bluuebunny/crossref_metadata_2025_split huggingface dataset:
Euglena gracilisascorbate peroxidase forms an intramolecular dimeric structure: its unique molecular characterization
Authors: Ishikawa Takahiro , Tajima Naoko , Nishikawa Hitoshi , Gao Yongshun , Rapolu Madhusudhan , Shibata Hitoshi , Sawa Yoshihiro , Shigeoka Shigeru 
Published: December 2009

Euglena gracilis lacks a catalase and contains a single APX (ascorbate peroxidase) and enzymes related to the redox cycle of ascorbate in the cytosol. In the present study, a full-length cDNA clone encoding the Euglena APX was isolated and found to contain an open reading frame encoding a protein of 649 amino acids with a calculated molecular mass of 70.5 kDa. Interestingly, the enzyme consisted of two entirely homologous catalytic domains, designated APX-N and APX-C, and an 102 amino acid extension in the N-terminal region, which had a typical class II signal proposed for plastid targeting in Euglena. A computer-assisted analysis indicated a novel protein structure with an intramolecular dimeric structure. The analysis of cell fractionation showed that the APX protein is distributed in the cytosol, but not the plastids, suggesting that Euglena APX becomes mature in the cytosol after processing of the precursor. The kinetics of the recombinant mature FL (full-length)-APX and the APX-N and APX-C domains with ascorbate and H2O2 were almost the same as that of the native enzyme. However, the substrate specificity of the mature FL-APX and the native enzyme was different from that of APX-N and APX-C. The mature FL-APX, but not the truncated forms, could reduce alkyl hydroperoxides, suggesting that the dimeric structure is correlated with substrate recognition. In Euglena cells transfected with double-stranded RNA, the silencing of APX expression resulted in a significant increase in the cellular level of H2O2, indicating the physiological importance of APX to the metabolism of H2O2.
Pericellular activation of hepatocyte growth factor by the transmembrane serine proteases matriptase and hepsin, but not by the membrane-associated protease uPA
Authors: Owen Kate A. , Qiu Deyi , Alves Juliano , Schumacher Andrew M. , Kilpatrick Lynette M. , Li Jun , Harris Jennifer L. , Ellis Vincent 
Published: December 2009

HGF (hepatocyte growth factor) is a pleiotropic cytokine homologous to the serine protease zymogen plasminogen that requires canonical proteolytic cleavage to gain functional activity. The activating proteases are key components of its regulation, but controversy surrounds their identity. Using quantitative analysis we found no evidence for activation by uPA (urokinase plasminogen activator), despite reports that this is a principal activator of pro-HGF. This was unaffected by a wide range of experimental conditions, including the use of various molecular forms of both HGF and uPA, and the presence of uPAR (uPA receptor) or heparin. In contrast the catalytic domains of the TTSPs (type-II transmembrane serine proteases) matriptase and hepsin were highly efficient activators (50% activation at 0.1 and 3.4 nM respectively), at least four orders of magnitude more efficient than uPA. PS-SCL (positional-scanning synthetic combinatorial peptide libraries) were used to identify consensus sequences for the TTSPs, which in the case of hepsin corresponded to the pro-HGF activation sequence, demonstrating a high specificity for this reaction. Both TTSPs were also found to be efficient activators at the cell surface. Activation of pro-HGF by PC3 prostate carcinoma cells was abolished by both protease inhibition and matriptase-targeting siRNA (small interfering RNA), and scattering of MDCK (Madin–Darby canine kidney) cells in the presence of pro-HGF was abolished by inhibition of matriptase. Hepsin-transfected HEK (human embryonic kidney)-293 cells also activated pro-HGF. These observations demonstrate that, in contrast with the uPA/uPAR system, the TTSPs matriptase and hepsin are direct pericellular activators of pro-HGF, and that together these proteins may form a pathway contributing to their involvement in pathological situations, including cancer.
Intonation Contrast in Cantonese Speakers With Hypokinetic Dysarthria Associated With Parkinson’s Disease
Authors: Ma Joan K.-Y. , Whitehill Tara L. , So Susanne Y.-S. 
Published: December 2009

PurposeSpeech produced by individuals with hypokinetic dysarthria associated with Parkinson’s disease (PD) is characterized by a number of features including impaired speech prosody. The purpose of this study was to investigate intonation contrasts produced by this group of speakers.MethodSpeech materials with a question–statement contrast were collected from 14 Cantonese speakers with PD. Twenty listeners then classified the productions as either questions or statements. Acoustic analyses of F0, duration, and intensity were conducted to determine which acoustic cues distinguished the production of questions from statements, and which cues appeared to be exploited by listeners in identifying intonational contrasts.ResultsThe results show that listeners identified statements with a high degree of accuracy, but the accuracy of question identification ranged from 0.56% to 96% across the 14 speakers. The speakers with PD used similar acoustic cues as nondysarthric Cantonese speakers to mark the question–statement contrast, although the contrasts were not observed in all speakers. Listeners mainly used F0 cues at the final syllable for intonation identification.ConclusionThese data contribute to the researchers' understanding of intonation marking in speakers with PD, with specific application to the production and perception of intonation in a lexical tone language.
Perception of Wet Vocal Quality in Identifying Penetration/Aspiration During Swallowing
Authors: Groves-Wright Kathy Jean , Boyce Suzanne , Kelchner Lisa 
Published: December 2009

Purpose
In the present study, the authors investigated the association between wet vocal quality (WVQ) and prandial material in the larynx during phonation. The presence of such material is indicative of oropharyngeal dysphagia and results from entry of material into the laryngeal vestibule during swallowing. The primary aim of the study was to determine whether clinicians reliably perceive WVQ during phonation when prandial material is in the larynx.

Method
Seventy-eight subjects underwent videofluoroscopic swallow study, and simultaneous recording of time-linked videofluoroscopic and acoustic data was conducted during postswallow phonation. Experienced dysphagia clinicians then rated randomized audio samples for presence or absence of WVQ.

Results
WVQ is not reliably perceived by clinicians when material is present in the larynx in the region of the glottis during phonation, and there is a high degree of interrater variability for perceptual judgments of wetness.

Conclusions
Material in the larynx during phonation may result in multiple voice quality percepts, and even experienced clinicians may not be adept at identifying the perceptual consequences of this. Observation of laryngeal physiology during voicing when material is in the larynx using vocal tract imaging can improve reliability in the identification of wet vocal quality.
Randomized Controlled Trial of Video Self-Modeling Following Speech Restructuring Treatment for Stuttering
Authors: Cream Angela , O’Brian Sue , Jones Mark , Block Susan , Harrison Elisabeth , Lincoln Michelle , Hewat Sally , Packman Ann , Menzies Ross , Onslow Mark 
Published: December 2009

Purpose
In this study, the authors investigated the efficacy of video self-modeling (VSM) following speech restructuring treatment to improve the maintenance of treatment effects.

Method
The design was an open-plan, parallel-group, randomized controlled trial. Participants were 89 adults and adolescents who undertook intensive speech restructuring treatment. Post treatment, participants were randomly assigned to 2 trial arms: standard maintenance and standard maintenance plus VSM. Participants in the latter arm viewed stutter-free videos of themselves each day for 1 month.

Results
The addition of VSM did not improve speech outcomes, as measured by percent syllables stuttered, at either 1 or 6 months postrandomization. However, at the latter assessment, self-rating of worst stuttering severity by the VSM group was 10% better than that of the control group, and satisfaction with speech fluency was 20% better. Quality of life was also better for the VSM group, which was mildly to moderately impaired compared with moderate impairment in the control group.

Conclusions
VSM intervention after treatment was associated with improvements in self-reported outcomes. The clinical implications of this finding are discussed.
Saccharomyces cerevisiae
Msh2-Msh6 DNA binding kinetics reveal a mechanism of targeting sites for DNA mismatch repair
Authors: Zhai Jie , Hingorani Manju M. 
Published: December 2009

The DNA mismatch repair system (MMR) identifies replication errors and damaged bases in DNA and functions to preserve genomic integrity. MutS performs the task of locating mismatched base pairs, loops and lesions and initiating MMR, and the fundamental question of how this protein targets specific sites in DNA is unresolved. To address this question, we examined the interactions between
Saccharomyces cerevisiae
Msh2-Msh6, a eukaryotic MutS homolog, and DNA in real time. The reaction kinetics reveal that Msh2-Msh6 binds a variety of sites at similarly fast rates (
k
ON
∼ 10
7
M
-1
s
-1
), and its selectivity manifests in differential dissociation rates; e.g., the protein releases a 2-Aminopurine:T base pair approximately 90-fold faster than a G:T mismatch. On releasing the 2-Ap:T site, Msh2-Msh6 is able to move laterally on DNA to locate a nearby G:T site. The long-lived Msh2-Msh6·G:T complex triggers the next step in MMR—formation of an ATP-bound clamp—more effectively than the short-lived Msh2-Msh6·2-Ap:T complex. Mutation of Glu in the conserved Phe-X-Glu DNA binding motif stabilizes Msh2-Msh6
E339A
·2-Ap:T complex, and the mutant can signal 2-Ap:T repair as effectively as wild-type Msh2-Msh6 signals G:T repair. These findings suggest a targeting mechanism whereby Msh2-Msh6 scans DNA, interrogating base pairs by transient contacts and pausing at potential target sites, and the longer the pause the greater the likelihood of MMR.
Actin polymerization driven mitochondrial transport in mating
S. cerevisiae
Authors: Senning Eric N. , Marcus Andrew H. 
Published: December 2009

The dynamic microenvironment of cells depends on macromolecular architecture, equilibrium fluctuations, and nonequilibrium forces generated by cytoskeletal proteins. We studied the influence of these factors on the motions of mitochondria in mating
S. cerevisiae
using Fourier imaging correlation spectroscopy (FICS). Our measurements provide detailed length-scale dependent information about the dynamic behavior of mitochondria. We investigate the influence of the actin cytoskeleton on mitochondrial motion and make comparisons between conditions in which actin network assembly and disassembly is varied either by using disruptive pharmacological agents or mutations that alter the rates of actin polymerization. Under physiological conditions, nonequilibrium dynamics of the actin cytoskeleton leads to 1.5-fold enhancement of the long-time mitochondrial diffusion coefficient and a transient subdiffusive temporal scaling of the mean-square displacement (MSD ∝
τ

α

, with
α
= 2/3). We find that nonequilibrium forces associated with actin polymerization are a predominant factor in driving mitochondrial transport. Moreover, our results lend support to an existing model in which these forces are directly coupled to mitochondrial membrane surfaces.
R loops stimulate genetic instability of CTG·CAG repeats
Authors: Lin Yunfu , Dent Sharon Y. R. , Wilson John H. , Wells Robert D. , Napierala Marek 
Published: December 2009

Transcription stimulates the genetic instability of trinucleotide repeat sequences. However, the mechanisms leading to transcription-dependent repeat length variation are unclear. We demonstrate, using biochemical and genetic approaches, that the formation of stable RNA·DNA hybrids enhances the instability of CTG·CAG repeat tracts. In vitro transcribed CG-rich repeating sequences, unlike AT-rich repeats and nonrepeating sequences, form stable, ribonuclease A-resistant structures. These RNA·DNA hybrids are eliminated by ribonuclease H treatment. Mutation in thernhA1gene that decreases the activity of ribonuclease HI stimulates the instability of CTG·CAG repeats inE. coli. Importantly, the effect of ribonuclease HI depletion on repeat instability requires active transcription. We also showed that transcription-dependent CTG·CAG repeat instability in human cells is stimulated by siRNA knockdown of RNase H1 and H2. In addition, we used bisulfite modification, which detects single-stranded DNA, to demonstrate that the nontemplate DNA strand at transcribed CTG·CAG repeats remains partially single-stranded in human genomic DNA, thus indicating that it is displaced by an RNA·DNA hybrid. These studies demonstrate that persistent hybrids between the nascent RNA transcript and the template DNA strand at CTG·CAG tracts promote instability of DNA trinucleotide repeats.
Orthologs of the Class A4 Heat Shock Transcription Factor HsfA4a Confer Cadmium Tolerance in Wheat and Rice
Authors: Shim Donghwan , Hwang Jae-Ung , Lee Joohyun , Lee Sichul , Choi Yunjung , An Gynheung , Martinoia Enrico , Lee Youngsook 
Published: December 2009

Abstract
Cadmium (Cd) is a widespread soil pollutant; thus, the underlying molecular controls of plant Cd tolerance are of substantial interest. A screen for wheat (Triticum aestivum) genes that confer Cd tolerance to a Cd hypersensitive yeast strain identified Heat shock transcription factor A4a (HsfA4a). Ta HsfA4a is most similar to the class A4 Hsfs from monocots. The most closely related rice (Oryza sativa) homolog, Os HsfA4a, conferred Cd tolerance in yeast, as did Ta HsfA4a, but the second most closely related rice homolog, Os HsfA4d, did not. Cd tolerance was enhanced in rice plants expressing Ta HsfA4a and decreased in rice plants with knocked-down expression of Os HsfA4a. An analysis of the functional domain using chimeric proteins constructed from Ta HsfA4a and Os HsfA4d revealed that the DNA binding domain (DBD) of HsfA4a is critical for Cd tolerance, and within the DBD, Ala-31 and Leu-42 are important for Cd tolerance. Moreover, Ta HsfA4a–mediated Cd resistance in yeast requires metallothionein (MT). In the roots of wheat and rice, Cd stress caused increases in HsfA4a expression, together the MT genes. Our findings thus suggest that HsfA4a of wheat and rice confers Cd tolerance by upregulating MT gene expression in planta.
The Small Subunit of Snapdragon Geranyl Diphosphate Synthase Modifies the Chain Length Specificity of Tobacco Geranylgeranyl Diphosphate Synthase in Planta
Authors: Orlova Irina , Nagegowda Dinesh A. , Kish Christine M. , Gutensohn Michael , Maeda Hiroshi , Varbanova Marina , Fridman Eyal , Yamaguchi Shinjiro , Hanada Atsushi , Kamiya Yuji , Krichevsky Alexander , Citovsky Vitaly , Pichersky Eran , Dudareva Natalia 
Published: December 2009

AbstractGeranyl diphosphate (GPP), the precursor of many monoterpene end products, is synthesized in plastids by a condensation of dimethylallyl diphosphate and isopentenyl diphosphate (IPP) in a reaction catalyzed by homodimeric or heterodimeric GPP synthase (GPPS). In the heterodimeric enzymes, a noncatalytic small subunit (GPPS.SSU) determines the product specificity of the catalytic large subunit, which may be either an active geranylgeranyl diphosphate synthase (GGPPS) or an inactive GGPPS-like protein. Here, we show that expression of snapdragon (Antirrhinum majus) GPPS.SSU in tobacco (Nicotiana tabacum) plants increased the total GPPS activity and monoterpene emission from leaves and flowers, indicating that the introduced catalytically inactive GPPS.SSU found endogenous large subunit partner(s) and formed an active snapdragon/tobacco GPPS in planta. Bimolecular fluorescence complementation and in vitro enzyme analysis of individual and hybrid proteins revealed that two of four GGPPS-like candidates from tobacco EST databases encode bona fide GGPPS that can interact with snapdragon GPPS.SSU and form a functional GPPS enzyme in plastids. The formation of chimeric GPPS in transgenic plants also resulted in leaf chlorosis, increased light sensitivity, and dwarfism due to decreased levels of chlorophylls, carotenoids, and gibberellins. In addition, these transgenic plants had reduced levels of sesquiterpene emission, suggesting that the export of isoprenoid intermediates from the plastids into the cytosol was decreased. These results provide genetic evidence that GPPS.SSU modifies the chain length specificity of phylogenetically distant GGPPS and can modulate IPP flux distribution between GPP and GGPP synthesis in planta.
Breeding requirements of Nahan’s Francolin, Francolinus nahan, in Budongo forest reserve, Uganda
Authors: Sande Eric , Dranzoa Christine , Wegge Per , Carroll John P. 
Published: December 2009

AbstractThe Nahan’s Francolin Francolinus nahani is a globally threatened species associated with remnant forests of the eastern equatorial lowlands of the Democratic Republic of the Congo and Uganda. We studied the species in the Budongo Forest Reserve during March 1998 to January 2000 in an attempt to document some aspects of breeding requirements. We located nests by physically searching the forest and through following radio‐tagged adults. We measured demographical and habitat parameters associated with each nest. Our data suggest that trees of large diameter at breast height with appropriate buttress formation are important for long‐time survival of Nahan’s Francolins.
Has the final countdown to wildlife extinction in Northern Central African Republic begun?
Authors: Bouché Philippe , Renaud Pierre‐Cyril , Lejeune Philippe , Vermeulen Cédric , Froment Jean‐Marc , Bangara Alfred , Fiongai Okclefort , Abdoulaye Antoine , Abakar Raymond , Fay Mike 
Published: December 2009

AbstractThe wildlife populations of Northern Central African Republic experienced precipitous declines during the 1970s and 1980s. While anecdotes coming out of the region indicate that the wildlife populations remain under serious threat, little is known about their status. An aerial sample count was carried out in the Northern Central African Republic at the end of the dry season in June 2005 and covered an 85,000 km2complex landscape containing national parks, hunting reserves and community hunting areas. Results show a dramatic decline of wildlife since the previous survey in 1985. In 20 years, large mammals’ numbers decreased by 65%, probably because of poaching and diseases brought by illegal cattle transhumance. Elephant (Loxodonta africana) and Buffon kob (Kobus kob) populations showed the greatest decline (over 80% each), while buffalo (Syncerus caffer), roan antelope (Hippotragus equinus) and Giant Lord’s Derby Eland (Taurotragus derbianus) populations seem stable or increasing over these last 20 years. The analysis of the wildlife population distribution by status of the different types of protected areas (national parks, hunting areas) showed that individual encounter rates of elephant and buffalo were lower in national parks than in neighbouring hunting areas, while those for roan, giraffe (Giraffa camelopardalis) and Buffon kob were higher in the national parks.
Blistering skin diseases: a bridge between dermatopathology and molecular biology
Authors: Nagy Nikoletta , McGrath John A 
Published: December 2009

Nagy N & McGrath J A (2010) Histopathology56, 91–99 Blistering skin diseases: a bridge between dermatopathology and molecular biologyAlthough dermatopathology and molecular biology are often considered to be separate laboratory disciplines, the respective approaches are far from mutually exclusive. This is certainly the case for understanding the pathology of blistering skin diseases, both acquired and inherited. For example, in toxic epidermal necrolysis, dermatopathology in isolation may provide few clues to disease pathogenesis. There is widespread keratinocyte apoptosis and a variable infiltrate of cytotoxic T cells, but morphology alone offers little insight into what causes the epidermal destruction. In contrast, molecular biology studies have revealed several key processes that help explain the keratinocyte death, including increased expression of death receptors and their ligands on keratinocyte cell membranes as well as the presence of local or systemic immunocyte‐derived cytolytic granules. For some inherited blistering diseases, however, such as epidermolysis bullosa, the molecular pathology is complex and difficult to unravel in isolation, yet the addition of dermatopathology is helpful in focusing molecular investigations. Notably, immunolabelling of cell adhesion proteins using specific antibody probes can identify reduced or absent immunoreactivity for candidate genes/proteins. Bridging dermatopathology and molecular biology investigations facilitates a greater understanding of disease processes, improves diagnostic accuracy, and provides a basis for the development and appraisal of new treatments.
The histological assessment of cutaneous vasculitis
Authors: Carlson J Andrew 
Published: December 2009

Carlson J A (2010) Histopathology56, 3–23 The histological assessment of cutaneous vasculitisVasculitis is defined as inflammation directed at vessels, which compromises or destroys the vessel wall leading to haemorrhagic and/or ischaemic events. Skin biopsy is the gold standard for the diagnosis of cutaneous vasculitis, whose manifestations include urticaria, infiltrative erythema, petechiae, purpura, purpuric papules, haemorrhagic vesicles and bullae, nodules, livedo racemosa, deep (punched out) ulcers and digital gangrene. These varied morphologies are a direct reflection of size of the vessels and extent of the vascular bed affected, ranging from a vasculitis affecting few superficial, small vessels in petechial eruptions to extensive pan‐dermal small vessel vasculitis in haemorrhagic bullae to muscular vessel vasculitis in lower extremity nodules with livedo racemosa. Skin biopsy, extending to subcutis and taken from the earliest, most symptomatic, reddish or purpuric lesion is crucial for obtaining a high‐yielding diagnostic sample. Based on histology, vasculitis can be classified on the size of vessels affected and the dominant immune cell mediating the inflammation (e.g. neutrophilic, granulomatous, lymphocytic, or eosinophilic). Disruption of small vessels by inflammatory cells, deposition of fibrin within the lumen and/or vessel wall coupled with nuclear debris allows for the confident recognition of small vessel, mostly neutrophilic vasculitis (also known as leukocytoclastic vasculitis). In contrast, muscular vessel vasculitis can be identified solely by infiltration of its wall by inflammatory cells. Extravasation of red blood cells (purpura) and necrosis are supportive, but not diagnostic of vasculitis as they are also seen in haemorrhagic and/or vaso‐occlusive disorders (pseudovasculitis). Vasculitic foci associated with extravascular granulomas (palisaded neutrophilic and granulomatous dermatitis), tissue eosinophilia, or tissue neutrophilia signal the risk for, or co‐existence of systemic disease. This essential histological information coupled with direct immunofluorescence and anti‐neutrophil cytoplasmic data and clinical findings enables more precise and accurate diagnosis of localized and systemic vasculitis syndromes.