of “stick-and-slip” parasite motility and for development of sporozoite subunit vaccines.
Evolution of the receptor binding properties of the influenza A(H3N2) hemagglutinin
Authors: Lin Yi Pu , Xiong Xiaoli , Wharton Stephen A. , Martin Stephen R. , Coombs Peter J. , Vachieri Sebastien G. , Christodoulou Evangelos , Walker Philip A. , Liu Junfeng , Skehel John J. , Gamblin Steven J. , Hay Alan J. , Daniels Rodney S. , McCauley John W.
Published: December 2012

The hemagglutinin (HA) of influenza A(H3N2) virus responsible for the 1968 influenza pandemic derived from an avian virus. On introduction into humans, its receptor binding properties had changed from a preference for avian receptors (α2,3-linked sialic acid) to a preference for human receptors (α2,6-linked sialic acid). By 2001, the avidity of human H3 viruses for avian receptors had declined, and since then the affinity for human receptors has also decreased significantly. These changes in receptor binding, which correlate with increased difficulties in virus propagation in vitro and in antigenic analysis, have been assessed by virus hemagglutination of erythrocytes from different species and quantified by measuring virus binding to receptor analogs using surface biolayer interferometry. Crystal structures of HA–receptor analog complexes formed with HAs from viruses isolated in 2004 and 2005 reveal significant differences in the conformation of the 220-loop of HA1, relative to the 1968 structure, resulting in altered interactions between the HA and the receptor analog that explain the changes in receptor affinity. Site-specific mutagenesis shows the HA1 Asp-225→Asn substitution to be the key determinant of the decreased receptor binding in viruses circulating since 2005. Our results indicate that the evolution of human influenza A(H3N2) viruses since 1968 has produced a virus with a low propensity to bind human receptor analogs, and this loss of avidity correlates with the marked reduction in A(H3N2) virus disease impact in the last 10 y.
Avatar pre-tRNAs help elucidate the properties of tRNA-splicing endonucleases that produce tRNA from permuted genes
Authors: Tocchini-Valentini Giuseppe D. , Tocchini-Valentini Glauco P.
Published: December 2012

Unusual tRNA genes, found in some algae, have their mature terminal 3′ portion in front of their 5′ portion in the genome. The transcripts from such genes must be cleaved by a pre-tRNA endonuclease to form a functional tRNA. We present a mechanism for the generation of “corrected” tRNAs from such a “permuted” pre-tRNA configuration. We used two avatar (av) or model pre-tRNAs and two splicing endonucleases with distinct mechanisms of recognition of the pre-tRNA. The splicing results are compatible with an evolutionary route in which permuted genes result from a duplication event followed by DNA rearrangement. The model pre-tRNAs permit description of the features that a transcript, derived from a rearranged duplicated gene, must have to give rise to functional tRNA. The two tRNA endonucleases are a eukaryal enzyme that normally acts in a mature domain-dependent mode and an archaeal enzyme that acts in a mature domain-independent mode. Both av pre-tRNAs are able to fold into two conformations: 1 and 2. We find that only conformation 2 can yield a corrected functional tRNA. This result is consistent with contemporary algae representing snapshots of different evolutionary stages, with duplicated genes preceding recombinatorial events generating a permutated gene. In a scenario elucidated by the use of the av pre-tRNAs, algal permuted tRNA genes could have further lost one of two mature domains, eliminating steric problems for the algal tRNA endonuclease, which remains a typical eukaryal enzyme capable of correcting the permuted transcript to a functional tRNA.
Thresholds for boreal biome transitions
Authors: Scheffer Marten , Hirota Marina , Holmgren Milena , Van Nes Egbert H. , Chapin F. Stuart
Published: December 2012

Although the boreal region is warming twice as fast as the global average, the way in which the vast boreal forests and tundras may respond is poorly understood. Using satellite data, we reveal marked alternative modes in the frequency distributions of boreal tree cover. At the northern end and at the dry continental southern extremes, treeless tundra and steppe, respectively, are the only possible states. However, over a broad intermediate temperature range, these treeless states coexist with boreal forest (∼75% tree cover) and with two more open woodland states (∼20% and ∼45% tree cover). Intermediate tree covers (e.g., ∼10%, ∼30%, and ∼60% tree cover) between these distinct states are relatively rare, suggesting that they may represent unstable states where the system dwells only transiently. Mechanisms for such instabilities remain to be unraveled, but our results have important implications for the anticipated response of these ecosystems to climatic change. The data reveal that boreal forest shows no gradual decline in tree cover toward its limits. Instead, our analysis suggests that it becomes less resilient in the sense that it may more easily shift into a sparse woodland or treeless state. Similarly, the relative scarcity of the intermediate ∼10% tree cover suggests that tundra may shift relatively abruptly to a more abundant tree cover. If our inferences are correct, climate change may invoke massive nonlinear shifts in boreal biomes.
Estimating Spatial and Temporal Components of Variation for Fisheries Count Data Using Negative Binomial Mixed Models
Authors: Irwin Brian J. , Wagner Tyler , Bence James R. , Kepler Megan V. , Liu Weihai , Hayes Daniel B.
Published: December 2012

Partitioning total variability into its component temporal and spatial sources is a powerful way to better understand time series and elucidate trends. The data available for such analyses of fish and other populations are usually nonnegative integer counts of the number of organisms, often dominated by many low values with few observations of relatively high abundance. These characteristics are not well approximated by the Gaussian distribution. We present a detailed description of a negative binomial mixed‐model framework that can be used to model count data and quantify temporal and spatial variability. We applied these models to data from four fishery‐independent surveys of Walleyes Sander vitreus across the Great Lakes basin. Specifically, we fitted models to gill‐net catches from Wisconsin waters of Lake Superior; Oneida Lake, New York; Saginaw Bay in Lake Huron, Michigan; and Ohio waters of Lake Erie. These long‐term monitoring surveys varied in overall sampling intensity, the total catch of Walleyes, and the proportion of zero catches. Parameter estimation included the negative binomial scaling parameter, and we quantified the random effects as the variations among gill‐net sampling sites, the variations among sampled years, and site × year interactions. This framework (i.e., the application of a mixed model appropriate for count data in a variance‐partitioning context) represents a flexible approach that has implications for monitoring programs (e.g., trend detection) and for examining the potential of individual variance components to serve as response metrics to large‐scale anthropogenic perturbations or ecological changes.
Longitudinal Length Back‐Calculations from Otoliths and Scales Differ Systematically in Haddock
Authors: Baumann Hannes , Sutherland Sandra J. , McBride Richard S.
Published: December 2012

Parallel macrostructure analysis of otoliths versus scales was conducted on Georges Bank Haddock Melanogrammus aeglefinus sampled in spring 2011 to test whether annuli widths of both structures yield comparable estimates of back‐calculated length at age. While generally similar in number, scale and otolith annuli were found to differ systematically in their relative widths, mainly because initial annuli are deposited closer to the origin in scales than in otoliths. Accounting for the delayed onset of scale versus otolith formation did not remove the systematic bias. To make both structures comparable, we developed an age‐independent correction approach that can adjust cumulative relative annuli widths (RAWs) of Haddock scales to otolith RAWs by the quadratic formula loge(RAWoto) = 0.7244·loge(RAWscale) + 0.0751·loge(RAWscale)2. Our study comprises a necessary step towards extracting and comparing longitudinal growth data over the entire time series of archived Haddock scales (1931–1993) and otoliths (1994–present) to improve understanding of decadal drivers of growth patterns in this fish stock. Historical longitudinal growth data for exploited stocks are currently underutilized despite their high potential value, given that such data do not confound growth and mortality the way population‐based age–length relationships do. Mixed archives consisting of multiple growth structures exist not only for Haddock but for many commercial fish species; hence, prior to mining these valuable time series of longitudinal data the comparability not only of age but also of back‐calculated growth estimates between structures needs to be ascertained.
Apparent Digestibility of 12 Protein-Origin Ingredients for Pacific White Shrimp Litopenaeus vannamei
Authors: Liu Xiang-He , Ye Ji-Dan , Kong Jiang-Hong , Wang Kun , Wang An-li
Published: December 2012

Using 0.5% chromic oxide as an external indicator, apparent digestibility coefficients (ADCs) were determined for 12 protein feed ingredients (fish meal [FM], blood meal [BM], meat-and-bone meal [MBM], poultry byproduct meal [PBM], shrimp head meal [SHM], squid visceral meal [SVM], soybean meal [SBM], rapeseed meal [RM], cottonseed meal [CM], peanut meal [PM], corn gluten meal [CGM], and brewer's yeast [BY]) fed to Pacific white shrimp Litopenaeus vannamei (mean initial weight ± SD = 4.45 ± 0.21 g). The shrimp were randomly allocated to thirty-nine 150-L tanks (20 shrimp/tank) and were hand-fed a reference diet or test diet (70% reference diet and 30% test feed by weight) twice daily to satiation. Feces were collected by siphoning. The observed range of ADCs of the 12 ingredients was 48.6–87.0% for dry matter, 55.7–92.3% for crude protein, 2.1–92.5% for crude lipid, 52.1–79.9% for phosphorus, and 51.1–97.2% for gross energy. Relatively high ADCs were observed for dry matter in FM (87.0%) and MBM (76.5%); for crude protein in FM (90.9%), SBM (92.3%), and PM (88.8%); for crude lipid in FM (92.5%) and SVM (88.5%); and for phosphorus (79.9, 72.7, 72.5, and 78.5%) and gross energy (97.2, 82.3, 84.0, and 84.6%) in FM, MBM, PBM, and BY. The ADCs of amino acids for the 12 ingredients were 86.7–97.4% (FM), 58.4–98.8% (BM), 46.9–99.6% (MBM), 54.8–95.4% (PBM), 79.0–100.0% (SHM), 58.3–93.0% (SVM), 60.7–99.4% (SBM), 62.6–99.6% (RM), 52.9–91.4% (CM), 60.1–99.9% (PM), 15.6–97.8% (CGM), and 30.3–98.4% (BY). Fish meal, SBM, and PM showed high average ADCs for total amino acids (>90%). Crude protein ADCs corresponded with amino acid ADCs. Resultant digestibility data may provide more accurate information pertinent to formulating commercial feeds for Pacific white shrimp.
RetroSeq: transposable element discovery from next-generation sequencing data
Authors: Keane Thomas M. , Wong Kim , Adams David J.
Published: December 2012

Summary: A significant proportion of eukaryote genomes consist of transposable element (TE)-derived sequence. These elements are known to have the capacity to modulate gene function and genome evolution. We have developed RetroSeq for detecting non-reference TE insertions from Illumina paired-end whole-genome sequencing data. We evaluate RetroSeq on a human trio from the 1000 Genomes Project, showing that it produces highly accurate TE calls.

Availabilty: RetroSeq is open-source and available from https://github.com/tk2/RetroSeq.

Contact:  tk2@sanger.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cytokinins Act Synergistically with Salicylic Acid to Activate Defense Gene Expression in Rice
Authors: Jiang Chang-Jie , Shimono Masaki , Sugano Shoji , Kojima Mikiko , Liu Xinqiong , Inoue Haruhiko , Sakakibara Hitoshi , Takatsuji Hiroshi
Published: December 2012

Hormone crosstalk is pivotal in plant–pathogen interactions. Here, we report on the accumulation of cytokinins (CK) in rice seedlings after infection of blast fungus Magnaporthe oryzae and its potential significance in rice–M. oryzae interaction. Blast infection to rice seedlings increased levels of N6-(Δ2-isopentenyl) adenine (iP), iP riboside (iPR), and iPR 5′-phosphates (iPRP) in leaf blades. Consistent with this, CK signaling was activated around the infection sites, as shown by histochemical staining for β-glucuronidase activity driven by a CK-responsive OsRR6 promoter. Diverse CK species were also detected in the hyphae (mycelium), conidia, and culture filtrates of blast fungus, indicating that M. oryzae is capable of production as well as hyphal secretion of CK. Co-treatment of leaf blades with CK and salicylic acid (SA), but not with either one alone, markedly induced pathogenesis-related genes OsPR1b and probenazole-induced protein 1 (PBZ1). These effects were diminished by RNAi-knockdown of OsNPR1 or WRKY45, the key regulators of the SA signaling pathway in rice, indicating that the effects of CK depend on these two regulators. Taken together, our data imply a coevolutionary rice–M. oryzae interaction, wherein M. oryzae probably elevates rice CK levels for its own benefits such as nutrient translocation. Rice plants, on the other hand, sense it as an infection signal and activate defense reactions through the synergistic action with SA.
Gene-for-Gene Tolerance to Bacterial Wilt in Arabidopsis
Authors: Van der Linden Liesl , Bredenkamp Jane , Naidoo Sanushka , Fouché-Weich Joanne , Denby Katherine J. , Genin Stephane , Marco Yves , Berger Dave K.
Published: December 2012

Bacterial wilt caused by Ralstonia solanacearum is a disease of widespread economic importance that affects numerous plant species, including Arabidopsis thaliana. We describe a pathosystem between A. thaliana and biovar 3 phylotype I strain BCCF402 of R. solanacearum isolated from Eucalyptus trees. A. thaliana accession Be-0 was susceptible and accession Kil-0 was tolerant. Kil-0 exhibited no wilting symptoms and no significant reduction in fitness (biomass, seed yield, and germination efficiency) after inoculation with R. solanacearum BCCF402, despite high bacterial numbers in planta. This was in contrast to the well-characterized resistance response in the accession Nd-1, which limits bacterial multiplication at early stages of infection and does not wilt. R. solanacearum BCCF402 was highly virulent because the susceptible accession Be-0 was completely wilted after inoculation. Genetic analyses, allelism studies with Nd-1, and RRS1 cleaved amplified polymorphic sequence marker analysis showed that the tolerance phenotype in Kil-0 was dependent upon the resistance gene RRS1. Knockout and complementation studies of the R. solanacearum BCCF402 effector PopP2 confirmed that the tolerance response in Kil-0 was dependent upon the RRS1–PopP2 interaction. Our data indicate that the gene-for-gene interaction between RRS1 and PopP2 can contribute to tolerance, as well as resistance, which makes it a useful model system for evolutionary studies of the arms race between plants and bacterial pathogens. In addition, the results alert biotechnologists to the risk that deployment of RRS1 in transgenic crops may result in persistence of the pathogen in the field.
Phytoplasma-Triggered Ca2+ Influx Is Involved in Sieve-Tube Blockage
Authors: Musetti Rita , Buxa Stefanie V. , De Marco Federica , Loschi Alberto , Polizzotto Rachele , Kogel Karl-Heinz , van Bel Aart J. E.
Published: December 2012

Phytoplasmas are obligate, phloem-restricted phytopathogens that are disseminated by phloem-sap-sucking insects. Phytoplasma infection severely impairs assimilate translocation in host plants and might be responsible for massive changes in phloem physiology. Methods to study phytoplasma- induced changes thus far provoked massive, native occlusion artifacts in sieve tubes. Hence, phytoplasma-phloem relationships were investigated here in intact Vicia faba host plants using a set of vital fluorescent probes and confocal laser-scanning microscopy. We focused on the effects of phytoplasma infection on phloem mass-flow performance and evaluated whether phytoplasmas induce sieve-plate occlusion. Apparently, phytoplasma infection brings about Ca2+ influx into sieve tubes, leading to sieve-plate occlusion by callose deposition or protein plugging. In addition, Ca2+ influx may confer cell wall thickening of conducting elements. In conclusion, phytoplasma effectors may cause gating of sieve-element Ca2+ channels leading to sieve-tube occlusion with presumptive dramatic effects on phytoplasma spread and photoassimilate distribution.
Identification of Functional Genic Components of Major Fusarium Head Blight Resistance Quantitative Trait Loci in Wheat Cultivar Sumai 3
Authors: Zhuang Yongbin , Gala Aravind , Yen Yang
Published: December 2012

Fusarium head blight (FHB) is a devastating disease worldwide, affecting wheat and other small grains. To identify key wheat genes involved in FHB pathogenesis, 406 FHB-related wheat expressed sequence tags functionally identified in Sumai 3 were investigated for their association with FHB-resistance quantitative trait loci (QTL) Fhb1 and Fhb_6BL in 2010 and 2011. A total of 47 candidate genes were identified by bulk analysis, near-isogenic screening and expression QTL mapping, and were finally mapped to their carrier chromosomes with Chinese Spring nulli-tetra deficiency lines. One gene, designated WFhb1_c1 (wheat Fhb1 candidate gene 1), was both functionally associated with and physically located within Fhb1 and was found to be weakly similar (E = 5e+0) to an Arabidopsis gene encoding pectin methyl esterase inhibitor. Two other genes, designated WFI_6BL1 and WFI_6BL2 (wheat-Fusarium interaction genes 6BL1 and 6BL2), were functionally associated with Fhb_6BL but physically mapped on chromosomes 7D and 5A, respectively. WFI_6BL1 was annotated as a 13- lipoxygenase gene and WFI_6BL2 might encode a PR-4-like protein. Our data suggested that i) Fhb1 seems to contribute to FHB resistance by reducing susceptibility in the first 60 h, ii) Fhb_6BL makes its contribution via the jasmonate-mediated pathways, and iii) wheat seems to activate its defense mechanism in the biotrophic phase of FHB pathogenesis.
Monitoring Current-Season Spread of Potato virus Y in Potato Fields Using ELISA and Real-Time RT-PCR
Authors: Fageria Manphool S. , Singh Mathuresh , Nanayakkara Upeksha , Pelletier Yvan , Nie Xianzhou , Wattie David
Published: December 2012

The current-season spread of Potato virus Y (PVY) was investigated in New Brunswick, Canada, in 11 potato fields planted with six different cultivars in 2009 and 2010. In all, 100 plants selected from each field were monitored for current-season PVY infections using enzyme-linked immunosorbent assay (ELISA) and real-time reverse-transcription polymerase chain reaction (RT-PCR) assay. Average PVY incidence in fields increased from 0.6% in 2009 and 2% in 2010 in the leaves to 20.3% in 2009 and 21.9% in 2010 in the tubers at the time of harvest. In individual fields, PVY incidence in tubers reached as high as 37% in 2009 and 39% in 2010 at the time of harvest. Real-time RT-PCR assay detected more samples with PVY from leaves than did ELISA. A higher number of positive samples was also detected with real-time RT-PCR from growing tubers compared with the leaves collected from the same plant at the same sampling time. PVY incidence determined from the growing tubers showed a significant positive correlation with the PVY incidence of tubers after harvest. Preharvest testing provides another option to growers to either top-kill the crop immediately to secure the seed market when the PVY incidence is low or leave the tubers to develop further for table or processing purposes when incidence of PVY is high.