bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of tomato BRANCHED1‐like genes in the control of shoot branching
Authors: Martín‐Trillo Mar , Grandío Eduardo González , Serra François , Marcel Fabien , Rodríguez‐Buey María Luisa , Schmitz Gregor , Theres Klaus , Bendahmane Abdelhafid , Dopazo Hernán , Cubas Pilar
Published: May 2011

In angiosperms, shoot branching greatly determines overall plant architecture and affects fundamental aspects of plant life. Branching patterns are determined by genetic pathways conserved widely across angiosperms. In Arabidopsis thaliana (Brassicaceae, Rosidae) BRANCHED1 (BRC1) plays a central role in this process, acting locally to arrest axillary bud growth. In tomato (Solanum lycopersicum, Solanaceae, Asteridae) we have identified two BRC1‐like paralogues, SlBRC1a and SlBRC1b. These genes are expressed in arrested axillary buds and both are down‐regulated upon bud activation, although SlBRC1a is transcribed at much lower levels than SlBRC1b. Alternative splicing of SlBRC1a renders two transcripts that encode two BRC1‐like proteins with different C‐t domains due to a 3′‐terminal frameshift. The phenotype of loss‐of‐function lines suggests that SlBRC1b has retained the ancestral role of BRC1 in shoot branch suppression. We have isolated the BRC1a and BRC1b genes of other Solanum species and have studied their evolution rates across the lineages. These studies indicate that, after duplication of an ancestral BRC1‐like gene, BRC1b genes continued to evolve under a strong purifying selection that was consistent with the conserved function of SlBRC1b in shoot branching control. In contrast, the coding sequences of Solanum BRC1a genes have evolved at a higher evolution rate. Branch‐site tests indicate that this difference does not reflect relaxation but rather positive selective pressure for adaptation.
Wheat flowering repressor VRN2 and promoter CO2 compete for interactions with NUCLEAR FACTOR‐Y complexes
Authors: Li Chengxia , Distelfeld Assaf , Comis Alfio , Dubcovsky Jorge
Published: May 2011

The transition from vegetative to reproductive development in the temperate cereals is mainly regulated by seasonal cues including vernalization (determined mainly by VRN1 and VRN2 genes) and photoperiod (determined mainly by PPD1 and CO2 genes). The wheat VRN3 gene, which is similar to Arabidopsis FT, plays a central role in the integration of the competing signals from these two pathways. Under long days, VRN3 transcription is down‐regulated by VRN2, a unique flowering repressor in cereals, and up‐regulated by CO2. Overexpression of VRN3 overcomes VRN2 repression and promotes VRN1 transcription and flowering initiation. Using yeast two‐ and three‐hybrid assays we show here that the CCT domains present in VRN2 and CO2 proteins interact with the same subset of eight NF‐Y proteins, and that these CCT proteins compete with NF‐YA for interactions with NF‐YB proteins. We have confirmed all these interactions in vitro, and the interactions between VRN2 and two of the three NF‐YB proteins were further confirmed in planta. In addition, we show that mutations in the CCT domain of VRN2 that eliminate the vernalization requirement in winter wheat also reduce the strength of the interactions between VRN2 and NF‐Y proteins, and the ability of VRN2 to compete with CO2. Taken together, our results suggest that the interactions between CCT and NF‐Y proteins play an important role in the integration of the vernalization and photoperiod seasonal signals, and provide a flexible combinatorial system to integrate multiple developmental and environmental signals in the regulation of flowering initiation in the temperate cereals.
Pseudomonas syringae colonizes distant tissues in Nicotiana benthamiana through xylem vessels
Authors: Misas‐Villamil Johana C. , Kolodziejek Izabella , van der Hoorn Renier A. L.
Published: May 2011

The ability to move from the primary infection site and colonize distant tissue in the leaf is an important property of bacterial plant pathogens, yet this aspect has hardly been investigated for model pathogens. Here we show that GFP‐expressing Pseudomonas syringae pv. syringae DC3000 that lacks the HopQ1‐1 effector (PtoDC3000ΔhQ) has a strong capacity to colonize distant leaf tissue from wound‐inoculated sites in N. benthamiana. Distant colonization occurs within 1 week after toothpick inoculation and is characterized by distant colonies in the apoplast along the vasculature. Distant colonization is blocked by the non‐host resistance response triggered by HopQ1‐1 in an SGT1‐dependent manner and is associated with an explosive growth of the bacterial population, and displays robust growth differences between compatible and incompatible interactions. Scanning electron microscopy revealed that PtoDC3000ΔhQ bacteria are present in xylem vessels, indicating that they use the xylem to move through the leaf blade. Distant colonization does not require flagellin‐mediated motility, and is common for P. syringae pathovars that represent different phylogroups.
3D position of pericentromeric heterochromatin within the nucleus of a patient with ICF syndrome
Authors: Dupont C , Guimiot F , Perrin L , Marey I , Smiljkovski D , Le Tessier D , Lebugle C , Baumann C , Bourdoncle P , Tabet A‐C , Aboura A , Benzacken B , Dupont J‐M
Published: May 2011

Dupont C, Guimiot F, Perrin L, Marey I, Smiljkovski D, Le Tessier D, Lebugle C, Baumann C, Bourdoncle P, Tabet A‐C, Aboura A, Benzacken B, Dupont J‐M. 3D position of pericentromeric heterochromatin within the nucleus of a patient with ICF syndrome.

ICF (immunodeficiency, centromeric region instability, facial anomalies) syndrome is a rare autosomal recessive disorder characterised by severe immunodeficiency, craniofacial anomalies and chromosome instability. Chromosome analyses from blood samples show a high frequency of decondensation of pericentromeric heterochromatin (PH) and rearrangements involving chromosomes 1 and 16. It is the first and, as far as we know, the only disease associated with a mutation in a DNA methyltransferase gene, DNMT3B, with significant hypomethylation of the classical satellite DNA, the major component of the juxtacentromeric heterochromatin. To better understand the complex links between the hypomethylation of the satellite DNA, the cytogenetic anomalies and the clinical features of ICF syndrome, we performed three‐dimensional (3D) FISH on preserved cells from a patient with a suspected ICF phenotype. Analysis of DNMT3B did not reveal any mutation in our patient, making this case an ICF type 2. The results of 3D‐FISH showed a statistically significant change in the intranuclear position of PH of chromosome 1 in cells of the patient as compared to normal cells. It is difficult to understand how a defect in the methylation pathway can be responsible for the various symptoms of this condition. From our observations we suggest a mechanistic link between the reorganisation of the nuclear architecture and the altered gene expression.
CHD7 mutations causing CHARGE syndrome are predominantly of paternal origin
Authors: Pauli S , von Velsen N , Burfeind P , Steckel M , Mänz J , Buchholz A , Borozdin W , Kohlhase J
Published: May 2011

Pauli S, von Velsen N, Burfeind P, Steckel M, Mänz J, Buchholz A, Borozdin W, Kohlhase J. CHD7 mutations causing CHARGE syndrome are predominantly of paternal origin.

CHARGE (coloboma, heart defects, atresia of the choanae, retarded growth and development, genital hypoplasia, ear anomalies and deafness) syndrome is a congenital malformation syndrome caused by mutations in the CHD7 gene in approximately 2/3 of cases. In the vast majority of cases, CHARGE syndrome is sporadic. There are only a few reports of parent‐to‐child transmission and somatic or gonadal mosaicism. To determine the parental origin of CHD7 mutations in sporadic CHARGE syndrome, we screened 30 families for informative exonic or intronic polymorphisms located near the detected CHD7 mutation. An informative polymorphism could be identified in 13 out of 30 families. Linkage analysis was performed between the CHD7 mutation and the polymorphism in the child. In 12 out of 13 families, the mutation affected the paternal allele (92.3%). In our cohort, the mean paternal age at birth was 32.92 years. Comparing the age of fathers of an affected CHARGE patient with the paternal age of the German population in general, we could not observe any paternal age effect. Taken together, we show in this study that de novo CHD7 mutations occur predominantly in the male germ line.
Inhibition of peripheral blood natural killer cell cytotoxicity in patients with myasthenia gravis treated with plasmapheresis
Authors: Chien P. J. , Yeh J. H. , Chiu H. C. , Hsueh Y. M. , Chen C. T. , Chen M. C. , Shih C. M.
Published: May 2011

Background and purpose:  Myasthenia gravis (MG) is an autoimmune disorder that may involve natural killer (NK) cells. Although NK cells are part of the innate immune system, they also influence adaptive immune responses. Double‐filtration plasmapheresis (DFP) is an effective therapy for MG crisis. Thus, we examined the effects of DFP on the cytotoxicity of NK cells.

Methods:  A total of 20 patients with MG and 16 healthy controls were recruited for the study. Ficoll‐Paque‐isolated peripheral blood mononuclear cells (PBMCs) and K562 cells were used as the effector and target cells, respectively. NK cell cytotoxicity was analyzed using flow cytometry immediately before and after DFP and upon course completion.

Results:  Double‐filtration plasmapheresis treatment decreased significantly the NK cell cytotoxicity in patients with MG, especially in good responders, those who were positive for acetylcholine receptor (AChR) antibodies, and those receiving immunosuppressants.

Conclusions:  The decrease in NK cell cytotoxicity after DFP and the decline of AChR antibody titer were observed in good responders indicating that this could benefit patients with MG.
Optimizing the risk estimation after a transient ischaemic attack – the ABCDE⊕ score
Authors: Engelter S. T. , Amort M. , Jax F. , Weisskopf F. , Katan M. , Burow A. , Bonati L. H. , Hatz F. , Wetzel S. G. , Fluri F. , Lyrer P. A.
Published: May 2011

Background and purpose:  The risk of stroke after a transient ischaemic attack (TIA) can be predicted by scores incorporating age, blood pressure, clinical features, duration (ABCD‐score), and diabetes (ABCD2‐score). However, some patients have strokes despite a low predicted risk according to these scores. We designed the ABCDE+ score by adding the variables ‘etiology’ and ischaemic lesion visible on diffusion‐weighted imaging (DWI) –‘DWI‐positivity’– to the ABCD‐score. We hypothesized that this refinement increases the predictability of recurrent ischaemic events.

Methods:  We performed a prospective cohort study amongst all consecutive TIA patients in a university hospital emergency department. Area under the computed receiver‐operating curves (AUCs) were used to compare the predictive values of the scores with regard to the outcome stroke or recurrent TIA within 90 days.

Results:  Amongst 248 patients, 33 (13.3%, 95%‐CI 9.3–18.2%) had a stroke (n = 13) or a recurrent TIA (n = 20). Patients with recurrent ischaemic events more often had large‐artery atherosclerosis as the cause for TIA (46% vs. 14%, P < 0.001) and positive DWI (61% vs. 35%; P = 0.01) compared with patients without recurrent events. Patients with and those without events did not differ with regard to age, clinical symptoms, duration, blood pressure, risk factors, and stroke preventive treatment. The comparison of AUCs [95%CI] showed superiority of the ABCDE+ score (0.67[0.55–0.75]) compared to the ABCD2‐score (0.48[0.37–0.58]; P = 0.04) and a trend toward superiority compared to the ABCD‐score (0.50[0.40–0.61]; P = 0.07).

Conclusion:  In TIA patients, the addition of the variables ‘etiology’ and ‘DWI‐positivity’ to the ABCD‐score seems to enhance the predictability of subsequent cerebral ischaemic events.
Muscle cells and motoneurons differentially remove mutant SOD1 causing familial amyotrophic lateral sclerosis
Authors: Onesto Elisa , Rusmini Paola , Crippa Valeria , Ferri Nicola , Zito Arianna , Galbiati Mariarita , Poletti Angelo
Published: May 2011

J. Neurochem. (2011) 118, 266–280.

Amyotrophic lateral sclerosis (ALS) is a fatal motoneuronal disease which occurs in sporadic or familial forms, clinically indistinguishable. About 15% of familial ALS cases are linked to mutations of the superoxide dismutase 1 (SOD1) gene that may induce misfolding in the coded protein, exerting neurotoxicity to motoneurons. However, other cell types might be target of SOD1 toxicity, because muscle‐restricted expression of mutant SOD1 correlates with muscle atrophy and motoneurons death. We analysed the molecular behaviour of mutant SOD1 in motoneuronal NSC34 and muscle C2C12 cells. We found that misfolded mutant SOD1 clearance is much more efficient in muscle C2C12 than in motoneuronal NSC34 cells. Mutant SOD1 forms aggregates and impairs the proteasome only in motoneuronal NSC34 cells. Interestingly, NSC34 cells expressing mutant SOD1 are more sensitive to a superoxide‐induced oxidative stress. Moreover, in muscle C2C12 cells mutant SOD1 remains soluble even when proteasome is inhibited with MG132. The higher mutant SOD1 clearance in muscle cells correlates with a more efficient proteasome activity, combined with a robust autophagy activation. Therefore, muscle cells seem to better manage misfolded SOD1 species, not because of an intrinsic property of the mutant protein, but in function of the cell environment, indicating also that the SOD1 toxicity at muscle level may not directly depend on its aggregation rate.
β‐N‐Oxalyl‐l‐α,β‐diaminopropionic acid regulates mitogen‐activated protein kinase signaling by down‐regulation of phosphatidylethanolamine‐binding protein 1
Authors: Jammulamadaka Nalini , Burgula Sandeepta , Medisetty Rajesh , Ilavazhagan Govindan , Rao S. L. N. , Singh Surya S.
Published: May 2011

J. Neurochem. (2011) 118, 176–186.

β‐N‐Oxalyl‐l‐α,β‐diaminopropionic acid (l‐ODAP) an α‐amino‐3‐hydroxy‐5‐ methyl‐4‐isoxazole propionic acid (AMPA) receptor agonist activates protein kinase C in white leghorn chick brain. The current study focuses on the protein kinase C downstream signaling targets associated with l‐ODAP excitotoxicity in SK‐N‐MC human neuroblastoma cells and white leghorn male chick (Gallus domesticus) brain extracts. l‐ODAP treatment in SK‐N‐MC cells (1.5 mM) and chicks (0.5 mg/g body weight) results in a decreased expression and increased phosphorylation of phosphatidylehthanolamine‐binding protein 1 (PEBP1) up to 4 h which however, returns to normal by 8 h. d‐ODAP, the non‐toxic enantiomer however, did not affect PEBP1 levels in either chick brain or SK‐N‐MC cells. Decreased PEBP1 expression correlated with subsequent activation of Raf‐1, MEK and ERK signaling components of the mitogen‐activated protein kinase cascade and nuclear translocation of hypoxia inducible factor‐1α (HIF‐1α) in chick brain nuclear extracts and SK‐N‐MC cells. SK‐N‐MC cells over‐expressing PEBP1 inhibited nuclear translocation of HIF‐1α when treated with l‐ODAP, indicating that down‐regulation of PEBP1 is responsible for HIF‐1α stabilization and nuclear localization. Excitotoxicity of l‐ODAP may thus be the result of phosphorylation and down‐regulation of PEBP1, a crucial signaling protein regulating diverse signaling cascades. l‐ODAP induced convulsions and seizures in chicks could be the result of a hypoxic insult to brain.
rho1 GABAC receptors are expressed in fibrous and cartilaginous layers of chick sclera and located on sclera fibroblasts and chondrocytes
Authors: Cheng Zhen‐Ying , Chebib Mary , Schmid Katrina L.
Published: May 2011

J. Neurochem. (2011) 118, 281–287.

rho1 GABAC receptor antagonists inhibit myopia in chick but the site of this effect is not known. The sclera ultimately determines the shape and size of the globe and thus an untested possibility is that GABA agents have a scleral mechanism. Whether rho1 GABAC receptors are expressed and located in chick sclera is unknown. Real‐time PCR, western blot and immunohistochemistry were used to determine whether rho1 GABAC receptors are expressed and located in chick fibrous and cartilaginous sclera. Both layers of the chick sclera were positive for rho1 GABAC receptor mRNA (PCR) and protein (western blot) expression and labeling was observed in both fibroblasts and chondrocytes of the fibrous and cartilaginous layers (immunohistochemistry). These investigations clearly show that chick sclera possesses rho1 GABAC receptors. The sclera is thus a potential previously unrecognized site for activity of rho1 GABAC agents.
Intersectionality, Metaphors, and the Multiplicity of Gender
Authors: Garry Ann
Published: May 2011

Although intersectional analyses of gender have been widely adopted by feminist theorists in many disciplines, controversy remains over their character, limitations, and implications. I support intersectionality, cautioning against asking too much of it. It provides standards for the uses of methods or frameworks rather than theories of power, oppression, agency, or identity. I want feminist philosophers to incorporate intersectional analyses more fully into our work so that our theories can, in fact, have the pluralistic and inclusive character to which we give lip service. To this end, I advocate an intersectional family resemblance strategy that does not create philosophical problems for feminists. I test my approach against María Lugones's argument in “Heterosexualism and the Colonial/Modern Gender System” (Lugones 2007) to determine, in particular, whether we can successfully resist a move to create multiple genders for women. If we can successfully resist this move, then we can answer the objection that intersectionality fragments women both theoretically and politically. I also argue that my approach avoids Lugones's critique of forms of intersectionality that fall within “the logic of purity.”
Conceptions of Care: Altruism, Feminism, and Mature Care
Authors: Pettersen Tove
Published: May 2011

In “Conceptions of Care,” Tove Pettersen discusses and articulates select ways in which care can be comprehended. Several difficulties related to an altruistic understanding of care are examined before the author presents the case for a more favorable concept: mature care. Mature care is intended to take into account the interests of both parties to the caring relationship. This understanding of care facilitates the expression of the relational and reciprocal aspects of caring while emphasizing the equal worth of all involved. Also attended to is the embeddedness of care in wider cultural and political contexts.
Donna Haraway's Cyborg Touching (Up/On) Luce Irigaray's Ethics and the Interval Between: Poethics as Embodied Writing
Authors: Toye Margaret E.
Published: May 2011

In this article, I argue that Donna Haraway's figure of the cyborg needs to be reassessed and extricated from the many misunderstandings that surround it. First, I suggest that we consider her cyborg as an ethical concept. I propose that her cyborg can be productively placed within the ethical framework developed by Luce Irigaray, especially in relationship to her concept of the “interval between.” Second, I consider how Haraway's “cyborg writing” can be understood as embodied ethical writing, that is, as a contemporary écriture feminine. I believe that this cyborgian “writing the body” offers us a way of both creating and understanding texts that think through ethics, bodies, aesthetics, and politics together as part of a vital and relevant contemporary feminist ethics of embodiment. I employ the term “poethics” as a useful way to describe such a practice.
Ocular Blood Flow Analysis Detects Microvascular Abnormalities in Impaired Glucose Tolerance
Authors: QUINN CATHERINE E. , HAMILTON PAUL K. , McCANN AARON J. , AGNEW CHRISTINA E. , MILLAR AULEEN M. , LOCKHART CHRISTOPHER J. , HARBINSON MARK T. , McVEIGH GARY E.
Published: May 2011

Please cite this paper as: Quinn, Hamilton, McCann, Agnew, Millar, Lockhart, Harbinson and McVeigh (2011). Ocular Blood Flow Analysis Detects Microvascular Abnormalities in Impaired Glucose Tolerance. Microcirculation 18(7), 532–540.

Objective:  Waveform analysis has been used to assess vascular resistance and predict cardiovascular events. We aimed to identify microvascular abnormalities in patients with IGT using ocular waveform analysis. The effects of pioglitazone were also assessed.

Methods:  Forty patients with IGT and 24 controls were studied. Doppler velocity recordings were obtained from the central retinal, ophthalmic, and common carotid arteries, and sampled at 200 Hz. A discrete wavelet‐based analysis method was employed to quantify waveforms. The RI was also determined. Patients with IGT were randomized to pioglitazone or placebo, and measurements were repeated after 12‐week treatment.

Results:  In the ocular waveforms, significant differences in power spectra were observed in frequency band 4 (corresponding to frequencies between 6.25 and 12.50 Hz) between groups (p < 0.05). No differences in RI occurred. No association was observed between waveform parameters and fasting glucose or insulin resistance. Pioglitazone had no effect on waveform structure, despite significantly reducing insulin resistance, fasting glucose, and triglycerides (p < 0.05).

Conclusions:  Analysis of ocular Doppler flow waveforms using the discrete wavelet transform identified microvascular abnormalities that were not apparent using RI. Pioglitazone improved glucose, insulin sensitivity, and triglycerides without influencing the contour of the waveforms.
Differential expression of toll‐like receptor mRNAs in recurrent aphthous ulceration
Authors: Gallo Camila , Barros Fabiana , Sugaya Norberto , Nunes Fabio , Borra Ricardo
Published: May 2011

J Oral Pathol Med (2012) 41: 80–85

Background:  Toll‐like receptors (TLR) are membrane proteins that recognize conserved molecules derived from bacterial, viral, fungal or host tissues. They are responsible for promoting the production of cytokines and chemokines, increasing the expression of costimulatory molecules and influencing the T Helper response (Th) toward either a Th1 or Th2 profile, thereby modulating the regulatory T cell response and controlling the integrity of the epithelial barrier. The key factors responsible for increased susceptibility to recurrent aphthous ulceration (RAU) are unclear, and because TLRs are involved in both immune regulation and control of the epithelial barrier, a deficiency in TLR activity is likely to cause increased susceptibility.

Methods:  We investigated the gene expression of TLRs one through 10 in tissue samples and peripheral blood mononuclear cells (PBMC) of RAU patients in comparison to healthy controls using real‐time quantitative reverse transcription PCR.

Results:  The analysis of mRNA expression levels in oral lesion showed significant (P < 0.01) overexpression of the TLR2 (∼6‐fold) gene and decreased expression of the TLR3 (∼5‐fold) and TLR5 (∼6‐fold) genes in comparison with healthy oral mucosa. The analysis of mRNA expression in PBMC indicated a down‐regulation of TLR5 gene expression in the cells from RAU patients (P < 0.05; ∼2‐fold).

Conclusion:  Our results support the hypothesis that a subset of RAU patients has fewer TLR expression that have been tentatively implicated in anti‐inflammatory effects. This derangement of TLR gene expression may cause an overlay exuberant inflammation reaction in situations where normal individuals are resistant.
Cysteine Ubiquitination of PTS1 Receptor Pex5p Regulates Pex5p Recycling
Authors: Okumoto Kanji , Misono Sachi , Miyata Non , Matsumoto Yui , Mukai Satoru , Fujiki Yukio
Published: May 2011

Pex5p is the cytosolic receptor for peroxisome matrix proteins with peroxisome‐targeting signal (PTS) type 1 and shuttles between the cytosol and peroxisomes. Here, we show that Pex5p is ubiquitinated at the conserved cysteine11 in a manner sensitive to dithiothreitol, in a form associated with peroxisomes. Pex5p with a mutation of the cysteine11 to alanine, termed Pex5p‐C11A, abrogates peroxisomal import of PTS1 and PTS2 proteins in wild‐type cells. Pex5p‐C11A is imported into peroxisomes but not exported, resulting in its accumulation in peroxisomes. These results suggest an essential role of the cysteine residue in the export of Pex5p. Furthermore, domain mapping indicates that N‐terminal 158‐amino‐acid region of Pex5p‐C11A, termed 158‐CA, is sufficient for such dominant‐negative activity by binding to membrane peroxin Pex14p via its two pentapeptide WXXXF/Y motifs. Stable expression of either Pex5p‐C11A or 158‐CA likewise inhibits the wild‐type Pex5p import into peroxisomes, strongly suggesting that Pex5p‐C11A exerts the dominant‐negative effect at the translocation step via Pex14p. Taken together, these findings show that the cysteine11 of Pex5p is indispensable for two distinct steps, its import and export. The Pex5p‐C11A would be a useful tool for gaining a mechanistic insight into the matrix protein import into peroxisomes.
Perceptions of community trust and safety – consequences for children’s well‐being in rural and urban contexts
Authors: Eriksson Ulrika , Hochwälder Jacek , Sellström Eva
Published: May 2011

Aim:  To explore the associations between subjective well‐being and perceptions of community trust and safety amongst children in rural and urban areas.

Methods:  The study used self‐reported data from the 2001/2002 Swedish cross‐national WHO study Health Behaviour in School‐aged Children. The sample consisted of 3852 children aged 11–15 years, living in different residential areas. Bivariate analyses and multivariate logistic regression were performed.

Results:  The results indicated that a greater proportion of children in urban areas perceived low community trust and safety, compared with children in rural areas. Further, the multivariate analysis revealed that perceived community trust and safety significantly impacts upon children’s subjective well‐being in both rural and urban contexts.

Conclusion:  Children’s perceptions of trust and safety have different magnitudes in urban and rural areas. The associations of perceptions of community trust and safety for children’s subjective well‐being are relevant in both urban and rural areas. As perceptions of low trust and safety in the community seem to be related to low subjective well‐being, efforts to encourage community trust and safety should be included amongst the key priorities in community health promotion.
Unique ganglioside binding by botulinum neurotoxins C and D‐SA
Authors: Kroken Abby R. , Karalewitz Andrew P.‐A. , Fu Zhuji , Baldwin Michael R. , Kim Jung‐Ja P. , Barbieri Joseph T.
Published: May 2011

The botulinum neurotoxins (BoNTs) are the most potent protein toxins for humans. There are seven serotypes of BoNTs (A–G), based on a lack of cross‐antiserum neutralization. The BoNT/C and BoNT/D serotypes include mosaic toxins that are organized as D–C and C–D toxins. One BoNT D–C mosaic toxin, BoNT/D‐South Africa (BoNT/D‐SA), was not fully neutralized by immunization with a vaccine composed of either prototype BoNT/C‐Stockholm or BoNT/D‐1873. Whereas several BoNT serotypes utilize dual receptors (gangliosides and proteins) to bind to and enter neurons, the basis for BoNT/C and BoNT/D entry into neurons is less well understood. Recent studies solved the crystal structures of the receptor‐binding domains of BoNT/C, BoNT/D, and BoNT/D‐SA. Comparative structural analysis showed that BoNT/C, BoNT/D and BoNT/D‐SA lacked components of the ganglioside‐binding pocket that exists within other BoNT serotypes. With the use of structure‐based alignments, biochemical analyses, and cell‐binding approaches, BoNT/C and BoNT/D‐SA have been shown to possess a unique ganglioside‐binding domain, the ganglioside‐binding loop. Defining how BoNTs enter host cells provides insights towards understanding the evolution and extending the potential therapeutic and immunological values of the BoNT serotypes.
Roles of conserved arginines in ATP‐binding domains of AAA+ chaperone ClpB from Thermus thermophilus
Authors: Yamasaki Takashi , Nakazaki Yosuke , Yoshida Masasuke , Watanabe Yo‐hei
Published: May 2011

ClpB, a member of the expanded superfamily of ATPases associated with diverse cellular activities (AAA+), forms a ring‐shaped hexamer and cooperates with the DnaK chaperone system to reactivate aggregated proteins in an ATP‐dependent manner. The ClpB protomer consists of an N‐terminal domain, an AAA+ module (AAA‐1), a middle domain, and a second AAA+ module (AAA‐2). Each AAA+ module contains highly conserved WalkerA and WalkerB motifs, and two arginines (AAA‐1) or one arginine (AAA‐2). Here, we investigated the roles of these arginines (Arg322, Arg323, and Arg747) of ClpB from Thermus thermophilus in the ATPase cycle and chaperone function by alanine substitution. These mutations did not affect nucleotide binding, but did inhibit the hydrolysis of the bound ATP and slow the threading of the denatured protein through the central pore of the T. thermophilus ClpB ring, which severely impaired the chaperone functions. Previously, it was demonstrated that ATP binding to the AAA‐1 module induced motion of the middle domain and stabilized the ClpB hexamer. However, the arginine mutations of the AAA‐1 module destabilized the ClpB hexamer, even though ATP‐induced motion of the middle domain was not affected. These results indicated that the three arginines are crucial for ATP hydrolysis and chaperone activity, but not for ATP binding. In addition, the two arginines in AAA‐1 and the ATP‐induced motion of the middle domain independently contribute to the stabilization of the hexamer.

Structured digital abstract

 TClpB binds to TClpB by molecular sieving (View Interaction 1, 2)
The lipid translocase, ABCA4: seeing is believing
Authors: Pollock Naomi Laura , Callaghan Richard
Published: May 2011

Mutations to members of the A subfamily of ATP binding cassette (ABC) proteins are responsible for a number of diseases; typically they are associated with aberrant cellular lipid transport processes. Mutations to the ABCA4 protein are linked to a number of visual disorders including Stargardt’s disease and retinitis pigmentosa. Over 500 disease‐associated mutations in ABCA4 have been demonstrated; however, the genotype–phenotype link has not been firmly established. This shortfall is primarily because the function of ABCA4 in the visual cycle is not yet fully understood. One hypothesis suggests that ABCA4 mediates the trans‐bilayer translocation of retinal‐phosphatidylethanolamine conjugates to facilitate the retinal regeneration process in the visual cycle. This review examines the evidence to support, or refute, this working hypothesis on the function of this clinically important protein.
Function and regulation of ABCA1 – membrane meso‐domain organization and reorganization
Authors: Nagao Kohjiro , Tomioka Maiko , Ueda Kazumitsu
Published: May 2011

The ATP‐binding cassette protein A1 (ABCA1) mediates the secretion of cellular‐free cholesterol and phospholipids to an extracellular acceptor, apolipoprotein A‐I, to form high‐density lipoprotein. Because ABCA1 is a key factor in cholesterol homeostasis, elaborate transcriptional and post‐transcriptional regulations of ABCA1 have evolved to maintain cholesterol homeostasis. Recent studies suggest that ABCA1 moves lipids not only between membranes but also within membranes to organize and reorganize membrane meso‐domains to modulate cell proliferation and immunity.
ABCG transporters and disease
Authors: Woodward Owen M. , Köttgen Anna , Köttgen Michael
Published: May 2011

ATP‐binding cassette (ABC) transporters form a large family of transmembrane proteins that facilitate the transport of specific substrates across membranes in an ATP‐dependent manner. Transported substrates include lipids, lipopolysaccharides, amino acids, peptides, proteins, inorganic ions, sugars and xenobiotics. Despite this broad array of substrates, the physiological substrate of many ABC transporters has remained elusive. ABC transporters are divided into seven subfamilies, A–G, based on sequence similarity and domain organization. Here we review the role of members of the ABCG subfamily in human disease and how the identification of disease genes helped to determine physiological substrates for specific ABC transporters. We focus on the recent discovery of mutations in ABCG2 causing hyperuricemia and gout, which has led to the identification of urate as a physiological substrate for ABCG2.
Novel Chiral Skeletons for Drug Discovery: Antibacterial Tetramic Acids
Authors: Holloway Chloe A. , Matthews Christopher J. , Jeong Yong‐Chul , Moloney Mark G. , Roberts Christine F. , Yaqoob Muhammad
Published: May 2011

Modification of the ring nucleus of tetramic acids derived from serine gives chiral heterocyclic libraries that exhibit antibacterial activity, and correlation with various physicochemical parameters indicates that chiral tetramic acids may provide a potentially valuable non‐aromatic skeleton for fragment‐based drug discovery.
Monitoring the Metabolic Status of Geobacter Species in Contaminated Groundwater by Quantifying Key Metabolic Proteins with Geobacter-Specific Antibodies
Authors: Yun Jiae , Ueki Toshiyuki , Miletto Marzia , Lovley Derek R.
Published: May 2011

Simple and inexpensive methods for assessing the metabolic status and bioremediation activities of subsurface microorganisms are required before bioremediation practitioners will adopt molecular diagnosis of the bioremediation community as a routine practice for guiding the development of bioremediation strategies. Quantifying gene transcripts can diagnose important aspects of microbial physiology during bioremediation but is technically challenging and does not account for the impact of translational modifications on protein abundance. An alternative strategy is to directly quantify the abundance of key proteins that might be diagnostic of physiological state. To evaluate this strategy, an antibody-based quantification approach was developed to investigate subsurface
Geobacter
communities. The abundance of citrate synthase corresponded with rates of metabolism of
Geobacter bemidjiensis
in chemostat cultures. During
in situ
bioremediation of uranium-contaminated groundwater the quantity of
Geobacter
citrate synthase increased with the addition of acetate to the groundwater and decreased when acetate amendments stopped. The abundance of the nitrogen-fixation protein, NifD, increased as ammonium became less available in the groundwater and then declined when ammonium concentrations increased. In a petroleum-contaminated aquifer, the abundance of BamB, an enzyme subunit involved in the anaerobic degradation of mono-aromatic compounds by
Geobacter
species, increased in zones in which
Geobacter
were expected to play an important role in aromatic hydrocarbon degradation. These results suggest that antibody-based detection of key metabolic proteins, which should be readily adaptable to standardized kits, may be a feasible method for diagnosing the metabolic state of microbial communities responsible for bioremediation, aiding in the rational design of bioremediation strategies.
Composition and Variability of Biofouling Organisms in Seawater Reverse Osmosis Desalination Plants
Authors: Zhang Minglu , Jiang Sunny , Tanuwidjaja Dian , Voutchkov Nikolay , Hoek Eric M. V. , Cai Baoli
Published: May 2011

Seawater reverse osmosis (SWRO) membrane biofouling remains a common challenge in the desalination industry, but the marine bacterial community that causes membrane fouling is poorly understood. Microbial communities at different stages of treatment processes (intake, cartridge filtration, and SWRO) of a desalination pilot plant were examined by both culture-based and culture-independent approaches. Bacterial isolates were identified to match the genera
Shewanella
,
Alteromonas
,
Vibrio
, and
Cellulophaga
based on 16S rRNA gene sequencing analysis. The 16S rRNA gene clone library of the SWRO membrane biofilm showed that a filamentous bacterium,
Leucothrix mucor
, which belongs to the gammaproteobacteria, accounted for nearly 30% of the clone library, while the rest of the microorganisms (61.2% of the total clones) were related to the alphaproteobacteria. 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) analysis indicated that bacteria colonizing the SWRO membrane represented a subportion of microbes in the source seawater; however, they were quite different from those colonizing the cartridge filter. The examination of five SWRO membranes from desalination plants located in different parts of the world showed that although the bacterial communities from the membranes were not identical to each other, some dominant bacteria were commonly observed. In contrast, bacterial communities in source seawater were significantly different based on location and season. Microbial profiles from 14 cartridge filters collected from different plants also revealed spatial trends.
The Genotype of the Calcium/Calmodulin-Dependent Protein Kinase Gene (
CCaMK
) Determines Bacterial Community Diversity in Rice Roots under Paddy and Upland Field Conditions
Authors: Ikeda Seishi , Okubo Takashi , Takeda Naoya , Banba Mari , Sasaki Kazuhiro , Imaizumi-Anraku Haruko , Fujihara Shinsuke , Ohwaki Yoshinari , Ohshima Kenshiro , Fukuta Yoshimichi , Eda Shima , Mitsui Hisayuki , Hattori Masahira , Sato Tadashi , Shinano Takuro , Minamisawa Kiwamu
Published: May 2011

The effects of the
Oryza sativa
calcium/calmodulin-dependent protein kinase
OsCCaMK
genotype (dominant homozygous [D], heterozygous [H], recessive homozygous [R]) on rice root-associated bacteria, including endophytes and epiphytes, were examined by using a
Tos17
rice mutant line under paddy and upland field conditions. Roots were sampled at the flowering stage and were subjected to clone library analyses. The relative abundance of
Alphaproteobacteria
was noticeably decreased in R plants under both paddy and upland conditions (0.8% and 3.0%, respectively) relative to those in D plants (10.3% and 17.4%, respectively). Population shifts of the
Sphingomonadales
and
Rhizobiales
were mainly responsible for this low abundance in R plants. The abundance of
Anaerolineae
(
Chloroflexi
) and
Clostridia
(
Firmicutes
) was increased in R plants under paddy conditions. The abundance of a subpopulation of
Actinobacteria
(
Saccharothrix
spp. and unclassified
Actinosynnemataceae
) was increased in R plants under upland conditions. Principal coordinate analysis revealed unidirectional community shifts in relation to
OsCCaMK
gene dosage under both conditions. In addition, shoot length, tiller number, and plant weight decreased as the
OsCCaMK
gene dosage decreased under upland conditions. These results suggest significant impacts of
OsCCaMK
on both the diversity of root-associated bacteria and rice plant growth under both paddy and upland field conditions.
Anaerobic Oxidation of Methane in Sediments of Lake Constance, an Oligotrophic Freshwater Lake
Authors: Deutzmann Jörg S. , Schink Bernhard
Published: May 2011

Anaerobic oxidation of methane (AOM) with sulfate as terminal electron acceptor has been reported for various environments, including freshwater habitats, and also, nitrate and nitrite were recently shown to act as electron acceptors for methane oxidation in eutrophic freshwater habitats. Radiotracer experiments with sediment material of Lake Constance, an oligotrophic freshwater lake, were performed to follow
14
CO
2
formation from
14
CH
4
in sediment incubations in the presence of different electron acceptors, namely, nitrate, nitrite, sulfate, or oxygen. Whereas
14
CO
2
formation without and with sulfate addition was negligible, addition of nitrate increased
14
CO
2
formation significantly, suggesting that AOM could be coupled to denitrification. Nonetheless, denitrification-dependent AOM rates remained at least 1 order of magnitude lower than rates of aerobic methane oxidation. Using molecular techniques, putative denitrifying methanotrophs belonging to the NC10 phylum were detected on the basis of the
pmoA
and 16S rRNA gene sequences. These findings show that sulfate-dependent AOM was insignificant in Lake constant sediments. However, AOM can also be coupled to denitrification in this oligotrophic freshwater habitat, providing first indications that this might be a widespread process that plays an important role in mitigating methane emissions.
Significant Alteration of Gene Expression in Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium by Plant Species
Authors: Vanden Wymelenberg Amber , Gaskell Jill , Mozuch Michael , Splinter BonDurant Sandra , Sabat Grzegorz , Ralph John , Skyba Oleksandr , Mansfield Shawn D. , Blanchette Robert A. , Grigoriev Igor V. , Kersten Philip J. , Cullen Dan
Published: May 2011

Identification of specific genes and enzymes involved in conversion of lignocellulosics from an expanding number of potential feedstocks is of growing interest to bioenergy process development. The basidiomycetous wood decay fungi
Phanerochaete chrysosporium
and
Postia placenta
are promising in this regard because they are able to utilize a wide range of simple and complex carbon compounds. However, systematic comparative studies with different woody substrates have not been reported. To address this issue, we examined gene expression of these fungi colonizing aspen (
Populus grandidentata
) and pine (
Pinus strobus
). Transcript levels of genes encoding extracellular glycoside hydrolases, thought to be important for hydrolytic cleavage of hemicelluloses and cellulose, showed little difference for
P. placenta
colonizing pine versus aspen as the sole carbon source. However, 164 genes exhibited significant differences in transcript accumulation for these substrates. Among these, 15 cytochrome P450s were upregulated in pine relative to aspen. Of 72
P. placenta
extracellular proteins identified unambiguously by mass spectrometry, 52 were detected while colonizing both substrates and 10 were identified in pine but not aspen cultures. Most of the 178
P. chrysosporium
glycoside hydrolase genes showed similar transcript levels on both substrates, but 13 accumulated >2-fold higher levels on aspen than on pine. Of 118 confidently identified proteins, 31 were identified in both substrates and 57 were identified in pine but not aspen cultures. Thus,
P. placenta
and
P. chrysosporium
gene expression patterns are influenced substantially by wood species. Such adaptations to the carbon source may also reflect fundamental differences in the mechanisms by which these fungi attack plant cell walls.
Validation of Heavy-Water Stable Isotope Probing for the Characterization of Rapidly Responding Soil Bacteria
Authors: Aanderud Zachary T. , Lennon Jay T.
Published: May 2011

Rapid responses of bacteria to sudden changes in their environment can have important implications for the structure and function of microbial communities. In this study, we used heavy-water stable isotope probing (H
2
18
O-SIP) to identify bacteria that respond to soil rewetting. First, we conducted experiments to address uncertainties regarding the H
2
18
O-SIP method. Using liquid chromatography-mass spectroscopy (LC-MS), we determined that oxygen from H
2
18
O was incorporated into all structural components of DNA. Although this incorporation was uneven, we could effectively separate
18
O-labeled and unlabeled DNAs derived from laboratory cultures and environmental samples that were incubated with H
2
18
O. We found no evidence for
ex vivo
exchange of oxygen atoms between DNA and extracellular H
2
O, suggesting that
18
O incorporation into DNA is relatively stable. Furthermore, the rate of
18
O incorporation into bacterial DNA was high (within 48 to 72 h), coinciding with pulses of CO
2
generated from soil rewetting. Second, we examined shifts in the bacterial composition of grassland soils following rewetting, using H
2
18
O-SIP and bar-coded pyrosequencing of 16S rRNA genes. For some groups of soil bacteria, we observed coherent responses at a relatively course taxonomic resolution. Following rewetting, the relative recovery of
Alphaproteobacteria
,
Betaproteobacteria
, and
Gammaproteobacteria
increased, while the relative recovery of
Chloroflexi
and
Deltaproteobacteria
decreased. Together, our results suggest that H
2
18
O-SIP is effective at identifying metabolically active bacteria that influence soil carbon dynamics. Our results contribute to the ecological classification of soil bacteria while providing insight into some of the functional traits that influence the structure and function of microbial communities under dynamic soil moisture regimes.
Effect of Chemical Chaperones in Improving the Solubility of Recombinant Proteins in Escherichia coli
Authors: Prasad Shivcharan , Khadatare Prashant B. , Roy Ipsita
Published: May 2011

The recovery of active proteins from inclusion bodies usually involves chaotrope-induced denaturation, followed by refolding of the unfolded protein. The efficiency of renaturation is low, leading to reduced yield of the final product. In this work, we report that recombinant proteins can be overexpressed in the soluble form in the host expression system by incorporating compatible solutes during protein expression. Green fluorescent protein (GFP), which was otherwise expressed as inclusion bodies, could be made to partition off into the soluble fraction when sorbitol and arginine, but not ethylene glycol, were present in the growth medium. Arginine and sorbitol increased the production of soluble protein, while ethylene glycol did not. Production of ATP increased in the presence of sorbitol and arginine, but not ethylene glycol. A control experiment with fructose addition indicated that protein solubilization was not due to a simple ATP increase. We have successfully reproduced these results with the N-terminal domain of HypF (HypF-N), a bacterial protein which forms inclusion bodies inEscherichia coli. Instead of forming inclusion bodies, HypF-N could be expressed as a soluble protein in the presence of sorbitol, arginine, and trehalose in the expression medium.
Pantethine Rescues Phosphopantothenoylcysteine Synthetase and Phosphopantothenoylcysteine Decarboxylase Deficiency in Escherichia coli but Not in Pseudomonas aeruginosa
Authors: Balibar Carl J. , Hollis-Symynkywicz Micah F. , Tao Jianshi
Published: May 2011

Coenzyme A (CoA) plays a central and essential role in all living organisms. The pathway leading to CoA biosynthesis has been considered an attractive target for developing new antimicrobial agents with novel mechanisms of action. By using an arabinose-regulated expression system, the essentiality of
coaBC
, a single gene encoding a bifunctional protein catalyzing two consecutive steps in the CoA pathway converting 4′-phosphopantothenate to 4′-phosphopantetheine, was confirmed in
Escherichia coli
. Utilizing this regulated
coaBC
strain, it was further demonstrated that
E. coli
can effectively metabolize pantethine to bypass the requirement for
coaBC
. Interestingly, pantethine cannot be used by
Pseudomonas aeruginosa
to obviate
coaBC
. Through reciprocal complementation studies in combination with biochemical characterization, it was demonstrated that the differential characteristics of pantethine utilization in these two microorganisms are due to the different substrate specificities associated with endogenous pantothenate kinase, the first enzyme in the CoA biosynthetic pathway encoded by
coaA
in
E. coli
and
coaX
in
P. aeruginosa
.
Complete Genome Sequence of Aeromonas veronii Strain B565
Authors: Li Yanxia , Liu Yuchun , Zhou Zhemin , Huang Huoqing , Ren Yan , Zhang Yuting , Li Guannan , Zhou Zhigang , Wang Lei
Published: May 2011

Aeromonas veronii
strain B565 was isolated from aquaculture pond sediment in China. We present here the complete genome sequence of B565 and compare it with 2 published genome sequences of pathogenic strains in the
Aeromonas
genus. The result represents an independent stepwise acquisition of virulence factors of pathogenic strains in this genus.