bluuebunny/crossref_metadata_2025 huggingface dataset:
Acupuncture as a Treatment Technique for Aphasia and Cognitive Impairments
Authors: Laures-Gore Jacqueline , Marshall Rebecca Shisler
Published: October 2008

Purpose:
In response to the growing interest and use of acupuncture by Americans who are searching for effective treatments of aphasia and cognitive impairments, this paper serves to (a) briefly explain the technique of acupuncture, (b) describe its biologic mechanisms, and (c) summarize studies investigating the effectiveness of acupuncture in treating cognitive impairment associated with vascular dementia and stroke-related language impairments.

Methods:
Published reports of the use and effectiveness of acupuncture in treating cognitive impairments related to vascular dementia and aphasia related to stroke are reviewed and reported.

Results and Conclusions:
Rigorously designed studies investigating acupuncture and vascular neuropathologies are too few in number to produce any definite conclusions about the efficacy of this technique in treating aphasia related to stroke or cognitive impairments related to vascular dementia. Although there is some empirical evidence indicating that acupuncture may be a valuable adjunct to conventional therapies, speech-language pathologists should remain cautious of acupuncture's promise until further, well-designed studies are conducted.
Herbal Contributions to the Management of the Multi-Factorial Cognitive Disorders — Alzheimer's Disease and Vascular Dementia
Authors: Hecht S. Wyler
Published: October 2008

Purpose:
Multi-factorial disorders of cognition such as Alzheimer's disease and vascular dementia are increasing as the general population ages. The small number of drugs currently approved for the treatment of such disorders provide palliative and temporary benefit with only modest efficacy; thus, it stands to reason that alternative approaches should be explored.

Method:
Certain plants and plant derivatives are currently under study for their effects on memory and other domains of cognition. These plants and the compounds derived from them have minimal adverse effects and have multi-functional properties (anti-oxidant, pro-cholinergic, antiplatelet aggregation, amyloid beta peptide inhibiting) with relevant application in the treatment of dementia and other cognitive impairment. This paper reviews four herbal medicines (Ginkgo biloba, Bacopa monniera, Huperzine Alpha, and Vinpocetine) with varying degrees of proven benefit for the treatment of dementias and other cognitive impairment.

Results and Conclusions:
These herbal medicines are promising alternative or adjunct treatment modalities. The plants or plant derivatives discussed here have, in many cases, proven to be equally or more effective than conventional drug therapy in the treatment of dementia.
RTI Services for Children With Mild Articulation Needs: Four Years of Data
Authors: Taps Jennifer
Published: October 2008

This article summarizes 4 years of data from San Diego Unified School District's Speech Improvement Class model for students with mild articulation needs. The district made a gradual shift from special education to general education. Data demonstrate that most students complete the class in 17-20 treatment hours. Three factors have been fundamental to the success of this program: the Articulation Resource Center, ongoing professional development, and a well-defined set of procedures. Challenges and concerns are also discussed. Overall, speech-language pathologists in San Diego Unified are implementing this class effectively and have branched out into other response to intervention supports.
Response to Intervention: Grassroots Efforts in Ohio
Authors: Jillson Kathryn D.
Published: October 2008

While states and school districts work to grasp the Response to Intervention (RTI) process, speech-language pathologists question their role in this process and the skills needed to fully participate in RTI. Is it possible to put into place response to intervention elements that are beneficial to students, even if the framework is not in place throughout the district? This article will review Ohio's history regarding (RTI). The current support for RTI within the state and the needs expressed by school-based speech-language pathologists in respect to RTI will be discussed and considerations for the future will be provided.
Tissue Engineering Applications for Cleft Palate Reconstruction
Authors: Gupta Deepak M. , Panetta Nicholas J. , Longaker Michael T. , Lorenz H. Peter
Published: October 2008

Cleft palate is a common birth defect that carries significant biomedical and psychosocial implications throughout the lives of affected children and their families. To date, numerous etiopathogenetic factors have been identified that can lead to isolated and syndromic forms of cleft palate. The management of patients with cleft palate has improved significantly over the last several decades with important surgical advances and an increasingly multidisciplinary approach to patient care. Technological innovations have become focused on improving functional results, with current research and clinical reports of cleft palate reconstruction promising even greater improvements and further “minimalization” of surgery in the future. As part of this evolution, research in tissue engineering approaches for cleft palate reconstruction promise increased functionality, improved aesthetics, fewer complications, and reduced disease burden. The current review discusses several aspects of tissue engineering research that promise innovation in cleft palate repair including distraction osteogenesis, biologic implants, fetal surgery, in utero medical therapy, and prevention.
Bacterial leaching from dairy shed effluent applied to a fine sandy loam under irrigated pasture
Authors: Jiang Shuang , Buchan Graeme D. , Noonan Mike J. , Smith Neil , Pang Liping , Close Murray
Published: October 2008

This experiment investigated bacterial transport from land-applied dairy shed effluent (DSE), via field lysimeter studies, using 2 contrasting irrigation methods. Transient water flow and bacterial transport were studied, and the factors controlling faecal coliform (FC) transport are discussed. Two trials (Trial 1, summer; Trial 2, autumn) were carried out, using 6 undisturbed soil monolith lysimeters, 500 mm diameter by 700 mm deep, with a free-draining, Templeton fine sandy loam. DSE with inert chemical tracers was applied at the start of both trials using the same method, followed with repeated 14-day cycles of either flood or spray irrigation of water. A bacterial tracer, antibiotic-resistant faecal coliform, was added to the DSE in Trial 2 only, to distinguish applied FC from external or resident FC. Leachates were collected after each water application (or heavy rainfall when applicable) for enumeration of FC and measurement of tracers. All lysimeters were instrumented for monitoring volumetric water content, matric potential, and soil temperature at 4 depths (100, 250, 450, and 600 mm). The results showed that bacteria could readily penetrate through 700-mm-deep soil columns, when facilitated by water flow. The highest post-water irrigation concentration was 3.4 × 103 cfu/100 mL under flood irrigation, which resulted in more bacterial and Br– leaching than spray irrigation. Trial 2 (autumn) results also showed significant differences between irrigation treatments in lysimeters sharing similar drainage class (moderate or moderately rapid), flood irrigation again gave more bacterial and tracer (Cl–) leaching. In the summer trial, FC in leachate as high as 1.4 × 106 cfu/100 mL, similar to the concentration of DSE, was detected in one lysimeter that had a higher clay content in the topsoil immediately after DSE application, and before any water irrigation. This indicates that applied DSE leached through preferential flow paths without any dilution. Bacterial concentration in the leachate was positively correlated with both volumetric water content and water potential, and sometimes drainage rate. Greater bacterial leaching was found in the lysimeter with rapid whole-column effective hydraulic conductivity, Keff, for both flood and spray treatments. Occasionally, the effect of Keff on water movement and bacterial transport overrode the effect of irrigation. The ‘seasonal condition’ of the soil (including variation in initial water content) also influenced bacterial leaching, with less risk of leaching in autumn than in summer. These findings contribute to our increased understanding of bacterial transport processes on the field scale.
Mms19 protein functions in nucleotide excision repair by sustaining an adequate cellular concentration of the TFIIH component Rad3
Authors: Kou Haiping , Zhou Ying , Gorospe R. M. Charlotte , Wang Zhigang
Published: October 2008

Nucleotide excision repair (NER) is a major cellular defense mechanism against DNA damage. We have investigated the role of Mms19 in NER in the yeast
Saccharomyces cerevisiae
. NER was deficient in the
mms19
deletion mutant cell extracts, which was complemented by the NER/transcription factor TFIIH, but not by purified Mms19 protein. In
mms19
mutant cells, protein levels of the core TFIIH component Rad3 (XPD homologue) and Ssl2 (XPB homologue) were significantly reduced by up to 3.5- and 2.2-fold, respectively. The other four essential subunits of the core TFIIH, Tfb1, Tfb2, Ssl1, and Tfb4, and the TFIIK subunits Tfb3, Kin28, and Ccl1 of the holo TFIIH were not much affected by Mms19. Elevating Rad3 protein concentration by overexpressing the protein from a plasmid under the
GAL1
promoter control restored proficient NER in
mms19
mutant cells, as indicated by complementation for UV sensitivity. Overexpression of Ssl2 had no effect on repair. Overexpression of Rad3, Ssl2, or both proteins, however, could not correct the temperature-sensitive growth defect of
mms19
mutant cells. These results show that Mms19 functions in NER by sustaining an adequate cellular concentration of the TFIIH component Rad3 and suggest that Mms19 has distinct and separable functions in NER and cell growth, thus implicating Mms19 protein as a novel multifunctional regulator in cells.
Interferon regulatory factor 4 differentially regulates the production of Th2 cytokines in naïve vs. effector/memory CD4+T cells
Authors: Honma Kiri , Kimura Daisuke , Tominaga Norio , Miyakoda Mana , Matsuyama Toshifumi , Yui Katsuyuki
Published: October 2008

Interferon regulatory factor (IRF) 4 is a member of the IRF family of transcription factors and plays critical roles in the development of CD4+T cells into Th2 and Th17 cells. Using the infection model ofNippostrongyrus brasiliensis, we have confirmed the critical roles of IRF-4 in Th2 developmentin vivoby using IRF-4−/−BALB/c mice. However, naïve IRF-4−/−CD4+T cells produced Th2 cytokines, including IL-4, IL-5, and IL-10, but not IL-2 or IFN-γ, at levels higher than wild-type BALB/c CD4+T cells in response to T cell receptor stimulation. In contrast, effector/memory IRF-4−/−CD4+T cells did not exhibit increased production of Th2 cytokines. Knockdown of IRF-4 expression by using small interfering RNA promoted IL-4 production in naïve CD4+T cells but inhibited it in effector/memory CD4+T cells. These results indicate that IRF-4 plays differential roles in the regulation of Th2 cytokine production in naïve CD4+T cells and effector/memory CD4+T cells. IRF-4 inhibits Th2 cytokine production in naïve CD4+T cells, whereas it promotes Th2 cytokine production in effector/memory CD4+T cells.
Cell surface targeting of μ-δ opioid receptor heterodimers by RTP4
Authors: Décaillot Fabien M. , Rozenfeld Raphael , Gupta Achla , Devi Lakshmi A.
Published: October 2008

μ opioid receptors are G protein–coupled receptors that mediate the pain-relieving effects of clinically used analgesics, such as morphine. Accumulating evidence shows that μ-δ opioid heterodimers have a pharmacologic profile distinct from those of the μ or δ homodimers. Because the heterodimers exhibit distinct signaling properties, the protein and mechanism regulating their levels have significant effects on morphine-mediated physiology. We report the characterization of RTP4, a Golgi chaperone, as a regulator of the levels of heterodimers at the cell surface. We show that the association with RTP4 protects μ-δ receptors from ubiquitination and degradation. This leads to increases in surface heterodimer levels, thereby affecting signaling. Thus, the oligomeric organization of opioid receptors is controlled by RTP4, and this governs their membrane targeting and functional activity. This work is the first report of the identification of a chaperone involved in the regulation of the biogenesis of a family A GPCR heterodimer. The identification of such factors as RTP4 controlling dimerization will provide insight into the regulation of heterodimers
in vivo.
This has implications in the modulation of pharmacology of their endogenous ligands, and in the development of drugs with specific therapeutic effects.
Efficient cell-free production of olfactory receptors: Detergent optimization, structure, and ligand binding analyses
Authors: Kaiser Liselotte , Graveland-Bikker Johanna , Steuerwald Dirk , Vanberghem Mélanie , Herlihy Kara , Zhang Shuguang
Published: October 2008

High-level production of membrane proteins, particularly of G protein-coupled receptors (GPCRs) in heterologous cell systems encounters a number of difficulties from their inherent hydrophobicity in their transmembrane domains, which frequently cause protein aggregation and cytotoxicity and thus reduce the protein yield. Recent advances in cell-free protein synthesis circumvent those problems to produce membrane proteins with a yield sometimes exceeding the cell-based approach. Here, we report cell-free production of a human olfactory receptor 17-4 (hOR17-4) using the wheat germ extract. Using the simple method, we also successful produced two additional olfactory receptors. To obtain soluble olfactory receptors and to increase yield, we directly added different detergents in varying concentrations to the cell-free reaction. To identify a purification buffer system that maintained the receptor in a nonaggregated form, we developed a method that uses small-volume size-exclusion column chromatography combined with rapid and sensitive dot-blot detection. Different buffer components including salt concentration, various detergents and detergent concentration, and reducing agent and its concentrations were evaluated for their ability to maintain the cell-free produced protein stable and nonaggregated. The purified olfactory receptor displays a typical a α-helical CD spectrum. Surface plasmon resonance measurements were used to show binding of a known ligand undecanal to hOR17-4. Our approach to produce a high yield of purified olfactory receptor is a milestone toward obtaining a large quantity of olfactory receptors for designing bionic sensors. Furthermore, this simple approach may be broadly useful not only for other classes of GPCRs but also for other membrane proteins.
Syntaxin 5 regulates the endoplasmic reticulum channel-release properties of polycystin-2
Authors: Geng Lin , Boehmerle Wolfgang , Maeda Yoshiko , Okuhara Dayne Y. , Tian Xin , Yu Zhiheng , Choe Chi-un , Anyatonwu Georgia I. , Ehrlich Barbara E. , Somlo Stefan
Published: October 2008

Polycystin-2 (PC2), the gene product of one of two genes mutated in dominant polycystic kidney disease, is a member of the transient receptor potential cation channel family and can function as intracellular calcium (Ca
2+
) release channel. We performed a yeast two-hybrid screen by using the NH
2
terminus of PC2 and identified syntaxin-5 (Stx5) as a putative interacting partner. Coimmunoprecipitation studies in cell lines and kidney tissues confirmed interaction of PC2 with Stx5
in vivo. In vitro
binding assays showed that the interaction between Stx5 and PC2 is direct and defined the respective interaction domains as the t-SNARE region of Stx5 and amino acids 5 to 72 of PC2. Single channel studies showed that interaction with Stx5 specifically reduces PC2 channel activity. Epithelial cells overexpressing mutant PC2 that does not bind Stx5 had increased baseline cytosolic Ca
2+
levels, decreased endoplasmic reticulum (ER) Ca
2+
stores, and reduced Ca
2+
release from ER stores in response to vasopressin stimulation. Cells lacking PC2 altogether had reduced cytosolic Ca
2+
levels. Our data suggest that PC2 in the ER plays a role in cellular Ca
2+
homeostasis and that Stx5 functions to inactivate PC2 and prevent leaking of Ca
2+
from ER stores. Modulation of the PC2/Stx5 interaction may be a useful target for impacting dysregulated intracellular Ca
2+
signaling associated with polycystic kidney disease.
Petroleomics: Chemistry of the underworld
Authors: Marshall Alan G. , Rodgers Ryan P.
Published: October 2008

Each different molecular elemental composition—e.g., C
c
H
h
N
n
O
o
S
s
—has a different exact mass. With sufficiently high mass resolving power (
m
/Δ
m
50%
≈ 400,000, in which
m
is molecular mass and Δ
m
50%
is the mass spectral peak width at half-maximum peak height) and mass accuracy (<300 ppb) up to ≈800 Da, now routinely available from high-field (≥9.4 T) Fourier transform ion cyclotron resonance mass spectrometry, it is possible to resolve and identify uniquely and simultaneously each of the thousands of elemental compositions from the most complex natural organic mixtures, including petroleum crude oil. It is thus possible to separate and sort petroleum components according to their heteroatom class (N
n
O
o
S
s
), double bond equivalents (DBE = number of rings plus double bonds involving carbon, because each ring or double bond results in a loss of two hydrogen atoms), and carbon number. “Petroleomics” is the characterization of petroleum at the molecular level. From sufficiently complete characterization of the organic composition of petroleum and its products, it should be possible to correlate (and ultimately predict) their properties and behavior. Examples include molecular mass distribution, distillation profile, characterization of specific fractions without prior extraction or wet chemical separation from the original bulk material, biodegradation, maturity, water solubility (and oil:water emulsion behavior), deposits in oil wells and refineries, efficiency and specificity of catalytic hydroprocessing, “heavy ends” (asphaltenes) analysis, corrosion, etc.
Up-regulation of the proapoptotic caspase 2 splicing isoform by a candidate tumor suppressor, RBM5
Authors: Fushimi Kazuo , Ray Payal , Kar Amar , Wang Lei , Sutherland Leslie C. , Wu Jane Y.
Published: October 2008

Similar to many genes involved in programmed cell death (PCD), the caspase 2 (casp-2) gene generates both proapoptotic and antiapoptotic isoforms by alternative splicing. Using a yeast RNA–protein interaction assay, we identified RBM5 (also known as LUCA-15) as a protein that binds to casp-2 pre-mRNA. In both transfected cells and
in vitro
splicing assay, RBM5 enhances the formation of proapoptotic Casp-2L. RBM5 binds to a U/C-rich sequence immediately upstream of the previously identified In100 splicing repressor element. Our mutagenesis experiments demonstrate that RBM5 binding to this intronic sequence regulates the ratio of proapoptotic/antiapoptotic casp-2 splicing isoforms, suggesting that casp-2 splicing regulation by RBM5 may contribute to its tumor suppressor activity. Our work has uncovered a player in casp-2 alternative splicing regulation and revealed a link between the alternative splicing regulator and the candidate tumor suppressor gene. Together with previous studies, our work suggests that splicing control of cell death genes may be an important aspect in tumorigenesis. Enhancing the expression or activities of splicing regulators that promote the production of proapoptotic splicing isoforms might provide a therapeutic approach to cancer.
Hypertonic stress increases claudin-4 expression and tight junction integrity in association with MUPP1 in IMCD3 cells
Authors: Lanaspa Miguel A. , Andres-Hernando Ana , Rivard Christopher J. , Dai Yue , Berl Tomas
Published: October 2008

We reported that the multiple PDZ protein 1 (MUPP1) is an osmotic response protein in kidney cells. This up-regulation was found to be necessary for the maintenance of tight epithelial properties in these cells. We investigated whether an interaction with one or more members of the claudin family is responsible for this observation. In response to hypertonicity, the up-regulation of claudin-4 (Cldn4) expression, and not other claudins, was initially identified in inner medullary collecting duct (IMCD3) cells by gene array and further verified by quantitative PCR and Western blotting. In kidney tissues, Cldn4 expression was substantial in the papilla and absent in the cortex. Furthermore, Cldn4 expression significantly increased in the papilla of mice after 36 h of thirsting. Cldn4 immunofluorescence in hypertonically stressed cells revealed colocalization with MUPP1 at the tight junctions. Interaction between Cldn4 and MUPP1 was also demonstrated by coimmunoprecipitation of both proteins from IMCD3 cells chronically adapted to hypertonicity. In IMCD3 cells stably silenced for MUPP1 expression under hypertonic conditions, a significant decrement in Cldn4 expression was observed that was restored after inhibition of lysosome activity. Immunofluorescence detection identified that in these MUPP1-silenced cells Cldn4 was mistargeted to the lysosomes. Functionally, silencing Cldn4 expression in IMCD3 cells resulted in a decrease in the transepithelial resistance to the same degree as observed when MUPP1 expression was silenced, suggesting that MUPP1 contributes to the maintenance of a tight epithelium in the medulla of the kidney under hypertonic stress by correctly localizing Cldn4 to the tight junctions.
Restoration of visual function in retinal degeneration mice by ectopic expression of melanopsin
Authors: Lin Bin , Koizumi Amane , Tanaka Nobushige , Panda Satchidananda , Masland Richard H.
Published: October 2008

The rod and cone cells of the mammalian retina are the principal photoreceptors for image-forming vision. They transmit information by means of a chain of intermediate cells to the retinal ganglion cells, which in turn send signals from the retina to the brain. Loss of photoreceptor cells, as happens in a number of human diseases, leads to irreversible blindness. In a mouse model (
rd/rd
) of photoreceptor degeneration, we used a viral vector to express in a large number of retinal ganglion cells the light sensitive protein melanopsin, normally present in only a specialized subset of the cells. Whole-cell patch–clamp recording showed photoresponses in these cells even after degeneration of the photoreceptors and additional pharmacological or Cd
2+
block of synaptic function. Interestingly, similar responses were observed across a wide variety of diverse types of ganglion cell of the retina. The newly melanopsin-expressing ganglion cells provided an enhancement of visual function in
rd
/
rd
mice: the pupillary light reflex (PLR) returned almost to normal; the mice showed behavioral avoidance of light in an open-field test, and they could discriminate a light stimulus from a dark one in a two-choice visual discrimination alley. Recovery of the PLR was stable for at least 11 months. It has recently been shown that ectopic retinal expression of a light sensitive bacterial protein, channelrhodopsin-2, can restore neuronal responsiveness and simple visual abilities in
rd/rd
mice. For therapy in human photodegenerations, channelrhodopsin-2 and melanopsin have different advantages and disadvantages; both proteins (or modifications of them) should be candidates.
A genetic timer through noise-induced stabilization of an unstable state
Authors: Turcotte Marc , Garcia-Ojalvo Jordi , Süel Gürol M.
Published: October 2008

Stochastic fluctuations affect the dynamics of biological systems. Typically, such noise causes perturbations that can permit genetic circuits to escape stable states, triggering, for example, phenotypic switching. In contrast, studies have shown that noise can surprisingly also generate new states, which exist solely in the presence of fluctuations. In those instances noise is supplied externally to the dynamical system. Here, we present a mechanism in which noise intrinsic to a simple genetic circuit effectively stabilizes a deterministically unstable state. Furthermore, this noise-induced stabilization represents a unique mechanism for a genetic timer. Specifically, we analyzed the effect of noise intrinsic to a prototypical two-component gene-circuit architecture composed of interacting positive and negative feedback loops. Genetic circuits with this topology are common in biology and typically regulate cell cycles and circadian clocks. These systems can undergo a variety of bifurcations in response to parameter changes. Simulations show that near one such bifurcation, noise induces oscillations around an unstable spiral point and thus effectively stabilizes this unstable fixed point. Because of the periodicity of these oscillations, the lifetime of the noise-dependent stabilization exhibits a polymodal distribution with multiple, well defined, and regularly spaced peaks. Therefore, the noise-induced stabilization presented here constitutes a minimal mechanism for a genetic circuit to function as a timer that could be used in the engineering of synthetic circuits.
Eukaryotic-like protein kinases in the prokaryotes and the myxobacterial kinome
Authors: Pérez J. , Castañeda-García A. , Jenke-Kodama H. , Müller R. , Muñoz-Dorado J.
Published: October 2008

Ser/Thr/Tyr kinases, which together comprise a major class of regulatory proteins in eukaryotes, were not believed to play an important role in prokaryotes until recently. However, our analysis of 626 prokaryotic genomes reveals that eukaryotic-like protein kinases (ELKs) are found in nearly two-thirds of the sequenced strains. We have identified 2697 ELKs, most of which are encoded by multicellular strains of the phyla Proteobacteria (
Myxococcales
), Actinobacteria, Cyanobacteria, and Chloroflexi, and 2 Acidobacteria and 1 Planctomycetes. Astonishingly, 7 myxobacterial strains together encode 892 ELKs, with 4 of the strains exhibiting a genomic ELK density similar to that observed in eukaryotes. Most myxobacterial ELKs show a modular organization in which the kinase domain is located at the N terminus. The C-terminal portion of the ELKs is highly diverse and often contains sequences with similarity to characterized domains, most of them involved in signaling mechanisms or in protein–protein interactions. However, many of these architectures are unique to the myxobacteria, an observation that suggests that this group exploits sophisticated and novel signal transduction systems. Phylogenetic reconstruction using the kinase domains revealed many orthologous sequence pairs and a huge number of gene duplications that probably occurred after speciation. Furthermore, studies of the microsynteny in the ELK-encoding regions reveal only low levels of synteny among
Myxococcus xanthus
,
Plesiocystis pacifica
, and
Sorangium cellulosum
. However, extensive similarities between
M. xanthus
,
Stigmatella aurantiaca
, and 3
Anaeromyxobacter
strains were observed, indicating that they share regulatory pathways involving various ELKs.
The role of host protein YajQ in the temporal control of transcription in bacteriophage Φ6
Authors: Qiao Xueying , Sun Yang , Qiao Jian , Mindich Leonard
Published: October 2008

Bacteriophage Φ6 contains three dsRNA genomic segments L, M, and S. The RNA is located inside a core particle composed of multiple copies of a major structural protein, an RNA-dependent RNA polymerase, a hexameric NTPase, and an auxiliary protein. The virion RNA polymerase in the core particle transcribes segments M and S
in vitro
. Yet early in infection, the transcription of L is highly active. Late in infection, transcription of L is low, and that of M and S is high. A host protein encoded by
yajQ
is responsible for the activation of L transcription. Knockout mutants of
yajQ
do not support the replication of Φ6, although they do support the replication of distantly related members of the Cystoviridae. Φ6 can mutate to independence of YajQ. This requires two mutations in the gene for the RNA-dependent RNA polymerase. YajQ acts indirectly on the polymerase by binding to P1, the major structural protein of the core. Previous studies have shown that the activity of the polymerase in the core is controlled by the conformation of the core particle structure.
The pretranslocation ribosome is targeted by GTP-bound EF-G in partially activated form
Authors: Hauryliuk Vasili , Mitkevich Vladimir A. , Eliseeva Natalia A. , Petrushanko Irina Yu. , Ehrenberg Måns , Makarov Alexander A.
Published: October 2008

Translocation of the tRNA·mRNA complex through the bacterial ribosome is driven by the multidomain guanosine triphosphatase elongation factor G (EF-G). We have used isothermal titration calorimetry to characterize the binding of GDP and GTP to free EF-G at 4°C, 20°C, and 37°C. The binding affinity of EF-G is higher to GDP than to GTP at 4°C, but lower at 37°C. The binding enthalpy and entropy change little with temperature in the case of GDP binding but change greatly in the case of GTP binding. These observations are compatible with a large decrease in the solvent-accessible hydrophobic surface area of EF-G on GTP, but not GDP, binding. The explanation we propose is the locking of the switch 1 and switch 2 peptide loops in the G domain of EF-G to the γ-phosphate of GTP. From these data, in conjunction with previously reported structural data on guanine nucleotide-bound EF-G, we suggest that EF-G enters the pretranslocation ribosome as an “activity chimera,” with the G domain activated by the presence of GTP but the overall factor conformation in the inactive form typical of a GDP-bound multidomain guanosine triphosphatase. We propose that the active overall conformation of EF-G is attained only in complex with the ribosome in its “ratcheted state,” with hybrid tRNA binding sites.
The N-terminal domain of MyoD is necessary and sufficient for its nuclear localization-dependent degradation by the ubiquitin system
Authors: Sadeh Ronen , Breitschopf Kristin , Bercovich Beatrice , Zoabi Muhammad , Kravtsova-Ivantsiv Yelena , Kornitzer Daniel , Schwartz Alan , Ciechanover Aaron
Published: October 2008

A growing number of proteins, including the myogenic transcription factor MyoD, are targeted for proteasomal degradation after N-terminal ubiquitination (NTU) where the first ubiquitin moiety is conjugated to the N-terminal residue rather than to an internal lysine. NTU might be essential in targeting both lysine-containing and naturally occurring lysine-less proteins such as p16
INK4a
and p14
ARF
; however, the mechanisms that underlie this process are largely unknown. Specifically, the recognition motif(s) in the target substrates and the ubiquitin ligase(s) that catalyze NTU are still obscure. Here we show that the N-terminal domain of MyoD is critical for its degradation and that its destabilizing effect depends on nuclear localization of the protein. Deletion of the first 15 aa of MyoD blocked completely its lysine-independent degradation. Importantly, transfer of the first 30 N-terminal residues of MyoD to GFP destabilized this otherwise stable protein, and, here too, targeting for degradation depended on localization of the protein to the nucleus. Deletion of the N-terminal domain of lysine-less MyoD did not abolish completely ubiquitination of the protein, suggesting that this domain may be required for targeting the protein also in a postubiquitination step. Interestingly, NTU is evolutionarily conserved: in the yeast
Saccharomyces cerevisiae
lysine-less (LL) MyoD is degraded in a ubiquitin-, N-terminal domain-, and nuclear localization-dependent manner. Taken together, our data suggest that a short N-terminal segment of MyoD is necessary and sufficient to render MyoD susceptible for ubiquitin- and nuclear-dependent degradation.
Analysis of intergenic transcription and histone modification across the human immunoglobulin heavy-chain locus
Authors: Chowdhury Muslima , Forouhi Omid , Dayal Sandeep , McCloskey Natalie , Gould Hannah J. , Felsenfeld Gary , Fear David J.
Published: October 2008

Ig class switch recombination (CSR) is initiated by activation-induced cytidine deaminase (AID) mediated deamination of the switch (S) regions; the resultant mismatch is processed to yield the DNA breaks required for recombination. Whereas many of the pathways involved in the mechanism of recombination have been identified, little is known about how CSR is regulated. AID action is known to require transcription of the Ig heavy-chain genes. However, it is not understood how AID is restricted to the Ig genes. Many aspects of gene expression are known to be regulated by modification of chromatin structure. In turn, chromatin is known to be regulated by several RNA-dependent activities. We have mapped the transcriptional and chromatin landscape of the human Ig heavy-chain locus to investigate the effect these activities have on CSR. We demonstrate that the Ig heavy-chain constant genes and 3′-regulatory regions are in an active chromatin conformation in unstimulated total human B cells: the locus undergoes both genic and intergenic transcription and possesses histone modifications associated with “active” chromatin (acetylated H3 and H4 and lysine 4 trimethylated H3). However, on cytokine stimulation, these modifications spread into the S regions, demonstrating a chromatin remodeling activity associated with switching. Surprisingly, after stimulation, the S regions also accumulate lysine 9 trimethylated H3, a modification previously associated with gene silencing. These data demonstrates that the Ig locus is maintained with a complex pattern of both positive and negative histone marks and suggest that some of these marks may have dual functions.
Estimation of ejection fraction and stroke volume using single- and biplane magnetic resonance imaging of the left cardiac ventricle
Authors: Thunberg P. , Emilsson K. , Rask P. , Kähäri A.
Published: October 2008

Background: In cardiac magnetic resonance imaging (MRI), left ventricular stroke volume (SV) and ejection fractions (EF) are occasionally calculated using single-plane and biplane ellipsoid models. In previous studies, the calculated SV and EF using single- and biplane ellipsoid models have been compared to reference values calculated from short-axis (SA) images. In these studies, however, it has been emphasized that through-plane motion of the basal SA images represents an important source of error, which may result in incorrect reference values.

Purpose: To compare the calculated SV and EF using single-plane and biplane ellipsoid models with SV and EF calculated from SA images in which compensation was made for through-plane motion.

Material and Methods: A group of 20 patients who underwent MRI examination were included in the study. SV and EF were calculated using the stack of SA images (which had been compensated for through-plane motion) and compared to the SV and EF calculated according to the single- and biplane ellipsoid models.

Results: The mean difference between the single-plane model and the reference was -0.3±6.5 for EF and 7.2±17.1 ml for SV. Corresponding comparison between the biplane method and the reference resulted in a mean difference of 0.3±6.1 for EF and 11.8±14.9 ml for SV.

Conclusion: The results from this study show that left ventricular EF can be adequately estimated using the single- and biplane ellipsoid models, while SV tends to be overestimated using both geometrical models.
Building Up Goodwill: British Business, Development and Economic Nationalism in Ghana and Nigeria, 1945–1977
Authors: Decker Stephanie
Published: October 2008

Contemporary sub-Saharan Africa presents a puzzle to many observers, and has generally been perceived as a hostile environment to modern business. It is indeed difficult to make sense of politics and business on the continent without understanding how African colonies turned into independent countries since the late 1950s, and how they evolved into postcolonial states from the 1970s onwards. Imperial business was witness to these fundamental changes in African societies and deeply affected by it. Although some economic indicators in the 1970s were relatively favorable (many commodity prices were high), this was the decade when the severe decline of Africa, both in relative and absolute terms, began.
The C-Terminal Half of the HrpN Virulence Protein of the Fire Blight PathogenErwinia amylovoraIs Essential for Its Secretion and for Its Virulence and Avirulence Activities
Authors: Sinn Judith P. , Oh Chang-Sik , Jensen Philip J. , Carpenter Sara C. D. , Beer Steven V. , McNellis Timothy W.
Published: October 2008

The HrpN (harpin) protein of the fire blight pathogen Erwinia amylovora is an essential virulence factor secreted via the bacterial type III secretion system. HrpN also has avirulence activity when delivered to tobacco by E. amylovora and has defense elicitor activity when applied to plants as a cell-free protein extract. Here, we characterize a series of random mutations in hrpN that altered the predicted amino acid sequence of the protein. Amino acid substitutions and deletions in the highly conserved, C-terminal portion of HrpN disrupted the virulence and avirulence activities of the protein. Several of these mutations produced a dominant-negative effect on E. amylovora avirulence on tobacco. None of the mutations clearly separated the virulence and avirulence activities of HrpN. Some C-terminal mutations abolished secretion of HrpN by E. amylovora. The results indicate that the C-terminal half of HrpN is essential for its secretion by E. amylovora, for its virulence activity on apple and pear, and for its avirulence activity on tobacco. In contrast, the C-terminal half of HrpN was not required for cell-free elicitor activity. This suggests that the N-terminal and C-terminal halves of HrpN mediate cell-free elicitor activity and avirulence activity, respectively.
The cAMP-Dependent Signaling Pathway and Its Role in Conidial Germination, Growth, and Virulence of the Gray Mold Botrytis cinerea
Authors: Schumacher Julia , Kokkelink Leonie , Huesmann Christina , Jimenez-Teja Daniel , Collado Isidro G. , Barakat Radwan , Tudzynski Paul , Tudzynski Bettina
Published: October 2008

In Botrytis cinerea, some components of the cAMP-dependent pathway, such as α subunits of heterotrimeric G proteins and the adenylate cyclase BAC, have been characterized and their impact on growth, conidiation, germination, and virulence has been demonstrated. Here, we describe the functions of more components of the cAMP cascade: the catalytic subunits BcPKA1 and BcPKA2 and the regulatory subunit BcPKAR of the cAMP-dependent protein kinase (PKA). Although Δbcpka2 mutants showed no obvious phenotypes, growth and virulence were severely affected by deletion of both bcpka1 and bcpkaR. Similar to Δbac, lesion development of Δbcpka1 and ΔbcpkaR was slower than in controls and soft rot of leaves never occurred. In contrast to Δbac, Δbcpka1 and ΔbcpkaR mutants sporulated in planta, and growth rate, conidiation, and conidial germination were not impaired, indicating PKA-independent functions of cAMP. Unexpectedly, Δbcpka1 and ΔbcpkaR showed identical phenotypes, suggesting the total loss of PKA activity in both mutants. The deletion of bcras2 encoding the fungal-specific Ras GTPase resulted in significantly delayed germination and decreased growth rates. Both effects could be partially restored by exogenous cAMP, suggesting that BcRAS2 activates the adenylate cyclase in addition to the Gα subunits BCG1 and BCG3, thus influencing cAMP-dependent signal transduction.
Induction of Plant Defense Gene Expression by Plant Activators and Pseudomonas syringae pv. tomato in Greenhouse-Grown Tomatoes
Authors: Herman M. A. B. , Davidson J. K. , Smart C. D.
Published: October 2008

Plant activators provide an appealing management option for bacterial diseases of greenhouse-grown tomatoes. Two types of plant activators, one that induces systemic acquired resistance (SAR) and a second that activates induced systemic resistance (ISR), were evaluated for control of Pseudomonas syringae pv. tomato and effect on plant defense gene activation. Benzothiadiazole (BTH, SAR-inducing compound) effectively reduced bacterial speck incidence and severity, both alone and in combination with the ISR-inducing product. Application of BTH also led to elevated activation of salicylic acid and ethylene-mediated responses, based on real-time polymerase chain reaction analysis of marker gene expression levels. In contrast, the ISR-inducing product (made up of plant growth-promoting rhizobacteria) inconsistently modified defense gene expression and did not provide disease control to the same level as did BTH. No antagonism was observed by combining the two activators as control of bacterial speck was similar to or better than BTH alone.
Fluctuations as a source of information in fluorescence microscopy
Authors: Petrášek Zdeněk , Schwille Petra
Published: October 2008

Fluctuations in fluorescence spectroscopy and microscopy have traditionally been regarded as noise—they lower the resolution and contrast and do not permit high acquisition rates. However, fluctuations can also be used to gain additional information about a system. This fact has been exploited in single-point microscopic techniques, such as fluorescence correlation spectroscopy and analysis of single molecule trajectories, and also in the imaging field, e.g. in spatio-temporal image correlation spectroscopy. Here, we discuss how fluctuations are used to obtain more quantitative information from the data than that given by average values, while minimizing the effects of noise due to stochastic photon detection.
Molecular circuits for associative learning in single-celled organisms
Authors: Fernando Chrisantha T , Liekens Anthony M.L , Bingle Lewis E.H , Beck Christian , Lenser Thorsten , Stekel Dov J , Rowe Jonathan E
Published: October 2008

We demonstrate how a single-celled organism could undertake associative learning. Although to date only one previous study has found experimental evidence for such learning, there is no reason in principle why it should not occur. We propose a gene regulatory network that is capable of associative learning between any pre-specified set of chemical signals, in a Hebbian manner, within a single cell. A mathematical model is developed, and simulations show a clear learned response. A preliminary design for implementing this model using plasmids within
Escherichia coli
is presented, along with an alternative approach, based on double-phosphorylated protein kinases.
Global stability for thermal convection in a fluid overlying a highly porous material
Authors: Hill Antony A , Straughan Brian
Published: October 2008

This paper investigates the instability thresholds and global nonlinear stability bounds for thermal convection in a fluid overlying a highly porous material. A two-layer approach is adopted, where the Darcy–Brinkman equation is employed to describe the fluid flow in the porous medium. An excellent agreement is found between the linear instability and unconditional nonlinear stability thresholds, demonstrating that the linear theory accurately emulates the physics of the onset of convection.
Principles of transcriptional regulation and evolution of the metabolic system inE. coli
Authors: Seshasayee Aswin S.N. , Fraser Gillian M. , Babu M. Madan , Luscombe Nicholas M.
Published: October 2008

Organisms must adapt to make optimal use of the metabolic system in response to environmental changes. In the long-term, this involves evolution of the genomic repertoire of enzymes; in the short-term, transcriptional control ensures that appropriate enzymes are expressed in response to transitory extracellular conditions. Unicellular organisms are particularly susceptible to environmental changes; however, genome-scale impact of these modulatory effects has not been explored so far in bacteria. Here, we integrate genome-scale data to investigate the evolutionary trends and transcriptional control of metabolism inEscherichia coliK12. Globally, the regulatory system is organized in a clear hierarchy of general and specific transcription factors (TFs) that control differing ranges of metabolic functions. Further, catabolic, anabolic, and central metabolic pathways are targeted by distinct combinations of these TFs. Locally, enzymes catalyzing sequential reactions in a metabolic pathway are co-regulated by the same TFs. Regulation is more complex at junctions: General TFs control the overall activity of all connecting reactions, whereas specific TFs control individual enzymes. Divergent junctions play a special role in delineating metabolic pathways and decouple the regulation of incoming and outgoing reactions. We find little evidence for differential usage of isozymes, which are generally co-expressed in similar conditions, and thus are likely to reinforce the metabolic system through redundancy. Finally, we show that enzymes controlled by the same TFs have a strong tendency to co-evolve, suggesting a significant constraint to maintain similar regulatory regimes during evolution. Catabolic, anabolic, and central energy pathways evolve differently, emphasizing the role of the environment in shaping the metabolic system. Many of the observations also occur in yeast, and our findings may apply across large evolutionary distances.
E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites
Authors: Rabinovich Alina , Jin Victor X. , Rabinovich Roman , Xu Xiaoqin , Farnham Peggy J.
Published: October 2008

We have previously shown that most sites bound by E2F family members in vivo do not contain E2F consensus motifs. However, differences between in vivo target sites that contain or lack a consensus E2F motif have not been explored. To understand how E2F binding specificity is achieved in vivo, we have addressed how E2F family members are recruited to core promoter regions that lack a consensus motif and are excluded from other regions that contain a consensus motif. Using chromatin immunoprecipitation coupled with DNA microarray analysis (ChIP-chip) assays, we have shown that the predominant factors specifying whether E2F is recruited to an in vivo binding site are (1) the site must be in a core promoter and (2) the region must be utilized as a promoter in that cell type. We have tested three models for recruitment of E2F to core promoters lacking a consensus site, including (1) indirect recruitment, (2) looping to the core promoter mediated by an E2F bound to a distal motif, and (3) assisted binding of E2F to a site that weakly resembles an E2F motif. To test these models, we developed a new in vivo assay, termed eChIP, which allows analysis of transcription factor binding to isolated fragments. Our findings suggest that in vivo (1) a consensus motif is not sufficient to recruit E2Fs, (2) E2Fs can bind to isolated regions that lack a consensus motif, and (3) binding can require regions other than the best match to the E2F motif.