bluuebunny/crossref_metadata_2025 huggingface dataset:
Topographically specific regeneration of sensory axons in the spinal cord
Authors: Harvey Pamela , Gong BangJian , Rossomando Anthony J. , Frank Eric
Published: June 2010

Artemin, a member of the glial-derived neurotrophic factor family, promotes robust regeneration of sensory axons after dorsal root crush. We report here that several classes of sensory axons regenerate to topographically appropriate regions of the dorsal horn with artemin treatment. Projections of regenerated muscle and cutaneous myelinated sensory afferents are restricted to the correct spinal segments and to appropriate regions within spinal gray matter. Regenerated unmyelinated axons expressing calcitonin gene-related peptide project only to superficial laminae of the dorsal horn, where uninjured nociceptive afferents project normally. In contrast, intraventricular infusion of a soluble form of the Nogo receptor that blocks the action of several myelin-associated inhibitory proteins promotes relatively unrestricted regeneration of sensory axons throughout the dorsal white and gray matter of the spinal cord. These results demonstrate that cues capable of guiding regenerating axons to appropriate spinal targets persist in the adult mammalian cord, but only some methods of stimulating regeneration allow the use of these cues by growing axons.
Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition
Authors: Ni Lisheng , Xu Weijun , Kumaraswami Muthiah , Schumacher Maria A.
Published: June 2010

The segregation of plasmid DNA typically requires three elements: a DNA centromere site, an NTPase, and a centromere-binding protein. Because of their simplicity, plasmid partition systems represent tractable models to study the molecular basis of DNA segregation. Unlike eukaryotes, which utilize the GTPase tubulin to segregate DNA, the most common plasmid-encoded NTPases contain Walker-box and actin-like folds. Recently, a plasmid stability cassette on
Bacillus thuringiensis
pBtoxis encoding a putative FtsZ/tubulin-like NTPase called TubZ and DNA-binding protein called TubR has been described. How these proteins collaborate to impart plasmid stability, however, is unknown. Here we show that the TubR structure consists of an intertwined dimer with a winged helix-turn-helix (HTH) motif. Strikingly, however, the TubR recognition helices mediate dimerization, making canonical HTH–DNA interactions impossible. Mutagenesis data indicate that a basic patch, encompassing the two wing regions and the N termini of the recognition helices, mediates DNA binding, which indicates an unusual HTH–DNA interaction mode in which the N termini of the recognition helices insert into a single DNA groove and the wings into adjacent DNA grooves. The TubZ structure shows that it is as similar structurally to eukaryotic tubulin as it is to bacterial FtsZ. TubZ forms polymers with guanine nucleotide-binding characteristics and polymer dynamics similar to tubulin. Finally, we show that the exposed TubZ C-terminal region interacts with TubR-DNA, linking the TubR-bound pBtoxis to TubZ polymerization. The combined data suggest a mechanism for TubZ-polymer powered plasmid movement.
Injectable hydrogel properties influence infarct expansion and extent of postinfarction left ventricular remodeling in an ovine model
Authors: Ifkovits Jamie L. , Tous Elena , Minakawa Masahito , Morita Masato , Robb J. Daniel , Koomalsingh Kevin J. , Gorman Joseph H. , Gorman Robert C. , Burdick Jason A.
Published: June 2010

A recent trend has emerged that involves myocardial injection of biomaterials, containing cells or acellular, following myocardial infarction (MI) to influence the remodeling response through both biological and mechanical effects. Despite the number of different materials injected in these approaches, there has been little investigation into the importance of material properties on therapeutic outcomes. This work focuses on the investigation of injectable hyaluronic acid (MeHA) hydrogels that have tunable mechanics and gelation behavior. Specifically, two MeHA formulations that exhibit similar degradation and tissue distribution upon injection but have differential moduli (~8 versus ~43 kPa) were injected into a clinically relevant ovine MI model to evaluate the associated salutary effect of intramyocardial hydrogel injection on the remodeling response based on hydrogel mechanics. Treatment with both hydrogels significantly increased the wall thickness in the apex and basilar infarct regions compared with the control infarct. However, only the higher-modulus (MeHA High) treatment group had a statistically smaller infarct area compared with the control infarct group. Moreover, reductions in normalized end-diastolic and end-systolic volumes were observed for the MeHA High group. This group also tended to have better functional outcomes (cardiac output and ejection fraction) than the low-modulus (MeHA Low) and control infarct groups. This study provides fundamental information that can be used in the rational design of therapeutic materials for treatment of MI.
Denatured states of low-complexity polypeptide sequences differ dramatically from those of foldable sequences
Authors: Tzul Franco O. , Bowler Bruce E.
Published: June 2010

How the primary sequence of a protein encodes conformational preferences that operate early in folding to promote efficient formation of the correct native topology is still poorly understood. To address this issue, we have prepared a set of yeast iso-1-cytochrome
c
variants that contain polyalanine inserts ranging from 6 to 30 residues in length near the N terminus of the protein. We study the thermodynamics and kinetics of His-heme loop formation in the denatured state at 3 and 6 M guanidine-HCl concentration. We find that polyalanine closely approximates a random coil with excluded volume giving scaling exponents,
ν
3
, for equilibrium loop formation of 2.26 ± 0.13 and 1.97 ± 0.04 in 3 and 6 M guanidine-HCl, respectively. The rate of loop breakage initially decreases and then becomes independent of loop size as would be expected for a random coil. Comparison with previously reported data for denatured state His-heme loop formation for iso-1-cytochrome
c
and
Rhodopseudomonas palustris
cytochrome
c
′, shows that foldable sequences deviate significantly from random coil behavior and that the deviation is fold-dependent.
Role of kinase-independent and -dependent functions of FAK in endothelial cell survival and barrier function during embryonic development
Authors: Zhao Xiaofeng , Peng Xu , Sun Shaogang , Park Ann Y.J. , Guan Jun-Lin
Published: June 2010

Focal adhesion kinase (FAK) is essential for vascular development as endothelial cell (EC)–specific knockout of FAK (conditional FAK knockout [CFKO] mice) leads to embryonic lethality. In this study, we report the differential kinase-independent and -dependent functions of FAK in vascular development by creating and analyzing an EC-specific FAK kinase-defective (KD) mutant knockin (conditional FAK knockin [CFKI]) mouse model. CFKI embryos showed apparently normal development through embryonic day (E) 13.5, whereas the majority of CFKO embryos died at the same stage. Expression of KD FAK reversed increased EC apoptosis observed with FAK deletion in embryos and in vitro through suppression of up-regulated p21. However, vessel dilation and defective angiogenesis of CFKO embryos were not rescued in CFKI embryos. ECs without FAK or expressing KD FAK showed increased permeability, abnormal distribution of vascular endothelial cadherin (VE-cadherin), and reduced VE-cadherin Y658 phosphorylation. Together, our data suggest that kinase-independent functions of FAK can support EC survival in vascular development through E13.5 but are insufficient for maintaining EC function to allow for completion of embryogenesis.
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function
Authors: Zhao Huiying , Yang Yuedong , Zhou Yaoqi
Published: June 2010

Motivation: Template-based prediction of DNA binding proteins requires not only structural similarity between target and template structures but also prediction of binding affinity between the target and DNA to ensure binding. Here, we propose to predict protein–DNA binding affinity by introducing a new volume-fraction correction to a statistical energy function based on a distance-scaled, finite, ideal-gas reference (DFIRE) state.

Results: We showed that this energy function together with the structural alignment program TM-align achieves the Matthews correlation coefficient (MCC) of 0.76 with an accuracy of 98%, a precision of 93% and a sensitivity of 64%, for predicting DNA binding proteins in a benchmark of 179 DNA binding proteins and 3797 non-binding proteins. The MCC value is substantially higher than the best MCC value of 0.69 given by previous methods. Application of this method to 2235 structural genomics targets uncovered 37 as DNA binding proteins, 27 (73%) of which are putatively DNA binding and only 1 protein whose annotated functions do not contain DNA binding, while the remaining proteins have unknown function. The method provides a highly accurate and sensitive technique for structure-based prediction of DNA binding proteins.

Availability: The method is implemented as a part of the Structure-based function-Prediction On-line Tools (SPOT) package available at http://sparks.informatics.iupui.edu/spot

Contact:  yqzhou@iupui.edu
The effects of adding torasemide to standard therapy on peak oxygen consumption, natriuretic peptides, and quality of life in patients with compensated left ventricular systolic dysfunction
Authors: Gupta Sanjay , Waywell Carolyn , Gandhi Nandkumar , Clayton Nigel , Keevil Brian , Clark Andrew L. , Ng Leong L. , Brooks Nicholas , Neyses Ludwig
Published: June 2010

Aims

Diuretics, when used to treat congestion in patients with chronic heart failure, improve symptoms and, perhaps, prognosis but little information is available to guide their use in patients with left ventricular systolic dysfunction (LVSD) who are not congested. Chronic diuretic therapy causes persistent and potentially harmful neuroendocrine activation. Alternatively, in patients in whom neuroendocrine activation is blocked with angiotensin‐converting enzyme (ACE)‐inhibitors and β‐blockers, diuretics may be beneficial by decreasing preload and afterload and preventing congestion. We aimed to assess the effect of the loop diuretic, torasemide on quality of life, and surrogate markers of prognosis when given to patients with LVSD who were not clinically congested and who were optimally treated with ACE‐inhibitors (or angiotensin receptor antagonists) and β‐blockers.

Methods and results

Thirty patients with stable LVSD who had no clinically detectable fluid overload were randomized to receive either torasemide 5 mg daily or placebo for 3 months (Phase A), and after a washout phase of 2 months, cross‐over was performed for 3 months (Phase B). Diuretic therapy did not cause significant change in peak VO2, mean N‐terminal pro‐hormone brain natriuretic peptide (NT‐proBNP) levels, or measures of quality of life compared with placebo. Diuretic therapy did however lead to significant fall in systolic and diastolic blood pressures and increase in plasma renin levels compared with placebo.

Conclusion

Diuretic therapy with torasemide is not superior to placebo in improving peak VO2 or reducing NT‐proBNP levels in patients with left ventricular dysfunction who are not clinically congested.
Estimating the target strength of live, free-swimming chokka squid Loligo reynaudii at 38 and 120 kHz
Authors: Soule Michael A. , Hampton Ian , Lipiński Marek R.
Published: June 2010

Soule, M. A., Hampton, I., and Lipiński, M. R. 2010. Estimating the target strength of live, free-swimming chokka squid Loligo reynaudii at 38 and 120 kHz. – ICES Journal of Marine Science, 67: 1381–1391. Estimates of the target strength (TS) of the loliginid squid Loligo reynaudii at 120 kHz were made from ex situ experiments on 38 caged, but free-swimming animals, and at 38 and 120 kHz from 17 in situ experiments on spawning aggregations in the wild conducted from a research vessel and from small boats. The cage experiments suggested that the backscattering cross section is proportional to mantle length (ML), which would not be expected from simple considerations of ML in relation to wavelength. A similar relationship was found during the in situ experiments conducted from the research vessel. The TS estimates from the research vessel agreed well with those from the cage experiments, for both of the two methods used to extract squid TS distributions from the overall TS distributions, but were some 2–3 dB lower than those from the small boats. This suggests that in situ estimates are affected by the vessel and/or the way in which squid react to it. It is concluded that ex situ experiments on L. reynaudii TS are of most value as a complement to in situ experiments, which should be made concurrently while surveying, using systems capable of having higher volume resolution than in the current experiments, to maximize the applicability of the estimates to the survey data.
Behavioural system identification of visual flight speed control inDrosophila melanogaster
Authors: Rohrseitz Nicola , Fry Steven N.
Published: June 2010

Behavioural control in many animals involves complex mechanisms with intricate sensory-motor feedback loops. Modelling allows functional aspects to be captured without relying on a description of the underlying complex, and often unknown, mechanisms. A wide range of engineering techniques are available for modelling, but their ability to describe time-continuous processes is rarely exploited to describe sensory-motor control mechanisms in biological systems. We performed a system identification of visual flight speed control in the fruitflyDrosophila, based on an extensive dataset of open-loop responses previously measured under free flight conditions. We identified a second-order under-damped control model with just six free parameters that well describes both the transient and steady-state characteristics of the open-loop data. We then used the identified control model to predict flight speed responses after a visual perturbation under closed-loop conditions and validated the model with behavioural measurements performed in free-flying flies under the same closed-loop conditions. Our system identification of the fruitfly's flight speed response uncovers the high-level control strategy of a fundamental flight control reflex without depending on assumptions about the underlying physiological mechanisms. The results are relevant for future investigations of the underlying neuromotor processing mechanisms, as well as for the design of biomimetic robots, such as micro-air vehicles.
Streptomyces coacervatus sp. nov., isolated from the intestinal tract of Armadillidium vulgare
Authors: Shibazaki Azusa , Omoto Yuta , Kudo Takuji , Yaguchi Takashi , Saito Akihiro , Ando Akikazu , Mikami Yuzuru , Gonoi Tohru
Published: June 2010

A Gram-staining-positive bacterium, designated AS-0823T, which formed spiral spore chains on the aerial mycelium, was isolated from the intestinal tract of Armadillidium vulgare, a small terrestrial crustacean commonly found on the ground around houses in Japan. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus Streptomyces and was most closely related to Streptomyces longisporus ISP 5166T (98.6 % 16S rRNA gene sequence similarity), Streptomyces curacoi NBRC 12761T (98.4 %) and Streptomyces griseoruber NBRC 12873T (98.4 %). The affiliation of strain AS-0823T to the genus Streptomyces was supported by chemotaxonomic data: iso-C16 : 0, anteiso-C15 : 0, C16 : 0, iso-C15 : 0 and anteiso-C17 : 0 as the major cellular fatty acids, ll-diaminopimelic acid as the characteristic diamino acid in the peptidoglycan and the absence of mycolic acids. DNA–DNA hybridization and physiological and biochemical analysis supported the differentiation of strain AS-0823T from S. longisporus JCM 4395T. Therefore, strain AS-0823T represents a novel species, for which the name Streptomyces coacervatus sp. nov. is proposed. The type strain is AS-0823T ( = IFM 11055T  = DSM 41983T  = JCM 17138T).
Lysobacter dokdonensis sp. nov., isolated from soil
Authors: Oh Ki-Hoon , Kang So-Jung , Jung Yong-Taek , Oh Tae-Kwang , Yoon Jung-Hoon
Published: June 2010

A Gram-negative, non-motile, rod-shaped bacterial strain, DS-58T, was isolated from a soil sample from Dokdo, an island of Korea, and its taxonomic position was investigated. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-58T fell within the family Xanthomonadaceae. The isolate showed 96.9 % 16S rRNA gene sequence similarity with its closest phylogenetic neighbour, Lysobacter niastensis GH41-7T, and 93.4–95.7 % 16S rRNA gene sequence similarity with other members of the genus Lysobacter. Strain DS-58T contained Q-8 as the predominant ubiquinone and iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1ω9c as the major fatty acids. The DNA G+C content was 68.1 mol%. Strain DS-58T could be distinguished phenotypically from type strains of closely related species of the genus Lysobacter and phylogenetically from all members of the genus Lysobacter. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DS-58T is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter dokdonensis sp. nov. is proposed. The type strain is DS-58T ( = KCTC 12822T  = DSM 17958T).
Streptomyces youssoufiensis sp. nov., isolated from a Moroccan phosphate mine
Authors: Hamdali H. , Virolle M. J. , von Jan M. , Spröer C. , Klenk H.-P. , Ouhdouch Y.
Published: June 2010

A novel actinomycete, strain X4T, was isolated from a phosphate mine in Youssoufia, 100 km north of Marrakesh, Morocco. The taxonomic status of this strain was evaluated by a polyphasic approach. Strain X4Thad white aerial mycelium withRectiflexibilesspore chains bearing smooth-surfaced spores and did not produce diffusible pigments. Chemotaxonomic analysis showed that the cell wall of strain X4Tcontainedll-diaminopimelic acid and glycine. Phylogenetic analysis based on the almost complete 16S rRNA gene sequence indicated that strain X4Tbelongs to the Group I streptomycetes, branching off next toStreptomyces ramulosusNRRL B-2714TandStreptomyces kasugaensisM338-M1T. DNA–DNA relatedness and phenotypic data enabled strain X4Tto be distinguished from the phylogenetically most closely related type strains. It is therefore proposed that strain X4Trepresents a novel species of the genusStreptomyces, for which the nameStreptomyces youssoufiensissp. nov. is proposed; the type strain is X4T( = CCMM B709T = DSM 41920T).
Streptomyces tacrolimicus sp. nov., a low producer of the immunosuppressant tacrolimus (FK506)
Authors: Martínez-Castro Miriam , Barreiro Carlos , Romero Francisco , Fernández-Chimeno Rosa Isabel , Martín Juan F.
Published: June 2010

The number of tacrolimus (FK506)-producing isolates has increased remarkably because of the clinical importance of tacrolimus as an immunosuppressant. However, the taxonomy of several of these isolates has not been studied. The taxonomic status of strain ATCC 55098T, a tacrolimus-producing strain, was determined in this study. The genotypic, phenotypic and chemotaxonomic properties were consistent with the inclusion of strain ATCC 55098T in the genus Streptomyces. The 16S rRNA gene sequence of strain ATCC 55098T was determined and used to generate phylogenetic trees with corresponding sequences of the most closely related type strains (≥98 % 16S rRNA gene sequence similarity) of species of the genus Streptomyces. Strain ATCC 55098T formed a distinct phylogenetic branch adjacent to a cluster comprising Streptomyces fulvissimus NBRC 13482T and Streptomyces flavofungini NBRC 13371T. However, morphological and physiological tests and DNA–DNA relatedness distinguished strain ATCC 55098T from its closest phylogenetic neighbours. On the basis of these results, strain ATCC 55098T represents a novel species of the genus Streptomyces, for which the name Streptomyces tacrolimicus sp. nov. is proposed. The type strain is ATCC 55098T ( = CECT 7664T).
Variation in Antiherbivore Defense Responses in Synthetic Nicotiana Allopolyploids Correlates with Changes in Uniparental Patterns of Gene Expression
Authors: Anssour Samir , Baldwin Ian T.
Published: June 2010

We examined the expression of Nicotiana  attenuata (Na) and Nicotiana obtusifolia (No) herbivore-induced genes in synthetic autopolyploids (NaT and NoT) and five independent allopolyploid Nicotiana × obtusiata (N×o) lines to understand how the expression of genes regulating complex polygenetic defense traits is altered in the early stages of allopolyploid hybridization. In Na, applying Manduca sexta oral secretions (OS) to wounds rapidly increased the transcript accumulation of wound-induced protein kinase (WIPK), lipoxygenase 3 (LOX3), nonexpressor of pathogenesis-related 1 (NPR1), and jasmonate-resistant 4 (JAR4) genes; these were correlated with increases in accumulation of jasmonic acid (JA), jasmonate-isoleucine, and trypsin protease inhibitors (TPIs). In No, OS elicitation reduced NPR1 transcripts and increased the level of salicylic acid (SA) that appeared to antagonize JA and JA-mediated defenses. OS elicited N×o lines, accumulated high levels of the uniparental transcript of WIPK, LOX3, JAR4, and TPI, but low levels of both parental NPR1 transcripts that in turn were correlated with an increase in SA and a decrease in JA levels, suggesting SA/JA antagonism in the allopolyploid crosses. Methyl jasmonate treatment of N×o lines elicited transcripts of both parental LOX3, JAR4, and TPIs, demonstrating that the uniparental pattern observed after OS elicitation was not due to gene inactivation. TPIs were induced at different levels among N×o lines; some lines expressed high levels comparable to Na, others low levels similar to No, suggesting that synthetic neoallopolyploids rapidly readjust the expression of their parental defensive genes to generate diverse antiherbivore responses. Changes in the expression of key genes and posttranscriptional events likely facilitate adaptive radiations during allopolyploid speciation events.
Myosin XI Is Essential for Tip Growth inPhyscomitrella patens
Authors: Vidali Luis , Burkart Graham M. , Augustine Robert C. , Kerdavid Erin , Tüzel Erkan , Bezanilla Magdalena
Published: June 2010

Class XI myosins are plant specific and responsible for cytoplasmic streaming. Because of the large number of myosin XI genes in angiosperms, it has been difficult to determine their precise role, particularly with respect to tip growth. The moss Physcomitrella patens provides an ideal system to study myosin XI function. P. patens has only two myosin XI genes, and these genes encode proteins that are 94% identical to each other. To determine their role in tip growth, we used RNA interference to specifically silence each myosin XI gene using 5′ untranslated region sequences. We discovered that the two myosin XI genes are functionally redundant, since silencing of either gene does not affect growth or polarity. However, simultaneous silencing of both myosin XIs results in severely stunted plants composed of small rounded cells. Although similar to the phenotype resulting from silencing of other actin-associated proteins, we show that this phenotype is not due to altered actin dynamics. Consistent with a role in tip growth, we show that a functional, full-length fusion of monomeric enhanced green fluorescent protein (mEGFP) to myosin XI accumulates at a subcortical, apical region of actively growing protonemal cells.
DWA1 and DWA2, Two Arabidopsis DWD Protein Components of CUL4-Based E3 Ligases, Act Together as Negative Regulators in ABA Signal Transduction
Authors: Lee Jae-Hoon , Yoon Hye-Jin , Terzaghi William , Martinez Cristina , Dai Mingqiu , Li Jigang , Byun Myung-Ok , Deng Xing Wang
Published: June 2010

To elucidate potential roles of CUL4-DDB1-DWD (for Cullin 4-Damaged DNA Binding1-DDB1 binding WD40) E3 ligases in abscisic acid (ABA) signaling, we examined ABA sensitivities of T-DNA mutants of a number of Arabidopsis thaliana DWD genes, which encode substrate receptors for CUL4 E3 ligases. Mutants in two DWD genes, DWA1 and DWA2 (DWD hypersensitive to ABA1 and 2), had ABA-hypersensitive phenotypes. Both proteins interacted with DDB1 in yeast two-hybrid assays and associated with DDB1 and CUL4 in vivo, implying they could form CUL4-based complexes. Several ABA-responsive genes were hyperinduced in both mutants, and the ABA-responsive transcription factors ABA INSENSITIVE 5 (ABI5) and MYC2 accumulated to high levels in the mutants after ABA treatment. Moreover, ABI5 interacted with DWA1 and DWA2 in vivo. Cell-free degradation assays showed ABI5 was degraded more slowly in dwa1 and dwa2 than in wild-type cell extracts. Therefore, DWA1 and/or DWA2 may be the substrate receptors for a CUL4 E3 ligase that targets ABI5 for degradation. Our data indicate that DWA1 and DWA2 can directly interact with each other, and their double mutants exhibited enhanced ABA and NaCl hypersensitivities, implying they can act together. This report thus describes a previously unknown heterodimeric cooperation between two independent substrate receptors for CUL4-based E3 ligases.
Phospholipase A2 Is Required for PIN-FORMED Protein Trafficking to the Plasma Membrane in theArabidopsisRoot
Authors: Lee Ok Ran , Kim Soo Jin , Kim Hae Jin , Hong Jeum Kyu , Ryu Stephen Beungtae , Lee Sang Ho , Ganguly Anindya , Cho Hyung-Taeg
Published: June 2010

Phospholipase A2 (PLA2), which hydrolyzes a fatty acyl chain of membrane phospholipids, has been implicated in several biological processes in plants. However, its role in intracellular trafficking in plants has yet to be studied. Here, using pharmacological and genetic approaches, the root hair bioassay system, and PIN-FORMED (PIN) auxin efflux transporters as molecular markers, we demonstrate that plant PLA2s are required for PIN protein trafficking to the plasma membrane (PM) in the Arabidopsis thaliana root. PLA2α, a PLA2 isoform, colocalized with the Golgi marker. Impairments of PLA2 function by PLA2α mutation, PLA2-RNA interference (RNAi), or PLA2 inhibitor treatments significantly disrupted the PM localization of PINs, causing internal PIN compartments to form. Conversely, supplementation with lysophosphatidylethanolamine (the PLA2 hydrolytic product) restored the PM localization of PINs in the pla2α mutant and the ONO-RS-082–treated seedling. Suppression of PLA2 activity by the inhibitor promoted accumulation of trans-Golgi network vesicles. Root hair–specific PIN overexpression (PINox) lines grew very short root hairs, most likely due to reduced auxin levels in root hair cells, but PLA2 inhibitor treatments, PLA2α mutation, or PLA2-RNAi restored the root hair growth of PINox lines by disrupting the PM localization of PINs, thus reducing auxin efflux. These results suggest that PLA2, likely acting in Golgi-related compartments, modulates the trafficking of PIN proteins.
ArabidopsisRETINOBLASTOMA-RELATED Is Required for Stem Cell Maintenance, Cell Differentiation, and Lateral Organ Production
Authors: Borghi Lorenzo , Gutzat Ruben , Fütterer Johannes , Laizet Yec'han , Hennig Lars , Gruissem Wilhelm
Published: June 2010

Several genes involved in the regulation of postembryonic organ initiation and growth have been identified. However, it remains largely unclear how developmental cues connect to the cell cycle. RETINOBLASTOMA RELATED (RBR) is a plant homolog of the tumor suppressor Retinoblastoma (pRb), which is a key regulator of the cell cycle. Using inducible RNA interference (RNAi) against Arabidopsis thaliana  RBR (RBRi), we reduced RBR expression levels at different stages of plant development. Conditional reduction or loss of RBR function disrupted cell division patterns, promoted context-dependent cell proliferation, and negatively influenced establishment of cell differentiation. Several lineages of toti- and pluripotent cells, including shoot apical meristem stem cells, meristemoid mother cells, and procambial cells, failed to produce appropriately differentiated cells. Meristem activity was altered, leading to a disruption of the CLAVATA-WUSCHEL feedback loop and inhibition of lateral organ formation. Release of RBR from RNAi downregulation restored meristem activity. Gene profiling analyses soon after RBRi induction revealed that a change in RBR homeostasis is perceived as a stress, even before genes regulated by RBR-E2F become deregulated. The results establish RBR as a key cell cycle regulator required for coordination of cell division, differentiation, and cell homeostasis.
The Conserved Splicing Factor SUA Controls Alternative Splicing of the Developmental Regulator ABI3 in Arabidopsis
Authors: Sugliani Matteo , Brambilla Vittoria , Clerkx Emile J.M. , Koornneef Maarten , Soppe Wim J.J.
Published: June 2010

ABSCISIC ACID INSENSITIVE3 (ABI3) is a major regulator of seed maturation in Arabidopsis thaliana. We detected two ABI3 transcripts, ABI3-α and ABI3-β, which encode full-length and truncated proteins, respectively. Alternative splicing of ABI3 is developmentally regulated, and the ABI3-β transcript accumulates at the end of seed maturation. The two ABI3 transcripts differ by the presence of a cryptic intron in ABI3-α, which is spliced out in ABI3-β. The suppressor of abi3-5 (sua) mutant consistently restores wild-type seed features in the frameshift mutant abi3-5 but does not suppress other abi3 mutant alleles. SUA is a conserved splicing factor, homologous to the human protein RBM5, and reduces splicing of the cryptic ABI3 intron, leading to a decrease in ABI3-β transcript. In the abi3-5 mutant, ABI3-β codes for a functional ABI3 protein due to frameshift restoration.
Seniority and gender differences in 360‐degree assessments of influencing, leadership and team behaviours. Part 2: Gender differences, conclusions and implications
Authors: Manning Tony , Robertson Bob
Published: June 2010

Purpose

The purpose of this two‐part paper is to present and discuss research into gender and seniority differences in 360‐degree assessments of influencing, leadership and team behaviours.

Design/methodology/approach

The article builds on a previous article on influencing behaviour and 360‐degree assessments that found a statistically significant positive relationship between these two sets of variables. However, the strength of this relationship was found to vary, depending on the seniority and gender of individuals. This article extends the previous one in two ways. Firstly, it examines four hypotheses to explain the earlier findings. Secondly, it introduces data on two other types of behaviour – leadership and team behaviour – in relation to 360‐degree performance assessments.

Findings

The authors found support for the first hypothesis. The 360‐degree assessments are affected by seniority. Influencing behaviour is more closely linked to 360‐degree assessments of middle managers who tend to have less legitimate power. The authors found little support for the second hypothesis. The 360‐degree assessments were strongly related to leadership and team behaviours in senior managers, as well as middle managers. The authors found clear evidence to support the third hypothesis that male and female managers were judged by different gender stereotypes. The authors also found support for the fourth hypothesis that male and female managers tended to do different jobs.

Originality/value

The originality and value of this paper lies in its examination of the relationship between three different types of behaviour (i.e. influencing, leadership and team working) and 360‐degree assessments of performance, including seniority and gender differences. It combines theory and research as a basis for practice. It draws on relevant theory on influencing, team working and leadership, presents empirical evidence, examines possible interpretations, draws practical conclusions and discusses their implications. The findings have implications for the use of 360‐degree assessments, challenge universal prescriptions about leadership and management, provide guidelines about the development needs of managers as they move from middle to senior management levels, and highlight particular problems for female managers making the transition.
Rural small business finance: evidence from the 1998 survey of small business finances
Authors: Gustafson Cole R.
Published: June 2010

The 1998 Survey of Small Business Finances provides robust information on the financing of small businesses, including an overview of the firms’ organization, financial characteristics, and credit use. Information from the survey is used in this study to compare the financial characteristics of metro and rural small businesses. While many financial characteristics are similar, rural small businesses do own more land and depreciable assets, and have lower inventory and other current assets when compared to metro firms. Rural firms have relatively similar access to technology and financial services, although utilization varies. Both metro and rural small businesses rely on a wide variety of sources for financing; however, rural small businesses have significantly more mortgages, loans from shareholders, and other types of loans, but fewer credit cards. Use of nonparametric rank order statistical methods was required because normality assumptions were violated due to asymmetric distribution of small firms.
Risk management strategy evaluation for corn and soybean producers
Authors: Pritchett James G. , Patrick George F. , Collins Kurt J. , Rios Ana
Published: June 2010

Returns to a model farm are simulated to assess the impact of marketing and insurance risk management tools as measured by mean net returns and returns at 5% value‐at‐risk (VaR). Results indicate that revenue insurance strategies and strategies involving a combination of price and yield protection provide substantial downside revenue protection, while mean net returns only modestly differ from the benchmark harvest sale strategy when considering all years between 1986 and 2000.
Bank risk ratings and the pricing of agricultural loans
Authors: Walraven Nick , Barry Peter J.
Published: June 2010

This paper reviews the prevalence of the use of risk ratings by commercial banks that participated in the Federal Reserve’s Survey of Terms of Bank Lending to Farmers between 1997 and 2002. Adoption of risk rating procedures held about steady over the period, with a little less than half the banks on the panel either not using a risk rating system, or reporting the same rating for all their loans in the survey. However, most of these banks were small, and roughly four‐fifths of all sample loans carried an informative risk rating. After controlling for the size and performance of the bank and as many nonprice terms of the loan as possible, findings reveal that banks consistently charged higher rates of interest for the farm loans they characterized as riskier, with an average difference in rates between the most risky and least risky loans of about 1 and a half percentage points.
Economic analysis of the standard reinsurance agreement
Authors: Vedenov Dmitry V. , Miranda Mario J. , Dismukes Robert , Glauber Joseph W.
Published: June 2010

An economic analysis is presented of the Standard Reinsurance Agreement (SRA), the contract governing the relationship between the Federal Crop Insurance Corporation and the private insurance companies that deliver crop insurance products to farmers. The paper outlines provisions of the SRA and describes the modeling methodology behind the SRA simulator, a computer program developed to assist crop insurers and policy makers in assessing the economic impact of the Agreement. The simulator is then used to analyze how the SRA affects returns from underwriting crop insurance. The results are presented in aggregate and also at the regional and individual company levels.
Competition in farm credit markets: identifying market segments served by the farm credit system and commercial banks
Authors: Dodson Charles B. , Koenig Steven R.
Published: June 2010

Agricultural credit markets are dominated by two institutional retail lender groups, the cooperative Farm Credit System (FCS) and commercial banks. Analysis of farm loans made over the 1991S1993 and 2001S2002 periods indicates that FCS lenders were more likely to serve full‐time commercial farmers and farmers located in regions with less competitive credit markets. In contrast, commercial banks were more likely to serve small, part‐time, and hobby farmers. This segmentation of farm credit markets is consistent with federal regulations requiring the FCS to provide credit to “bona fide” farmers with a basis for credit.
Farm financial structure
Authors: Featherstone Allen M. , Ibendahl Gregory A. , Randy Winter J. , Spaulding Aslihan
Published: June 2010

The structure of U.S. agriculture is a topic of relevance to farmers, policy makers, farm organizations, and academics. Over the last century, farm financial structure issues have become extremely important as the United States moved from an agrarian economy to a more industrialized one. Traditionally analyzed topics such as optimal capital structure, equity capital markets, entry into production agriculture by beginning farmers, and tax issues remain important. Societal effects caused by changing farm financial structure and the effect on the rural landscape are issues needing further research. Finally, research is needed on farm financial structure changes in other regions of the world that may affect the competitiveness of U.S. agriculture.
The sustainability of return on assets among sectors in the food economy
Authors: Boland Michael , Schumacher Sara
Published: June 2010

Using return on assets as a proxy for profitability, this study evaluates the sustainability of profits in the food economy with respect to industry, corporate, and business‐specific effects for low‐ and high‐performing firms. The food economy is broken into its four major sectors: food processing, wholesale grocery, retail supermarket, and restaurant. Industry incremental effects are not significantly different between low and high performers except in processing. On average, high performance has been more sustainable than low performance. Corporate and segment sustainability rates were larger for high performers as compared to low performers. Within the retail industry, there is no significant difference between sustainability rates of high and low performers. High performers in the retail industry had significantly greater industry, business‐segment, and total‐sum sustainability rates than the other three sectors, suggesting the retail sector has important characteristics that merit further research.
Farmland valuation and asset performance
Authors: Moss Charles B. , Katchova Ani L.
Published: June 2010

The first theme addressed in this paper is agricultural asset performance. The low rate of return on agricultural assets has been of particular interest to policy makers. From a market portfolio perspective, several studies have analyzed the relationship between farm asset returns and systematic market factors, concluding that farmland adds little systematic risk to a well‐diversified portfolio. Because asset values adjust so that the return to each asset is in equilibrium with its relative risk, any persistent low return on agricultural assets may be due to differences in relative risk. The paper’s second theme is the valuation of farmland in the United States. Numerous studies have examined the factors affecting farmland values. Most have used the standard present value capitalization formula relating land values to land rents, although these models have been rejected by empirical data. Several studies have reformulated and improved the performance of the present value models. Since changes in rates of return of agricultural assets and land values can have drastic consequences for farmers’ wealth and sector solvency, future research needs in this area will continue.
U.S. macroeconomic and tax policy: impacts on U.S. farm operations
Authors: Covey Ted , Durst Ron , Ryan Jim
Published: June 2010

Agricultural economists have generally concluded that macroeconomic and tax policy matters regarding the financial wellbeing of U.S. farm operations. Farm operations react more quickly and with greater response to both anticipated and unanticipated macroeconomic policy changes than do the commercial business operations, sometimes resulting in overshooting in the agricultural economy. In the early 1980s, the Federal Reserve’s disinflationary policy and large federal budget deficits had disproportionately large effects on real agricultural interest rates. This paper concludes with a presentation of numerous potential researchable issues regarding macroeconomic and tax policy’s impact on farm financial well‐being.
Research on USDA farm credit programs: past, present, and future
Authors: Ahrendsen Bruce L. , Dodson Charles B. , Dixon Bruce L. , Koenig Steven R.
Published: June 2010

Federal farm credit programs currently administered by the USDA were initiated in the early 1900s to help the farm sector cope with natural disasters, and these programs have continued to evolve. There has been a rich history of research analyzing USDA farm credit programs and the effects they have had on farmers, ranchers, and credit markets. This paper highlights past research and offers a view of the future direction of research on federal farm credit programs.
Permanent and expanded: chapter 12 bankruptcy regulations following BAPCPA
Authors: O’Neill Barbara
Published: June 2010

The purpose of this article is to describe Chapter 12 of the Federal Bankruptcy Code and recent changes in federal bankruptcy legislation that affect family farmers and fishermen. Chapter 12 provides debt relief to financially stressed family farmers and, since 2005, fishermen with regular income. It was first enacted in 1986, in response to the farm financial crisis of the early‐ to mid‐1980s, and was subsequently renewed by Congress until being made a permanent part of the Bankruptcy Code on July 1, 2005. This article provides an overview of the history and procedural aspects of Chapter 12 bankruptcy for family farmers and fishermen who are experiencing financial distress. It also discusses changes to the Bankruptcy Code enacted in 2005 under the Bankruptcy Abuse Prevention and Consumer Protection Act (BAPCPA) that affect the agricultural community.
Managing economic risk caused by insects: bug options
Authors: Richards Timothy J. , Eaves James , Fournier Valerie , Naranjo S.E. , Chu C.‐C. , Henneberry T.J.
Published: June 2010

The market for insuring insect damage is far from complete. This study introduces a new type of derivative instrument‐insect derivatives‐that provide growers a market‐based means of transferring insect risk to speculators or others who may profit from higher insect populations. A risk‐neutral valuation model is developed and applied to Bemisia tabaci population data. Economic simulation models show how insect derivatives can improve risk‐return results for a representative cotton farm in the Imperial Valley of California. The results suggest that insect derivatives may become important risk management tools for a wide range of growers.
Rates of return on U.S. farm investments, 1940‐2003: a comparison of imputed returns versus residual income approaches
Authors: Moss Charles B. , Mishra Ashok K. , Erickson Kenneth W.
Published: June 2010

The rate of return on farm assets is a key indicator of the profitability of farm sector investments. The residual income approach is most commonly used to estimate the returns to farm assets, farmland, and labor and management. However this approach may be sensitive to the underlying assumptions. This study examines the implications of the residual return assumption by using alternative formulations for computing the rate of return to farm assets. Specifically, we develop the rate of return on agricultural assets using an alternative imputation method. We demonstrate that the presence of multiple quasi‐fixed factors implies the rate of return to farm assets may be understated by the residual income approach.
An overview of recent developments in the microfinance literature
Authors: Hartarska Valentina M. , Holtmann Martin
Published: June 2010

This paper presents an overview of microfinance and microfinance research. The objective is to show that microfinance research has come full circle: from policies to lending methodologies and to organizations in the 1990s, and back to a focus on policies. Specifically, developments in the theoretical literature on asymmetric information, transaction costs, contracts, and banking identify the challenges that MFIs must overcome. Recent trends toward intermediation and commercialization have brought about renewed focus on identifying appropriate policies to promote a viable microfinance industry. The paper concludes by describing some current challenges faced by the industry and offers a possible research agenda for agricultural economists.
Microfinance in developing countries: accomplishments, debates, and future directions
Authors: Meyer Richard L. , Nagarajan Geetha
Published: June 2010

This paper provides an overview of the microfinance industry in developing countries. It highlights the early development of the concept of microfinance and identifies some of the key issues and debates concerning its performance in terms of outreach, sustainability, and impact. Studies are summarized that report on industry performance by region. The frontiers for the industry involve broadening the range and diversity of services provided to existing clients and expanding services to difficult‐to‐reach populations, especially the remote, poorest, and the youth. In countries where the industry is still small and fledgling, the challenge is often one of addressing the problems of reaching people in remote and conflict‐affected areas.
A comparative review of major types of rural microfinance institutions in developing countries
Authors: Zeller Manfred
Published: June 2010

This paper describes different types of rural microfinance institutions, and examines their comparative advantages as well as related challenges to and strategies for deepening rural financial systems. The focus is not about which type of institution is better or worse for a particular target clientele in a particular operating environment. Instead, one of the major recommendations of this study is that there is no blueprint for rural microfinance. Institutional diversity is desired to enhance competition, depth and breadth of outreach, and welfare impact.
The Uganda rural farmers scheme: women’s accessibility to agricultural credit
Authors: Abaru Biruma M. , Mugera Amin W. , Norman David W. , Featherstone Allen M.
Published: June 2010

This study investigates factors related to loan approval, disbursement, repayment, and loan rationing among 1,012 farmers in the Rural Farmers Scheme (RFS), Uganda, between 1987 and May 1995. Results indicate that women had a higher loan approval rate and loan repaid/loan borrowed ratio than men, but lower actual disbursement levels. Loan rationing among women and men was not statistically different, and no justification was found for microfinance institutions discriminating against women in giving loans based on repayment rates. A wide gap exists between loan amounts approved and disbursed. Strategies are outlined for improving the pool of women loan applicants.
A dynamic model of individual and group lending in developing countries
Authors: Katchova Ani L. , Miranda Mario J. , Gonzalez‐Vega Claudio
Published: June 2010

This paper examines the contract design problem of microfinance institutions seeking to maximize outreach to the poor while remaining financially sustainable. A dynamic model of group lending is developed that shows how optimal interest rates depend on information regarding moral hazard and adverse selection problems, correlated project risks, and strategic default. Relative to traditional static models, the results indicate a dynamic model better explains the current experience with individual and group lending in developing countries.